Mark Yandell

Mark Yandell, PhD

Languages spoken: English

Academic Information

Departments Primary - Human Genetics , Adjunct - Biomedical Informatics

Academic Office Information

myandell@genetics.utah.edu

Research Interests

  • Computational Biology
  • Human Population Genetics
  • Image Processing, Computer-Assisted
  • bioinformatics
  • Comparative Genomics

Mark Yandell, PhD has led software development groups in both industry and academia. As a postdoc at the Human Genome Project at Washington University, St. Louis, he was a co-developer of the PolyBayes package, the first probabilistic algorithm for sequence variant discovery. Thereafter, he joined Celera Genomics, where he directed the group that wrote much of the software used to annotate and analyze the Drosophila, Human, Mouse, and mosquito genomes. From 2001-2005 he was a senior scientist for Howard Hughes Medical Institute (HHMI), where he led the comparative genomics group at the Berkeley Drosophila Genome Project. Since 2005, he has been a faculty member in the Eccles Institute of Human Genetics at the University of Utah. Dr. Yandell is an internationally recognized expert in software for comparative and functional genomics. He has served on the Scientific Advisory Boards of numerous genome projects. He is Director of the Eccles Institute’s Bioinformatics program, and frequent guest lecturer in several CSHL courses on genomics, programming and sequence analysis. He is also co-author of the O’Reilly Book on BLAST. Current projects in his laboratory include an NSF program grant for annotation of plant genomes; NIGMS support for genomics-based venom studies using the cone snail Conus bullatus; and support from the NHGRI and NIGMS for VAAST, a probabilistic disease gene finder for personal genome sequences. Dr. Yandell is technical director of the Utah Genome Project (UGP), an intramural, multi-million dollar effort to improve patient care and facilitate research on undiagnosed diseases, Co-director of the Utah Center for Genetic Discovery, Adjunct Professor of Biomedical Informatics, a member of the Huntsman Cancer Institute’s Cancer Control and Population Sciences Program, and H.A. and Edna Benning Presidential Endowed Chair at the University of Utah.

Research in his group is genomics-based and focused on two areas: genome annotation and understanding the consequences of sequence variants. Toward these ends, they have developed two highly successful tools: MAKER, an easy-to-use genome annotation pipeline, and VAAST, a probabilistic disease-gene finder for personal genome sequences. Software abounds in the genomics domain; what distinguishes MAKER and VAAST is their scalability and scope of application. Both tools are designed to operate on very large and heterogeneous next-generation sequencing datasets. The outputs of these tools don’t merely result in publications, they nucleate communities. Consequently, his lab has become an international nexus for genomics collaborations. Recent MAKER collaborations include the genome-annotation and analyses of Maize, venomous snails, the Coelacanth, the sacred lotus, the alga Nannochloropsis, the Gibbon, the Lamprey and the King Cobra. VAAST collaborations include searches for genes and alleles involved in autism, breast cancer, Crohn disease, cardiovascular disease, cavernous angiomas, and atypical cystic fibrosis. Also underway are extensions to VAAST that enable computation upon large pedigrees (pVAAST), and Phevor, a tool that combines phenotype with genotype for patient diagnosis. VAAST, pVAAST, and Phevor comprise the backbone of the Utah Genome Project, a multimillion-dollar investment by the University of Utah in translational genomic medicine. Going forward, the integration of MAKER and VAAST will also provide a coordinated means to search the genomes of plant cultivars, animal breeds, and wild populations of flora and fauna for the genes and variants that underlie phenotypic traits.

Education History

Other Training Marine Biological Laboratories
Marine Biological Laboratories
Postdoctoral Fellowship Washington University
 Postdoctoral Fellow
University of Colorado
 PhD
Undergraduate University of Texas
 BA

