Los Alamos National Laboratory

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Patrick Sam Guy Chain

Patrick Chain

Email
Phone (505) 665-4019

Capabilities

  • Biosciences
  • Biosecurity
  • Pre-symptomatic diagnosis of infection,
  • Pathogen studies
  • Strategies for disease surveillance and management
  • Biological threat identification, characterization, detection/diagnosis,
  • Transcriptomics
  • Next generation genome sequencing
  • Metagenomic
  • Single cell genomics
  • Genome annotation
  • Microbial biochemistry
  • Epidemiology modeling
  • Computer and Computational Sciences
  • Exascale
  • Computational Co-Design
  • Data-Intensive computing
  • Machine learning,
  • Data mining
  • High performance computing
  • Earth and Space Sciences
  • Carbon fluxes
  • Information Science and Technology
  • Visualization
  • Biological systems

Expertise

Genomics and Bioinformatics: Use of sequencing to characterize and understand biological systems, ranging from microbial, to plants and humans, with special focus on microbial communities, or microbiomes. Development of algorithms and methods (with a focus on metagenomics) to make better use of next generation seqeuncing technologies, and to develop platforms that allow more traditional biologists to interpret high throughput sequencing data. Development of ontologies for pathogens and epidemiology, in order to better make use of streaming sequencing data to advance biosurveillance efforts. Development of methods to integrate various omics data to relate gene content and metabolic potential, to gene/protein expression, and metabolite exchange within key biological systems.

Molecular Biology and GeneticsMicrobial Ecology and Evolution: Studies of bacteria and archaea in a variety of environments, including within or living with eukaryotic host systems, such as fungi, algae, plants and animals (including humans). Conduct directed, experimental evolution studies to better understand antimicrobial resistance, and utilize comparative genomics methods to infer evolutionary history of strains and species. Development of methods to capture and sort combinations of bacterial/eukaryotic cells to better understand cell to cell dynamics.

Websites

Video

Education

B.Sc. Molecular Biology and Biotechnology 1992-1996 McMaster University, Hamilton, Ont., Canada M.Sc. Molecular Microbiology 1996-1998 McMaster University, Hamilton, Ont., Canada

Ph.D. Microbiology and Molecular Genetics 2006-2011 Michigan State University, East Lansing, MI, USA  

 

LANL Positions

2000-2013, Scientist, Microbial Genome Program Finishing Lead, Microbial Interaction Program Head, Metagenomics Program Assembly Lead, DOE Joint Genome Institute

2009-present, Scientist, Metagenomics Applications Team Leader, Bioinformatics and Analytics Team Leader, Genome Programs Lead, Biosciences Division

 

Professional Societies

American Academy for the Advancement in Science 

American Society for Microbiology

International Society for Microbial Ecology

 

Awards

1992 Canada Scholarship

1992 Recipient of the McMaster University A. G. Reilly Scholarship

1992 Governor General’s Award

1996 Honours Distinction, McMaster University

2000 Joint Genome Institute Achievement Award

2004 ISME Best Poster Award

2004 LLNL Biology and Biotechnology Research Program Achievement Award

2007 Natural Sciences and Engineering Research Council Scholarship

2007 LLNL Chemistry, Materials and Life Sciences (CMLS) Award

2007 LLNL CMLS Biosciences and Biotechnology Division Award

2012 LAAP (Los Alamos Awards Program) Achievement Award

2013 PNNL Outstanding Lecturer Award

2014 LANL Fellow’s Prize Award2016 LANL Distinguished Performance Award

2016 LANL Distinguished Performance Award

 

Publications

Relevant publications below in reverse chronological order; more complete and updated lists can be found here:

Li, P. E., Lo, C. C., Anderson, J. J., Davenport, K. W., Bishop-Lilly, K. A., Xu, Y., Ahmed, S., Feng, S., Mokashi, V. P., and Chain, P. S. (2017) Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. Nucleic acids research 45, 67-80

Wang, S., Zhang, H., Scharadin, T. M., Zimmermann, M., Hu, B., Pan, A. W., Vinall, R., Lin, T. Y., Cimino, G., Chain, P., Vuyisich, M., Gleasner, C., McMurry, K., Malfatti, M., Turteltaub, K., de Vere White, R., Pan, C. X., and Henderson, P. T. (2016) Molecular Dissection of Induced Platinum Resistance through Functional and Gene Expression Analysis in a Cell Culture Model of Bladder Cancer. PloS one 11, e0146256

Ramirez, M. S., Xie, G., Traglia, G. M., Johnson, S. L., Davenport, K. W., van Duin, D., Ramazani, A., Perez, F., Jacobs, M. R., Sherratt, D. J., Bonomo, R. A., Chain, P. S., and Tolmasky, M. E. (2016) Whole-Genome Comparative Analysis of Two Carbapenem-Resistant ST-258 Klebsiella pneumoniae Strains Isolated during a North-Eastern Ohio Outbreak: Differences within the High Heterogeneity Zones. Genome biology and evolution 8, 2036-2043

Oulas, A., Polymenakou, P. N., Seshadri, R., Tripp, H. J., Mandalakis, M., Paez-Espino, A. D., Pati, A., Chain, P., Nomikou, P., Carey, S., Kilias, S., Christakis, C., Kotoulas, G., Magoulas, A., Ivanova, N. N., and Kyrpides, N. C. (2016) Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environmental microbiology 18, 1122-1136

