Mark Yandell, PhD

Research Interests

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

Languages

  • 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 USTAR 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
Ph.D.
Undergraduate University of Texas
Biology
B.A.

Selected Publications

Journal Article

  1. 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.
  2. Li Q, Watkins M, Robinson SD, Safavi-Hemami H, Yandell M (2018). Discovery of Novel Conotoxin Candidates Using Machine Learning. Toxins (Basel), 10(12).
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. Eilbeck K, Quinlan A, Yandell M (2017). Settling the score: variant prioritization and Mendelian disease. Nat Rev Genet, 18(10), 599-612.
  15. 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.
  16. 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.
  17. 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.
  18. 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).
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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).
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. Yandell MB, Zelik KE (2016). Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate. Sci Rep, 6, 23243.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. Campbell MS, Yandell M (2015). An Introduction to Genome Annotation. Curr Protoc Bioinformatics, 52, 4.1.1-17.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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.
  55. 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.
  56. 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.
  57. 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.
  58. 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.
  59. 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.
  60. Safavi-Hemami H, Hu H, Gorasia DG, Bandyopadhyay PK, Veith PD, Young ND, Reynolds EC, Yandell M, Olivera BM, Purcell AW (2014). Combined proteomic and transcriptomic interrogation of the venom gland of Conus geographus uncovers novel components and functional compartmentalization. Mol Cell Proteomics, 13(4), 938-53.
  61. Manuck TA, Watkins WS, Moore B, Esplin MS, Varner MW, Jackson GM, Yandell M, Jorde L (2014). Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention. Am J Obstet Gynecol, 210(4), 321.e1-321.e21.
  62. Kumar P P, Franklin S, Emechebe U, Hu H, Moore B, Lehman C, Yandell M, Moon AM (2014). TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome. PLoS Genet, 10(3), e1004247.
  63. 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, Dworzyski 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, Lovrei L, Palandai 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, Gonzlez-Lamuo 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 (2014). An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Genome Biol, 15(3), R53.
  64. Chapin A, Hu H, Rynearson SG, Hollien J, Yandell M, Metzstein MM (2014). In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. G3 (Bethesda), 4(3), 485-96.
  65. Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martnez-Garca PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marais 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 (2014). Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies. Genome Biol, 15(3), R59.
  66. Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martnez-Garca 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 (2014). Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics, 196(3), 891-909.
  67. 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 (2014). Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Curr Biol, 24(4), 459-64.
  68. 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 (2014). MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol, 164(2), 513-24.
  69. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wster 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 (2013). The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proc Natl Acad Sci U S A, 110(51), 20651-6.
  70. 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 (2013). The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proc Natl Acad Sci U S A, 110(51), 20645-50.
  71. Ul-Hasan S, Burgess DM, Gajewiak J, Li Q, Hu H, Yandell M, Olivera BM, Bandyopadhyay PK (2013). Characterization of the peptidylglycine α-amidating monooxygenase (PAM) from the venom ducts of neogastropods, Conus bullatus and Conus geographus. Toxicon, 74, 215-24.
  72. Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M (2013). VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet Epidemiol, 37(6), 622-34.
  73. Flygare S, Campbell M, Ross RM, Moore B, Yandell M (2013). ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea. J Comput Biol, 20(8), 583-92.
  74. 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 (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol, 14(5), R41.
  75. Amemiya CT, Alfldi 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 (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311-6.
  76. 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 (2013). Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet, 45(4), 415-21, 421e1-2.
  77. Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C (2013). Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet, 9(4), e1003470.
  78. 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 (2013). Genomic diversity and evolution of the head crest in the rock pigeon. Science, 339(6123), 1063-7.
  79. Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2012). Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct. BMC Genomics, 13, 284.
  80. Yandell M, Ence D (2012). A beginner's guide to eukaryotic genome annotation. Nat Rev Genet, 13(5), 329-42.
  81. 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.
  82. Holt C, Yandell M (2011). MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12, 491.
  83. 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.
  84. 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.
  85. 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.
  86. 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.
  87. 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.
  88. 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.
  89. 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.
  90. Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2011). Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genomics, 12, 60.
  91. 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.
  92. 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.
  93. 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.
  94. Eilbeck K, Moore B, Holt C, Yandell M (2009). Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics, 10, 67.
  95. 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.
  96. 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.
  97. 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.
  98. 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.
  99. 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.
  100. 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.
  101. Majoros WH, Subramanian GM, Yandell MD (2003). Identification of key concepts in biomedical literature using a modified Markov heuristic. Bioinformatics, 19(3), 402-7.
  102. 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.
  103. 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.
  104. 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 (2002). A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science, 296(5573), 1661-71.
  105. 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.
  106. 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, Guigo 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.
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. 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.

Review

  1. Yandell MD, Majoros WH (2002). Genomics and natural language processing. [Review]. Nat Rev Genet, 3(8), 601-10.

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. 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.
  6. 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.
  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.