Selected Publications

Journal Article

  1. 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 (2024). The impact of damaging epilepsy and cardiac genetic variant burden in sudden death in the young. Genome Med, 16(1), 13. (Read full article)
  2. Maclary ET, Holt C, Concepcion GT, Sovi I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro MD (2023). Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid. G3 (Bethesda). (Read full article)
  3. 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 (2023). Genetic and clinical variables act synergistically to impact neurodevelopmental outcomes in children with single ventricle heart disease. Commun Med (Lond), 3(1), 127. (Read full article)
  4. McMahon KL, OBrien 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 (2023). Identification of sodium channel toxins from marine cone snails of the subgenera Textilia and Afonsoconus. Cell Mol Life Sci, 80(10), 287. (Read full article)
  5. Johnstone EB, Gorsi B, Coelho E, Moore B, Farr AM, Cooper AR, Mardis ER, Rajkovic A, Chow CY, Yandell M, Welt CK (2022). DIS3 Variants are Associated With Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis. J Clin Endocrinol Metab, 108(9), 2330-2335. (Read full article)
  6. Zimmerman RM, Hernandez EJ, Watkins WS, Blue N, Tristani-Firouzi M, Yandell M, Steinberg BA (2023). An Explainable Artificial Intelligence Approach for Discovering Social Determinants of Health and Risk Interactions for Stroke in Patients With Atrial Fibrillation. Am J Cardiol, 201, 224-226. (Read full article)
  7. 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 (2023). Neurite outgrowth deficits caused by rare PLXNB1 mutation in pediatric bipolar disorder. Mol Psychiatry, 28(6), 2525-2539. (Read full article)
  8. Timoshevskaya N, Ekut 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 (2023). An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes. Cell Rep, 42(3), 112263. (Read full article)
  9. 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 (2023). Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning. Genome Med, 15(1), 18. (Read full article)
  10. 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 (2022). Comprehensive Genomic Profiling of Cell-Free DNA in Men With Advanced Prostate Cancer: Differences in Genomic Landscape Based on Race. Oncologist, 27(10), e815-e818. (Read full article)
  11. 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 (2022). Genomic landscape of advanced prostate cancer patients with BRCA1 versus BRCA2 mutations as detected by comprehensive genomic profiling of cell-free DNA. Front Oncol, 12, 966534. (Read full article)
  12. Simeone CA, Wilkerson JL, Poss AM, Banks JA, Varre JV, Guevara JL, Hernandez EJ, Gorsi B, Atkinson DL, Turapov T, Frodsham SG, Morales JCF, ONeil K, Moore B, Yandell M, Summers SA, Krolewski AS, Holland WL, Pezzolesi MG (2022). A dominant negative ADIPOQ mutation in a diabetic family with renal disease, hypoadiponectinemia, and hyperceramidemia. NPJ Genom Med, 7(1), 43. (Read full article)
  13. 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 (2021). Family Screening After Sudden Death in a Population-Based Study of Children. Pediatrics, 149(4). (Read full article)
  14. 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 (2022). Comprehensive variant calling from whole-genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia. Mol Genet Genomic Med, 10(4), e1888. (Read full article)
  15. Wesoowski 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 (2022). An explainable artificial intelligence approach for predicting cardiovascular outcomes using electronic health records. PLOS Digit Health, 1(1). (Read full article)
  16. Maclary ET, Phillips B, Wauer R, Boer EF, Bruders R, Gilvarry T, Holt C, Yandell M, Shapiro MD (2021). Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Mol Biol Evol, 38(12), 5376-5390. (Read full article)
  17. Hberle J, Moore MB, Haskins N, Rfenacht V, Rokicki D, Rubio-Gozalbo E, Tuchman M, Longo N, Yandell M, Andrews A, AhMew N, Caldovic L (2021). Noncoding sequence variants define a novel regulatory element in the first intron of the N-acetylglutamate synthase gene. Hum Mutat, 42(12), 1624-1636. (Read full article)
  18. Boer EF, Van Hollebeke HF, Maclary ET, Holt C, Yandell M, Shapiro MD (2021). A ROR2 coding variant is associated with craniofacial variation in domestic pigeons. Curr Biol, 31(22), 5069-5076.e5. (Read full article)
  19. 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 S, Scott Watkins W, Karren MA, Knight S, Brent Muhlestein J, Carlquist JF, Anderson JL, Chahine KG, Shah KU, Ball CA, Benjamin IJ, Yandell M, Tristani-Firouzi M (2021). The history and geographic distribution of a KCNQ1 atrial fibrillation risk allele. Nat Commun, 12(1), 6442. (Read full article)
  20. 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 (2021). Causal and Candidate Gene Variants in a Large Cohort of Women with Primary Ovarian Insufficiency. J Clin Endocrinol Metab, 107, 685-714. (Read full article)