Li, N., Hennelly, S. P., Stubben, C. J., Micheva-Viteva, S., Hu, B., Shou, Y., Vuyisich, M., Tung, C. S., Chain, P. S., Sanbonmatsu, K. Y., and Hong-Geller, E. (2016) Functional and Structural Analysis of a Highly-Expressed Yersinia pestis Small RNA following Infection of Cultured Macrophages. PloS one 11, e0168915

Filippidou, S., Jaussi, M., Junier, T., Wunderlin, T., Jeanneret, N., Palmieri, F., Palmieri, I., Roussel-Delif, L., Vieth-Hillebrand, A., Vetter, A., Chain, P. S., Regenspurg, S., and Junier, P. (2016) Anoxybacillusgeothermalis sp. nov., a facultatively anaerobic, endospore-forming bacterium isolated from mineral deposits in a geothermal station. Int J Syst Evol Microbiol 66, 2944-2951

Feng, S., Lo, C. C., Li, P. E., and Chain, P. S. (2016) ADEPT, a dynamic next generation sequencing data error-detection program with trimming. BMC bioinformatics 17, 109

Doggett, N. A., Mukundan, H., Lefkowitz, E. J., Slezak, T. R., Chain, P. S., Morse, S., Anderson, K., Hodge, D. R., and Pillai, S. (2016) Culture-Independent Diagnostics for Health Security. Health Secur 14, 122-142

Willias, S. P., Chauhan, S., Lo, C. C., Chain, P. S., and Motin, V. L. (2015) CRP-Mediated Carbon Catabolite Regulation of Yersinia pestis Biofilm Formation Is Enhanced by the Carbon Storage Regulator Protein, CsrA. PloS one 10, e0135481

Wang, D., Dorosky, R. J., Han, C. S., Lo, C. C., Dichosa, A. E., Chain, P. S., Yu, J. M., Pierson, L. S., 3rd, and Pierson, E. A. (2015) Adaptation genomics of a small-colony variant in a Pseudomonas chlororaphis 30-84 biofilm. Applied and environmental microbiology 81, 890-899

Oulas, A., Polymenakou, P. N., Seshadri, R., Tripp, H. J., Mandalakis, M., Paez-Espino, A. D., Pati, A., Chain, P., Nomikou, P., Carey, S., Kilias, S., Christakis, C., Kotoulas, G., Magoulas, A., Ivanova, N. N., and Kyrpides, N. C. (2015) Metagenomic investigation of the geologically unique Hellenic Volcanic Arc reveals a distinctive ecosystem with unexpected physiology. Environmental microbiology

Kruse, T., van de Pas, B. A., Atteia, A., Krab, K., Hagen, W. R., Goodwin, L., Chain, P., Boeren, S., Maphosa, F., Schraa, G., de Vos, W. M., van der Oost, J., Smidt, H., and Stams, A. J. (2015) Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. Journal of bacteriology 197, 893-904

Hua, Z. S., Han, Y. J., Chen, L. X., Liu, J., Hu, M., Li, S. J., Kuang, J. L., Chain, P. S., Huang, L. N., and Shu, W. S. (2015) Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics. The ISME journal 9, 1280-1294

Howe, A., and Chain, P. S. (2015) Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial). Frontiers in microbiology 6, 678

Hemme, C. L., Tu, Q., Shi, Z., Qin, Y., Gao, W., Deng, Y., Nostrand, J. D., Wu, L., He, Z., Chain, P. S., Tringe, S. G., Fields, M. W., Rubin, E. M., Tiedje, J. M., Hazen, T. C., Arkin, A. P., and Zhou, J. (2015) Comparative metagenomics reveals impact of contaminants on groundwater microbiomes. Frontiers in microbiology 6, 1205

Freitas, T. A., Li, P. E., Scholz, M. B., and Chain, P. S. (2015) Accurate read-based metagenome characterization using a hierarchical suite of unique signatures. Nucleic acids research 43, e69

Filippidou, S., Junier, T., Wunderlin, T., Lo, C. C., Li, P. E., Chain, P. S., and Junier, P. (2015) Under-detection of endospore-forming Firmicutes in metagenomic data. Computational and structural biotechnology journal 13, 299-306

Cui, H. H., Erkkila, T., Chain, P. S., and Vuyisich, M. (2015) Building International Genomics Collaboration for Global Health Security. Frontiers in public health 3, 264

Chapman, C., Henry, M., Bishop-Lilly, K. A., Awosika, J., Briska, A., Ptashkin, R. N., Wagner, T., Rajanna, C., Tsang, H., Johnson, S. L., Mokashi, V. P., Chain, P. S., and Sozhamannan, S. (2015) Scanning the landscape of genome architecture of non-O1 and non-O139 Vibrio cholerae by whole genome mapping reveals extensive population genetic diversity. PloS one 10, e0120311

Xie, G., Lo, C. C., Scholz, M., and Chain, P. S. (2014) Recruiting human microbiome shotgun data to site-specific reference genomes. PloS one 9, e84963

Vuyisich, M., Arefin, A., Davenport, K., Feng, S., Gleasner, C., McMurry, K., Parson-Quintana, B., Price, J., Scholz, M., and Chain, P. (2014) Facile, high quality sequencing of bacterial genomes from small amounts of DNA. International journal of genomics 2014, 434575

Swan, B. K., Chaffin, M. D., Martinez-Garcia, M., Morrison, H. G., Field, E. K., Poulton, N. J., Masland, E. D., Harris, C. C., Sczyrba, A., Chain, P. S., Koren, S., Woyke, T., and Stepanauskas, R. (2014) Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres. PloS one 9, e95380

