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Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia. bioRxiv [Preprint]. 2024 Mar 16:2024.03.15.585298. doi: 10.1101/2024.03.15.585298. PMID: 38559060; PMCID: PMC10979946.

Differences in molecular sampling and data processing explain variation among single-cell and single-nucleus RNA-seq experiments

Chamberlin JT, Lee Y, Marth G, Quinlan AR.  Genome Res. 2024 Feb 14:gr.278253.123. doi: 10.1101/gr.278253.123. Epub ahead of print. PMID: 38355308.

The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young

Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Karthik F, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Faulkner M, MacLeod HM, Burns KM, Yandell M, Tristani-Firouzi M, George AL Jr, McNally EM. T Genome Med. 2024 Jan 16;16(1):13. doi: 10.1186/s13073-024-01284-w. PMID: 38229148; PMCID: PMC10792876.

A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data

Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT.  Genome Res. 2024 Jan 9. doi: 10.1101/gr.278234.123. Epub ahead of print. PMID: 38195207.

Effects of parental age and polymer composition on short tandem repeat de novo mutation rates

Goldberg ME, Noyes MD, Eichler EE, Quinlan AR, Harris K. bioRxiv [Preprint]. 2023 Dec 23:2023.12.22.573131. doi: 10.1101/2023.12.22.573131. PMID: 38187618; PMCID: PMC10769404.

Characterization and visualization of tandem repeats at genome scale

Dolzhenko E, English A, Dashnow H, De Sena Brandine G, Mokveld T, Rowell WJ, Karniski C, Kronenberg Z, Danzi MC, Cheung WA, Bi C, Farrow E, Wenger A, Chua KP, Martínez-Cerdeño V, Bartley TD, Jin P, Nelson DL, Zuchner S, Pastinen T, Quinlan AR, Sedlazeck FJ, Eberle MA.  Nat Biotechnol. 2024 Jan 2. doi: 10.1038/s41587-023-02057-3. Epub ahead of print. PMID: 38168995.

Single-Cell Long-Read Sequencing Enables the Dissection of BTK Subclonal Dynamics in CLL Treatment

Gage BlackXiaomeng HuangYi QiaoPhilip MoosDeborah M. StephensGabor MarthJennifer A. Woyach;  Blood 2023; 142 (Supplement 1): 1893. doi:

Genome sequencing of Pakistani families with male infertility identifies deleterious genotypes in SPAG6, CCDC9, TKTL1, TUBA3C, and M1AP

Khan MR, Akbari A, Nicholas TJ, Castillo-Madeen H, Ajmal M, Haq TU, Laan M, Quinlan AR, Ahuja JS, Shah AA, Conrad DF. Andrology. 2023 Dec 10. doi: 10.1111/andr.13570. Epub ahead of print. PMID: 38073178.

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid

Maclary ET, Holt C, Concepcion GT, Sović I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD. bioRxiv [Preprint]. 2023 Oct 14:2023.10.11.561892. doi: 10.1101/2023.10.11.561892. PMID: 37873124; PMCID: PMC10592783.

The status of the human gene catalogue

Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL. Nature. 2023 Oct;622(7981):41-47. doi: 10.1038/s41586-023-06490-x. Epub 2023 Oct 4. PMID: 37794265.

Genetic and clinical variables act synergistically to impact neurodevelopmental outcomes in children with single ventricle heart disease

Miller TA, Hernandez EJ, Gaynor JW, Russell MW, Newburger JW, Chung W, Goldmuntz E, Cnota JF, Zyblewski SC, Mahle WT, Zak V, Ravishankar C, Kaltman JR, McCrindle BW, Clarke S, Votava-Smith JK, Graham EM, Seed M, Rudd N, Bernstein D, Lee TM, Yandell M, Tristani-Firouzi M. Commun Med (Lond). 2023 Sep 27;3(1):127. doi: 10.1038/s43856-023-00361-2. PMID: 37758840.

Identification of sodium channel toxins from marine cone snails of the subgenera Textilia and Afonsoconus

McMahon KL, O'Brien H, Schroeder CI, Deuis JR, Venkatachalam D, Huang D, Green BR, Bandyopadhyay PK, Li Q, Yandell M, Safavi-Hemami H, Olivera BM, Vetter I, Robinson SD. Cell Mol Life Sci. 2023 Sep 9;80(10):287. doi: 10.1007/s00018-023-04935-0. PMID: 37689602; PMCID: PMC10492761.

quickBAM: a parallelized BAM file access API for high throughput sequence analysis informatics

Pitman TA, Huang X, Marth GT, Qiao Y.  Bioinformatics. 2023 Jul 27:btad463. doi: 10.1093/bioinformatics/btad463. Epub ahead of print. PMID: 37498562.

An Explainable Artificial Intelligence Approach for Discovering Social Determinants of Health and Risk Interactions for Stroke in Patients With Atrial Fibrillation

Zimmerman RM, Hernandez EJ, Watkins WS, Blue N, Tristani-Firouzi M, Yandell M, Steinberg BA. Am J Cardiol. 2023 Jun 27;201:224-226. doi: 10.1016/j.amjcard.2023.05.064. Epub ahead of print. PMID: 37385178.

Epistasis between mutator alleles contributes to germline mutation rate variability in laboratory mice

Sasani TA, Quinlan AR, Harris K. 2023 Apr 25:2023.04.25.537217. doi: 10.1101/2023.04.25.537217. PMID: 37162999; PMCID: PMC10168256.

Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder

Yang G, Ullah HMA, Parker E, Gorsi B, Libowitz M, Maguire C, King JB, Coon H, Lopez-Larson M, Anderson JS, Yandell M, Shcheglovitov A. Mol Psychiatry. 2023 Apr 10. doi: 10.1038/s41380-023-02035-w. Epub ahead of print. PMID: 37032361.

The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young

Puckelwartz MJ, Pesce LL, Hernandez EJ, Webster G, Dellefave-Castillo LM, Russell MW, Geisler SS, Kearns SD, Etheridge FK, Etheridge SP, Monroe TO, Pottinger TD, Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, MacLeod H, Burns KM, Yandell M, Tristani-Firouzi M, George AL, McNally EM. medRxiv [Preprint]. 2023 Mar 29:2023.03.27.23287711. doi: 10.1101/2023.03.27.23287711. PMID: 37034657; PMCID: PMC10081419.

Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning

Peterson B, Hernandez EJ, Hobbs C, Malone Jenkins S, Moore B, Rosales E, Zoucha S, Sanford E, Bainbridge MN, Frise E, Oriol A, Brunelli L, Kingsmore SF, Yandell M. Genome Med. 2023 Mar 16;15(1):18. doi: 10.1186/s13073-023-01166-7. PMID: 36927505; PMCID: PMC10018992.

An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes

Timoshevskaya N, Eşkut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, Mountcastle J, Haase B, Balacco JR, Formenti G, Pelan S, Sims Y, Howe K, Fedrigo O, Jarvis ED, Smith JJ. Cell Rep. 2023 Mar 15;42(3):112263. doi: 10.1016/j.celrep.2023.112263. Epub ahead of print. PMID: 36930644.

DIS3 Variants are Associated with Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis

Johnstone EB, Gorsi B, Coelho E, Moore B, Farr AM, Cooper AR, Mardis ER, Rajkovic A, Chow CY, Yandell M, Welt CK.  J Clin Endocrinol Metab. 2023 Mar 3:dgad126. doi: 10.1210/clinem/dgad126. Epub ahead of print. PMID: 36869713.

Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study

Workalemahu T, Avery C, Lopez S, Blue NR, Wallace A, Quinlan AR, Coon H, Warner D, Varner MW, Branch DW, Jorde LB, Silver RM. PLoS One. 2023 Feb 17;18(2):e0281934. doi: 10.1371/journal.pone.0281934. PMID: 36800380; PMCID: PMC9937472.

Random allelic expression in the adult human body

Kravitz SN, Ferris E, Love MI, Thomas A, Quinlan AR, Gregg C. Cell Rep. 2023 Jan 5;42(1):111945. doi: 10.1016/j.celrep.2022.111945. Epub ahead of print. PMID: 36640362.

STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. Genome Biol. 2022 Dec 14;23(1):257. doi: 10.1186/s13059-022-02826-4. PMID: 36517892.

Extensive Recombination-driven Coronavirus Diversification Expands the Pool of Potential Pandemic Pathogens.

Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC. Genome Biol Evol. 2022 Dec 8;14(12):evac161. doi: 10.1093/gbe/evac161. PMID: 36477201.

Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate

Nicholas TJ, Cormier MJ, Quinlan AR. BMC Bioinformatics. 2022 Nov 16;23(1):490. doi: 10.1186/s12859-022-05008-y. PMID: 36384437; PMCID: PMC9670370.

Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies.

Cormier MJ, Pedersen BS, Bayrak-Toydemir P, Quinlan AR.  BMC Bioinformatics. 2022 Nov 14;23(1):482. doi: 10.1186/s12859-022-05041-x. PMID: 36376793.

Genomic landscape of advanced prostate cancer patients with BRCA1 versus BRCA2 mutations as detected by comprehensive genomic profiling of cell-free DNA

Swami U, Zimmerman RM, Nussenzveig RH, Hernandez EJ, Jo Y, Sayegh N, Wesolowski S, Kiedrowski LA, Barata PC, Lemmon GH, Bilen MA, Heath EI, Nandagopal L, Babiker HM, Pal SK, Lilly M, Maughan BL, Haaland B, Yandell M, Sartor O, Agarwal N. Front Oncol. 2022 Sep 15;12:966534. doi: 10.3389/fonc.2022.966534. PMID: 36185208; PMCID: PMC9521349.

Familial aggregation of stillbirth: a pedigree analysis of a matched case control study

Workalemahu T, Page JM, Meeks H, Yu Z, Guinto E, Fraser A, Varner MW, Theilen LH, Quinlan A, Coon H, Enquobahrie DA, Ananth CV, Tekola-Ayele F, Jorde LB, Silver RM. BJOG. 2022 Sep 26. doi: 10.1111/1471-0528.17301. Epub ahead of print. PMID: 36161750.

Poxviruses capture host genes by LINE-1 retrotransposition.

Fixsen SM, Cone KR, Goldstein SA, Sasani TA, Quinlan AR, Rothenburg S, Elde NC. Elife. 2022 Sep 7;11:e63332. doi: 10.7554/eLife.63332. Epub ahead of print. PMID: 36069526.


Comprehensive Genomic Profiling of Cell-Free DNA in Men With Advanced Prostate Cancer: Differences in Genomic Landscape Based on Race

Zimmerman R, Bilen MA, Heath EI, Nandagopal L, Swami U, Kessel A, Jaeger E, Wesolowski S, Hernanadez EJ, Chipman J, Mack A, Ravindranathan D, Maughan BL, Nussenzveig R, Yandell M, Kohli M, Lilly MB, Sartor AO, Agarwal N, Barata PC. Oncologist. 2022 Aug 29:oyac176. doi: 10.1093/oncolo/oyac176. Epub ahead of print. PMID: 36036607

Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer

Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V.  Cell Syst. 2022 Aug 15:S2405-4712(22)00313-1. doi: 10.1016/j.cels.2022.07.006. Epub ahead of print. PMID: 35981544.

 A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia.

Simeone CA, Wilkerson JL, Poss AM, Banks JA, Varre JV, Guevara JL, Hernandez EJ, Gorsi B, Atkinson DL, Turapov T, Frodsham SG, Morales JCF, O'Neil K, Moore B, Yandell M, Summers SA, Krolewski AS, Holland WL, Pezzolesi MG. NPJ Genom Med. 2022 Jul 22;7(1):43. doi: 10.1038/s41525-022-00314-z. PMID: 35869090.

Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take?

Kunisaki J, Quinlan A, Aston KI, Hotaling J. Integrating Precision Medicine into the Standard of Care for Male Infertility: What Will it Take? Eur Urol. 2022 Jul 7:S0302-2838(22)02465-4. doi: 10.1016/j.eururo.2022.06.015. Epub ahead of print. PMID: 35811191.


Searching thousands of genomes to classify somatic and novel structural variants using STIX

Chowdhury M, Pedersen BS, Sedlazeck FJ, Quinlan AR, Layer RM.

Nat Methods. 2022 Jun;19(6):770. doi: 10.1038/s41592-022-01538-8. Erratum for: Nat Methods. 2022 Apr;19(4):445-448. PMID: 35618956; PMCID: PMC9184272.

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Subclonal evolution of CLL driver mutations is associated with relapse in ibrutinib and acalabrutinib treated patients

Black GS, Huang X, Qiao Y, Tarapcsak S, Rogers KA, Misra S, Byrd JC, Marth GT, Stephens DM, Woyach JA

Blood. 2022 Apr 27:blood.2021015132. doi: 10.1182/blood.2021015132. Epub ahead of print. PMID: 35476648.

Family Screening After Sudden Death in a Population-Based Study of Children

Kannankeril PJ, Shoemaker MB, Fountain D, Roden DM, Yandell M, Tristani-Firouzi M, Etheridge SP, Webster G, George AL, McNally EM, MacLeod H, Burns KM. Family Screening After Sudden Death in a Population-Based Study of Children. Pediatrics. 2022 Apr 1;149(4):e2021054432. doi: 10.1542/peds.2021-054432. PMID: 35284934; PMCID: PMC9153292.


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Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency

Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK. Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency. J Clin Endocrinol Metab. 2022 Feb 17;107(3):685-714. doi: 10.1210/clinem/dgab775. PMID: 34718612; PMCID: PMC9006976.


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Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia

Nicholas TJ, Al-Sweel N, Farrell A, Mao R, Bayrak-Toydemir P, Miller CE, Bentley D, Palmquist R, Moore B, Hernandez EJ, Cormier MJ, Fredrickson E, Noble K, Rynearson S, Holt C, Karren MA, Bonkowsky JL, Tristani-Firouzi M, Yandell M, Marth G, Quinlan AR, Brunelli L, Toydemir RM, Shayota BJ, Carey JC, Boyden SE, Malone Jenkins S. Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med. 2022 Apr;10(4):e1888. doi: 10.1002/mgg3.1888. Epub 2022 Feb 4. PMID: 35119225; PMCID: PMC9000945.


