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.

We are the data coordinating center for the Alzheimer's Disease Sequencing Project (ADSP), a White House/NIH initiative to sequence more than 11,000 Alzheimer's patients and cognitively unaffected controls. We are the Data management and Information transfer (DMIT) core for the Consortium for Alzheimer's Sequence Analysis (CASA), a UF1 cooperative research agreement with NIA to analyze genomic data from ADSP and other related studies.

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 Members

Dawn Alessandrine (Administrative Assistant)
Fanny Leung (Postdoc)
Tianyan Hu (Postdoc)
Pavel Kuksa (Postdoc)
Weixin Wang (Postdoc)
Chiao-Feng Lin (Data Analyst Sr.)
Mugdha Khaladkar (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

Jean-Charles Lambert, Carla A Ibrahim-Verbaas, Denise Harold, Adam C Naj, Rebecca Sims, Céline Bellenguez, Gyungah Jun, Anita L DeStefano, Joshua C Bis, Gary W Beecham, Benjamin Grenier-Boley, Giancarlo Russo, Tricia A Thornton-Wells, Nicola Jones, Albert V Smith, Vincent Chouraki, Charlene Thomas, M Arfan Ikram, Diana Zelenika, Badri N Vardarajan, Yoichiro Kamatani, Chiao-Feng Lin, Amy Gerrish, Helena Schmidt, Brian Kunkle, Melanie L Dunstan, Agustin Ruiz, Marie-Thérèse Bihoreau, Seung-Hoan Choi, Christiane Reitz, Florence Pasquier, Paul Hollingworth, Alfredo Ramirez, Olivier Hanon, Annette L Fitzpatrick, Joseph D Buxbaum, Dominique Campion, Paul K Crane, Clinton Baldwin, Tim Becker, Vilmundur Gudnason, Carlos Cruchaga, David Craig, Najaf Amin, Claudine Berr, Oscar L Lopez, Philip L De Jager, Vincent Deramecourt, Janet A Johnston, Denis Evans, Simon Lovestone, Luc Letenneur, Francisco J Morón, David C Rubinsztein, Gudny Eiriksdottir, Kristel Sleegers, Alison M Goate, Nathalie Fiévet, Matthew J Huentelman, Michael Gill, Kristelle Brown, M Ilyas Kamboh, Lina Keller, Pascale Barberger-Gateau, Bernadette McGuinness, Eric B Larson, Robert Green, Amanda J Myers, Carole Dufouil, Stephen Todd, David Wallon, Seth Love, Ekaterina Rogaeva, John Gallacher, Peter St George-Hyslop, Jordi Clarimon, Alberto Lleo, Anthony Bayer, Debby W Tsuang, Lei Yu, Magda Tsolaki, Paola Bossù, Gianfranco Spalletta, Petroula Proitsi, John Collinge, Sandro Sorbi, Florentino Sanchez-Garcia, Nick C Fox, John Hardy, Maria Candida Deniz Naranjo, Paolo Bosco, Robert Clarke, Carol Brayne, Daniela Galimberti, Michelangelo Mancuso, Fiona Matthews, European Alzheimer's Disease Initiative (EADI), Genetic and Environmental Risk in Alzheimer's Disease (GERAD), Alzheimer's Disease Genetic Consortium (ADGC), Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), Susanne Moebus, Patrizia Mecocci, Maria Del Zompo, Wolfgang Maier, Harald Hampel, Alberto Pilotto, Maria Bullido, Francesco Panza, Paolo Caffarra, Benedetta Nacmias, John R Gilbert, Manuel Mayhaus, Lars Lannfelt, Hakon Hakonarson, Sabrina Pichler, Minerva M Carrasquillo, Martin Ingelsson, Duane Beekly, Victoria Alvarez, Fanggeng Zou, Otto Valladares, Steven G Younkin, Eliecer Coto, Kara L Hamilton-Nelson, Wei Gu, Cristina Razquin, Pau Pastor, Ignacio Mateo, Michael J Owen, Kelley M Faber, Palmi V Jonsson, Onofre Combarros, Michael C O'Donovan, Laura B Cantwell, Hilkka Soininen, Deborah Blacker, Simon Mead, Thomas H Mosley Jr, David A Bennett, Tamara B Harris, Laura Fratiglioni, Clive Holmes, Renee F A G de Bruijn, Peter Passmore, Thomas J Montine, Karolien Bettens, Jerome I Rotter, Alexis Brice, Kevin Morgan, Tatiana M Foroud, Walter A Kukull, Didier Hannequin, John F Powell, Michael A Nalls, Karen Ritchie, Kathryn L Lunetta, John S K Kauwe, Eric Boerwinkle, Matthias Riemenschneider, Mercè Boada, Mikko Hiltunen, Eden R Martin, Reinhold Schmidt, Dan Rujescu, Li-San Wang, Jean-François Dartigues, Richard Mayeux, Christophe Tzourio, Albert Hofman, Markus M Nöthen, Caroline Graff, Bruce M Psaty, Lesley Jones, Jonathan L Haines, Peter A Holmans, Mark Lathrop, Margaret A Pericak-Vance, Lenore J Launer, Lindsay A Farrer, Cornelia M van Duijn, Christine Van Broeckhoven, Valentina Moskvina, Sudha Seshadri, Julie Williams, Gerard D Schellenberg & Philippe Amouyel: Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nature Genetics 2013 Notes: doi:10.1038/ng.2802.

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.

Paul Ryvkin, Yuk Yee Leung, Ian M. Silverman, Micah Childress, Otto Valladares, Isabelle Dragomir, Brian D. Gregory, and Li-San Wang: HAMR: High throughput Annotation of Modified Ribonucleotides. RNA 2013 Notes: in press.

Chiao-Feng Lin, Otto Valladares, D. Micah Childress, Egor Klevak, Evan T. Geller, Yih-Chii Hwang, Ellen A. Tsai, Gerard D. Schellenberg, and Li-San Wang: DRAW+SneakPeek: Analysis Workflow and Quality Metric Management for DNA-Seq Experiments. Bioinformatics August 2013 Notes: 10.1093/bioinformatics/btt422.

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.

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.

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.

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Last updated: 11/05/2014
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