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Faculty

Duke-NUS Centre for Computational Biology Faculty:



Steven George Rozen

Professor

Laboratory of Computational Systems Biology and Human Genetics

Email

Contact: 65164945

Steve Rozen's research has ranged over bioinformatics, human genetics & cancer genomics. Rozen founded and directs the Duke-NUS Centre for Computational Biology. The Centre's 5 regular-rank faculty have published > 250 scientific papers since 2013 and the Centre offers a PhD program in bioinformatics.

Rozen's own laboratory focuses on bioinformatics and cancer genomics, and is part of team-science efforts in cancer genomics that have led to multiple papers, including 5 in Nature Genetics. This research was also recognized by the American Association for Cancer Research (AACR) 2018 Team Science Award to the "Genomic Approaches to Preventing and Treating Asian-Prevalent Cancers Team" for work on aristolochic acid mutagenesis in liver and urinary tract cancers and for genomic studies of biliary tract cancers, lymphomas, and gastric cancers.

Within cancer genomics, the Rozen Lab studies alternative splicing, lncRNAs, and use of mutational signatures as tools for studying the molecular epidemiology of cancer. Rozen also created and maintains the widely-used Primer3 software for PCR primer design. Previously, he also worked extensively on identifying mutations in human Y chromosomes and their clinical consequences, as reported in multiple publications in Nature Genetics and Nature.

The Rozen laboratory also co-led a major study that used machine learning to computationally mine mutation data from almost 24,000 human cancer samples to identify 81 "mutational signatures" that will help reveal the origins and development of various types of cancer (published in Nature, 2020  https://doi.org/10.1038/s41586-020-1943-3).

 

Mutational signatures of cigarette smoking (blue, black, and red bars, top) and aristolochic acid (AA), a carcinogen in some herbal medicine (grey bars, bottom). The circles in the middle provide a partial view of which cancer types have which signatures – each column is a cancer type; each row is a signature.

LB Alexandrov, J Kim, NJ Haradhvala, MN Huang, AWT Ng, AB Boot, KR Covington, DA Gordenin, E Bergstrom, N Lopez-Bigas, LJ Klimczak, JR McPherson, S Morganella, S Sabarinathan, DA Wheeler, V Mustonen, the PCAWG Mutational Signatures Working Group, G Getz, SG Rozen*, MR Stratton*, PCAWG Consortium. "The repertoire of mutational signatures in human cancer" Nature 578 94-101, https://doi.org/10.1038/s41586-020-1943-3 (2020) (* = corresponding author) IF 43.07

J Zavadil, SG Rozen. "Experimental Delineation of Mutational Signatures Is an Essential Tool in Cancer Epidemiology and Prevention" Chemical Research in Toxicology, 32:2153-2155 (2019) IF 3.278

EN Bergstrom, MN Huang, U Mahto, M Barnes, MR Stratton, SG Rozen, LB Alexandrov. "SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events" BMC Genomics 20, doi: 10.1186/s12864-019-6041-2 (2019) IF 3.730

Y.S. Low, C. Bloecker, J.R. McPherson, S.A. Tang, Y.Y. Cheng, J.Y.S. Wong, C. Chua, T.K.H. Lim, C.L. Tang, M.H. Chew, P.T. Tan, I.B. Tan*, S.G. Rozen*, P.Y. Cheah*. "A formalin-fixed paraffin-embedded (FFPE)-based prognostic signature to predict metastasis in clinically low risk stage I/II microsatellite stable colorectal cancer" Cancer Lett 403:3-20 (2017) (* = corresponding author) IF 5.62

M.N. Huang, W. Yu, W.W. Teoh, M. Ardin, A. Jusakul, A. Ng, A. Boot, B. Abedi-Ardekani, S. Villar, S.S .Myint, R .Othman, S.L. Poon, A. Heguy, M. Olivier, M. Hollstein, P. Tan, B.T. Teh, K. Sabapathy, J. Zavadil, S. Rozen. "Genome-scale mutational signatures of aflatoxin in cells, mice and human tumors" Genome Res, doi:10.1101/gr.220038.116 (2017) IF 11.35

A. Jusakul, I. Cutcutache, C.H. Yong, J.Q. Lim, M.N. Huang, N. Padmanabhan, V. Nellore, S. Kongpetch, A.W.T. Ng, L.M. Ng, S.P. Choo, S.S. Myint, R. Thanan, S. Nagarajan, W.K. Lim, C.C.Y. Ng, A. Boot, M. Liu, C.K. Ong, V. Rajasegaran, S. Lie, AS-T Lim, T.H. Lim, J. Tan, M.J. Liang, J. Mcpherson, N. Khuntikeo, V. Bhudhisawasdi, P. Yongvanit, S. Wongkham, Y. Totoki, H. Nakamura, Y. Arai, S. Yamasaki, P. Chow, A.Y.F. Chung, L.L.P.J .Ooi, T. Lim, S. Dima, D. Duda, I. Popescu, P. Broet, S-Y Hsieh, M-C Yu, A. Scarpa, J. Lai, D. Luo, A.L. Carvalho, A. Vettore, H. Rhee, Y.N. Park, L. Alexandrov, R. Gordan*, S .Rozen*, T. Shibata*, C. Pairojkul*, B.T. Teh*, P. Tan*. "Whole-genome and epigenomic landscapes of etiologically distinct subtypes of cholangiocarcinoma" Cancer Discov, doi:10.1158/2159-8290.CD-17-0368 (2017) (* = corresponding author) IF 19.78

