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Stephen Richards, Ph.D.

Assistant Professor, Department of Molecular and Human Genetics

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Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions., Anstead, Clare A., Korhonen Pasi K., Young Neil D., Hall Ross S., Jex Aaron R., Murali Shwetha C., Hughes Daniel S. T., Lee Siu F., Perry Trent, Stroehlein Andreas J., et al. , Nature communications, 2015, Volume 6, p.7344, (2015) Abstract
The genomes of two key bumblebee species with primitive eusocial organization., Sadd, Ben M., Barribeau Seth M., Bloch Guy, de Graaf Dirk C., Dearden Peter, Elsik Christine G., Gadau Jürgen, Grimmelikhuijzen Cornelis J. P., Hasselmann Martin, Lozier Jeffrey D., et al. , Genome biology, 2015 Apr 24, Volume 16, Issue 1, p.76, (2015) Abstract
Best Practices in Insect Genome Sequencing: What Works and What Doesn't., Richards, Stephen, and Murali Shwetha C. , Current opinion in insect science, 2015 Feb 1, Volume 7, p.1-7, (2015) Abstract
Genomic Signatures of Cooperation and Conflict in the Social Amoeba., Ostrowski, Elizabeth A., Shen Yufeng, Tian Xiangjun, Sucgang Richard, Jiang Huaiyang, Qu Jiaxin, Katoh-Kurasawa Mariko, Brock Debra A., Dinh Christopher, Lara-Garduno Fremiet, et al. , Current biology : CB, 2015 Jun 15, Volume 25, Issue 12, p.1661-5, (2015) Abstract
A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor., Zhao, Chaoyang, Escalante Lucio Navarro, Chen Hang, Benatti Thiago R., Qu Jiaxin, Chellapilla Sanjay, Waterhouse Robert M., Wheeler David, Andersson Martin N., Bao Riyue, et al. , Current biology : CB, 2015 Mar 2, Volume 25, Issue 5, p.613-20, (2015) Abstract
Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines, Huang, W., Massouras A., Inoue Y., Peiffer J., Ramia M., Tarone A. M., Turlapati L., Zichner T., Zhu D., Lyman R. F., et al. , Genome Research, 07/2014, Volume 24, Issue 7, p.1193 - 1208, (2014)
Comparative validation of the D. melanogaster modENCODE transcriptome annotation., Chen, Zhen-Xia, Sturgill David, Qu Jiaxin, Jiang Huaiyang, Park Soo, Boley Nathan, Suzuki Ana Maria, Fletcher Anthony R., Plachetzki David C., FitzGerald Peter C., et al. , Genome research, 2014 Jul, Volume 24, Issue 7, p.1209-23, (2014) Abstract
The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima., Chipman, Ariel D., Ferrier David E. K., Brena Carlo, Qu Jiaxin, Hughes Daniel S. T., Schröder Reinhard, Torres-Oliva Montserrat, Znassi Nadia, Jiang Huaiyang, Almeida Francisca C., et al. , PLoS biology, 2014 Nov, Volume 12, Issue 11, p.e1002005, (2014) Abstract
Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura., Fuller, Zachary L., Haynes Gwilym D., Zhu Dianhui, Batterton Matthew, Chao Hsu, Dugan Shannon, Javaid Mehwish, Jayaseelan Joy C., Lee Sandra, Li Mingmei, et al. , G3 (Bethesda, Md.), 2014 Oct 17, (2014) Abstract
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species., Bradnam, Keith R., Fass Joseph N., Alexandrov Anton, Baranay Paul, Bechner Michael, Birol Inanç, Boisvert Sébastien, Chapman Jarrod A., Chapuis Guillaume, Chikhi Rayan, et al. , GigaScience, 2013 Jul 22, Volume 2, Issue 1, p.10, (2013) Abstract
Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster., Ober, Ulrike, Ayroles Julien F., Stone Eric A., Richards Stephen, Zhu Dianhui, Gibbs Richard A., Stricker Christian, Gianola Daniel, Schlather Martin, Mackay Trudy F. C., et al. , PLoS genetics, 2012, Volume 8, Issue 5, p.e1002685, (2012) Abstract
Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing., Fondon, John W., Martin Andy, Richards Stephen, Gibbs Richard A., and Mittelman David , PloS one, 2012, Volume 7, Issue 3, p.e33036, (2012) Abstract
Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology., English, Adam C., Richards Stephen, Han Yi, Wang Min, Vee Vanesa, Qu Jiaxin, Qin Xiang, Muzny Donna M., Reid Jeffrey G., Worley Kim C., et al. , PloS one, 2012, Volume 7, Issue 11, p.e47768, (2012) Abstract
