Jiangxi Medical College, China (Bachelor of Medicine)
Shandong Medical University, China (Master of Medicine)
Swiss Institute for Experimental Cancer Research, University of Lausanne, Switzerland (M.D.)
Richard Morimoto laboratory of Northwestern University (Postdoctoral fellow)
Janet Rowley laboratory of University of Chicago (Postdoctoral fellow)
My research interest is in genomics. The rapid progress of genomics science in recent years has made revolutionary impact on biology and medicine studies. Analyzing life process at genome level provides systems information to understand the basis of physiology, and to study diseases. In the past years, I have been working on multiple genomics topics, as exemplified by the followings:
Gene expression reflects biological activities of the genome under physiological or pathological conditions. In the past years, we used SAGE (serial analysis of gene expression)-based approach to study transcriptome extensively, covering the area of annotating the transcribed regions in the human, Drosophila and rice genomes, gene expression in human hematopoiesis including stem/progenitor cells, pre-B cells, pre-T cells, myeloid progenitors, NK progenitors, erythroid progenitors, and myeloid leukemia with major chromosomal abnormalities. Currently, we are performing an ARRA RC1 grant-funded large-scale study to identify fusion genes in leukemia.
Genome structural studies
Genetic abnormalities include insertion, deletion, amplification and translocation and SNPs. Comprehensive mapping these changes are essential to reveal the genetic basis of diseases. Currently, we are actively exploring the potential of using next-generation DNA sequencing technologies for high-resolution analysis of genome structure in inherited diseases and cancer genome.
Developing genomics technologies
With the large size and high complexity of the genomes, genomics study relies heavily on the use of technologies with high-throughput capacity for information acquisition and the use of computational tools for data interpretation. We have developed next-generation DNA sequencing-based technologies (454, Illumina platforms) for genome structural and transcriptome studies. We are also developing bioinformatics tools for large-scale genome data collection, analysis and interpretation.
My study has been supported by grants from the National Human Genome Research Institute, National Cancer Institute of National Institute of Health, the Department of Defense, and multiple private foundations.
- Wang SM, Fears SC, Zhang L, Chen JJ, Rowley JD. Screening poly dA/dT(-) cDNAs for gene identification. Proc. Natl. Acad. Sci. USA 97:4162-4167, 2000
- Müschen M, Lee S, Zhou G, Feldhahn N, Barath VS, Chen J, Moers C, Krönke M, Rowley JD, Wang SM. Molecular portraits of B cell lineage commitment. Proc. Natl. Acad. Sci. USA 99:10014-10019, 2002
- Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl. Acad. Sci. USA 99:12257-12262, 2002
- Lee S, Bao J, Zhou G, Shapiro J, Xu J, Shi RZ, Lu X, Clark T, Johnson D, Kim YC, Wing C, Tseng C, Sun M, Lin W, Wang J, Yang H, Wang J, Du W, Wu CI, Zhang X, Wang SM. Detecting novel low-abundant transcripts in Drosophila. RNA 11:939-946, 2005
- Bao J, Lee S, Chen C, Zhang X, Zhang Y, Liu S, Clark T, Wang J, Cao M, Yang H, Wang SM, Yu J. Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiology, 138:1216-1231, 2005
- Lee S, Johnson D, Dunbar K, Dong H, Ge X, Kim YC, Wing C, Jayathilaka N, Emmanuel N, Zhou CQ, Gerber HL, Tseng CC, Wang SM. 2.45 GHz Radiofrequency fields alter gene expression in cultured human cells. FEBS Letters 579:4829-4836, 2005
- SAGE: Current Technologies and Applications. p1-375. Horizon Scientific Press, UK. Editor: Wang SM, 2005
- Lee S, Chen J, Zhou G, Shi RZ, Bouffard GG, Kocherginsky M, Ge X, Sun M, Jayathilaka N, Kim YC, Emmanuel N, Bohlander SK, Minden M, Kline J, Ozer O, Larson RA, LeBeau MM, Green ED, Trent J, Karrison T, Liu PP, Wang SM, Rowley JD. Gene Expression Profiles in Acute Myeloid Leukemia with Common Translocations using SAGE, Proc. Natl. Acad. Sci. USA 103:1030-1035, 2006
- Ge X, Wu Q, Jung YC, Chen J, Wang SM. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics. 22: 2475-2479, 2006. (“the Hot Paper in Computer Science” assigned by Thompson Scientific in 2008)
- Wang SM. Understanding SAGE data. Trends in Genetics 23:42-50, 2007
- Lu J, Shen Y, Wu Q, Kumar S, He B, Shi S, Carthew RW, Wang SM, Wu CI. The birth and death of microRNA genes in Drosophila. Nature Genetics 40:351-355, 2008.
- Chen J, Kim YC, Jung YC, Xuan Z, Dworkin G, Zhang Y, Zhang MQ, Wang SM. Scanning the human genome at kilobase resolution. Genome Research 18:751-762, 2008
- Wu Q, Kim YC, Lu J, Xuan Z, Chen J, Zheng Y, Zhou T, Zhang MQ, Wu CI, Wang SM. Poly A- transcripts expressed in HeLa cells. PLoS ONE 3:e2803. 2008
- Kim YC, Wu Q, Chen J, Xuan Z, Jung YC, Zhang MQ, Rowley JD, Wang SM. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc. Natl. Acad. Sci. USA 106:8278-8283, 2009
- Kim YC, Jung YC, Chen J, Alhasan AH, Kaewsaard P, Zhang Y, Ma S, Rosen S, Wang SM. Evidence for widely presence of genomic aberrations in chronic lymphocytic leukemia. BMC Research Notes 3:341, 2010
- Wen H, Li Y, Malek SN, Kim YC, Xu J, Chen P, Xiao F, Huang X, Zhou X, Xuan Z, Mankala S, Hou G, Rowley JD, Zhang MQ, Wang SM. New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One. 7:e51203., 2012
- Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, Wang SM. Can unknown predisposition in familial breast cancer be family-specific? The Breast Journal, 2013 (in press)