Scholars@Duke

• Background
• 

  Education, Training, & Certifications

  • Ph.D., New York University 1993
• 

  Previous Appointments & Affiliations

  • Associate Professor of Psychiatry and Behavioral Sciences, Psychiatry & Behavioral Sciences, Clinical Science Departments 2013 - 2020
  • Associate Professor of Psychiatry and Behavioral Sciences, Psychiatry & Behavioral Sciences, Clinical Science Departments 2010 - 2013
  • Instructor, Temporary of Medical Psychology in the Department of Psychiatry and Behavioral Sciences, Psychiatry & Behavioral Sciences, Clinical Science Departments 2008 - 2010
• Recognition
• 

  In the News

  • NOV 4, 2013

    Duke Today

    Duke-NUS Scientists Advance Research on Bile Duct Cancers

  • AUG 27, 2013

    Duke Today

    Three Subtypes of Gastric Cancer Suggest Different Treatment Approaches
• Research
• 

  Selected Grants

  • The Molecular Genetics of High Myopia awarded by National Institutes of Health 2003 - 2014
  • Metabolic Signatures for Alzheimer's Disease awarded by National Institutes of Health 2007 - 2011
• 

  External Relationships

  • Duke-National University of Singapore
• Publications & Artistic Works
• 

  Selected Publications

  • Academic Articles

    • Tan, Yu G., Yan M. Law, Nye T. Ngo, Li Y. Khor, Puay H. Tan, Enya H. W. Ong, John S. P. Yuen, et al. “Patient-reported functional outcomes and oncological control after primary focal cryotherapy for clinically significant prostate cancer: A Phase II mandatory biopsy-monitored study.” Prostate 83, no. 8 (June 2023): 781–91. https://doi.org/10.1002/pros.24517.
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    • Liu, Mo, Yang Wu, Nanhai Jiang, Arnoud Boot, and Steven G. Rozen. “mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery.” Nar Genom Bioinform 5, no. 1 (March 2023): lqad005. https://doi.org/10.1093/nargab/lqad005.
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    • Alexandrov, Ludmil B., Jaegil Kim, Nicholas J. Haradhvala, Mi Ni Huang, Alvin Wei Tian Ng, Yang Wu, Arnoud Boot, et al. “Author Correction: The repertoire of mutational signatures in human cancer.” Nature 614, no. 7948 (February 2023): E41. https://doi.org/10.1038/s41586-022-05600-5.
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    • Islam, SM Ashiqul, Marcos Díaz-Gay, Yang Wu, Mark Barnes, Raviteja Vangara, Erik N. Bergstrom, Yudou He, et al. “Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor.” Cell Genom 2, no. 11 (November 9, 2022): None. https://doi.org/10.1016/j.xgen.2022.100179.
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    • Terlouw, Diantha, Frederik J. Hes, Manon Suerink, Arnoud Boot, Alexandra M. J. Langers, Carli M. Tops, Monique E. van Leerdam, et al. “APC mosaicism, not always isolated: two first-degree relatives with apparently distinct APC mosaicism.” Gut, October 28, 2022. https://doi.org/10.1136/gutjnl-2022-328540.
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    • Lim, Jing Quan, Dachuan Huang, Jason Yongsheng Chan, Yurike Laurensia, Esther Kam Yin Wong, Daryl Ming Zhe Cheah, Burton Kuan Hui Chia, et al. “A genomic-augmented multivariate prognostic model for the survival of natural-killer/T-cell lymphoma patients from an international cohort.” Am J Hematol 97, no. 9 (September 2022): 1159–69. https://doi.org/10.1002/ajh.26636.
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    • Ling, Li, Fangfang Li, Pinglan Yang, Robert D. Oates, Sherman Silber, Cornelia Kurischko, Francis C. Luca, et al. “Genetic characterization of a missense mutation in the X-linked TAF7L gene identified in an oligozoospermic man†.” Biol Reprod 107, no. 1 (July 25, 2022): 157–67. https://doi.org/10.1093/biolre/ioac093.
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    • Assante, Gabriella, Sriram Chandrasekaran, Stanley Ng, Aikaterini Tourna, Carolina H. Chung, Kowsar A. Isse, Jasmine L. Banks, et al. “Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease.” Genome Med 14, no. 1 (June 23, 2022): 67. https://doi.org/10.1186/s13073-022-01071-5.
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    • Boot, Arnoud, Mo Liu, Nicole Stantial, Viraj Shah, Willie Yu, Karin C. Nitiss, John L. Nitiss, Sue Jinks-Robertson, and Steven G. Rozen. “Recurrent mutations in topoisomerase IIα cause a previously undescribed mutator phenotype in human cancers.” Proc Natl Acad Sci U S A 119, no. 4 (January 25, 2022). https://doi.org/10.1073/pnas.2114024119.
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    • Wu, Yang, Ellora Hui Zhen Chua, Alvin Wei Tian Ng, Arnoud Boot, and Steven G. Rozen. “Accuracy of mutational signature software on correlated signatures.” Sci Rep 12, no. 1 (January 10, 2022): 390. https://doi.org/10.1038/s41598-021-04207-6.
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    • Bylstra, Yasmin, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R Ryanne Wu, Jing Xian Teo, Sonia Davila, et al. “Correction to: Family history assessment significantly enhances delivery of precision medicine in the genomics era.” Genome Med 13, no. 1 (July 5, 2021): 109. https://doi.org/10.1186/s13073-021-00916-9.
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    • Padmanabhan, Nisha, Huang Kie Kyon, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, et al. “Author Correction: Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation.” Genome Biol 22, no. 1 (June 17, 2021): 181. https://doi.org/10.1186/s13059-021-02405-z.
