Stephen W. Schaeffer, B.S., M.S., Ph.D. - Publications

Affiliations: 
Biology Pennsylvania State University, State College, PA, United States 
Area:
Evolutionary Genetics and Genomics
Website:
http://www.personal.psu.edu/sws4/

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Fuller ZL, Koury SA, Phadnis N, Schaeffer SW. How chromosomal rearrangements shape adaptation and speciation: Case studies in Drosophila pseudoobscura and its sibling species D. persimilis. Molecular Ecology. PMID 30402909 DOI: 10.1111/mec.14923  0.56
2018 Fuller ZL, Leonard CJ, Young RE, Schaeffer SW, Phadnis N. Ancestral polymorphisms explain the role of chromosomal inversions in speciation. Plos Genetics. 14: e1007526. PMID 30059505 DOI: 10.1371/journal.pgen.1007526  0.56
2017 Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of Natural Populations: Evolutionary Forces that Establish and Maintain Gene Arrangements in Drosophila pseudoobscura. Molecular Ecology. PMID 29055159 DOI: 10.1111/mec.14381  1
2016 Huang C, Schaeffer SW, Fisher CR, Cowart DA. Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci. Peerj. 4: e2366. PMID 27635334 DOI: 10.7717/peerj.2366  1
2016 Fuller ZL, Haynes GD, Richards S, Schaeffer SW. Genomics of Natural Populations: How Differentially Expressed Genes Shape the Evolution of Chromosomal Inversions in Drosophila pseudoobscura. Genetics. PMID 27401754 DOI: 10.1534/genetics.116.191429  1
2015 Projecto-Garcia J, Jollivet D, Mary J, Lallier FH, Schaeffer SW, Hourdez S. Selective forces acting during multi-domain protein evolution: the case of multi-domain globins. Springerplus. 4: 354. PMID 26191481 DOI: 10.1186/s40064-015-1124-2  1
2015 Faure B, Schaeffer SW, Fisher CR. Species distribution and population connectivity of deep-sea mussels at hydrocarbon seeps in the Gulf of Mexico. Plos One. 10: e0118460. PMID 25859657 DOI: 10.1371/journal.pone.0118460  1
2015 Yin Z, Tang J, Schaeffer SW, Bader DA. Exemplar or matching: modeling DCJ problems with unequal content genome data Journal of Combinatorial Optimization. DOI: 10.1007/s10878-015-9940-4  1
2014 Fuller ZL, Haynes GD, Zhu D, Batterton M, Chao H, Dugan S, Javaid M, Jayaseelan JC, Lee S, Li M, Ongeri F, Qi S, Han Y, Doddapaneni H, Richards S, ... Schaeffer SW, et al. Evidence for stabilizing selection on codon usage in chromosomal rearrangements of Drosophila pseudoobscura. G3 (Bethesda, Md.). 4: 2433-49. PMID 25326424 DOI: 10.1534/g3.114.014860  1
2014 Cowart DA, Halanych KM, Schaeffer SW, Fisher CR. Depth-dependent gene flow in Gulf of Mexico cold seep Lamellibrachia tubeworms (Annelida, Siboglinidae) Hydrobiologia. 736: 139-154. DOI: 10.1007/s10750-014-1900-y  1
2014 Yin Z, Tang J, Schaeffer SW, Bader DA. A lin-kernighan heuristic for the DCJ median problem of genomes with unequal contents Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8591: 227-238. DOI: 10.1007/978-3-319-08783-2_20  1
2013 Cowart DA, Huang C, Arnaud-Haond S, Carney SL, Fisher CR, Schaeffer SW. Restriction to large-scale gene flow vs. regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae). Molecular Ecology. 22: 4147-62. PMID 23879204 DOI: 10.1111/mec.12379  1
2013 Wallace AG, Detweiler D, Schaeffer SW. Molecular population genetics of inversion breakpoint regions in Drosophila pseudoobscura. G3 (Bethesda, Md.). 3: 1151-63. PMID 23665879 DOI: 10.1534/g3.113.006122  1
2013 Yin Z, Tang J, Schaeffer SW, Bader DA. Streaming breakpoint graph analytics for accelerating and parallelizing the computation of DCJ median of three genomes Procedia Computer Science. 18: 561-570. DOI: 10.1016/j.procs.2013.05.220  1
2013 Cowart DA, Huang C, Schaeffer SW. Identification and amplification of microsatellite loci in deep-sea tubeworms of the genus Escarpia (Polychaeta, Siboglinidae) Conservation Genetics Resources. 5: 479-482. DOI: 10.1007/s12686-012-9832-1  1
2011 Kang S, Tang J, Schaeffer SW, Bader DA. Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time. Plos One. 6: e22483. PMID 21887219 DOI: 10.1371/journal.pone.0022483  1
2011 Wallace AG, Detweiler D, Schaeffer SW. Evolutionary history of the third chromosome gene arrangements of Drosophila pseudoobscura inferred from inversion breakpoints. Molecular Biology and Evolution. 28: 2219-29. PMID 21339510 DOI: 10.1093/molbev/msr039  1
