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.
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.
Prashant Mali is a Professor in the Department of Bioengineering at the University of California, San Diego . His research bridges genome engineering, RNA biology, and biomedical applications, with a focus on CRISPR-Cas systems and ADAR-mediated RNA editing. Education : Ph.D. in Bioengineering Key Affiliations : UC San Diego, Altman Clinical and Translational Research Institute Dr. Mali's work centers on CRISPR-Cas9 technology , RNA editing , and human pluripotent stem cells . His lab develops tools for programmable gene regulation, synthetic lethal screens, and metabolic pathway analysis in disease contexts. Recent publications highlight innovations in circular RNA engineering , ADAR activity mapping , and metabolic reprogramming in cancer . His team employs multi-omics approaches and in vivo models to translate genome editing into clinical applications. Students and Collaborators Current Lab Members : Sami Nourreddine (Postdoc), Amir Dailamy (Graduate), Andrew Portell (Graduate), Michael Tong (Graduate) Alumni : Kyle Ford (PhD 2022), Nathan Palmer (PhD 2022), Udit Parekh (PhD 2021) Research Themes CRISPR Screens : Synthetic lethal interactions, oncogenic pathways, metabolic vulnerabilities RNA Editing : ADAR engineering, circular guide RNAs, clinical translation Tissue Engineering : Vascularized organoids, cardiac maturation, ex vivo models
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.
Zechuan Lin is a Lecturer at the Department of Neurology , Yale School of Medicine, and a member of the Adams Center for Parkinson's Disease Research . He previously held a postdoctoral research fellowship at Harvard Medical School/Brigham and Women's Hospital in 2023 and earned his PhD from Peking University, College of Life Sciences in 2019. His research bridges computational biology , genomics , and plant genetics , focusing on genetic improvement in crops like rice and maize. Key methodologies include heterosis analysis , transcriptomic profiling , and QTL mapping to dissect agronomic traits and environmental adaptation. Lin's publications highlight advancements in hybrid rice breeding , genome-wide selection , and computational tools for allelic imbalance and daylength-sensing models. His work integrates bioinformatics and genetic networks to address both fundamental and applied biological questions. He is affiliated with Scherzer's Lab , which employs interdisciplinary approaches to neurogenomics and personalized medicine for neurological disorders like Parkinson's disease. His contributions to big data analysis and cross-species genetic studies reflect a unique intersection of plant and neurogenomics.
Ueli Grossniklaus is an Ordinary Professor at the University of Zurich within the Faculty of Mathematical and Natural Sciences , affiliated with the Department of Plant and Microbiology . His work focuses on plant developmental biology, particularly epigenetic and genetic mechanisms governing reproduction and adaptation. Key Courses: Epigenetics, Plant Biology Workshop, Group Seminars on Current Research Laboratory Techniques: Advanced methods in plant cell mechanics, transcriptomics, and genome editing Research Interests span plant epigenetics, reproductive biology, and the interplay between environmental stress and genetic regulation. He investigates: Mechanistic control of gametogenesis and fertilization Epigenetic contributions to plant adaptation Evolutionary implications of asexual reproduction Biophysical forces in plant cell growth Publication Trends (2025–2018) reveal expertise in: Arabidopsis and fern model systems Epigenetic regulation (DNA methylation, histone dynamics) Apomixis and hybrid seed failure mechanisms Biomechanics of pollen tubes and carnivorous plants Genome editing tools (CRISPR) and long-read sequencing Scientific Collaborations include interdisciplinary projects on: Microfluidic devices for plant cell analysis Gene drive ecology and ethics 3D imaging of plant reproductive structures Advising and Grants focus on mentoring through research internships in developmental biology, genetics, and systems biology. His lab engages in: Epigenetic response to environmental stress Cell wall mechanics in reproduction Computational modeling of plant growth Laboratory Teams integrate plant biologists, bioengineers, and computational scientists to study: Mechanistic gene regulation Evolutionary developmental biology Microrobotics for cellular force measurement
