Mark Yandell

Mark Yandell, PhD

Languages spoken: English

Academic Information

Departments Primary - Human Genetics , Adjunct - Biomedical Informatics

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

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

Selected Publications

Journal Article

  1. 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)
  2. 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. (Read full article)
  3. 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. (Read full article)
  4. 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.
  5. 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.
  6. 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)
  7. 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)
  8. 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, O'Hare 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.
  9. 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)
  10. Häberle J, Moore MB, Haskins N, Rüfenacht 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)
  11. 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)
  12. 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. (Read full article)
  13. Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Cañestro C, Sydes J, Beaudry FE, Sun Y, Hertel J, Beam MJ, Fasold M, Ishiyama M, Johnson J, Kehr S, Lara M, Letaw JH, Litman GW, Litman RT, Mikami M, Ota T, Saha NR, Williams L, Stadler PF, Wang H, Taylor JS, Fontenot Q, Ferrara A, Searle SM, Aken B, Yandell M, Schneider I, Yoder JA, Volff JN, Meyer A, Amemiya CT, Venkatesh B, Holland PW, Guiguen Y, Bobe J, Shubin NH, Di Palma F, Alföldi J, Lindblad-Toh K, Postlethwait JH (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat Genet, 48(4), 427-37. (Read full article)
  14. 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 (2017). Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nature genetics, 49(11), 1593-1601. (Read full article)
  15. 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 C (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature genetics, 50(2), 270-277. (Read full article)
  16. Suzuki Y, Yandell MD, Roy PJ, Krishna S, Savage-Dunn C, Ross RM, Padgett RW, Wood W (1999). A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans. Development (Cambridge, England), 126(2), 241-50. (Read full article)
  17. Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami (2017). Hormone-like peptides in the venoms of marine cone snails. General and comparative endocrinology, 244, 11-18. (Read full article)
  18. Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell (2013). VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genetic epidemiology, 37(6), 622-34. (Read full article)
  19. Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martínez-García PJ, Holt C, Yandell M, Zimin AV, Yorke JA, Crepeau MW, Puiu D, Salzberg SL, Dejong PJ, Mockaitis K, Main D, Langley CH, Neale D (2014). Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation. Genetics, 196(3), 891-909. (Read full article)
  20. Smith CD, Edgar RC, Yandell MD, Smith DR, Celniker SE, Myers EW, Karpen G (2007). Improved repeat identification and masking in Dipterans. Gene, 389(1), 1-9. (Read full article)
  21. 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 (Baltimore, Md.), 70(3), 899-910. (Read full article)
  22. Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson C (2014). DisAp-dependent striated fiber elongation is required to organize ciliary arrays. The Journal of cell biology, 207(6), 705-15. (Read full article)
  23. King SB, Yandell MA, Stephansen AB, Neumark D (2014). Time-resolved radiation chemistry: dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes. The Journal of chemical physics, 141(22), 224310. (Read full article)
  24. King SB, Stephansen AB, Yokoi Y, Yandell MA, Kunin A, Takayanagi T, Neumark D (2015). Electron accommodation dynamics in the DNA base thymine. The Journal of chemical physics, 143(2), 024312. (Read full article)
  25. Al-Agha AE, Ahmed IA, Nuebel E, Moriwaki M, Moore B, Peacock KA, Mosbruger T, Neklason DW, Jorde LB, Yandell M, Welt C (2018). Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. The Journal of clinical endocrinology and metabolism, 103(2), 555-563. (Read full article)
  26. 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 C (2021). Causal and Candidate Gene Variants in a Large Cohort of Women with Primary Ovarian Insufficiency. The Journal of clinical endocrinology and metabolism, 107(3), 685-714. (Read full article)
  27. Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg (2016). Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. Journal of clinical microbiology, 54(4), 1000-7. (Read full article)
  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 (2017). Viral Pathogen Detection by Metagenomics and Pan-Viral Group Polymerase Chain Reaction in Children With Pneumonia Lacking Identifiable Etiology. The Journal of infectious diseases, 215(9), 1407-1415. (Read full article)