An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records

Wesołowski S, Lemmon G, Hernandez EJ, Henrie A, Miller TA, Weyhrauch D, Puchalski MD, Bray BE, Shah RU, Deshmukh VG, Delaney R, Yostl HJ, Eilbeck K, Tristani-Firouzi M, Yandell M. An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records. PLOS Digit Health. 2022;1(1):e0000004. doi: 10.1371/journal.pdig.0000004. Epub 2022 Jan 18. PMID: 35373216; PMCID: PMC8975108.


Clin.iobio: A Collaborative Diagnostic Workflow to Enable Team-Based Precision Genomics

Ward A, Velinder M, Di Sera T, Ekawade A, Malone Jenkins S, Moore B, Mao R, Bayrak-Toydemir P, Marth G. . J Pers Med. 2022 Jan 8;12(1):73. doi: 10.3390/jpm12010073. PMID: 35055388; PMCID: PMC8780189

The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming

Primo VA Jr, Rezvani Y, Farrell A, Murphy CQ, Lou J, Vajdi A, Marth GT, Zarringhalam K, Gubbels MJ. T. mSystems. 2021 Dec 21;6(6):e0119621. doi: 10.1128/mSystems.01196-21. Epub 2021 Dec 7. PMID: 34874774; PMCID: PMC8651083

A ROR2 coding variant is associated with craniofacial variation in domestic pigeons

Boer ER, Van Hollebeke HF, Maclary ET, Holt C, Yandell M, Shapiro MD

Current Biology. 2021. Nov 22. 31:1–8.


The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele

Hateley S, Lopez-Izquierdo A, Jou CJ, Cho S, Schraiber JG, Song S, Maguire CT, Torres N, Riedel M, Bowles NE, Arrington CB, Kennedy BJ. Etheridge SP, Lai S, Pribble C, Meyers L, Lundahl D, Byrnes J, Granka JM, Kauffman CA, Lemmon G, Boyden A, Watkins SW, Karren MA, Knight A, Muhlestein JB, Carlquist JF, Anderson JL, Chahine KG, Shah KU, Ball CA, Benjamin IJ, Yandell M, Tristani-Firouzi M

Nat Commun. 2021; 12: 6442. Published online 2021 Nov 8. doi: 10.1038/s41467-021-26741-7


Addressing ethical and laboratory challenges for initiation of a rapid whole genome sequencing program

Jenkins SM, Palmquist R, Kapron AL, Torr C, Best DH, Karren MA, Brunelli L, Yandell M, Tristani-Firouzi M, Dimmock D, Watts B, Botkin JR, Johnson A, Bonkowsky JL

J Clin Transl Sci. 2021. Oct 28. 5(1):e177. doi:


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A Poisson binomial based statistical testing framework for comprehensive comorbidity discovery across massive Electronic Health Record

Lemmon G, Wesolowski S, Henrie A, Tristani-Firouzi M, Yandell M. A Poisson binomial-based statistical testing framework for comorbidity discovery across electronic health record datasets. Nat Comput Sci. 2021 Oct;1(10):694-702. doi: 10.1038/s43588-021-00141-9. Epub 2021 Oct 21. PMID: 35252879; PMCID: PMC8896515.

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

De La Vega FM, Chowdhury S, Moore B, Frise E, McCarthy J, Hernandez EJ, Wong T, James K, Guidugli L, Agrawal PB, Genetti CA, Brownstein CA, Beggs AH, Löscher BS, Franke A, Boone B, Levy SE, Õunap K, Pajusalu S, Huentelman M, Ramsey K, Naymik M, Narayanan V, Veeraraghavan N, Billings P, Reese MG, Yandell M, Kingsmore SF. Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med. 2021 Oct 14;13(1):153. doi: 10.1186/s13073-021-00965-0. PMID: 34645491; PMCID: PMC8515723.

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Identifying anatomical regions associated with endometriosis pain using neighbor-joining clustering

Kiser AC, Eilbeck K, Hernandez EJ, Schliep KC, Peterson M, Yandell M

Fertil Steril. 2021 Sept. 16(3):e207-e208. doi:10.1016/j.fertnstert.2021.07.568

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC

bioRxiv . 2021 Jun 28;2021.02.03.429646. doi: 10.1101/2021.02.03.429646

PMID: 33564759

Mobile element insertions and associated structural variants in longitudinal breast cancer samples

Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB

Sci Rep. 2021. Jun 22;11(1):13020. doi: 10.1038/s41598-021-92444-0

PMID: 34158539

Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools

Hou, H, Pedersen B, Quinlan A

Nature Comp Sci. 2021. June 21;1:441–447.

Unfazed: parent-of-origin detection for large and small de novo variants. Bioinformatics

Belyeu JR, Sasani TA, Pedersen BS, Quinlan AR

Bioinformatics. 2021. Jun 19:btab454. doi: 10.1093/bioinformatics/btab454

Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform

Lin E, Hahn AW, Nussenzveig RH, Wesolowski S, Sayegh N, Maughan BL, McFarland T, Rathi N, Sirohi D, Sonpavde G, Swami U, Kohli M, Rich T, Sartor O, Yandell M, Agarwal N

Oncologist. 2021. Jun 22. doi: 10.1002/onco.13869

PMID: 34157173

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Genes affecting ionizing radiation survival identified through combined exome sequencing and functional screening

Gupta M, Liu X, Teraoka SN, Wright JA, Gatti RA, Quinlan A, Concannon P

Human Mutation. 2021. June 13;1–15. Human Mutation. 2021;1–15

PMID: 34153142

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Genomic predictors of response to PD-1 axis inhibitors in metastatic urothelial cancer (mUC) patients using machine learning analysis of tissue comprehensive genomic profiling (CGP).

Reisinger R, Santos VS, Nussenzveig R, Wesolowski S, Hernandez EJ, Henrie AR, Maughan BL, Swami U, Yandell M, Grivas P, Agarwal N.

Raquel Reisinger, Victor Sacristan Santos, Roberto Nussenzveig, Sergiusz Wesolowski, Edgar Javier Hernandez, Alexander Ryan Henrie, Benjamin L. Maughan, Umang Swami, Mark Yandell, Petros Grivas, and Neeraj Agarwal Journal of Clinical Oncology 2021 39:15_suppl, 4542-4542

10.1200/JCO.2021.39.15_suppl.4542 Journal of Clinical Oncology 39, no. 15_suppl (May 20, 2021) 4542-4542.

Samplot: a platform for structural variant visual validation and automated filtering

Belyeu JR, Chowdhury M, Brown J, Pedersen BS, Cormier MJ, Quinlan AR, Layer RM

Genome Biol. 2021. May 25;22(1):161. doi: 10.1186/s13059-021-02380-5.

PMID: 34034781

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The genomic basis of evolutionary differentiation among honey bees

Fouks B, Brand P, Nguyen HN, Herman J, Camara F, Ence D, Hagen DE, Hoff KJ, Nachweide S, Romoth L, Walden KKO, Guigo R, Stanke M, Narzisi G, Yandell M, Robertson HM, Koeniger N, Chantawannakul P, Schatz MC, Worley KC, Robinson GE, Elsik CG, Rueppell O

Genome Res. 2021. May 4;31(7):1203-1215. doi: 10.1101/gr.272310.120

PMID: 33947700

Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses

Tollis M, Ferris E, Campbell MS, Harris VK, Rupp SM, Harrison TM, Kiso WK, Schmitt DL, Garner MM, Athena Aktipis C, Maley CC, Boddy AM, Yandell M, Gregg C, Schiffman JD, Abegglen LM

Mol Biol Evol. 2021. May 3;msab127. doi: 10.1093/molbev/msab127.

PMID: 33944920

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Common Variation in Cytoskeletal Genes is Associated with Conotruncal Heart Defects

Musfee FI, Agopian AJ, Goldmuntz E, Hakonarson H, Morrow BE, Taylor DM, Tristani-Firouzi M, Watkins WS, Yandell M, Mitchell LE

Genes (Basel). 2021. Apr 27;12(5):655. doi: 10.3390/genes12050655

PMID: 33925651

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data

Cormier MJ, Belyeu JR, Pedersen BS, Brown J, Köster J, Quinlan AR

Nat Commun . 2021 Apr 12;12(1):2151. doi: 10.1038/s41467-021-22381-z

PMID: 33846313

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CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

Wallace AD, Sasani TA, Swanier J, Gates BL, Greenland J, Pedersen BS, Varley KE, Quinlan AR.

PLoS One . 2021 Apr 8;16(4):e0241253. doi: 10.1371/journal.pone.0241253. eCollection 2021

PMID: 33830997 PMCID: PMC8031414

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De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families.

Belyeu JR, Brand H, Wang H, Zhao X, Pedersen BS, Feusier J, Gupta M, Nicholas TJ, Brown J, Baird L, Devlin B, Sanders SJ, Jorde LB, Talkowski ME, Quinlan AR.

Am J Hum Genet . 2021 Apr 1;108(4):597-607. doi: 10.1016/j.ajhg.2021.02.012. Epub 2021 Mar 5

PMID: 33675682

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OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR.

Genome Med . 2021 Mar 26;13(1):46. doi: 10.1186/s13073-021-00854-6

PMID: 33771218 PMCID: PMC7995589

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Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens

Goldstein SA, Brown J, Pedersen BS, Quinlan AR, Elde NC

bioRxiv . 2021 Feb 4;2021.02.03.429646. doi: 10.1101/2021.02.03.429646. Preprint

PMID: 33564759 PMCID: PMC7872347

Disruption of human meiotic telomere complex genes TERB1, TERB2 and MAJIN in men with non-obstructive azoospermia

Salas-Huetos A, Tüttelmann F, Wyrwoll MJ, Kliesch S, Lopes AM, Goncalves J, Boyden SE, Wöste M, Hotaling JM; GEMINI Consortium, Nagirnaja L, Conrad DF, Carrell DT, Aston KI

Hum Genet. 2021. Jan;140(1):217-227. doi: 10.1007/s00439-020-02236-1. Epub 2020 Nov 19. PMID: 33211200

PMID: 33211200

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ped_draw: pedigree drawing with ease.

Velinder M, Lee D, Marth G.

BMC Bioinformatics. 2020 Dec 9;21(1):569. doi: 10.1186/s12859-020-03917-4.

PMID: 33297934

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gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization.

Di Sera T, Velinder M, Ward A, Qiao Y, Georges S, Miller C, Pitman A, Richards W, Ekawade A, Viskochil D, Carey JC, Pace L, Bale J, Clardy SL, Andrews A, Botto L, Marth G.

medRxiv. 2020 Nov 6:2020.11.05.20224865. doi: 10.1101/2020.11.05.20224865. Preprint.

PMID: 33173897

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Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias.

Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G.

HGG Adv. 2020 Oct 22;1(1):100008. doi: 10.1016/j.xhgg.2020.100008. Epub 2020 Aug 25.

PMID: 33263113

Development of a Portable Tool to Identify Patients With Atrial Fibrillation Using Clinical Notes From the Electronic Medical Record

Shah RU, Mutharasan RK, Ahmad FS, Rosenblatt AG, Gay HC, Steinberg BA, Yandell M, Tristani-Firouzi M, Klewer J, Mukherjee R, Lloyd-Jones DM

Circulation: Cardiovascular Quality and Outcomes, 13(10) October 2020, e006516

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Clinical and molecular epidemiology of invasive Staphylococcus aureus infection in Utah children; continued dominance of MSSA over MRSA

Crandall H, Kapusta A, Killpack J, Heyrend C, Nilsson K, Dickey M, Daly JA, mpofo K, Pavia AT, Mulvey MA, Yandell M, Hulten KG, Blaschke AJ.

PLoSONE 15(9):e0238991

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Genomic analyses implicate noncoding de novo variants in congenital heart disease.

Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA Jr, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD.

Nat Genet. 2020 Aug;52(8):769-777. doi: 10.1038/s41588-020-0652-z. Epub 2020 Jun 29.

PMID: 32601476

Curses or Cures: A Review of the Numerous Benefits Versus the Biosecurity Concerns of Conotoxin Research.

Bjørn-Yoshimoto WE, Ramiro IBL, Yandell M, McIntosh JM, Olivera BM, Ellgaard L, Safavi-Hemami H

Biomedicines . 2020 Jul 22;8(8):E235. doi: 10.3390/biomedicines8080235.

PMID: 32708023

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches.

Pedersen BS, Bhetariya PJ, Brown J, Kravitz SN, Marth G, Jensen RL, Bronner MP, Underhill HR, Quinlan AR

Genome Med. 2020; 12: 62. Published online 2020 Jul 14. doi: 10.1186/s13073-020-00761-2


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MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate.

Ireland AS, Micinski AM, Kastner DW, Guo B, Wait SJ, Spainhower KB, Conley CC, Chen OS, Guthrie MR, Soltero D, Qiao Y, Huang X, Tarapcsák S, Devarakonda S, Chalishazar MD, Gertz J, Moser JC, Marth G, Puri S, Witt BL, Spike BT, Oliver TG

Cancer Cell . 2020 Jul 13;38(1):60-78.e12. doi: 10.1016/j.ccell.2020.05.001. Epub 2020 May 30.

PMID: 32473656

Regulatory sharing between estrogen receptor α bound enhancers.

Carleton JB, Ginley-Hidinger M, Berrett KC, Layer RM, Quinlan AR, Gertz J

Nucleic Acids Res. 2020 Jul 9;48(12):6597-6610. doi: 10.1093/nar/gkaa454

PMID: 32479598

Pulmonary Eosinophilic Granulomatosis with Polyangiitis Has IgG4 Plasma Cells and Immunoregulatory Features.

