Peer-Reviewed Publications

Xu Y, Cao H, Liu H, Sun H, Martin B, Zhao Y, Wang Q, Deng G, Xue J, Zong Y, Zhu J, Wen F, Long LP, Wong SS, Zhao N, Fu X, Liao M, Hu G, Webby R, Gao GF, Wan XF (2015) Identification of the source of A (H10N8) virus causing human infection. Infection, Genetics and Evolution 30: 159-163. DOI: 10.1016/j.meegid.2014.12.026 • SCOPUS ID: 2-s2.0-84920741596 • SCOPUS CITATION COUNT: 24

Pang B, Schlessman D, Kuang X, Zhao N, Shyu D, Korkin D, Shyu C-R (2015) An integrated approach to sequence-independent local alignment of protein binding sites. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12(2): 298-308. DOI: 10.1109/TCBB.2014.2355208 • SCOPUS ID: 2-s2.0-84927664817 • SCOPUS CITATION COUNT: 0

Herrera F, Aboughanem-Sabanadzovic N, Valverde RA (2015) A begomovirus associated with yellow vein symptoms of Oxalis debilis. European Journal of Plant Pathology 142: 203-209. DOI: 10.1007/s10658-015-0594-y • SCOPUS ID: 2-s2.0-84939998906 • SCOPUS CITATION COUNT: 6

Huang X, Jennings SF, Bruce B, Buchan A, Cai L, Chen P, Cramer CL, Guan W, Hilgert UK, Jiang H, Li Z, McClure G, McMullen DF, Nanduri B, Perkins A, Rekepalli B, Salem S, Specker J, Walker K, Wunsch D, Xiong D, Zhang S, Zhang Y, Zhao Z, Moore JH (2015) Big data - a 21st century science Maginot Line? No-boundary thinking: shifting from the big data paradigm. BioData Mining 8: 7. DOI: 10.1186/s13040-015-0037-5 • SCOPUS ID: 2-s2.0-84924094267 • SCOPUS CITATION COUNT: 8

Martin BE, Jia K, Sun H, Ye J, Hall C, Ware D, Wan XF (2015) Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays. Virology 476: 151-158. DOI: 10.1016/j.virol.2014.11.029 • SCOPUS ID: 2-s2.0-84921270479 • SCOPUS CITATION COUNT: 5

Hanna ME, Bednarova A, Rakshit K, Chaudhuri A, O'Donnell JM, Krishnan N (2015) Perturbations in dopamine synthesis lead to discrete physiological effects and impact oxidative stress response in Drosophila. Journal of Insect Physiology 73: 11-19. DOI: 10.1016/j.jinsphys.2015.01.001 • SCOPUS ID: 2-s2.0-84921260303 • SCOPUS CITATION COUNT: 32

Garcia-Reyero N (2015) Are adverse outcome pathways here to stay?. Environmental Science and Technology 49(1): 3-9. DOI: 10.1021/es504976d • SCOPUS ID: 2-s2.0-84924981770 • SCOPUS CITATION COUNT: 43

Natarajan C, Hoffmann FG, Lanier HC, Wolf CJ, Cheviron ZA, Spangler ML, Weber RE, Fago A, Storz JF (2015) Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin. Molecular Biology and Evolution 32(4): 978-997. DOI: 10.1093/molbev/msu403 • SCOPUS ID: 2-s2.0-84926654384 • SCOPUS CITATION COUNT: 84

Blake JA, Christie KR, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Burgess S, Buza T, Gresham C, McCarthy F, Pillai L, Wang H, Carbon S, Dietze H, Lewis SS, Mungall CJ, Munoz-Torres MC, Feuermann M, Gaudet P, Basu S, Chisholm RL, Dodson RJ, Fey P, Mi H, Thomas PD, Muruganujan A, Poudel S, Hu J, Aleksander SA, McIntosh BK, Renfro DP, Siegele DA, Attrill H, Brown NH, Tweedie S, Lomax J, Osumi-Sutherland D, Parkinson H, Roncaglia P, Lovering RC, Talmud PJ, Humphries SE, Denny P, Campbell NH, Foulger RE, Chibucos MC, Gwinn Giglio M, Chang HY, Finn R, Fraser M, Mitchell A, Nuka G, Pesseat S, Sangrador A, Scheremetjew M, Young SY, Stephan R, Harris MA, Oliver SG, Rutherford K, Wood V, Bahler J, Lock A, Kersey PJ, McDowall MD, Staines DM, Dwinell M, Shimoyama M, Laulederkind S, Hayman GT, Wang SJ, Petri V, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Costanzo MC, Demeter J, Dwight SS, Engel SR, Hitz BC, Inglis DO, Lloyd P, Miyasato SR, Paskov K, Roe G, Simison M, Nash RS, Skrzypek MS, Weng S, Wong ED, Berardini TZ, Li D, Huala E, Argasinska J, Arighi C, Auchincloss A, Axelsen K, Argoud-Puy G, Bateman A, Bely B, Blatter MC, Bonilla C, Bougueleret L, Boutet E, Breuza L, Bridge A, Britto R, Casals C, Cibrian-Uhalte E, Coudert E, Cusin I, Duek-Roggli P, Estereicher A, Famiglietti L, Gane P, Garmiri P, Gos A, Gruaz-Gumowski N, Hatton-Ellis E, Hinz U, Hulo C, Huntley R, Jungo F, Keller G, Laiho K, Lemercier P, Lieberherr D, MacDougall A, Magrane M, Martin M, Masson P, Mutowo P, O'Donovan C, Pedruzzi I, Pichler K, Poggioli D, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Shypitsyna A, Stutz A, Sundaram S, Tognolli M, Wu C, Xenarios I, Chan J, Kishore R, Sternberg PW, Van Auken K, Muller HM, Done J, Li Y, Howe D, Westerfield M (2015) Gene Ontology Consortium: going forward. Nucleic Acids Research 43(Database issue): D1049-D1056. DOI: 10.1093/nar/gku1179 • SCOPUS ID: 2-s2.0-84946735654 • SCOPUS CITATION COUNT: 2613

