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John Heidelberg

Research Profile

Genes & Molecular Sequences

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Genomics

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Sequence Analysis, DNA

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TOP 3
Esther Singer; John F Heidelberg; Ashita Dhillon; Katrina J Edwards
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l.
William C Nelson; Devaki Bhaya; John F Heidelberg
Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population.
Christian G Klatt; Michael Kühl; Douglas B Rusch; Mary M Bateson; Devaki Bhaya; Donald A Bryant; Frederick M Cohan; Arthur R Grossman; Natsuko Hamamura; John F Heidelberg; Jason M Wood; David M Ward
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.

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All Publications

2013: Esther Singer; John F Heidelberg; Ashita Dhillon; Katrina J Edwards
Metagenomic insights into the dominant Fe(II) oxidizing Zetaproteobacteria from an iron mat at Lō´ihi, Hawai´l.
Frontiers in microbiology 2013;4():52.
2012: William C Nelson; Devaki Bhaya; John F Heidelberg
Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population.
Journal of bacteriology 2012;194(14):3636-42.
2011: Christian G Klatt; Michael Kühl; Douglas B Rusch; Mary M Bateson; Devaki Bhaya; Donald A Bryant; Frederick M Cohan; Arthur R Grossman; Natsuko Hamamura; John F Heidelberg; Jason M Wood; David M Ward
Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential.
The ISME journal 2011;5(8):1262-78.
2011: William C Nelson; Lori Wollerman; Devaki Bhaya; John F Heidelberg
Analysis of insertion sequences in thermophilic cyanobacteria: exploring the mechanisms of establishing, maintaining, and withstanding high insertion sequence abundance.
Applied and environmental microbiology 2011;77(15):5458-66.
2011: Jennifer F Biddle; William J Brazelton; Katrina J Edwards; John F Heidelberg; Craig L Moyer; Jason B Sylvan; Benjamin J Tully; William C Nelson
Prospects for the study of evolution in the deep biosphere.
Frontiers in microbiology 2011;2():285.
2011: Esther Singer; Eric A Webb; Roman A Barco; Clara S Chan; Luis R Comolli; David Emerson; Steve Ferriera; John F Heidelberg; Justin Johnson; J Gijs Kuenen; William C Nelson; Katrina J Edwards
Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium.
PloS one 2011;6(9):e25386.
2008: Marie L Cuvelier; Alejandra Ortiz; Eunsoo Kim; Heike Moehlig; David E Richardson; John F Heidelberg; John M Archibald; Alexandra Z Worden
Widespread distribution of a unique marine protistan lineage.
Environmental microbiology 2008;10(6):1621-34.
2008: David M Ward; Frederick M Cohan; Devaki Bhaya; John F Heidelberg; Michael Kühl; A Grossman
Genomics, environmental genomics and the issue of microbial species.
Heredity 2008;100(2):207-19.
2007: Devaki Bhaya; Arthur R Grossman; Anne-Soisig Steunou; Natalia Khuri; Frederick M Cohan; Natsuko Hamamura; Melanie C Melendrez; Mary M Bateson; David M Ward; John F Heidelberg
Population level functional diversity in a microbial community revealed by comparative genomic and metagenomic analyses.
The ISME journal 2007;1(8):703-13.
2007: Donald A Bryant; Amaya M Garcia Costas; Julia A Maresca; Aline Gomez Maqueo Chew; Christian G Klatt; Mary M Bateson; Luke J Tallon; Jessica Hostetler; William C Nelson; John F Heidelberg; David M Ward
Candidatus Chloracidobacterium thermophilum: an aerobic phototrophic Acidobacterium.
Science (New York, N.Y.) 2007;317(5837):523-6.
2007: George A Kowalchuk; John F Heidelberg; Mark J Bailey
The ISME journal: multidisciplinary journal of microbial ecology.
The ISME journal 2007;1(1):1-3.
2007: Fabrice Not; Rudolf Gausling; Farooq Azam; John F Heidelberg; Alexandra Z Worden
Vertical distribution of picoeukaryotic diversity in the Sargasso Sea.
Environmental microbiology 2007;9(5):1233-52.