Scholz, M., Lo, C. C., and Chain, P. S. (2014) Improved assemblies using a source-agnostic pipeline for MetaGenomic Assembly by Merging (MeGAMerge) of contigs. Scientific reports 4, 6480

Luo, C., Rodriguez, R. L., Johnston, E. R., Wu, L., Cheng, L., Xue, K., Tu, Q., Deng, Y., He, Z., Shi, J. Z., Yuan, M. M., Sherry, R. A., Li, D., Luo, Y., Schuur, E. A., Chain, P., Tiedje, J. M., Zhou, J., and Konstantinidis, K. T. (2014) Soil microbial community responses to a decade of warming as revealed by comparative metagenomics. Applied and environmental microbiology 80, 1777-1786

Lo, C. C., and Chain, P. S. (2014) Rapid evaluation and quality control of next generation sequencing data with FaQCs. BMC bioinformatics 15, 366

Ladner, J. T., Beitzel, B., Chain, P. S., Davenport, M. G., Donaldson, E. F., Frieman, M., Kugelman, J. R., Kuhn, J. H., O'Rear, J., Sabeti, P. C., Wentworth, D. E., Wiley, M. R., Yu, G. Y., Threat Characterization, C., Sozhamannan, S., Bradburne, C., and Palacios, G. (2014) Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio 5, e01360-01314

Kyrpides, N. C., Hugenholtz, P., Eisen, J. A., Woyke, T., Goker, M., Parker, C. T., Amann, R., Beck, B. J., Chain, P. S., Chun, J., Colwell, R. R., Danchin, A., Dawyndt, P., Dedeurwaerdere, T., DeLong, E. F., Detter, J. C., De Vos, P., Donohue, T. J., Dong, X. Z., Ehrlich, D. S., Fraser, C., Gibbs, R., Gilbert, J., Gilna, P., Glockner, F. O., Jansson, J. K., Keasling, J. D., Knight, R., Labeda, D., Lapidus, A., Lee, J. S., Li, W. J., Ma, J., Markowitz, V., Moore, E. R., Morrison, M., Meyer, F., Nelson, K. E., Ohkuma, M., Ouzounis, C. A., Pace, N., Parkhill, J., Qin, N., Rossello-Mora, R., Sikorski, J., Smith, D., Sogin, M., Stevens, R., Stingl, U., Suzuki, K., Taylor, D., Tiedje, J. M., Tindall, B., Wagner, M., Weinstock, G., Weissenbach, J., White, O., Wang, J., Zhang, L., Zhou, Y. G., Field, D., Whitman, W. B., Garrity, G. M., and Klenk, H. P. (2014) Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS biology 12, e1001920

Cooper, K. K., Mandrell, R. E., Louie, J. W., Korlach, J., Clark, T. A., Parker, C. T., Huynh, S., Chain, P. S., Ahmed, S., and Carter, M. Q. (2014) Comparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7. BMC genomics 15, 17

Oh, S., Tandukar, M., Pavlostathis, S. G., Chain, P. S., and Konstantinidis, K. T. (2013) Microbial community adaptation to quaternary ammonium biocides as revealed by metagenomics. Environmental microbiology 15, 2850-2864

Mitter, B., Petric, A., Shin, M. W., Chain, P. S., Hauberg-Lotte, L., Reinhold-Hurek, B., Nowak, J., and Sessitsch, A. (2013) Comparative genome analysis of Burkholderia phytofirmans PsJN reveals a wide spectrum of endophytic lifestyles based on interaction strategies with host plants. Frontiers in plant science 4, 120

Ishii, S., Suzuki, S., Norden-Krichmar, T. M., Tenney, A., Chain, P. S., Scholz, M. B., Nealson, K. H., and Bretschger, O. (2013) A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. Nature communications 4, 1601

Fitzsimons, M. S., Novotny, M., Lo, C. C., Dichosa, A. E., Yee-Greenbaum, J. L., Snook, J. P., Gu, W., Chertkov, O., Davenport, K. W., McMurry, K., Reitenga, K. G., Daughton, A. R., He, J., Johnson, S. L., Gleasner, C. D., Wills, P. L., Parson-Quintana, B., Chain, P. S., Detter, J. C., Lasken, R. S., and Han, C. S. (2013) Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome research 23, 878-888

Dodsworth, J. A., Blainey, P. C., Murugapiran, S. K., Swingley, W. D., Ross, C. A., Tringe, S. G., Chain, P. S., Scholz, M. B., Lo, C. C., Raymond, J., Quake, S. R., and Hedlund, B. P. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nature communications 4, 1854

D'Haeseleer, P., Gladden, J. M., Allgaier, M., Chain, P. S., Tringe, S. G., Malfatti, S. A., Aldrich, J. T., Nicora, C. D., Robinson, E. W., Pasa-Tolic, L., Hugenholtz, P., Simmons, B. A., and Singer, S. W. (2013) Proteogenomic analysis of a thermophilic bacterial consortium adapted to deconstruct switchgrass. PloS one 8, e68465

Boscaro, V., Felletti, M., Vannini, C., Ackerman, M. S., Chain, P. S., Malfatti, S., Vergez, L. M., Shin, M., Doak, T. G., Lynch, M., and Petroni, G. (2013) Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria. Proceedings of the National Academy of Sciences of the United States of America 110, 18590-18595

Zeytun, A., Malfatti, S. A., Vergez, L. M., Shin, M., Garcia, E., and Chain, P. S. (2012) Complete genome sequence of Francisella philomiragia ATCC 25017. Journal of bacteriology 194, 3266