  29. 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 A (2017). Human Bocavirus Capsid Messenger RNA Detection in Children With Pneumonia. The Journal of infectious diseases, 216(6), 688-696. (Read full article)
  30. Cone KR, Kronenberg ZN, Yandell M, Elde N (2017). Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus. Journal of virology, 91(4), (Read full article)
  31. Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Zabriskie MS, Yan D, Pomicter AD, Reynolds KR, Eiring AM, Kronenberg Z, Sherman RL, Tyner JW, Dalley BK, Dao KH, Yandell M, Druker BJ, Gotlib J, O'Hare T, Deininger M (2016). Age-related mutations and chronic myelomonocytic leukemia. Leukemia, 30(4), 906-13. (Read full article)
  32. Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera B (2016). Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. Molecular biology and evolution, 33(11), 2924-2934. (Read full article)
  33. 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 L (2021). Elephant Genomes Reveal Accelerated Evolution in Mechanisms Underlying Disease Defenses. Molecular biology and evolution, 38(9), 3606-3620. (Read full article)
  34. Maclary ET, Phillips B, Wauer R, Boer EF, Bruders R, Gilvarry T, Holt C, Yandell M, Shapiro M (2021). Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia). Molecular biology and evolution, 38(12), 5376-5390. (Read full article)
  35. Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311-6. (Read full article)
  36. Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs R (2014). Gibbon genome and the fast karyotype evolution of small apes. Nature, 513(7517), 195-201. (Read full article)
  37. Kerlavage A, Bonazzi V, di Tommaso M, Lawrence C, Li P, Mayberry F, Mural R, Nodell M, Yandell M, Zhang J, Thomas (2002). The Celera Discovery System. Nucleic acids research, 30(1), 129-36. (Read full article)
  38. Yu Y, Hu H, Bohlender RJ, Hu F, Chen JS, Holt C, Fowler J, Guthery SL, Scheet P, Hildebrandt MAT, Yandell M, Huff C (2018). XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. Nucleic acids research, 46(6), e32. (Read full article)
  39. 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 (2014). MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant physiology, 164(2), 513-24. (Read full article)
  40. 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 (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 physiology, 167(1), 25-39. (Read full article)
  41. Yandell MD, Edgar LG, Wood W (1994). Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans. Proceedings of the National Academy of Sciences of the United States of America, 91(4), 1381-5. (Read full article)
  42. Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine A (2000). Identification and characterization of a p53 homologue in Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America, 97(13), 7301-6. (Read full article)
  43. Yandell M, Bailey AM, Misra S, Shu S, Wiel C, Evans-Holm M, Celniker SE, Rubin G (2005). A computational and experimental approach to validating annotations and gene predictions in the Drosophila melanogaster genome. Proceedings of the National Academy of Sciences of the United States of America, 102(5), 1566-71. (Read full article)
  44. Smith CD, Zimin A, Holt C, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave MJ, Fernandes V, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Helmkampf M, Holley JA, Hu H, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Laird J, Mathis KA, Moeller JA, Muñoz-Torres MC, Murphy MC, Nakamura R, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Robertson HM, Smith CR, Suarez AV, Suen G, Suhr EL, Tao S, Torres CW, van Wilgenburg E, Viljakainen L, Walden KK, Wild AL, Yandell M, Yorke JA, Tsutsui N (2011). Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile). Proceedings of the National Academy of Sciences of the United States of America, 108(14), 5673-8. (Read full article)
  45. Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Favé MJ, Fernandes V, Gibson JD, Graur D, Gronenberg W, Grubbs KJ, Hagen DE, Viniegra AS, Johnson BR, Johnson RM, Khila A, Kim JW, Mathis KA, Munoz-Torres MC, Murphy MC, Mustard JA, Nakamura R, Niehuis O, Nigam S, Overson RP, Placek JE, Rajakumar R, Reese JT, Suen G, Tao S, Torres CW, Tsutsui ND, Viljakainen L, Wolschin F, Gadau (2011). Draft genome of the red harvester ant Pogonomyrmex barbatus. Proceedings of the National Academy of Sciences of the United States of America, 108(14), 5667-72. (Read full article)
  46. Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wüster W, Woods AE, Logan JM, Harrison RA, Castoe TA, de Koning AP, Pollock DD, Yandell M, Calderon D, Renjifo C, Currier RB, Salgado D, Pla D, Sanz L, Hyder AS, Ribeiro JM, Arntzen JW, van den Thillart GE, Boetzer M, Pirovano W, Dirks RP, Spaink HP, Duboule D, McGlinn E, Kini RM, Richardson M (2013). The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system. Proceedings of the National Academy of Sciences of the United States of America, 110(51), 20651-6. (Read full article)