2007: Shah M Faruque; Vincent C Tam; Nityananda Chowdhury; Pornphan Diraphat; Michelle Dziejman; John F Heidelberg; John D Clemens; John J Mekalanos; G Balakrish Nair
Genomic analysis of the Mozambique strain of Vibrio cholerae O1 reveals the origin of El Tor strains carrying classical CTX prophage.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(12):5151-6.
2006: Rekha Seshadri; joseph sam; Ashok K Chopra; Jian Sha; Jonathan Shaw; Joerg Graf; Daniel H Haft; Martin Wu; Qinghu Ren; Mary J Rosovitz; Ramana Madupu; Luke J Tallon; Mary Kim; Shaohua Jin; Hue Vuong; O Colin Stine; Afsar Ali; Amy J Horneman; John F Heidelberg
Genome sequence of Aeromonas hydrophila ATCC 7966T: jack of all trades.
Journal of bacteriology 2006;188(23):8272-82.
2006: Brian Palenik; Qinghu Ren; Chris L Dupont; Garry S A Myers; John F Heidelberg; Jonathan H Badger; Ramana Madupu; William C Nelson; Lauren M Brinkac; Robert J Dodson; A Scott Durkin; Sean C Daugherty; Steven A Sullivan; Hoda Khouri; Yasmin Mohamoud; Rebecca Halpin; Ian Paulsen
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(36):13555-9.
2006: Stefan Pukatzki; Amy T Ma; Derek Sturtevant; Bryan Krastins; David A Sarracino; William C Nelson; John F Heidelberg; John J Mekalanos
Identification of a conserved bacterial protein secretion system in Vibrio cholerae using the Dictyostelium host model system.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(5):1528-33.
2005: Rekha Seshadri; John F Heidelberg
Bacteria to the rescue.
Nature biotechnology 2005;23(10):1236-7.
2005: Michelle Dziejman; Davide Serruto; Vincent C Tam; Derek Sturtevant; Pornphan Diraphat; Shah M Faruque; M Hasibur Rahman; John F Heidelberg; Jeremy Decker; Li Li; Kate T Montgomery; George Grills; Raju Kucherlapati; John J Mekalanos
Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(9):3465-70.
2005: Rekha Seshadri; Lorenz Adrian; Derrick E Fouts; Jonathan Eisen; Adam M Phillippy; Barbara A Methe; Naomi L Ward; William C Nelson; Robert T Deboy; Hoda Khouri; James F Kolonay; Robert J Dodson; Sean C Daugherty; Lauren M Brinkac; Steven A Sullivan; Ramana Madupu; Karen E Nelson; Katherine H Kang; Marjorie Impraim; Kevin Tran; Jeffrey M Robinson; Heather A Forberger; Claire M Fraser-Liggett; Stephen H Zinder; John F Heidelberg
Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes.
Science (New York, N.Y.) 2005;307(5706):105-8.
2004: J Craig Venter; Karin Remington; John F Heidelberg; Aaron L Halpern; Douglas B Rusch; Jonathan Eisen; Dongying Wu; Ian Paulsen; Karen E Nelson; William Nelson; Derrick E Fouts; Samuel Levy; Anthony H Knap; Michael W Lomas; Ken Nealson; Owen R White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O Smith
Environmental genome shotgun sequencing of the Sargasso Sea.
Science (New York, N.Y.) 2004;304(5667):66-74.
2003: José R de la Torre; Lynne M Christianson; Oded Béjà; Marcelino Suzuki; David M Karl; John F Heidelberg; Edward F DeLong
Proteorhodopsin genes are distributed among divergent marine bacterial taxa.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(22):12830-5.
2003: Joseph G Leahy; Zafar M Khalid; Ernesto J Quintero; Joanne M Jones-Meehan; John F Heidelberg; Patricia J Batchelor; Rita R Colwell
The concentrations of hexadecane and inorganic nutrients modulate the production of extracellular membrane-bound vesicles, soluble protein, and bioemulsifier by Acinetobacter venetianus RAG-1 and Acinetobacter sp. strain HO1-N.
Canadian journal of microbiology 2003;49(9):569-75.
2003: Eric S Miller; John F Heidelberg; Jonathan Eisen; William C Nelson; A Scott Durkin; Ann Ciecko; Tamara Feldblyum; Owen R White; Ian Paulsen; William C Nierman; Jong Lee; Bridget Szczypinski; Claire M Fraser-Liggett
Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.
Journal of bacteriology 2003;185(17):5220-33.
