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Bioscience Division, B


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

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Contact Information

han_cliff at lanl dot gov

Media Contact

B Div Communications
Rebecca McDonald
(505) 665-4650

Other Resources

News Releases

Cliff S. Han

Sequencing, Finishing & Metagenomics

Cliff S. Han is the computational finishing team leader at the Joint Genome Institute in Los Alamos National Laboratory. He received his undergraduate degree from Jining Medical College in medicine, his Masters Degree from Suzhou Medical College in psychiatry. He worked in a mental hospital for 4 years as a psychiatrist before completing a Ph.D. in 1996 from Fudan University in genetics. Since then, he has spent the last 16 years working at LANL on genomics, starting with human genome project and later on sequencing microbial genomes.

Research Interests

  • Genome sequencing and finishing
  • Single cell genomics
  • Metagenomics

Representative Publications

Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A; Genomic Standards Consortium Human Microbiome Project Jumpstart Consortium, Detter JC. Genomics. Genome project standards in a new era of sequencing. Science. 2009;326(5950):236-7.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009 Dec 24;462(7276):1056-60.

Lauro FM, McDougald D, Thomas T, Williams TJ, Egan S, Rice S, DeMaere MZ, Ting L, Ertan H, Johnson J, Ferriera S, Lapidus A, Anderson I, Kyrpides N, Munk AC, Detter C, Han CS, Brown MV, Robb FT, Kjelleberg S, Cavicchioli R. The genomic basis of trophic strategy in marine bacteria. Proc Natl Acad Sci U S A. 2009;106(37):15527-33.

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;106(36):15442-7.

Wattam AR, Williams KP, Snyder EE, Almeida NF Jr, Shukla M, Dickerman AW, Crasta OR, Kenyon R, Lu J, Shallom JM, Yoo H, Ficht TA, Tsolis RM, Munk C, Tapia R, Han CS, Detter JC, Bruce D, Brettin TS, Sobral BW, Boyle SM, Setubal JC. Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle. J Bacteriol. 2009;191(11):3569-79.

Aliyari R, Wu Q, Li HW, Wang XH, Li F, Green LD, Han CS, Li WX, Ding SW. Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila. Cell Host Microbe. 2008 Oct 16;4(4):387-97.

Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG et al: The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environmental microbiology 2008.

Chistoserdova L, Lapidus A, Han C, Goodwin L, Saunders L, Brettin T, Tapia R, Gilna P, Lucas S, Richardson PM et al: Genome of Methylobacillus flagellatus, molecular basis for obligate methylotrophy, and polyphyletic origin of methylotrophy. Journal of bacteriology 2007, 189(11):4020-4027.

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. 2006 Dec 15

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. (2007) The complete genome sequence of Bacillus thuringiensis Al Hakam. J. Bacteriology 189:3680-1.

Norman A. Doggett, Gary Xie, Linda J. Meincke, Robert D. Sutherland, Mark O. Mundt, Nicolas S. Berbaria, Brian E. Davya, Michael L. Robinsona,b, M. Katharine Ruddc, James L. Weberd, Raymond L. Stallingse, and Cliff Han. (2006) A 360 Kb Interchromosomal Duplication of the Human HYDIN Locus. Genomics, accepted.

Dennis L. Maeder, Iain Anderson, Thomas S. Brettin, David C. Bruce, Paul Gilna, Cliff S. Han, Alla Lapidus, William W. Metcalf, Elizabeth Saunders, Roxanne Tapia, and Kevin R. Sowers. 2006. The Methanosarcina barkeri Genome: Comparative Analysis with Methanosarcina acetivorans and Methanosarcina mazei Reveals Extensive Rearrangement within Methanosarcinal Genomes. J. Bacteriology 199(22): 7922-7931

Cliff S. Han, Gary Xie, Jean F. Challacombe, Michael R. Altherr, Smriti S. Bhotika, David Bruce, Connie S. Campbell, Mary L. Campbell, Jin Chen, Olga Chertkov, Cathy Cleland, M. Dimitrijevic, Norman A. Doggett, John J. Fawcett, Tijana Glavina, Lynne A. Goodwin, Karen K. Hill, Penny Hitchcock, Paul J. Jackson, Paul Keim, Avinash Ramesh Kewalramani, Jon Longmire, Susan Lucas, Stephanie Malfatti, Kim McMurry, Linda J. Meincke, Monica Misra, Bernice L. Moseman, Mark Mundt, A. Christine Munk, Richard T. Okinaka, B. Parson-Quintana, Lee Philip Reilly, Paul Richardson, Donna L. Robinson, Eddy Rubin, Elizabeth Saunders, Roxanne Tapia, Judith G. Tesmer, Nina Thayer, Linda S. Thompson, Hope Tice, Lawrence O. Ticknor, Patti L. Wills, Thomas S. Brettin, Paul Gilna. 2006. The Pathogenomic Sequence Analysis of B. cereus and B. thuringiensis isolates closely related to Bacillus anthracis. J. Bacteriology 188(9): 3382-3390.

Cliff S. Han, Patrick Chain. 2006. Finishing repeat regions automatically with Dupfinisher. in Proceeding of the 2006 international conference on bioinformatics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26-29, 2006: 141-146.

Yvonne C. Rogers, A. Christine Munk, Linda J. Meincke, and Cliff S. Han. 2005. Closing bacterial genomic sequence gaps with adaptor-PCR. BioTechniques 39: 31-34.

Rasko, AR, M.R. Altherr, C.S. Han, and J. Ravel. 2005. Genomics of the bacillus cereus group of organisms. FEMS Microbiology Reviews 29 303-329.

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