Contact Information

Course Outlines

HSCI3004 Genomics and Bioinformatics

HSCI7004 Healthcare Analytics

Advanced Genetics and Bioinformatics

Research Team
Siddharth SinhaPost-doctoral FellowN22-2027+853 8822
Shanmuga Priya BhaskaranResearch AssistantN22-2027+853 8822
Benjamin TAMResearch AssistantN22-2027+853 8822
Lei WANGResearch AssistantN22-2027+853 8822
Li ZHANGPhD StudentN22-2027+853 8822 4217
Xiaobing WUPhD StudentN22-2027+853 8822 4217
Xiaoyu WANGPhD StudentN22-2027+853 8822 4217
Maoni GUOPhD StudentN22-3008+853 8822 4217
Teng HUANGPhD StudentN22-3008+853 8822 4217
Zixin QINPhD StudentN22-2027+853 8822 4217
Jiasheng CHIANPhD StudentN22-2027+853 8822 4217
Jiaheng LIPhD StudentN22-2027+853 8822 4217
1996 – 1998Postdoctoral fellow, Laboratory of Dr. Janet Rowley, Department of Medicine, University of Chicago
1994 – 1996Postdoctoral fellow, laboratory of Dr. Richard Morimoto, Department of Molecular Sciences, Northwestern University
1989 — 1994Doctor of Medicine, Swiss Institute for Experimental Cancer Research (ISREC), University of Lausanne, Switzerland
1986 – 1989Assistant Researcher, Department of Immunology, Institute for Basic Research, China Academy of Traditional Chinese Medicine, Beijing, China
1983 — 1986Master of Medicine, Shandong Medical University, China
1978 — 1983Bachelor of Medicine, Jiangxi Medical College, China
2017 – presentProfessor, Faculty of Health Sciences, University of Macau
2010 – 2016Associate Professor, Department of Genetics, Cell Biology & Anatomy,
University of Nebraska Medical Center, Nebraska, USA
2008 – 2010Adjunct Professor, McCormick School of Engineering and Applied Science, Northwestern University, Illinois, USA
2004 – 2009Assistant Professor, Northwestern University;
Director, Center for Functional Genomics, ENH Research Institute, Illinois, USA
1998 – 2003Research Assistant Professor, Department of Medicine, University of Chicago, USA
Research Interests
  • Cancer genomics and genetics
  • Hereditary breast cancer
  • Next-generation DNA sequencing
  • Bioinformatics
  • Whole genome sequencing
  • Exome sequencing
  • Transcriptome
Representative Publications
  1. SM Wang, JD Rowley. A Strategy for Gene Identification: Integrated Procedure for Gene Identification. Proc. Natl. Acad. Sci. USA 95: 11909-11914, 1998
  2. J Chen, JD Rowley, SM Wang. Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proc. Natl. Acad. Sci. USA 97: 349-353, 2000
  3. SM Wang, SC Fears, L Zhang, J-J Chen, JD Rowley. Screening poly dA/dT(-) cDNAs for gene identification. Proc. Natl. Acad. Sci. USA 97:4162-4167, 2000. (Commentary by KJ Martin and AB Pardee. Identifying expressed genes. Proc. Natl. Acad. Sci. USA 97: 3789-3791, 2000)
  4. S Lee, G Zhou, T Clark, J Chen, JD Rowley, SM Wang. The pattern of gene expression in human CD15+ myeloid progenitor cells. Proc. Natl. Acad. Sci. USA 98: 3340-3345, 2001
  5. G Zhou, J Chen, S Lee, T Clark, JD Rowley, SM Wang. The pattern of gene expression in human CD34+ hematopoietic stem/progenitor cells. Proc. Natl. Acad. Sci. USA 98: 13966-13971, 2001
  6. D Nam, S Lee, G Zhou, X Cao, C Wang, J Chen, T Clark, JD Rowley, SM Wang. Oligo dT primer generates a high frequency of truncated cDNAs through internal poly A priming during reverse transcription. Proc. Natl. Acad. Sci. USA. 99: 6152-6156, 2002
  7. T Clark, S Lee, LR Scott, SM Wang. Computational analysis of gene identification with SAGE. Journal of Computational Biology 3: 513-526, 2002
  8. M Müschen, S Lee, G Zhou, N Feldhahn, VS Barath, J Chen, C Moers, M Krönke, JD Rowley, SM Wang. Molecular portraits of B cell lineage commitment. Proc. Natl. Acad. Sci. USA 99:10014-10019, 2002
  9. J Chen, M Sun, S Lee, G Zhou, JD Rowley, SM Wang. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc. Natl. Acad. Sci. USA 99: 12257-12262, 2002
  10. S Lee, J Bao, G Zhou, J Shapino, J Xu, RZ Shi, X Lu, T Clark, D Johnson, YC Kim, C Wing, C Tseng, M Sun, W Lin, J Wang, W Du, CI Wu, X Zhang, SM Wang. Detecting novel low-abundant transcripts in Drosophila. RNA 11: 939-946, 2005
  11. S Lee, J Chen, G Zhou, RZ Shi, G Bouffard, M Kocherginsky, X Ge, M Sun, N Jayathilaka, YC Kim, N Emmanuel, S Bohlander, M Minden, J Kline, O Ozer, R Larson, M LeBeau, E Green, J Trent, T Karrison, P Liu, SM Wang, JD Rowley. Gene Expression Profiles in Acute Myeloid Leukemia with Common Translocations using SAGE, Proc. Natl. Acad. Sci. USA 103: 1030-1035, 2006