  47. 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 D (2013). The Burmese python genome reveals the molecular basis for extreme adaptation in snakes. Proceedings of the National Academy of Sciences of the United States of America, 110(51), 20645-50. (Read full article)
  48. 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 B (2015). Specialized insulin is used for chemical warfare by fish-hunting cone snails. Proceedings of the National Academy of Sciences of the United States of America, 112(6), 1743-8. (Read full article)
  49. 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 (2015). Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade. Proceedings of the National Academy of Sciences of the United States of America, 112(52), 15976-81. (Read full article)
  50. Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard (2016). Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides. Proceedings of the National Academy of Sciences of the United States of America, 113(12), 3227-32. (Read full article)
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  151. 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 C (2018). Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature genetics, 50(11), 1617. (Read full article)
  152. 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 C (2018). Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature genetics, 50(5), 768. (Read full article)
  153. Juarez EF, Peterson B, Sanford Kobayashi E, Gilmer S, Tobin LE, Schultz B, Lenberg J, Carroll J, Bai-Tong S, Sweeney NM, Beebe C, Stewart L, Olsen L, Reinke J, Kiernan EA, Reimers R, Wigby K, Tackaberry C, Yandell M, Hobbs C, Bainbridge M (2025). A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit. NPJ digital medicine, 8(1), 72. (Read full article)
  154. Zimmerman RM, Hernandez EJ, Yandell M, Tristani-Firouzi M, Silver RM, Grobman W, Haas D, Saade G, Steller J, Blue N (2024). AI-based analysis of fetal growth restriction in a prospective obstetric cohort quantifies compound risks for perinatal morbidity and mortality and identifies previously unrecognized high risk clinical scenarios. Research square, (Read full article)
  155. Espino S, Watkins M, Probst R, Koch TL, Chase K, Imperial J, Robinson SD, Flórez Salcedo P, Taylor D, Gajewiak J, Yandell M, Safavi-Hemami H, Olivera B (2024). ¿-Conotoxins are an Evolutionary Innovation of Mollusk-Hunting Cone Snails as a Counter-Adaptation to Prey Defense. Molecular biology and evolution, 41(11), (Read full article)
  156. Kingsmore SF, Wright M, Smith LD, Liang Y, Mowrey WR, Protopsaltis L, Bainbridge M, Baker M, Batalov S, Blincow E, Cao B, Caylor S, Chambers C, Ellsworth K, Feigenbaum A, Frise E, Guidugli L, Hall KP, Hansen C, Kiel M, Van Der Kraan L, Krilow C, Kwon H, Madhavrao L, Lefebvre S, Leipzig J, Mardach R, Moore B, Oh D, Olsen L, Ontiveros E, Owen MJ, Reimers R, Scharer G, Schleit J, Shelnutt S, Mehtalia SS, Oriol A, Sanford E, Schwartz S, Wigby K, Willis MJ, Yandell M, Kunard CM, Defay (2024). Prequalification of genome-based newborn screening for severe childhood genetic diseases through federated training based on purifying hyperselection. American journal of human genetics, 111(12), 2618-2642. (Read full article)
  157. Kiser AC, Schliep KC, Hernandez EJ, Peterson CM, Yandell M, Eilbeck (2024). An artificial intelligence approach for investigating multifactorial pain-related features of endometriosis. PloS one, 19(2), e0297998. (Read full article)
  158. Maclary ET, Holt C, Concepcion GT, Sovi¿ I, Vickrey AI, Yandell M, Kronenberg Z, Shapiro M (2023). Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F(1) hybrid. bioRxiv, (Read full article)
  159. 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 S (2023). The status of the human gene catalogue. ArXiv, (Read full article)
  160. Zimmerman RM, Hernandez EJ, Yandell M, Tristani-Firouzi M, Silver RM, Grobman W, Haas D, Saade G, Steller J, Blue N (2025). AI-based analysis of fetal growth restriction in a prospective obstetric cohort quantifies compound risks for perinatal morbidity and mortality and identifies previously unrecognized high risk clinical scenarios. BMC pregnancy and childbirth, 25(1), 80. (Read full article)
  161. Koch TL, Robinson SD, Salcedo PF, Chase K, Biggs J, Fedosov AE, Yandell M, Olivera BM, Safavi-Hemami (2024). Prey Shifts Drive Venom Evolution in Cone Snails. Molecular biology and evolution, 41(8), (Read full article)
  162. Allen-Brady K, Moore B, Verrilli LE, Alvord MA, Kern M, Camp N, Kelley K, Letourneau J, Cannon-Albright L, Yandell M, Johnstone EB, Welt C (2024). Breast Cancer is Increased in Women with Primary Ovarian Insufficiency. The Journal of clinical endocrinology and metabolism, 110(5), e1678-e1686. (Read full article)

