Speakers
Meaghan O'Malley Morris, MD PhD
Dr. Meaghan Morris is an Assistant Professor in the Divisions of Bayview Surgical Pathology and Neuropathology, The Johns Hopkins School of Medicine. In addition to her clinical practice in pathology, she leads a basic research program focusing on understanding the molecular basis for Alzheimer’s disease and other age-related dementias, with the ultimate goal of identifying new therapeutic targets for Alzheimer’s disease treatment. These investigations combine insights from brain tissue donated by patients with age-related neurodegenerative diseases, studies in cell culture models, and cutting edge molecular techniques to uncover new pathways involved in Alzheimer’s disease. Currently, her research is focused on how neuronal function and neuronal synapses are regulated by the microtubule-associated protein tau, a key pathologic protein which aggregates in Alzheimer’s disease and related dementias.
Shikhar Uttam, PhD
Dr. Uttam is an Assistant Professor at Department of Computational and System Biology, The University of Pittsburgh School of Medicine. The primary focus of his research program is computational imaging and optics, signal and systems, machine learning and imaging science applied to cancer systems biology, cancer epigenetics, early cancer detection, and precision medicine. The secondary focus is computational biology and bioinformatics. Other interests of his lab includes radar imaging and quantum information theory.
Hatice U. Osmanbeyoglu, MS PhD
Dr. Osmanbeyoglu is an Assistant Professor at Department of Biomedical Informatics, The University of Pittsburgh. The primary focus of her group is developing integrative statistical and machine learning approaches for extracting therapeutic insight from highly heterogenous omic datasets, clinical and drug response data for the purpose of precision medicine. Her lab's research projects are in the areas of cancer genomics, epigenetics of drug response, and immunotherapy and are executed through multi-disciplinary collaborations. Her lab has a particular interest in developing statistical methods for single cell multi-omics integration.
Osama Shiraz Shah
Osama Shiraz Shah is a 5th Year Graduate Student in The University of Pittsburgh Integrative System Biology PhD Program. He is a breast cancer researcher and bioinformatician. His dissertation mentors are Drs. Adrian Lee and Steffi Oesterreich. Osama's research interests include utilizing genomic assays and bioinformatic analyses to investigate understudied subtypes of breast cancer (BC). In a subset of BC cases, the lobular growth appears admixed with ductal growth patterns. This subset of morphological heterogenous BCs is known as mixed ductal and lobular carcinoma (mDLC). These are rare and elusive disease with little known about its molecular features. To improve our understanding of this elusive disease, he performed digital spatial profiling towards identify molecular differences between lobular and ductal regions. These features were associated with clinical significance suggesting that ductal and lobular phenotypes in mDLC can result in prognostic uncertainty in terms of treatment response and disease evolution.
James Zou, PhD
Dr. Zou is an Assistant Professor of Biomedical Data Science and, by courtesy, of Computer Science and Electrical Engineering at Stanford University. He works on making machine learning more reliable, human-compatible and statistically rigorous, and is especially interested in applications in human disease and health. Several of his lab's algorithms are widely used in tech and biotech industries. He received a Ph.D from Harvard in 2014, and was a member of Microsoft Research, a Gates Scholar at Cambridge and a Simons fellow at U.C. Berkeley. He joined Stanford in 2016 and was an inaugural Chan-Zuckerberg Investigator and the faculty director of the university-wide Stanford Data4Health hub. Dr. Zou is also a member of the Stanford AI Lab. His research is supported by the Sloan Fellowship, the NSF CAREER Award, and Google, Amazon and Adobe AI awards.
Rita Strack, PhD
Dr. Strack obtained her Ph.D. in Biochemistry and Molecular Biology from the University of Chicago. While there, she worked with Benjamin Glick and Robert Keenan to engineer improved variants of the red fluorescent protein DsRed, and also studied the chemical mechanism of chromophore formation in DsRed. She continued her research as a postdoctoral fellow in Samie Jaffrey's laboratory at Weill Cornell Medical College, where she developed fluorescent reporters for live-cell imaging of RNA such as Spinach2. She handles imaging, microscopy and probes, along with protein and RNA biochemistry content for the journal. Rita joined Nature Methods in November 2014.
Jian Ma, PhD
Dr. Ma is the Ray and Stephanie Lane Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University. He also has an Affiliated Faculty appointment in Machine Learning. His group started at the University of Illinois at Urbana-Champaign in August 2009. His lab moved to Carnegie Mellon in January 2016. The main focus of his ongoing research is the development of machine learning algorithms to reveal fundamental connections between human genome structure and function and their implications in human diseases. Recent interests include nuclear genome organization, single-cell epigenomics, spatial omics, comparative genomics, and complex molecular interactions. His lab is currently leading a UM1 Center in the Phase 2 of NIH 4D Nucleome (4DN) Program. He also serves as a co-chair (with Geeta Narlikar and Ana Pombo) of the Steering Committee of the 4DN Consortium. In addition, his lab is currently involved in the NIH SenNet Consortium and the IGVF Consortium. Dr. Ma has received numerous awards, including, among others, being named "Tomorrow's PI" by Genome Technology (2011), a National Science Foundation CAREER award (2011), and a Guggenheim Fellowship (2020).
