Lior S. Pachter is the Bren Professor of Computational Biology and Computing and Mathematical Sciences at the California Institute of Technology (Caltech). He holds a B.S. from Caltech (1994) and a Ph.D. from MIT (1999). His affiliations include the Division of Biology and Biological Engineering at Caltech. Roles: Faculty member, Principal Investigator Departments: Computational Biology and Computing and Mathematical Sciences Research interests span computational and experimental genomics, with a focus on single-cell sequencing technologies and RNA biology. His lab develops tools like kallisto, sleuth, and gget for genomic analysis. Key contributions include methods for quantifying RNA-Seq data and analyzing high-dimensional genomic datasets. Publications highlight advancements in spatial genomics, bioinformatics tools, and genomic data retrieval. His work emphasizes open-source software, with repositories hosted on GitHub.
Dr. Michael Baym is an Associate Professor of Biomedical Informatics at Harvard Medical School with affiliate appointments in Microbiology and the Laboratory of Systems Pharmacology, and as an Associate Member of the Broad Institute. He leads the Baym Lab, which studies microbial evolutionary genomics and antibiotic resistance through a hybrid of experimental, computational, and theoretical approaches. His research focuses on: Antibiotic Resistance Evolution and practical interventions Mobile Genetic Elements (plasmids, phages, transposons) Computational Genomic Algorithms for big data analysis Synthetic Biology tools and technologies Key recent publications explore phage discovery systems , phylogenetic compression of microbial genomes, and RNA-guided gene drives in plasmids. His work is supported by multiple NIH/NIGMS and NSF grants including a MIRA award. Scientific honors include: Packard Fellowship (2018) Pew Biomedical Scholarship (2020) Sloan Research Fellowship (2020) A. Clifford Barger Excellence in Mentoring Award (2021) SSQBio Mentorship Award (2022) The lab actively trains PhD students and postdoctoral fellows with alumni occupying academic and industry positions globally. Current team members include researchers from interdisciplinary backgrounds working at the intersection of experiment, computation, and theory .
Dana Pe'er is a Professor and Chair of the Computational and Systems Biology Program at the Sloan Kettering Institute (SKI) of Memorial Sloan Kettering Cancer Center. She is also an Investigator of the Howard Hughes Medical Institute and holds the Alan and Sandra Gerry Endowed Chair. Dr. Pe'er leads an interdisciplinary research group that combines advanced genomics approaches with machine learning to address fundamental questions in biomedical science, with particular focus on cancer biology, developmental biology, and immunology. Dr. Pe'er earned her PhD from Hebrew University in Jerusalem, Israel. Her academic journey includes a postdoctoral fellowship with George Church at Harvard Medical School. Before joining Memorial Sloan Kettering Cancer Center in 2016, she held faculty positions at Columbia University. Dr. Pe'er's research focuses on understanding cellular plasticity, the consequences of intra-tumor heterogeneity, cancer evolution and metastasis, and the mechanisms by which regulatory circuits go awry in disease. Her lab combines single-cell and spatial profiling technologies with machine learning approaches to investigate gene regulation, cellular plasticity, and cell-cell communication in the contexts of cancer, immunity, and development. They are particularly interested in how organisms develop from a single cell to generate diverse cell types, how epigenetic control rewires during development, and how cells communicate to execute multicellular responses. Analysis of Dr. Pe'er's recent publications reveals a strong focus on developing computational methods for single-cell and spatial genomics data analysis. Her work spans cancer types including pancreatic, prostate, colorectal, and breast cancer, with emphasis on tumor heterogeneity, metastasis mechanisms, and cellular plasticity. A significant portion of her research involves creating novel algorithms and tools like CellRank, REUNION, and SEACells that enable researchers to extract meaningful biological insights from complex genomic datasets. 