Peer-Reviewed Publications

Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K (2011) The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477(7366): 587-591.

CiteScore: 53.1 • DOI: 10.1038/nature10390 • PMID: 21881562 • SCOPUS ID: 2-s2.0-80053359585 • SCOPUS CITATION COUNT: 474

Paterson AH, Wendel JF, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker KC, Shu S, Udall J, Yoo MJ, Byers R, Chen W, Doron-Faigenboim A, Duke MV, Gong L, Grimwood J, Grover C, Grupp K, Hu G, Lee TH, Li J, Lin L, Liu T, Marler BS, Page JT, Roberts AW, Romanel E, Sanders WS, Szadkowski E, Tan X, Tang H, Xu C, Wang J, Wang Z, Zhang D, Zhang L, Ashrafi H, Bedon F, Bowers JE, Brubaker CL, Chee PW, Das S, Gingle AR, Haigler CH, Harker D, Hoffmann LV, Hovav R, Jones DC, Lemke C, Mansoor S, Rahman M, Rainville LN, Rambani A, Reddy UK, Rong JK, Saranga Y, Scheffler BE, Scheffler JA, Stelly DM, Triplett BA, Van Deynze A, Vaslin MF, Waghmare VN, Walford SA, Wright RJ, Zaki EA, Zhang T, Dennis ES, Mayer KF, Peterson DG, Rokhsar DS, Wang X, Schmutz J (2012) Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492(7429): 423-427.

CiteScore: 51 • DOI: 10.1038/nature11798 • PMID: 23257886 • SCOPUS ID: 2-s2.0-84871428041 • SCOPUS CITATION COUNT: 926

Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, Zimin AV, Hughes DST, Ferguson LC, Martin SH, Salazar C, Lewis JJ, Adler S, Ahn SJ, Baker DA, Baxter SW, Chamberlain NL, Chauhan R, Counterman BA, Dalmay T, Gilbert LE, Gordon K, Heckel DG, Hines HM, Hoff KJ, Holland PWH, Jacquin-Joly E, Jiggins FM, Jones RT, Kapan DD, Kersey P, Lamas G, Lawson D, Mapleson D, Maroja LS, Martin A, Moxon S, Palmer WJ, Papa R, Papanicolaou A, Pauchet Y, Ray DA, Rosser N, Salzberg SL, Supple MA, Surridge A, Tenger-Trolander A, Vogel H, Wilkinson PA, Wilson D, Yorke JA, Yuan F, Balmuth AL, Eland C, Gharbi K, Thomson M, Gibbs RA, Han Y, Jayaseelan JC, Kovar C, Mathew T, Muzny DM, Ongeri F, Pu LL, Qu J, Thornton RL, Worley KC, Wu YQ, Linares M, Blaxter ML, Ffrench-Constant RH, Joron M, Kronforst MR, Mullen SP, Reed RD, Scherer SE, Richards S, Mallet J, Owen McMillan W, Jiggins CD (2012) Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature 487(7405): 94-98.

CiteScore: 51 • DOI: 10.1038/nature11041 • PMID: 22722851 • SCOPUS ID: 2-s2.0-84863496231 • SCOPUS CITATION COUNT: 799

Simmonds P, Adams MJ, Benko M, Breitbart M, Brister JR, Carstens EB, Davison AJ, Delwart E, Gorbalenya AE, Harrach B, Hull R, King AM, Koonin EV, Krupovic M, Kuhn JH, Lefkowitz EJ, Nibert ML, Orton R, Roossinck MJ, Sabanadzovic S, Sullivan MB, Suttle CA, Tesh RB, van der Vlugt RA, Varsani A,Zerbini FM (2017) Consensus statement: Virus taxonomy in the age of metagenomics. Nature Reviews Microbiology 15(3): 161-168.

CiteScore: 50.6 • DOI: 10.1038/nrmicro.2016.177 • PMID: 28134265 • SCOPUS ID: 2-s2.0-85008394347 • SCOPUS CITATION COUNT: 442

Chen ZJ, Sreedasyam A, Ando A, Song Q, De Santiago LM, Hulse-Kemp AM, Ding M, Ye W, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin Y-M, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu G, Conover JL, Carlson JW, Shu S, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J (2020) Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nature Genetics 52(5): 525-533.

CiteScore: 50.5 • DOI: 10.1038/s41588-020-0614-5 • PMID: 32313247 • SCOPUS ID: 2-s2.0-85084077674 • SCOPUS CITATION COUNT: 177

Natarajan C, Hoffmann FG, Weber RE, Fago A, Witt CC, Storz JF (2016) Predictable convergence in hemoglobin function has unpredictable molecular underpinnings. Science 354(6310): 336-339.

CiteScore: 49.5 • DOI: 10.1126/science.aaf9070 • PMID: 27846568 • SCOPUS ID: 2-s2.0-84992153922 • SCOPUS CITATION COUNT: 155

Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, Chen J, Milucka J, Viehweger B, Becker KW, Dong X, Stairs CW, Hinrichs KU, Brown MW, Roger AJ, Strous M (2016) Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature 534(7606): 254-258.