Yang, F., Zeng, X., Ning, K., Liu, K. L., Lo, C. C., Wang, W., Chen, J., Wang, D., Huang, R., Chang, X., Chain, P. S., Xie, G., Ling, J., and Xu, J. (2012) Saliva microbiomes distinguish caries-active from healthy human populations. The ISME journal 6, 1-10

Steven, B., Gallegos-Graves, L. V., Starkenburg, S. R., Chain, P. S., and Kuske, C. R. (2012) Targeted and shotgun metagenomic approaches provide different descriptions of dryland soil microbial communities in a manipulated field study. Environmental microbiology reports 4, 248-256

Scholz, M. B., Lo, C. C., and Chain, P. S. (2012) Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis. Current opinion in biotechnology 23, 9-15

Ramirez, M. S., Xie, G., Marshall, S. H., Hujer, K. M., Chain, P. S., Bonomo, R. A., and Tolmasky, M. E. (2012) Multidrug-resistant (MDR) Klebsiella pneumoniae clinical isolates: a zone of high heterogeneity (HHZ) as a tool for epidemiological studies. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases 18, E254-258

Pester, M., Brambilla, E., Alazard, D., Rattei, T., Weinmaier, T., Han, J., Lucas, S., Lapidus, A., Cheng, J. F., Goodwin, L., Pitluck, S., Peters, L., Ovchinnikova, G., Teshima, H., Detter, J. C., Han, C. S., Tapia, R., Land, M. L., Hauser, L., Kyrpides, N. C., Ivanova, N. N., Pagani, I., Huntmann, M., Wei, C. L., Davenport, K. W., Daligault, H., Chain, P. S., Chen, A., Mavromatis, K., Markowitz, V., Szeto, E., Mikhailova, N., Pati, A., Wagner, M., Woyke, T., Ollivier, B., Klenk, H. P., Spring, S., and Loy, A. (2012) Complete genome sequences of Desulfosporosinus orientis DSM765T, Desulfosporosinus youngiae DSM17734T, Desulfosporosinus meridiei DSM13257T, and Desulfosporosinus acidiphilus DSM22704T. Journal of bacteriology 194, 6300-6301

Mason, O. U., Hazen, T. C., Borglin, S., Chain, P. S., Dubinsky, E. A., Fortney, J. L., Han, J., Holman, H. Y., Hultman, J., Lamendella, R., Mackelprang, R., Malfatti, S., Tom, L. M., Tringe, S. G., Woyke, T., Zhou, J., Rubin, E. M., and Jansson, J. K. (2012) Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill. The ISME journal 6, 1715-1727

Martinez-Garcia, M., Brazel, D. M., Swan, B. K., Arnosti, C., Chain, P. S., Reitenga, K. G., Xie, G., Poulton, N. J., Lluesma Gomez, M., Masland, D. E., Thompson, B., Bellows, W. K., Ziervogel, K., Lo, C. C., Ahmed, S., Gleasner, C. D., Detter, C. J., and Stepanauskas, R. (2012) Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PloS one 7, e35314

Leung, K., Zahn, H., Leaver, T., Konwar, K. M., Hanson, N. W., Page, A. P., Lo, C. C., Chain, P. S., Hallam, S. J., and Hansen, C. L. (2012) A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proceedings of the National Academy of Sciences of the United States of America 109, 7665-7670

Kaplan, J. B., Lo, C., Xie, G., Johnson, S. L., Chain, P. S., Donnelly, R., Kachlany, S. C., and Balashova, N. V. (2012) Genome sequence of Kingella kingae septic arthritis isolate PYKK081. Journal of bacteriology 194, 3017

Dichosa, A. E., Fitzsimons, M. S., Lo, C. C., Weston, L. L., Preteska, L. G., Snook, J. P., Zhang, X., Gu, W., McMurry, K., Green, L. D., Chain, P. S., Detter, J. C., and Han, C. S. (2012) Artificial polyploidy improves bacterial single cell genome recovery. PloS one 7, e37387

Beckloff, N., Starkenburg, S., Freitas, T., and Chain, P. (2012) Bacterial genome annotation. Methods in molecular biology 881, 471-503

Ahmed, S. A., Awosika, J., Baldwin, C., Bishop-Lilly, K. A., Biswas, B., Broomall, S., Chain, P. S., Chertkov, O., Chokoshvili, O., Coyne, S., Davenport, K., Detter, J. C., Dorman, W., Erkkila, T. H., Folster, J. P., Frey, K. G., George, M., Gleasner, C., Henry, M., Hill, K. K., Hubbard, K., Insalaco, J., Johnson, S., Kitzmiller, A., Krepps, M., Lo, C. C., Luu, T., McNew, L. A., Minogue, T., Munk, C. A., Osborne, B., Patel, M., Reitenga, K. G., Rosenzweig, C. N., Shea, A., Shen, X., Strockbine, N., Tarr, C., Teshima, H., van Gieson, E., Verratti, K., Wolcott, M., Xie, G., Sozhamannan, S., Gibbons, H. S., and Threat Characterization, C. (2012) Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2. PloS one 7, e48228

