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Jean F. Challacombe

Jean Challacombe

Capabilities

  • Biosciences
  • Human genome
  • Biosecurity
  • Pathogen studies
  • Biological threat identification, characterization, detection/diagnosis,
  • Transcriptomics
  • Next generation genome sequencing
  • Metagenomic
  • Genome annotation
  • Microbial biochemistry
  • Information Science and Technology
  • Biological systems
  • Science of Signatures - Remote and Standoff Sensing
  • Machine learning,

Expertise

Comparative genomics

Bioinformatics algorithm and tool development

Data management, data processing, data integration

Metabolic pathway analysis and network modeling

Machine learning

Education

B.S., Pharmacology, University of California, Santa Barbara, CA, 1983 - 1988

Ph.D., Neuroscience, Florida State University, Tallahassee, FL, 1989 - 1994

Coursework in Computer Science, University of Minnesota, Minneapolis, MN, 1995 - 1996

Coursework in Computer Science, University of New Mexico, 1997 - 1999

 

LANL Positions

Scientist, Biosecurity & Public Health Group, Bioscience Division, 2010 - present

Bioinformatics and Genome Analysis Team Leader, Bioscience Division, 2008 - 2010

Technical Staff Member/Scientist, Bioscience Division, 2000 - 2008

Programmer, Los Alamos National Laboratory (LANL), Los Alamos, NM, 1998 - 1999

 

Professional Societies

American Society for Microbiology

 

Awards

Two Los Alamos LAAP awards for noteworthy achievements

 

Publications

[Han, CS * Xie, G * Challacombe, JF * Altherr, MR * Bhotika, SS * Bruce, D * Campbell, CS * Campbell, ML * Chen, J * Chertkov, O * Cleland, C * Dimitrijevic, M * Doggett, NA * Fawcett, JJ * Glavina, T * Goodwin, LA * Hill, KK * Hitchcock, P * Jackson, PJ * Keim, P * Kewalramani, AR * Longmire, J * Lucas, S * Malfatti, S * McMurry, K * Meincke, LJ * Misra, M * Moseman, BL * Mundt, M * Munk, AC * Okinaka, RT * Parson-Quintana, B * Reilly, LP * Richardson, P * Robinson, DL * Rubin, E * Saunders, E * Tapia, R * Tesmer, JG * Thayer, N * Thompson, LS * Tice, H * Ticknor, LO * Wills, PL * Brettin, TS * Gilna, P], "Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis", JOURNAL OF BACTERIOLOGY, Vol.188, iss.9, p.3382-3390, MAY 2006.

[Challacombe, JF * Duncan, AJ * Brettin, TS * Bruce, D * Chertkov, O * Detter, JC * Han, CS * Misra, M * Richardson, P * Tapia, R * Thayer, N * Xie, G * Inzana, TJ], "Complete genome sequence of Haemophilus somnus (Histophilus somni) strain 129Pt and comparison to Haemophilus ducreyi 35000HP and Haemophilus influenzae Rd", JOURNAL OF BACTERIOLOGY, Vol.189, iss.5, p.1890-1898, MAR 2007.

[Xie, G * Bruce, DC * Challacombe, JF * Chertkov, O * Detter, JC * Gilna, P * Han, CS * Lucas, S * Misra, M * Myers, GL * Richardson, P * Tapia, R * Thayer, N * Thompson, LS * Brettin, TS * Henrissat, B * Wilson, DB * McBride, MJ], "Genome sequence of the cellulolytic gliding bacterium Cytophaga hutchinsonii", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol.73, iss.11, p.3536-3546, JUN 2007.

[Challacombe, J. F. * Duncan, A. J. * Xie, G. * Bruce, D. C. * Chertkov, O. * Gilna, P. * Han, C. S. * Lucas, S. * Richardson, P. M. * Tapia, R. * Thompson, L. S. * Inzana, T. J. * Brettin, T. S.], "The complete genome sequence of Haemophilus somnus 129Pt and comparison to related organisms", Abstracts of the General Meeting of the American Society for Microbiology, Vol.106, p.201, 2006.

