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, as an extension of his dissertation on mapping hte human genome, he has spent the last 16 years working at LANL on the Human Genome Project. He developed the overgo (overlapped oligonucleotide) probes in mapping chromosome 16. The whole chromosome was mapped with artificial bacterial chromosomes in less than six months. He then worked on analyzing human chromosome 16, resulting in a publication in Nature. Han established and has been leading the computational finishing team since 2003. He developed more than a hundred software tools to make the finishing process more efficient.

Research Interests

• Genome sequencing and finishing
• Single cell genomics
• Metagenomics

Representative Publications

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.

Avinash Kewalramani, Olga Chertkov, Riley Arnaudville, Cliff Han and Thomas Brettin A Novel Approach to High Throughput Microbial Genome Finishing: Incorporation of 454 Sequence Data for Gap Closure in Low Quality Sanger Data Proceedings of 2007 International Conference on Bioinformatics and Computational Biology (BIOCOMP'07: June 25-28, 2007)

Gary Xie, David C. Bruce, Jean F. Challacombe, Olga Chertkov, John C. Detter, Paul Gilna, Cliff S. Han, Susan Lucas, Monica Misra, Gerald L. Myers, Paul Richardson, Roxanne Tapia, Nina Thayer, Linda S. Thompson, Thomas S. Brettin, Bernard Henrissat, David B. Wilson, and Mark J. McBride Genome Sequence of the Cellulolytic Gliding Bacterium Cytophaga hutchinsonii Applied and Environmental Microbiology, June 2007, p.3536-3546

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.