Mark Yandell, PhD

Research Interests

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

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

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. Hormone-like peptides in the venoms of marine cone snails.Robinson SD, Li Q, Bandyopadhyay PK, Gajewiak J, Yandell M, Papenfuss AT, Purcell AW, Norton RS, Safavi-Hemami H (2017). Hormone-like peptides in the venoms of marine cone snails. Gen Comp Endocrinol, 244, 11-18.
  2. Emergence of a Viral RNA Polymerase Variant during Gene Copy Number Amplification Promotes Rapid Evolution of Vaccinia Virus.LID - e01428-16 [pii]LID - 10.1128/JVI.01428-16 [doi]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.LID - e01428-16 [pii]LID - 10.1128/JVI.01428-16 [doi]. J Virol, 91(4).
  3. Viral Pathogen Detection by Metagenomics and Pan Viral Group PCR in Children with Pneumonia Lacking Identifiable Etiology.LID - 10.1093/infdis/jix148 [doi]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 PCR in Children with Pneumonia Lacking Identifiable Etiology.LID - 10.1093/infdis/jix148 [doi]. (Epub ahead of print) J Infect Dis.
  4. Age-related mutations and chronic myelomonocytic leukemia.Mason CC, Khorashad JS, Tantravahi SK, Kelley TW, Zabriskie MS, Yan D, Pomicter AD, Reynolds KR, Eiring AM, Kronenberg Z, Sherman RL, Tyner JW, Dalley BK, Dao KH, Yandell M, Druker BJ, Gotlib J, OHare T, Deininger MW (2016). Age-related mutations and chronic myelomonocytic leukemia. Leukemia, 30(4), 906-13.
  5. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel.Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, Yandell M, Schlaberg R (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.
  6. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons.Braasch I, Gehrke AR, Smith JJ, Kawasaki K, Manousaki T, Pasquier J, Amores A, Desvignes T, Batzel P, Catchen J, Berlin AM, Campbell MS, Barrell D, Martin KJ, Mulley JF, Ravi V, Lee AP, Nakamura T, Chalopin D, Fan S, Wcisel D, Canestro 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, Alfoldi 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.
  7. Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides.Safavi-Hemami H, Li Q, Jackson RL, Song AS, Boomsma W, Bandyopadhyay PK, Gruber CW, Purcell AW, Yandell M, Olivera BM, Ellgaard L (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.
  8. Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species.Domyan ET, Kronenberg Z, Infante CR, Vickrey AI, Stringham SA, Bruders R, Guernsey MW, Park S, Payne J, Beckstead RB, Kardon G, Menke DB, Yandell M, Shapiro MD (2016). Molecular shifts in limb identity underlie development of feathered feet in two domestic avian species. Elife, 5, e12115.
  9. Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate.Yandell MB, Zelik KE (2016). Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate. Sci Rep, 6, 23243.
  10. Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.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.
  11. Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol, 17(1), 111.
  12. Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa.Safavi-Hemami H, Lu A, Li Q, Fedosov AE, Biggs J, Showers Corneli P, Seger J, Yandell M, Olivera BM (2016). Venom Insulins of Cone Snails Diversify Rapidly and Track Prey Taxa. Mol Biol Evol, 33(11), 2924-2934.
  13. VARPRISM: incorporating variant prioritization in tests of de novo mutation association.Hu H, Coon H, Li M, Yandell M, Huff CD (2016). VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Med, 8(1), 91.
  14. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.LID - btw799 [pii]LID - 10.1093/bioinformatics/btw799 [doi]Majoros WH, Campbell MS, Holt C, DeNardo E, Ware D, Allen AS, Yandell M, Reddy TE (2016). High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.LID - btw799 [pii]LID - 10.1093/bioinformatics/btw799 [doi]. (Epub ahead of print) Bioinformatics.
  15. 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.
  16. 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.
  17. 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.
  18. Specialized insulin is used for chemical warfare by fish-hunting cone snails.Safavi-Hemami H, Gajewiak J, Karanth S, Robinson SD, Ueberheide B, Douglass AD, Schlegel A, Imperial JS, Watkins M, Bandyopadhyay PK, Yandell M, Li Q, Purcell AW, Norton RS, Ellgaard L, Olivera BM (2015). Specialized insulin is used for chemical warfare by fish-hunting cone snails. Proc Natl Acad Sci U S A, 112(6), 1743-8.
  19. Muscle stem cells contribute to myofibres in sedentary adult mice.Keefe AC, Lawson JA, Flygare SD, Fox ZD, Colasanto MP, Mathew SJ, Yandell M, Kardon G (2015). Muscle stem cells contribute to myofibres in sedentary adult mice. Nat Commun, 6, 7087.
  20. Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ED, Simoes 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.
