Affiliate Faculty

Ivet Bahar

Adjunct Professor, State University of New York at Stony Brook

• Biomolecular systems dynamics, multiscale modeling and simulations, computer-aided drug design, molecular and systems pharmacology, bridging sequence evolution, structure and function.

Publications

Shiladitya Banerjee

Associate Professor, Physics, CMU

• Theory and computational models of living systems and processes

Fore Systems Professor of Computer Science, Computational Biology, Machine Learning, CMU

• Our group develops computational methods for understanding the interactions, dynamics and conservation of complex biological systems.

Takis Benos

Adjunct Professor, University of Florida

• We develop new computational methods to model biological processes and mine high-dimensional, multi-modal biomedical data.

Jeremy Berg

Professor, Computational & Systems Biology, Pitt

Professor, Assoc. Vice Chancellor, Science Strategy & Planning (HS), Pitt
Pittsburgh Foundation Professor and Director, Pitt
Institute for Personalized Medicine, Pitt

• Dr. Berg’s research focuses the relationships between the structures and functions of biological molecules.

Chakra Chennubhotla

• We investigate the molecular and cellular origins of human epithelial malignancies through computational approaches.

Yu-Chiao (Chris) Chiu

• We study precision cancer medicine by integrating machine and deep learning technology with complex multi-omics data.

Panos Chrysanthis

Professor, Computer Science, Pitt
Director of Advanced Data Management Technologies Lab, Pitt

• Database Systems, Mobile and Pervasive Data Management, Distributed Computing, Operating Systems, Real-Time Systems.

Gregory Cooper

Professor, Biomedical Informatics, Pitt

• Application of decision theory, probability theory, Bayesian statistics, and artificial intelligence to biomedical informatics research problems.

Lance Davidson

Professor, Bioengineering, Pitt

• Reverse Engineering Morphogenesis – From Cell Motility & ECM to Tissue Mechanics.

Mo R. Ebrahimkhani, MD

Associate Professor, Pathology, UPMC, Pitt

• Synthetic Biology and genetic circuit engineering, Programming multicellular systems and organoids via integration of systems and synthetic biology, Synthetic living machines, Morphogenetic engineering using human stem cells, Study and recreate multicellular evolution, computation, recording, and their emergent behaviors.

G. Bard Ermentrout

Distinguished University Professor, Mathematics, Pitt

• Dr. Ermentrout’s main focus is in the area of mathematical neuroscience where he tries to understand the patterns of activity in networks of neurons.

Christos Faloutsos

Fredkin Professor of Computer Science, CMU

• Data Mining for graphs and streams. Fractals, self-similarity and power laws. Indexing and data mining for video, biological and medical databases.

Madhavi Ganapathiraju

Associate Professor, Biomedical Informatics, Pitt

• Pattern mining whole-genome and whole-proteome sequences, with application of suffix array data structures for preprocessing genome sequences.

Vanathi Gopalakrishnan

Associate Professor, Computing & Information, Pitt

• The design and development of computational methods for solving clinically relevant biological problems.

Angela Gronenborn

UPMC Rosalind Franklin Professor and Chair, Structural Biology, Pitt
Distinguished Professor of Structural Biology, Pitt
Professor of Bioengineering, Pitt

• The molecular and atomic details that govern specificity in a variety of cellular interactions and that result in the amazing functional diversity observed in living organisms.

Aditi U. Gurkar

Assistant Professor of Medicine, Division of Geriatric Medicine, Aging Institute, Pitt

• Understanding the biology of aging and age-related diseases with focuses on identifying the signaling mechanisms that drive aging in response to endogenous DNA damage. By defining these molecular mechanism(s), she hopes to identify novel therapeutic targets that can be exploited to extend healthspan.

Publications

Graham Hatfull

Eberly Family Professor of Biotechnology, HHMI Professor, Biological Sciences, Pitt

• The molecular genetics of the mycobacteria and their mycobacteriophages.