2023 Class of 2023 Inductee - American Academy of Cancer Research (AACR) Academy 2023 Innovator Award - International Society for Computational Biology (ISCB) 2021 Fellow - International Society for Computational Biology (ISCB) Howard Hughes Medical Institute Investigator (2021) 2019 Ernst W. Bertner Memorial Award - University of Texas MD Anderson Cancer Center 2016 Lenfest Distinguished Faculty Award - Columbia University 2014 Director's Pioneer Award - National Institutes of Health 2014 Overton Prize - International Society for Computational Biology (ISCB) Dr. Pe'er is known for her dedicated mentorship approach, describing herself as "a mama bear" who cares deeply about her trainees while expecting independence, innovation, and hard work. She mentors numerous PhD students and postdocs in her lab. Her HHMI Investigator award provides approximately $9 million over seven years, enabling ambitious research directions. She also collaborates extensively with the Single-cell Analytics and Innovation Lab (SAIL) at MSK to generate new data from emerging technologies, working closely with wet-lab collaborators at MSK and beyond to apply computational methods to cutting-edge datasets across multiple disease areas. The Pe'er Lab is an interdisciplinary group of computational biologists with diverse backgrounds ranging from pure mathematics to clinical medicine. They work closely with wet-lab collaborators to apply their computational methods to cutting-edge datasets across cancer, immunology, and developmental biology. The lab is described as open, supportive, collaborative, and fun, with access to world-class facilities at the Sloan Kettering Institute. Dr. Pe'er's work continues to push the boundaries of computational biology and cancer research, with the ultimate goal of developing more effective, personalized therapies for cancer patients.
Dr. Rong Fan is the Harold Hodgkinson Professor of Biomedical Engineering and Professor of Pathology at Yale University. His research focuses on developing and applying single-cell and spatial omics technologies to study immune systems, cancer, and aging. His lab has pioneered technologies like the IsoCode microchip for high-throughput protein profiling, and spatial multi-omics platforms (e.g., DBiT-seq, spatial-ATAC-seq) to analyze tissue complexity at cellular resolution. He co-founded IsoPlexis, Singleron Biotechnologies, and AtlasXomics to commercialize these innovations. Education: PhD in Chemistry from UC Berkeley (2006), B.S. in Applied Chemistry from University of Science and Technology of China (1999). Postdoctoral training at Caltech before joining Yale in 2010. Research interests include CAR-T cell therapy optimization, spatial epigenomics, and multi-omics integration. Key achievements include discovering biomarkers predictive of CAR-T efficacy and defining spatial genomic landscapes in cancer and neuroinflammation. Awards: NSF CAREER Award, Packard Fellowship, election to AIMBE, CASE, and NAI. Serves on advisory boards for Bio-Techne and Yale Ventures. Active in training future scientists via the Yale Biomedical Engineering and Yale School of Medicine programs.
Vitaly Kheyfets, PhD, serves as Associate Professor in the Department of Pediatrics-Critical Care Medicine at the University of Colorado Anschutz Medical Campus School of Medicine, where he directs research at the intersection of pediatric critical care and cardiopulmonary pathophysiology with emphasis on pulmonary arterial hypertension (PAH). His primary research focuses on right ventricular adaptation to pulmonary hypertension, utilizing machine learning-driven multi-omics analysis to identify disease biomarkers and molecular networks. He pioneers computational fluid dynamics approaches for hemodynamic modeling in congenital heart conditions like Glenn physiology, while also investigating sleep oscillatory patterns as neurodegenerative biomarkers. His methodology integrates proteomics, spatial transcriptomics, and pressure waveform analysis to dissect vascular remodeling mechanisms. Publication trends reveal a strong emphasis on translating computational models into clinical applications for PAH prognostication, with recent work developing AI-cooperative diagnostic platforms and characterizing microvascular changes in the right ventricle. Cross-disciplinary collaborations span proteomics, imaging, and sleep neuroscience, demonstrating consistent innovation in both pulmonary hypertension and neurodegenerative disease biomarker discovery.