  21. Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR).Nash D, Arrington CB, Kennedy BJ, Yandell M, Wu W, Zhang W, Ware S, Jorde LB, Gruber PJ, Yost HJ, Bowles NE, Bleyl SB (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.
  22. Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade.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.
  23. Campbell MS, Yandell M (2015). An introduction to Genome Annotation. Curr Protoc Bioinformatics, 52, 4.1-4.1.17.
  24. Wham: Identifying Structural Variants of Biological Consequence.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.
  25. 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.
  26. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes.Law M, Childs KL, Campbell MS, Stein JC, Olson AJ, Holt C, Panchy N, Lei J, Jiao D, Andorf CM, Lawrence CJ, Ware D, Shiu SH, Sun Y, Jiang N, Yandell M (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.
  27. Transposable element islands facilitate adaptation to novel environments in an invasive species.Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stokl 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.
  28. DisAp-dependent striated fiber elongation is required to organize ciliary arrays.Galati DF, Bonney S, Kronenberg Z, Clarissa C, Yandell M, Elde NC, Jerka-Dziadosz M, Giddings TH, Frankel J, Pearson CG (2014). DisAp-dependent striated fiber elongation is required to organize ciliary arrays. J Cell Biol, 207(6), 705-15.
  29. Genome Annotation and Curation Using MAKER and MAKER-P.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.
  30. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations.Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M (2014). MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol, 164(2), 513-24.
  31. In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila.Chapin A, Hu H, Rynearson SG, Hollien J, Yandell M, Metzstein MM (2014). In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila. G3 (Bethesda), 4(3), 485-96.
  32. Combined proteomic and transcriptomic interrogation of the venom gland of Conus geographus uncovers novel components and functional compartmentalization.Safavi-Hemami H, Hu H, Gorasia DG, Bandyopadhyay PK, Veith PD, Young ND, Reynolds EC, Yandell M, Olivera BM, Purcell AW (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.
  33. Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.Domyan ET, Guernsey MW, Kronenberg Z, Krishnan S, Boissy RE, Vickrey AI, Rodgers C, Cassidy P, Leachman SA, Fondon JW 3rd, Yandell M, Shapiro MD (2014). Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon. Curr Biol, 24(4), 459-64.
  34. Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention.Manuck TA, Watkins WS, Moore B, Esplin MS, Varner MW, Jackson GM, Yandell M, Jorde L (2014). Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention. Am J Obstet Gynecol, 210(4), 321.e1-321.e21.
  35. Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, Puiu D, Crepeau MW, Cardeno C, Koriabine M, Holtz-Morris AE, Liechty JD, Martinez-Garcia PJ, Vasquez-Gross HA, Lin BY, Zieve JJ, Dougherty WM, Fuentes-Soriano S, Wu LS, Gilbert D, Marcais 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.
  36. Unique features of the loblolly pine (Pinus taeda L.) megagenome revealed through sequence annotation.Wegrzyn JL, Liechty JD, Stevens KA, Wu LS, Loopstra CA, Vasquez-Gross HA, Dougherty WM, Lin BY, Zieve JJ, Martinez-Garcia 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.
  37. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzynski 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, Lovrecic L, Palandacic 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, Gonzalez-Lamuno 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.
  38. TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.Kumar P P, Franklin S, Emechebe U, Hu H, Moore B, Lehman C, Yandell M, Moon AM (2014). TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome. PLoS Genet, 10(3), e1004247.
  39. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families.Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M (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.
  40. Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data.Kennedy B, Kronenberg Z, Hu H, Moore B, Flygare S, Reese MG, Jorde LB, Yandell M, Huff C (2014). Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. Curr Protoc Hum Genet, 81, 6.14.1-25.
  41. An improved genome release (version Mt4.0) for the model legume Medicago truncatula.Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, Gentzbittel L, Childs KL, Yandell M, Gundlach H, Mayer KF, Schwartz DC, Town CD (2014). An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics, 15, 312.