Milos Hauskrecht

Professor, Computer Science, Pitt

• The development of modern machine learning technologies for analysis of high dimensional time-series data in electronic health record (EHR) data and their application in clinical decision support and clinical alerting.

Luisa Hiller

Eberly Family Career Development Associate Professor, Biological Sciences, CMU

• Understanding the role of bacteria in both health and disease.

Veronica Hinman

Department Head and Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences, Biological Sciences, CMU

• How genomes control cell fate decisions during embryonic development and also later regeneration.

Xia Jiang

Associate Professor, Biomedical Informatics, Pitt

• We apply artificial intelligence, machine learning, Bayesian, and other computational methods to problems in biology, medicine, and translational research.

Alok Joglekar

Assistant Professor, Immunology, Computational & Systems Biology, Pitt

• Characterizing the antigenic targets of CD8+ T cells and regulatory T cells in anti-tumor and autoimmune T cell responses and probing the mechanistic basis of cross-reactivity of T cells between self- and pathogen-derived targets

Kenneth Jordan

Richard King Mellon Professor and Distinguished Professor of Computational Chemistry, Pitt 
Associate Director, Center for Research Computing, Pitt

• Theory and experimental studies of molecules and clusters, reaction at surfaces, electron and proton localization transfer in polyatomic molecules and waterclusters.

Maria Kurnikova

Professor, Chemistry, CMU

• Understanding the work of membrane proteins, such as receptors, signal transduction proteins, toxins, and ion channels.

Alexandros Labrinidis

Professor and Chair, Computer Science, Pitt
Co-Director, Advanced Data Management Technologies Laboratory, Pitt

• Big data, user-centric data management, scientific data management, data stream management systems and data-intensive computing.

Jeffrey Lawrence

Professor and Chair, Biological Sciences, Pitt

• Elucidating the evolution of bacterial genomes, including their size, composition, variability, and organization.

Philip LeDuc

William J. Brown Professor, Biomedical Engineering, CMU
Director, Center for the Mechanics and Engineering of Cellular Systems, CMU

• To investigate biological systems with mechanical engineering approaches, which we enable by synthesizing novel technologies.

Miler T. Lee

Assistant Professor, Biological Sciences, Pitt

• My research addresses how gene expression programs change, leading to changes to cellular identity.

Guillaume Marçais

Project Scientist, Computational Biology Department, CMU

• My research is focused on algorithm development and improvement in Bioinformatics such as genome assembly, RNA transcript assembly, sequence alignment, biological data storage, search and retrieval.

Publications

C. Joel McManus

Associate Professor, Biological Sciences, CMU

• Understanding the genetic causes of variation in gene expression.

Natasa Miskov-Zivanov

Assistant Professor, Electrical and Computer Engineering, Bioengineering, Pitt

• Biological design automation and systems and synthetic biology.

Tom Mitchell

Founders University Professor, Machine Learning, CMU

• Machine learning to understand how the human brain uses neural activity to represent information, and statistical learning algorithms for natural language processing.

Robert F. Murphy

Ray and Stephanie Lane Professor of Computational Biology, Emeritus, CMU

• Cell and computational biology. Experimental and computational methods to learn and represent how proteins are organized within eukaryotic cells.

Hyun Jung (HJ) Park

Assistant Professor, Human Genetics & Biostatistics, Pitt

• Investigates large-scale behavior of molecular dynamics in human diseases using bioinformatics, identifying molecular mechanisms of human diseases across diverse types of genetic and epigenetic data through big data analysis and machine learning algorithms.

R. Ravi

Andris A. Zoltners Professor of Business, CMU
Professor of Operations Research and Computer Science, CMU
Director of Analytics Strategy, Tepper School of Business, CMU

• Models, methods, and applications of discrete optimization.

Mark Rebeiz

Professor, Biological Science, Pitt

• We study the evolution of gene regulatory networks that control differences in morphology.

Kathryn Roeder

Professor, Statistics, Computational Biology, CMU

• The use of statistical tools to understand the workings of the human genome and the nature of inherited diseases.