  12. X Ge, Q Wu, YC Jung, J Chen, SM Wang. A large quantity of novel human antisense transcripts detected by LongSAGE. Bioinformatics. 22: 2475-2479, 2006. (“the Hot Paper in Computer Science” in 2008 by Essential Science Indicators of Thompson Scientific)
  13. S Lee, J Hwang, J Ulaszek, YC Kim, H Dong, HS Kim, JW Seok, BK Suh, SJ Yim, D Johnson, NH Choe, KT Chang, ZY Ryoo, CC Tseng, A Wickrema, SM Wang. Stable transcriptional status in the apoptotic erythroid genome. Biochem Biophys Res Commun. 359: 556-562, 2007
  14. SM Wang. Understanding SAGE data. Trends in Genetics 23: 42-50, 2007
  15. J Lu, Y Shen, Q Wu, S Kumar, B He, RW Carthew, SM Wang, CI Wu. The birth and death of microRNA genes in Drosophila. Nature Genetics 40: 351-355, 2008.
  16. J Chen, YC. Kim, Y-C Jung, Z Xuan, G Dworkin, Y Zhang, MQ Zhang, SM Wang. Scanning the human genome at kilobase resolution. Genome Research 18: 751-762, 2008
  17. Q Wu, YC Kim, J Lu, Z Xuan, J Chen, YL Zheng, T Zhou, MQ Zhang, CI Wu, SM Wang. Poly A- transcripts expressed in HeLa cells. PLoS ONE 3: e2803, 2008
  18. YC. Kim, Q Wu, J Chen, Z Xuan, Y-C Jung, MQ Zhang, JD Rowley, SM Wang. The transcriptome of human CD34+ hematopoietic stem-progenitor cells. Proc. Natl. Acad. Sci. USA 106: 8278-8283, 2009
  19. X Huang, H Guo, S Tammana, YC Jung, E Mellgren, P Bassi, L Ma, ZJ Tu, SC Ekker, X Wu, SM Wang, XZ Zhou. Gene Transfer Efficiency and Genome-Wide Integration Profiling of Sleeping Beauty, Tol2 and PiggyBac Transposons in Human Primary T Cells. Molecular Therapy. 18(10):1803-13, 2010
  20. 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, SM Wang. New fusion transcripts identified in normal karyotype acute myeloid leukemia. PLoS One 7:e51203, 2012
  21. Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, SM Wang. Can unknown predisposition in familial breast cancer be family-specific? The Breast Journal, 19:520-528, 2013
  22. COMPLEXO, Southey MC, Park DJ, Nguyen-Dumont T, Campbell I, Thompson E, Trainer AH, Chenevix-Trench G, Simard J, Dumont M, Soucy P, Thomassen M, Jønson L, Pedersen IS, Hansen TV, Nevanlinna H, Khan S, Sinilnikova O, Mazoyer S, Lesueur F, Damiola F, Schmutzler R, Meindl A, Hahnen E, Dufault MR, Chris Chan T, Kwong A, Barkardóttir R, Radice P, Peterlongo P, Devilee P, Hilbers F, Benitez J, Kvist A, Törngren T, Easton D, Hunter D, Lindstrom S, Kraft P, Zheng W, Gao YT, Long J, Ramus S, Feng BJ, Weitzel JN, Nathanson K, Offit K, Joseph V, Robson M, Schrader K, SM Wang, Kim YC, Lynch H, Snyder C, Tavtigian S, Neuhausen S, Couch FJ, Goldgar DE. COMPLEXO: identifying the missing heritability of breast cancer via next generation collaboration. Breast Cancer Res. 15(3):402, 2013
  23. Xiao F, Kim YC, Snyder C, Wen H, Chen PX, Luo J, Becirovic D, Downs B, Cowan KH, Lynch H, SM Wang. Genome instability in blood cells of a BRCA1+ breast cancer family. BMC Cancer 14:342, 2014.
  24. Wen H, Kim Y, Snyder C, Xiao F, Fleissner EA, Becirovic D, Luo J, Downs B, Sherman S, Cowan KH, Lynch HT, SM Wang. Family-specific, novel, deleterious germline variants provide a rich source to identify genetic predispositions for BRCAx familial breast cancer. BMC Cancer, 14:470, 2014.
  25. Lynch H, Synder C, SM Wang. Considerations for comprehensive assessment of genetic predisposition in familial breast cancer. Breast J. 21(1):67-75, 2015.
  26. Angulo-Ibáñez M, Rovira-Clavé X, Downs B, Kim YC, SM Wang, Tournier C, Reina M, Espel E. Erk5 contributes to balance cellular nucleotide levels and avoid replicative stress, Cell Cycle, 14(24):3864-76, 2015.
  27. Kim KC, Zhao L, Zhang H, Huang Y, Cui J, Xiao F, Downs F, SM Wang. Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients. Oncotarget 7(8):9600-12, 2016.
  28. Cui J, Luo L, KimYC, Synder C, Becirovic D, Downs B, Lynch H, SM Wang. Differences of variable number tandem repeats in XRCC5 promoter are associated with increased or decreased risk of familial breast cancer. Frontiers in Oncology, 6:00092, 2016.
  29. Zhang Y, Zhang Y, Geng L, Yi H, Huo W, Talmon G, Kim YC, SM Wang, Wang J. Transforming growth factor β mediates drug resistance by regulating expression of pyruvate dehydrogenase kinase 4 in colorectal cancer. JBC 291(33):17405-16, 2016.
  30. Kim YC, Cui J, Luo J, Xiao F, Downs B, Wang SM. Exome-based Variant Detection in Core Promoters. Sci Rep. 6:30716, 2016.

