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.
David Serre is a Professor in the Department of Microbiology and Immunology at the University of Maryland School of Medicine, with an additional appointment at the Institute for Genome Sciences. His research focuses on developing genomic approaches to study eukaryotic pathogens, particularly Plasmodium vivax, the leading cause of malaria outside Africa. His laboratory investigates parasite responses to antimalarial drugs, host immune responses, and mosquito vector biology using genomic and transcriptomic techniques. Education 1997–2000: Engineering degree in Chemistry, École Nationale Supérieure de Chimie, Montpellier, France 2000–2004: PhD in Biology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 2004–2007: Postdoctoral fellowship, McGill University and Genome Quebec Innovation Centre, Montreal, Canada Research Focus Dr. Serre’s work integrates genomics to study Plasmodium vivax’s drug resistance, relapse mechanisms, and interactions with hosts and vectors. Key areas include: Genomic assays to characterize parasite drug responses Transcriptomic analysis of host immune responses Genomic studies of Anopheles mosquitoes as malaria vectors Recent Trends in Publications Recent work highlights genomic and transcriptomic approaches to dissect Plasmodium vivax biology, including: Single-cell RNA sequencing to resolve transcript isoforms and stage-specific expression Analysis of relapse dynamics and drug resistance mechanisms Microbiome studies in mosquitoes and environmental contexts Grants & Advising No explicit grants or advisee names are listed in the provided text. Collaborators include institutions like the Max Planck Institute, McGill University, and the Institute for Genome Sciences. Labs & Teams His lab is affiliated with the University of Maryland School of Medicine and the Institute for Genome Sciences, focusing on genomic and molecular approaches to infectious diseases.
Dr. Gary Brewer is a Professor in the Department of Entomology at the University of Nebraska-Lincoln, with a 60% research and 40% teaching appointment. He has served as department head at NDSU (1997-2006) and UNL (2006-2018). His research focuses on field crops entomology, IPM of pasture cattle flies, salt creek tiger beetle conservation, and pollinator health. He has pioneered a push-pull strategy using coconut oil-derived repellents and led curriculum design for Rwanda’s Conservation Agriculture program. Education: B.S. in Zoology, University of Nebraska-Lincoln (1974) M.S. in Entomology, University of Nebraska-Lincoln (1978) Ph.D. in Entomology, Kansas State University (1984) Research Interests: Brewer’s work spans insect ecology, pest management, and conservation. Key areas include stable fly and horn fly control, pollinator protection, and endangered species recovery (e.g., Salt Creek tiger beetle). His lab develops natural product-based pest repellents and evaluates biopesticides for sustainable agriculture. Grants & Contributions: $362,150 USDA grant for undergraduate research in beneficial insect protection (2018) $325,000 USDA grant for multi-tactic stable fly control (2017) NE Game and Parks funded salt creek tiger beetle reintroduction programs Labs & Teams: Brewer’s team collaborates with industry (e.g., Vestergaard Frandsen) and international partners to advance IPM strategies. His work bridges field research with applied solutions for farmers and conservationists.
Donald Rio holds the Richard and Rhoda Goldman Distinguished Chair in the Biological Sciences and is a Professor of Biochemistry, Biophysics, and Structural Biology. He is affiliated with the Division of Biochemistry and Molecular Biology and the Center for Integrative Genetics. His lab focuses on nucleic acid transactions, including transposable element mobilization (P elements) and RNA binding protein mechanisms controlling alternative splicing. Research highlights include studies on THAP9 proteins in humans/zebrafish, cryo-EM structural analysis of transposase-DNA complexes, and splicing regulation in neurodegenerative diseases like ALS and Parkinson’s. His work combines biochemical, genetic, and computational approaches, including the development of the Junction Usage Model (JUM) for splicing analysis. Research interests span transposition mechanisms linked to HIV integration, immune system recombination, and evolutionary genome dynamics. His team investigates how RNA binding proteins like hnRNPA1 influence splicing in disease contexts, with projects involving CRISPR-based models and patient RNA-seq data analysis. Collaborations include studies on splicing accuracy across tissues and age, and the impact of splicing defects in neurodegenerative disorders. Key awards include the Goldman Chair. His lab’s contributions bridge fundamental molecular mechanisms with translational applications in genetic disease modeling and drug discovery. Recent work focuses on isogenic stem cell models (iSCORE-PD) for Parkinson’s research and structural biology insights into transposase function. Grants and projects involve NIH funding for ALS splicing studies and collaborations with institutions like the Buck Institute. His lab actively publishes in top journals such as Genome Research , PNAS , and Nature , with a strong emphasis on cryo-EM and bioinformatic methods.