Yilmaz, P., Kottmann, R., Field, D., Knight, R., Cole, J. R., Amaral-Zettler, L., Gilbert, J. A., Karsch-Mizrachi, I., Johnston, A., Cochrane, G., Vaughan, R., Hunter, C., Park, J., Morrison, N., Rocca-Serra, P., Sterk, P., Arumugam, M., Bailey, M., Baumgartner, L., Birren, B. W., Blaser, M. J., Bonazzi, V., Booth, T., Bork, P., Bushman, F. D., Buttigieg, P. L., Chain, P. S., Charlson, E., Costello, E. K., Huot-Creasy, H., Dawyndt, P., DeSantis, T., Fierer, N., Fuhrman, J. A., Gallery, R. E., Gevers, D., Gibbs, R. A., San Gil, I., Gonzalez, A., Gordon, J. I., Guralnick, R., Hankeln, W., Highlander, S., Hugenholtz, P., Jansson, J., Kau, A. L., Kelley, S. T., Kennedy, J., Knights, D., Koren, O., Kuczynski, J., Kyrpides, N., Larsen, R., Lauber, C. L., Legg, T., Ley, R. E., Lozupone, C. A., Ludwig, W., Lyons, D., Maguire, E., Methe, B. A., Meyer, F., Muegge, B., Nakielny, S., Nelson, K. E., Nemergut, D., Neufeld, J. D., Newbold, L. K., Oliver, A. E., Pace, N. R., Palanisamy, G., Peplies, J., Petrosino, J., Proctor, L., Pruesse, E., Quast, C., Raes, J., Ratnasingham, S., Ravel, J., Relman, D. A., Assunta-Sansone, S., Schloss, P. D., Schriml, L., Sinha, R., Smith, M. I., Sodergren, E., Spo, A., Stombaugh, J., Tiedje, J. M., Ward, D. V., Weinstock, G. M., Wendel, D., White, O., Whiteley, A., Wilke, A., Wortman, J. R., Yatsunenko, T., and Glockner, F. O. (2011) Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nature biotechnology 29, 415-420

Weilharter, A., Mitter, B., Shin, M. V., Chain, P. S., Nowak, J., and Sessitsch, A. (2011) Complete genome sequence of the plant growth-promoting endophyte Burkholderia phytofirmans strain PsJN. Journal of bacteriology 193, 3383-3384

van Passel, M. W., Kant, R., Zoetendal, E. G., Plugge, C. M., Derrien, M., Malfatti, S. A., Chain, P. S., Woyke, T., Palva, A., de Vos, W. M., and Smidt, H. (2011) The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes. PloS one 6, e16876

Starkenburg, S. R., Reitenga, K. G., Freitas, T., Johnson, S., Chain, P. S., Garcia-Pichel, F., and Kuske, C. R. (2011) Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide. Journal of bacteriology 193, 4569-4570

Hu, B., Xie, G., Lo, C. C., Starkenburg, S. R., and Chain, P. S. (2011) Pathogen comparative genomics in the next-generation sequencing era: genome alignments, pangenomics and metagenomics. Briefings in functional genomics 10, 322-333

Chain, P. S., Xie, G., Starkenburg, S. R., Scholz, M. B., Beckloff, N., Lo, C. C., Davenport, K. W., Reitenga, K. G., Daligault, H. E., Detter, J. C., Freitas, T. A., Gleasner, C. D., Green, L. D., Han, C. S., McMurry, K. K., Meincke, L. J., Shen, X., and Zeytun, A. (2011) Genomics for key players in the N cycle from guinea pigs to the next frontier. Methods in enzymology 496, 289-318

Chain, P. S., Lang, D. M., Comerci, D. J., Malfatti, S. A., Vergez, L. M., Shin, M., Ugalde, R. A., Garcia, E., and Tolmasky, M. E. (2011) Genome of Ochrobactrum anthropi ATCC 49188 T, a versatile opportunistic pathogen and symbiont of several eukaryotic hosts. Journal of bacteriology 193, 4274-4275

Campbell, M. A., Chain, P. S., Dang, H., El Sheikh, A. F., Norton, J. M., Ward, N. L., Ward, B. B., and Klotz, M. G. (2011) Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world's oceans: calls to validate the names 'Nitrosococcus halophilus' and 'Nitrosomonas mobilis'. FEMS microbiology ecology 76, 39-48

Xie, G., Chain, P. S., Lo, C. C., Liu, K. L., Gans, J., Merritt, J., and Qi, F. (2010) Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing. Molecular oral microbiology 25, 391-405

Walker, C. B., de la Torre, J. R., Klotz, M. G., Urakawa, H., Pinel, N., Arp, D. J., Brochier-Armanet, C., Chain, P. S., Chan, P. P., Gollabgir, A., Hemp, J., Hugler, M., Karr, E. A., Konneke, M., Shin, M., Lawton, T. J., Lowe, T., Martens-Habbena, W., Sayavedra-Soto, L. A., Lang, D., Sievert, S. M., Rosenzweig, A. C., Manning, G., and Stahl, D. A. (2010) Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea. Proceedings of the National Academy of Sciences of the United States of America 107, 8818-8823

Kielak, A., Rodrigues, J. L., Kuramae, E. E., Chain, P. S., van Veen, J. A., and Kowalchuk, G. A. (2010) Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS microbiology ecology 71, 23-33

Hather, G. J., Haynes, W., Higdon, R., Kolker, N., Stewart, E. A., Arzberger, P., Chain, P., Field, D., Franza, B. R., Lin, B., Meyer, F., Ozdemir, V., Smith, C. V., van Belle, G., Wooley, J., and Kolker, E. (2010) The United States of America and scientific research. PloS one 5, e12203

Ayala-del-Rio, H. L., Chain, P. S., Grzymski, J. J., Ponder, M. A., Ivanova, N., Bergholz, P. W., Di Bartolo, G., Hauser, L., Land, M., Bakermans, C., Rodrigues, D., Klappenbach, J., Zarka, D., Larimer, F., Richardson, P., Murray, A., Thomashow, M., and Tiedje, J. M. (2010) The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Applied and environmental microbiology 76, 2304-2312