Dr. Pamela D. Roberts is a Professor of Plant Pathology and State Extension Specialist for Vegetable Pathology at the University of Florida's Southwest Florida Research and Education Center (SWFREC) in Immokalee, FL. She holds a B.Sc. in Horticultural Sciences from Kansas State University, an M.S. in Plant Pathology from the University of Hawaii, and a Ph.D. in Plant Pathology from the University of Florida. Her research focuses on sustainable disease management in vegetables and specialty crops, emphasizing integrated management strategies for bacterial and fungal-like pathogens. She leads the Florida Extension Plant Disease Diagnostic Laboratory at SWFREC, offering diagnostic services and disease management recommendations. Her extension programs include educational outreach on plant diseases and field demonstrations of integrated management techniques. Dr. Roberts has received prestigious awards such as the UF/IFAS Jim App Team Award and the Dallas Townsend Distinguished Extension Award. She serves as Editor-in-Chief of the American Phytopathological Society journal Plant Health Progress . Her work spans disease diagnosis, epidemiology, and pathogen evolution, with a strong emphasis on crops like tomato, pepper, and citrus. Her research publications address topics such as Xanthomonas pathogen diversity, remote sensing for disease detection, and sustainable agricultural practices. She collaborates on projects involving molecular diagnostics, pest management strategies, and crop resilience. Ongoing efforts include combating bacterial spot diseases, whitefly-transmitted viruses, and citrus black spot.
James Zou is an Associate Professor of Biomedical Data Science at Stanford University, with courtesy appointments in Computer Science and Electrical Engineering. His research focuses on advancing machine learning methodologies for healthcare applications, emphasizing reliability, fairness, and statistical rigor. He holds a Ph.D. from Harvard University and has held positions at Microsoft Research, Cambridge University (as a Gates Scholar), and UC Berkeley (Simons Fellow). Zou leads the Stanford Data4Health hub and is a Chan-Zuckerberg Investigator. His work spans AI-driven diagnostics, spatial transcriptomics, and ethical AI frameworks. Key achievements include the EchoNet AI system for echocardiography and foundational contributions to data valuation (e.g., Data Shapley). Awards include the Sloan Fellowship, NSF CAREER Award, and Google/Tencent AI awards. Education: Ph.D., Harvard University (2014); Postdoctoral roles at Microsoft Research, Cambridge, and Berkeley. Research Interests: Machine learning for healthcare, algorithmic fairness, interpretable AI, spatial omics, and translational bioinformatics. His lab develops tools like TextGrad (PyTorch for text agents) and frameworks for evaluating medical AI systems. Recent work addresses LLMs in peer review and clinical decision-making. Grants/Grants: Supported by NSF, Sloan Foundation, Chan-Zuckerberg Initiative, and industry partnerships (Google, Amazon, Adobe). Advises on over 20 doctoral students, many contributing to high-impact papers in Nature , Science , and top conferences (NeurIPS, ICML). Leads collaborations in cardiology, oncology, and veterinary medicine. Labs/Teams: Stanford AI Lab, Stanford Data4Health, and interdisciplinary groups in precision medicine. Active in open-source projects like FrugalML and MetaViz.
