Research > Research Areas
Data Services and Informatics Tools
The department plays a key role in coordinating healthcare data, infrastructure, and services for the health sciences. Jonathan C. Silverstein, MD, MS, chief research informatics officer (CRIO); Eugene M. Sadhu, MD. associate CRIO; and Shyam Visweswaran, MD, PhD, director of the Biomedical Informatics Core of the Clinical and Translational Science Institute, work closely together to develop research data services and informatics tools to support biomedical data science and artificial intelligence research.
Our work spans biomedical data infrastructure and research informatics, providing the analytical backbone for health sciences research across the University of Pittsburgh and UPMC. From harmonizing electronic health records and managing large-scale clinical data warehouses to developing tools for cohort discovery, federated queries and translational data integration, this work enables investigators to conduct rigorous, reproducible research.
Projects
Cellular Senescence Network (SenNet) Program
A national initiative to comprehensively identify and characterize senescent cells across tissues, health states, and the human lifespan, the Cellular Senescence Network (SenNet) Program will produce publicly accessible atlases documenting the diversity of senescent cells, their distinguishing molecular features and the factors they secrete. To detect and profile these rare cells, SenNet develops innovative tools that build on advances in single-cell analysis and works to establish common terminology and classification standards to unite the broader cellular senescence research community. In partnership with Carnegie Mellon University and the Pittsburgh Supercomputing Center, the Consortium Organization and Data Coordinating Center serves as the organizational and computational hub for the entire SenNet consortium.
Faculty: Jonathan C. Silverstein, MD, MS
Collaborators: Ziv Bar-Joseph, PhD, and Philip D. Blood, PhD
Sample Publication: SenNet Consortium. NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nat Aging. 2022 Dec;2(12):1090-1100.
Human BioMolecular Atlas Program (HuBMAP)
The University of Pittsburgh and the Pittsburgh Supercomputing Center lead the infrastructure component and coordinating center for the Human BioMolecular Atlas Program (HuBMAP). The coordinating center develops a flexible, scalable hybrid cloud environment that connects HuBMAP with the storage and computing resources needed to deposit, access, query, search, analyze, and visualize both raw and processed data, in close coordination with the HIVE Collaboratory, the HuBMAP Consortium, and stakeholders worldwide.
Faculty: Jonathan C. Silverstein, MD, MS
Collaborators: Ziv Bar-Joseph, PhD, and Philip D. Blood, PhD
Sample Publication: Börner K, Blood PD, Silverstein JC, Ruffalo M, Satija R, Teichmann SA, Pryhuber GJ, Misra RS, Purkerson JM, Fan J, Hickey JW, Molla G, Xu C, Zhang Y, Weber GM, Jain Y, Qaurooni D, Kong Y; HRA Team; Bueckle A, Herr BW 2nd. Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nat Methods. 2025 Apr;22(4):845-860.
Breast Cancer Research Foundation (BCRF) Global Data Hub
Designed to foster data sharing, enable new analyses, and catalyze collaboration, the Breast Cancer Research Foundation (BCRF) Global Data Hub is a centralized research portal aggregating molecular and clinical data from breast cancer studies worldwide. The University of Pittsburgh developed and operates the hub in partnership with BCRF, leading data coordination, ensuring that regulatory and privacy standards are met, and simplifying data access for investigators worldwide.
Faculty: Jonathan C. Silverstein, MD, MS, and Eugene M. Sadhu, MD
Collaborator: Alexander Ropelewski
Sample Publication SGarcia-Recio S, Hinoue T, Wheeler GL, Kelly BJ, Garrido-Castro AC, Pascual T, De Cubas AA, Xia Y, Felsheim BM, McClure MB, Rajkovic A, Karaesmen E, Smith MA, Fan C, Ericsson PIG, Sanders ME, Creighton CJ, Bowen J, Leraas K, Burns RT, Coppens S, Wheless A, Rezk S, Garrett AL, Parker JS, Foy KK, Shen H, Park BH, Krop I, Anders C, Gastier-Foster J, Rimawi MF, Nanda R, Lin NU, Isaacs C, Marcom PK, Storniolo AM, Couch FJ, Chandran U, Davis M, Silverstein J, Ropelewski A, Liu MC, Hilsenbeck SG, Norton L, Richardson AL, Symmans WF, Wolff AC, Davidson NE, Carey LA, Lee AV, Balko JM, Hoadley KA, Laird PW, Mardis ER, King TA; AURORA US Network; Perou CM. Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis. Nat Cancer. 2023 Jan;4(1):128-147.
