Epernicus: Stephen Schaeffer, Ph.D.

Stephen Schaeffer, Ph.D.

Position:
Associate Professor

Biology

Pennsylvania State University (University Park, PA)
Degrees:

Ph.D., Genetics, University of Georgia (Athens, GA)

M.Sc., Biology, West Virginia University (Morgantown, WV)

B.Sc., Biology, West Virginia Wesleyan College (Buckhannon, WV)
Past Advisors:

Wyatt W. Anderson (as Graduate Student - Ph.D.)

Edward C. Keller (as Graduate Student - Masters)
Research:
I examine the evolution of genome rearrangements within and among Drosophila species using population genetic and comparative genomic methods.
Other Experience:
1985-1988 Post-Doctoral Fellow, Harvard University, Richard C. Lewontin Laboratory

Communities:

Stephen Schaeffer's Genealogy

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Stephen Schaeffer's Publications (29)

Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura.
Schaeffer SW

Evolution; international journal of organic evolution. 2008 Dec;62(12):3082-99
Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes.
Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM

Genetics. 2008 Jul;179(3):1657-80
Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps.
Schaeffer SW, Bhutkar A, McAllister BF, Matsuda M, Matzkin LM, O'Grady PM, Rohde C, Valente VL, Aguadé M, Anderson WW, Edwards K, Garcia AC, Goodman J, Hartigan J, Kataoka E, Lapoint RT, Lozovsky ER, Machado CA, Noor MA, Papaceit M, Reed LK, Richards S, Rieger TT, Russo SM, Sato H, Segarra C, Smith DR, Smith TF, Strelets V, Tobari YN, Tomimura Y, Wasserman M, Watts T, Wilson R, Yoshida K, Markow TA, Gelbart WM, Kaufman TC

Genetics. 2008 Jul;179(3):1601-55
Phylogenomic resources at the UCSC Genome Browser.
Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W

Methods in molecular biology (Clifton, N.J.). 2008;422:133-44
Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions.
Noor MA, Garfield DA, Schaeffer SW, Machado CA

Genetics. 2007 Nov;177(3):1417-28
Evolution of genes and genomes on the Drosophila phylogeny.
Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, Grabherr M, Kleber M, Mauceli E, MacCallum I

Nature. 2007 Nov 8;450(7167):203-18
Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae.
Carney SL, Flores JF, Orobona KM, Butterfield DA, Fisher CR, Schaeffer SW

Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology. 2007 Mar;146(3):326-37
Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements.
Meisel RP, Schaeffer SW

PLoS ONE. 2007;2(6):e530
The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source.
Steglich C, Schaeffer SW

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2006 May;6(3):205-19
Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura.
Schaeffer SW, Anderson WW

Genetics. 2005 Dec;171(4):1729-39
Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.
Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE

Proceedings of the National Academy of Sciences of the United States of America. 2005 Feb 22;102(8):2713-8
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
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, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA

Genome research. 2005 Jan;15(1):1-18
Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis.
Schaeffer SW, Goetting-Minesky MP, Kovacevic M, Peoples JR, Graybill JL, Miller JM, Kim K, Nelson JG, Anderson WW

Proceedings of the National Academy of Sciences of the United States of America. 2003 Jul 8;100(14):8319-24
Evolutionary rearrangement of the amylase genomic regions between Drosophila melanogaster and Drosophila pseudoobscura.
Schaeffer SW, Bernhardt MJ, Anderson WW

The Journal of heredity. 2003 Nov-Dec;94(6):464-71
Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura.
Schaeffer SW

Genetical research. 2002 Dec;80(3):163-75
Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles.
Schaeffer SW, Walthour CS, Toleno DM, Olek AT, Miller EL

Genetics. 2001 Oct;159(2):673-87
Polymorphism and divergence at a Drosophila pseudogene locus.
Pritchard JK, Schaeffer SW

Genetics. 1997 Sep;147(1):199-208
Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila.
Akashi H, Schaeffer SW

Genetics. 1997 May;146(1):295-307
S-allele sequence diversity in natural populations of Solanum carolinense (Horsenettle).
Richman AD, Kao TH, Schaeffer SW, Uyenoyama MK

Heredity. 1995 Oct;75 ( Pt 4):405-15
Molecular population genetics of sex determination genes: the transformer gene of Drosophila melanogaster.
Walthour CS, Schaeffer SW

Genetics. 1994 Apr;136(4):1367-72
Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura.
Schaeffer SW, Miller EL

Genetics. 1993 Oct;135(2):541-52
Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region.
Schaeffer SW, Miller EL

Genetics. 1992 Oct;132(2):471-80
Molecular population genetics of an electrophoretically monomorphic protein in the alcohol dehydrogenase region of Drosophila pseudoobscura.
Schaeffer SW, Miller EL

Genetics. 1992 Sep;132(1):163-78
Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura.
Schaeffer SW, Miller EL

Proceedings of the National Academy of Sciences of the United States of America. 1991 Jul 15;88(14):6097-101
Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region.
Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW

Proceedings of the National Academy of Sciences of the United States of America. 1991 Jan 1;88(1):305-9

Show more publications...

One Figure

Gene order changes among the eight Drosophila species. Each thin line represents a single gene and its position in the different species. See Bhutkar et al. 2008 Genetics 179: 1657-1680 for more details.

Websites

Schaeffer Laboratory Page

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