  42. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.Hu H, Roach JC, Coon H, Guthery SL, Voelkerding KV, Margraf RL, Durtschi JD, Tavtigian SV, Shankaracharya, Wu W, Scheet P, Wang S, Xing J, Glusman G, Hubley R, Li H, Garg V, Moore B, Hood L, Galas DJ, Srivastava D, Reese MG, Jorde LB, Yandell M, Huff CD (2014). A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol, 32(7), 663-9.
  43. Coordinated control of senescence by lncRNA and a novel T-box3 co-repressor complex.LID - 10.7554/eLife.02805 [doi]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.LID - 10.7554/eLife.02805 [doi]. Elife, 3.
  44. Gibbon genome and the fast karyotype evolution of small apes.Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvak 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.
  45. Transiently active Wnt/beta-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration.Murphy MM, Keefe AC, Lawson JA, Flygare SD, Yandell M, Kardon G (2014). Transiently active Wnt/beta-catenin signaling is not required but must be silenced for stem cell function during muscle regeneration. Stem Cell Reports, 3(3), 475-88.
  46. Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma.Darlington TM, Pimentel R, Smith K, Bakian AV, Jerominski L, Cardon J, Camp NJ, Callor WB, Grey T, Singleton M, Yandell M, Renshaw PF, Yurgelun-Todd DA, Gray D, Coon H (2014). Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma. Transl Psychiatry, 4, e471.
  47. Genomic diversity and evolution of the head crest in the rock pigeon.Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, Huff CD, Hu H, Vickrey AI, Nielsen SC, Stringham SA, Hu H, Willerslev E, Gilbert MT, Yandell M, Zhang G, Wang J (2013). Genomic diversity and evolution of the head crest in the rock pigeon. Science, 339(6123), 1063-7.
  48. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution.Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SM, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner ME, Warren WC, Clifton SW, Wilson RK, Li W (2013). Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nat Genet, 45(4), 415-21, 421e1-2.
  49. The African coelacanth genome provides insights into tetrapod evolution.Amemiya CT, Alfoldi 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.
  50. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs.Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C (2013). Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet, 9(4), e1003470.
  51. ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea.Flygare S, Campbell M, Ross RM, Moore B, Yandell M (2013). ImagePlane: an automated image analysis pipeline for high-throughput screens using the planarian Schmidtea mediterranea. J Comput Biol, 20(8), 583-92.
  52. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix.Hu H, Huff CD, Moore B, Flygare S, Reese MG, Yandell M (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.
  53. Characterization of the peptidylglycine alpha-amidating monooxygenase (PAM) from the venom ducts of neogastropods, Conus bullatus and Conus geographus.Ul-Hasan S, Burgess DM, Gajewiak J, Li Q, Hu H, Yandell M, Olivera BM, Bandyopadhyay PK (2013). Characterization of the peptidylglycine alpha-amidating monooxygenase (PAM) from the venom ducts of neogastropods, Conus bullatus and Conus geographus. Toxicon, 74, 215-24.
  54. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system.Vonk FJ, Casewell NR, Henkel CV, Heimberg AM, Jansen HJ, McCleary RJ, Kerkkamp HM, Vos RA, Guerreiro I, Calvete JJ, Wuster 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.
  55. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes.Castoe TA, de Koning AP, Hall KT, Card DC, Schield DR, Fujita MK, Ruggiero RP, Degner JF, Daza JM, Gu W, Reyes-Velasco J, Shaney KJ, Castoe JM, Fox SE, Poole AW, Polanco D, Dobry J, Vandewege MW, Li Q, Schott RK, Kapusta A, Minx P, Feschotte C, Uetz P, Ray DA, Hoffmann FG, Bogden R, Smith EN, Chang BS, Vonk FJ, Casewell NR, Henkel CV, Richardson MK, Mackessy SP, Bronikowski AM, Yandell M, Warren WC, Secor SM, Pollock DD (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.
  56. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min XJ, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R, Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, Shen-Miller J (2013). Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biol, 14(5), R41.
  57. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.Vieler A, Wu G, Tsai CH, Bullard B, Cornish AJ, Harvey C, Reca IB, Thornburg C, Achawanantakun R, Buehl CJ, Campbell MS, Cavalier D, Childs KL, Clark TJ, Deshpande R, Erickson E, Armenia Ferguson A, Handee W, Kong Q, Li X, Liu B, Lundback S, Peng C, Roston RL, Sanjaya, Simpson JP, Terbush A, Warakanont J, Zauner 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.
  58. Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct.Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2012). Elucidation of the molecular envenomation strategy of the cone snail Conus geographus through transcriptome sequencing of its venom duct. BMC Genomics, 13, 284.