PaTH Clinical Research Network
Funded by the Patient-Centered Outcomes Research Institute, PaTH is focused on building a learning health system for the mid-Atlantic region. The network brings together Geisinger Health System, Johns Hopkins University and Health System, Penn State College of Medicine and Milton S. Hershey Medical Center, Temple Health System and Lewis Katz School of Medicine, the University of Utah and University of Utah Health Care, and the University of Pittsburgh and UPMC. The University of Pittsburgh serves as the network's coordinating center and leads the informatics component of PaTH.
Faculty: Michael J. Becich, MD, PhD
Collaborator: Kathleen M. McTigue, MD, MS, MPH
Sample Publication: Boyer AR, Friedman CP, Chuang CH, Hamm ME, Wyncott A, Merritt JG, Becich MJ, Fernandez SA, Ford DE, Kirchner HL, Paranjape A, Williams DA, McTigue KM. The PaTH from discovery to implementation: using a PCORnet Clinical Research Network's own research to prioritize topics for collaborative health improvement activities. Learn Health Syst. 2025 Sep 1;9(4):e70037.
National Mesothelioma Virtual Bank (NMVB)
The National Mesothelioma Virtual Bank (NMVB) is a multi-institutional virtual biospecimen registry whose mission is to accelerate basic science, clinical and translational research on mesothelioma. The University of Pittsburgh serves as the coordinating site and houses the NMVB in the departments of Biomedical Informatics and Pathology. By linking biospecimen resources across partner institutions, including the University of Pennsylvania, NYU Langone Medical Center, Roswell Park Cancer Institute, and the University of Maryland, the NMVB supports investigators working to advance understanding of mesothelioma pathophysiology and to expedite the discovery of preventive measures, novel therapeutic interventions, and, ultimately, cures.
Faculty: Michael J. Becich, MD, Ph.
Collaborators: Brooke T. Mossman, PhD, Haining Yang, MD, PhD, and Tobias Peikert, MD
Sample Publication: Amin W, Parwani AV, Melamed J, Flores R, Pennathur A, Valdivieso F, Whelan NB, Landreneau R, Luketich J, Feldman M, Pass HI, Becich MJ. National Mesothelioma Virtual Bank: A platform for collaborative research and mesothelioma biobanking resource to support translational research. Lung Cancer Int. 2013;2013:765748.
All of Us (AoU) Research Program
The University of Pittsburgh leads the All of Us (AoU) Pennsylvania as an enrollment site in the national AoU Research Program, a landmark National Institutes of Health initiative to collect health data from 1 million people across the United States. The AoU program aims to transform the prevention and treatment of disease by accounting for individual differences in lifestyle, environment and genetics. Notably, Pitt enrolled the first adult and pediatric participants in the program.
Faculty: Shyam Visweswaran, MD, PhD
Collaborator: Steven E. Reis, MD
Sample Publication: All of Us Research Program Investigators; Denny JC, Rutter JL, Goldstein DB, Philippakis A, Smoller JW, Jenkins G, Dishman E. The "All of Us" Research Program. N Engl J Med. 2019 Aug 15;381(7):668-676.
Evolve to Next-Gen Accrual to Clinical Trials (ENACT) Network
The Accrual to Clinical Trials (ACT) Network and its successor, the Evolve to Next-Gen ACT (ENACT) Network, form a federated network connecting academic medical centers nationwide through shared electronic health record data. Funded through the National Center for Advancing Translational Sciences' Clinical and Translational Science Awards Program, ENACT is built on the i2b2/SHRINE platform and operates under shared data standards, common terminology, and a governance framework designed to ensure regulatory compliance and institutional accountability. Data available through the network are used to identify patient cohorts for clinical studies and to support a broad range of biomedical research.