Dong ZM, Lin E, Wechsler ME, Weller PF, Klion AD, Bochner BS, Delker DA, Hazel MW, Fairfax K, Khoury P, Akuthota P, Merkel PA, Dyer AM, Langford C, Specks U, Gleich GJ, Chinchilli VM, Raby B, Yandell M, Clayton F

Am J Pathol . 2020 Jul;190(7):1438-1448. doi: 10.1016/j.ajpath.2020.03.005. Epub 2020 Apr 3.

PMID: 32251643

Germline mutation rates in young adults predict longevity and reproductive lifespan.

Cawthon RM, Meeks HD, Sasani TA, Smith KR, Kerber RA, O'Brien E, Baird L, Dixon MM, Peiffer AP, Leppert MF, Quinlan AR, Jorde LB

PMID: 32561805

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A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia).

Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD

PLoS Genet . 2020 May 20;16(5):e1008274. doi: 10.1371/journal.pgen.1008274. eCollection 2020 May.

PMID: 32433666

Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus.

Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE

Genome Biol Evol . 2020 May 1;12(5):684-700. doi: 10.1093/gbe/evaa083.

PMID: 32333764

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Comprehensive Analysis of AR Alterations in Circulating Tumor DNA from Patients with Advanced Prostate Cancer.

Ledet EM, Lilly MB, Sonpavde G, Lin E, Nussenzveig RH, Barata PC, Yandell M, Nagy RJ, Kiedrowski L, Agarwal N, Sartor O

Oncologist . 2020 Apr;25(4):327-333. doi: 10.1634/theoncologist.2019-0115. Epub 2019 Nov 11.

PMID: 32297439

The stochastic nature of errors in next-generation sequencing of circulating cell-free DNA.

Nix DA, Hellwig S, Conley C, Thomas A, Fuertes CL, Hamil CL, Bhetariya PJ, Garrido-Laguna I, Marth GT, Bronner MP, Underhill HR.

PLoS One. 2020 Feb 21;15(2):e0229063. doi: 10.1371/journal.pone.0229063. eCollection 2020.

PMID: 32084206

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XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.

Berg JA, Belyeu JR, Morgan JT, Ouyang Y, Bott AJ, Quinlan AR, Gertz J, Rutter J

PLoS Comput Biol . 2020 Jan 31;16(1):e1007625. doi: 10.1371/journal.pcbi.1007625. eCollection 2020 Jan.

PMID: 32004313

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Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists

Ekawade A, Velinder M, Ward A, DiSera T, Miller C, Qiao Y, Marth G

BMC Medical Genomics 12:190

PMID: 31829207

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De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes.

Watkins WS, Hernandez EJ, Wesolowski S, Bisgrove BW, Sunderland RT, Lin E, Lemmon G, Demarest BL, Miller TA, Bernstein D, Brueckner M, Chung WK, Gelb BD, Goldmuntz E, Newburger JW, Seidman CE, Shen Y, Yost HJ, Yandell M, Tristani-Firouzi M

Nat Commun. 2019 Oct 17;10(1):4722. doi: 10.1038/s41467-019-12582-y.

PMID: 31624253

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Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation.

Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR.

Elife. 2019 Sep 24;8. pii: e46922. doi: 10.7554/eLife.46922.

PMID: 31549960

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Identification of Polycystic Kidney Disease 1 Like 1 Gene Variants in Children With Biliary Atresia Splenic Malformation Syndrome

Berauer JP, Mezina AI, Okou DT, Sabo A, Muzny DM, Gibbs RA, Hegde MR, Chopra P, Cutler DJ, Perlmutter DH, Bull LN, Thompson RJ, Loomes KM, Spinner NB, Rajagopalan R, Guthery SL, Moore B, Yandell M, Harpavat S, Magee JC, Kamath BM, Molleston JP, Bezerra JA, Murray KF, Alonso EM, Rosenthal P, Squires RH, Wang KS, Finegold MJ, Russo P, Sherker AH, Sokol RJ, Karpen SJ; Childhood Liver Disease Research Network (ChiLDReN).

Hepatology. 2019 Sep;70(3):899-910. doi: 10.1002/hep.30515. Epub 2019 Mar 21

PMID: 30664273

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Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy

Bhatia A, BC, Cogan J, Koziura ME, Brokamp E, Phillips J, Newman J, Undiagnosed Diseases Network (UDN), Moore SA, Hamid R

Clinical Imaging 58:108-113

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A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia).

Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Yandell M, Shapiro MD

BioRxiv doi:

Immune correlates of CD73 expression in patients with urothelial carcinoma (UC).

Lin E, Roberto Nussenzveig R, Hahn AW, Yandell M, Harshman LC, Agarwal N, Tripathi A

J Clin Oncol 37 suppl 15:4548

NT5E expression and the immune landscape of prostate cancer (PC): An analysis from The Cancer Genome Atlas database

Hahn AW, Edwin Lin E, Esther J, Anderson N, Rathi N, Yandell M, Maughan BL, Agarwal N

J Clin Oncol 37 suppl 15:5043

Profiling of genomic alterations in MAPK/ERK signaling in a large cohort of metastatic prostate cancer (mPC) patients

Lin E, Hahn AW, Sonpavde G, Lilly MB, Nussenzveig R, Ledet E, Pal SK, Grivas P, Rich TA, Raymond VM, Sartor AO, Yandell M, Agarwal N

J Clin Oncol 37 suppl 15:5032

Overlooked roles of DNA damage and maternal age in generating human germline mutations

Gao Z, Moorjani P, Sasani TA, Pedersen BS Quinlan AR, Jorde LB, Amster G, Przeworski M

Proc Natl Acad Sci U S A. 2019 May 7; 116(19): 9491–9500

PMCID: PMC6511033

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Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls

Pedersen BS, Quinlan AR

Gigascience. 2019 Apr; 8(4): giz040. doi: 10.1093/gigascience/giz040

PMCID: PMC6479422

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Coexpression patterns define epigenetic regulators associated with neurological dysfunction

Boukas L, Havrilla JM, Hickey PF, Quinlan AR, Bjornsson HT, Hansen KD

Genome Res. 2019 Apr;29(4):532-542. doi: 10.1101/gr.239442.118. Epub 2019 Mar 1

PMID: 30858344

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Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson MP, et al.

Nat Commun. 2019; 10: 1784. Published online 2019 Apr 16. doi: 10.1038/s41467-018-08148-z

PMCID: PMC6467913

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Discovery of targetable mutational signatures in advanced prostate cancer (aPC) using machine learning and next-generation sequencing (NGS) of circulating tumor DNA (ctDNA)

Lin E, Hahn AW, Sonpavde G, Lilly MB, Nussenzveig R, Ledet E, Pal SK, Grivas P, Rich TA, Raymond VM, Sartor AO, Yandell M, Agarwal N

J Clin Oncol 37 suppl 7:226

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder.

An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ

Science. 2018 Dec 14;362(6420). pii: eaat6576. doi: 10.1126/science.aat6576.

PMID: 30545852

A map of constrained coding regions in the human genome

Havrilla JM, Pedersen BS, Layer RM, Quinlan AR

Nat Genet. 2018 Dec 10. doi: 10.1038/s41588-018-0294-6. [Epub ahead of print]

PMID: 30531870

Discovery of Novel Conotoxin Candidates Using Machine Learning

Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M

Toxins (Basel). 2018 Dec 1;10(12). pii: E503. doi: 10.3390/toxins10120503

PMID: 30513724

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Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia

Wooderchak-Donahue WL, McDonald J, Farrell A, Akay G, Velinder M, Johnson P, VanSant-Webb C, Margraf R, Briggs E, Whitehead KJ, Thomson J, Lin AE, Pyeritz RE, Marth G, Bayrak-Toydemir P

J Med Genet. 2018 Dec;55(12):824-830. doi: 10.1136/jmedgenet-2018-105561. Epub 2018 Sep 2

PMID: 30244195

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Fine-mapping and functional studies highlight potential causal variants for rheumatoid arthritis and type 1 diabetes

Westra HJ, Martínez-Bonet M, Onengut-Gumuscu S, Lee A, Luo Y, Teslovich N, Worthington J, Martin J, Huizinga T, Klareskog L, Rantapaa-Dahlqvist S, Chen WM, Quinlan A, Todd JA, Eyre S, Nigrovic PA, Gregersen PK, Rich SS, Raychaudhuri S.

Nat Genet. 2018 Oct;50(10):1366-1374. doi: 10.1038/s41588-018-0216-7. Epub 2018 Sep 17

PMID: 30224649

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

Sasani TA, Cone KR, Quinlan AR, Elde NC

Elife. 2018 Aug 29;7. pii: e35453. doi: 10.7554/eLife.35453

PMCID: PMC6115191

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Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy

Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR

NPJ Genom Med. 2018 Aug 13;3:22. doi: 10.1038/s41525-018-0061-8. eCollection 2018

PMCID: PMC6089881

Automated size selection for short cell-free DNA fragments enriches for circulating tumor DNA and improves error correction during next generation sequencing

Hellwig S, Nix DA, Gligorich KM, O'Shea JM, Thomas A, Fuertes CL, Bhetariya PJ, Marth GT, Bronner MP, Underhill HR

PLoS One. 2018 Jul 25;13(7):e0197333. doi: 10.1371/journal.pone.0197333. eCollection 201

PMID: 30044795

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Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon

Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD

Elife. 2018 Jul 17;7. pii: e34803. doi: 10.7554/eLife.34803

PMCID: PMC6050045

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Coloc-stats: a unified web interface to perform colocalization analysis of genomic features

Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Quinlan AR, Sheffield NC, Trynka G, Sandve GK

Nucleic Acids Res. 2018 Jul 2;46(W1):W186-W193. doi: 10.1093/nar/gky474

PMCID: PMC6030976

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RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis

Peterson KA, Yoshigi M, Hazel MW, Delker DA, Lin E, Krishnamurthy C, Consiglio N, Robson J, Yandell M, Clayton F

Aliment Pharmacol Ther. 2018 Jul;48(2):219-225. doi: 10.1111/apt.14825. Epub 2018 Jun 4

PMID: 29863285

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SV-plaudit: A cloud-based framework for manually curating thousands of structural variants

Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Quinlan AR, Layer RM

Gigascience. 2018 May 31. doi: 10.1093/gigascience/giy064. [Epub ahead of print]

PMID: 29860504

Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato

Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH

Plant Cell. 2018 May 9. pii: tpc.00194.2018. doi: 10.1105/tpc.18.00194. [Epub ahead of print]

PMID: 29743197

hts-nim: scripting high-performance genomic analyses

Pedersen BS, Quinlan AR

Bioinformatics. 2018 Apr 30. doi: 10.1093/bioinformatics/bty358. [Epub ahead of print]

PMID: 29718142

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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

Werling DM, Brand H, An JY, Stone MR, Zhu L, Glessner JT, Collins RL, Dong S, Layer RM, Markenscoff-Papadimitriou E, Farrell A, Schwartz GB, Wang HZ, Currall BB, Zhao X, Dea J, Duhn C, Erdman CA, Gilson MC, Yadav R, Handsaker RE, Kashin S, Klei L, Mandell JD, Nowakowski TJ, Liu Y, Pochareddy S, Smith L, Walker MF, Waterman MJ, He X, Kriegstein AR, Rubenstein JL, Sestan N, McCarroll SA, Neale BM, Coon H, Willsey AJ, Buxbaum JD, Daly MJ, State MW, Quinlan AR, Marth GT, Roeder K, Devlin B, Talkowski ME, Sanders SJ

Nat Genet. 2018 Apr 26. doi: 10.1038/s41588-018-0107-y. [Epub ahead of print]

PMID: 29700473

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features

Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE

Bioinformatics. 2018 Apr 25. doi: 10.1093/bioinformatics/bty324. [Epub ahead of print]

PMID: 29701825

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Nanopore sequencing and assembly of a human genome with ultra-long reads

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O’Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29

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Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective

Than H, Qiao Y, Huang X, Yan D, Khorashad JS, Pomicter AD, Kovacsovics TJ, Marth GT, O'Hare T, Deininger MW

Leukemia. 2018 Mar 27. doi: 10.1038/s41375-018-0050-z. [Epub ahead of print]

PMID: 29588547

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Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)

Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, Domyan E, Suh AWarren WCYandell M, Gilbert TP, Shapiro MD

G3 (Bethesda). 2018 Mar 8. pii: g3.300443.2017. doi: 10.1534/g3.117.300443. [Epub ahead of print]

PMID: 29519939

mosdepth: quick coverage calculation for genomes and exomes

Pedersen BS, Quinlan AR

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699

PMID: 29096012

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The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool.

Flygare S, Hernandez EJ, Phan L, Moore B, Li M, Fejes A, Hu H, Eilbeck K, Huff C, Jorde L, G Reese M, Yandell M.

BMC Bioinformatics. 2018 Feb 20;19(1):57. doi: 10.1186/s12859-018-2056-y.