Ben Raphael is a Professor in the Department of Computer Science at Princeton University, with affiliations at the Lewis-Sigler Institute for Integrative Genomics, Omenn-Darling Bioengineering Institute, and Center for Statistics and Machine Learning. He is also an Affiliate Faculty member at the Rutgers Cancer Institute of New Jersey, Irving Institute for Cancer Dynamics at Columbia University, and New York Genome Center. His research focuses on computational methods for analyzing large-scale biological data, emphasizing cancer evolution, network/pathway analysis, and structural variation in genomes. Research Trends: His recent work spans cancer lineage trees, spatial transcriptomics, optimal transport for developmental models, and network analysis of mutations. Articles highlight applications in prostate cancer, pancreatic cancer, and single-cell genomics. Scientific Awards: 2024 ACM Fellow 2023 RECOMB Test of Time Award 2022 RECOMB Test of Time Runner-Up 2021 ISCB Innovator Award 2021 RECOMB Best Paper Runner-Up 2020 ISCB Fellow 2020 AACR Team Science Award 2011 NSF CAREER Award 2013 RECOMB Best Paper 2010-2012 Sloan Research Fellowship Advising: He has mentored numerous Ph.D. students and postdoctoral fellows, many of whom have transitioned to academic and industry roles. Current advisees include Uthsav Chitra, Gillian Chu, and Alexander Strzalkowski. Labs & Teams: Raphael leads the Raphael Lab at Princeton, developing tools like HotNet2, CHISEL, and HATCHet for cancer genomics and network analysis.
Miler T. Lee is an Associate Professor at the University of Pittsburgh , focusing on gene regulation during early embryonic development through high-throughput experimental and computational genomics. He earned his Ph.D. in Genomics and Computational Biology in 2009 from the University of Pennsylvania under Dr. Junhyong Kim, followed by postdoctoral work with Dr. Antonio Giraldez at Yale University. Joining the university in 2016, his research spans maternal-to-zygotic transition (MZT), RNA stability, pluripotency networks, and evolutionary developmental biology, utilizing model organisms like zebrafish, Xenopus, and Hydractinia symbiolongicarpus. Key Research Themes: Maternally inherited RNA dynamics during embryogenesis Mechanisms of RNA degradation and transcriptome remodeling Evolution of pluripotency networks in hybrid species Role of zinc signaling in fertilization barriers Computational tools for RNA regulation and sensing Scientific Awards: Pan-American Society for Evolutionary Developmental Biology Junior Faculty Award (2024) Outstanding New Investigator – International Xenopus Board (2023) Basil O'Connor Scholar – March of Dimes (2017-2019) Recent publications highlight his work on enhancer classification, RNA degradation mechanisms, and cross-species MZT comparisons. His lab develops innovative methods like RESA for regulatory sequence analysis and studies evolutionary divergence in RNA localization patterns. While the articles span computational and experimental approaches, they consistently address RNA's role in cellular identity, developmental timing, and evolutionary adaptation. Applications include understanding pluripotency, designing RNA biosensors, and elucidating fertilization barriers. Prospective Ph.D. students are encouraged to contact him for opportunities in gene regulation, development, evo-devo, and computational genomics.