Yoder-Himes, D. R., Chain, P. S., Zhu, Y., Wurtzel, O., Rubin, E. M., Tiedje, J. M., and Sorek, R. (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America 106, 3976-3981

Wu, D., Hugenholtz, P., Mavromatis, K., Pukall, R., Dalin, E., Ivanova, N. N., Kunin, V., Goodwin, L., Wu, M., Tindall, B. J., Hooper, S. D., Pati, A., Lykidis, A., Spring, S., Anderson, I. J., D'Haeseleer, P., Zemla, A., Singer, M., Lapidus, A., Nolan, M., Copeland, A., Han, C., Chen, F., Cheng, J. F., Lucas, S., Kerfeld, C., Lang, E., Gronow, S., Chain, P., Bruce, D., Rubin, E. M., Kyrpides, N. C., Klenk, H. P., and Eisen, J. A. (2009) A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060

Foster, J. T., Beckstrom-Sternberg, S. M., Pearson, T., Beckstrom-Sternberg, J. S., Chain, P. S., Roberto, F. F., Hnath, J., Brettin, T., and Keim, P. (2009) Whole-genome-based phylogeny and divergence of the genus Brucella. Journal of bacteriology 191, 2864-2870

Donaher, N., Tanifuji, G., Onodera, N. T., Malfatti, S. A., Chain, P. S., Hara, Y., and Archibald, J. M. (2009) The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome biology and evolution 1, 439-448

Chain, P. S., Grafham, D. V., Fulton, R. S., Fitzgerald, M. G., Hostetler, J., Muzny, D., Ali, J., Birren, B., Bruce, D. C., Buhay, C., Cole, J. R., Ding, Y., Dugan, S., Field, D., Garrity, G. M., Gibbs, R., Graves, T., Han, C. S., Harrison, S. H., Highlander, S., Hugenholtz, P., Khouri, H. M., Kodira, C. D., Kolker, E., Kyrpides, N. C., Lang, D., Lapidus, A., Malfatti, S. A., Markowitz, V., Metha, T., Nelson, K. E., Parkhill, J., Pitluck, S., Qin, X., Read, T. D., Schmutz, J., Sozhamannan, S., Sterk, P., Strausberg, R. L., Sutton, G., Thomson, N. R., Tiedje, J. M., Weinstock, G., Wollam, A., Genomic Standards Consortium Human Microbiome Project Jumpstart, C., and Detter, J. C. (2009) Genomics. Genome project standards in a new era of sequencing. Science 326, 236-237

Starkenburg, S. R., Larimer, F. W., Stein, L. Y., Klotz, M. G., Chain, P. S., Sayavedra-Soto, L. A., Poret-Peterson, A. T., Gentry, M. E., Arp, D. J., Ward, B., and Bottomley, P. J. (2008) Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter. Applied and environmental microbiology 74, 2852-2863

Sievert, S. M., Scott, K. M., Klotz, M. G., Chain, P. S., Hauser, L. J., Hemp, J., Hugler, M., Land, M., Lapidus, A., Larimer, F. W., Lucas, S., Malfatti, S. A., Meyer, F., Paulsen, I. T., Ren, Q., Simon, J., and Class, U. S. F. G. (2008) Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans. Applied and environmental microbiology 74, 1145-1156

Oda, Y., Larimer, F. W., Chain, P. S., Malfatti, S., Shin, M. V., Vergez, L. M., Hauser, L., Land, M. L., Braatsch, S., Beatty, J. T., Pelletier, D. A., Schaefer, A. L., and Harwood, C. S. (2008) Multiple genome sequences reveal adaptations of a phototrophic bacterium to sediment microenvironments. Proceedings of the National Academy of Sciences of the United States of America 105, 18543-18548

Norton, J. M., Klotz, M. G., Stein, L. Y., Arp, D. J., Bottomley, P. J., Chain, P. S., Hauser, L. J., Land, M. L., Larimer, F. W., Shin, M. W., and Starkenburg, S. R. (2008) Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Applied and environmental microbiology 74, 3559-3572

Isabel, S., Leblanc, E., Boissinot, M., Boudreau, D. K., Grondin, M., Picard, F. J., Martel, E. A., Parham, N. J., Chain, P. S., Bader, D. E., Mulvey, M. R., Bryden, L., Roy, P. H., Ouellette, M., and Bergeron, M. G. (2008) Divergence among genes encoding the elongation factor Tu of Yersinia Species. Journal of bacteriology 190, 7548-7558

Garcia, E., Chain, P., Elliott, J. M., Bobrov, A. G., Motin, V. L., Kirillina, O., Lao, V., Calendar, R., and Filippov, A. A. (2008) Molecular characterization of L-413C, a P2-related plague diagnostic bacteriophage. Virology 372, 85-96

Trojian, T. H., Mody, K., and Chain, P. (2007) Exercise and colon cancer: primary and secondary prevention. Current sports medicine reports 6, 120-124

Stein, L. Y., Arp, D. J., Berube, P. M., Chain, P. S., Hauser, L., Jetten, M. S., Klotz, M. G., Larimer, F. W., Norton, J. M., Op den Camp, H. J., Shin, M., and Wei, X. (2007) Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation. Environmental microbiology 9, 2993-3007

Kane, S. R., Chakicherla, A. Y., Chain, P. S., Schmidt, R., Shin, M. W., Legler, T. C., Scow, K. M., Larimer, F. W., Lucas, S. M., Richardson, P. M., and Hristova, K. R. (2007) Whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium Methylibium petroleiphilum PM1. Journal of bacteriology 189, 1931-1945