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    • Padmanabhan, Nisha, Huang Kie Kyon, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, et al. “Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation.” Genome Biol 22, no. 1 (June 1, 2021): 167. https://doi.org/10.1186/s13059-021-02375-2.
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    • Wang, C., J. R. McPherson, L. H. Zhang, S. Rozen, and K. Sabapathy. “Corrigendum to "Transcription-associated mutation of lasR in Pseudomonas aeruginosa".” Dna Repair (Amst) 100 (April 2021): 103073. https://doi.org/10.1016/j.dnarep.2021.103073.
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    • Campbell, Benjamin R., Zhishan Chen, Daniel L. Faden, Nishant Agrawal, Ryan J. Li, Glenn J. Hanna, N Gopalakrishna Iyer, et al. “The mutational landscape of early- and typical-onset oral tongue squamous cell carcinoma.” Cancer 127, no. 4 (February 15, 2021): 544–53. https://doi.org/10.1002/cncr.33309.
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    • Liu, Mo, Arnoud Boot, Alvin W. T. Ng, Raluca Gordân, and Steven G. Rozen. “Mutational processes in cancer preferentially affect binding of particular transcription factors.” Sci Rep 11, no. 1 (February 8, 2021): 3339. https://doi.org/10.1038/s41598-021-82910-0.
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    • Thean, Lai Fun, Christopher Blöcker, Hui Hua Li, Michelle Lo, Michelle Wong, Choong Leong Tang, Emile K. W. Tan, Steven G. Rozen, and Peh Yean Cheah. “Enhancer-derived long non-coding RNAs CCAT1 and CCAT2 at rs6983267 has limited predictability for early stage colorectal carcinoma metastasis.” Sci Rep 11, no. 1 (January 11, 2021): 404. https://doi.org/10.1038/s41598-020-79906-7.
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    • Bylstra, Yasmin, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R Ryanne Wu, Jing Xian Teo, Sonia Davila, et al. “Family history assessment significantly enhances delivery of precision medicine in the genomics era.” Genome Med 13, no. 1 (January 7, 2021): 3. https://doi.org/10.1186/s13073-020-00819-1.
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    • Bailey, Matthew H., William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, et al. “Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.” Nat Commun 11, no. 1 (November 30, 2020): 6232. https://doi.org/10.1038/s41467-020-20128-w.
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    • Chan, Jason Yongsheng, Jing Quan Lim, Joe Yeong, Vinod Ravi, Peiyong Guan, Arnoud Boot, Timothy Kwang Yong Tay, et al. “Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma.” J Clin Invest 130, no. 11 (November 2, 2020): 5833–46. https://doi.org/10.1172/JCI139080.
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    • Rozen, Steven G. “Mutational selection in normal urothelium.” Science 370, no. 6512 (October 2, 2020): 34–35. https://doi.org/10.1126/science.abe0955.
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    • Bailey, Matthew H., William U. Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, et al. “Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.” Nat Commun 11, no. 1 (September 21, 2020): 4748. https://doi.org/10.1038/s41467-020-18151-y.
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    • Li, Constance H., Stephenie D. Prokopec, Ren X. Sun, Fouad Yousif, Nathaniel Schmitz, Nathaniel PCAWG Tumour Subtypes and Clinical Translation, Paul C. Boutros, and Paul C. PCAWG Consortium. “Sex differences in oncogenic mutational processes.” Nat Commun 11, no. 1 (August 28, 2020): 4330. https://doi.org/10.1038/s41467-020-17359-2.
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    • Ray, Debleena, Yu Chye Yun, Muhammad Idris, Shanshan Cheng, Arnoud Boot, Tan Bee Huat Iain, Steven G. Rozen, Patrick Tan, and David M. Epstein. “A tumor-associated splice-isoform of MAP2K7 drives dedifferentiation in MBNL1-low cancers via JNK activation.” Proc Natl Acad Sci U S A 117, no. 28 (July 14, 2020): 16391–400. https://doi.org/10.1073/pnas.2002499117.
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    • Sinnakannu, Joanna R., Kian Leong Lee, Shanshan Cheng, Jia Li, Mengge Yu, Siew Peng Tan, Clara Chong Hui Ong, et al. “SRSF1 mediates cytokine-induced impaired imatinib sensitivity in chronic myeloid leukemia.” Leukemia 34, no. 7 (July 2020): 1787–98. https://doi.org/10.1038/s41375-020-0732-1.
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    • Cheng, Shanshan, Debleena Ray, Raymond Teck Ho Lee, Kishore Babu Naripogu, Permeen Akhtar Bt Mohamed Yusoff, Pamela Bee Leng Goh, Yujing Liu, et al. “A functional network of gastric-cancer-associated splicing events controlled by dysregulated splicing factors.” Nar Genom Bioinform 2, no. 2 (June 2020): lqaa013. https://doi.org/10.1093/nargab/lqaa013.
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    • Boot, Arnoud, Alvin W. T. Ng, Fui Teen Chong, Szu-Chi Ho, Willie Yu, Daniel S. W. Tan, N Gopalakrishna Iyer, and Steven G. Rozen. “Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types.” Genome Res 30, no. 6 (June 2020): 803–13. https://doi.org/10.1101/gr.255620.119.
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    • Ooi, Wen Fong, Amrita M. Nargund, Kevin Junliang Lim, Shenli Zhang, Manjie Xing, Amit Mandoli, Jing Quan Lim, et al. “Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma.” Gut 69, no. 6 (June 2020): 1039–52. https://doi.org/10.1136/gutjnl-2018-317612.