PMID: 29463208

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Primary Ovarian Insufficiency and Azospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation

Al-Agha AE, Ahmed IA, Nuebel E, Moriwaki M, Moore B, Peacock KA, Mosbruger T, Neklason DW, Jorde LB, Yandell M, Welt CK

J Clin Endocrinol Metab. 2018 Feb 1;103(2):555-563. doi: 10.1210/jc.2017-01966

PMID: 29240891

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Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study

Manuck TA, Watkins WS, Esplin MS, Biggio J, Bukowski R, Parry S, Zhan H, Huang H, Andrews W, Saade G, Sadovsky Y, Reddy UM, Ilekis J, Yandell M, Varner MW, Jorde LB, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Genomics and Proteomics Network for Preterm Birth Research (GPN-PBR)

BJOG. 2018 Feb;125(3):343-350. doi: 10.1111/1471-0528.14485. Epub 2017 Jan 31

PMID: 28139890

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The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution

Smith JJ, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT

Nat Genet. 2018 Jan 22. doi: 10.1038/s41588-017-0036-1. [Epub ahead of print]

PMID: 29358652

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GIGGLE: a search engine for large-scale integrated genome analysis

Layer RM, Pedersen BS, DiSera T, Marth GT, Gertz J, Quinlan AR

Nat Methods. 2018 Jan 8. doi: 10.1038/nmeth.4556. [Epub ahead of print]

PMID: 29309061

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Identification of ATIC as a Novel Target for Chemoradiosensitization

Liu X, Paila UD, Teraoka SN, Wright JA, Huang X, Quinlan AR, Gatti RA, Concannon P

Int J Radiat Oncol Biol Phys. 2018 Jan 1;100(1):162-173. doi: 10.1016/j.ijrobp.2017.08.033. Epub 2017 Sep 21

PMID: 29029884

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XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets

Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MA, Yandell M, Huff CD

Nucleic Acids Res. 2017 Dec 23. doi: 10.1093/nar/gkx1280. [Epub ahead of print]

PMID: 29294048

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Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools

Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT

J Clin Transl Sci. 2017 Dec;1(6):381-386. doi: 10.1017/cts.2017.311.

PMID: 29707261

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Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, Zeng X, Qi H, Chang W, Sierant MC, Hung WC, Haider S, Zhang J, Knight J, Bjornson RD, Castaldi C, Tikhonoa IR, Bilguvar K, Mane SM, Sanders SJ, Mital S, Russell MW, Gaynor JW, Deanfield J, Giardini A, Porter GA Jr, Srivastava D, Lo CW, Shen Y, Watkins WS, Yandell M, Yost HJ, Tristani-Firouzi M, Newburger JW, Roberts AE, Kim R, Zhao H, Kaltman JR, Goldmuntz E, Chung WK, Seidman JG, Gelb BD, Seidman CE, Lifton RP, Brueckner M

Nat Genet. 2017 Nov;49(11):1593-1601. doi: 10.1038/ng.3970. Epub 2017 Oct 9

PMID: 28991257

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Combating subclonal evolution of resistant cancer phenotypes

Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH

Nat Commun. 2017 Nov 1;8(1):1231. doi: 10.1038/s41467-017-01174-3

PMID: 29093439

Indexcov: fast coverage quality control for whole-genome sequencing

Pedersen BS, Collins RL, Talkowski ME, Quinlan AR

Gigascience. 2017 Nov 1;6(11):1-6. doi: 10.1093/gigascience/gix090

PMID: 29048539

Settling the score: variant prioritization and Mendelian disease

Eilbeck K, Quinlan A, Yandell M

Nat Rev Genet. 2017 Oct;18(10):599-612. doi: 10.1038/nrg.2017.52. Epub 2017 Aug 14.

PMID: 28804138

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Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia

Schlaberg R, Ampofo K, Tardif KD, Stockmann C, Simmon KE, Hymas W, Flygare S, Kennedy B, Blaschke A, Eilbeck K, Yandell M, McCullers JA, Williams DJ, Edwards K, Arnold SR, Bramley A, Jain S, Pavia AT

J Infect Dis. 2017 Sep 15;216(6):688-696. doi: 10.1093/infdis/jix352.

PMID: 28934425

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Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus

Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H

Genome Biol Evol. 2017 Sep 1;9(9):2211-2225. doi: 10.1093/gbe/evx157

PMID: 28922871

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The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae

Neale DB, McGuire PE, Wheeler NC, Stevens KA, Crepeau MW, Cardeno C, Zimin AV, Puiu D, Pertea GM, Sezen UU, Casola C, Koralewski TE, Paul R, Gonzalez-Ibeas D, Zaman S, Cronn R, Yandell M, Holt C, Langley CH, Yorke JA, Salzberg SL, Wegrzyn JL

G3 (Bethesda). 2017 Jul 27. pii: g3.300078.2017. doi: 10.1534/g3.117.300078. [Epub ahead of print]

PMID: 28751502

The evolving genetic risk for sporadic ALS

Gibson SB, Downie JM, Tsetsou S, Feusier JE, Figueroa KP, Bromberg MB, Jorde LB, Pulst SM

Neurology. 2017 Jul 18;89(3):226-233. doi: 10.1212/WNL.0000000000004109. Epub 2017 Jun 22

PMID: 28642336

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Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings

Lubin IM, Aziz N, Babb LJ, Ballinger D, Bisht H, Church DM, Cordes S, Eilbeck K, Hyland F, Kalman L, Landrum M, Lockhart ER, Maglott D, Marth G, Pfeifer JD, Rehm HL, Roy S, Tezak Z, Truty R, Ullman-Cullere M, Voelkerding KV, Worthey EA, Zaranek AW, Zook JM

J Mol Diagn. 2017 May;19(3):417-426. doi: 10.1016/j.jmoldx.2016.12.001. Epub 2017 Mar 18.

PMCID: PMC5417043

Extremely low-coverage whole genome sequencing in South Asians captures population genomics information

Rustagi N, Zhou A, Watkins WS, Gedvilaite E, Wang S, Ramesh N, Muzny D, Gibbs RA, Jorde LB, Yu F, Xing J

BMC Genomics. 2017 May 22;18(1):396. doi: 10.1186/s12864-017-3767-6

PMCID: PMC5440948

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The Venom Repertoire of Conus gloriamaris (Chemnitz, 1777), the Glory of the Sea

Robinson SD, Li Q, Lu A, Bandyopadhyay PK, Yandell M, Olivera BM, Safavi-Hemami H

Mar Drugs. 2017 May 20;15(5). pii: E145

PMID: 28531118

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Evolutionary history of Tibetans inferred from whole-genome sequencing

Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, Downie JM, Roach JC, Cole AM, Lorenzo FR, Rogers AR, Brunkow ME, Cavalleri G, Hood L, Alpatty SM, Prchal JT, Jorde LB, Robbins PA, Simonson TS, Huff CD

PLoS Genet. 2017 Apr 27;13(4):e1006675. doi: 10.1371/journal.pgen.1006675. eCollection 2017 Apr

PMCID: PMC5407610

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Hormone-like peptides in the venoms of marine cone snails

Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H

Gen Comp Endocrinol. 2017 Apr 1;244:11-18. doi: 10.1016/j.ygcen.2015.07.012. Epub 2015 Aug 22.

PMCID: PMC4762756 [Available on 2018-04-01]

Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology

Schlaberg R, Queen K, Simmon K, Tardif K, Stockmann C, Flygare S, Kennedy B, Voelkerding K, Bramley A, Zhang J, Eilbeck K, Yandell M, Jain S, Pavia AT, Tong S, Ampofo K

J Infect Dis. 2017 Mar 25. doi: 10.1093/infdis/jix148. [Epub ahead of print]

PMID: 28368491

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POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women

Moriwaki M, Moore B, Mosbruger T, Neklason DW, Yandell M, Jorde LB, Welt CK

J. Endocr. Soc. (2017) 1 (3): 162-173

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cyvcf2: fast, flexible variant analysis with Python

Pedersen BS, Quinlan AR

Bioinformatics. 2017 Feb 6. doi: 10.1093/bioinformatics/btx057

PMID: 28165109

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Who's Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy

Pedersen BS, Quinlan AR

Am J Hum Genet. 2017 Jan 30. pii: S0002-9297(17)30017-4. doi: 10.1016/j.ajhg.2017.01.017. [Epub ahead of print]

PMID: 28190455

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High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE

Majoros WH, Campbell MS, Holt C, DeNardo E, Ware D, Allen AS, Yandell M, Reddy TE

Bioinformatics. 2016 Dec 23. pii: btw799. doi: 10.1093/bioinformatics/btw799. [Epub ahead of print]

PMID: 28011790

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Emergence of a viral RNA polymerase variant during gene copy number amplification promotes rapid evolution of vaccinia virus.

Cone KR, Kronenberg ZN, Yandell M, Elde NC

J Virol. 2016 Dec 7. pii: JVI.01428-16. [Epub ahead of print]

PMID: 27928012

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VARPRISM: incorporating variant prioritization in tests of de novo mutation association

Hu H, Coon H, Li M, Yandell M, Huff CD

Genome Med. 2016 Aug 25;8(1):91. doi: 10.1186/s13073-016-0341-9

PMID: 27562213

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Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa

Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM

Mol Biol Evol. 2016 Aug 14. pii: msw174. [Epub ahead of print]

PMID: 27524826

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Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy.

Khorashad JS, Tantravahi SK, Yan D, Mason CC, Qiao Y, Eiring AM, Gligorich K, Hein T, Pomicter AD, Reid AG, Kelley TW, Marth GT, O'Hare T, Deininger MW.

Leukemia. 2016 Aug 2. doi: 10.1038/leu.2016.218.

PMID: 27480386

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The draft genome sequence and annotation of the desert woodrat Neotoma lepida

Campbell M, Oakeson KF, Yandell M, Halpert JR, Dearing D

Genom Data. 2016 Jun 23;9:58-9. doi: 10.1016/j.gdata.2016.06.008

PMCID: PMC4927542

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Association of TMTC2 With Human Nonsyndromic Sensorineural Hearing Loss

Runge CL, Indap A, Zhou Y, Kent JW Jr, King E, Erbe CB, Cole R, Littrell J, Merath K, James R, Rüschendorf F, Kerschner JE, Marth G, Hübner N, Göring HH, Friedland DR, Kwok WM, Olivier M.

JAMA Otolaryngol Head Neck Surg. 2016 Jun 16. doi: 10.1001/jamaoto.2016.1444

PMID: 27311106

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Vcfanno: fast, flexible annotation of genetic variants.

Pedersen BS, Layer RM, Quinlan AR

Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5

PMCID: PMC4888505

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Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA profiling

Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Gabor Marth G, Yandell M, Schlaberg R  

Genome Biol. 2016 May 26;17(1):111. doi: 10.1186/s13059-016-0969-1

PMID: 27224977

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Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans

Barber MF, Kronenberg Z, Yandell M, Elde NC

PLoS Genet. 2016 May 20;12(5):e1006063. doi: 10.1371/journal.pgen.1006063. eCollection 2016.

PMID: 27203426

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OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data

Huang J, Gutierrez F, Strachan HJ, Dou D, Huang W, Smith B, Blake JA, Eilbeck K, Natale DA, Lin Y, Wu B, Silva Nd, Wang X1, Liu Z, Borchert GM, Tan M, Ruttenberg A

J Biomed Semantics. 2016 May 10;7:25. doi: 10.1186/s13326-016-0064-2. eCollection 2016

PMID: 27175225

The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology

Huang J, Eilbeck K, Smith B, Blake JA, Dou D, Huang W, Natale D, Ruttenberg A, Huan J, Zimmermann MT, Jiang G, Lin Y, Wu B, Strachan HJ, He Y, Zhang S, Wang X, Liu Z, Borchert GM, Tan M

J Biomed Semantics. 2016 May 4;7:24. doi: 10.1186/s13326-016-0066-0. eCollection 2016

PMID: 27152146

A proposed clinical decision support architecture capable of supporting whole genome sequence information

Welch BM, Loya SR, Eilbeck K, Kawamoto K

J Pers Med. 2014 Apr 4;4(2):176-99. doi: 10.3390/jpm4020176.

PMID: 25411644

Age-related mutations and chronic myelomonocytic leukemia

Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Zabriskie MS, Yan D, Pomicter AD, Reynolds KR, Eiring AM, Kronenberg Z, Sherman RL, Tyner JW, Dalley BK, Dao KH, Yandell M, Druker BJ, Gotlib J, O'Hare T, Deininger MW

Leukemia. 2016 April. 30(4):906-13. doi: 10.1038/leu.2015.337. [Epub ahead of print]

PMID: 26648538

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The genomic CDS sandbox: An assessment among domain experts

Aziz A, Kawamoto K, Eilbeck K, Williams MS, Freimuth RR, Hoffman MA, Rasmussen LV, Overby CL, Shirts BH, Hoffman JM, Welch BM

J Biomed Inform. 2016 Apr;60:84-94. doi: 10.1016/j.jbi.2015.12.019. Epub 2016 Jan 15

PMID: 26778834

Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species

Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD

Elife. 2016 Mar 15;5. pii: e12115. doi: 10.7554/eLife.12115

PMID: 26977633

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Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides.

Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L

Proc Natl Acad Sci U S A. 2016 Mar 8. pii: 201525790 [Epub ahead of print]

PMID: 26957604

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The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH

Nat Genet. 2016 Mar 7. doi: 10.1038/ng.3526. [Epub ahead of print]

PMID: 26950095

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Targeted Deep Sequencing in Multiple-Affected Sibships of European Ancestry Identifies Rare Deleterious Variants in PTPN22 that Confer Risk for Type 1 Diabetes

Ge Y, Onengut-Gumuscu S, Quinlan AR, Mackey AJ, Wright JA, Buckner JH, Habib T, Rich SS, Concannon P

Diabetes. 2016 Mar;65(3):794-802. pii: db150322. [Epub ahead of print]

PMCID: PMC4764149

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Unbiased Detection of Respiratory Viruses Using RNA-seq-Based Metagenomics: A Systematic Comparison to A Commercial PCR Panel.

Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R

J Clin Microbiol. 2016 Apr;54(4):1000-7. doi: 10.1128/JCM.03060-15

PMID: 26818672

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Genetic variation may influence response to 17-alpha hydroxyprogesterone caproate (17P) for recurrent preterm birth (PTB) prevention

Manuck TA, Watkins S, Esplin MS, Parry S, Zhang H, Huang H, Biggio JR, Bukowski R, Saade G, Andrews W, Baldwin D, Sadovsky Y, Reddy U, Ilekis J, Varner MW, Yandell M, Jorde LB

Am J Obstet Gynecol 214(1):S9–S10

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Gene set enrichment investigation of maternal exome variation in spontaneous preterm birth (SPTB)

Manuck TA, Watkins S, Eplin MS, Parry S, Zhang H, Huang H, Biggio JR, Bukowski R, Saade G, Andrews W, Baldwin D, Sadovsky Y, Reddy U, Ilekis J, Varner MW, Jorde LJ, Yandell M.

