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Bioscience Division, B

Contacts

  • Division Leader
    Jose A. Olivares
  • Deputy Division Leader
    vacant
  • Chief of Staff
    Kathy Kelly
  • Executive Office Administrator
    Nicole Voight
  • Division Office
    505 667 2690


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Contact Information

(505) 665 1485
jchalla at lanl dot gov

Media Contact

B Div Communications
Rebecca McDonald
(505) 665-4650

Other Resources

Joint Genome Institute

News Releases

Jean Challacombe

Biodefense Informatics Team

Jean F. Challacombe was trained in pharmacology at the University of California, Santa Barbara. She received her Ph.D. in neuroscience at Florida State University, and spent three years as a postdoc working in developmental neuroscience and cell biology at the University of Minnesota. She started her training in computer science while doing postdoctoral research at the University of Minnesota, took courses in computer science at the University of New Mexico and worked as a Java software developer in private industry prior to coming to Los Alamos National Laboratory in 2000. At LANL, she began working in the area of bioinformatics, applying her computer science and programming skills while becoming an expert in database design, administration, and Perl-CGI web applications. She began working for the DOE Joint Genome Institute in 2001, as a member of the informatics team, applying her Java programming skills in support of the laboratory information management system for genome finishing, then joined the annotation and analysis team in 2003 to work on annotating and analyzing human chromosomes 19, 5 and 16. Since then, she has contributed to numerous genome annotation and analysis efforts, involving eukaryotic, viral and bacterial genomes, and has authored or coauthored peer-reviewed publications in the fields of bioinformatics and genomics, as well as several invited book chapters and reviews.

Research Interests

  • Comparative genome analysis
  • Bioinformatics tool development to facilitate genome and metagenome data analysis
  • Algorithm development and implementation
  • Data integration, pattern recognition, data management/data mining

Representative Publications

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. Proc Natl Acad Sci U S A. 2009 Sep 8;106(36):15442-7.

Barabote RD, Xie G, Leu D, Normand P, Necsulea A, Daubin V, Médigue C, Adney WS, Xu XC, Lapidus A, Detter C, Pujic P, Bruce D, Challacombe JF, Brettin TS, Richardson P, Berry AM. Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations. Genome Res. 2009. 19(6): 1033-1043

Ward NL, Challacombe JF, Janssen PH, Henrissat B, Coutinho PM, Wu M, Xie G, Haft DH, 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, Ganapaty A, Gwinn-Giglio M, Han CS, Khouri H, Kiss H, Kothari SP, Madupu R, Nelson RK, Nelson WC, Paulsen I, Penn K, Ren Q, Rosovitz MJ, Selengut JD, Shrivastava S, Sullivan SA, Tapia R, Thompson LS, Watkins KL, Yang Q, Yu C, Zafar N, Zhou L, and Kuske CR. Three genomes from the phylum Acidobacteria provide evidence of their lifestyles in soils. Appl Environ Microbiol. 2009. 75(7): 2046-2056.

Martinez D, Challacombe J, Morgenstern I, Hibbett D, Monika Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas F, Martinez, AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Splinter BonDurant S, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavín JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker S, Bruno K, Keneally W, Hoegger PJ, Kues U, Ramiaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee C, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev I, 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. Proc Natl Acad Sci USA 2009. 106(6):1954-59.

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.
Appl Environ Microbiol. 2007. 73(11):3536-46.

Challacombe JF, Altherr MR, Xie G, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett NA, Fawcett JJ, Glavina T, Goodwin LA, Green LD, Han CS, Hill KK, Hitchcock P, Jackson PJ, Keim P, Kewalramani AR, Longmire J, Lucas S, Malfatti S, Martinez D, McMurry K, Meincke LJ, Misra M, Moseman BL, Mundt M, Munk AC, Okinaka RT, Parson-Quintana B, Reilly LP, Richardson P, Robinson DL, Saunders E, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Ticknor LO, Wills PL, Gilna P, Brettin TS. The Complete Genome Sequence of Bacillus thuringiensis Al Hakam. J Bacteriol. 2007. 189(9):3680-1.

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 H. ducreyi 35000HP and H. influenzae Rd. J Bacteriol. 2007. 189(5):1890-1898.

Han CS, Xie G, Challacombe JF*, Altherr MR, Bhotika SS, Brown N, Bruce D, Campbell CS, Campbell ML, Chen J, Chertkov O, Cleland C, Dimitrijevic M, Doggett NA, Fawcett JJ, Glavina T, Goodwin LA, Green LD, 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. J Bacteriol. 2006 May;188(9):3382-90. *The first three authors contributed equally to this work.

Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA. The sequence and analysis of duplication-rich human chromosome 16. Nature 432(7020):988-942004 (2004).

Author list available upon request. Finishing the euchromatic sequence of the human genome. Nature 431:931-945(2004).

Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. The DNA sequence and comparative analysis of human chromosome 5. Nature 431(7006):268-74 (2004).

Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, Altherr MR, Brettin TS. Evaluation of the host transcriptional response to human cytomegalovirus infection. Physiol Genomics. 2004 18(1):51-62.

Book Chapters and Invited Reviews

Challacombe JF, Okinaka RT, Munk AC, Brettin TS, Keim P. Bacillus anthracis. In: Genomes of Food- and Water-borne Pathogens, ASM Press, in press 2009.

Keim P, Gruendike JM, Klevytska AM, Schupp, JM, Challacombe J, Okinaka R. The genome and variation of Bacillus anthracis. In: Molecular Aspects of Medicine, Elsevier Press, 2009.

Challacombe JF, Inzana TJ. Comparative Genomics of Pasteurellaceae. In Pasteurellaceae: Biology, Genomics and Molecular Aspects. Horizon Scientific Press, 2008.

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