  21. 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, Lscher BS, Franke A, Boone B, Levy SE, unap K, Pajusalu S, Huentelman M, Ramsey K, Naymik M, Narayanan V, Veeraraghavan N, Billings P, Reese MG, Yandell M, Kingsmore SF (2021). Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. Genome Med, 13(1), 153. (Read full article)
  22. Lemmon G, Wesolowski S, Henrie A, Tristani-Firouzi M, Yandell M (2021). A Poisson binomial-based statistical testing framework for comorbidity discovery across electronic health record datasets. Nat Comput Sci, 1(10), 694-702. (Read full article)
  23. 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 (2021). Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform. Oncologist, 26(9), 751-760. (Read full article)
  24. Tollis M, Ferris E, Campbell MS, Harris VK, Rupp SM, Harrison TM, Kiso WK, Schmitt DL, Garner MM, Aktipis CA, Maley CC, Boddy AM, Yandell M, Gregg C, Schiffman JD, Abegglen LM (2021). Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. Mol Biol Evol, 38(9), 3606-3620. (Read full article)
  25. Malone Jenkins S, 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 (2021). Addressing ethical and laboratory challenges for initiation of a rapid whole genome sequencing program. J Clin Transl Sci, 5(1), e177. (Read full article)
  26. 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 (2021). The genomic basis of evolutionary differentiation among honey bees. Genome Res. (Read full article)
  27. Musfee FI, Agopian AJ, Goldmuntz E, Hakonarson H, Morrow BE, Taylor DM, Tristani-Firouzi M, Watkins WS, Yandell M, Mitchell LE (2021). Common Variation in Cytoskeletal Genes is Associated with Conotruncal Heart Defects. Genes (Basel), 12(5). (Read full article)
  28. Bogenschutz EL, Fox ZD, Farrell A, Wynn J, Moore B, Yu L, Aspelund G, Marth G, Yandell M, Shen Y, Chung WK, Kardon G (2020). Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias. HGG Adv, 1(1). (Read full article)
  29. Shah RU, Mutharasan RK, Ahmad FS, Rosenblatt AG, Gay HC, Steinberg BA, Yandell M, Tristani-Firouzi M, Klewer J, Mukherjee R, Lloyd-Jones DM (2020). Development of a Portable Tool to Identify Patients With Atrial Fibrillation Using Clinical Notes From the Electronic Medical Record. Circ Cardiovasc Qual Outcomes, 13(10), e006516. (Read full article)
  30. Crandall H, Kapusta A, Killpack J, Heyrend C, Nilsson K, Dickey M, Daly JA, Ampofo K, Pavia AT, Mulvey MA, Yandell M, Hulten KG, Blaschke AJ (2020). Clinical and molecular epidemiology of invasive Staphylococcus aureus infection in Utah children; continued dominance of MSSA over MRSA. PLoS One, 15(9), e0238991. (Read full article)
  31. Bjrn-Yoshimoto WE, Ramiro IBL, Yandell M, McIntosh JM, Olivera BM, Ellgaard L, Safavi-Hemami H (2020). Curses or Cures: A Review of the Numerous Benefits Versus the Biosecurity Concerns of Conotoxin Research. Biomedicines, 8(8). (Read full article)
  32. 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 (2020). Pulmonary Eosinophilic Granulomatosis with Polyangiitis Has IgG4 Plasma Cells and Immunoregulatory Features. Am J Pathol, 190(7), 1438-1448. (Read full article)
  33. Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD (2020). A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet, 16(5), e1008274. (Read full article)
  34. Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE (2020). Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus. Genome Biol Evol, 12(5), 684-700. (Read full article)
  35. Ledet EM, Lilly MB, Sonpavde G, Lin E, Nussenzveig RH, Barata PC, Yandell M, Nagy RJ, Kiedrowski L, Agarwal N, Sartor O (2019). Comprehensive Analysis of AR Alterations in Circulating Tumor DNA from Patients with Advanced Prostate Cancer. Oncologist, 25(4), 327-333. (Read full article)
  36. Ledet EM, Lilly MB, Sonpavde G, Lin E, Nussenzveig RH, Barata PC, Yandell M, Nagy RJ, Kiedrowski L, Agarwal N, Sartor O (2019). Comprehensive Analysis of AR Alterations in Circulating Tumor DNA from Patients with Advanced Prostate Cancer. Oncologist. (Read full article)
  37. 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 (2019). De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes. Nat Commun, 10(1), 4722. (Read full article)
  38. 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 (2019). Identification of Polycystic Kidney Disease 1 Like 1 Gene Variants in Children With Biliary Atresia Splenic Malformation Syndrome. Hepatology, 70(3), 899-910. (Read full article)
  39. Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M (2018). Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins (Basel), 10(12). (Read full article)
  40. 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 (2018). Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet, 50(11), 1617. (Read full article)
  41. Majoros WH, Holt C, Campbell MS, Ware D, Yandell M, Reddy TE (2018). Predicting gene structure changes resulting from genetic variants via exon definition features. Bioinformatics, 34(21), 3616-3623. (Read full article)
  42. Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD (2018). Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. Elife, 7. (Read full article)