  59. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.Holt C, Yandell M (2011). MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics, 12, 491.
  60. A probabilistic disease-gene finder for personal genomes.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.
  61. Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications.Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, Tian L, Robison RJ, Clement M, Lin Y, Zhang P, Liu Y, Moore B, Glessner JT, Elia J, Reimherr F, van Solinge WW, Yandell M, Hakonarson H, Wang J, Johnson WE, Wei Z, Wang K (2011). Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med, 12(62), 41-55.
  62. Characterization of the Conus bullatus genome and its venom-duct transcriptome.Hu H, Bandyopadhyay PK, Olivera BM, Yandell M (2011). Characterization of the Conus bullatus genome and its venom-duct transcriptome. BMC Genomics, 12, 60.
  63. Draft genome of the red harvester ant Pogonomyrmex barbatus.Smith CR, Smith CD, Robertson HM, Helmkampf M, Zimin A, Yandell M, Holt C, Hu H, Abouheif E, Benton R, Cash E, Croset V, Currie CR, Elhaik E, Elsik CG, Fave 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.
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  65. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Fave 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, Munoz-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.
  66. The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB (2010). The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, 11, 420.
  67. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire.Levesque 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.
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  69. Quantitative measures for the management and comparison of annotated genomes.Eilbeck K, Moore B, Holt C, Yandell M (2009). Quantitative measures for the management and comparison of annotated genomes. BMC Bioinformatics, 10, 67.
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  72. Improved repeat identification and masking in Dipterans.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.
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  84. Identification and characterization of a p53 homologue in Drosophila melanogaster.Jin S, Martinek S, Joo WS, Wortman JR, Mirkovic N, Sali A, Yandell MD, Pavletich NP, Young MW, Levine AJ (2000). Identification and characterization of a p53 homologue in Drosophila melanogaster. Proc Natl Acad Sci U S A, 97(13), 7301-6.
  85. A BMP homolog acts as a dose-dependent regulator of body size and male tail patterning in Caenorhabditis elegans.Suzuki Y, Yandell MD, Roy PJ, Krishna S, Savage-Dunn C, Ross RM, Padgett RW, Wood WB (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.
  86. A general approach to single-nucleotide polymorphism discovery.Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR (1999). A general approach to single-nucleotide polymorphism discovery. Nat Genet, 23(4), 452-6.
  87. Trimethylpsoralen induces small deletion mutations in Caenorhabditis elegans.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. A beginner's guide to eukaryotic genome annotation.Yandell M, Ence D (2012). A beginner's guide to eukaryotic genome annotation. [Review]. Nat Rev Genet, 13(5), 329-42.
  2. Genomics and natural language processing.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. 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.
  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. 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.
  4. 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.
  5. 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.
  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. 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.
  8. 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.
  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, MD (2003). Using genome annotations for high-throughput comparative-genomics. Genome Informatics.

Commentary

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

Case Report

  1. Exome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locus.Bowles NE, Jou CJ, Arrington CB, Kennedy BJ, Earl A, Matsunami N, Meyers LL, Etheridge SP, Saarel EV, Bleyl SB, Yost HJ, Yandell M, Leppert MF, Tristani-Firouzi M, Gruber PJ (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.
  2. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency.Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, Hakonarson H, Lillehaug JR, Biesecker LG, Yandell M, Arnesen T, Lyon GJ (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.

Letter

  1. Autoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutations.Chen K, Wu W, Mathew D, Zhang Y, Browne SK, Rosen LB, McManus MP, Pulsipher MA, Yandell M, Bohnsack JF, Jorde LB, Notarangelo LD, Walter JE (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.