Hristova, K. R., Schmidt, R., Chakicherla, A. Y., Legler, T. C., Wu, J., Chain, P. S., Scow, K. M., and Kane, S. R. (2007) Comparative transcriptome analysis of Methylibium petroleiphilum PM1 exposed to the fuel oxygenates methyl tert-butyl ether and ethanol. Applied and environmental microbiology 73, 7347-7357

Garcia, E., Worsham, P., Bearden, S., Malfatti, S., Lang, D., Larimer, F., Lindler, L., and Chain, P. (2007) Pestoides F, an atypical Yersinia pestis strain from the former Soviet Union. Advances in experimental medicine and biology 603, 17-22

Arp, D. J., Chain, P. S., and Klotz, M. G. (2007) The impact of genome analyses on our understanding of ammonia-oxidizing bacteria. Annual review of microbiology 61, 503-528

Starkenburg, S. R., Chain, P. S., Sayavedra-Soto, L. A., Hauser, L., Land, M. L., Larimer, F. W., Malfatti, S. A., Klotz, M. G., Bottomley, P. J., Arp, D. J., and Hickey, W. J. (2006) Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Applied and environmental microbiology 72, 2050-2063

Scott, K. M., Sievert, S. M., Abril, F. N., Ball, L. A., Barrett, C. J., Blake, R. A., Boller, A. J., Chain, P. S., Clark, J. A., Davis, C. R., Detter, C., Do, K. F., Dobrinski, K. P., Faza, B. I., Fitzpatrick, K. A., Freyermuth, S. K., Harmer, T. L., Hauser, L. J., Hugler, M., Kerfeld, C. A., Klotz, M. G., Kong, W. W., Land, M., Lapidus, A., Larimer, F. W., Longo, D. L., Lucas, S., Malfatti, S. A., Massey, S. E., Martin, D. D., McCuddin, Z., Meyer, F., Moore, J. L., Ocampo, L. H., Jr., Paul, J. H., Paulsen, I. T., Reep, D. K., Ren, Q., Ross, R. L., Sato, P. Y., Thomas, P., Tinkham, L. E., and Zeruth, G. T. (2006) The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2. PLoS biology 4, e383

Mavromatis, K., Doyle, C. K., Lykidis, A., Ivanova, N., Francino, M. P., Chain, P., Shin, M., Malfatti, S., Larimer, F., Copeland, A., Detter, J. C., Land, M., Richardson, P. M., Yu, X. J., Walker, D. H., McBride, J. W., and Kyrpides, N. C. (2006) The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies. Journal of bacteriology 188, 4015-4023

Loots, G. G., Chain, P. S., Mabery, S., Rasley, A., Garcia, E., and Ovcharenko, I. (2006) Array2BIO: from microarray expression data to functional annotation of co-regulated genes. BMC bioinformatics 7, 307

Klotz, M. G., Arp, D. J., Chain, P. S., El-Sheikh, A. F., Hauser, L. J., Hommes, N. G., Larimer, F. W., Malfatti, S. A., Norton, J. M., Poret-Peterson, A. T., Vergez, L. M., and Ward, B. B. (2006) Complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium Nitrosococcus oceani ATCC 19707. Applied and environmental microbiology 72, 6299-6315

Chain, P. S., Hu, P., Malfatti, S. A., Radnedge, L., Larimer, F., Vergez, L. M., Worsham, P., Chu, M. C., and Andersen, G. L. (2006) Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. Journal of bacteriology 188, 4453-4463

Chain, P. S., Denef, V. J., Konstantinidis, K. T., Vergez, L. M., Agullo, L., Reyes, V. L., Hauser, L., Cordova, M., Gomez, L., Gonzalez, M., Land, M., Lao, V., Larimer, F., LiPuma, J. J., Mahenthiralingam, E., Malfatti, S. A., Marx, C. J., Parnell, J. J., Ramette, A., Richardson, P., Seeger, M., Smith, D., Spilker, T., Sul, W. J., Tsoi, T. V., Ulrich, L. E., Zhulin, I. B., and Tiedje, J. M. (2006) Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proceedings of the National Academy of Sciences of the United States of America 103, 15280-15287

Brotcke, A., Weiss, D. S., Kim, C. C., Chain, P., Malfatti, S., Garcia, E., and Monack, D. M. (2006) Identification of MglA-regulated genes reveals novel virulence factors in Francisella tularensis. Infection and immunity 74, 6642-6655

Beller, H. R., Chain, P. S., Letain, T. E., Chakicherla, A., Larimer, F. W., Richardson, P. M., Coleman, M. A., Wood, A. P., and Kelly, D. P. (2006) The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. Journal of bacteriology 188, 1473-1488

Larsson, P., Oyston, P. C., Chain, P., Chu, M. C., Duffield, M., Fuxelius, H. H., Garcia, E., Halltorp, G., Johansson, D., Isherwood, K. E., Karp, P. D., Larsson, E., Liu, Y., Michell, S., Prior, J., Prior, R., Malfatti, S., Sjostedt, A., Svensson, K., Thompson, N., Vergez, L., Wagg, J. K., Wren, B. W., Lindler, L. E., Andersson, S. G., Forsman, M., and Titball, R. W. (2005) The complete genome sequence of Francisella tularensis, the causative agent of tularemia. Nature genetics 37, 153-159

