Publications – Page 5

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.

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.

King SB, Yandell MA, Stephansen AB, Neumark DM (2014).

Time-resolved radiation chemistry: dynamics of electron attachment to uracil following UV excitation of iodide-uracil complexes.

J Chem Phys, 141(22), 224310.

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(10), e471

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.