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Daniel Dykhuizen

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Publications

TOP 3
Sujay Chattopadhyay; Daniel E Dykhuizen; Sandip Paul; Evgeni V Sokurenko
Tracking recent adaptive evolution in microbial species using TimeZone.
Sujay Chattopadhyay; Rohinee N Paranjpye; Daniel E Dykhuizen; Evgeni V Sokurenko; Mark Strom
Comparative evolutionary analysis of the major structural subunit of Vibrio vulnificus type IV pili.
Sujay Chattopadhyay; Scott Weissman; Vladimir N Minin; Thomas A Russo; Daniel E Dykhuizen; Evgeni V Sokurenko
High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection.

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All Publications

2013: Sujay Chattopadhyay; Daniel E Dykhuizen; Sandip Paul; Evgeni V Sokurenko
Tracking recent adaptive evolution in microbial species using TimeZone.
Nature protocols 2013;8(4):652-65.
2009: Sujay Chattopadhyay; Rohinee N Paranjpye; Daniel E Dykhuizen; Evgeni V Sokurenko; Mark Strom
Comparative evolutionary analysis of the major structural subunit of Vibrio vulnificus type IV pili.
Molecular biology and evolution 2009;26(10):2185-96.
2009: Sujay Chattopadhyay; Scott Weissman; Vladimir N Minin; Thomas A Russo; Daniel E Dykhuizen; Evgeni V Sokurenko
High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(30):12412-7.
2008: Daniel E Dykhuizen; Dustin Brisson; Sabina Sandigursky; Gary P Wormser; John Nowakowski; Robert B Nadelman; Ira Schwartz
The propensity of different Borrelia burgdorferi sensu stricto genotypes to cause disseminated infections in humans.
The American journal of tropical medicine and hygiene 2008;78(5):806-10.
2008: Daniel M Stoebel; Antony M Dean; Daniel E Dykhuizen
The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products.
Genetics 2008;178(3):1653-60.
2008: Dustin Brisson; Daniel E Dykhuizen; Richard S Ostfeld
Conspicuous impacts of inconspicuous hosts on the Lyme disease epidemic.
Proceedings. Biological sciences / The Royal Society 2008;275(1631):227-35.
2007: Natalia Korotkova; Sujay Chattopadhyay; Tami A Tabata; Viktoriya Beskhlebnaya; Vladimir Vigdorovich; Brett K Kaiser; Roland K Strong; Daniel E Dykhuizen; Evgeni V Sokurenko; Steve L Moseley
Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli.
Molecular microbiology 2007;64(1):180-94.
2007: Sujay Chattopadhyay; Michael Feldgarden; Scott Weissman; Daniel E Dykhuizen; Gerald van Belle; Evgeni V Sokurenko
Haplotype diversity in "source-sink" dynamics of Escherichia coli urovirulence.
Journal of molecular evolution 2007;64(2):204-14.
2007: Sujay Chattopadhyay; Daniel E Dykhuizen; Evgeni V Sokurenko
ZPS: visualization of recent adaptive evolution of proteins.
BMC bioinformatics 2007;8():187.
2006: Evgeni V Sokurenko; Richard Gomulkiewicz; Daniel E Dykhuizen
Source-sink dynamics of virulence evolution.
Nature reviews. Microbiology 2006;4(7):548-55.
2006: Dustin Brisson; Daniel E Dykhuizen
A modest model explains the distribution and abundance of Borrelia burgdorferi strains.
The American journal of tropical medicine and hygiene 2006;74(4):615-22.
2006: Scott Weissman; Sujay Chattopadhyay; Pavel Aprikian; Mana Obata Yasuoka; Yuliya Yarova-Yarovaya; Ann Stapleton; William Ba-Thein; Daniel E Dykhuizen; James R Johnson; Evgeni V Sokurenko
Clonal analysis reveals high rate of structural mutations in fimbrial adhesins of extraintestinal pathogenic Escherichia coli.
Molecular microbiology 2006;59(3):975-88.
2004: Dustin Brisson; Daniel E Dykhuizen
ospC diversity in Borrelia burgdorferi: different hosts are different niches.
Genetics 2004;168(2):713-22.
2004: Shaobin Zhong; Arkady B Khodursky; Daniel E Dykhuizen; Antony M Dean
Evolutionary genomics of ecological specialization.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(32):11719-24.
2004: Daniel E Dykhuizen; Antony M Dean
Evolution of specialists in an experimental microcosm.
Genetics 2004;167(4):2015-26.
2004: Evgeni V Sokurenko; Michael Feldgarden; Elena Trintchina; Scott Weissman; Serine Avagyan; Sujay Chattopadhyay; James R Johnson; Daniel E Dykhuizen
Selection footprint in the FimH adhesin shows pathoadaptive niche differentiation in Escherichia coli.
Molecular biology and evolution 2004;21(7):1373-83.
2003: Scott Weissman; Steve L Moseley; Daniel E Dykhuizen; Evgeni V Sokurenko
Enterobacterial adhesins and the case for studying SNPs in bacteria.
Trends in microbiology 2003;11(3):115-7.
2002: Mark Michael Lunzer; Arvind Natarajan; Daniel E Dykhuizen; Antony M Dean
Enzyme kinetics, substitutable resources and competition: from biochemistry to frequency-dependent selection in lac.
Genetics 2002;162(1):485-99.
2002: Wei-Gang Qiu; Daniel E Dykhuizen; Michael S Acosta; Benjamin J Luft