Am J Obstet Gynecol 214(1):S142–S143.

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An Introduction to Genome Annotation

Campbell MS, Yandell M

Curr Protoc Bioinformatics. 2015 Dec 17;52:4.1.1-4.1.17. doi: 10.1002/0471250953.bi0401s52

PMID: 26678385

Shared genetic variants among streptococcus pneumonia isolates causing complicated pneumonia and empyema in children

Osborne E, Blaschke AJ, Ampofo K, Crandall H, Killpack J, Stockmann CR, Farrell AP, Fischer KF, Pavla A, Eilbeck K, Schlaberg R, Yandell M, Byington CL

Open Forum Infect Dis 2 (Suppl 1):S8. doi: 10.1093/ofid/ofv131.20

Wham: Identifying Structural Variants of Biological Consequence

Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M

PLoS Comput Biol. 2015 Dec 1;11(12):e1004572. doi: 10.1371/journal.pcbi.1004572. eCollection 2015

PMID: 26625158

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miRNA Nomenclature: A View Incorporating Genetic Origins, Biosynthetic Pathways, and Sequence Variants

Desvignes T, Batzel P, Berezikov E, Eilbeck K, Eppig JT, McAndrews MS, Singer A, Postlethwait JH

Trends Genet. 2015 Nov;31(11):613-26. doi: 10.1016/j.tig.2015.09.002. Epub 2015 Oct 8

PMID: 26453491

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Osborne Nishimura E, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B

Proc Natl Acad Sci U S A. 2015 Nov 23. pii: 201510461

PMID: 26598659

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Efficient genotype compression and analysis of large genetic-variation data sets.

Layer RM, Kindlon N, Karczewski KJ; Exome Aggregation Consortium, Quinlan AR.

Nat Methods. 2015 Nov 9. doi: 10.1038/nmeth.3654. [Epub ahead of print]

PMID: 26550772

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Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

Singh R, Kuscu C, Quinlan A, Qi Y, Adli M

Nucleic Acids Res. 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575. Epub 2015 Jun 1

PMCID: PMC4605288

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A global reference for human genetic variation

1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR

Nature 526, 68–74 (01 October 2015) doi:10.1038/nature15393

PMID: 26432245

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An integrated map of structural variation in 2,504 human genomes

Peter H. Sudmant,    Tobias Rausch,    Eugene J. Gardner,    Robert E. Handsaker,    Alexej Abyzov, John Huddleston,    Yan Zhang,    Kai Ye,    Goo Jun,    Markus Hsi-Yang Fritz,    Miriam K. Konkel,    Ankit Malhotra,    Adrian M. Stütz,    Xinghua Shi,    Francesco Paolo Casale,    Jieming Chen,    Fereydoun Hormozdiari,    Gargi Dayama,    Ken Chen,    Maika Malig,    Mark J. P. Chaisson,    Klaudia Walter, Sascha Meiers,    Seva Kashin,    Erik Garrison,    Adam Auton,    Hugo Y. K. Lam,    Xinmeng Jasmine Mu,    Can Alkan,    Danny Antaki,    Taejeong Bae,    Eliza Cerveira,    Peter Chines,    Zechen Chong, Laura Clarke,    Elif Dal,    Li Ding,    Sarah Emery,    Xian Fan,    Madhusudan Gujral,    Fatma Kahveci, Jeffrey M. Kidd,    Yu Kong,    Eric-Wubbo Lameijer,    Shane McCarthy,    Paul Flicek,    Richard A. Gibbs,    Gabor Marth,    Christopher E. Mason,    Androniki Menelaou,    Donna M. Muzny,    Bradley J. Nelson,    Amina Noor,    Nicholas F. Parrish,    Matthew Pendleton,    Andrew Quitadamo,    Benjamin Raeder,    Eric E. Schadt,    Mallory Romanovitch,    Andreas Schlattl,    Robert Sebra,    Andrey A. Shabalin,    Andreas Untergasser,    Jerilyn A. Walker,    Min Wang,    Fuli Yu,    Chengsheng Zhang, Jing Zhang,    Xiangqun Zheng-Bradley,    Wanding Zhou,    Thomas Zichner,    Jonathan Sebat,    Mark A. Batzer,    Steven A. McCarroll,    The 1000 Genomes Project Consortium,    Ryan E. Mills,    Mark B. Gerstein,    Ali Bashir,    Oliver Stegle,    Scott E. Devine,    Charles Lee,    Evan E. Eichler    & Jan O. Korbel

Nature 526, 75–81 (01 October 2015) doi:10.1038/nature15394

PMCID: PMC4617611

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Sequence Analysis and Characterization of Active Human Alu subfamilies Based on the 1000 Genomes Pilot Project.

Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT; 1000 Genomes Consortium, Batzer MA.

Genome Biol Evol. 2015 Aug 29. pii: evv167. [Epub ahead of print]

PMID: 26319576

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A high-throughput next-generation sequencing assay for the mitochondrial genome

Dames S, Eilbeck K, Mao R

Methods Mol Biol. 2015;1264:77-88. doi: 10.1007/978-1-4939-2257-4_8

PMID: 25631005

Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

Thibault JC, Roe DR, Eilbeck K, Cheatham Iii TE, Facelli JC

SAR QSAR Environ Res. 2015;26(7-9):577-93. doi: 10.1080/1062936X.2015.1076515. Epub 2015 Sep 21

PMID: 26387907

Hormone-like peptides in the venoms of marine cone snails.

Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H.

Gen Comp Endocrinol. 2015 Aug 22. pii: S0016-6480(15)00214-2. doi: 10.1016/j.ygcen.2015.07.012. [Epub ahead of print]

PMID: 26301480

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Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.

Bowles NE, Jou CJ, Arrington CB, Kennedy BJ, Earl A, Matsunami N, Meyers LL, Etheridge SP, Saarel EV, Bleyl SB, Yost HJ, Yandell M, Leppert MF, Tristani-Firouzi M, Gruber PJ; Baylor Hopkins Centers for Mendelian Genomics.

Am J Med Genet Part A. 2015 Aug 18; 167A:2975-2984doi: 10.1002/ajmg.a.37297. [Epub ahead of print]

PMID: 26284702

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SpeedSeq: ultra-fast personal genome analysis and interpretation

Chiang C, Layer RM, Faust GG, Lindberg MR, Rose DB, Garrison EP, Marth GT, Quinlan AR, Hall IM.

Nat Methods. 2015 Aug 10. doi: 10.1038/nmeth.3505. [Epub ahead of print]

PMID: 26258291

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Improving the Sequence Ontology terminology for genomic variant annotation

Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K

J Biomed Semantics. 2015 Jul 31;6:32. doi: 10.1186/s13326-015-0030-4. eCollection 2015

PMID: 26229585

Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project.

Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT Jr, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS; National Heart, Lung, and Blood Institute Exome Sequencing Project.

JAMA Neurol. 2015 Jul 1;72(7):781-8. doi: 10.1001/jamaneurol.2015.0582.

PMID: 25961151

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Building an Ontology for Identity Resolution in Healthcare and Public Health

Duncan J, Eilbeck K, Narus SP, Clyde S, Thornton S, Staes C

Online J Public Health Inform. 2015 Jul 1;7(2):e219. doi: 10.5210/ojphi.v7i2.6010. eCollection 2015.

PMID: 26392849

Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).

Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB.

PLoS One. 2015 Jun 29;10(6):e0131514. doi: 10.1371/journal.pone.0131514. eCollection 2015

PMID: 26121141

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Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ÉD, Simões ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G.

Science. 2015 Jun 5;348(6239):1139-43. doi: 10.1126/science.aaa4788. Epub 2015 May 14.

PMID: 25977371

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Muscle stem cells contribute to myofibres in sedentary adult mice.

Keefe AC, Lawson JA, Flygare SD, Fox ZD, Colasanto MP, Mathew SJ, Yandell M, Kardon G.

Nat Commun. 2015 May 14;6:7087. doi: 10.1038/ncomms8087

PMID: 25971691

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GFVO: the Genomic Feature and Variation Ontology

Baran J, Durgahee BS, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M

PeerJ. 2015 May 5;3:e933. doi: 10.7717/peerj.933. eCollection 2015

PMID: 26019997

Birth of identity: understanding changes to birth certificates and their value for identity resolution

Duncan J, Narus SP, Clyde S, Eilbeck K, Thornton S, Staes C

J Am Med Inform Assoc. 2015 Apr;22(e1):e120-9. doi: 10.1136/amiajnl-2014-002774. Epub 2014 Jul 30.

PMID: 25080533

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P; Type 1 Diabetes Genetics Consortium, Todd JA,Wallace C, Concannon P, Rich SS.

Nat Genet. 2015 Apr;47(4):381-6. doi: 10.1038/ng.3245. Epub 2015 Mar 9.

PMID: 25751624 [PubMed - indexed for MEDLINE] PMCID: PMC4380767 [Available on 2015-10-01]

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The distribution and mutagenesis of short coding INDELs from 1,128 whole exomes

Challis D, Antunes L, Garrison E, Banks E, Evani US, Muzny D, Poplin R, Gibbs RA, Marth G, Yu F

BMC Genomics. 2015 Feb 28;16:143. doi: 10.1186/s12864-015-1333-7

PMCID: PMC4352271

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Toolbox for mobile-element insertion detection on cancer genomes

Lee WP, Wu J, Marth GT

Cancer Inform. 2015 Feb 12;14(Suppl 1):37-44. doi: 10.4137/CIN.S24657. eCollection 2015

PMCID: PMC4338948

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Specialized insulin is used for chemical warfare by fish-hunting cone snails.

Safavi-Hemami H, Gajewiak J, Karanth S, Robinson SD, Ueberheide B, Douglass AD, Schlegel A, Imperial JS, Watkins M, Bandyopadhyay PK, Yandell M, Li Q, Purcell AW, Norton RS, Ellgaard L, Olivera BM.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1743-8. doi: 10.1073/pnas.1423857112. Epub 2015 Jan 20.

PMID: 25605914

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Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction

Do R, Stitziel NO, Won HH, Jørgensen AB, Duga S, Angelica Merlini P, Kiezun A, Farrall M, Goel A, Zuk O, Guella I, Asselta R, Lange LA, Peloso GM, Auer PL; NHLBI Exome Sequencing Project, Girelli D, Martinelli N, Farlow DN, DePristo MA, Roberts R, Stewart AF, Saleheen D, Danesh J, Epstein SE, Sivapalaratnam S, Hovingh GK, Kastelein JJ, Samani NJ, Schunkert H, Erdmann J, Shah SH, Kraus WE, Davies R, Nikpay M, Johansen CT, Wang J, Hegele RA, Hechter E, Marz W, Kleber ME, Huang J, Johnson AD, Li M, Burke GL, Gross M, Liu Y, Assimes TL, Heiss G, Lange EM, Folsom AR, Taylor HA, Olivieri O, Hamsten A, Clarke R, Reilly DF, Yin W, Rivas MA, Donnelly P, Rossouw JE, Psaty BM, Herrington DM, Wilson JG, Rich SS, Bamshad MJ, Tracy RP, Cupples LA, Rader DJ, Reilly MP, Spertus JA, Cresci S, Hartiala J, Tang WH, Hazen SL, Allayee H, Reiner AP, Carlson CS, Kooperberg C, Jackson RD, Boerwinkle E, Lander ES, Schwartz SM, Siscovick DS, McPherson R, Tybjaerg-Hansen A, Abecasis GR, Watkins H, Nickerson DA, Ardissino D, Sunyaev SR, O'Donnell CJ, Altshuler D, Gabriel S, Kathiresan S

Nature. 2015 Feb 5;518(7537):102-6. doi: 10.1038/nature13917. Epub 2014 Dec 10

PMCID: PMC4319990

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Extending reference assembly models.

Church DM, Schneider VA, Steinberg KM, Schatz MC, Quinlan AR, Chin CS, Kitts PA, Aken B, Marth GT, Hoffman MM, Herrero J, Mendoza ML, Durbin R, Flicek P.

Genome Biol. 2015 Jan 24;16:13. doi: 10.1186/s13059-015-0587-3.

PMID: 25651527

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Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.

Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2015 Jan;167(1):25-39. doi: 10.1104/pp.114.245027. Epub 2014 Nov 10.

PMID: 25384563

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DisAp-dependent striated fiber elongation is required to organize ciliary arrays

Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG.

J Cell Biol. 2014 Dec 22;207(6):705-15. doi: 10.1083/jcb.201409123.

PMID: 25533842

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Transposable element islands facilitate adaptation to novel environments in an invasive species

Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, Oettler J.

Nat Commun. 2014 Dec 16;5:5495. doi: 10.1038/ncomms6495.

PMID: 25510865

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Genome Annotation and Curation Using MAKER and MAKER-P

Campbell MS, Holt C, Moore B, Yandell M.

Curr Protoc Bioinformatics. 2014 Dec 12;48:4.11.1-4.11.39. doi: 10.1002/0471250953.bi0411s48.

PMID: 25501943

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bam.iobio: a web-based, real-time, sequence alignment file inspector.

Miller CA, Qiao Y, DiSera T, D'Astous B, Marth GT.

Nat Methods. 2014 Dec;11(12):1189. doi: 10.1038/nmeth.3174.

PMID: 25423016

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Population-based structural variation discovery with Hydra-Multi.

Lindberg MR, Hall IM, Quinlan AR.

Bioinformatics. 2015 Apr 15;31(8):1286-9. doi: 10.1093/bioinformatics/btu771. Epub 2014 Dec 2.

