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Computational and Systems Biology Faculty

Program Chair

Gaudenz Danuser, Ph.D.
Gaudenz Danuser, Ph.D.

Professor

Research Interests: Computer vision; computational cell biology; regulation of cell morphogenesis; roles of cell morphogenesis in cancer

Technical Expertise: Computer vision; time-series analysis; model regression; continuum mechanics; software engineering

Faculty

Maria Chahrour, Ph.D.

Assistant Professor

Research Interests: Genomic, genetic, and molecular approaches to autism spectrum disorders

Technical Expertise: Genetic linkage and mapping, whole exome and genome sequence analysis

Maria Chahrour, Ph.D.
Lindsay Cowell, Ph.D.

Associate Professor

Research Interests: Somatic diversification of antigen receptor genes; repertoire characteristics as biomarkers of immune status and disease; host-pathogen interactions

Lindsay Cowell, Ph.D.
Nick Grishin (Nikolai Grichine), Ph.D.

Professor

Research Interests: Computational biology; analysis of protein sequences and structures

Nick Grishin, Ph.D.
Dustin Hancks, Ph.D.

Assistant Professor

Research Interests: Host-pathogen interactions, genetic conflicts, positive selection​, genome evolution, innate immunity, evolutionary immunology, horizontal gene transfer, poxviruses, mutation, genetic disease, genomics

Technical Expertise: Evolutionary analysis

Dustin Hancks, Ph.D.
Gary Hon, Ph.D.

Assistant Professor

Research Interests: Developing (epi)genomic/bioinformatic tools to assess and predict the functions of regulatory elements, epigenetic biomarkers of disease state, epigenetics in development and disease, global regulation of mammalian gene expression, non-coding genome function

Technical Expertise: Single-cell genomics, genome engineering, gene regulation, cell state engineering

Gary Hon, Ph.D.
Khuloud Jaqaman, Ph.D.

Assistant Professor

Research Interests: Quantitative spatiotemporal structure-function relationships of multi-molecular assemblies; linking molecular and cellular behavior across multiple scales; computational image analysis and mathematical modeling

Technical Expertise: Computer vision, stochastic modeling and model calibration, time series analysis

Khuloud Jaqaman, Ph.D.
Steve Jiang, Ph.D.

Professor

Research Interests: Personal high performance computing device to improve the efficiency and more importantly, to change the way we diagnose and treat patients in cancer radiotherapy

Steve Jiang, Ph.D.
Lukasz Joachimiak, Ph.D.

Assistant Professor

Research Interests: Molecular recognition in protein folding, chaperone structural biology, and neurodegeneration

Technical Expertise: Biochemistry, biophysics, structural biology, chemical biology and protein modeling

Lukasz Joachimiak, Ph.D.
Daehwan Kim, Ph.D.

Assistant Professor

Research Interests: DNA and RNA sequence alignment, graph alignment to population of genomes, genotyping, personalized medicine

Technical Expertise: Computer Algorithms, Commercial-grade Software Development, Deep Learning, Biostatistics, Medical Data Analysis

Daehwan Kim, Ph.D.
Genevieve Konopka, Ph.D.

Associate Professor

Research Interests: Comparative genomics, epigenetics, and alternative splicing analyses relevant to brain evolution and cognitive disorders

Technical Expertise: Transcriptomics, weighted gene co-expression network analyses, single-cell RNA-sequencing analyses

Genevieve Konopka, Ph.D.
W. Lee Kraus, Ph.D.

Professor

Research Interests: Computational genomics. Using molecular, genetic, genomic, and computational approaches to understanding signal-regulated gene expression. Integrating data from different genomic platforms using computational approaches

W. Lee Kraus, Ph.D.
Bo Li, Ph.D.

Assistant Professor

Research Interests: Cancer immunology; statistical modeling for cancer genomics data; data mining; tumor-infiltrating immune repertoire profiling

Technical Expertise: Immune receptor repertoire, computational prediction of cancer antigens, machine learning, cancer-immune interactions, hypervariable immune receptors, cancer biomarker identification

Bo Li, Ph.D.
Milo Lin, Ph.D.

Assistant Professor

Research Interests: Optimization in conformational and network space.

