FACULTY & RESEARCH
Our Expertise and Leadership
Our outstanding faculty, staff, trainees and alumni have come to Colorado from around the world. Before joining our program, they trained at Harvard, Yale, Stanford, Berkeley, Johns Hopkins, and other top universities.
The Computational Bioscience core and affiliated faculty work in a wide range of areas, including genomics, metabolomics, microbiome research, systems genetics, cancer research, image analysis, clinical research informatics, and many other fields that span the spectrum of biomedical research from the molecular to the clinical. They have appointments in numerous departments on three CU campuses, including Medicine, Pharmacology, Biostatistics and Informatics, Biochemistry & Molecular Genetics, Computer Science, and Bioengineering; including faculty from National Jewish Health.
Research Areas
- Biological Visualization Data
- Biomedical Ontology
- Cell Image Analysis
- Clinical Informatics
- Clinical Research Informatics
- Clinical Decision Support
- Health Care Process Modeling & Analysis
- Gene Expression
- Computational Pharmacology
- Genomics
- Metagenomics
- Microbiome
- Molecular Evolution
- Natural Language Processing
- Network Analysis
- Neuroscience
- Next Generation Sequence Analysis
- Personalized Medicine
- Statistical Methods in Genomics
- Electronic Health Record Data Analysis
- Biostatistics
- Text Mining
- Translational Bioinformatics
- Visual Analytics
- Physical simulations of biological macromolecules and their dynamics
Faculty
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Mazen Al Borno PhD
Assistant Professor
Without being conscious of it, our motor system is constantly solving computationally challenging problems in ways that astonish both roboticists and neuroscientists. We develop computational models of animal movement to understand how the brain generates movement and design novel rehabilitation therapies and assistive devices for patients with movement disorders. We collaborate closely with neuroscientists, clinicians and roboticists to study the brain and help patients achieve a better quality of life.
David Albers PhD
Associate Professor
Dr. David Albers lab focuses on advancing biomedicine using:
-data assimilation of both clinician and patient collected data to forecast physiology and compute new phenotypes
-health care process modeling and analysis
-temporal-focused spectral analysis and information theoretic tools
-mechanistic physiologic models using clinical data
-discovering phenotypes using temporal information within clinical data
-visualizing patient health evolution in an intensive care setting
-deconvolving biases present in clinical data
-computational machinery based on variational inference to discover features that can be used to define phenotypes and other clinically actionable quantities
Tell Bennett MD
Professor
We focus on clinical decision-making, particularly in high-risk environments such as intensive care units, and on the development and implementation of informatics and data science methods and tools to improve outcomes.
James Costello PhD
(he/him/his)
Associate Professor
Director, Pharmacology Program
Within the broad scope of systems biology, my lab focuses on 3 research areas: 1) Network inference for identifying drug targets, 2) Predicting drug sensitivity from -omics datasets, and 3) Modeling temporal effects of drug combinations.
Robin Dowell DSc
Professor
Our primary interest is in understanding transcriptional regulation: how does it work, evolve, and respond to perturbations? To this end, we are leveraging a variety of experimental and computational approaches. In general, we seek to develop principled, biologically informed machine learning approaches to identify causal relationships within transcriptional regulatory networks.
Debashis Ghosh MS, PhD
Professor
My research interests focus on the use of machine learning, multiple comparisons and multivariate statistical methods for the analysis of high-throughput data. I have focused most of my research on combining genomic data from either multiple datasets or from multiple studies. I have worked with transcriptomic, copy number, methylation and more recently, metabolomics and imaging data. Application areas I have worked in include cancer, diabetes, and ophthalmology. I have advised 12 Ph.D. students and one postdoctoral fellow in Biostatistics and Statistics on these topics. Students who would work with me in the future could expect to work on new analytical methods for large-scale datasets as well as begin to examine computational issues to enhance scalability.
Carsten Goerg PhD
Assistant Professor
Design, development, and evaluation of visualizations and visual analytics tools for supporting biologists in analyzing large and complex datasets. Also, application of text analytics research approaches to the biomedical literature.
Casey Greene PhD
Professor
We focus on bringing together publicly available big data, developing new computational methods to analyze that data, and creating tools to put those resources into the hands of every biologist.
Melissa Haendel PhD
Professor
TISLab is unique in that it focuses on unifying data across sources, disciplines and forms to make them informative for new kinds of translational questions. It brings together people and their data across extremely diverse disciplinary divides, leading advances in science that aim to: (1) Cope with Climate Change; (2) Facilitate knowledge discovery for Covid-19; (3) Improve Rare Disease Diagnosis and Treatment; (4) Accelerate Cancer Research; and (5) Promote Healthy Lifestyles.