Jonathan Rubin

Professor and Department Chair, Mathematics, Pitt

• Modeling and analysis of neuronal network dynamics, especially respiratory, locomotor and pathological rhythms; modeling acute inflammation, including in traumatic brain injury; multiple time scale dynamics and parameter estimation for biological models.

Matt Ruffalo

Systems Scientist, Computational Biology, CMU

Gordon Rule

Head, CMU Qatar Biological Sciences Program
Professor, Biological Sciences, CMU

• My research is directed at understanding inter-molecular interactions in biological systems.

Hanna Salman

Associate Professor, Physics & Astronomy, Pitt

• Our research aims to understand mechanisms of collective behavior and variability in bacterial cultures and their effect on responses to changing environments.

Tuomas Sandholm

Angel Jordan University Professor, Computer Science, CMU
Co-Director, CMU AI
Director, Electronic Marketplace Laboratory, CMU

• Steering evolution and biological adaptation using computational game theory and opponent exploitation techniques; generating multi-step treatment plans; optimization, game theory, artificial intelligence, and market design.

Gerald Schatten

Director, Pittsburgh Development Center, Pitt
Professor of Obstetrics, Gynecology, Reproductive Sciences, Cell Biology, and Bioengineering, Pitt
Director of the Division of Development and Regenerative Medicine, Pitt

•  The molecular biology of cell function in gametes, embryos, stem cells, maternal/fetal efficacy of assisted reproduction technologies, the origins of developmental diseases...

Jason Shoemaker

Associate Professor, Chemical/Petroleum Engineering, Pitt

• Computationally Driven Discovery in Health Biological information – from molecular events to personal genomics – has exploded. Our group aims to develop computational approaches to exploit large-scale data to promote disease treatment discovery and optimization.

Ian Sigal 

Associate Professor, Ophthalmology & Bioengineering Ocular Biomechanics Laboratory, Pitt
Director, Image Acquisition and Analysis Core Module, Ophthalmology and Visual Science Center, Pitt

• We study soft tissue architecture and biomechanics. We use computational and experimental tools to figure out natural strategies to make tissues robust and last a lifetime. We do this primarily by studying the eye.

David Swigon

Associate Professor, Mathematics, Pitt

• My research is in the area of mathematical biology. We construct mathematical models of biological systems within the framework of continuum mechanics and stochastic dynamic systems.

Pei Tang

Professor, Anesthesiology and Perioperative Medicine, Pharmacology & Chemical Biology and Computational & Systems Biology, Pitt

• We are interested in the action of low-affinity drugs, such as general anesthetics and alcohols, on the neurotransmitter-gated receptor channels.

D. Lansing Taylor

Director, Drug Discovery Institute, Pitt
Distinguished Professor and Allegheny Foundation Professor of Computational & Systems Biology, Pitt

• I am focusing my efforts in Quantitative Systems Pharmacology in order to change the paradigm in drug discovery and development.

Shyam Visweswaran

Associate Professor, Computing and Information, Pitt

• Application of AI, machine learning, data mining of biomedical data, and Bayesian methods to problems in clinical medicine and bioinformatics with focus on patient-specific predictive modeling.

Yoram Vodovotz

Professor, Surgery, Immunology, Bioengineering, Computational & Systems Biology, Clinical & Translational Science, and Communication Science & Disorders, Pitt

• Our group’s research focuses on studying mechanisms of inflammation and gaining a systems-level perspective into this central physiological and pathological process.

Junmei Wang

Associate Professor of Pharmaceutical Sciences, Pitt

• Computational Chemistry and Biophysics, Drug Discovery and Development, Systems Pharmacology and Outcomes

Xiaosong Wang

Associate Professor, Pathology & Biomedical Informatics, Pitt

• Develop novel bioinformatics tools and models to predict therapeutic responses of cancer targeted therapies and immunotherapies, as well as to facilitate clinically important decisions. Develop integrative computational genomics approaches to discover causal genetic alternations, viable therapeutic targets, and predictive biomarkers in cancer. Characterize the landscape of driving genetic aberrations, therapeutic targets, and predictive biomarkers for the development of new cancer precision medicine.