[Challacombe, Jean F. * Inzana, Thomas J.], "Comparative genomics of Pasteurellaceae", Pasteurellacea: Biology, Genomics, and Molecular Aspects, p.53-77, 2008. 

[Martinez, D * Challacombe, J * Morgenstern, I * Hibbett, D * Schmoll, M * Kubicek, CP * Ferreira, P * Ruiz-Duenas, FJ * Martinez, AT * Kersten, P * Hammel, KE * Wymelenberg, AV * Gaskell, J * Lindquist, E * Sabat, G * BonDurant, SS * Larrondo, LF * Canessa, P * Vicuna, R * Yadav, J * Doddapaneni, H * Subramanian, V * Pisabarro, AG * Lavin, JL * Oguiza, JA * Master, E * Henrissat, B * Coutinho, PM * Harris, P * Magnuson, JK * Baker, SE * Bruno, K * Kenealy, W * Hoegger, PJ * Kues, U * Ramaiya, P * Lucash, S * Salamov, A * Shapiro, H * Tu, H * Chee, CL * Misra, M * Xie, G * Teter, S * Yaver, D * James, T * Mokrejs, M * Pospisek, M * Grigoriev, IV * Brettin, T * Rokhsar, D * Berka, R * Cullen, D], "Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol.106, iss.6, p.1954-1959, FEB 10 2009.

[Ward, NL * Challacombe, JF * Janssen, PH * Henrissat, B * Coutinho, PM * Wu, M * Xie, G * Haft, DH * Sait, M * Badger, J * Barabote, RD * Bradley, B * Brettin, TS * Brinkac, LM * Bruce, D * Creasy, T * Daugherty, SC * Davidsen, TM * Deboy, RT * Detter, JC * Dodson, RJ * Durkin, AS * Ganapathy, A * Gwinn-Giglio, M * Han, CS * Khouri, H * Kiss, H * Kothari, SP * Madupu, R * Nelson, KE * Nelson, WC * Paulsen, I * Penn, K * Ren, QH * Rosovitz, MJ * Selengut, JD * Shrivastava, S * Sullivan, SA * Tapia, R * Thompson, LS * Watkins, KL * Yang, Q * Yu, CH * Zafar, N * Zhou, LW * Kuske, CR], "Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol.75, iss.7, p.2046-2056, APR 1 2009.

[Barabote, RD * Xie, G * Leu, DH * Normand, P * Necsulea, A * Daubin, V * Medigue, C * Adney, WS * Xu, XC * Lapidus, A * Parales, RE * Detter, C * Pujic, P * Bruce, D * Lavire, C * Challacombe, JF * Brettin, TS * Berry, AM], "Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations", GENOME RESEARCH, Vol.19, iss.6, p.1033-1043, JUN 2009.

[Chun, J * Grim, CJ * Hasan, NA * Lee, JH * Choi, SY * Haley, BJ * Taviani, E * Jeon, YS * Kim, DW * Lee, JH * Brettin, TS * Bruce, DC * Challacombe, JF * Detter, JC * Han, CS * Munk, AC * Chertkov, O * Meincke, L * Saunders, E * Walters, RA * Huq, A * Nair, GB * Colwell, RR], "Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol.106, iss.36, p.15442-15447, SEP 8 2009.

[Keim, P * Gruendike, JM * Klevytska, AM * Schupp, JM * Challacombe, J * Okinaka, R], "The genome and variation of Bacillus anthracis", MOLECULAR ASPECTS OF MEDICINE, Vol.30, iss.6, spec. iss.SI, p.397-405, DEC 2009.

[Grim, CJ * Hasan, NA * Taviani, E * Haley, B * Chun, J * Brettin, TS * Bruce, DC * Detter, JC * Han, CS * Chertkov, O * Challacombe, J * Huq, A * Nair, GB * Colwell, RR], "Genome Sequence of Hybrid Vibrio cholerae O1 MJ-1236, B-33, and CIRS101 and Comparative Genomics with V. cholerae", JOURNAL OF BACTERIOLOGY, Vol.192, iss.13, p.3524-3533, JUL 2010.