Faculty: Shyam Visweswaran, MD, PhD
Collaborator: Steven E. Reis, MD
Sample Publication: Visweswaran S, Becich MJ, D'Itri VS, Sendro ER, MacFadden D, Anderson NR, Allen KA, Ranganathan D, Murphy SN, Morrato EH, Pincus HA, Toto R, Firestein GS, Nadler LM, Reis SE. Accrual to Clinical Trials (ACT): a Clinical and Translational Science Award consortium network. JAMIA Open. 2018 Oct;1(2):147-152.
Genomic Information Commons (GIC)
As founding members of the Genomic Information Commons (GIC) consortium, the University of Pittsburgh and UPMC Children's Hospital of Pittsburgh helped to establish this federated network alongside Boston Children's Hospital, Cincinnati Children's Hospital Medical Center, the Children's Hospital of Philadelphia, and Washington University in St. Louis. The GIC provides researchers with two complementary access pathways: a Prep-to-Research Portal, through which investigators can execute genotype, phenotype, or combined queries and receive aggregate results in real time; and a Study Portal, through which patient-level data are transferred to a cloud-hosted analytic environment for investigators with appropriate approvals.
Faculty: Shyam Visweswaran, MD, PhD
Collaborators: Jerry Vockley, MD, PhD, Lina Ghaloul Gonzalez, MD, and Kathryn Kernan, MD
Sample Publication: Mandl KD, Glauser T, Krantz ID, Avillach P, Bartels A, Beggs AH, Biswas S, Bourgeois FT, Corsmo J, Dauber A, Devkota B, Fleisher GR, Heath AP, Helbig I, Hirschhorn JN, Kilbourn J, Kong SW, Kornetsky S, Majzoub JA, Marsolo K, Martin LJ, Nix J, Schwarzhoff A, Stedman J, Strauss A, Sund KL, Taylor DM, White PS, Marsh E, Grimberg A, Hawkes C; Genomics Research and Innovation Network. The Genomics Research and Innovation Network: creating an interoperable, federated, genomics learning system. Genet Med. 2020 Feb;22(2):371-380.
Medication Error Avoidance at Regional Scale (MEARS)
The Medication Error Avoidance at Regional Scale (MEARS) initiative is a University of Pittsburgh effort dedicated to advancing patient safety at a regional scale. Operating within the framework of the Jewish Healthcare Foundation's Regional Autonomous Patient Safety (RAPS) program, MEARS works to identify, analyze, and reduce medication errors across health care settings, with a particular focus on preventable adverse drug events among patients transitioning between hospitals and skilled nursing facilities.
Faculty: Richard Boyce, PhD, Eugene M. Sadhu, MD, and Michael J. Becich, MD, PhD
Collaborator: Carl Kingsford, Ph.D.
Sample Publication: Kane-Gill SL, Wong A, Culley CM, Perera S, Reynolds MD, Handler SM, Kellum JA, Aspinall MB, Pellett ME, Long KE, Nace DA, Boyce RD. Transforming the medication regimen review process using telemedicine to prevent adverse events. J Am Geriatr Soc. 2021 Feb;69(2):530-538.
Models of Infectious Disease Agent Study (MIDAS) Network Coordination Center
Mathematical models of infectious disease progression can provide public health officials and policymakers with valuable projections of the timing and magnitude of both emerging outbreaks and recurring waves of seasonal infections. The Models of Infectious Disease Agent Study (MIDAS) is a global network of scientists and practitioners who develop and use computational, statistical and mathematical models to improve understanding of infectious disease dynamics. Launched by the National Institutes of Health in 2004 to help the nation prepare for infectious disease threats, the network has grown into a broad, open research infrastructure.
Faculty: Harry Hochheiser, PhD
Collaborators: Bruce Childers, MD, and Willem G Van Panhuis, MD, PhD
Sample Publication: Pokutnaya D, Childers B, Arcury-Quandt AE, Hochheiser H, Van Panhuis WG. An implementation framework to improve the transparency and reproducibility of computational models of infectious diseases. PLoS Comput Biol. 2023 Mar 16;19(3):e1010856.