Feil, H., Feil, W. S., Chain, P., Larimer, F., DiBartolo, G., Copeland, A., Lykidis, A., Trong, S., Nolan, M., Goltsman, E., Thiel, J., Malfatti, S., Loper, J. E., Lapidus, A., Detter, J. C., Land, M., Richardson, P. M., Kyrpides, N. C., Ivanova, N., and Lindow, S. E. (2005) Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proceedings of the National Academy of Sciences of the United States of America 102, 11064-11069

Chain, P. S., Comerci, D. J., Tolmasky, M. E., Larimer, F. W., Malfatti, S. A., Vergez, L. M., Aguero, F., Land, M. L., Ugalde, R. A., and Garcia, E. (2005) Whole-genome analyses of speciation events in pathogenic Brucellae. Infection and immunity 73, 8353-8361

Larimer, F. W., Chain, P., Hauser, L., Lamerdin, J., Malfatti, S., Do, L., Land, M. L., Pelletier, D. A., Beatty, J. T., Lang, A. S., Tabita, F. R., Gibson, J. L., Hanson, T. E., Bobst, C., Torres, J. L., Peres, C., Harrison, F. H., Gibson, J., and Harwood, C. S. (2004) Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris. Nature biotechnology 22, 55-61

Chain, P. S., Carniel, E., Larimer, F. W., Lamerdin, J., Stoutland, P. O., Regala, W. M., Georgescu, A. M., Vergez, L. M., Land, M. L., Motin, V. L., Brubaker, R. R., Fowler, J., Hinnebusch, J., Marceau, M., Medigue, C., Simonet, M., Chenal-Francisque, V., Souza, B., Dacheux, D., Elliott, J. M., Derbise, A., Hauser, L. J., and Garcia, E. (2004) Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences of the United States of America 101, 13826-13831

Rocap, G., Larimer, F. W., Lamerdin, J., Malfatti, S., Chain, P., Ahlgren, N. A., Arellano, A., Coleman, M., Hauser, L., Hess, W. R., Johnson, Z. I., Land, M., Lindell, D., Post, A. F., Regala, W., Shah, M., Shaw, S. L., Steglich, C., Sullivan, M. B., Ting, C. S., Tolonen, A., Webb, E. A., Zinser, E. R., and Chisholm, S. W. (2003) Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424, 1042-1047

Palenik, B., Brahamsha, B., Larimer, F. W., Land, M., Hauser, L., Chain, P., Lamerdin, J., Regala, W., Allen, E. E., McCarren, J., Paulsen, I., Dufresne, A., Partensky, F., Webb, E. A., and Waterbury, J. (2003) The genome of a motile marine Synechococcus. Nature 424, 1037-1042

Garcia, E., Elliott, J. M., Ramanculov, E., Chain, P. S., Chu, M. C., and Molineux, I. J. (2003) The genome sequence of Yersinia pestis bacteriophage phiA1122 reveals an intimate history with the coliphage T3 and T7 genomes. Journal of bacteriology 185, 5248-5262

Chain, P., Lamerdin, J., Larimer, F., Regala, W., Lao, V., Land, M., Hauser, L., Hooper, A., Klotz, M., Norton, J., Sayavedra-Soto, L., Arciero, D., Hommes, N., Whittaker, M., and Arp, D. (2003) Complete genome sequence of the ammonia-oxidizing bacterium and obligate chemolithoautotroph Nitrosomonas europaea. Journal of bacteriology 185, 2759-2773

Chain, P., Kurtz, S., Ohlebusch, E., and Slezak, T. (2003) An applications-focused review of comparative genomics tools: capabilities, limitations and future challenges. Briefings in bioinformatics 4, 105-123

Hernandez-Lucas, I., Mavingui, P., Finan, T., Chain, P., and Martinez-Romero, E. (2002) In vivo cloning strategy for Rhizobium plasmids. BioTechniques 33, 782, 784, 786-788

Galibert, F., Finan, T. M., Long, S. R., Puhler, A., Abola, P., Ampe, F., Barloy-Hubler, F., Barnett, M. J., Becker, A., Boistard, P., Bothe, G., Boutry, M., Bowser, L., Buhrmester, J., Cadieu, E., Capela, D., Chain, P., Cowie, A., Davis, R. W., Dreano, S., Federspiel, N. A., Fisher, R. F., Gloux, S., Godrie, T., Goffeau, A., Golding, B., Gouzy, J., Gurjal, M., Hernandez-Lucas, I., Hong, A., Huizar, L., Hyman, R. W., Jones, T., Kahn, D., Kahn, M. L., Kalman, S., Keating, D. H., Kiss, E., Komp, C., Lelaure, V., Masuy, D., Palm, C., Peck, M. C., Pohl, T. M., Portetelle, D., Purnelle, B., Ramsperger, U., Surzycki, R., Thebault, P., Vandenbol, M., Vorholter, F. J., Weidner, S., Wells, D. H., Wong, K., Yeh, K. C., and Batut, J. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293, 668-672

Finan, T. M., Weidner, S., Wong, K., Buhrmester, J., Chain, P., Vorholter, F. J., Hernandez-Lucas, I., Becker, A., Cowie, A., Gouzy, J., Golding, B., and Puhler, A. (2001) The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proceedings of the National Academy of Sciences of the United States of America 98, 9889-9894

Chain, P. S., Hernandez-Lucas, I., Golding, B., and Finan, T. M. (2000) oriT-directed cloning of defined large regions from bacterial genomes: identification of the Sinorhizobium meliloti pExo megaplasmid replicator region. Journal of bacteriology 182, 5486-5494