Mark Yandell, PhD

Research Interests

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


  • English

Academic Information

  • Departments: Biomedical Informatics - Adjunct Associate Professor, Human Genetics - Professor

Academic Office Information

  • 801-581-4422
  • George and Dolores Eccles Institute of Human Genetics
    Human Genetics
    15 N 2030 E, Room: 2100
    Salt Lake City, UT 84112

Academic Bio

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

Type School Degree
Other Training Marine Biological Laboratories
Advanced Quantitative Light Microscopy Course
Postdoctoral Fellowship Washington University
Computational Biology
Postdoctoral Fellow
Other Training Marine Biological Laboratories
Molecular Evolution
Doctoral Training University of Colorado
Molecular, Cellular, & Developmental Biology
Undergraduate University of Texas

Selected Publications

Journal Article

  1. 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.
  2. 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).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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. (Epub ahead of print) Oncologist.
  8. 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.
  9. 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.
  10. Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M (2018). Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins (Basel), 10(12).
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. Eilbeck K, Quinlan A, Yandell M (2017). Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet, 18(10), 599-612.
  23. 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.
  24. 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.
  25. 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.
  26. 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).
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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).
  32. 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.
  33. 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.
  34. Hu H, Coon H, Li M, Yandell M, Huff CD (2016). VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Medicine, 8(1), 91.
  35. 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.
  36. 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, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biology, 17(1), 111.
  37. Barber MF, Kronenberg Z, Yandell M, Elde NC (2016). Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans. PLoS Genet, 12(5), e1006063.
  38. 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, Caestro 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, Alfldi J, Lindblad-Toh K, Postlethwait JH (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet, 48(4), 427-37.
  39. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R (2016). Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. J Clin Microbiol, 54(4), 1000-7.
  40. 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, OHare T, Deininger MW (2016). Age-related mutations and chronic myelomonocytic leukemia. Leukemia, 30(4), 906-13.
  41. Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L (2016). Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides. Proc Natl Acad Sci U S A, 113(12), 3227-32.
  42. Yandell MB, Zelik KE (2016). Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate. Sci Rep, 6, 23243.
  43. 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 (2016). Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. eLife, 5, e12115.
  44. 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 (2016). Genetic variation may influence response to 17-alpha hydroxyprogesterone caproate (17P) for recurrent preterm birth (PTB) prevention. Am J Obstet Gynecol, 214(1), S9-S10.
  45. 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 (01/01/2016). Gene set enrichment investigation of maternal exome variation in spontaneous preterm birth (SPTB). Am J Obstet Gynecol, 241(1), S142-S143.
  46. Boothby TC, Tenlen JR, Smith FW, Wang JR, Patanella KA, Nishimura EO, Tintori SC, Li Q, Jones CD, Yandell M, Messina DN, Glasscock J, Goldstein B (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proc Natl Acad Sci U S A, 112(52), 15976-81.
  47. Campbell MS, Yandell M (2015). An Introduction to Genome Annotation. Curr Protoc Bioinformatics, 52, 4.1.1-4.1.17.
  48. Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M (2015). Wham: Identifying Structural Variants of Biological Consequence. PLoS Comput Biol, 11(12), e1004572.
  49. 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 (2015). Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus. Am J Med Genet A, 167A(12), 2975-84.
  50. Mason C, Khorashad JS, Tantravahi SK, Kelley TW, Pomicter AD, Iovino AJ, Reynolds KR, Eiring AM, Zabriskie MS, Kronenberg Z, Tyner JW, Dalley B, Dao KHT, OHare T, Yandell M, Druker BJ, Gotlib JR, Deininger MW (2014). Next Generation Sequencing to Delineate the Mutational Landscape of Chronic Myelomonocytic Leukemia (CMML): Novel Disease Genes and Correlations with Survival. Blood, 124(21), 4367.
  51. King SB, Stephansen AB, Yokoi Y, Yandell MA, Kunin A, Takayanagi T, Neumark DM (2015). Electron accommodation dynamics in the DNA base thymine. J Chem Phys, 143(2), 024312.
  52. Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB (2015). Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR). PLoS ONE, 10(6), e0131514.
  53. 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 D, Simes 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 (2015). Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science, 348(6239), 1139-43.
  54. Keefe AC, Lawson JA, Flygare SD, Fox ZD, Colasanto MP, Mathew SJ, Yandell M, Kardon G (2015). Muscle stem cells contribute to myofibres in sedentary adult mice. Nat Commun, 6, 7087.
  55. 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 (2015). Specialized insulin is used for chemical warfare by fish-hunting cone snails. Proc Natl Acad Sci U S A, 112(6), 1743-8.
  56. 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 (2015). 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. Plant Physiol, 167(1), 25-39.
  57. Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG (2014). DisAp-dependent striated fiber elongation is required to organize ciliary arrays. J Cell Biol, 207(6), 705-15.
  58. Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stkl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J, Oettler J (2014). Transposable element islands facilitate adaptation to novel environments in an invasive species. Nat Commun, 5, 5495.
  59. Campbell MS, Holt C, Moore B, Yandell M (2014). Genome Annotation and Curation Using MAKER and MAKER-P. Curr Protoc Bioinformatics, 48, 4.11.1-39.
  60. 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 (2014). Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma. Transl Psychiatry, 4, e471.
  61. 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, Izsvk 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, OBleness 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 (2014). Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201.
  62. Murphy MM, Keefe AC, Lawson JA, Flygare SD, Yandell M, Kardon G (2014). Transiently active Wnt/β-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration. Stem Cell Reports, 3(3), 475-88.
  63. 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 (2014). A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol, 32(7), 663-9.
  64. Kumar P P, Emechebe U, Smith R, Franklin S, Moore B, Yandell M, Lessnick SL, Moon AM (2014). Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex. eLife, 3.
  65. 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 (2014). An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics, 15, 312.
  66. Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C (2014). Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. Curr Protoc Hum Genet, 81, 6.14.1-25.
  67. Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M (2014). Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet, 94(4), 599-610.
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  1. Yandell MD, Majoros WH (2002). Genomics and natural language processing. [Review]. Nat Rev Genet, 3(8), 601-10.


  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.


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


  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.