PMID: 25527832

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Poretools: a toolkit for analyzing nanopore sequence data

Loman NJ, Quinlan AR

Bioinformatics. 2014 Dec 1;30(23):3399-401. doi: 10.1093/bioinformatics/btu555

PMCID: PMC4296151

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Evaluation of need for ontologies to manage domain content for the Reportable Conditions Knowledge Management System

Eilbeck KL, Lipstein J, McGarvey S, Staes CJ

AMIA Annu Symp Proc. 2014 Nov 14;2014:496-505. eCollection 2014

PMID: 25954354

Clinical decision support for whole genome sequence information leveraging a service-oriented architecture: a prototype

Welch BM, Rodriguez-Loya S, Eilbeck K, Kawamoto K

AMIA Annu Symp Proc. 2014 Nov 14;2014:1188-97. eCollection 2014

PMID: 25954430

Technical desiderata for the integration of genomic data with clinical decision support

Welch BM, Eilbeck K, Del Fiol G, Meyer LJ, Kawamoto K

J Biomed Inform. 2014 Oct;51:3-7. doi: 10.1016/j.jbi.2014.05.014. Epub 2014 Jun 12

PMID: 24931434

Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma.

Darlington TM, Pimentel R, Smith K, Bakian AV, Jerominski L, Cardon J, Camp NJ, Callor WB, Grey T, Singleton M, Yandell M, Renshaw PF, Yurgelun-Todd DA, Gray D, Coon H.

Transl Psychiatry. 2014 Oct 21;4:e471. doi: 10.1038/tp.2014.111.

PMID: 25335167

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A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer.

Quick J, Quinlan AR, Loman NJ.

Gigascience. 2014 Oct 20;3:22. doi: 10.1186/2047-217X-3-22. eCollection 2014.

PMID: 25386338

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Toolbox for mobile-element insertion detection on cancer genomes.

Lee WP, Wu J, Marth GT.

Cancer Inform. 2014 Oct 15;13(Suppl 4):45-52. doi: 10.4137/CIN.S13979. eCollection 2014.

PMID: 25452688

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Tangram: a comprehensive toolbox for mobile element insertion detection.

Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT.

BMC Genomics. 2014 Sep 16;15:795. doi: 10.1186/1471-2164-15-795.

PMID: 25228379

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Gibbon genome and the fast karyotype evolution of small apes.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA.

Nature. 2014 Sep 11;513(7517):195-201. doi: 10.1038/nature13679.

PMID: 25209798

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Transiently active Wnt/β-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration.

Murphy MM, Keefe AC, Lawson JA, Flygare SD, Yandell M, Kardon G

Stem Cell Reports. 2014 Sep 9;3(3):475-88. doi: 10.1016/j.stemcr.2014.06.019. Epub 2014 Jul 31.

PMID: 25241745

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BEDTools: The Swiss-Army Tool for Genome Feature Analysis.

Quinlan AR.

Curr Protoc Bioinformatics. 2014 Sep 8;47:11.12.1-11.12.34. doi: 10.1002/0471250953.bi1112s47.

PMID: 25199790

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SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization.

Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT.

Genome Biol. 2014 Aug 26;15(8):443. doi: 10.1186/s13059-014-0443-x.

PMID: 25160522

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OMIT: dynamic, semi-automated ontology development for the microRNA domain

Huang J, Dang J, Borchert GM, Eilbeck K, Zhang H, Xiong M, Jiang W, Wu H, Blake JA, Natale DA, Tan M

PLoS One. 2014 Jul 15;9(7):e100855. doi: 10.1371/journal.pone.0100855. eCollection 2014

PMID: 25025130

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C; 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Genome Biol. 2014 Jun 30;15(6):R88. doi: 10.1186/gb-2014-15-6-r88.

PMID: 24980144

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LUMPY: a probabilistic framework for structural variant discovery.

Layer RM, Chiang C, Quinlan AR, Hall IM.

Genome Biol. 2014 Jun 26;15(6):R84. doi: 10.1186/gb-2014-15-6-r84.

PMID: 24970577

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Forward genetic screening identifies a small molecule that blocks Toxoplasma gondii growth by inhibiting both host- and parasite-encoded kinases

Brown KM, Suvorova E2 Farrell A, McLain A, Dittmar A, Wiley GB, Marth G, Gaffney PM, Gubbels MJ, White M, Blader IJ

PLoS Pathog. 2014 Jun 12;10(6):e1004180. doi: 10.1371/journal.ppat.1004180. eCollection 2014

PMCID: PMC4055737

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Novel somatic and germline mutations in intracranial germ cell tumours

Wang L, Yamaguchi S, Burstein MD, Terashima K, Chang K, Ng HK, Nakamura H, He Z, Doddapaneni H, Lewis L, Wang M, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adekunle A, Sun J, Qiao Y, Marth G, Muzny DM, Gibbs RA, Leal SM, Wheeler DA, Lau CC

Nature. 2014 Jul 10;511(7508):241-5. doi: 10.1038/nature13296. Epub 2014 Jun 4

PMCID: PMC4532372

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Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex.

Kumar P P, Emechebe U, Smith R, Franklin S, Moore B, Yandell M, Lessnick SL, Moon AM.

Elife. 2014 May 29;3. doi: 10.7554/eLife.02805.

PMID: 24876127

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A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.

Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD.

Nat Biotechnol. 2014 Jul;32(7):663-9. doi: 10.1038/nbt.2895. Epub 2014 May 18.

PMID: 24837662

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Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii.

Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ.

BMC Genomics. 2014 May 10;15:354. doi: 10.1186/1471-2164-15-354.

PMID: 24885922

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An improved genome release (version Mt4.0) for the model legume Medicago truncatula.

Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD.

BMC Genomics. 2014 Apr 27;15:312. doi: 10.1186/1471-2164-15-312.

PMID: 24767513

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Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.

Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C.

Curr Protoc Hum Genet. 2014 Apr 24;81:6.14.1-6.14.25. doi: 10.1002/0471142905.hg0614s81.

PMID: 24763993

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Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset

Gordon AS, Tabor HK, Johnson AD, Snively BM, Assimes TL, Auer PL, Ioannidis JP, Peters U, Robinson JG, Sucheston LE, Wang D, Sotoodehnia N, Rotter JI, Psaty BM, Jackson RD, Herrington DM, O'Donnell CJ, Reiner AP, Rich SS, Rieder MJ, Bamshad MJ, Nickerson DA; NHLBI GO Exome Sequencing Project

Hum Mol Genet. 2014 Apr 15;23(8):1957-63. doi: 10.1093/hmg/ddt588. Epub 2013 Nov 26

PMCID: PMC3959810

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Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.

Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M.

Am J Hum Genet. 2014 Apr 3;94(4):599-610. doi: 10.1016/j.ajhg.2014.03.010.

PMID: 24702956

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Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.

Manuck TA, Watkins WS, Moore B, Esplin MS, Varner MW, Jackson GM, Yandell M, Jorde L.

Am J Obstet Gynecol. 2014 Apr;210(4):321.e1-321.e21. doi: 10.1016/j.ajog.2014.01.013. Epub 2014 Mar 1.

PMID: 24594138

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TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

Kumar P P, Franklin S, Emechebe U, Hu H, Moore B, Lehman C, Yandell M, Moon AM.

PLoS Genet. 2014 Mar 27;10(3):e1004247. doi: 10.1371/journal.pgen.1004247. eCollection 2014 Mar.

PMID: 24675841

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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM.

Genome Biol. 2014 Mar 25;15(3):R53. doi: 10.1186/gb-2014-15-3-r53.

PMID: 24667040

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In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila.

Chapin A, Hu H, Rynearson SG, Hollien J, Yandell M, Metzstein MM.

G3 (Bethesda). 2014 Mar 20;4(3):485-96. doi: 10.1534/g3.113.009357.

PMID: 24429422

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Homozygous mutation of MTPAP causes cellular radiosensitivity and persistent DNA double-strand breaks.

Martin NT, Nakamura K, Paila U, Woo J, Brown C, Wright JA, Teraoka SN, Haghayegh S, McCurdy D, Schneider M, Hu H, Quinlan AR, Gatti RA, Concannon P.

Cell Death Dis. 2014 Mar 20;5:e1130. doi: 10.1038/cddis.2014.99.

PMID: 24651433

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Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.

Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale DB.

Genetics. 2014 Mar;196(3):891-909. doi: 10.1534/genetics.113.159996.

PMID: 24653211

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MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT.

PLoS One. 2014 Mar 5;9(3):e90581. doi: 10.1371/journal.pone.0090581. eCollection 2014.

PMID: 24599324

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Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martínez-García PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marçais G, Roberts M, Holt C, Yandell M, Davis JM, Smith KE, Dean JF, Lorenz WW, Whetten RW, Sederoff R, Wheeler N, McGuire PE, Main D, Loopstra CA, Mockaitis K, deJong PJ, Yorke JA, Salzberg SL, Langley CH.

Genome Biol. 2014 Mar 4;15(3):R59. doi: 10.1186/gb-2014-15-3-r59.

PMID: 24647006

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Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.

Domyan ET, Guernsey MW, Kronenberg Z, Krishnan S, Boissy RE, Vickrey AI, Rodgers C, Cassidy P, Leachman SA, Fondon JW 3rd, Yandell M, Shapiro MD.

Curr Biol. 2014 Feb 17;24(4):459-64. doi: 10.1016/j.cub.2014.01.020. Epub 2014 Feb 6.

PMID: 24508169

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Combined proteomic and transcriptomic interrogation of the venom gland of Conus geographus uncovers novel components and functional compartmentalization.

Safavi-Hemami H, Hu H, Gorasia DG, Bandyopadhyay PK, Veith PD, Young ND, Reynolds EC, Yandell M, Olivera BM, Purcell AW.

Mol Cell Proteomics. 2014 Apr;13(4):938-53. doi: 10.1074/mcp.M113.031351. Epub 2014 Jan 29.

PMID: 24478445

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Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations.

Chen K, Wu W, Mathew D, Zhang Y, Browne SK, Rosen LB, McManus MP, Pulsipher MA, Yandell M, Bohnsack JF, Jorde LB, Notarangelo LD, Walter JE.

J Allergy Clin Immunol. 2014 Mar;133(3):880-2.e10. doi: 10.1016/j.jaci.2013.11.038. Epub 2014 Jan 25.

PMID: 24472623

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Joint linkage and association analysis with exome sequence data implicates SLC25A40 in hypertriglyceridemia

Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, Brunzell JD, Motulsky AG, Nickerson DA; NHLBI GO Exome Sequencing Project, Wijsman EM, Jarvik GP

Am J Hum Genet. 2013 Dec 5;93(6):1035-45. doi: 10.1016/j.ajhg.2013.10.019. Epub 2013 Nov 21

PMCID: PMC3852929

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SSW library: an SIMD Smith-Waterman C/C++ library for use in genomic applications.

Zhao M, Lee WP, Garrison EP, Marth GT.

PLoS One. 2013 Dec 4;8(12):e82138. doi: 10.1371/journal.pone.0082138. eCollection 2013.

PMID: 24324759

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MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.

Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M.

Plant Physiol. 2014 Feb;164(2):513-24. doi: 10.1104/pp.113.230144. Epub 2013 Dec 4

PMID: 24306534

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The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.

Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson MK.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20651-6. doi: 10.1073/pnas.1314702110. Epub 2013 Dec 2.

PMID: 24297900

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The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.

Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, Pollock DD.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20645-50. doi: 10.1073/pnas.1314475110. Epub 2013 Dec 2.

PMID: 24297902

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Integrating precision medicine in the study and clinical treatment of a severely mentally ill person

O'Rawe JA, Fang H, Rynearson S, Robison R, Kiruluta ES, Higgins G, Eilbeck K, Reese MG, Lyon GJ

PeerJ. 2013 Oct 3;1:e177. doi: 10.7717/peerj.177. eCollection 2013

PMID: 24109560

Integrative annotation of variants from 1092 humans: application to cancer genomics.

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium, Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M.

Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587.

PMID: 24092746

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Characterization of the peptidylglycine α-amidating monooxygenase (PAM) from the venom ducts of neogastropods, Conus bullatus and Conus geographus.

Ul-Hasan S, Burgess DM, Gajewiak J, Li Q, Hu H, Yandell M, Olivera BM, Bandyopadhyay PK.

Toxicon. 2013 Nov;74:215-24. doi: 10.1016/j.toxicon.2013.08.054. Epub 2013 Aug 29.

PMID: 23994590

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Recurrent gain-of-function mutation in PRKG1 causes thoracic aortic aneurysms and acute aortic dissections

Guo DC, Regalado E, Casteel DE, Santos-Cortez RL, Gong L, Kim JJ, Dyack S, Horne SG, Chang G, Jondeau G, Boileau C, Coselli JS, Li Z, Leal SM, Shendure J, Rieder MJ, Bamshad MJ, Nickerson DA; GenTAC Registry Consortium; National Heart, Lung, and Blood Institute Grand Opportunity Exome Sequencing Project, Kim C, Milewicz DM

J Hum Genet. 2013 Aug 8;93(2):398-404. doi: 10.1016/j.ajhg.2013.06.019. Epub 2013 Aug 1

PMCID: PMC3738837

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The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders

Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, Eilbeck K, Mao R.

J Mol Diagn. 2013 Jul;15(4):526-34. doi: 10.1016/j.jmoldx.2013.03.005. Epub 2013 May 9.

PMID: 23665194

Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project

Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP; NHLBI Exome Sequencing Project

Blood. 2013 Jul 25;122(4):590-7. doi: 10.1182/blood-2013-02-485094. Epub 2013 May 20

PMCID: PMC3724194

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GEMINI: integrative exploration of genetic variation and genome annotations.

Paila U, Chapman BA, Kirchner R, Quinlan AR.

PLoS Comput Biol. 2013;9(7):e1003153. doi: 10.1371/journal.pcbi.1003153. Epub 2013 Jul 18.

PMID: 23874191

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Genetic basis for phenotypic differences between different Toxoplasma gondii type I strains.

Yang N, Farrell A, Niedelman W, Melo M, Lu D, Julien L, Marth GT, Gubbels MJ, Saeij JP.