CiteScore: 49.2 • DOI: 10.1038/nature18297 • PMID: 27279223 • SCOPUS ID: 2-s2.0-84973889511 • SCOPUS CITATION COUNT: 47

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.

CiteScore: 46 • DOI: 10.1126/science.1254449 • PMID: 25504731 • SCOPUS ID: 2-s2.0-84917697073 • SCOPUS CITATION COUNT: 242

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.

CiteScore: 46 • DOI: 10.1126/science.1253451 • PMID: 25504713 • SCOPUS ID: 2-s2.0-84917708482 • SCOPUS CITATION COUNT: 1245

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.

CiteScore: 46 • DOI: 10.1126/science.1251385 • PMID: 25504712 • SCOPUS ID: 2-s2.0-84917678595 • SCOPUS CITATION COUNT: 650

Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, Garcia-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Di Palma F, Blumberg AJ, Wakeley J, Jaffe D, Mallet J (2019) Genomic architecture and introgression shape a butterfly radiation. Science 366(6465): 594-599.

CiteScore: 45.3 • DOI: 10.1126/science.aaw2090 • PMID: 31672890 • SCOPUS ID: 2-s2.0-85074347910 • SCOPUS CITATION COUNT: 220

Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR, Chen R, Halder G, Nijhout HF,McMillan WO (2011) Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science 333(6046): 1137-41.

CiteScore: 44.7 • DOI: 10.1126/science.1208227 • PMID: 21778360 • SCOPUS ID: 2-s2.0-80052151984 • SCOPUS CITATION COUNT: 308

Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X, Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W, Li R, Chen ZJ (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology 33(5): 531-537.

CiteScore: 39.6 • DOI: 10.1038/nbt.3207 • PMID: 25893781 • SCOPUS ID: 2-s2.0-84929171720 • SCOPUS CITATION COUNT: 1177

Brown MW, Tice AK (2020) A genetic toolbox for marine protists. Nature Methods 17(5): 469-470.

CiteScore: 33.9 • DOI: 10.1038/s41592-020-0794-z • PMID: 32251395 • SCOPUS ID: 2-s2.0-85083185980 • SCOPUS CITATION COUNT: 1

Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE (2015) Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nature Biotechnology 32(9): 915-925.

CiteScore: 33.9 • DOI: 10.1038/nbt.2972 • PMID: 25150835 • SCOPUS ID: 2-s2.0-84922578455 • SCOPUS CITATION COUNT: 158

Gorbalenya AE, Krupovic M, Mushegian A, Kropinski AM, Siddell SG, Varsani A, Adams MJ, Davison AJ, Dutilh BE, Harrach B, Harrison RL, Junglen S, King AMQ, Knowles NJ, Lefkowitz EJ, Nibert ML, Rubino L, Sabanadzovic S, Sanfacon H, Simmonds P, Walker PJ, Zerbini FM, Kuhn JH, International Committee on Taxonomy of Viruses Executive Committee (2020) The new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nature Microbiology 5(5): 668-674.

CiteScore: 28.2 • DOI: 10.1038/s41564-020-0709-x • PMID: 32341570 • SCOPUS ID: 2-s2.0-85083987153 • SCOPUS CITATION COUNT: 138

Nadeau NJ, Ruiz M, Salazar P, Counterman B, Medina JA, Ortiz-Zuazaga H, Morrison A, McMillan WO, Jiggins CD, Papa R (2014) Population genomics of parallel hybrid zones in the mimetic butterflies, H. melpomene and H. erato. Genome Research 24(8): 1316-1333.

CiteScore: 26.3 • DOI: 10.1101/gr.169292.113 • PMID: 24823669 • SCOPUS ID: 2-s2.0-84905666210 • SCOPUS CITATION COUNT: 85

Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, Nielsen DM, Lavoie C, Ray DA, Salazar C, McMillan WO, Counterman BA (2013) Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research 23(8): 1248-1257.

CiteScore: 25.8 • DOI: 10.1101/gr.150615.112 • PMID: 23674305 • SCOPUS ID: 2-s2.0-84881119383 • SCOPUS CITATION COUNT: 54

Platt RN, Vandewege MW, Kern C, Schmidt CJ, Hoffmann FG, Ray DA (2014) Large Numbers of Novel miRNAs Originate from DNA Transposons and Are Coincident with a Large Species Radiation in Bats. Molecular Biology and Evolution 31(6): 1536-1545.

CiteScore: 24.9 • DOI: 10.1093/molbev/msu112 • PMID: 24692655 • SCOPUS ID: 2-s2.0-84901467575 • SCOPUS CITATION COUNT: 55

Suga H, Torruella G, Burger G, Brown MW, Ruiz-Trillo I (2014) Earliest Holozoan expansion of phosphotyrosine signaling. Molecular Biology and Evolution 31(3): 517-528.

CiteScore: 24.9 • DOI: 10.1093/molbev/mst241 • PMID: 24307687 • SCOPUS ID: 2-s2.0-84895771214 • SCOPUS CITATION COUNT: 34