2003: Shelley A Haveman; Véronique Brunelle; Johanna K Voordouw; Gerrit Voordouw; John F Heidelberg; Ralf Rabus
Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase.
Journal of bacteriology 2003;185(15):4345-53.
2003: Rekha Seshadri; Ian Paulsen; Jonathan Eisen; Timothy D Read; Karen E Nelson; William C Nelson; Naomi L Ward; Hervé Tettelin; Tanja M Davidsen; Maureen J Beanan; Robert T Deboy; Sean C Daugherty; Lauren M Brinkac; Ramana Madupu; Robert J Dodson; Hoda Khouri; Kathy H Lee; Heather A Carty; David Scanlan; Robert A Heinzen; Herbert A Thompson; James E Samuel; Claire M Fraser-Liggett; John F Heidelberg
Complete genome sequence of the Q-fever pathogen Coxiella burnetii.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(9):5455-60.
2003: Timothy D Read; Garry S A Myers; Robert brunham; William C Nelson; Ian Paulsen; John F Heidelberg; Erik Holtzapple; Hoda Khouri; N B Federova; H A Carty; Lowell Umayam; Daniel H Haft; J Peterson; Maureen J Beanan; Owen R White; Steven L Salzberg; Ruching Hsia; Grant McClarty; Roger Rank; Patrik M Bavoil; Claire M Fraser-Liggett
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae.
Nucleic acids research 2003;31(8):2134-47.
2002: John F Heidelberg; Karla Heidelberg; Rita R Colwell
Bacteria of the gamma-subclass Proteobacteria associated with zooplankton in Chesapeake Bay.
Applied and environmental microbiology 2002;68(11):5498-507.
2002: John F Heidelberg; Karla Heidelberg; Rita R Colwell
Seasonality of Chesapeake Bay bacterioplankton species.
Applied and environmental microbiology 2002;68(11):5488-97.
2002: Oded Béjà; Marcelino Suzuki; John F Heidelberg; William C Nelson; Christina M Preston; Tohru Hamada; Jonathan Eisen; Claire M Fraser-Liggett; Edward F DeLong
Unsuspected diversity among marine aerobic anoxygenic phototrophs.
Nature 2002;415(6872):630-3.
2002: Michelle Dziejman; Emmy Balon; Dana Boyd; Claire M Fraser-Liggett; John F Heidelberg; John J Mekalanos
Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(3):1556-61.
2002: Alex S Beliaev; Dorothea K Thompson; Tripti Khare; Hanjo Lim; Craig C Brandt; Guangshan Li; Alison E Murray; John F Heidelberg; Carol S Giometti; John Yates; Kenneth H Nealson; James M Tiedje; Jizhong Zhoui
Gene and protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors.
Omics : a journal of integrative biology 2002;6(1):39-60.
2000: Karen E Nelson; Ian Paulsen; John F Heidelberg; Claire M Fraser-Liggett
Status of genome projects for nonpathogenic bacteria and archaea.
Nature biotechnology 2000;18(10):1049-54.
2000: Timothy D Read; Robert brunham; C Shen; Steven R Gill; John F Heidelberg; Owen R White; EK Hickey; J Peterson; Teresa Utterback; K Berry; S Bass; K Linher; Janice Weidman; Hoda Khouri; B Craven; C Bowman; Robert J Dodson; Michelle G Giglio; W Nelson; Robert T Deboy; James F Kolonay; Grant McClarty; Steven L Salzberg; Jonathan Eisen; Claire M Fraser-Liggett
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
Nucleic acids research 2000;28(6):1397-406.
2000: Jonathan Eisen; John F Heidelberg; Owen R White; Steven L Salzberg
Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Genome biology 2000;1(6):RESEARCH0011.
1999: Karen E Nelson; RA Clayton; Steven R Gill; Michelle G Giglio; Robert J Dodson; Daniel H Haft; EK Hickey; J D Peterson; William C Nelson; KA Ketchum; L McDonald; Teresa Utterback; JA Malek; K D Linher; M M Garrett; A M Stewart; M D Cotton; M S Pratt; C A Phillips; D Richardson; John F Heidelberg; Granger Sutton; Robert D Fleischmann; Jonathan Eisen; Owen R White; Steven L Salzberg; Hamilton O Smith; J Craig Venter; Claire M Fraser-Liggett
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nature 1999;399(6734):323-9.
1997: John F Heidelberg; M Shahamat; M Levin; I Rahman; G Stelma; C Grim; Rita R Colwell
Effect of aerosolization on culturability and viability of gram-negative bacteria.
Applied and environmental microbiology 1997;63(9):3585-8.