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    • Xing, Manjie, Wen Fong Ooi, Jing Tan, Aditi Qamra, Po-Hsien Lee, Zhimei Li, Chang Xu, et al. “Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.” J Clin Invest 130, no. 6 (June 1, 2020): 3005–20. https://doi.org/10.1172/JCI126726.
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    • Kongpetch, Sarinya, Apinya Jusakul, Jing Quan Lim, Cedric Chuan Young Ng, Jason Yongsheng Chan, Vikneswari Rajasegaran, Tse Hui Lim, et al. “Lack of Targetable FGFR2 Fusions in Endemic Fluke-Associated Cholangiocarcinoma.” Jco Glob Oncol 6 (April 2020): 628–38. https://doi.org/10.1200/GO.20.00030.
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    • Wang, Xiang-Ming, Yang Lu, Yi-Meng Song, Jun Dong, Ruo-Yan Li, Guo-Liang Wang, Xu Wang, et al. “Integrative genomic study of Chinese clear cell renal cell carcinoma reveals features associated with thrombus.” Nat Commun 11, no. 1 (February 6, 2020): 739. https://doi.org/10.1038/s41467-020-14601-9.
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    • ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, R. “Pan-cancer analysis of whole genomes.” Nature 578, no. 7793 (February 2020): 82–93. https://doi.org/10.1038/s41586-020-1969-6.
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    • Bylstra, Yasmin, Weng Khong Lim, Sylvia Kam, Koei Wan Tham, R Ryanne Wu, Jing Xian Teo, Sonia Davila, et al. “Family History Assessment Significantly Enhances Delivery of Precision Medicine in the Genomics Era,” January 30, 2020. https://doi.org/10.1101/2020.01.29.926139.
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    • Boot, Arnoud, Nanhai Jiang, and Steven G. Rozen. “Toward clinical understanding of aristolochic acid upper-tract urothelial carcinoma.” Theranostics 10, no. 12 (2020): 5578–80. https://doi.org/10.7150/thno.46489.
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    • Boot, Arnoud, and Steven Rozen. “Recurrent mutations in topoisomerase 2a cause a novel mutator phenotype in human cancers,” 2020. https://doi.org/10.1101/2020.05.22.111666.
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    • Bylstra, Y., S. Davila, W. K. Lim, R. Wu, J. X. Teo, S. Kam, T. Lysaght, et al. “Implementation of genomics in medical practice to deliver precision medicine for an Asian population.” Npj Genomic Medicine 4, no. 1 (December 1, 2019). https://doi.org/10.1038/s41525-019-0085-8.
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    • Sundar, Raghav, Alvin Ng, Hermioni Zouridis, Nisha Padmanabhan, Taotao Sheng, Shenli Zhang, Ming Hui Lee, et al. “DNA epigenetic signature predictive of benefit from neoadjuvant chemotherapy in oesophageal adenocarcinoma: results from the MRC OE02 trial.” Eur J Cancer 123 (December 2019): 48–57. https://doi.org/10.1016/j.ejca.2019.09.016.
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    • Zavadil, Jiri, and Steven G. Rozen. “Experimental Delineation of Mutational Signatures Is an Essential Tool in Cancer Epidemiology and Prevention.” Chem Res Toxicol 32, no. 11 (November 18, 2019): 2153–55. https://doi.org/10.1021/acs.chemrestox.9b00339.
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    • Teo, Jing Xian, Sonia Davila, Chengxi Yang, An An Hii, Chee Jian Pua, Jonathan Yap, Swee Yaw Tan, et al. “Digital phenotyping by consumer wearables identifies sleep-associated markers of cardiovascular disease risk and biological aging.” Commun Biol 2, no. 1 (October 4, 2019): 361. https://doi.org/10.1038/s42003-019-0605-1.
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    • Bergstrom, Erik N., Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R. Stratton, Steven G. Rozen, and Ludmil B. Alexandrov. “SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events.” Bmc Genomics 20, no. 1 (August 30, 2019): 685. https://doi.org/10.1186/s12864-019-6041-2.
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    • Xue, Ruidong, Lu Chen, Chong Zhang, Masashi Fujita, Ruoyan Li, Shu-Mei Yan, Choon Kiat Ong, et al. “Genomic and Transcriptomic Profiling of Combined Hepatocellular and Intrahepatic Cholangiocarcinoma Reveals Distinct Molecular Subtypes.” Cancer Cell 35, no. 6 (June 10, 2019): 932-947.e8. https://doi.org/10.1016/j.ccell.2019.04.007.
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    • Zhivagui, Maria, Alvin W. T. Ng, Maude Ardin, Mona I. Churchwell, Manuraj Pandey, Claire Renard, Stephanie Villar, et al. “Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans.” Genome Res 29, no. 4 (April 2019): 521–31. https://doi.org/10.1101/gr.242453.118.
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    • Teo, Jing Xian, Sonia Davila, Chengxi Yang, An An Hii, Chee Jian Pua, Jonathan Yap, Swee Yaw Tan, et al. “Digital phenotyping by consumer wearables identifies sleep-associated markers of cardiovascular disease risk and biological aging.” Commun Biol 2 (2019): 361. https://doi.org/10.1038/s42003-019-0605-1.
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    • Bergstrom, Erik, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael Stratton, Steven Rozen, and Ludmil Alexandrov. “SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events,” 2019. https://doi.org/10.1101/653097.
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    • Bylstra, Yasmin, Jyn Ling Kuan, Weng Khong Lim, Jaydutt Digambar Bhalshankar, Jing Xian Teo, Sonia Davila, Bin Tean Teh, et al. “Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders.” Genet Med 21, no. 1 (January 2019): 207–12. https://doi.org/10.1038/s41436-018-0008-6.
