Publications

Filters: Author is Richards, Stephen  [Clear All Filters]
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C
Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Correction to: Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Ecol Evol. 2021 ;21(1):146.
Chen Z-X, Sturgill D, Qu J, Jiang H, Park S, Boley N, Suzuki AMaria, Fletcher AR, Plachetzki DC, FitzGerald PC, Artieri CG, Atallah J, Barmina O, Brown JB, Blankenburg KP, Clough E, Dasgupta A, Gubbala S, Han Y, Jayaseelan JC, Kalra D, Kim Y-A, Kovar CL, Lee SL, Li M, Malley JD, Malone JH, Mathew T, Mattiuzzo NR, Munidasa M, Muzny DM, Ongeri F, Perales L, Przytycka TM, Pu L-L, Robinson G, Thornton RL, Saada N, Scherer SE, Smith HE, Vinson C, Warner CB, Worley KC, Wu Y-Q, Zou X, Cherbas P, Kellis M, Eisen MB, Piano F, Kionte K, Fitch DH, Sternberg PW, Cutter AD, Duff MO, Hoskins RA, Graveley BR, Gibbs RA, Bickel PJ, Kopp A, Carninci P, Celniker SE, Oliver B, Richards S. Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res. 2014 ;24(7):1209-23.
Newton ILG, Clark ME, Kent BN, Bordenstein SR, Qu J, Richards S, Kelkar YD, Werren JH. Comparative Genomics of Two Closely Related Wolbachia with Different Reproductive Effects on Hosts. Genome Biol Evol. 2016 ;8(5):1526-42.
Lindsey ARI, Kelkar YD, Wu X, Sun D, Martinson EO, Yan Z, Rugman-Jones PF, Hughes DST, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Ye G, Gibbs RA, Richards S, Yi SV, Stouthamer R, Werren JH. Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum. BMC Biol. 2018 ;16(1):54.
Lindsey ARI, Werren JH, Richards S, Stouthamer R. Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont. G3 (Bethesda). 2016 ;6(7):2113-23.
Bechsgaard J, Vanthournout B, Funch P, Vestbo S, Gibbs RA, Richards S, Sanggaard KW, Enghild JJ, Bilde T. Comparative genomic study of arachnid immune systems indicates loss of beta-1,3-glucanase-related proteins and the immune deficiency pathway. J Evol Biol. 2016 ;29(2):277-91.
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, K Durbin J, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MAF, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 ;15(1):1-18.
B
Sparks ME, Bansal R, Benoit JB, Blackburn MB, Chao H, Chen M, Cheng S, Childers C, Dinh H, Doddapaneni H, Dugan S, Elpidina EN, Farrow DW, Friedrich M, Gibbs RA, Hall B, Han Y, Hardy RW, Holmes CJ, Hughes DST, Ioannidis P, Jarvela AMCheatle, J Johnston S, Jones JW, Kronmiller BA, Kung F, Lee SL, Martynov AG, Masterson P, Maumus F, Munoz-Torres M, Murali SC, Murphy TD, Muzny DM, Nelson DR, Oppert B, Panfilio KA, Paula DPires, Pick L, Poelchau MF, Qu J, Reding K, Rhoades JH, Rhodes A, Richards S, Richter R, Robertson HM, Rosendale AJ, Tu ZJake, Velamuri AS, Waterhouse RM, Weirauch MT, Wells JT, Werren JH, Worley KC, Zdobnov EM, Gundersen-Rindal DE. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics. 2020 ;21(1):227.
Richards S, Murali SC. Best Practices in Insect Genome Sequencing: What Works and What Doesn't. Curr Opin Insect Sci. 2015 ;7:1-7.
A
Zhao C, Shukle R, Navarro-Escalante L, Chen M, Richards S, Stuart JJ. Avirulence gene mapping in the Hessian fly (Mayetiola destructor) reveals a protein phosphatase 2C effector gene family. J Insect Physiol. 2016 ;84:22-31.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou W-C, Corbeil J, Del Fabbro C, T Docking R, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam T-W, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, J Ruby G, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu S-M, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2013 ;2(1):10.
Richards S. Arthropod Genome Sequencing and Assembly Strategies. Methods Mol Biol. 2019 ;1858:1-14.
Rane RV, Walsh TK, Pearce SL, Jermiin LS, Gordon KHj, Richards S, Oakeshott JG. Are feeding preferences and insecticide resistance associated with the size of detoxifying enzyme families in insect herbivores?. Curr Opin Insect Sci. 2016 ;13:70-76.
Park Y, Aikins J, Wang LJ, Beeman RW, Oppert B, Lord JC, Brown SJ, Lorenzen MD, Richards S, Weinstock GM, Gibbs RA. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum. Insect Biochem Mol Biol. 2008 ;38(4):380-6.
Fondon JW, Martin A, Richards S, Gibbs RA, Mittelman D. Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing. PLoS One. 2012 ;7(3):e33036.