Bioinformatics Faculty and Staff

Song Liu, PhD
Phone: 716-845-1628

Dr. Liu has overall responsibility for shared resource direction and oversight, and coordinates bioinformatics support assignments for all work done by the resource personnel. He supervises the faculty members, staff bioinformaticians and research assistants in the Resource and prepares written documentation as required by the profession, the Institute and various regulatory agencies.

His responsibilities also include promoting the resource through both internal and external presentations, and coordinating the efforts with other Shared Resources (e.g., Genomics Shared Resource). Dr. Liu serves on RPCI’s Information Technology (IT) Advisory Board Research Committee, Education Roundtable Committee, Internal Funding Review Committee, Genomics Shared Resource Advisory Committee, and Center for Personalized Medicine Steering Committee. Dr. Liu is Vice Chair for Bioinformatics and Professor of the RPCI Department of Biostatistics and Bioinformatics, and Director of the Master of Science program in Bioinformatics and Biostatistics through RPCI’s graduate division.

Jianmin Wang, PhD
Phone: 716-845-1499

Dr. Wang assists Dr. Liu in the day-to-day operation of the Bioinformatics Shared Resource. In collaboration with Dr. Liu, he reviews the bioinformatics section of new protocols, grants, and manuscripts, directs the experimental design and analysis plan of clinical, laboratory, and population-based studies utilizing high-resolution, high-throughput platforms, oversees ongoing bioinformatics support regarding the project, and presents on the progress of the Resource to the Advisory Committee.

His responsibilities also include directing the development of analysis pipelines for various next-generation sequencing, high-density microarray, and proteomics applications utilizing the high-performance computing facility, and working on solutions to integrate different analytic tools and unify the analysis interface. In collaboration with the IT department, he is actively involved in the design and deployment of various data warehousing and computing resources. Dr. Wang serves on RPCI’s IT Advisory Board Research Committee and Center for Personalized Medicine Steering Committee.

Lei Wei, PhD
Faculty Bioinformatician
Phone: 716-845-1176

Dr. Wei joined the faculty of RPCI in 2013 as Assistant Professor of Oncology. Specialized in genetic variation and somatic mutation detection through creating and utilizing sophisticated computational and statistical methods of Next-Generation Sequencing (NGS), he has developed his research interests which lie within integrative analysis of large-scale, multi-dimensional data to unveil the molecular mechanism of cancer initiation, progression and prognosis.

Prior to his arrival at Buffalo, he joined the bioinformatics team of the Pediatric Cancer Genome Project (PCGP), St. Jude Children's Research Hospital and Washington University in 2010. Since then, he has been working as the Disease Coordinator and Lead Analyst of four major cancer types, analyzed over 150 pairs of Whole-Genome Sequencing (WGS) data, and numerous exome, RNASeq and targeted sequencing data sets. Besides human cancers, he dissected NGS data of mouse model and influenza virus, and developed analytic pipelines with high sensitivity and specificity, which have been adopted by several genome centers to analyze data for multiple projects, and yield a number of published and in-progress high-impact publications.

An example of a recent publication is “The genomic landscape of hypodiploid acute lymphoblastic leukemia” published in Nature Genetics (45: 242-52, 2013). He has also served as a core member of the pilot Clinical Sequencing group at St. Jude Children’s Research Hospital.

Martin Morgan, PhD
Director, R/Bioconductor
Department of Biostatistics and Bioinformatics
Phone: 716-845-6503

Dr. Morgan earned his undergraduate and Master's degrees in Botany at the University of Toronto. Dr. Morgan's PhD studies at the University of Chicago involved the evolutionary consequences of frequency-dependent selection, and of multilocus deleterious mutation.

Dr. Morgan spent 10 years as an Assistant and then Associate Professor at Washington State University, before joining the Fred Hutchinson Cancer Research Center in 2005. At the Hutch, Dr. Morgan worked on the Bioconductor project for the analysis and comprehension of high-throughput genomic data; he has led Bioconductor since 2008. Dr. Morgan recently moved to Roswell Park Comprehensive Cancer Center in Buffalo, NY, where the Bioconductor project is now based.

Qianqian Zhu, PhD
Faculty Bioinformatician
Phone: 716-845-1300 x5659

Dr. Zhu joined the faculty of RPCI in April of 2012 as Assistant Professor of Oncology. She has an interdisciplinary training in biostatistics, bioinformatics, and human genetics, and has accumulated extensive collaboration experience with biologists and clinicians in genetic epidemiology studies utilizing approaches of GWAS and NGS.

Dr. Zhu completed her postdoctoral training in statistical genetics at Center for Human Genetic Variation at Duke University from 2010 to 2012. Prior to that, she received her PhD education in Bioinformatics and MA education in Biostatistics from the University at Buffalo (UB). She has authored a number of publications in premier journals, including American Journal of Human Genetics, Genome Biology, and Bioinformatics. Dr. Zhu’s primary research interest is in developing statistically sound and computationally efficient methods to pinpoint the causal genetic variants of human diseases utilizing high-throughput genetics and genomics data.

Her areas of expertise include: 1) computational method development for causal genetic variant identification; 2) statistical and bioinformatics analysis of genome, epigenome, and transcriptome data; and 3) pharmacogenomics, genetic testing, and personalized medicine. She has conducted a number of cutting-edge studies in dissecting genetic contributors to complex human traits.

Li Yan, PhD
Senior Bioinformatician
Phone: 716-845-7757

Dr. Yan joined the staff of RPCI in 2011. He completed his PhD in Physics at the University of Rochester and PhD in Biostatistics at UB. Dr. Yan has more than 12 years of experience in both academic and non-profit research foundation environments, collaborating with clinical and other scientific colleagues on a wide range of activities including study design, analysis plans, project reports, abstracts, manuscripts, and presentations.

He has extensive experience in many programming languages, including R and C++, as well as extensive experience in directing the design and deployment of various high-throughput platforms in cancer-oriented studies. An example of a recently developed tool is OSAT (Yan et al. BMC Genomics. 2012; 13:689. PMC3548766), which is a computational package for sample-to-batch allocations in omics experiments in order to minimize the impact of batch effects.

Qiang Hu, MD, PhD
Senior Bioinformatician
Phone: 716-845-1630

Dr. Hu joined the RPCI faculty in 2010. He graduated from Peking University with a degree in medicine and received his PhD in Bioinformatics from Tsinghua University. He is skilled in PERL and R computing languages, and has extensive experience in utilizing parallel computing in high-performance servers to process, analyze and interpret high-dimension, high-complexity data. An example of a recently developed tool is VPA (Hu et al. BMC Research Note. 2012; 5:31 PMC3293055), which is a customized package for analyzing variants with user-specified frequency pattern from NGS studies.

Research Assistants, MS/MA

The RAs in the Bioinformatics Shared Resource work under the mentorship of the faculty on appropriately chosen bioinformatics projects. They are graduate trainees enrolled in the RPCI MS program Bioinformatics & Bioinformatics and/or the UB graduate program in Biostatistics.