Tao Liu

PhD

Specializing In:

Bioinformatics Computational biology

Research Interests:

Bioinformatics algorithm development

About Tao Liu

Biography:

I joined Roswell Park Comprehensive Cancer Center in 2019. Before that, I was an assistant professor in the Department of Biochemistry at University at Buffalo since 2013. My research group focuses on building bioinformatics algorithms for single-cell genomics assays to study transcriptional and epigenetic regulatory mechanisms and the influence of the genetic variations at regulatory elements. Before my career as a faculty member, I was a postdoctoral fellow at the Dana-Farber Cancer Institute, where I had extensive experience working in the Analysis Working Group of the ENCODE and modENCODE consortium. I developed and am maintaining widely-used open-source algorithms, including MACS (cited over 5,000 times according to Google Scholar) to analyze ChIP-seq data, and an integrative platform for comprehensive analyses on cis-regulatory elements, which has over 3,000 users. I have authored or co-authored over 40 peer-reviewed methodological and collaborative publications.

Positions

Roswell Park Comprehensive Cancer
  • Associate Professor of Oncology
  • Department of Biostatistics & Bioinformatics
  • Associate Director, Cancer Genomics and Computational Oncology

Jacobs School of Medicine and Biomedical Sciences, University at Buffalo

  • Research Assistant
  • Professor of Biochemistry

Background

Education and Training:

  • 2007 - PhD - Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
  • 2002 - BS - Physics, Nanjing University, China

Fellowship:

  • 2007-2012 - Postdoctoral Research Fellow in bioinformatics, Dana-Farber Cancer Institute, Boston, MA

Professional Experience:

  • 2007-2012 - Postdoctoral Research Fellow, Dana-Farber Cancer Institute, Boston MA
  • 2012-2019 - Assistant Professor, Department of Biochemistry, University at Buffalo, Buffalo NY

Honors & Awards:

  • 2002 - Excellent Graduate Student Award, Graduate School of Chinese Academy of Sciences
  • 2000 - Excellent Student Award, Nanjing University
  • 2009 - Winner of ChIP-seq Community Challenge hosted by SeqAnswer

Research

Research Overview:

My long-term research interest is to develop and apply computational approaches for studying transcriptional and epigenetic regulation. My group at Roswell Park Comprehensive Cancer Center focuses on building bioinformatics algorithms for single-cell genomics assays to study gene regulatory mechanisms and the influence of the genetic variations at cis-regulatory elements. I am maintaining some widely used bioinformatics algorithms for genomics analysis such as MACS for Chromatin Immunoprecipitation with High-throughput Sequencing. I have close collaborations with experimentalists, biologists and clinicians in various fields.

Publications

Full Publications list on PubMed
  1. Tarbell, E. and Liu, T. (2019) HMMRATAC: a Hidden Markov ModeleR for ATAC-seq. Nucleic Acid Research. [in press]
  2. Ho, J.*, Jung, Y.*, Liu, T.*, Alver, B., Lee, S., Ikegami, K., & et al. (2014) Comparative analysis of metazoan chromatin organization. Nature, 512(7515), 449. PMCID: PMC4227084
  3. Bailey, T.*, Krajewski, P.*, Ladunga, I.*, Lefebvre, C.*, Li, Q.*, Liu, T.*, Madrigal, P.*, Taslim, C.*, & Zhang, J.*. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Computational Biology, 9 (11), e1003326 PMCID: PMC3828144
  4. Liu, T.*, Ortiz, J.A.*, Taing, L., Meyer, C.A., Lee, B., Zhang, Y., & et al. (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biology, 12(8), R83. PMCID: PMC3245621
  5. Zhang, Y.*, Liu, T.*, Meyer, C.A., Eeckhoute, J., Johnson, D.S., Bernstein, B.E., & et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biology, 9(9), R137. PMCID: PMC2592715