  43. Liu MJ, Sugimoto K, Uygun S, Panchy N, Campbell MS, Yandell M, Howe GA, Shiu SH (2018). Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato. Plant Cell, 30(7), 1445-1460. (Read full article)
  44. Peterson KA, Yoshigi M, Hazel MW, Delker DA, Lin E, Krishnamurthy C, Consiglio N, Robson J, Yandell M, Clayton F (2018). RNA sequencing confirms similarities between PPI-responsive oesophageal eosinophilia and eosinophilic oesophagitis. Aliment Pharmacol Ther, 48(2), 219-225. (Read full article)
  45. Holt C, Campbell M, Keays DA, Edelman N, Kapusta A, Maclary E, T Domyan E, Suh A, Warren WC, Yandell M, Gilbert MTP, Shapiro MD (2018). Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia). G3 (Bethesda), 8(5), 1391-1398. (Read full article)
  46. 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 (2018). Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet, 50(5), 768. (Read full article)
  47. Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MAT, Yandell M, Huff CD (2017). XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. Nucleic Acids Res, 46(6), e32. (Read full article)
  48. 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 (2018). The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool. BMC Bioinformatics, 19(1), 57. (Read full article)
  49. 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 (2018). Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study. BJOG, 125(3), 343-350. (Read full article)
  50. 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 (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nat Genet, 50(2), 270-277. (Read full article)
  51. Al-Agha AE, Ahmed IA, Nuebel E, Moriwaki M, Moore B, Peacock KA, Mosbruger T, Neklason DW, Jorde LB, Yandell M, Welt CK (2018). Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. J Clin Endocrinol Metab, 103(2), 555-563. (Read full article)
  52. 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 (2017). Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet, 49(11), 1593-1601. (Read full article)
  53. Eilbeck K, Quinlan A, Yandell M (2017). Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet, 18(10), 599-612. (Read full article)
  54. 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 (2017). Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia. J Infect Dis, 216(6), 688-696. (Read full article)
  55. 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 (2017). The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3 (Bethesda), 7(9), 3157-3167. (Read full article)
  56. Li Q, Barghi N, Lu A, Fedosov AE, Bandyopadhyay PK, Lluisma AO, Concepcion GP, Yandell M, Olivera BM, Safavi-Hemami H (2017). Divergence of the Venom Exogene Repertoire in Two Sister Species of Turriconus. Genome Biol Evol, 9(9), 2211-2225. (Read full article)
  57. Robinson SD, Li Q, Lu A, Bandyopadhyay PK, Yandell M, Olivera BM, Safavi-Hemami H (2017). The Venom Repertoire of Conus gloriamaris (Chemnitz, 1777), the Glory of the Sea. Mar Drugs, 15(5). (Read full article)
  58. Majoros WH, Campbell MS, Holt C, DeNardo EK, Ware D, Allen AS, Yandell M, Reddy TE (2017). High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics, 33(10), 1437-1446. (Read full article)
  59. 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 (2017). Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology. J Infect Dis, 215(9), 1407-1415. (Read full article)
  60. Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H (2017). Hormone-like peptides in the venoms of marine cone snails. Gen Comp Endocrinol, 244, 11-18. (Read full article)
  61. Moriwaki M, Moore B, Mosbruger T, Neklason DW, Yandell M, Jorde LB, Welt CK (2017). POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women. J Endocr Soc, 1(3), 162-173. (Read full article)
  62. Cone KR, Kronenberg ZN, Yandell M, Elde NC (2017). Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus. J Virol, 91(4). (Read full article)
  63. Campbell M, Oakeson KF, Yandell M, Halpert JR, Dearing D (2016). The draft genome sequence and annotation of the desert woodrat Neotoma lepida. Genom Data, 9, 58-9.
  64. Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM (2016). Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. Mol Biol Evol, 33(11), 2924-2934. (Read full article)
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  121. 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, Zuner 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 (2012). Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779. PLoS Genet, 8(11), e1003064. (Read full article)
  122. Holt C, Yandell M (2011). MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12, 491. (Read full article)
  123. Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, Jorde LB, Reese MG (2011). A probabilistic disease-gene finder for personal genomes. Genome Res, 21(9), 1529-42. (Read full article)
  124. 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 (2011). Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet, 89(1), 28-43. (Read full article)
