Li-San Wang, Ph.D.

faculty photo
Associate Professor of Pathology and Laboratory Medicine
Department: Pathology and Laboratory Medicine
Graduate Group Affiliations

Contact information
Penn Center for Bioinformatics
1424 Blockley Hall
423 Guardian Drive
University of Pennsylvania
Philadelphia, PA 19104
Office: +1(215) 7467015
Education:
B.S. (Electrical Engineering)
National Taiwan University, 1994.
M.S. (Electrical Engineering)
National Taiwan University, 1996.
Ph.D. (Computer Sciences)
University of Texas at Austin, 2003.
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Description of Research Expertise

Our lab focuses on Alzheimer’s disease and other neurodegenerative disorders, aging, and psychiatric disorders including autism and bipolar disorder. Ongoing projects in our lab can be divided into the following two main directions:

Genetics and genomics of Alzheimer’s disease and other neurodegenerative disorders.

Our lab participated in the analysis of several large-scale genome-wide association (GWA) studies, which led to findings of new risk genes for frontotemporal dementia (FTD), progressive supranuclear palsy (PSP), and late-onset Alzheimer’s disease (AD).

Our lab is a participant of the Alzheimer’s Disease Genetics Consortium (ADGC), the largest collaborative project in United States to study AD genetics. In 2010, ADGC was one of the four founding consortia of International Genomics Alzheimer’s Project (IGAP) that substantially increased sample size and detected many additional candidate AD risk genes.

Our lab also contributes to the AD genetics research community in general. We have received a five-year grant that will develop the NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) into a one-stop portal for access to all AD genetics studies sponsored by NIA.

Informatics and algorithm development for genome-scale experiments.

Our lab actively develops novel algorithms and computer programs that analyze GWA and DNA-seq studies. Currently we are working on a pipeline that analyzes whole-exome or whole-genome resequencing studies. Our lab has also been collaborating with Brian Gregory’s lab in the Department of Biology on RNA-seq methodology, i.e. the analysis of RNA processing and function using high throughput sequencing.

Lab Personnel

Fanny Leung (Postdoc)
Tianyan Hu (Postdoc)
Pavel Kuksa (Postdoc)
Weixin Wang (Postdoc)
Chiao-Feng Lin (Data Analyst Sr.)
Otto Valladares (Programmer Analyst Sr.)
Micah Childress (Programmer Analyst)
Amanda Partch (Data Analyst)
Daniel Laufer (Research Administration Coordinator)
John Malamon (Data Analyst)
Yih-Chii Hwang (GCB Ph.D. candidate)
Alex Amlie-Wolf (GCB rotation graduate student)
Mitchell Tang (Undergraduate researcher)

Selected Publications

Hwang, Yih-Chii; Zheng, Qi; Gregory, Brian; Wang, Li-San: High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Research 41(9): 4835-46, May 2013.

Yuk Yee Leung, Paul Ryvkin, Lyle Ungar, Brian Gregory, Li-San Wang: CoRAL: Predicting non-coding RNAs from small RNA-sequencing data. Nucleic Acids Research 41(14): e137, August 2013 Notes: 10.1093/nar/gkt426.

Reitz C, Jun G, Naj A, Rajbhandary R, Vardarajan B N, San Wang L-, Valladares O, Lin C-F, Larson EB, Graff-Radford NR, Evans D, De Jager PL, Crane PK, Buxbaum JD, Murrell JR, Raj T, Ertekin-Taner N, Logue M, Baldwin CT, Green RC, Barnes LL, Cantwell LB, Fallin DM, Go RCP, Griffith P, Obisesan TO, Manly JJ, Lunetta KL, Kamboh IM, Lopez OL, Bennett DA, Hendrie H, Hall KS, Goate AM, Byrd GS, Kukull WA, Foroud TM, Haines JL, Farrer LA, Pericak-Vance MA, Schellenberg GD, Mayeux R, Alzheimer Disease Genetics Consortium: Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans. Journal of American Medical Association 309(14): 1483-92, April 2013.