Technical Expertise: Statistical mechanics, protein folding, non-equilibrium physics

Milo Lin, Ph.D.
Albert Montillo, Ph.D.

Assistant Professor

Research Interests: Developing state-of-the-art machine learning approaches to extract radiological imaging and imaging-genomic biomarkers and to engender personalized prognostics in neuroscience and oncological applications

Technical Expertise: Advanced image analysis, neuroimaging, MRI, MEG/EEG, PET/SPECT

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Zbyszek Otwinowski, Ph.D.

Professor

Research Interests: Development of methods to study next generation sequencing and X-ray crystallographic data

Zbyszek Otwinowski, Ph.D.
Satwik Rajaram, Ph.D.

Assistant Professor

Research Interests: Understanding tissue organization via machine learning; intra-tumor heterogeneity; computational image analysis and spatial statistics

Technical Expertise: Machine learning (both classical and deep).  Image analysis specifically for microscopy

Satwik Rajaram, Ph.D.
Kimberly Reynolds, Ph.D.

Assistant Professor

Research Interests: Statistical analysis and rational design of cellular systems

Technical Expertise: principal components analysis and matrix factorization, statistical analysis of protein sequences, python for large scale data analysis

Kimberly Reynolds, Ph.D.
Luke Rice, Ph.D.

Associate Professor

Research Interests: Integrating structure, kinetics, and computation to understand the molecular determinants and regulatory mechanisms of microtubule dynamics

Luke Rice, Ph.D.
Elliott Ross, Ph.D.

Professor

Research Interests: Cellular information processing; molecular mechanisms of G protein-mediated signaling: amplification, selectivity, response kinetics and signal integration

Elliott Ros, Ph.D.
Tao Wang, Ph.D.

Assistant Professor

Research Interests: Biostatistics, Machine learning, Immunogenomics, and Tumor genomics

Tao Wang, Ph.D.
Guanghua Xiao, Ph.D.

Professor

Research Interests: Improving treatments for cancer by applying computer science and statistical methodologies to analyzing high-throughput biological data. New models and tools are currently in development to assist the investigation of disease mechanisms and their related diagnostic innovations.

Guanghua Xiao, Ph.D.
Yang Xie, Ph.D.

Professor

Research Interests: Biostatistics, bioinformatics, statistical genomics, clinical trial design, and biomarker studies

Technical Expertise: Developing and applying statistical and computational approaches to decipher genetic and genomic problems, in particular, human complex traits.

Yang Xie, Ph.D.
Chao Xing, Ph.D.

Associate Professor

Research Interests: Statistical genetics, genetic epidemiology, bioinformatics, gene mapping for complex traits

Technical Expertise: Developing and applying statistical and computational approaches to decipher genetic and genomic problems, in particular, human complex traits.

Chao Xing, Ph.D.
Xiaowei Zhan, Ph.D.

Assistant Professor

Research Interests: Statistical genetics, forward genetics screening, statistical computation, next-generation sequencing, genetic association studies

Technical Expertise: Statistical genetics, microbiome, statistical computation, bioinformatics, deep learning

Xiaowei Zhan, Ph.D.
Jian Zhou, Ph.D.

Assistant Professor

Research Interests: Machine Learning and Statistical Methods for Genomics, Sequence Basis of Genome Regulation, Statistical Methods for Single-cell Data Analysis, The Evolution of Noncoding Genome.

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Associate Members

These faculty members do not accept graduate students. They participate in teaching, co-mentoring, exam and dissertation committees, and all other program responsibilities.

Dominika Borek, Ph.D.

Associate Professor

Research Interests: Development of methods to study heteroplasmy and the somatic evolution of cancers.

Dominika Borek, Ph.D.
Murat Cobanoglu, Ph.D.

Assistant Professor

Research Interests: Active machine learning driven cancer drug discovery

Murat Cobanoglu, Ph.D.
Dan Heitjan, Ph.D.

Professor

Research Interests: Clinical trial design and analysis; health economics; incomplete data; statistical modeling

Technical Expertise: Biostatistics, casual inference, clinical trials, incomplete data, observational studies

Daniel Heitjan, Ph.D.
Julia Kozlitina, Ph.D.

Associate Professor

Research Interests: Statistics, statistical genetics, genetic epidemiology, genome-wide association studies

Julia Kozlitina, Ph.D.