  125. 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 (2011). Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med, 12(62), 41-55. (Read full article)
  126. 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, Fav 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 (2011). Draft genome of the red harvester ant Pogonomyrmex barbatus. Proc Natl Acad Sci U S A, 108(14), 5667-72. (Read full article)
  127. 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, Muoz-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 (2011). Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proc Natl Acad Sci U S A, 108(14), 5673-8. (Read full article)
  128. Moore B, Hu H, Singleton M, De La Vega FM, Reese MG, Yandell M (2011). Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med, 13(3), 210-7. (Read full article)
  129. 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, Fav 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, Muoz-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 (2011). The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet, 7(2), e1002007. (Read full article)
  130. Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2011). Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genomics, 12, 60. (Read full article)
  131. Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB (2010). The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, 11, 420. (Read full article)
  132. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K (2010). A standard variation file format for human genome sequences. Genome Biol, 11(8), R88. (Read full article)
  133. Lvesque 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 (2010). Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol, 11(7), R73. (Read full article)
  134. Eilbeck K, Moore B, Holt C, Yandell M (2009). Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics, 10, 67. (Read full article)
  135. Yandell M, Moore B, Salas F, Mungall C, MacBride A, White C, Reese MG (2008). Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins. PLoS Comput Biol, 4(11), e1000218. (Read full article)
  136. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Snchez Alvarado A, Yandell M (2008). MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res, 18(1), 188-96. (Read full article)
  137. Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen GH (2007). Improved repeat identification and masking in Dipterans. Gene, 389(1), 1-9. (Read full article)
  138. Yandell M, Mungall CJ, Smith C, Prochnik S, Kaminker J, Hartzell G, Lewis S, Rubin GM (2006). Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol, 2(3), e15. (Read full article)
  139. Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, Rubin GM (2005). A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A, 102(5), 1566-71. (Read full article)
  140. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M (2005). The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol, 6(5), R44. (Read full article)
  141. Majoros WH, Subramanian GM, Yandell MD (2003). Identification of key concepts in biomedical literature using a modified Markov heuristic. Bioinformatics, 19(3), 402-7. (Read full article)
  142. 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 (2002). Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science, 298(5591), 149-59. (Read full article)
  143. 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, OBrochta 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 (2002). The genome sequence of the malaria mosquito Anopheles gambiae. Science, 298(5591), 129-49. (Read full article)
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  145. Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas P (2002). The Celera Discovery System. Nucleic Acids Res, 30(1), 129-36. (Read full article)
  146. 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, Guig 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 (2001). The sequence of the human genome. Science, 291(5507), 1304-51. (Read full article)
  147. Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ (2000). Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A, 97(13), 7301-6. (Read full article)
  148. 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, Sidn-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 (2000). The genome sequence of Drosophila melanogaster. Science, 287(5461), 2185-95. (Read full article)
  149. 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, OFarrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S (2000). Comparative genomics of the eukaryotes. Science, 287(5461), 2204-15. (Read full article)
  150. Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR (1999). A general approach to single-nucleotide polymorphism discovery. Nat Genet, 23(4), 452-6. (Read full article)
  151. Suzuki Y, Yandell MD, Roy PJ, Krishna S, Savage-Dunn C, Ross RM, Padgett RW, Wood WB (1999). A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans. Development, 126(2), 241-50. (Read full article)
  152. Yandell MD, Edgar LG, Wood WB (1994). Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans. Proc Natl Acad Sci U S A, 91(4), 1381-5. (Read full article)