Larry Hunter PhD
Professor
My research interests involve the development and application of advanced computational techniques to biomedicine, particularly the application of machine learning and statistical inference techniques to high-throughput molecular assays. I am also interested in automated processing of biomedical texts, anatomically realistic models of neural computation, and neurobiologically and evolutionarily informed computational models of cognition.
Katerina Kechris PhD
Professor
Director, Computational Bioscience Program
Our research focuses on the development and application of statistical and computational methods for analyzing omics data sets.
Arjun Krishnan PhD
Associate Professor
Our goal is to enable biomedical researches to effectively reuse massive collections of publicly-available data — e.g., omics, knowledgebases, unstructured text, genetic associations — to gain nuanced insights into the molecular mechanisms underlying heterogeneous traits and disease.
Ryan Layer PhD
Assistant Professor
The lab focuses on developing methods that can leverage population-scale datasets to understand better how genetic variation affects human health.
Catherine Lozupone PhD
Associate Professor
We combine bioinformatics and experimental work to understand the driving factors of human microbiota composition, host:microbe interactions, and the intersection with diet in a variety of disease contexts. Our work has a particular focus on HIV-positive and high HIV-risk populations, cancer and Clostridioides difficile infection.
Christopher Miller PhD
Associate Professor
We develop and use bioinformatic and genome-enabled approaches to study microbial communities. With the advent of new sequencing technologies, one can sequence billions or trillions of base pairs of DNA for relatively little money. One of the most powerful applications of this new economy is the direct sequencing of microbial DNA and RNA from the environment. The combination of deep sequencing and bioinformatics reveals that even “simple” natural microbial communities are in fact quite complex. We are interested in understanding this complexity at a systems level for microbial communities relevant to study of the environment, health, and disease.
David Pollock PhD
Professor
Protein, RNA, and other functional molecules that exist in living organisms are the product of millions of years of evolution. The substitutions that have occurred over the years had to have been compatible with the constraints of structure and function, and thus the evolutionary record provides critical data for understanding macromolecular structure/function/sequence relationships. In our laboratory, we use the techniques of molecular evolution, computational biology, and evolutionary genomics to exploit this record to make inferences about past biological events and to make testable predictions about the effects of mutations.
Antonio Porras Msc, PhD
Assistant Professor
Our team is working on the creation of normative statistical models of cranial growth that can be used as references to study developmental abnormalities quantitatively. Based on such models, we are creating new methods to identify and quantify abnormal developmental patterns associated with specific pathologies and genetic factors. Those methods will help us better understand developmental cranial disorders and create more informed and targeted treatments.
Janani Ravi PhD
Assistant Professor
We develop general-purpose computational approaches that integrate large-scale heterogeneous public datasets that lead to the mechanistic understanding of microbial genotypes, phenotypes, and diseases.
Laura Saba PhD
Associate Professor
We utilize and develop systems genetics tools to explore biological mechanisms responsible for disease.
Michael Strong PhD
Associate Professor
Dr. Strong’s research focuses on synergistic genomic, computational and molecular strategies to disease and disease pathogenesis. I am particularly interested in developing and applying computational methods to better generate, integrate and analyze genomic and proteomic information, with a focus on respiratory disease and disease pathogens, including Mycobacterium tuberculosis.
Email:strongm@njhealth.org
Anne Thessen PhD
Associate Professor
Linking phenomes, genomes, and exposomes using semantic technology.
Gregory Way PhD
Assistant Professor
We are specifically focused on the following research: (1) Reproducible software for processing high-dimensional microscopy readouts; (2) Microscopy representations of cell state; (3) Drug screening for pediatric diseases; and (4) New models of pediatric disease to aid drug screening.
Laura Wiley PhD
Assistant Professor
The Wiley Lab develops methods for using electronic health record data for clinical evidence generation and biomedical research in support of precision medicine. Ongoing projects include building and mining a clinical data repository to inform clinical management of intracranial aneurysms, developing tools to support abstraction of medical charts, and supporting informatics and data science needs of other collaborative projects in genomics and precision medicine. The Lab also has a strong emphasis on education, developing content to train clinical data scientists and research informaticians.
Fuyong Xing PhD
Assistant Professor
His research focuses on medical image computing, imaging informatics, and machine learning.
Fan Zhang PhD
Assistant Professor
We develop statistical machine learning for single-cell omics to study inflammatory disease for translational medicine.