Moyle RG, Hosner PA, Jones AW, Outlaw DC (2015) Phylogeny and biogeography of Ficedula flycatchers (Aves: Muscicapidae): novel results from fresh source material. Molecular Phylogenetics and Evolution 82 Pt A: 87-94. DOI: 10.1016/j.ympev.2014.09.029 • SCOPUS ID: 2-s2.0-84909979829 • SCOPUS CITATION COUNT: 19

Suh A, Churakov G, Ramakodi MP, Platt RN, Jurka J, Kojima KK, Caballero J, Smit AF, Vliet KA, Hoffmann FG, Brosius J, Green RE, Braun EL, Ray DA, Schmitz J (2015) Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes. Genome Biology and Evolution 7(1): 205-217. DOI: 10.1093/gbe/evu256 • SCOPUS ID: 2-s2.0-84919656263 • SCOPUS CITATION COUNT: 48

Ramakodi MP, Singh B, Wells JD, Guerrero F, Ray DA (2015) A 454 sequencing approach to dipteran mitochondrial genome research. Genomics 105(1): 53-60. DOI: 10.1016/j.ygeno.2014.10.014 • SCOPUS ID: 2-s2.0-84919372887 • SCOPUS CITATION COUNT: 41

Aboughanem-Sabanadzovic N, Sabanadzovic S (2015) First report of Grapevine leafroll-associated virus 2 infecting muscadine (Vitis rotundifolia) and summer grape (Vitis aestivalis) in the United States. Plant Disease 99(1): 163. DOI: 10.1094/PDIS-12-13-1252-PDN • SCOPUS ID: 2-s2.0-84923375197 • SCOPUS CITATION COUNT: 9

Collier SD, Branton SL, Evans JD, Leigh SA, Wan XF, Cooksey AM, Olanrewaju HA, Pharr GT (2015) Proteomic analysis of Mycoplasma gallisepticum vaccine strain F. International Journal of Poultry Science 14(1): 1-12. SCOPUS ID: 2-s2.0-84924287092 • SCOPUS CITATION COUNT: 0

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutierrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldon T, Paten B, Ray DA (2014) Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs. Science 346(6215): 1254449. DOI: 10.1126/science.1254449 • SCOPUS ID: 2-s2.0-84917697073 • SCOPUS CITATION COUNT: 274

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldon T, Capella-Gutierrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Nunez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jonsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alstrom P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346(6215): 1320-1331. DOI: 10.1126/science.1253451 • SCOPUS ID: 2-s2.0-84917708482 • SCOPUS CITATION COUNT: 1406

Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Odeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Nunez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farre M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Hastad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alstrom P, Fjeldsa J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J, Jarvis ED, Gilbert MT, Wang J (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346(6215): 1311-1320. DOI: 10.1126/science.1251385 • SCOPUS ID: 2-s2.0-84917678595 • SCOPUS CITATION COUNT: 768

Chong AY, Kojima KK, Jurka J, Ray DA, Smit AF, Isberg SR, Gongora J (2014) Evolution and gene capture in ancient endogenous retroviruses - insights from the crocodilian genomes. Retrovirology 11(1): 71. DOI: 10.1186/s12977-014-0071-2 • SCOPUS ID: 2-s2.0-84924230064 • SCOPUS CITATION COUNT: 30

Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J (2014) Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC. PLoS ONE 9(12): e114631. DOI: 10.1371/journal.pone.0114631 • SCOPUS ID: 2-s2.0-84901250709 • SCOPUS CITATION COUNT: 20

Wang RL, Bencic DC, Garcia-Reyero N, Perkins EJ, Villeneuve DL, Ankley GT, Biales AD (2014) Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PLoS ONE 9(12): e114178. DOI: 10.1371/journal.pone.0114178 • SCOPUS ID: 2-s2.0-84895895875 • SCOPUS CITATION COUNT: 18