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    • Bylstra, Yasmin, Jyn Ling Kuan, Weng Khong Lim, Jaydutt Digambar Bhalshankar, Jing Xian Teo, Sonia Davila, Bin Tean Teh, et al. “Correction: Population genomics in South East Asia captures unexpectedly high carrier frequency for treatable inherited disorders.” Genet Med 20, no. 12 (December 2018): 1692. https://doi.org/10.1038/s41436-018-0142-1.
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    • Boot, Arnoud, Mi Ni Huang, Alvin W. T. Ng, Szu-Chi Ho, Jing Quan Lim, Yoshiiku Kawakami, Kazuaki Chayama, Bin Tean Teh, Hidewaki Nakagawa, and Steven G. Rozen. “In-depth characterization of the cisplatin mutational signature in human cell lines and in esophageal and liver tumors.” Genome Res 28, no. 5 (May 2018): 654–65. https://doi.org/10.1101/gr.230219.117.
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    • Tang, Yew Chung, Szu-Chi Ho, Elisabeth Tan, Alvin Wei Tian Ng, John R. McPherson, Germaine Yen Lin Goh, Bin Tean Teh, Frederic Bard, and Steven G. Rozen. “Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer.” Breast Cancer Res 20, no. 1 (March 22, 2018): 22. https://doi.org/10.1186/s13058-018-0949-3.
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    • Thekkeparambil Chandrabose, Srijaya, Sandhya Sriram, Subha Subramanian, Shanshan Cheng, Wee Kiat Ong, Steve Rozen, Noor Hayaty Abu Kasim, and Shigeki Sugii. “Amenable epigenetic traits of dental pulp stem cells underlie high capability of xeno-free episomal reprogramming.” Stem Cell Res Ther 9, no. 1 (March 20, 2018): 68. https://doi.org/10.1186/s13287-018-0796-2.
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    • Lim, Weng Khong, Sonia Davila, Jing Xian Teo, Chengxi Yang, Chee Jian Pua, Christopher Blöcker, Jing Quan Lim, et al. “Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research.” Plos Biol 16, no. 2 (February 2018): e2004285. https://doi.org/10.1371/journal.pbio.2004285.
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    • Huang, Kie Kyon, Kalpana Ramnarayanan, Feng Zhu, Supriya Srivastava, Chang Xu, Angie Lay Keng Tan, Minghui Lee, et al. “Genomic and Epigenomic Profiling of High-Risk Intestinal Metaplasia Reveals Molecular Determinants of Progression to Gastric Cancer.” Cancer Cell 33, no. 1 (January 8, 2018): 137-150.e5. https://doi.org/10.1016/j.ccell.2017.11.018.
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    • Yan, TingDong, Wen Fong Ooi, Aditi Qamra, Alice Cheung, DongLiang Ma, Gopinath Meenakshi Sundaram, Chang Xu, et al. “HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis.” Nat Commun 9, no. 1 (January 8, 2018): 100. https://doi.org/10.1038/s41467-017-02601-1.
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    • Teh, Bin Tean, Kevin Lim, Chern Han Yong, Cedric Chuan Young Ng, Sushma Ramesh Rao, Vikneswari Rajasegaran, Weng Khong Lim, et al. “The draft genome of tropical fruit durian (Durio zibethinus).” Nat Genet 49, no. 11 (November 2017): 1633–41. https://doi.org/10.1038/ng.3972.
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    • Yao, Xiaosai, Jing Tan, Kevin Junliang Lim, Joanna Koh, Wen Fong Ooi, Zhimei Li, Dachuan Huang, et al. “VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma.” Cancer Discov 7, no. 11 (November 2017): 1284–1305. https://doi.org/10.1158/2159-8290.CD-17-0375.
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    • Ng, Alvin W. T., Song Ling Poon, Mi Ni Huang, Jing Quan Lim, Arnoud Boot, Willie Yu, Yuka Suzuki, et al. “Aristolochic acids and their derivatives are widely implicated in liver cancers in Taiwan and throughout Asia.” Sci Transl Med 9, no. 412 (October 18, 2017). https://doi.org/10.1126/scitranslmed.aan6446.
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    • Jusakul, Apinya, Ioana Cutcutache, Chern Han Yong, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Vishwa Nellore, et al. “Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.” Cancer Discov 7, no. 10 (October 2017): 1116–35. https://doi.org/10.1158/2159-8290.CD-17-0368.
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    • Low, Yee Syuen, Christopher Blöcker, John R. McPherson, See Aik Tang, Ying Ying Cheng, Joyner Y. S. Wong, Clarinda Chua, et al. “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 (September 10, 2017): 13–20. https://doi.org/10.1016/j.canlet.2017.05.031.
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    • Huang, Mi Ni, Willie Yu, Wei Wei Teoh, Maude Ardin, Apinya Jusakul, Alvin Wei Tian Ng, Arnoud Boot, et al. “Genome-scale mutational signatures of aflatoxin in cells, mice, and human tumors.” Genome Res 27, no. 9 (September 2017): 1475–86. https://doi.org/10.1101/gr.220038.116.
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    • Li, Xinjian, Willie Yu, Xu Qian, Yan Xia, Yanhua Zheng, Jong-Ho Lee, Wei Li, et al. “Nucleus-Translocated ACSS2 Promotes Gene Transcription for Lysosomal Biogenesis and Autophagy.” Mol Cell 66, no. 5 (June 1, 2017): 684-697.e9. https://doi.org/10.1016/j.molcel.2017.04.026.
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    • Qamra, Aditi, Manjie Xing, Nisha Padmanabhan, Jeffrey Jun Ting Kwok, Shenli Zhang, Chang Xu, Yan Shan Leong, et al. “Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma.” Cancer Discov 7, no. 6 (June 2017): 630–51. https://doi.org/10.1158/2159-8290.CD-16-1022.