Yu-Li Wang

Mehrabian Professor, Biomedical Engineering, CMU

• Mechanics represent a key aspect of live cells. Our lab seeks a cellular-level understanding of the mechanisms of actuating and sensing mechanical events.

Larry Wasserman

UPMC Professor of Statistics and Data Science, Statistics, ML, CMU

• We are group of faculty and students in Statistics and Machine Learning broadly interested in theoretical work at the intersection of these two disciplines.

Leila Wehbe

Assistant Professor, Machine Learning Department & Neuroscience Institute, CMU

• Our research is focused on computational modeling of the brain representation of language and other high-level tasks. We use machine learning and neuroimaging -- fMRI and MEG -- to study how the brain represents information during complex naturalistic tasks. Our research is at the interface between natural language processing, machine learning and cognitive neuroscience.

Publications

Wei Wu

Senior Systems Scientist, Computational Biology, CMU

• My research uses integrative approaches to study complex human diseases by combining biology, computational and statistical learning, bioinformatics, and genomics.

Shandong Wu

Associate Professor, Radiology, Biomedical Informatics, Bioengineering, Intelligent Systems, Clinical and Translational Science, Pitt
Director, Intelligent Computing for Clinical Imaging (ICCI) Lab, Pitt
Technical Director for AI Innovations in Radiology, Pitt

• Current research interests center on computational breast imaging and clinical studies for investigating quantitative imaging-derived biomarkers, models, and systems for breast cancer screening, risk assessment, diagnosis, prognosis, and treatment, towards improving individualized clinical decision-making and precision medicine.

Xiang-Qun (Sean) Xie

Associate Dean of PharmacoAnaltyics, Pitt
Professor, Pharmaceutical Sciences, Pitt

• Dr. Xie’s research group designs and discovers GPCRs chemical genomics-based drugs for osteoporosis, multiple myeloma and breast cancer research.

Yan Xu

Peter Winter Professor of Anesthesiology, Pitt
Professor of Pharmacology & Chemical Biology, Physics & Astronomy, and Structural Biology, Pitt
Vice Chair for Basic Sciences, Anesthesiology & Perioperative Medicine, Pitt

• High-Resolution Channel Protein Structure and Function; Molecular Mechanisms of General Anesthesia; MRI of Brain Protection after Cardiac Arrest and Resuscitation.

Da Yang

Associate Professor, Pharmaceutical Sciences, Pitt

• The Yang lab focuses on computational and functional studies to identify mechanisms of cancer drug resistance, and to develop approaches/markers for personalized cancer medicine.

Hassane Zarour, MD

Professor, Department of Medicine, Division of Hematology/Oncology
Professor, Department of Immunology
Professor, Department of Dermatology, Pitt

• Our research focuses on translational cancer immunotherapy from the laboratory into the clinic and includes:

  1. The mechanisms of tumor-induced immune cell dysfunction, including the role of multiple inhibitory receptor pathways (PD-1, Tim-3, BTLA and TIGIT). 

  2. Novel combinatorial immunotherapies in cancer patients, including dual immune checkpoint blockades and intratumoral TLR9 agonist together with PD-1 blockade.

  3. Studies of the gut microbiome in cancer Immunotherapy. 

Publications

Fang-Cheng Yeh, MD, PhD

Associate Professor, Neurological Surgery, Pitt
Director, High-Definition Fiber Tractography Lab, Pitt

• Diffusion MRI, tractography, network analysis, medical image analysis, pathology informatics.

Bokai Zhu

Assistant Professor, Department of Medicine, Division of Endocrinology and Metabolism, Aging Institute of UPMC, Pitt

• 12h-clock, Hepatic Metabolic Homeostasis, Aging-associated Diseases

Publications