2010 Meisel RP, Hilldorfer BB, Koch JL, Lockton S, Schaeffer SW. Adaptive evolution of genes duplicated from the Drosophila pseudoobscura neo-X chromosome. Molecular Biology and Evolution. 27: 1963-78. PMID 20351054 DOI: 10.1093/molbev/msq085  1
2010 Projecto-Garcia J, Zorn N, Jollivet D, Schaeffer SW, Lallier FH, Hourdez S. Origin and evolution of the unique tetra-domain hemoglobin from the hydrothermal vent scale worm Branchipolynoe. Molecular Biology and Evolution. 27: 143-52. PMID 19755665 DOI: 10.1093/molbev/msp218  1
2010 Pia Miglietta M, Hourdez S, Cowart DA, Schaeffer SW, Fisher C. Species boundaries of Gulf of Mexico vestimentiferans (Polychaeta, Siboglinidae) inferred from mitochondrial genes Deep-Sea Research Part Ii: Topical Studies in Oceanography. 57: 1916-1925. DOI: 10.1016/j.dsr2.2010.05.007  1
2010 McMullin ER, Nelson K, Fisher CR, Schaeffer SW. Population structure of two deep sea tubeworms, Lamellibrachia luymesi and Seepiophila jonesi, from the hydrocarbon seeps of the Gulf of Mexico Deep-Sea Research Part I: Oceanographic Research Papers. 57: 1499-1509. DOI: 10.1016/j.dsr.2010.07.012  1
2008 Schaeffer SW. Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura. Evolution; International Journal of Organic Evolution. 62: 3082-99. PMID 18764919 DOI: 10.1111/j.1558-5646.2008.00504.x  1
2008 Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W. Phylogenomic resources at the UCSC Genome Browser. Methods in Molecular Biology (Clifton, N.J.). 422: 133-44. PMID 18629665 DOI: 10.1007/978-1-59745-581-7_9  1
2008 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, et al. Polytene chromosomal maps of 11 Drosophila species: the order of genomic scaffolds inferred from genetic and physical maps. Genetics. 179: 1601-55. PMID 18622037 DOI: 10.1534/genetics.107.086074  1
2008 Bhutkar A, Schaeffer SW, Russo SM, Xu M, Smith TF, Gelbart WM. Chromosomal rearrangement inferred from comparisons of 12 Drosophila genomes. Genetics. 179: 1657-80. PMID 18622036 DOI: 10.1534/genetics.107.086108  1
2007 Noor MA, Garfield DA, Schaeffer SW, Machado CA. Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics. 177: 1417-28. PMID 18039875 DOI: 10.1534/genetics.107.070672  1
2007 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, ... ... Schaeffer SW, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18. PMID 17994087 DOI: 10.1038/nature06341  0.32
2007 Meisel RP, Schaeffer SW. Meiotic transmission of Drosophila pseudoobscura chromosomal arrangements. Plos One. 2: e530. PMID 17565383 DOI: 10.1371/journal.pone.0000530  1
2007 Carney SL, Flores JF, Orobona KM, Butterfield DA, Fisher CR, Schaeffer SW. Environmental differences in hemoglobin gene expression in the hydrothermal vent tubeworm, Ridgeia piscesae. Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology. 146: 326-37. PMID 17240180 DOI: 10.1016/j.cbpb.2006.11.002  1
2006 Steglich C, Schaeffer SW. The ornithine decarboxylase gene of Trypanosoma brucei: Evidence for horizontal gene transfer from a vertebrate source. Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases. 6: 205-19. PMID 16344004 DOI: 10.1016/j.meegid.2005.05.004  1
2006 Carney SL, Formica MI, Divatia H, Nelson K, Fisher CR, Schaeffer SW. Population structure of the mussel "Bathymodiolus" childressi from Gulf of Mexico hydrocarbon seeps Deep-Sea Research Part I: Oceanographic Research Papers. 53: 1061-1072. DOI: 10.1016/j.dsr.2006.03.002  1
2005 Schaeffer SW, Anderson WW. Mechanisms of genetic exchange within the chromosomal inversions of Drosophila pseudoobscura. Genetics. 171: 1729-39. PMID 16143625 DOI: 10.1534/genetics.105.041947  1
2005 Flores JF, Fisher CR, Carney SL, Green BN, Freytag JK, Schaeffer SW, Royer WE. Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. Proceedings of the National Academy of Sciences of the United States of America. 102: 2713-8. PMID 15710902 DOI: 10.1073/pnas.0407455102  1
2005 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, ... ... Schaeffer SW, et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Research. 15: 1-18. PMID 15632085 DOI: 10.1101/gr.3059305  1
2003 Schaeffer SW, Bernhardt MJ, Anderson WW. Evolutionary rearrangement of the amylase genomic regions between Drosophila melanogaster and Drosophila pseudoobscura. The Journal of Heredity. 94: 464-71. PMID 14691313 DOI: 10.1093/jhered/esg094  1