Ben Cosgrove is an Associate Professor in the Meinig School of Biomedical Engineering at Cornell University, serving as Director of Graduate Studies. His research focuses on systems bioengineering approaches to understand muscle stem cell dysfunction in aging and disease. He leads the Cosgrove Lab, a multidisciplinary group integrating biomedical engineering, stem cell biology, and systems biology to study microenvironmental signaling in muscle regeneration. His work includes developing biomimetic microenvironments for stem cell manufacturing and improving regenerative medicine therapies. Dr. Cosgrove holds a B.Eng. from the University of Minnesota (2003) and a Ph.D. in Bioengineering from MIT (2009). Postdoctoral training at Stanford University (with Dr. Helen Blau) followed. His research is supported by NIH grants (including R01, R21), the Glenn Medical Research Foundation, and others. He has been recognized with awards such as the BMES Graduate Research Award (2008), Rising Star Award (2015), and Swanson Teaching Excellence Award (2019). Research interests span bioengineering, biomechanics, computational science, and systems biology. His lab's innovations include spatial transcriptomic mapping and high-yield stem cell expansion platforms. Current projects aim to decode stem cell-niche interactions to treat muscle degeneration and aging. Grants: NIH K99/R00, R01, R21; Glenn Medical Research Foundation Labs/Teams: Cosgrove Lab (Cornell University) Future Work: Expanding applications of spatial transcriptomics and engineering regenerative therapies for muscle diseases
Dr. Christina Leslie is a Research Professor and Member of the Computational & Systems Biology Program at Memorial Sloan Kettering Cancer Center (MSK). She leads an active research laboratory focused on developing computational approaches to understand complex biological systems. Dr. Leslie earned her PhD from the University of California, Berkeley and has established herself as a leading computational biologist in cancer research and immunology. Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center Gerstner Sloan Kettering Graduate School of Biomedical Sciences Dr. Leslie's research focuses on developing novel computational methods to study cellular biological systems from a global and data-driven perspective. Her lab exploits diverse high-throughput functional and genomic data to understand molecular networks underlying fundamental cellular processes, including transcription regulation, pre-mRNA processing, signaling, and post-transcriptional gene silencing. Her algorithmic methods draw heavily on machine learning to build accurate predictive models from noisy and high-dimensional biological data. Key areas of interest include modeling cell-type specific transcriptional programs and dissecting co- and post-transcriptional regulation, particularly microRNA-mediated gene regulation. Analysis of Dr. Leslie's publication record over the last five years reveals a strong focus on computational approaches to cancer genomics, immunology, and epigenetics. Her work bridges multiple disciplines, with a particular emphasis on developing machine learning methods to interpret complex biological data. The publications demonstrate increasing sophistication in integrating multiple data types (genomic, transcriptomic, epigenomic) to understand cancer biology and immune responses. Recent work shows a growing emphasis on single-cell technologies and spatial analysis of tumor microenvironments. Introduction of string kernel methodology for SVM classification of biological sequences Development of algorithms for predictive modeling of gene regulation First systems-level analyses of competition between microRNAs and between target transcripts Dr. Leslie actively mentors numerous graduate students and research associates, with current lab members including Vianne Gao, Alireza Karbalaghareh, Erik Ladewig, and several others. Her lab has received significant research funding to support their work on computational approaches to cancer biology and immunology. The Leslie Lab maintains close collaborations with multiple experimental groups at MSK, facilitating the translation of computational insights into biological understanding. The Leslie Lab operates within the Computational & Systems Biology Program at MSK, with strong ties to both the research and clinical missions of the institution. The lab maintains state-of-the-art computational infrastructure for analyzing large-scale genomic and proteomic datasets and collaborates extensively with wet-lab researchers to validate computational predictions experimentally.
Maizie Zhou is an Assistant Professor in Biomedical Engineering and Computer Science at Vanderbilt University’s School of Engineering. She holds dual PhDs in Computer Science (Stanford University) and Neuroscience (Wake Forest School of Medicine), with additional degrees from Wake Forest University and Huazhong University of Science and Technology. Her research focuses on computational genomics, bioinformatics, and machine learning applied to problems in cancer genomics, single-cell and spatial transcriptomics, and computational neuroscience. She leads the Zhou Lab, which develops algorithms for structural variant detection, neural circuit analysis, and integrative omics approaches. Recent work includes tools like VolcanoSV and stDyer, and she has received grants from NIH, Vanderbilt Brain Institute, and industry partnerships. Key achievements include VUSE Best Paper Awards, Global Engagement Travel Grants, and mentoring students in prestigious programs like the Provost’s Pathbreaking Discovery Award. Her lab also explores the neural underpinnings of cognitive maturation in primates, combining computational and experimental neuroscience. Education: PhDs in Computer Science (Stanford) and Neuroscience (Wake Forest), MS (Computer Science, Wake Forest), BS (Biotechnology, Huazhong). Research interests span computational genomics (e.g., structural variant detection, haplotype phasing), spatial transcriptomics (clustering, integration), and computational neuroscience (neural circuit dynamics, prefrontal cortex plasticity). Her lab’s tools address challenges in precision medicine, cancer genomics, and understanding adolescent brain development. Recent projects include NIH-funded work on spatial transcriptomics and collaborations with Dr. Meltzer’s lab on cancer genomics. Publications highlight advancements in bioinformatics tools and neural mechanisms, with trends toward multi-omics integration and algorithmic innovation in genomics. Awards include the Global Engagement Travel Grant and CCSB Accelerator Fund. Students under her mentorship have excelled in qualifying exams and travel grants, reflecting her impactful training program.