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    • Alok, Anshula, Zhengdeng Lei, N Suhas Jagannathan, Simran Kaur, Nathan Harmston, Steven G. Rozen, Lisa Tucker-Kellogg, and David M. Virshup. “Wnt proteins synergize to activate β-catenin signaling.” J Cell Sci 130, no. 9 (May 1, 2017): 1532–44. https://doi.org/10.1242/jcs.198093.
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    • Ler, Lian Dee, Sujoy Ghosh, Xiaoran Chai, Aye Aye Thike, Hong Lee Heng, Ee Yan Siew, Sucharita Dey, et al. “Loss of tumor suppressor KDM6A amplifies PRC2-regulated transcriptional repression in bladder cancer and can be targeted through inhibition of EZH2.” Sci Transl Med 9, no. 378 (February 22, 2017). https://doi.org/10.1126/scitranslmed.aai8312.
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    • Suzuki, Yuka, Sarah Boonhsi Ng, Clarinda Chua, Wei Qiang Leow, Jermain Chng, Shi Yang Liu, Kalpana Ramnarayanan, et al. “Multiregion ultra-deep sequencing reveals early intermixing and variable levels of intratumoral heterogeneity in colorectal cancer.” Mol Oncol 11, no. 2 (February 2017): 124–39. https://doi.org/10.1002/1878-0261.12012.
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    • Ng, Sarah B., Clarinda Chua, Matthew Ng, Anna Gan, Polly Sy Poon, Melissa Teo, Cherylin Fu, et al. “Individualised multiplexed circulating tumour DNA assays for monitoring of tumour presence in patients after colorectal cancer surgery.” Sci Rep 7 (January 19, 2017): 40737. https://doi.org/10.1038/srep40737.
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    • Tompson, Stuart W., Charles Johnson, Diana Abbott, Benjamin Bakall, Vincent Soler, Tammy L. Yanovitch, Kristina N. Whisenhunt, et al. “Reduced penetrance in a large Caucasian pedigree with Stickler syndrome.” Ophthalmic Genet 38, no. 1 (2017): 43–50. https://doi.org/10.1080/13816810.2016.1275018.
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    • Huang, Kie Kyon, John R. McPherson, Su Ting Tay, Kakoli Das, Iain Beehuat Tan, Cedric Chuan Young Ng, Na-Yu Chia, et al. “SETD2 histone modifier loss in aggressive GI stromal tumours.” Gut 65, no. 12 (December 2016): 1960–72. https://doi.org/10.1136/gutjnl-2015-309482.
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    • Chan, Cheryl, Thomas Thurnherr, Jingbo Wang, Xavier Gallart-Palau, Siu Kwan Sze, Steve Rozen, and Caroline G. Lee. “Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein.” Mol Oncol 10, no. 8 (October 2016): 1183–95. https://doi.org/10.1016/j.molonc.2016.05.006.
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    • Chan, Tim Hon Man, Aditi Qamra, Kar Tong Tan, Jing Guo, Henry Yang, Lihua Qi, Jaymie Siqi Lin, et al. “ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer.” Gastroenterology 151, no. 4 (October 2016): 637-650.e10. https://doi.org/10.1053/j.gastro.2016.06.043.
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    • Wang, Chao, John R. McPherson, Lian-Hui Zhang, Steve Rozen, and Kanaga Sabapathy. “Transcription-associated mutation of lasR in Pseudomonas aeruginosa.” Dna Repair (Amst) 46 (October 2016): 9–19. https://doi.org/10.1016/j.dnarep.2016.09.001.
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    • Yao, J. K., G. G. Dougherty, R. D. Reddy, M. S. Keshavan, D. M. Montrose, W. R. Matson, S. Rozen, R. R. Krishnan, J. McEvoy, and R. Kaddurah-Daouk. “Altered interactions of tryptophan metabolites in first-episode neuroleptic-naive patients with schizophrenia.” Mol Psychiatry 15, no. 9 (September 2010): 938–53. https://doi.org/10.1038/mp.2009.33.
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    • Bellott, Daniel W., Helen Skaletsky, Tatyana Pyntikova, Elaine R. Mardis, Tina Graves, Colin Kremitzki, Laura G. Brown, et al. “Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition.” Nature 466, no. 7306 (July 29, 2010): 612–16. https://doi.org/10.1038/nature09172.
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    • Rozen, S. “Genome-scale technologies foster advances in neurological and behavioral research.” Current Psychiatry Reviews 6, no. 2 (May 1, 2010): 74–81. https://doi.org/10.2174/157340010791196457.
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    • Hughes, Jennifer F., Helen Skaletsky, Tatyana Pyntikova, Tina A. Graves, Saskia K. M. van Daalen, Patrick J. Minx, Robert S. Fulton, et al. “Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.” Nature 463, no. 7280 (January 28, 2010): 536–39. https://doi.org/10.1038/nature08700.
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    • Mannelli, Paolo, Ashwin Patkar, Steve Rozen, Wayne Matson, Ranga Krishnan, and Rima Kaddurah-Daouk. “Opioid use affects antioxidant activity and purine metabolism: preliminary results.” Hum Psychopharmacol 24, no. 8 (December 2009): 666–75. https://doi.org/10.1002/hup.1068.
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    • Rozen, Steve, Janet D. Marszalek, Raaji K. Alagappan, Helen Skaletsky, and David C. Page. “Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection.” Am J Hum Genet 85, no. 6 (December 2009): 923–28. https://doi.org/10.1016/j.ajhg.2009.11.011.
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    • Patkar, Ashwin A., Steve Rozen, Paolo Mannelli, Wayne Matson, Chi-Un Pae, K Ranga Krishnan, and Rima Kaddurah-Daouk. “Alterations in tryptophan and purine metabolism in cocaine addiction: a metabolomic study.” Psychopharmacology (Berl) 206, no. 3 (October 2009): 479–89. https://doi.org/10.1007/s00213-009-1625-1.