BMC Genomics. 2013 Jul 10;14:467. doi: 10.1186/1471-2164-14-467.

PMID: 23837824

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Variant discovery in targeted resequencing using whole genome amplified DNA.

Indap AR, Cole R, Runge CL, Marth GT, Olivier M.

BMC Genomics. 2013 Jul 10;14:468. doi: 10.1186/1471-2164-14-468.

PMID: 23837845

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VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.

Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M.

Genet Epidemiol. 2013 Sep;37(6):622-34. doi: 10.1002/gepi.21743. Epub 2013 Jul 8.

PMID: 23836555

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Fine-scale patterns of population stratification confound rare variant association tests

O'Connor TD, Kiezun A, Bamshad M, Rich SS, Smith JD, Turner E; NHLBIGO Exome Sequencing Project; ESP Population Genetics, Statistical Analysis Working Group, Leal SM, Akey JM

PLoS One. 2013 Jul 4;8(7):e65834. doi: 10.1371/journal.pone.0065834. Print 2013

PMCID: PMC3701690

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ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.

Flygare S, Campbell M, Ross RM, Moore B, Yandell M.

J Comput Biol. 2013 Aug;20(8):583-92. doi: 10.1089/cmb.2013.0025. Epub 2013 Jul 3.

PMID: 23822514

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Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).

Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J.

Genome Biol. 2013 May 10;14(5):R41. doi: 10.1186/gb-2013-14-5-r41.

PMID: 23663246

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Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.

Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C.

PLoS Genet. 2013 Apr;9(4):e1003470. doi: 10.1371/journal.pgen.1003470. Epub 2013 Apr 25.

PMID: 23637635

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The African coelacanth genome provides insights into tetrapod evolution

Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K

Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027

PMCID: PMC3633110

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Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W

Nat Genet. 2013 Apr;45(4):415-21, 421e1-2. doi: 10.1038/ng.2568. Epub 2013 Feb 24

PMCID: PMC3709584

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Scotty: a web tool for designing RNA-Seq experiments to measure differential gene expression.

Busby MA, Stewart C, Miller CA, Grzeda KR, Marth GT.

Bioinformatics. 2013 Mar 1;29(5):656-7. doi: 10.1093/bioinformatics/btt015. Epub 2013 Jan 12.

PMID: 23314327

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Genomic diversity and evolution of the head crest in the rock pigeon

Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, Yandell M, Zhang G, Wang J

Science. 2013 Mar 1;339(6123):1063-7. doi: 10.1126/science.1230422. Epub 2013 Jan 31

PMCID: PMC3778192

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Exome sequencing and genome-wide linkage analysis in 17 families illustrate the complex contribution of TTN truncating variants to dilated cardiomyopathy

Norton N, Li D, Rampersaud E, Morales A, Martin ER, Zuchner S, Guo S, Gonzalez M, Hedges DJ, Robertson PD, Krumm N, Nickerson DA, Hershberger RE; National Heart, Lung, and Blood Institute GO Exome Sequencing Project and the Exome Sequencing Project Family Studies Project Team

Circ Cardiovasc Genet. 2013 Apr;6(2):144-53. doi: 10.1161/CIRCGENETICS.111.000062. Epub 2013 Feb 15

PMCID: PMC3815606

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Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms.

Malhotra A, Lindberg M, Faust GG, Leibowitz ML, Clark RA, Layer RM, Quinlan AR, Hall IM.

Genome Res. 2013 May;23(5):762-76. doi: 10.1101/gr.143677.112. Epub 2013 Feb 14.

PMID: 23410887

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Scribl: an HTML5 Canvas-based graphics library for visualizing genomic data over the web

Miller CA, Anthony J, Meyer MM, Marth G

Bioinformatics. 2013 Feb 1;29(3):381-3. doi: 10.1093/bioinformatics/bts677. Epub 2012 Nov 19

PMCID: PMC3562066

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Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants

Fu W, O'Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ; NHLBI Exome Sequencing Project, Akey JM

Nature. 2013 Jan 10;493(7431):216-20. doi: 10.1038/nature11690. Epub 2012 Nov 2

PMCID: PMC3676746

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Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779

Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zäuner S, Farre EM, Hegg EL, Jiang N, Kuo MH, Lu Y, Niyogi KK, Ohlrogge J, Osteryoung KW, Shachar-Hill Y, Sears BB, Sun Y, Takahashi H, Yandell M, Shiu SH, Benning C

PLoS Genet. 2012;8(11):e1003064. doi: 10.1371/journal.pgen.1003064. Epub 2012 Nov 15PMCID: PMC3499364

PMCID: PMC3499364

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Copy Number Variation detection from 1000 Genomes Project exon capture sequencing data.

Wu J, Grzeda KR, Stewart C, Grubert F, Urban AE, Snyder MP, Marth GT.

BMC Bioinformatics. 2012 Nov 17;13:305. doi: 10.1186/1471-2105-13-305.

PMID: 23157288 Free

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Binary Interval Search: a scalable algorithm for counting interval intersections.

Layer RM, Skadron K, Robins G, Hall IM, Quinlan AR.

Bioinformatics. 2013 Jan 1;29(1):1-7. doi: 10.1093/bioinformatics/bts652. Epub 2012 Nov 4.

PMID: 23129298

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An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632.

PMID: 23128226

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Targeted proteomic dissection of Toxoplasma cytoskeleton sub-compartments using MORN1.

Lorestani A, Ivey FD, Thirugnanam S, Busby MA, Marth GT, Cheeseman IM, Gubbels MJ.

Cytoskeleton (Hoboken). 2012 Dec;69(12):1069-85. doi: 10.1002/cm.21077. Epub 2012 Oct 11.

PMID: 23027733

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TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome

Boileau C, Guo DC, Hanna N, Regalado ES, Detaint D, Gong L, Varret M, Prakash SK, Li AH, d'Indy H, Braverman AC, Grandchamp B, Kwartler CS, Gouya L, Santos-Cortez RL, Abifadel M, Leal SM, Muti C, Shendure J, Gross MS, Rieder MJ, Vahanian A, Nickerson DA, Michel JB; National Heart, Lung, and Blood Institute (NHLBI) Go Exome Sequencing Project, Jondeau G, Milewicz DM

Nat Genet. 2012 Jul 8;44(8):916-21. doi: 10.1038/ng.2348

PMCID: PMC4033668

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Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct

Hu H, Bandyopadhyay PK, Olivera BM, Yandell M

BMC Genomics. 2012 Jun 28;13:284. doi: 10.1186/1471-2164-13-284

PMCID: PMC3441800

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Copy number variation detection and genotyping from exome sequence data

Krumm N, Sudmant PH, Ko A, O'Roak BJ, Malig M, Coe BP; NHLBI Exome Sequencing Project, Quinlan AR, Nickerson DA, Eichler EE

Genome Res. 2012 Aug;22(8):1525-32. doi: 10.1101/gr.138115.112. Epub 2012 May 14

PMCID: PMC3409265

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The 1000 Genomes Project: data management and community access

Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium

Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974

PMCID: PMC3340611

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A beginner's guide to eukaryotic genome annotation

Yandell M, Ence D

Nat Rev Genet. 2012 Apr 18;13(5):329-42. doi: 10.1038/nrg3174

PMID: 22510764

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A DOC2 protein identified by mutational profiling is essential for apicomplexan parasite exocytosis.

Farrell A, Thirugnanam S, Lorestani A, Dvorin JD, Eidell KP, Ferguson DJ, Anderson-White BR, Duraisingh MT, Marth GT, Gubbels MJ.

Science. 2012 Jan 13;335(6065):218-21. doi: 10.1126/science.1210829.

PMID: 22246776

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Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis

Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA, Barnes KC; National Heart, Lung, and Blood Institute (NHLBI) GO Exome Sequencing Project; Lung GO, Gibson RL, Bamshad MJ

Nat Genet. 2012 Jul 8;44(8):886-9. doi: 10.1038/ng.2344

PMCID: PMC3702264

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Evidence for two independent associations with type 1 diabetes at the 12q13 locus

Keene KL, Quinlan AR, Hou X, Hall IM, Mychaleckyj JC, Onengut-Gumuscu S, Concannon P

Genes Immun. 2012 Jan;13(1):66-70. doi: 10.1038/gene.2011.56. Epub 2011 Aug 18

PMCID: PMC3285513

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Expression divergence measured by transcriptome sequencing of four yeast species.

Busby MA, Gray JM, Costa AM, Stewart C, Stromberg MP, Barnett D, Chuang JH, Springer M, Marth GT.

BMC Genomics. 2011 Dec 29;12:635. doi: 10.1186/1471-2164-12-635.

PMID: 22206443

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ART: a next-generation sequencing read simulator.

Huang W, Li L, Myers JR, Marth GT.

Bioinformatics. 2012 Feb 15;28(4):593-4. doi: 10.1093/bioinformatics/btr708. Epub 2011 Dec 23.

PMCID: PMC3278762

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MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Holt C, Yandell M

BMC Bioinformatics. 2011 Dec 22;12:491. doi: 10.1186/1471-2105-12-491

PMCID: PMC3280279

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Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

Dale RK, Pedersen BS, Quinlan AR

Bioinformatics. 2011 Dec 15;27(24):3423-4. doi: 10.1093/bioinformatics/btr539

PMCID: PMC3232365

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Detection and interpretation of genomic structural variation in mammals

Hall IM, Quinlan AR

Methods Mol Biol. 2012;838:225-48. doi: 10.1007/978-1-61779-507-7_11

PMID: 22228015

Characterizing complex structural variation in germline and somatic genomes

Quinlan AR, Hall IM

Trends Genet. 2012 Jan;28(1):43-53. doi: 10.1016/j.tig.2011.10.002. Epub 2011 Nov 15

PMCID: PMC3249479

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Genome sequencing of mouse induced pluripotent stem cells reveals retroelement stability and infrequent DNA rearrangement during reprogramming

Quinlan AR, Boland MJ, Leibowitz ML, Shumilina S, Pehrson SM, Baldwin KK, Hall IM

Cell Stem Cell. 2011 Oct 4;9(4):366-73. doi: 10.1016/j.stem.2011.07.018

PMCID: PMC3975295

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VAAST - A probabilistic disease-gene finder for personal genomes.

Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG.

Genome Res. 2011 Sep;21(9):1529-42. doi: 10.1101/gr.123158.111. Epub 2011 Jun 23.

PMID: 21700766

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The functional spectrum of low-frequency coding variation.

Marth GT, Yu F, Indap AR, Garimella K, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl C, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler D, Bustamante CD, Clark AG, Daly M, DePristo M, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R; 1000 Genomes Project.

Genome Biol. 2011 Sep 14;12(9):R84. doi: 10.1186/gb-2011-12-9-r84.

PMID: 21917140

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A comprehensive map of mobile element insertion polymorphisms in humans.

Stewart C, Kural D, Strömberg MP, Walker JA, Konkel MK, Stütz AM, Urban AE, Grubert F, Lam HY, Lee WP, Busby M, Indap AR, Garrison E, Huff C, Xing J, Snyder MP, Jorde LB, Batzer MA, Korbel JO, Marth GT; 1000 Genomes Project.

PLoS Genet. 2011 Aug;7(8):e1002236. doi: 10.1371/journal.pgen.1002236. Epub 2011 Aug 18.

PMID: 21876680

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The variant call format and VCFtools

Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group

Bioinformatics. 2011 Aug 1;27(15):2156-8. doi: 10.1093/bioinformatics/btr330. Epub 2011 Jun 7

PMCID: PMC3137218

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Demographic history and rare allele sharing among human populations.

Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA; 1000 Genomes Project, Bustamante CD.

Proc Natl Acad Sci U S A. 2011 Jul 19;108(29):11983-8. doi: 10.1073/pnas.1019276108. Epub 2011 Jul 5.

PMID: 21730125

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Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017. Epub 2011 Jun 23

PMCID: PMC3135802

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Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications

Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K

Discov Med. 2011 Jul;12(62):41-55

PMCID: PMC3544941

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Variation in genome-wide mutation rates within and between human families

Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P; 1000 Genomes Project

Nat Genet. 2011 Jun 12;43(7):712-4. doi: 10.1038/ng.862

PMCID: PMC3322360

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BamTools: a C++ API and toolkit for analyzing and managing BAM files

Barnett DW, Garrison EK, Quinlan AR, Strömberg MP, Marth GT

Bioinformatics. 2011 Jun 15;27(12):1691-2. doi: 10.1093/bioinformatics/btr174. Epub 2011 Apr 14

PMCID: PMC3106182

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Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile)

Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui ND

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5673-8. doi: 10.1073/pnas.1008617108. Epub 2011 Jan 31

PMCID: PMC3078359

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Draft genome of the red harvester ant Pogonomyrmex barbatus

Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau J

Proc Natl Acad Sci U S A. 2011 Apr 5;108(14):5667-72. doi: 10.1073/pnas.1007901108. Epub 2011 Jan 31

PMCID: PMC3078412

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Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics

Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M

Genet Med. 2011 Mar;13(3):210-7. doi: 10.1097/GIM.0b013e31820ed321

PMCID: PMC3558030

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Evolution of the Sequence Ontology terms and relationships

Mungall CJ, Batchelor C, Eilbeck K.

J Biomed Inform. 2011 Feb;44(1):87-93. doi: 10.1016/j.jbi.2010.03.002. Epub 2010 Mar 10

PMID: 20226267

The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle

Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR

PLoS Genet. 2011 Feb 10;7(2):e1002007. doi: 10.1371/journal.pgen.1002007

PMCID: PMC3037820

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Mapping copy number variation by population-scale genome sequencing

Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project

Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708.

PMCID: PMC3077050

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Characterization of the Conus bullatus genome and its venom-duct transcriptome

Hu H, Bandyopadhyay PK, Olivera BM, Yandell M

BMC Genomics. 2011 Jan 25;12:60. doi: 10.1186/1471-2164-12-60

PMCID: PMC3040727

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A map of human genome variation from population-scale sequencing

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA

Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534

PMCID: PMC3042601

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Diversity of human copy number variation and multicopy genes

Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J; 1000 Genomes Project, Eichler EE.