Y. Suzuki, S.B. Ng, C. Chua, W.Q. Leow, J. Chng, S.Y. Liu, K. Ramnarayanan, A. Gan, D.L. Ho, R. Ten, Y. Su, A. Lezhava, J. H. Lai, D. Koh, K.H. Lim, P. Tan, S.G Rozen*, I.B. Tan* "Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer" Mol Oncol doi:10.1002/1878-0261.12012 (2016) (* = corresponding author) IF 5.37

J. Tan, C.K. Ong, W.K. Lim, C.C.Y. Ng, A.A. Thike, L.M. Ng, V. Rajasegaran, S.S. Myint, S. Nagarajan, S. Thangaraju, S. Dey, N.D. Md Nasir, G.C. Wijaya, J.Q. Lim, D. Huang, Z. Li, B.H. Wong, J.Y.S. Chan, J.R. McPherson, I. Cutcutache, G. Poore, S.T. Tay, W.J. T. Tan, C. Putti, B.S. Ahmad, P. Iau, C.W. Chan, A.P.T. Tang, W.S. Yong, P. Madhukumar, G.H. Ho, V.K.M. Tan, C.Y. Wong, M. Hartman, K.W. Ong, B.K.T. Tan, S.G. Rozen*, P. Tan*, P.H. Tan*, B.T. Teh*. "Genomic landscapes of breast fibroepithelial tumors" Nat Genet 47:1341–1345 (2015) (* = corresponding author) IF 29.35

I. Cutcutache, A.Y. Wu, Y. Suzuki, J.R. McPherson, Z. Lei, N. Deng, S. Zhang, W.K. Wong, K.C. Soo, W.H. Chan, L.L. Ooi, R. Welsch, P. Tan, S.G. Rozen. "Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma" Gastric Cancer 1-13 (2015) IF 3.71

I. Cutcutache, Y. Suzuki, I. B. Tan, S. Ramgopal, S. Zhang, K. Ramnarayana, A. Gan, H.H. Lee, S.T. Tay, A. Ooi, C.K. Ong, J.T. Bolthouse, B.R. Lane, J.G. Anema, R.J. Kahnoski, P. Tan*, B.T. Teh*, S.G. Rozen*. "Exome-wide sequencing shows low mutation rates and identifies novel mutated genes in seminomas" Eur. Urol. 68(1):77-83 (2015) (* = corresponding author). Designated "Platinum Priority" and highlighted in a journal editorial. IF 13.93

S.L. Poon, M.N. Huang, Y. Choo, J.R. McPherson, W. Yu, H.L. Heng, A. Gan, S.S. Myint, E.Y. Siew, L.D. Ler, L.G. Ng, W.-H. Weng, C.-K. Chuang, J.S.P Yuen, S.-T. Pang*, P. Tan*, B.T. Teh*, S.G. Rozen*. "Mutation signatures implicate aristolochic acid in bladder cancer development" Genome Med. 7:38 (2015) (* = corresponding author) IF 4.94

W.K. Lim, C.K. Ong, J. Tan, A.A. Thike, C.C. Ng, V. Rajasegaran, S.S. Myint, S. Nagarajan, N.D. Nasir, J.R. McPherson, I. Cutcutache, G. Poore, S.T. Tay, W.S. Ooi, V.K. Tan, M. Hartman, K.W. Ong, B.K. Tan, S.G. Rozen*, P.H. Tan*, P. Tan*, B.T. Teh*. "Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma” Nat. Genet. 46:877-880 (2014) (* = corresponding author) IF 29.6

S.L. Poon, J.R. McPherson, P. Tan, B.T. Teh, S.G. Rozen. "Genome wide carcinogen signatures promise new opportunities for cancer prevention" Genome Med. (review) 6:24 (2014) IF 4.9

Z. Lei, I.B. Tan, K. Das, N. Deng, H. Zouridis, S. Pattison, C. Chua, Z. Feng, Y.K. Guan, C.H. Ooi, T. Ivanova, S. Zhang, M. Lee, J. Wu, A. Ngo, S. Manesh, E. Tan, B.T. Teh, J.B. Yan So, L.K. Goh, A. Boussioutas, T.K. Hon Lim, H. Flotow, P. Tan, S.G. Rozen. "Identification of molecular subtypes of gastric cancer with different responses to PI3-kinase Inhibitors and 5-fluorouracil” Gastroenterology 145:554-565 (2013) (received journal editorial) IF 13.9

S.L. Poon, S.-T. Pang*, J.R. McPherson, W. Yu, K.K. Huang, P. Guan, W.-H. Weng, E.Y. Siew, Y. Liu, H..L. Heng, S.C. Chong, A. Gan, S.T. Tay, W.K. Lim, I. Cutcutache, D. Huang, L.D. Ler, M.-L. Nairismägi, M.H. Lee, Y.-H. Chang, K.-J. Yu, W. Chan-on, B.-K. Li, Y.-F. Yuan, C.-N. Qian, K.-F. Ng, C.-F. Wu, C.-L. Hsu, R. M. Bunte, M.R. Stratton, P.A. Futreal, W.-K. Sung, C.-K. Chuang, C.K. Ong, S.G. Rozen*, P. Tan*, B.T. Teh* "Genome wide mutational signatures of aristolochic acid and its application as a screening tool. " Sci. Transl. Med. 5:197ra101 (2013) (Received journal cover image and focus article; also highlighted by Science Magazine and The Scientist; (* = corresponding author) IF 14.4

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B.C. Faircloth, M. Remm, S.G. Rozen. "Primer3 - New capabilities and interfaces” Nucleic Acids Res. 40:e115 (2012) IF 8.3