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    • Visser, L., G. H. Westerveld, C. M. Korver, S. K. M. van Daalen, S. E. Hovingh, S. Rozen, F. van der Veen, and S. Repping. “Y chromosome gr/gr deletions are a risk factor for low semen quality.” Hum Reprod 24, no. 10 (October 2009): 2667–73. https://doi.org/10.1093/humrep/dep243.
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    • Hughes, Jennifer F., Helen Skaletsky, Steve Rozen, Richard K. Wilson, and David C. Page. “Has the chimpanzee Y chromosome been sequenced?” Nat Genet 38, no. 8 (August 2006): 853–54. https://doi.org/10.1038/ng0806-853b.
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    • Ballabio, Andrea, David Nelson, and Steve Rozen. “Genetics of disease The sex chromosomes and human disease.” Curr Opin Genet Dev 16, no. 3 (June 2006): 209–12. https://doi.org/10.1016/j.gde.2006.04.016.
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    • Hughes, J. F., H. Skaletsky, T. Pyntikova, P. J. Minx, T. Graves, S. Rozen, R. K. Wilson, and D. C. Page. “Erratum: Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee (Nature (2005) 437 (101-104)).” Nature 441, no. 7090 (May 11, 2006): 248. https://doi.org/10.1038/nature04776.
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    • Repping, Sjoerd, Saskia K. M. van Daalen, Laura G. Brown, Cindy M. Korver, Julian Lange, Janet D. Marszalek, Tatyana Pyntikova, et al. “High mutation rates have driven extensive structural polymorphism among human Y chromosomes.” Nat Genet 38, no. 4 (April 2006): 463–67. https://doi.org/10.1038/ng1754.
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    • Hughes, Jennifer F., Helen Skaletsky, Tatyana Pyntikova, Patrick J. Minx, Tina Graves, Steve Rozen, Richard K. Wilson, and David C. Page. “Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee.” Nature 437, no. 7055 (September 1, 2005): 100–103. https://doi.org/10.1038/nature04101.
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    • Rozen, Steve, Merit E. Cudkowicz, Mikhail Bogdanov, Wayne R. Matson, Bruce S. Kristal, Chris Beecher, Scott Harrison, et al. “Metabolomic analysis and signatures in motor neuron disease.” Metabolomics 1, no. 2 (2005): 101–8. https://doi.org/10.1007/s11306-005-4810-1.
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    • Repping, Sjoerd, Cindy M. Korver, Robert D. Oates, Sherman Silber, Fulco van der Veen, David C. Page, and Steve Rozen. “Are sequence family variants useful for identifying deletions in the human Y chromosome?” Am J Hum Genet 75, no. 3 (September 2004): 514–17. https://doi.org/10.1086/423394.
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    • Repping, Sjoerd, Saskia K. M. van Daalen, Cindy M. Korver, Laura G. Brown, Janet D. Marszalek, Judith Gianotten, Robert D. Oates, et al. “A family of human Y chromosomes has dispersed throughout northern Eurasia despite a 1.8-Mb deletion in the azoospermia factor c region.” Genomics 83, no. 6 (June 2004): 1046–52. https://doi.org/10.1016/j.ygeno.2003.12.018.
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    • Repping, Sjoerd, Helen Skaletsky, Laura Brown, Saskia K. M. van Daalen, Cindy M. Korver, Tatyana Pyntikova, Tomoko Kuroda-Kawaguchi, et al. “Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection.” Nat Genet 35, no. 3 (November 2003): 247–51. https://doi.org/10.1038/ng1250.
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    • Rozen, Steve, Helen Skaletsky, Janet D. Marszalek, Patrick J. Minx, Holland S. Cordum, Robert H. Waterston, Richard K. Wilson, and David C. Page. “Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.” Nature 423, no. 6942 (June 19, 2003): 873–76. https://doi.org/10.1038/nature01723.
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    • Skaletsky, Helen, Tomoko Kuroda-Kawaguchi, Patrick J. Minx, Holland S. Cordum, LaDeana Hillier, Laura G. Brown, Sjoerd Repping, et al. “The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes.” Nature 423, no. 6942 (June 19, 2003): 825–37. https://doi.org/10.1038/nature01722.
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    • Repping, Sjoerd, Helen Skaletsky, Julian Lange, Sherman Silber, Fulco Van Der Veen, Robert D. Oates, David C. Page, and Steve Rozen. “Recombination between palindromes P5 and P1 on the human Y chromosome causes massive deletions and spermatogenic failure.” Am J Hum Genet 71, no. 4 (October 2002): 906–22. https://doi.org/10.1086/342928.
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    • Kuroda-Kawaguchi, T., H. Skaletsky, L. G. Brown, P. J. Minx, H. S. Cordum, R. H. Waterston, R. K. Wilson, et al. “The AZFc region of the Y chromosome features massive palindromes and uniform recurrent deletions in infertile men.” Nat Genet 29, no. 3 (November 2001): 279–86. https://doi.org/10.1038/ng757.
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    • Tilford, C. A., T. Kuroda-Kawaguchi, H. Skaletsky, S. Rozen, L. G. Brown, M. Rosenberg, J. D. McPherson, et al. “A physical map of the human Y chromosome.” Nature 409, no. 6822 (February 15, 2001): 943–45. https://doi.org/10.1038/35057170.
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    • Drenkard, E., B. G. Richter, S. Rozen, L. M. Stutius, N. A. Angell, M. Mindrinos, R. J. Cho, P. J. Oefner, R. W. Davis, and F. M. Ausubel. “A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis.” Plant Physiol 124, no. 4 (December 2000): 1483–92. https://doi.org/10.1104/pp.124.4.1483.