SAGE: Current Technologies and Applications. p1-375. Horizon Scientific Press, UK. Editor: SM Wang, 2005

Full Publications List
Research Grants
2017-2020Macau FDCT 085/2017/A2
Human genome core-promoter polymorphism and its application in cancer genome mutation studies.
2017-2020University of Macau Start-up Research Grant (SRG) – SRG2016-00097-FHS
Identification of key functional genes in genome instability caused by BRCA1 germline mutation.
2014 – 2016Eppley Cancer Institute grant (PI)
Middle East Breast Cancer Initiative (USD100,000)
2014 – 2016Eppley Cancer Institute grant (PI)
Genomics Study in a BRCA1+ Familial Breast Cancer Family (USD50,000)
2013 – 2015US National Institute of Health R21CA180008 (PI)
(PQD3) Genetic Basis of Breast Cancer Resistance in BRCA1+ Carrier (USD400,000)
2013 – 2014Eppley Cancer Institute grant (PI)
Identifying new germline mutation in familial breast cancer –phase 3 (USD50,000)
2012 – 2013University of Nebraska Global program (Co-PI)
UNMC and Beijing Genome Institute joint lymphoma genomics study (USD100,000)
2011 – 2012Eppley Cancer Institute grant (PI)
Identifying new germline mutation in familial breast cancer phase 1 (USD50,000)
2011 – 2012Leukemia Research Foundation (Co-PI)
Identification of driver mutation in peripheral T cell lymphoma (USD200,000)
2010 – 2016Nebraska University of Medical Center cancer genomics start-up grant (PI)(USD1,000,000)
2009 – 2012US National Institute of Health RC1 CA145889 (PI)
Comprehensive identification of fusion transcripts in leukemia (USD1,000,000)
2009 – 2012US National Institute of Health R01 GM83226 (Co-PI)
Large-scale expression analysis of natural antisense transcript (USD800,000)
2009 – 2010NorthShore University HealthSystem (co-PI)
Applying ditag genome scanning technology for genome-scale identification of breast cancer genetic mutation (USD50,000)
2009 – 2010Daniel F. and Ada L. Rice Foundation (PI)
Identifying new breast cancer susceptibility gene (USD100,000)
2007 – 2009NorthShore University HealthSystem grant (PI)
Career Development award (USD100,000)
2007 – 2008Guglielmi Fidelity Charitable Fund (PI)
Genetic Basis of CLL (USD50,000)
2006 – 2007Chicago Biomedical Consortium Catalyst Award (Co-PI)
Functions and Evolution of micro-RNAs (USD 200,000)
2005 – 2006Mazza Foundation (PI)
Identify genomic abnormalities in normal karyotype CLL (USD50,000)
2004 – 2010Evanston Northwestern Healthcare Foundation (PI)
Genomics Development Fund (USD1,400,000)
2003 – 2007US National Institute of Health R01 HG002600 (PI)
Identification of novel genes in human genome (USD1,300,000)
2002 – 2007US Department of Defense (Co-PI)
Bio-Effects of Radio Frequency for Homeland Defense (USD1,000,000)
2002 – 2004G. Harold and Lelia Y. Mathers Foundation (PI)
Identification of novel transcripts and novel genes in normal hematopoietic cells and acute myeloid leukemic cells (USD600,000)
1998 – 2000US National Institute of Health (R21 CA78862, Co-PI)
Develop 3’ SSH/SAGE technique for Gene Identification (USD400,000)
1998 – 1999American Cancer Society (IRG-58-004-40-IRG, PI)
Genome-wide identification of abnormally expressed genes in leukemia with MLL-AF9 fusion (USD30,000)
Professional Activities