Review

  1. 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 (2023). The status of the human gene catalogue. [Review]. Nature, 622(7981), 41-47. (Read full article)
  2. Yandell MD, Majoros WH (2002). Genomics and natural language processing. [Review]. Nat Rev Genet, 3(8), 601-10. (Read full article)

Book

  1. Korf I, Yandell M, Bedell J (2003). Blast. O'Reilly & Associates.

Conference Proceedings

  1. Robert Schlaberg, Heng Xie, Steven Flygare, Yuying Mei, Hajime Matsuzaki, Mark Yandell, Erin H Graf (2017). Detection of Previously Missed Pathogens in Immunocompromised Children with Pneumonia by a Fully-Validated Next-Generation Sequencing Test. American Thoracic Society 2017 International Conference, American Journal of Respiratory and Critical Care Medicine, 195, A7561.
  2. Lyon, G et al (2011). Returning research results in the context of next-generation sequencing for "simple" and "complex" disorders. CSHL Personal Genomes Meeting, Cold Spring Harbor Laboratories.
  3. Reese MG, de la Vega F, Chervitz S, Russell A, Kiruluta EE, Huff C, Hu H, Moore B, Jorde L, Lyon G, Yandell M (2011). A clinical genome interpretation system: variant prioritization in personal genome for clinical applications. CSHL Personal Genomes Meeting, Cold Spring Harbor Laboratories.
  4. Hu, H, Zimin, A, Kim, J, Gadau, J, Robertson, H, Suarez, AV, Smith, C, Tsutsui, N, Yandell, M, Smith, CD (2010). The genomes of the Argentine and Red Harvester ants. CSHL Biology of Genomes, Cold Spring Harbor Laboratories.
  5. Carson Holt, Hao Hu, Barry Moore, Ian Korf amp Mark Yandell (2009). MAKER: GENOME ANNOTATION MADE EASY. CSHL 2009 Biology of Genomes, Cold Spring Harbor Laboratories.
  6. Hao Hu, Carson Holt1, Barry Moore, Ian Korf amp Mark Yandell (2009). NOT CREATED EQUAL. EVALUATOR: TOOL FOR GENE ANNOTATION QUALITY CONTROL. CSHL Biology of Genomes.
  7. Mark Yandell, Barry Moore, Sofia MC Robb, Eric Ross amp Alejandro S225nchez Alvarado (2009). An image-based whole-genome screen for novel regulators of tissue homeostasis and regeneration. Janelia Farm BioImage Informatics.
  8. Yandell, M, Moore, B, MacBride, AR, Slas, F, Mikloos, G, Frise, E, Reese, M (2009). Progress towards individual whole genome sequence analysis mutations in protein coding genes in 8 published genomes. CSHL Personal Genomes, Cold Spring Harbor Laboratories.
  9. Mark Yandell, Brandi L Cantarel, Sofia MC Robb, Jason Pelletteri, Eric Ross, Hadi Islam, Bret Pearson, Alejandro Snchez Alvarado (2007). A NEW WORM ON THE BLOCK: USING THE PLANARIAN GENOME FOR FUNCTIONAL AND COMPARATIVE GENOMICS. The Biology of Genomes.
  10. Yandell, M, Eilbeck, K, Moore, B (2007). New measures for management and comparison of annotated genomes. In Cold Spring Harbor/ Wellcome Trust (Ed.), Cold Spring Harbor/Wellcome Trust Genome Informatics Meeting.
  11. Yandell, MD (2003). Using genome annotations for high-throughput comparative-genomics. Genome Informatics.

Commentary

  1. Yandell, MD (2004). Blending Biology and Bioinformatics. Science.

Letter

  1. 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 (2014). Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations. [Letter to the editor]. J Allergy Clin Immunol, 133(3), 880-2.e10. (Read full article)