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    • Sun, C., H. Skaletsky, S. Rozen, J. Gromoll, E. Nieschlag, R. Oates, and D. C. Page. “Deletion of azoospermia factor a (AZFa) region of human Y chromosome caused by recombination between HERV15 proviruses.” Hum Mol Genet 9, no. 15 (September 22, 2000): 2291–96. https://doi.org/10.1093/oxfordjournals.hmg.a018920.
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    • Rozen, S., and H. Skaletsky. “Primer3 on the WWW for general users and for biologist programmers.” Methods Mol Biol 132 (2000): 365–86. https://doi.org/10.1385/1-59259-192-2:365.
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    • Steen, R. G., A. E. Kwitek-Black, C. Glenn, J. Gullings-Handley, W. Van Etten, O. S. Atkinson, D. Appel, et al. “A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat.” Genome Res 9, no. 6 (June 1999): AP1-insert.
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    • Steen, R. G., A. E. Kwitek-Black, C. Glenn, J. Gullings-Handley, W. Van Etten, O. S. Atkinson, D. Appel, et al. “Erratum: A high-density integrated genetic linkage and radiation hybrid map of the laboratory rat (Genome Research (1999) 9, (AP1-AP8)).” Genome Research 9, no. 8 (January 1, 1999): 793.
    • Wang, J. T., S. Rozen, B. A. Shapiro, D. Shasha, Z. Wang, and M. Yin. “New techniques for DNA sequence classification.” J Comput Biol 6, no. 2 (1999): 209–18. https://doi.org/10.1089/cmb.1999.6.209.
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    • Deloukas, P., G. D. Schuler, G. Gyapay, E. M. Beasley, C. Soderlund, P. Rodriguez-Tomé, L. Hui, et al. “A physical map of 30,000 human genes.” Science 282, no. 5389 (October 23, 1998): 744–46. https://doi.org/10.1126/science.282.5389.744.
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    • Wang, D. G., J. B. Fan, C. J. Siao, A. Berno, P. Young, R. Sapolsky, G. Ghandour, et al. “Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome.” Science 280, no. 5366 (May 15, 1998): 1077–82. https://doi.org/10.1126/science.280.5366.1077.
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    • Kenmochi, N., T. Kawaguchi, S. Rozen, E. Davis, N. Goodman, T. J. Hudson, T. Tanaka, and D. C. Page. “A map of 75 human ribosomal protein genes.” Genome Res 8, no. 5 (May 1998): 509–23. https://doi.org/10.1101/gr.8.5.509.
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    • Goodman, N., S. Rozen, and L. D. Stein. “The LabFlow system for workflow management in large scale biology research laboratories.” Proc Int Conf Intell Syst Mol Biol 6 (1998): 69–77.
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    • Goodman, N., S. Rozen, L. D. Stein, and A. G. Smith. “The LabBase system for data management in large scale biology research laboratories.” Bioinformatics 14, no. 7 (1998): 562–74. https://doi.org/10.1093/bioinformatics/14.7.562.
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    • Bonnet, A., A. Shrufi, and S. Rozen. “LabFlow-l: A database benchmark for high-throughput workflow management.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 1057 LNCS (December 1, 1996): 463–78.
    • Saxena, R., L. G. Brown, T. Hawkins, R. K. Alagappan, H. Skaletsky, M. P. Reeve, R. Reijo, et al. “The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned.” Nat Genet 14, no. 3 (November 1996): 292–99. https://doi.org/10.1038/ng1196-292.
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    • Schuler, G. D., M. S. Boguski, T. J. Hudson, L. Hui, J. Ma, A. B. Castle, X. Wu, et al. “Genome maps .7. The human transcript map.” Science 274, no. 5287 (October 25, 1996): 547–58.
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    • Schuler, G. D., M. S. Boguski, T. J. Hudson, L. Hui, J. Ma, A. B. Castle, X. Wu, et al. “Genome maps 7. The human transcript map. Wall chart.” Science 274, no. 5287 (October 25, 1996): 547–62.
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    • Reijo, R., T. Y. Lee, P. Salo, R. Alagappan, L. G. Brown, M. Rosenberg, S. Rozen, et al. “Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA-binding protein gene.” Human Reproduction 11, no. SUPPL. 4 (January 1, 1996): 27–49. https://doi.org/10.1093/humrep/11.suppl_4.27.
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    • Hudson, T. J., L. D. Stein, S. S. Gerety, J. Ma, A. B. Castle, J. Silva, D. K. Slonim, et al. “An STS-based map of the human genome.” Science 270, no. 5244 (December 22, 1995): 1945–54. https://doi.org/10.1126/science.270.5244.1945.
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    • Reijo, R., T. Y. Lee, P. Salo, R. Alagappan, L. G. Brown, M. Rosenberg, S. Rozen, T. Jaffe, D. Straus, and O. Hovatta. “Diverse spermatogenic defects in humans caused by Y chromosome deletions encompassing a novel RNA-binding protein gene.” Nat Genet 10, no. 4 (August 1995): 383–93. https://doi.org/10.1038/ng0895-383.
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    • Rozen, S., L. Stein, and N. Goodman. “LabBase: Managing Lab Data in a Large-Scale Genome-Mapping Project.” Ieee Engineering in Medicine and Biology Magazine 14, no. 6 (January 1, 1995): 702–9. https://doi.org/10.1109/51.473263.
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    • Rozen, S., and D. Shasha. “Using a Relational System on Wall Street: The Good, the Bad, the Ugly, and the Ideal.” Communications of the Acm 32, no. 8 (January 8, 1989): 988–94. https://doi.org/10.1145/65971.65977.
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  • Book Sections