Sudin Bhattacharya is an Associate Professor at the BioMolecular Science Gateway, Michigan State University, with affiliations in the Genetics & Genome Sciences Program and Cell & Molecular Biology Program. His research bridges computational biology and toxicology to understand complex biological systems. Email: sbhattac@msu.edu Research Interests Dr. Bhattacharya specializes in systems toxicology, focusing on computational modeling of gene regulatory networks, single-cell transcriptomics, and molecular dynamics in response to environmental toxicants. His work examines how chemical exposures disrupt cellular pathways and contribute to disease mechanisms. Article Trends His recent publications emphasize: Single-cell and single-nucleus RNA sequencing for toxicological profiling Computational models of circadian rhythms and intercellular communication Dose-dependent responses to environmental chemicals like TCDD and heavy metals Mechanistic studies of adipose tissue remodeling and hypertension Applications of machine learning in chemical risk assessment Integrative approaches to liver metabolism and disease modeling Scientific Contributions Dr. Bhattacharya has pioneered multiscale modeling of biological systems, particularly in hepatic and vascular contexts. His work on the aryl hydrocarbon receptor and PPARα signaling networks has advanced predictive toxicology frameworks.
Dr. Qin Li is an Assistant Professor of Genetics at the University of Pennsylvania Perelman School of Medicine, affiliated with the Penn Institute for Immunology & Immune Health (I3H), the Penn Institute for RNA Innovation, and the Penn Center for Genomic Integrity. He earned his BS and PhD in Biological Science and Biochemistry & Molecular Biology from Peking University, followed by postdoctoral training at Stanford University. Education : BS (Peking University, 2009), PhD (Peking University, 2014) Dr. Li’s research focuses on the ADAR1-dsRNA-MDA5 axis, exploring how RNA editing mediates self/non-self discrimination in the immune system. His work connects RNA editing quantitative trait loci (edQTLs) to inflammatory disease heritability and develops computational/experimental tools for RNA editing and sensing. Recent publications highlight his contributions to understanding RNA editing’s role in autoimmune diseases, CRISPR-based regulatory principles, and novel RNA ligand engineering. He mentors PhD and Master’s students in Bioengineering, Cell and Molecular Biology, and related programs.