The Drosophila melanogaster Genetic Reference Panel., Mackay, Trudy F. C., Richards Stephen, Stone Eric A., Barbadilla Antonio, Ayroles Julien F., Zhu Dianhui, Casillas Sònia, Han Yi, Magwire Michael M., Cridland Julie M., et al. , Nature, 2012 Feb 9, Volume 482, Issue 7384, p.173-8, (2012) Abstract
Epistasis dominates the genetic architecture of Drosophila quantitative traits., Huang, Wen, Richards Stephen, Carbone Mary Anna, Zhu Dianhui, Anholt Robert R. H., Ayroles Julien F., Duncan Laura, Jordan Katherine W., Lawrence Faye, Magwire Michael M., et al. , Proceedings of the National Academy of Sciences of the United States of America, 2012 Sep 25, Volume 109, Issue 39, p.15553-9, (2012) Abstract
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species., Werren, John H., Richards Stephen, Desjardins Christopher A., Niehuis Oliver, Gadau Jürgen, Colbourne John K., Werren John H., Richards Stephen, Desjardins Christopher A., Niehuis Oliver, et al. , Science (New York, N.Y.), 2010 Jan 15, Volume 327, Issue 5963, p.343-8, (2010) Abstract
A full-length cDNA resource for the pea aphid, Acyrthosiphon pisum., Shigenobu, S., Richards S., Cree A. G., Morioka M., Fukatsu T., Kudo T., Miyagishima S., Gibbs R. A., Stern D. L., and Nakabachi A. , Insect molecular biology, 2010 Mar, Volume 19 Suppl 2, p.23-31, (2010) Abstract
A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome., Hampton, Oliver A., Den Hollander Petra, Miller Christopher A., Delgado David A., Li Jian, Coarfa Cristian, Harris Ronald A., Richards Stephen, Scherer Steven E., Muzny Donna M., et al. , Genome research, 2009 Feb, Volume 19, Issue 2, p.167-77, (2009) Abstract
Analysis of transcriptome data in the red flour beetle, Tribolium castaneum., Park, Yoonseong, Aikins Jamie, Wang L. J., Beeman Richard W., Oppert Brenda, Lord Jeffrey C., Brown Susan J., Lorenzen Marcé D., Richards Stephen, Weinstock George M., et al. , Insect biochemistry and molecular biology, 2008 Apr, Volume 38, Issue 4, p.380-6, (2008) Abstract
The genome of the model beetle and pest Tribolium castaneum., Richards, Stephen, Gibbs Richard A., Weinstock George M., Brown Susan J., Denell Robin, Beeman Richard W., Gibbs Richard, Beeman Richard W., Brown Susan J., Bucher Gregor, et al. , Nature, 2008 Apr 24, Volume 452, Issue 7190, p.949-55, (2008) Abstract
Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes., Dunning Hotopp, Julie C., Clark Michael E., Oliveira Deodoro C. S. G., Foster Jeremy M., Fischer Peter, Muñoz Torres Mónica C., Giebel Jonathan D., Kumar Nikhil, Ishmael Nadeeza, Wang Shiliang, et al. , Science (New York, N.Y.), 2007 Sep 21, Volume 317, Issue 5845, p.1753-6, (2007) Abstract
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects., Savard, Joël, Tautz Diethard, Richards Stephen, Weinstock George M., Gibbs Richard A., Werren John H., Tettelin Hervé, and Lercher Martin J. , Genome research, 2006 Nov, Volume 16, Issue 11, p.1334-8, (2006) Abstract
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes., Siepel, Adam, Bejerano Gill, Pedersen Jakob S., Hinrichs Angie S., Hou Minmei, Rosenbloom Kate, Clawson Hiram, Spieth John, Hillier Ladeana W., Richards Stephen, et al. , Genome research, 2005 Aug, Volume 15, Issue 8, p.1034-50, (2005) Abstract
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution., Richards, Stephen, Liu Yue, Bettencourt Brian R., Hradecky Pavel, Letovsky Stan, Nielsen Rasmus, Thornton Kevin, Hubisz Melissa J., Chen Rui, Meisel Richard P., et al. , Genome research, 2005 Jan, Volume 15, Issue 1, p.1-18, (2005) Abstract
The DNA sequence of the human X chromosome., Ross, Mark T., Grafham Darren V., Coffey Alison J., Scherer Steven, McLay Kirsten, Muzny Donna, Platzer Matthias, Howell Gareth R., Burrows Christine, Bird Christine P., et al. , Nature, 2005 Mar 17, Volume 434, Issue 7031, p.325-37, (2005) Abstract

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