2003 Schaeffer SW, Goetting-Minesky MP, Kovacevic M, Peoples JR, Graybill JL, Miller JM, Kim K, Nelson JG, Anderson WW. Evolutionary genomics of inversions in Drosophila pseudoobscura: evidence for epistasis. Proceedings of the National Academy of Sciences of the United States of America. 100: 8319-24. PMID 12824467 DOI: 10.1073/pnas.1432900100  1
2003 Mcmullin ER, Hourdez S, Schaeffer SW, Fisher CR. Phylogeny and biogeography of deep sea vestimentiferan tubeworms and their bacterial symbionts Symbiosis. 34: 1-41.  1
2002 Schaeffer SW. Molecular population genetics of sequence length diversity in the Adh region of Drosophila pseudoobscura. Genetical Research. 80: 163-75. PMID 12688655 DOI: 10.1017/S0016672302005955  1
2002 Carney SL, Peoples JR, Fisher CR, Schaeffer SW. AFLP analyses of genomic DNA reveal no differentiation between two phenotypes of the vestimentiferan tubeworm Ridgeia piscesae Cahiers De Biologie Marine. 43: 363-366.  1
2001 Schaeffer SW, Walthour CS, Toleno DM, Olek AT, Miller EL. Protein variation in Adh and Adh-related in Drosophila pseudoobscura. Linkage disequilibrium between single nucleotide polymorphisms and protein alleles. Genetics. 159: 673-87. PMID 11606543  1
2000 Kovacevic M, Schaeffer SW. Molecular population genetics of X-linked genes in Drosophila pseudoobscura. Genetics. 156: 155-72. PMID 10978282  1
2000 Mullineaux LS, Fisher CR, Peterson CH, Schaeffer SW. Tubeworm succession at hydrothermal vents: Use of biogenic cues to reduce habitat selection error? Oecologia. 123: 275-284.  1
1997 Pritchard JK, Schaeffer SW. Polymorphism and divergence at a Drosophila pseudogene locus. Genetics. 147: 199-208. PMID 9286680  1
1997 Akashi H, Schaeffer SW. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics. 146: 295-307. PMID 9136019  1
1994 Walthour CS, Schaeffer SW. Molecular population genetics of sex determination genes: the transformer gene of Drosophila melanogaster. Genetics. 136: 1367-72. PMID 8013913  1
1993 Schaeffer SW, Miller EL. Estimates of linkage disequilibrium and the recombination parameter determined from segregating nucleotide sites in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics. 135: 541-52. PMID 8244013  1
1992 Schaeffer SW, Miller EL. Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region. Genetics. 132: 471-80. PMID 1427038  1
1992 Schaeffer SW, Miller EL. Molecular population genetics of an electrophoretically monomorphic protein in the alcohol dehydrogenase region of Drosophila pseudoobscura. Genetics. 132: 163-78. PMID 1398051  1
1991 Schaeffer SW, Miller EL. Nucleotide sequence analysis of Adh genes estimates the time of geographic isolation of the Bogota population of Drosophila pseudoobscura. Proceedings of the National Academy of Sciences of the United States of America. 88: 6097-101. PMID 2068088  1
1991 Anderson WW, Arnold J, Baldwin DG, Beckenbach AT, Brown CJ, Bryant SH, Coyne JA, Harshman LG, Heed WB, Jeffery DE. Four decades of inversion polymorphism in Drosophila pseudoobscura. Proceedings of the National Academy of Sciences of the United States of America. 88: 10367-71. PMID 1946458  1
1991 Aquadro CF, Weaver AL, Schaeffer SW, Anderson WW. Molecular evolution of inversions in Drosophila pseudoobscura: the amylase gene region. Proceedings of the National Academy of Sciences of the United States of America. 88: 305-9. PMID 1702542  1
1988 Schaeffer SW, Aquadro CF, Langley CH. Restriction-map variation in the Notch region of Drosophila melanogaster. Molecular Biology and Evolution. 5: 30-40. PMID 2833676  1
1987 Schaeffer SW, Aquadro CF. Nucleotide sequence of the Adh gene region of Drosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication. Genetics. 117: 61-73. PMID 3666441  1
1987 Schaeffer SW, Aquadro CF, Anderson WW. Restriction-map variation in the alcohol dehydrogenase region of Drosophila pseudoobscura. Molecular Biology and Evolution. 4: 254-65. PMID 2833670  1
1986 Arnold J, Eckenrode VK, Lemke K, Phillips GJ, Schaeffer SW. A comprehensive package for DNA sequence analysis in FORTRAN IV for the PDP-11. Nucleic Acids Research. 14: 239-54. PMID 3003673 DOI: 10.1093/nar/14.1.239  1
1985 Schaeffer SW, Keller EC, Buroker NE. Population genetics of Melampus bidentatus (Gastropoda: Pulmonata): the effect of planktonic development on gene flow Genetica. 66: 223-229. DOI: 10.1007/BF00128043  1
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