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Computational Biology

Computational biology image

The Computational Biology Track curriculum is designed to help students learn how to leverage mathematical and computational approaches to understand biological and chemical processes. For more details, review the Computational Biology Degree Plan.


Research Topics

Mathematical and computational concepts, methods, and algorithms are being applied to all areas of basic and clinical life sciences, which results in a variety of research topics. Examples include:

  • Biophysics and Structural Biology – Protein structure and function prediction; analysis of biological sequences and 3D structures; macromolecular interactions and biological networks; molecular evolution
  • Chemical Biology – Analysis of small organic molecules; design of materials and drugs; chemical dynamics
  • Genetics and Genomics – Analysis of DNA/RNA sequences; genome association to cellular and organismal function; statistical genetics
  • Imaging – Computer vision and pattern recognition applied to medical imaging and microscopy data, statistical and mathematical modeling of the spatiotemporal organization of image events from molecular to macroscopic scales
  • Medical Informatics – Machine learning of patterns in multivariate clinical databases, predictive modeling of clinical outcomes by variable association
  • Systems Biology – Computational reconstruction and analysis of biological networks; modeling of complex, nonlinear systems; spatiotemporal integration of chemical and mechanical processes across scales

Track Director

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.
Daniel Heitjan, Ph.D.

Professor

Research Interests: Statistical methods, clinical trials, epidemiology, health economics

Daniel Heitjan, Ph.D.
Gary Hon, Ph.D.

Associate Professor

Research Interests: Single-cell regulatory genomics, cell fate engineering, function of non-coding elements and genetic variants.

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

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

Associate 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: Artificial intelligence in medical imaging, radiotherapy treatment planning, and adaptive radiotherapy etc

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.
Xiaochun Li, Ph.D.

Associate Professor

Research Interests: Structural and biochemical characterization of membrane proteins in cholesterol biosynthesis, metabolism and signaling

Xiaochun 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.
Weiguo Lu, Ph.D.

Professor

Research Interests: Adaptive radiation therapy; treatment-plan optimization; radiation-dose calculations

Weiguo Lu, 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

Albert Montillo, Ph.D.
Zbyszek Otwinowski, Ph.D.

Professor

Research Interests: Methods development for cryo-electron microscopy, X-ray crystallography, and next-generation sequencing; Structural studies of macromolecules with X-ray crystallography and cryo-EM single particle reconstruction; Higher-order structure of eukaryotic chromatin.

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.
Erdal Toprak, Ph.D.

Professor

Research Interests: Antibiotic resistance and sensitivity; single molecule biophysics; synthetic biology

Erdal Toprak, 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.

Professor

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

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

Associate 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.
Wenhao Zhang, Ph.D.

Assistant Professor

Research Interests: Computational Neuroscience

Wenhao Zhang, 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.

UTSW Distinguished Fellow

Research Interests: Active machine learning driven cancer drug discovery

Murat Cobanoglu, Ph.D.
Julia Kozlitina, Ph.D.

Associate Professor

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

Julia Kozlitina, Ph.D.