Ruxuan (Rosy) Li
Ruxuan (Rosy) Li is a 3rd Year Graduate Student in The University of Pittsburgh Bioengineering PhD Program. Her dissertation mentor is Dr. Ioannis (Yannis) Zervantonakis. Rosy received her bachelor’s degree in Biomedical Engineering from Southern University of Science and Technology in 2020. In her senior year, she went to Bone Bioengineering Lab, Columbia University for a one-year research program, where her work focused on the mechanobiology of bone modeling and remodeling. She joined Zervantonakis lab in Fall 2020. Rosy is interested in using bioinformatics and 3D tissue culture models to study the dynamics of immune cells in breast tumors. Outside the lab, she enjoys playing piano and singing.
Amanda C. Poholek, PhD
Dr. Poholek is an Assistant Professor at Department of Pediatrics and Department of Immunology, University of Pittsburgh. Her research focuses on understanding how immune cells integrate signals encountered in the environment to drive functional outcomes at the molecular and epigenetic level in both health and disease. While the basic mechanisms of immune cell differentiation have been defined, the role that transcription factors play in shaping the epigenetic landscape during differentiation remains unclear. Specific projects are focused on the role of Blimp-1 in allergic asthma, and the role of metabolism in shaping the epigenome of T cells during differentiation and function. Dr. Poholek is also the Director of the Health Sciences Sequencing Core at UPMC Children’s Hospital of Pittsburgh.
Tullia C. Bruno, PhD
Dr. Bruno is an Assistant Professor in the Department of Immunology at the University of Pittsburgh and a faculty member in the Tumor Microenvironment Center and the Cancer Immunology and Immunotherapy Program at the UPMC Hillman Cancer Center. She obtained her Ph.D. in Immunology from Johns Hopkins in 2010 and completed her postdoctoral fellowship at the University of Colorado in 2015—both with a focus in tumor immunology. While Dr. Bruno’s PhD training focused on inhibitory receptors on intratumoral T cells, she became interested in the role of B cells in the tumor microenvironment (TME) during her postdoctoral fellowship and has built her independent research program around understanding intratumoral B cell function within tertiary lymphoid structures in multiple human cancers. Dr. Bruno’s research lab has an overt focus on studying immunity within cancer patients, which makes her research highly translational with the potential for future clinical trials targeting B cells. Thus, Dr. Bruno’s overall research objective is to develop a B cell-specific immunotherapy in the next five to ten years.
Yufei Huang, PhD
Dr. Huang is Professor of Medicine at The University of Pittsburgh, and Leader of AI Research at UPMC Hillman Cancer Center. He is member of Hillman Cancer Virology Program. Dr. Huang’s research focuses on two main areas: 1. m6A methylation and its role in cancer. His lab uses a combination of computation/AI and high throughput profiling technologies to 1) delineate regulation of m6A deposition; 2) determine the mechanisms by which m6A regulates gene expression and downstream functions; 3) m6A’s role in cancer and viral infection. His lab developed many computation tools and resources for analyzing m6A profiling data and predicting m6A functions including the exomePeak pipeline for detecting m6A and differential m6A sites from MeRIP-seq, m6A-express for predicting m6A-regulation of gene expression, FunDMDeep-m6A for prioritizing functional differential m6A sites, and the MeT-DB database. 2. AI for precision oncology. His lab focuces on developing novel deep learning and AI models that can 1) perform cancer phenotype predictions and, at the same time, 2) identifying markers and generate explainable mechanisms. His lab has developed several genomics-based deep learning/AI tools for cancer prognosis and survival analysis, drug response prediction, and cancer gene dependence prediction.
Riyue Bao, PhD
Dr. Bao is an Associate Professor of Medicine at The University of Pittsburgh. She is a member of the Hillman Cancer Center (HCC) Cancer Biology Program and Co-Director of the UPMC HCC Cancer Bioinformatics. Her work bridges methodological advances and biomedical applications with a direct impact on accelerating the knowledge discovery to new clinical trials that could benefit patients. Dr. Bao's lab marries both dry and wet lab techniques, with a primary focus on the data-driven discovery of resistance mechanisms to cancer immunotherapy, integrating single-cell sequencing, spatial imaging, and deep learning-assisted digital pathology. Her work provides the scientific rationale that has directly led to the opening of new trials that combine targeted therapy with immune checkpoint inhibitors, such as ivosidenib plus nivolumab in IDH1 mutant tumors. Dr. Bao is Leader of Bioinformatics on the Melanoma and Skin Cancer SPORE and Head and Neck SPORE, member of the Society for Immunotherapy of Cancer (SITC) Big Data and Data Sharing Committee, and serves as the Ad-Hoc member of the Cancer Center Data Science Strategy Committee.