    • Fukawa, T., N. Shannon, D. Huang, J. Tan, X. Yao, S. G. Rozen, P. Tan, and B. T. Teh. “Molecular genetics of renal cell carcinoma.” In Renal Cell Carcinoma: Molecular Features and Treatment Updates, 83–103, 2017. https://doi.org/10.1007/978-4-431-55531-5_3.
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  • Conference Papers

    • Rozen, Steven G. “Opportunities and challenges in using mutational signature analysis to illuminate cancer biology and epidemiology.” In Environmental and Molecular Mutagenesis, 63:49–50, 2022.
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    • Boot, A., P. H. Lin, W. Yu, F. Y. Lo, J. Salk, V. Chew, C. C. I. I. I. Valentine, S. T. Pang, and S. G. Rozen. “Non-invasive Detection of Aristolochic Acid Exposure Using Ultra-Sensitive Duplex Sequencing.” In Environmental and Molecular Mutagenesis, 62:31–32, 2021.
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    • Rozen, S. G. “Utility of Mutational Spectra to Identify Tumor Origin.” In Environmental and Molecular Mutagenesis, 62:25–25, 2021.
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    • Boot, A., P. H. Lin, W. Yu, F. Y. Lo, J. J. Salk, C. C. Valentine, S. T. Pang, and S. G. Rozen. “Ultra-deep Sequencing of Blood and Urine to Test for Exposure to Aristolochic Acids.” In Environmental and Molecular Mutagenesis, 61:50–51, 2020.
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    • Rozen, S. G. “Mutational Signature Analysis for Molecular Cancer Epidemiology: The Example of Aristolochic Acid.” In Environmental and Molecular Mutagenesis, 60:50–50. WILEY, 2019.
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    • Rozen, S. G., A. Boot, N. H. Jiang, S. L. Zhang, and S. -. C. Ho. “Robust Experimental and Computational Methods for In-depth Characterization of Mutational Signatures.” In Environmental and Molecular Mutagenesis, 60:79–79. WILEY, 2019.
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    • Zavadil, J., M. Korenjak, M. Zhivagui, A. W. T. Ng, C. Renard, R. A. Herbert, E. Bergstrom, L. B. Alexandrov, and S. G. Rozen. “Non-Canonical Characteristics of Mutational Signatures Identified By Experimental Modelling.” In Environmental and Molecular Mutagenesis, 60:78–79. WILEY, 2019.
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    • Jusakul, Apinya, Chern Han Yong, Ioana Cutcutache, Jing Quan Lim, Mi Ni Huang, Nisha Padmanabhan, Sarinya Kongpetch, et al. “Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma.” In Cancer Science, 109:720–720. WILEY, 2018.
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    • Zhivaqui, M., A. W. T. Ng, M. Ardin, M. Churchwell, M. Pandey, C. Renard, S. Villar, et al. “Genome-wide mutational signature of glycidamide observed in human cancers using PCAWG data.” In Environmental and Molecular Mutagenesis, 59:69–70. WILEY, 2018.
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    • Ng, A. W. T., S. L. Poon, M. N. Huang, J. Q. Lim, S. Thangarajua, C. C. Y. Ng, P. Tan, et al. “Frequent mutational signature of aristolochic-acid derivatives in hepatocellular carcinomas in Asia and Taiwan.” In Environmental and Molecular Mutagenesis, 58:S32–S32. WILEY, 2017.
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    • Cutcutache, Ioana, Alice Yingting Wu, John R. McPherson, Zhengdeng Lei, Niantao Deng, Wai Keong Wong, Khee Chee Soo, et al. “Abstract 5168: Gastric adenocarcinomas show pervasive loss of heterozygosity and enrichment for “STOP” genes in regions of hemizygous deletion.” In Cancer Research, 74:5168–5168. American Association for Cancer Research (AACR), 2014. https://doi.org/10.1158/1538-7445.am2014-5168.
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    • Poon, Song Ling, See-Tong Pang, John R. McPherson, Steven G. Rozen, Patrick Tan, and Bin Tean Teh. “Abstract 4270: The use of mutational signatures in identifying carcinogen exposure.” In Cancer Research, 74:4270–4270. American Association for Cancer Research (AACR), 2014. https://doi.org/10.1158/1538-7445.am2014-4270.
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    • Lei, Zengdeng, Nian Tao Deng, Hermioni Zouridis, Iain Beehaut Tan, Chia Huey Ooi, Tatiana Ivanova, Shenli Zhang, et al. “Abstract 1200: Molecular subtypes of gastric cancer show systematic differences in response to PI3K inhibitors and fluorouracil.” In Cancer Research, 73:1200–1200. American Association for Cancer Research (AACR), 2013. https://doi.org/10.1158/1538-7445.am2013-1200.
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    • Stein, L., A. Marquis, E. Dredge, M. P. Reeve, M. Daly, S. Rozen, and N. Goodman. “Splicing UNIX into a genome mapping laboratory.” In Usenix Summer 1994 Technical Conference, 1994.
    • Stein, L., A. Marquis, E. Dredge, M. P. Reeve, M. Daly, S. Rozen, and N. Goodman. “Splicing UNIX into a genome mapping laboratory.” In Usenix Summer 1994 Technical Conference, 1994.
    • “Splicing UNIX into a genome mapping laboratory.” In Usenix Summer 1994 Technical Conference, 1994.

  • Preprints

    • Liu, Mo, Yang Wu, Nanhai Jiang, Arnoud Boot, and Steven Rozen. “mSigHdp: hierarchical Dirichlet process mixture modeling for mutational signature discovery.” BioRxiv, 2022. https://doi.org/10.1101/2022.01.31.478587.
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