Selected Publications: Stephen Richards, Ph.D.

Stephen Richards, Ph.D.

Butterfly genome reveals promiscuous exchange of mimicry adaptations among species
Kanchon K Dasmahapatra, James R Walters, Adriana D Briscoe, John W Davey, Annabel Whibley,Nicola J Nadeau, et al. in Nature (2012)

Ober U, Ayroles JF, Stone EA, Richards S, Zhu D, Gibbs RA, Stricker C, Gianola
D, Schlather M, Mackay TF, Simianer H. Using Whole-Genome Sequence Data to Predict Quantitative Trait Phenotypes in Drosophila melanogaster. PLoS Genet. 2012 May;8(5):e1002685. Epub 2012 May 3. [PubMed]

Trudy F. C. Mackay, Stephen Richards, Eric A. Stone, Antonio Barbadilla, Julien F. Ayroles, Dianhui Zhu, Sònia Casillas, Yi Han, Michael M. Magwire, Julie M. Cridland, et al. The Drosophila melanogaster Genetic Reference Panel. Nature. 2012 February 8; 482(7384): 173–178. doi: 10.1038/nature10811 [PubMed]

International Aphid Genomics Consortium, Genome sequence of the pea aphid Acyrthosiphon pisum.  PLoS Biol.  2010 Feb; 8(2):e1000313. [PubMed]

Nasonia Genome Working Group, Werren, JH, Richards, S, Desjardins, CA, Niehuis, O, Gadau, J, Colbourne, JK, Beukeboom, LW, Desplan, C et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.  Science  2010 Jan 15; 327(5963):343-8. [PubMed]

Hampton, OA, Den Hollander, P, Miller, CA, Delgado, DA, Li, J, Coarfa, C, Harris, RA, Richards, S, Scherer, SE et al. A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome.  Genome Res.  2008 Dec 3; . [PubMed]

Tribolium Genome Sequencing Consortium, Richards, S, Gibbs, RA, Weinstock, GM, Brown, SJ, Denell, R, Beeman, RW, Gibbs, R, Beeman, RW et al. The genome of the model beetle and pest Tribolium castaneum.  Nature  2008 Apr 24; 452(7190):949-55. [PubMed]

Park, Y, Aikins, J, Wang, LJ, Beeman, RW, Oppert, B, Lord, JC, Brown, SJ, Lorenzen, MD, Richards, S et al. Analysis of transcriptome data in the red flour beetle, Tribolium castaneum.  Insect Biochem. Mol. Biol.  2008 Apr; 38(4):380-6. [PubMed]

Hotopp, JC, Clark, ME, Oliveira, DC, Foster, JM, Fischer, P, Torres, MC, Giebel, JD, Kumar, N, Ishmael, N et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes.  Science  2007 Sep 21; 317(5845):1753-6. [PubMed]

Savard, J, Tautz, D, Richards, S, Weinstock, GM, Gibbs, RA, Werren, JH, Tettelin, H, Lercher, MJ. Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects.  Genome Res.  2006 Nov; 16(11):1334-8. [PubMed]

Honeybee Genome Sequencing Consortium, Insights into social insects from the genome of the honeybee Apis mellifera.  Nature  2006 Oct 26; 443(7114):931-49. [PubMed]

Siepel, A, Bejerano, G, Pedersen, JS, Hinrichs, AS, Hou, M, Rosenbloom, K, Clawson, H, Spieth, J, Hillier, LW et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.  Genome Res.  2005 Aug; 15(8):1034-50. [PubMed]

Ross, MT, Grafham, DV, Coffey, AJ, Scherer, S, McLay, K, Muzny, D, Platzer, M, Howell, GR, Burrows, C et al. The DNA sequence of the human X chromosome.  Nature  2005 Mar 17; 434(7031):325-37. [PubMed]

Richards, S, Liu, Y, Bettencourt, BR, Hradecky, P, Letovsky, S, Nielsen, R, Thornton, K, Hubisz, MJ, Chen, R et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.  Genome Res.  2005 Jan; 15(1):1-18. [PubMed]

Celniker, SE, Wheeler, DA, Kronmiller, B, Carlson, JW, Halpern, A, Patel, S, Adams, M, Champe, M, Dugan, SP et al. Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence.  Genome Biol.  2002; 3(12):RESEARCH0079. [PubMed]

Strausberg, RL, Feingold, EA, Grouse, LH, Derge, JG, Klausner, RD, Collins, FS, Wagner, L, Shenmen, CM, Schuler, GD et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.  Proc. Natl. Acad. Sci. U.S.A.  2002 Dec 24; 99(26):16899-903. [PubMed]

Adams, MD, Celniker, SE, Holt, RA, Evans, CA, Gocayne, JD, Amanatides, PG, Scherer, SE, Li, PW, Hoskins, RA et al. The genome sequence of Drosophila melanogaster.  Science  2000 Mar 24; 287(5461):2185-95. [PubMed]

Metzker, ML, Raghavachari, R, Richards, S, Jacutin, SE, Civitello, A, Burgess, K, Gibbs, RA. Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates.  Nucleic Acids Res.  1994 Oct 11; 22(20):4259-67. [PubMed]

Eichler, EE, Richards, S, Gibbs, RA, Nelson, DL. Fine structure of the human FMR1 gene.  Hum. Mol. Genet.  1993 Aug; 2(8):1147-53. [PubMed]

Fu, YH, Friedman, DL, Richards, S, Pearlman, JA, Gibbs, RA, Pizzuti, A, Ashizawa, T, Perryman, MB, Scarlato, G et al. Decreased expression of myotonin-protein kinase messenger RNA and protein in adult form of myotonic dystrophy.  Science  1993 Apr 9; 260(5105):235-8. [PubMed]

Civitello, AB, Richards, S, Gibbs, RA. A simple protocol for the automation of DNA cycle sequencing reactions and polymerase chain reactions.  DNA Seq.  1992; 3(1):17-23. [PubMed]