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.
Nicole C. Riddle is a Professor and Associate Chair for Research and Facilities in the Department of Biology at the University of Alabama at Birmingham (UAB). She holds a B.S. in Biology from the University of Missouri Columbia and a Ph.D. in Evolutionary and Population Biology from Washington University in St. Louis. Her research focuses on epigenetics and chromatin dynamics, particularly in the context of aging and sex differences using Drosophila melanogaster as a model system. Dr. Riddle's work explores how epigenetic mechanisms influence lifespan, genome stability, and phenotypic variation. She has pioneered the use of Drosophila to study exercise-induced physiological changes and their genetic underpinnings. Her lab investigates the roles of HP1 proteins in transcriptional regulation and chromatin organization, with recent studies emphasizing cross-species comparisons of aging mechanisms. Her research has been supported by grants including the BII: IISAGE project on sex-specific aging mechanisms. Notable contributions include developing novel tools like the Rotating Exercise Quantification System (REQS) to measure Drosophila activity levels. Dr. Riddle actively mentors students and postdoctoral researchers, inviting inquiries via riddlenc@uab.edu to join her lab.
Ramesh Shanmughom Pillai is a Full Professor at the Department of Molecular Biology, University of Geneva, Switzerland. He holds additional roles as a Visiting Professor at the University of Kumamoto, Japan, and has been a Group Leader at EMBL Grenoble and a postdoctoral fellow at the Friedrich Miescher Institute. His research focuses on RNA modifications, epigenetics, and piRNA pathways in germline biology. Pillai has received prestigious awards including the ERC Consolidator Grant and The RNA Society Scaringe Award. Education: BSc Botany (University of Kerala, India) MSc Biotechnology (IIT Roorkee, India) PhD in Cell Biology (University of Bern, Switzerland) Research Interests: Pillai’s work centers on RNA biology, particularly the role of RNA modifications (e.g., m6A, m6Am) in development and fertility. He investigates piRNA biogenesis, transposon silencing, and the molecular mechanisms of RNA-protein interactions. His studies bridge biochemistry, genetics, and structural biology to elucidate how RNA molecules regulate critical biological processes. Teaching & Service: At the University of Geneva, he teaches Molecular Biology courses (BSc/MSc levels) and advises 5 PhD students and 4 postdocs. He chairs the ERC Consolidator Grant Review Panel and organizes major conferences like the PIWI/piRNAs Meeting and Swiss RNA Workshop. Pillai also serves on editorial boards for Nucleic Acids Research and RNA . Awards: ERC Consolidator Grant (2015) Best PhD Thesis Award (2003) RNA Society Scaringe Award (2005) Grants & Labs: Funded by ERC Starting and Consolidator Grants, his lab explores RNA modification networks in germ cells. Former trainees include Professors Simon Conn (Flinders University) and Hao Wu (CAS, China).
Xian Wu, Ph.D., serves as a Research Assistant Professor in the Department of Pharmacology & Toxicology at East Carolina University's Brody School of Medicine. Her research leverages human stem cell models to investigate developmental vulnerabilities to environmental contaminants in cardiovascular and neural systems, with emphasis on epigenetic mechanisms and disease modeling. Dr. Wu's academic credentials include: Ph.D. in Toxicology from the University of Georgia M.S. in Biomedicine from East China Normal University B.S. in Biotechnology from Anhui University Her postdoctoral training comprised a Fellowship at the National Institute of Environmental Health Sciences and an ORISE Fellowship at the U.S. Food and Drug Administration. Research focuses on creating human stem cell-derived organoid systems to model developmental toxicology, particularly examining cardiac and neural development under chemical exposure. The laboratory employs fluorescence reporter systems and RNA-seq to identify critical vulnerability windows during early development, with recent work targeting Parkinson's disease mechanisms through dopaminergic neuron models and cardiac fibrosis via advanced organoids. Methodological innovations include high-content imaging for neurogenesis quantification and epigenetic pathway analysis. Publication trends (2016-2025) demonstrate consistent advancement in stem cell-based toxicology testing, with increasing emphasis on micro/nanoplastics risk assessment, arsenic neurotoxicity mechanisms, and doxorubicin cardiotoxicity modeling. The work bridges environmental health, epigenetics, and regenerative medicine through interdisciplinary approaches. Scientific recognition includes: 2025 SPARC Award (ECU) 2024 Top Abstract Award (Developmental Origins of Health and Disease Society) 2024 NIEHS P30 Center Travel Award 2023 ECU Research and Creative Activity Award Dr. Wu actively mentors graduate researchers including Ph.D. candidate Cate Duncan and M.S. students Kamilah Muhammad and Bailey Skeen, alongside undergraduate Bryce Tilghman. Former trainees McKyrah Brown and Monica Cross completed honors theses in the laboratory. Current grants include ECU's SPARC Award funding stem cell model development for environmental contaminant testing. The BSOM 6S-11 laboratory maintains specialized capabilities in cardiac and cerebral organoid generation, fluorescence-based toxicity screening, and RNA-seq epigenetic analysis. Collaborative networks include the National Institute of Environmental Health Sciences and ECU's Center for Human Health and the Environment, supporting translational research on developmental vulnerability periods.