Kai Mesa is an Assistant Professor in the Department of Molecular Biology at Princeton University, where he leads the Laboratory of Macrophage Dynamics. His research integrates immunology, stem cell biology, and advanced imaging to study macrophage behavior in tissue regeneration and aging, primarily using mouse skin models. Education: Ph.D., Yale University B.S., University of California, Berkeley Dr. Mesa's research focuses on understanding how macrophages establish niche-specific identities, influence wound healing outcomes, and contribute to age-related tissue dysfunction. By combining multiphoton intravital microscopy with spatial transcriptomics, his lab investigates the molecular and cellular dynamics governing immune cell integration, tissue regeneration, and aging. His work has significant implications for regenerative medicine and immunosenescence. The recent publications highlight a consistent trend in studying cellular dynamics in vivo, particularly in skin and immune systems. The research spans stem cell regulation, macrophage function, and immune-microenvironment interactions, with increasing focus on aging and spatial organization. Key methodologies include intravital imaging, lineage tracing, and single-cell spatial analysis. Scientific Awards: Charles H. Revson Senior Fellowship in Biomedical Science (2021) Jane Coffin Childs Postdoctoral Fellowship (2017) Carolyn Slayman Prize in Genetics, Yale University (2017) ASCB Beckman Coulter Distinguished Graduate Student Achievement Prize (2015) National Science Foundation Graduate Research Fellowship (2014) Dr. Mesa has been supported by competitive fellowships during his graduate and postdoctoral training. He mentors research in a dynamic lab environment and is actively recruiting new members. His advising focuses on interdisciplinary approaches combining imaging, molecular biology, and systems-level analysis of tissue-immune interactions. The Mesa Lab, also known as the Laboratory of Macrophage Dynamics, utilizes cutting-edge techniques such as multiphoton intravital microscopy and spatial transcriptomics to study macrophage behavior in living tissues. The lab explores fundamental questions about immune cell niche establishment, wound-induced immune dynamics, and age-related immune dysfunction in mammalian skin.
Nathan G. Swenson is a Professor in the Department of Biological Sciences at the University of Notre Dame and serves as the Gillen Director of the Environmental Research Center (UNDERC). He has held prior academic positions at the University of Maryland and Michigan State University, advancing from Assistant to full Professor. His research integrates genomics, ecology, and evolutionary biology to understand forest biodiversity and dynamics. Research Interests: Ecology and Environmental Biology Evolutionary Biology Genetics and Genomics Global Change Biology Forest Ecology Functional and Phylogenetic Ecology Tree Physiology and Demography His research focuses on leveraging intra- and interspecific variation in tree performance to predict forest biodiversity patterns. He employs integrative approaches from genomes to forest canopies and utilizes large-scale global datasets. Recent publications emphasize intraspecific trait variation, transcriptomic responses to drought, ecological forecasting, and functional group dynamics in tropical and temperate forests. Scientific Awards: Winner of 2017 British Ecological Society John Harper Prize (awarded to J. Zambrano; Swenson was senior author) Advising and Grants: Dr. Swenson has mentored numerous researchers, including M.N. Umana, S.J. Worthy, and J. Yang, who frequently co-author high-impact papers. His lab receives substantial research funding, evident from large collaborative projects and participation in global networks like ForestGEO and the TRY plant trait database. He has secured support for long-term ecological research, genomic studies, and international fieldwork. Labs and Teams: He leads the Swenson Lab, which conducts research on woody plant ecology in dynamic environments. The lab emphasizes community transcriptomics, functional trait analysis, and large-scale ecological modeling. It collaborates widely across institutions and is involved in major initiatives such as ForestGEO and NEON.
Guizhen Zhao is an Assistant Professor at the University of Houston College of Pharmacy , Department of Pharmacological and Pharmaceutical Sciences. Her research focuses on epigenetic and molecular mechanisms in cardiovascular diseases (CVD), particularly aortic aneurysm, dissection, and atherosclerosis, with a goal to drive drug discovery innovations. Major research areas: Metaboloepigenetic properties of vascular cells, chromatin remodeling, vascular cell crosstalk Methodologies: bulk RNA-seq, single-cell RNA-seq, ChIP-seq, ATAC-seq, spatial transcriptomics, metabolomics Ongoing projects include studying BAF60c-dependent epigenetic modifications in smooth muscle cell biology, BAF60c-mediated iPSC differentiation, BAF60a in endothelial dysfunction, and vascular cell interactions in CVD development. Scientific contributions include 15+ publications on abdominal aortic aneurysm, atherosclerosis, and chromatin remodeling mechanisms, with recent work on adenosine kinase inhibition and KLF11 as therapeutic targets. 2023-25: Career Development Award, American Heart Association 2021-22: Postdoctoral Fellowship, American Heart Association 2019: Young Investigator Award, American Heart Association