Review

  1. Yandell MD, Majoros W (2002). Genomics and natural language processing. Nature reviews. Genetics, 3(8), 601-10. (Read full article)
  2. 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 S (2023). The status of the human gene catalogue. Nature, 622(7981), 41-47. (Read full article)

Book

  1. Korf I, Yandell M, Bedell (2003). Blast. 360.

Conference Proceedings

  1. Mark Yandell, Brandi L. Cantarel, Sofia MC Robb, Jason Pelletteri, Eric Ross, Hadi Islam, Bret Pearson, Alejandro Sánchez Alvarad (2007). A NEW WORM ON THE BLOCK: USING THE PLANARIAN GENOME FOR FUNCTIONAL AND COMPARATIVE GENOMICS.
  2. Yandell, M (2003). Using genome annotations for high-throughput comparative-genomics.
  3. Mark Yandell, Barry Moore, Sofia MC Robb, Eric Ross & Alejandro Sánchez Alvarad (2009). An image-based whole-genome screen for novel regulators of tissue homeostasis and regeneration.
  4. Hao Hu, Carson Holt1, Barry Moore, Ian Korf & Mark Yandel (2009). NOT CREATED EQUAL. EVALUATOR: TOOL FOR GENE ANNOTATION QUALITY CONTROL.
  5. Carson Holt, Hao Hu, Barry Moore, Ian Korf & Mark Yandel (2009). MAKER: GENOME ANNOTATION MADE EASY.
  6. Yandell, M., Eilbeck, K., Moore, B (2007). New measures for management and comparison of annotated genomes.
  7. 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.
  8. 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.
  9. Lyon, G et a (2011). Returning research results in the context of next-generation sequencing for "simple" and "complex" disorders.
  10. 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.
  11. Robert Schlaberg , Heng Xie , Steven Flygare , Yuying Mei , Hajime Matsuzaki , Mark Yandell , Erin H. Gra (2017). Detection of Previously Missed Pathogens in Immunocompromised Children with Pneumonia by a Fully-Validated Next-Generation Sequencing Test. 195, A7561.

Commentary

  1. Yandell, M (2004). Blending Biology and Bioinformatics. Science (New York, N.Y.),

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 J (2014). Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations. The Journal of allergy and clinical immunology, 133(3), 880-2.e10. (Read full article)