Science. 2010 Oct 29;330(6004):641-6. doi: 10.1126/science.1197005.

PMCID: PMC3020103

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Rapid whole-genome mutational profiling using next-generation sequencing technologies

Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B, Shen L, Donahue WF, Tusneem N, Stromberg MP, Stewart DA, Zhang L, Ranade SS, Warner JB, Lee CC, Coleman BE, Zhang Z, McLaughlin SF, Malek JA, Sorenson JM, Blanchard AP, Chapman J, Hillman D, Chen F, Rokhsar DS, McKernan KJ, Jeffries TW, Marth GT, Richardson PM.

Genome Res. 2008 Oct;18(10):1638-42. doi: 10.1101/gr.077776.108. Epub 2008 Sep 4

PMCID: PMC2556265

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A standard variation file format for human genome sequences

Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K

Genome Biol. 2010;11(8):R88. doi: 10.1186/gb-2010-11-8-r88. Epub 2010 Aug 26

PMCID: PMC2945790

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Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire

Lévesque CA, Brouwer H, Cano L, Hamilton JP, Holt C, Huitema E, Raffaele S, Robideau GP, Thines M, Win J, Zerillo MM, Beakes GW, Boore JL, Busam D, Dumas B, Ferriera S, Fuerstenberg SI, Gachon CM, Gaulin E, Govers F, Grenville-Briggs L, Horner N, Hostetler J, Jiang RH, Johnson J, Krajaejun T, Lin H, Meijer HJ, Moore B, Morris P, Phuntmart V, Puiu D, Shetty J, Stajich JE, Tripathy S, Wawra S, van West P, Whitty BR, Coutinho PM, Henrissat B, Martin F, Thomas PD, Tyler BM, De Vries RP, Kamoun S, Yandell M, Tisserat N, Buell CR

Genome Biol. 2010;11(7):R73. doi: 10.1186/gb-2010-11-7-r73. Epub 2010 Jul 13

PMCID: PMC2926784

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Moore B, Fan G, Eilbeck K.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W161-4. doi: 10.1093/nar/gkq426. Epub 2010 May 21

PMID: 20494974

The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB

MC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420

PMCID: PMC2996948

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Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM.

Genome Res. 2010 May;20(5):623-35. doi: 10.1101/gr.102970.109. Epub 2010 Mar 22

PMCID: PMC2860164

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Novel sequence feature variant type analysis of the HLA genetic association in systemic sclerosis

Karp DR, Marthandan N, Marsh SG, Ahn C, Arnett FC, Deluca DS, Diehl AD, Dunivin R, Eilbeck K, Feolo M, Guidry PA, Helmberg W, Lewis S, Mayes MD, Mungall C, Natale DA, Peters B, Petersdorf E, Reveille JD, Smith B, Thomson G, Waller MJ, Scheuermann RH.

Hum Mol Genet. 2010 Feb 15;19(4):707-19. doi: 10.1093/hmg/ddp521. Epub 2009 Nov 18

PMID: 19933168

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan AR, Hall IM

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

PMCID: PMC2832824

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Population genomic inferences from sparse high-throughput sequencing of two populations of Drosophila melanogaster

Sackton TB, Kulathinal RJ, Bergman CM, Quinlan AR, Dopman EB, Carneiro M, Marth GT, Hartl DL, Clark AG

Genome Biol Evol. 2009 Nov 18;1:449-65. doi: 10.1093/gbe/evp048.

PMCID: PMC2839279

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The Sequence Alignment/Map format and SAMtools

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup

Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8

PMCID: PMC2723002

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Quantitative measures for the management and comparison of annotated genomes

Eilbeck K, Moore B, Holt C, Yandell M

BMC Bioinformatics. 2009 Feb 23;10:67. doi: 10.1186/1471-2105-10-67

PMCID: PMC2653490

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The Protein Feature Ontology: a tool for the unification of protein feature annotations

Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.

Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20

PMID: 18936051

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins

Yandell M, Moore B, Salas F, Mungall C, MacBride A, White C, Reese MG

PLoS Comput Biol. 2008 Nov;4(11):e1000218. doi: 10.1371/journal.pcbi.1000218. Epub 2008 Nov 7

PMCID: PMC2565504

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EagleView: a genome assembly viewer for next-generation sequencing technologies

Huang W, Marth G

Genome Res. 2008 Sep;18(9):1538-43. doi: 10.1101/gr.076067.108. Epub 2008 Jun 11

PMCID: PMC2527701

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Whole-genome sequencing and variant discovery in C. elegans

Hillier LW, Marth GT, Quinlan AR, Dooling D, Fewell G, Barnett D, Fox P, Glasscock JI, Hickenbotham M, Huang W, Magrini VJ, Richt RJ, Sander SN, Stewart DA, Stromberg M, Tsung EF, Wylie T, Schedl T, Wilson RK, Mardis ER

Nat Methods. 2008 Feb;5(2):183-8. doi: 10.1038/nmeth.1179. Epub 2008 Jan 20

PMID: 18204455

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Pyrobayes: an improved base caller for SNP discovery in pyrosequences

Quinlan AR, Stewart DA, Strömberg MP, Marth GT

Nat Methods. 2008 Feb;5(2):179-81. doi: 10.1038/nmeth.1172. Epub 2008 Jan 13.

PMID: 18193056

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MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes

Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M

Genome Res. 2008 Jan;18(1):188-96. Epub 2007 Nov 19

PMCID: PMC2134774

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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ; OBI Consortium, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S.

Nat Biotechnol. 2007 Nov;25(11):1251-5

PMID: 17989687

Primer-site SNPs mask mutations

Quinlan AR, Marth GT

Nat Methods. 2007 Mar;4(3):192

PMID: 17327845

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Improved repeat identification and masking in Dipterans

Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH

Gene. 2007 Mar 1;389(1):1-9. Epub 2006 Oct 12

PMCID: PMC1945102

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Analysis of concordance of different haplotype block partitioning algorithms

Indap AR, Marth GT, Struble CA, Tonellato P, Olivier M

BMC Bioinformatics. 2005 Dec 15;6:303

PMCID: PMC1343594

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The Sequence Ontology: a tool for the unification of genome annotations

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M

Genome Biol. 2005;6(5):R44. Epub 2005 Apr 29

PMCID: PMC1175956

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A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome

Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, Rubin GM

Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1566-71. Epub 2005 Jan 24

PMCID: PMC545494

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Eilbeck K, Lewis SE

Comp Funct Genomics. 2004;5(8):642-7. doi: 10.1002/cfg.446

PMID: 18629179

The Gene Ontology (GO) database and informatics resource

Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D258-61

PMID: 14681407

Computational SNP discovery in DNA sequence data

Marth GT

Methods Mol Biol. 2003;212:85-110

PMID: 12491905

STRP screening sets for the human genome at 5 cM density

Ghebranious N, Vaske D, Yu A, Zhao C, Marth G, Weber JL

BMC Genomics. 2003 Feb 24;4(1):6. Epub 2003 Feb 24

PMCID: PMC152641

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Identification of key concepts in biomedical literature using a modified Markov heuristic

Majoros WH, Subramanian GM, Yandell MD

Bioinformatics. 2003 Feb 12;19(3):402-7

PMID: 12584127

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Sequence variations in the public human genome data reflect a bottlenecked population history

Marth G, Schuler G, Yeh R, Davenport R, Agarwala R, Church D, Wheelan S, Baker J, Ward M, Kholodov M, Phan L, Czabarka E, Murvai J, Cutler D, Wooding S, Rogers A, Chakravarti A, Harpending HC, Kwok PY, Sherry ST

Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):376-81. Epub 2002 Dec 26

PMCID: PMC140982

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Human diallelic insertion/deletion polymorphisms

Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G

Am J Hum Genet. 2002 Oct;71(4):854-62. Epub 2002 Sep 4

PMCID: PMC378541

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The genome sequence of the malaria mosquito Anopheles gambiae

Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JM, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL

Science. 2002 Oct 4;298(5591):129-49

PMID: 12364791

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Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster

Zdobnov EM, von Mering C, Letunic I, Torrents D, Suyama M, Copley RR, Christophides GK, Thomasova D, Holt RA, Subramanian GM, Mueller HM, Dimopoulos G, Law JH, Wells MA, Birney E, Charlab R, Halpern AL, Kokoza E, Kraft CL, Lai Z, Lewis S, Louis C, Barillas-Mury C, Nusskern D, Rubin GM, Salzberg SL, Sutton GG, Topalis P, Wides R, Wincker P, Yandell M, Collins FH, Ribeiro J, Gelbart WM, Kafatos FC, Bork P

Science. 2002 Oct 4;298(5591):149-59

PMID: 12364792

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Genomics and natural language processing

Yandell MD, Majoros WH.

Nat Rev Genet. 2002 Aug;3(8):601-10

PMID: 12154383

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Mural RJ, Adams MD, Myers EW, Smith HO, Miklos GL, Wides R, Halpern A, Li PW, Sutton GG, Nadeau J, Salzberg SL, Holt RA, Kodira CD, Lu F, Chen L, Deng Z, Evangelista CC, Gan W, Heiman TJ, Li J, Li Z, Merkulov GV, Milshina NV, Naik AK, Qi R, Shue BC, Wang A, Wang J, Wang X, Yan X, Ye J, Yooseph S, Zhao Q, Zheng L, Zhu SC, Biddick K, Bolanos R, Delcher AL, Dew IM, Fasulo D, Flanigan MJ, Huson DH, Kravitz SA, Miller JR, Mobarry CM, Reinert K, Remington KA, Zhang Q, Zheng XH, Nusskern DR, Lai Z, Lei Y, Zhong W, Yao A, Guan P, Ji RR, Gu Z, Wang ZY, Zhong F, Xiao C, Chiang CC, Yandell M, Wortman JR, Amanatides PG, Hladun SL, Pratts EC, Johnson JE, Dodson KL, Woodford KJ, Evans CA, Gropman B, Rusch DB, Venter E, Wang M, Smith TJ, Houck JT, Tompkins DE, Haynes C, Jacob D, Chin SH, Allen DR, Dahlke CE, Sanders R, Li K, Liu X, Levitsky AA, Majoros WH, Chen Q, Xia AC, Lopez JR, Donnelly MT, Newman MH, Glodek A, Kraft CL, Nodell M, Ali F, An HJ, Baldwin-Pitts D, Beeson KY, Cai S, Carnes M, Carver A, Caulk PM, Center A, Chen YH, Cheng ML, Coyne MD, Crowder M, Danaher S, Davenport LB, Desilets R, Dietz SM, Doup L, Dullaghan P, Ferriera S, Fosler CR, Gire HC, Gluecksmann A, Gocayne JD, Gray J, Hart B, Haynes J, Hoover J, Howland T, Ibegwam C, Jalali M, Johns D, Kline L, Ma DS, MacCawley S, Magoon A, Mann F, May D, McIntosh TC, Mehta S, Moy L, Moy MC, Murphy BJ, Murphy SD, Nelson KA, Nuri Z, Parker KA, Prudhomme AC, Puri VN, Qureshi H, Raley JC, Reardon MS, Regier MA, Rogers YH, Romblad DL, Schutz J, Scott JL, Scott R, Sitter CD, Smallwood M, Sprague AC, Stewart E, Strong RV, Suh E, Sylvester K, Thomas R, Tint NN, Tsonis C, Wang G, Wang G, Williams MS, Williams SM, Windsor SM, Wolfe K, Wu MM, Zaveri J, Chaturvedi K, Gabrielian AE, Ke Z, Sun J, Subramanian G, Venter JC, Pfannkoch CM, Barnstead M, Stephenson LD

Science. 2002 May 31;296(5573):1661-71

PMID: 12040188

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The Celera Discovery System

Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas P

Nucleic Acids Res. 2002 Jan 1;30(1):129-36

PMID: 11752274

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Single-nucleotide polymorphisms in the public domain: how useful are they?

Marth G, Yeh R, Minton M, Donaldson R, Li Q, Duan S, Davenport R, Miller RD, Kwok PY

Nat Genet. 2001 Apr;27(4):371-2

PMID: 11279516

The sequence of the human genome

Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X.

Science. 2001 Feb 16;291(5507):1304-51

PMID: 11181995

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A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms

Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D; International SNP Map Working Group

Nature. 2001 Feb 15;409(6822):928-33

PMID: 11237013

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Conceptual modelling of genomic information

Paton NW, Khan SA, Hayes A, Moussouni F, Brass A, Eilbeck K, Goble CA, Hubbard SJ, Oliver SG.

Bioinformatics. 2000 Jun;16(6):548-57

PMID: 10980152

Identification and characterization of a p53 homologue in Drosophila melanogaster

Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ

Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7301-6


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Comparative genomics of the eukaryotes

Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O'Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S.

Science. 2000 Mar 24;287(5461):2204-15

PMCID: PMC2754258

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The genome sequence of Drosophila melanogaster

Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Sidén-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, WoodageT, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC.

Science. 2000 Mar 24;287(5461):2185-95

PMID: 10731132

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A general approach to single-nucleotide polymorphism discovery

Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR

Nat Genet. 1999 Dec;23(4):452-6

PMID: 10581034

A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans

Suzuki Y, Yandell MD, Roy PJ, Krishna S, Savage-Dunn C, Ross RM, Padgett RW, Wood WB

Development. 1999 Jan;126(2):241-50

PMID: 9847238

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Sequence assembly with CAFTOOLS

Dear S, Durbin R, Hillier L, Marth G, Thierry-Mieg J, Mott R

Genome Res. 1998 Mar;8(3):260-7

PMCID: PMC310697

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Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans

Yandell MD, Edgar LG, Wood WB

Proc Natl Acad Sci U S A. 1994 Feb 15;91(4):1381-5


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