  • Journal of Genetic Mutation Disorders (Editorial board member, 2015 –)
  • Advances in Modern Oncology Research (Editorial board member, 2015 –)
  • Journal of Medical Genomics & Biomarkers (Editorial board member, 2015 –)
  • Clinics in Oncology (Editorial board member, 2015 –)
  • microRNA (2014 –)
  • Methods in Next-Generation Sequencing (Editor 2013 – 2014)
Advisory board member

  • The Kamie K. Preston Hereditary Cancer Foundation, Board of Directors. (2015 –)
Journal reviewer
Analytical Biochemistry, Biochemistry Research International, Bioinformatics, BioTechniques, BMC Cancer, BMC Developmental Biology, BMC Evolutionary Biology, BMC Genomics, BMC Bioinformatics, BMC Medical Genetics, BMC Medical Genomics, Case Reports in Obstetrics and Gynecology, Cell Cycles, Cell Death and Differentiation, Current Medicinal Chemistry, Cancer Genetics, Cancer Biomarkers, Cancer Medicine, Differentiation, Experimental Hematology, Familial Cancer, The Breast Journal, FEBS Letters, Gene, Genes, Chromosomes & Cancer, Genome Biology, Genetics, Genome Research, Genomics, In Silico Bioinformatics, Insect MicroRNAs, Molecular Biology, Journal of Africa Biotechnology, Journal of Biology, Journal of Biotechnology, Journal of Biomedicine and Biotechnology, Molecular Pharmacology, Nature, Nature Biotechnology, Nature Communication, Nature Methods, Nature Review of Genetics, Nature Protocol, Neurotoxicity Research, Nucleic Acid Research, Oncogene, Oncotarget, Pathology – Research and Practice, Physiological Genomics, PLOS One, PNAS, Proteomics, Science, Stem Cell
Conference organization committee

  • 3rd World Congress and Expo on Oncology & Radiology, San Francisco, 2017
  • 2nd International Conference on Transcriptomics, Orlando, 2016
  • 20th International Conference on Intelligent System for Computational Biology and 11th European Conference on Computational Biology, 2013
  • 19th International Conference on Intelligent System for Computational Biology and 10th European Conference on Computational Biology, 2011
  • The 9th European Conference on Computational Biology 2010, Section of Gene Regulation and Transcriptomics, Ghent, Belgium, 2010
  • The 16th Annual International Conference on Intelligent Systems for Molecular Biology, Toronto, Canada. 2008
  • The 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Vienna, Austria. 2007
Visiting Professorship

  • Visiting Professor, Shandong University (2004 –)
  • Visiting Professor, Beijing Institute of Genomics, Chinese Academy of Sciences (2002 –)
Postdoctoral fellows trained
Graduate students trained
12 (MS), PhD (4)