Publications – Page 4

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.

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.

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.

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.

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.

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.

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.

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.

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.

Yandell MB, Zelik KE (2016).

Preferred Barefoot Step Frequency is Influenced by Factors Beyond Minimizing Metabolic Rate.

Sci Rep, 6, 23243.

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.

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.

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.

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.

Campbell MS, Yandell M (2015).

An Introduction to Genome Annotation.

Curr Protoc Bioinformatics, 52, 4.1.1-4.1.17.

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.

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.

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.

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.

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.

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.

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.

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.

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.