Benjamin M. Neale, Yan Kou, Li Liu, Avi Ma’ayan, Kaitlin E. Samocha, Aniko Sabo, Chiao-Feng Lin, Christine Stevens, Li-San Wang, Vladimir Makarov, Paz Polak, Seungtai Yoon, Jared Maguire, Emily L. Crawford, Nicholas G. Campbell, Evan T. Geller, Otto Valladares, Chad Schafer, Han Liu, Tuo Zhao, Guiqing Cai, Jayon Lihm, Ruth Dannenfelser, Omar Jabado, Zuleyma Peralta, Uma Nagaswamy, Donna Muzny, Jeffrey G. Reid, Irene Newsham, Yuanqing Wu, Lora Lewis, Yi Han, Benjamin F. Voight, Elaine Lim, Elizabeth Rossin, Andrew Kirby, Jason Flannick, Menachem Fromer, Khalid Shakir, Tim Fennell, Kiran Garimella, Eric Banks, Ryan Poplin, Stacey Gabriel, Mark DePristo, Jack R. Wimbish, Braden E. Boone, Shawn E. Levy, Catalina Betancur, Shamil Sunyaev, Eric Boerwinkle, Joseph D. Buxbaum, Edwin H. Cook, Bernie Devlin, Richard A. Gibbs, Kathryn Roeder, Gerard D. Schellenberg, James S. Sutcliffe & Mark J. Daly: Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature April 2012 Notes: doi:10.1038/nature11011.

Adam C Naj, Gyungah Jun, Gary W Beecham, Li-San Wang, Badri Narayan Vardarajan, Jacqueline Buros, Paul J Gallins, Joseph D Buxbaum, Gail P Jarvik, Paul K Crane, Eric B Larson, Thomas D Bird, Bradley F Boeve, Neill R Graff-Radford, Philip L De Jager, Denis Evans, Julie A Schneider, Minerva M Carrasquillo, Nilufer Ertekin-Taner, Steven G Younkin, Carlos Cruchaga, John S K Kauwe, Petra Nowotny, Patricia Kramer, John Hardy, Matthew J Huentelman, Amanda J Myers, Michael M Barmada, F Yesim Demirci, Clinton T Baldwin, Robert C Green, Ekaterina Rogaeva, Peter St George-Hyslop, Steven E Arnold, Robert Barber, Thomas Beach, Eileen H Bigio, James D Bowen, Adam Boxer, James R Burke, Nigel J Cairns, Chris S Carlson, Regina M Carney, Steven L Carroll, Helena C Chui, David G Clark, Jason Corneveaux, Carl W Cotman, Jeffrey L Cummings, Charles DeCarli, Steven T DeKosky, Ramon Diaz-Arrastia, Malcolm Dick, Dennis W Dickson, William G Ellis, Kelley M Faber, Kenneth B Fallon, Martin R Farlow, Steven Ferris, Matthew P Frosch, Douglas R Galasko, Mary Ganguli, Marla Gearing, Daniel H Geschwind, Bernardino Ghetti, John R Gilbert, Sid Gilman, Bruno Giordani, Jonathan D Glass, John H Growdon, Ronald L Hamilton, Lindy E Harrell, Elizabeth Head, Lawrence S Honig, Christine M Hulette, Bradley T Hyman, Gregory A Jicha, Lee-Way Jin, Nancy Johnson, Jason Karlawish, Anna Karydas, Jeffrey A Kaye, Ronald Kim, Edward H Koo, Neil W Kowall, James J Lah, Allan I Levey, Andrew P Lieberman, Oscar L Lopez, Wendy J Mack, Daniel C Marson, Frank Martiniuk, Deborah C Mash, Eliezer Masliah, Wayne C McCormick, Susan M McCurry, Andrew N McDavid, Ann C McKee, Marsel Mesulam, Bruce L Miller, Carol A Miller, Joshua W Miller, Joseph E Parisi, Daniel P Perl, Elaine Peskind, Ronald C Petersen, Wayne W Poon, Joseph F Quinn, Ruchita A Rajbhandary, Murray Raskind, Barry Reisberg, John M Ringman, Erik D Roberson, Roger N Rosenberg, Mary Sano, Lon S Schneider, William Seeley, Michael L Shelanski, Michael A Slifer, Charles D Smith, Joshua A Sonnen, Salvatore Spina, Robert A Stern, Rudolph E Tanzi, John Q Trojanowski, Juan C Troncoso, Vivianna M Van Deerlin, Harry V Vinters, Jean Paul Vonsattel, Sandra Weintraub, Kathleen A Welsh-Bohmer, Jennifer Williamson, Randall L Woltjer, Laura B Cantwell, Beth A Dombroski, Duane Beekly, Kathryn L Lunetta, Eden R Martin, M Ilyas Kamboh, Andrew J Saykin, Eric M Reiman, David A Bennett, John C Morris, Thomas J Montine, Alison M Goate, Deborah Blacker, Debby W Tsuang, Hakon Hakonarson, Walter A Kukull, Tatiana M Foroud, Jonathan L Haines, Richard Mayeux, Margaret A Pericak-Vance, Lindsay A Farrer & Gerard D Schellenberg : Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nature Genetics 43(5): 436-441, May 2011.