Jeremy Wang, PhD is an Assistant Professor in the Department of Genetics at the UNC School of Medicine . His research focuses on applying high-performance computational methods and machine learning to analyze high-throughput sequence data using long-read technologies (e.g., Oxford Nanopore) to advance precision personalized medicine . Key disease areas include Inflammatory Bowel Diseases (IBD) Respiratory Infectious Diseases His lab specializes in microbiome analysis , host-pathogen interactions , and computational genomics , working with collaborators in clinical, translational, and computational domains. His publications demonstrate expertise in long-read sequencing applications for Pediatric cancer classification SARS-CoV-2 genomic epidemiology Microbiome spatiotemporal dynamics Murine disease models Drosophilid genome assemblies Metagenomic bias analysis Collaborations span UNC and global institutions, with current work extending to clinical laboratory partnerships for pathogen sequencing and oral microbiome sampling methodology.
Dr. Andre Kahles is a Lecturer in the Department of Computer Science at ETH Zürich, specializing in biomedical informatics. His research focuses on computational methods for analyzing large-scale genomic and transcriptomic data, with applications in cancer genomics, metagenomics, and precision medicine. He has contributed to the development of tools such as SplAdder for alternative splicing analysis, MetaGraph for petascale genomic data exploration, and SECEDO for subclone detection in cancer genomes. His work bridges algorithmic innovation with biological insights, addressing challenges in single-cell analysis, genome graph alignment, and multi-omics integration. Key research themes include: Developing scalable algorithms for processing nanopore sequencing and metagenomic data Characterizing somatic mutations and non-coding drivers in cancer genomes Advancing genome graph-based alignment and annotation methods Integrating multi-omics data for clinical decision-making and tumor profiling His publications span topics like RNA-seq analysis, chromothripsis in cancers, and global urban microbiome tracking through the MetaSUB consortium. Kahles has collaborated on landmark projects including the Pan-Cancer Analysis of Whole Genomes (PCAWG) and the Tumor Profiler Study.
Istvan Albert is a Research Professor of Bioinformatics at Pennsylvania State University , affiliated with the Department of Biochemistry and Molecular Biology . He leads the Bioinformatics Consulting Center and teaches BMMB 852: Applied Bioinformatics . Research Interests: Specializing in bioinformatics, large-scale biological data analysis, microarray and sequence analysis, scientific programming, algorithm development, and database-driven web development. His work spans gene ontology visualization , RNA-Seq analysis , and coronavirus research . Software Development: Created GeneScape for gene function visualization and bio for bioinformatics workflows. Maintains the Biostar Handbook series and the Biostars Q&A Forum , a leading bioinformatics resource.
Jian Peng is an Assistant Professor in the Department of Computer Science at the University of Illinois at Urbana-Champaign. His research focuses on computational biology, machine learning, and their applications to protein structure prediction, drug design, and molecular modeling. He has contributed to advancements in antibody engineering, protein-ligand docking, and generative models for biological systems. Key research areas include: Machine Learning for Molecular Modeling Protein Structure Prediction Antibody and Peptide Design Genomics and Single-Cell Analysis Structure-Based Drug Discovery His work emphasizes integrating deep learning techniques with biological datasets to address challenges in precision medicine, drug development, and systems biology. Notable achievements include developing the FastFold system to accelerate AlphaFold training and pioneering flow-based methods for antibody design. Awards include the Overton Prize (2020), recognizing contributions to computational biology. His research has been published in top journals and conferences, spanning topics from protein mutation prediction to geodesic-based immune complex modeling.
