Steven Rozen

Expert in bioinformatics, cancer genomics, and genomics. Computer science PhD in databases and 20 years’ track record of impactful research as evidenced by a Google Scholar h-index of 81 and i10-index of 154. Experience in leading wet-lab as well as computational research.

Managing multidisciplinary teams: I founded the Duke-NUS Centre for Computational Biology, whose 5 faculty (including me) have published > 250 papers since 2016 and currently hold US$ 10 million in competitive funding. In addition to the faculty, the Centre has 9 PhD students, 12 research fellows, and 6 research assistants working in wet lab and computational research. I also co-led the International Cancer Genome Consortium working group on mutational signatures, and I am one of 2 corresponding authors on the resulting reference paper for these signatures, which has been cited 1,700 times since 2020.

Extensive background in software development and data science. I developed and maintained the widely used Primer3 program for PCR primer design. I and my lab released several R packages on CRAN and GitHub. We are also working on Python-based deep learning models for the analysis of variants of unknown significance in clinical genetics. Can meet the challenges of writing and maintaining robust software that meets users’ real needs and build systems for reproducible genomic analyses in the laboratory and the clinic.

Extensive background in oncology bioinformatics and major contributions to cancer genomics, as recognized by the 2018 American Association for Cancer Research Team Science Award. Used mutational signatures to discover widespread exposure to the carcinogen aristolochic acid in liver cancer (cited 275 times). Elucidated genomic landscapes of gastric cancer (cited 654 times), bile-duct cancer (3 papers, cited 1,400 times), and several other cancer types.

Associate and Full Professor, 2008 – present

Duke-NUS Medical School, Singapore

• Multiple high-impact publications in cancer genomics, many based on analysis of somatic mutations discovered by Illumina sequencing.
  • American Association for Cancer Research, Team Science Award to the “Genomic Approaches to

    Preventing and Treating Asian-Prevalent Cancers Team”.

  • Co-led the International Cancer Genome Consortium working group on mutational signatures; one of the 2 corresponding authors on the resulting reference for these signatures, cited 1,700 times since 2020.
  • Used mutational signatures to discover widespread mutagenesis by the carcinogen aristolochic acid in liver cancer and to discover a mutation in TOP2A gene that causes an indel hypermutator phenotype in human cancers.
  • Singapore President's Science Award “For Outstanding Integrative and Translational Research in Asian Cancer Genomics” along with Patrick Tan and Teh Bin Tean.
  • Secured US$ 7 million of competitive funding for my lab.
  • Mentored multiple PhD students and postdoctoral fellows; all but 2 are working in science.
  • Along with the Centre for Quantitative Medicine launched the PhD Programme in Quantitative Biology and Medicine and direct its keystone course “Core Concepts in Bioinformatics”.
  • Currently investigating deep learning protein language models as part of interpreting possible oncogenic somatic mutations and variants of unknown significance in clinical genetics.

Duke-NUS Medical School, Singapore

• Provide leadership for the strategic direction and oversight of computational, data, network, and security infrastructure for all research IT.
• Work closely with corporate IT to maintain solutions for large-scale, high-throughput scientific applications and data.
• Most recently oversaw procurement and deployment of and manage a US$ 1.8 million high-performance computing cluster: 20 compute nodes with 128 AMD EPYC 7763 cores each, 2 nodes with dual Nvidia A-100 GPUs, and 3 petabytes of Isilon storage.
• Support users of the high-performance computing cluster and facilitate other researcher IT needs vis-a-vis IT department and University policies.

Duke-NUS Medical School, Singapore

• Directed computational biology research center with the missions of (1) pursuing cutting-edge biomedical research with a strong computational component, (2) providing research collaborations and consulting in bioinformatics to the Duke-NUS and SingHealth research communities, and (3) providing graduate and continuing education in bioinformatics and computational biology.
• Recruited 4 highly productive faculty, all with independent research programs in addition to collaborations with the wider Duke-NUS and SingHealth research community.
• The faculty (including Rozen) have > 250 publications since 2016 and currently hold US$10 million in competitive funding as principal or co-investigator.
• The Centre is currently training 9 PhD students and 12 research fellows.

Whitehead Institute for Biomedical Research, Cambridge, MA

• Wrote and maintained Primer3, ubiquitously used software and web sites for PCR primer design, including at NCBI’s Primer-BLAST. The 3 publications describing Primer3 have been cited > 33,000 times and are still cited 1,700 times per year.
• At the Whitehead-MIT Genome Center, helped map the human genome for sequencing and helped with the first use of Affymetrix microarrays for SNP genotyping.
• Discovered the mechanisms and clinical consequences of multiple types of deletions in the human Y chromosome, as reported in first and senior author papers in Nature, Nature Genetics, the American Journal of Human Genetics, and others.

• Pioneered approaches to analyzing shotgun mass-spectrometry lipidomic data and HPLC-electrochemical metabolomics data.
• Developed and deployed a system for automatic analysis and warehousing of large amounts of Affymetrix gene-expression-array data for a major pharmaceutical company.

PhD Computer Science and > 20 years' experience in bioinformatics and genomics