Günter U Höglinger, Nadine M Melhem, Dennis W Dickson, Patrick M A Sleiman, Li-San Wang, Lambertus Klei, Rosa Rademakers, Rohan de Silva, Irene Litvan, David E Riley, John C van Swieten, Peter Heutink, Zbigniew K Wszolek, Ryan J Uitti, Jana Vandrovcova, Howard I Hurtig, Rachel G Gross, Walter Maetzler, Stefano Goldwurm, Eduardo Tolosa, Barbara Borroni, Pau Pastor, PSP Genetics Study Group, Laura B Cantwell, Mi Ryung Han, Allissa Dillman, Marcel P van der Brug, J Raphael Gibbs, Mark R Cookson, Dena G Hernandez, Andrew B Singleton, Matthew J Farrer, Chang-En Yu, Lawrence I Golbe, Tamas Revesz, John Hardy, Andrew J Lees, Bernie Devlin, Hakon Hakonarson, Ulrich Müller & Gerard D Schellenberg: Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy. Nature Genetics 43(7): 699–705, June 2011.

Van Deerlin VM, Sleiman PM, Martinez-Lage M, Chen-Plotkin A, Wang LS, Graff-Radford NR, Dickson DW, Rademakers R, Boeve BF, Grossman M, Arnold SE, Mann DM, Pickering-Brown SM, Seelaar H, Heutink P, van Swieten JC, Murrell JR, Ghetti B, Spina S, Grafman J, Hodges J, Spillantini MG, Gilman S, Lieberman AP, Kaye JA, Woltjer RL, Bigio EH, Mesulam M, Al-Sarraj S, Troakes C, Rosenberg RN, White CL 3rd, Ferrer I, Lladó A, Neumann M, Kretzschmar HA, Hulette CM, Welsh-Bohmer KA, Miller BL, Alzualde A, de Munain AL, McKee AC, Gearing M, Levey AI, Lah JJ, Hardy J, Rohrer JD, Lashley T, Mackenzie IR, Feldman HH, Hamilton RL, Dekosky ST, van der Zee J, Kumar-Singh S, Van Broeckhoven C, Mayeux R, Vonsattel JP, Troncoso JC, Kril JJ, Kwok JB, Halliday GM, Bird TD, Ince PG, Shaw PJ, Cairns NJ, Morris JC, McLean CA, DeCarli C, Ellis WG, Freeman SH, Frosch MP, Growdon JH, Perl DP, Sano M, Bennett DA, Schneider JA, Beach TG, Reiman EM, Woodruff BK, Cummings J, Vinters HV, Miller CA, Chui HC, Alafuzoff I, Hartikainen P, Seilhean D, Galasko D, Masliah E, Cotman CW, Tuñón MT, Martínez MC, Munoz DG, Carroll SL, Marson D, Riederer PF, Bogdanovic N, Schellenberg GD, Hakonarson H, Trojanowski JQ, Lee VM.: Common variants at 7p21 are associated with frontotemporal lobar degeneration with TDP-43 inclusions. Nature Genetics 42(3): 234-9, March 2010.

Qi Zheng, Paul Ryvkin, Fan Li, Isabelle Dragomir, Otto Valladares, Jamie Yang, Kajia Cao, Li-San Wang*, and Brian D. Gregory* (*: Co-corresponding authors): Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis. Public Library of Science (PLoS) Genetics 6(9): e1001141, September 2010.

Erika L. Pearce, Matthew C. Walsh, Pedro J. Cejas, Gretchen M. Harms, Hao Shen, Li-San Wang, Russell G. Jones and Yongwon Choi: Enhancing CD8 T-cell memory by modulating fatty acid metabolism. Nature 460(7251): 103-7, June 2009.

Steve G. Hershman, Qijun Chen, Julia Y. Lee, Marina L. Kozak, Peng Yue, Li-San Wang, and F. Brad Johnson: Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae. Nucleic Acids Research 36(1): 144-156, November 2008.

Wang, L.-S., Warnow, T.: Reconstructing Chromosomal Evolution. SIAM Journal on Computing 36(1): 99-131, July 2006.

Hannenhalli, S., Wang, L.-S.: Enhanced position weight matrices using mixture models. Bioinformatics 21(Supp.1): i204-i212, June 2005.

Moret, B.M.E., Wang, L.-S., Warnow, T., Wyman, S.: New Approaches for Reconstructing Phylogenies Based on Gene Order Bioinformatics 17(Supp.1): 165–173, June 2001.

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Last updated: 07/26/2014
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