[Haley, BJ * Grim, CJ * Hasan, NA * Choi, SY * Chun, J * Brettin, TS * Bruce, DC * Challacombe, JF * Detter, JC * Han, CS * Huq, A * Colwell, RR], "Comparative genomic analysis reveals evidence of two novel Vibrio species closely related to V. cholerae", BMC MICROBIOLOGY, Vol.10, 154, MAY 27 2010.

[Hasan, NA * Grim, CJ * Haley, BJ * Chun, J * Alam, M * Taviani, E * Hoq, M * Munk, AC * Saunders, E * Brettin, TS * Bruce, DC * Challacombe, JF * Detter, JC * Han, CS * Xie, G * Nair, GB * Huq, A * Colwell, RR], "Comparative genomics of clinical and environmental Vibrio mimicus", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol.107, iss.49, p.21134-21139, DEC 7 2010.

[McKinlay, JB * Laivenieks, M * Schindler, BD * McKinlay, AA * Siddaramappa, S * Challacombe, JF * Lowry, SR * Clum, A * Lapidus, AL * Burkhart, KB * Harkins, V * Vieille, C], "A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production", BMC GENOMICS, Vol.11, 680, NOV 30 2010.

[Challacombe, Jean F. * Okinaka, Richard T. * Munk, A. Christine * Brettin, Thomas S. * Keim, Paul], "Bacillus anthracis", Genomes of Foodborne and Waterborne Pathogens, p.165-183, 2011.

[Challacombe, JF * Eichorst, SA * Hauser, L * Land, M * Xie, G * Kuske, CR], "Biological Consequences of Ancient Gene Acquisition and Duplication in the Large Genome of Candidatus Solibacter usitatus Ellin6076", PLOS ONE, Vol.6, iss.9, e24882, SEP 15 2011.

[Siddaramappa, S * Challacombe, JF * Petersen, JM * Pillai, S * Hogg, G * Kuske, CR], "Common Ancestry and Novel Genetic Traits of Francisella novicida-Like Isolates from North America and Australia as Revealed by Comparative Genomic Analyses", APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Vol.77, iss.15, p.5110-5122, AUG 2011.

[Okinaka, RT * Price, EP * Wolken, SR * Gruendike, JM * Chung, WK * Pearson, T * Xie, G * Munk, C * Hill, KK * Challacombe, J * Ivins, BE * Schupp, JM * Beckstrom-Sternberg, SM * Friedlander, A * Keim, P], "An attenuated strain of Bacillus anthracis (CDC 684) has a large chromosomal inversion and altered growth kinetics", BMC GENOMICS, Vol.12, 477, SEP 30 2011.

[Siddaramappa, S * Challacombe, JF * Duncan, AJ * Gillaspy, AF * Carson, M * Gipson, J * Orvis, J * Zaitshik, J * Barnes, G * Bruce, D * Chertkov, O * Detter, JC * Han, CS * Tapia, R * Thompson, LS * Dyer, DW * Inzana, TJ], "Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses", BMC GENOMICS, Vol.12, 570, NOV 23 2011.

[Siddaramappa, S * Challacombe, JF * DeCastro, RE * Pfeiffer, F * Sastre, DE * Gimenez, MI * Paggi, RA * Detter, JC * Davenport, KW * Goodwin, LA * Kyrpides, N * Tapia, R * Pitluck, S * Lucas, S * Woyke, T * Maupin-Furlow, JA], "A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099(T)", BMC GENOMICS, Vol.13, 165, MAY 4 2012.

[Siddaramappa, S * Challacombe, JF * Delano, SF * Green, LD * Daligault, H * Bruce, D * Detter, C * Tapia, R * Han, SS * Goodwin, L * Han, J * Woyke, T * Pitluck, S * Pennacchio, L * Nolan, M * Land, M * Chang, YJ * Kyrpides, NC * Ovchinnikova, G * Hauser, L * Lapidus, A * Yan, J * Bowman, KS * da Costa, MS * Rainey, FA * Moe, WM], "Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9(T)) and comparison to Dehalococcoides strains", STANDARDS IN GENOMIC SCIENCES, Vol.6, iss.2, p.251-264, 2012.

[Siddaramappa, S * Challacombe, JF * Petersen, JM * Pillai, S * Kuske, CR], "Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources", BMC GENOMICS, Vol.13, 422, AUG 24 2012