Geographic uniformity of the Lyme disease spirochete (Borrelia burgdorferi) and its shared history with tick vector (Ixodes scapularis) in the Northeastern United States.
Genetics 2002;160(3):833-49.
2001: James R Johnson; Scott Weissman; Adam L Stell; Elena Trintchina; Daniel E Dykhuizen; Evgeni V Sokurenko
Clonal and pathotypic analysis of archetypal Escherichia coli cystitis isolate NU14.
The Journal of infectious diseases 2001;184(12):1556-65.
2001: Daniel E Dykhuizen; G Baranton
The implications of a low rate of horizontal transfer in Borrelia.
Trends in microbiology 2001;9(7):344-50.
2001: Ing-Nang Wang; Daniel E Dykhuizen
Variation of enzyme activities at a branched pathway involved in the utilization of gluconate in Escherichia coli.
Evolution; international journal of organic evolution 2001;55(5):897-908.
2001: Guy Baranton; G Seinost; G Theodore; Danièle Postic; Daniel E Dykhuizen
Distinct levels of genetic diversity of Borrelia burgdorferi are associated with different aspects of pathogenicity.
Research in microbiology 2001;152(2):149-56.
2000: Maria J C Gomes-Solecki; John J Dunn; Benjamin J Luft; J Castillo; Daniel E Dykhuizen; X Yang; John D Glass; Raymond J Dattwyler
Recombinant chimeric Borrelia proteins for diagnosis of Lyme disease.
Journal of clinical microbiology 2000;38(7):2530-5.
2000: Bruce Rannala; Wei-Gang Qiu; Daniel E Dykhuizen
Methods for estimating gene frequencies and detecting selection in bacterial populations.
Genetics 2000;155(2):499-508.
1999: Gerald Seinost; William T Golde; B W Berger; John J Dunn; D Qiu; D S Dunkin; Daniel E Dykhuizen; Benjamin J Luft; Raymond J Dattwyler
Infection with multiple strains of Borrelia burgdorferi sensu stricto in patients with Lyme disease.
Archives of dermatology 1999;135(11):1329-33.
1999: Gerald Seinost; Daniel E Dykhuizen; Raymond J Dattwyler; William T Golde; John J Dunn; Ing-Nang Wang; Gary P Wormser; M E Schriefer; Benjamin J Luft
Four clones of Borrelia burgdorferi sensu stricto cause invasive infection in humans.
Infection and immunity 1999;67(7):3518-24.
1999: Evgeni V Sokurenko; David L Hasty; Daniel E Dykhuizen
Pathoadaptive mutations: gene loss and variation in bacterial pathogens.
Trends in microbiology 1999;7(5):191-5.
1999: Ing-Nang Wang; Daniel E Dykhuizen; W Qiu; John J Dunn; Elizabeth M Bosler; Benjamin J Luft
Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto.
Genetics 1999;151(1):15-30.
1998: Evgeni V Sokurenko; Veronika Chesnokova; Daniel E Dykhuizen; Itzhak Ofek; X R Wu; Karen A Krogfelt; Carsten Struve; Mark A Schembri; David L Hasty
Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(15):8922-6.
1998: William T Golde; B Robinson-Dunn; M G Stobierski; Daniel E Dykhuizen; Ing-Nang Wang; V Carlson; H Stiefel; S Shiflett; G L Campbell
Culture-confirmed reinfection of a person with different strains of Borrelia burgdorferi sensu stricto.
Journal of clinical microbiology 1998;36(4):1015-9.
1998: Daniel E Dykhuizen
Santa Rosalia revisited: why are there so many species of bacteria?
Antonie van Leeuwenhoek 1998;73(1):25-33.
1997: Wei-Gang Qiu; Elizabeth M Bosler; J R Campbell; G D Ugine; Ing-Nang Wang; Benjamin J Luft; Daniel E Dykhuizen
A population genetic study of Borrelia burgdorferi sensu stricto from eastern Long Island, New York, suggested frequency-dependent selection, gene flow and host adaptation.
Hereditas 1997;127(3):203-16.
1996: David Guttman; P W Wang; Ing-Nang Wang; Elizabeth M Bosler; Benjamin J Luft; Daniel E Dykhuizen
Multiple infections of Ixodes scapularis ticks by Borrelia burgdorferi as revealed by single-strand conformation polymorphism analysis.
Journal of clinical microbiology 1996;34(3):652-6.
1995: B C McGrath; John J Dunn; G Gorgone; D Guttman; Daniel E Dykhuizen; Benjamin J Luft
Identification of an immunologically important hypervariable domain of major outer surface protein A of Borrelia burgdorferi.
Infection and immunity 1995;63(4):1356-61.
1994: David Guttman; Daniel E Dykhuizen
Detecting selective sweeps in naturally occurring Escherichia coli.
Genetics 1994;138(4):993-1003.
1994: David Guttman; Daniel E Dykhuizen
Clonal divergence in Escherichia coli as a result of recombination, not mutation.
Science (New York, N.Y.) 1994;266(5189):1380-3.
1993: Daniel E Dykhuizen; D S Polin; John J Dunn; B Wilske; V Preac-Mursic; Raymond J Dattwyler; Benjamin J Luft
Borrelia burgdorferi is clonal: implications for taxonomy and vaccine development.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(21):10163-7.
1993: Daniel E Dykhuizen
Chemostats used for studying natural selection and adaptive evolution.
Methods in enzymology 1993;224():613-31.
1991: Daniel E Dykhuizen; L Green
Recombination in Escherichia coli and the definition of biological species.
Journal of bacteriology 1991;173(22):7257-68.