Professor Alexander J. Hartemink holds dual appointments in the Department of Computer Science and Department of Biology at Duke University, Trinity College of Arts & Sciences. He is also a Bass Fellow in Computer Science. His research focuses on computational biology, machine learning, and systems biology, with applications to genomics, epigenomics, and transcriptional regulation. Hartemink leads the Duke Office of University Scholars and Fellows and has directed the Computational Biology and Bioinformatics graduate program. He earned a PhD from MIT (2001), MPhil from the University of Oxford (1996), and BS from Duke (1994). Research Interests His work integrates computational methods to study chromatin dynamics, transcriptional networks, and epigenetic mechanisms. Key areas include modeling chromatin accessibility, predicting transcription factor binding, and understanding cell-cycle regulation. Techniques employed include Bayesian networks, dynamic systems modeling, and machine learning algorithms. Publications & Trends Recent work emphasizes single-cell multi-omics integration, chromatin occupancy modeling (RoboCOP framework), and transcriptional regulation in response to genetic perturbations. Themes include epigenetic plasticity, disease-associated enhancers, and systems-level analysis of gene expression. Awards & Grants Hartemink has received the Sloan Research Fellowship (2005) and NSF CAREER Award (2004). Active grants include NIH funding for chromatin-transcription interplay studies and NSF support for regulatory genome research. He collaborates on projects like the Data+ initiative, promoting interdisciplinary data science. Affiliations & Labs Associated with Duke’s Center for Genomic and Computational Biology and Center for Advanced Genomic Technologies. His lab develops computational tools for genomic analysis, including software for chromatin modeling and epigenetic data integration.
Maria Chikina is an Assistant Professor at the University of Pittsburgh School of Medicine's Department of Computational and Systems Biology. She holds a PhD in Molecular Biology from Princeton University. Her research focuses on developing computational methods to analyze large-scale genomic datasets, bridging statistical rigor with biological insights to overcome experimental biases. Key research areas include latent variable modeling (e.g., PLIER, CellCODE), interpretable neural networks for sequence-to-function modeling, evolutionary rate analysis (RERconverge), and applications in tumor immunology, exercise genomics, and infectious disease (e.g., SARS-CoV-2). Her lab has developed tools like InstaPrism, NIFA, and L0 segmentation for data-driven biological discovery. Her work spans collaborations with institutions like UPMC (on tumor microenvironment) and the Molecular Transducers of Physical Activity Consortium (MoTraPAC). Notable projects include analyzing convergent evolution in marine mammals and subterranean species, and developing epigenetic biomarkers for disease states through the ECHO program. Lab members include PhD students (Rezwan Hosseini, Tugrul Balci) and postdocs (Tina Subic, Anish Sevekari). Past students Wynn Meyer now leads a group at Lehigh University. Her group emphasizes open-source tools (GitHub repository ChikinaLab) and interdisciplinary approaches to systems biology challenges.
Ash A. Alizadeh is the Moghadam Family Professor of Medicine, Oncology, and Hematology (by courtesy) at Stanford University, where he serves as leader of the Cancer Genomics Program at Stanford Cancer Institute. He holds multiple academic appointments including Professor in Medicine - Oncology, and membership in Bio-X, the Institute for Stem Cell Biology and Regenerative Medicine, and the Maternal & Child Health Research Institute (MCHRI). Dr. Alizadeh received his BS in Biochemistry from UCLA (1994), MD from Stanford Medical School, and PhD in Biophysics from Stanford. He completed additional training at the National Cancer Institute (NCI), the National Institutes of Health (NIH), and the Howard Hughes Medical Institute (HHMI). His primary research focuses on developing and applying genome technologies and computing (machine learning & data science) to problems in human disease, with special emphasis on cancer detection, classification, monitoring, and tumor immunology. His laboratory pioneers noninvasive cancer genomic techniques including CAPP-Seq, PhasED-Seq, and EPIC-Seq for "liquid biopsies" that analyze circulating nucleic acids for early cancer detection and monitoring therapeutic response. Using machine learning approaches, his group studies how cellular compositional variation impacts cancer behavior and therapeutic response, including anti-tumor immunity. His work spans molecular, cellular, organism and population levels of tumor behavior analysis. Dr. Alizadeh has received numerous prestigious awards including the Scholar Award from the American Society of Hematology (ASH), the Leukemia & Lymphoma Society (LLS), the V-Foundation, as well as awards from the American Red Cross, Damon Runyon Cancer Research Foundation, and Doris Duke Charitable Research Foundation. He is an elected member of the American Society for Clinical Investigation (ASCI) and serves on the Scientific Advisory Board of the Lymphoma Research Foundation (LRF). As an educator and mentor, Dr. Alizadeh advises numerous doctoral students, postdoctoral fellows, and medical scholars. He teaches in the Department of Medicine and Immunology and serves on various admissions panels at Stanford. His laboratory, the Alizadeh Lab, is a hub for interdisciplinary cancer genomics research that combines computational biology, molecular genetics, and clinical oncology to develop novel cancer diagnostics and therapeutics.