Dr. Chad J. Brenner is an Associate Professor in the Department of Otolaryngology-Head and Neck Surgery and Pharmacology at the University of Michigan Medical School. He also directs the U-M Program in Cellular and Molecular Biology, the Otolaryngology Clinical Laboratory (CLIA), and the Head & Neck Oncology Program. His research focuses on developing liquid biopsy tools for cancer detection and precision therapy, particularly in HPV-driven head and neck cancers. Key roles include membership in the Rogel Cancer Center, Kresge Hearing Research Institute, and Center for Computational Medicine & Bioinformatics. Education: B.S. in Biomedical Engineering, M.S. in Bioelectrical Engineering, and Ph.D. in Cellular and Molecular Biology from the University of Michigan, with doctoral work on prostate cancer mechanisms. Research Interests: HPV integration and cancer heterogeneity Urine- and blood-based liquid biopsies for real-time cancer monitoring Combination immunotherapy strategies for improving checkpoint inhibitor responses Genetic engineering to identify cancer vulnerabilities Clinical trial innovation for adaptive therapies Recent Work Highlights: Development of the MyHPVscore blood test for HPV-related head and neck cancer detection, and exploration of tumor-immune interactions through PD-L1 and T-cell profiling. Ongoing projects include PET-guided radiotherapy optimization and multi-omics analyses of tumor heterogeneity. Labs & Teams: Leads the Michigan Otolaryngology and Translational Oncology (MiOTO) lab and collaborates with interdisciplinary teams across computational medicine, immunology, and clinical oncology.
Xiaoning Qian is a Professor in the Department of Electrical and Computer Engineering at Texas A&M University, where he also serves on the Faculty Advisory Committee for the Texas A&M Institute of Data Science (TAMIDS) and the Executive Committee for the Texas A&M TRIPODS Research Institute for Foundations of Interdisciplinary Data Science (FIDS). He holds a joint appointment in the Applied Math group within the Computational Science Initiative at Brookhaven National Laboratory (BNL). Previously, he was an Associate Professor (2018-2022) and Assistant Professor (2013-2018) at Texas A&M, and an Assistant Professor in the Department of Computer Science and Engineering at the University of South Florida (2009-2013). Dr. Qian received his B.S.E. and M.S.E. degrees from Shanghai Jiaotong University, China, and his M.Ph. and Ph.D. degrees in Electrical Engineering from Yale University. Dr. Qian's research focuses on developing mathematical models and computational algorithms in signal processing, machine learning, and Bayesian methods, particularly in learning, uncertainty quantification, and experimental design. His work spans multiple disciplines, with applications in life sciences and materials science. His research group, the Biomedical Imaging, Sensing, and Genomic Signal Processing Group, actively applies probabilistic models and optimization algorithms to solve complex problems in interdisciplinary domains. His research has evolved from foundational work in bioinformatics and biomedical image processing to more recent applications in materials science and broader AI for science initiatives. Dr. Qian has received numerous scientific awards and recognitions including: National Science Foundation (NSF) CAREER Award Segers Family Dean's Excellence Professorship II in the College of Engineering TEES (Texas A&M Engineering Experiment Station) Senior Faculty Fellow Montague-Center for Teaching Excellence Scholar J. T. Oden Faculty Fellow at the University of Texas, Austin Finalist of the 2023 INFORMS QSR Best Paper Faculty Impact Fellow from the Department of Electrical & Computer Engineering As an advisor , Dr. Qian has mentored numerous graduate students through their PhD and MS programs, with many of his alumni securing positions at prestigious institutions and companies including NIH/NCBI, Microsoft, Baidu Research Lab, and Qualcomm. His research has been supported by multiple grants, including an NSF CAREER award and collaborative research funding from the Information Integration and Informatics program. He is actively recruiting postdoc and graduate student research assistants for projects in machine learning and optimization methods with applications in bioinformatics and materials science. Dr. Qian is involved with several research initiatives including the Objective-Based Uncertainty Quantification (ObjectiveUQ) project, which provides a mathematical framework for integrating prior knowledge and data while enabling effective operational and experimental design under uncertainty. He also co-organizes the Bio-Seminar series for the Biomedical Imaging, Sensing & Genomic Signal Processing group at Texas A&M.
Daniela Strenkert is an Assistant Professor at Michigan State University, affiliated with the MSU-DOE Plant Research Laboratory, Plant Biology Department, Molecular Plant Sciences Program, BioMolecular Science Gateway, and Cell & Molecular Biology Program. Her research focuses on systems biology approaches to understand gene regulation in photosynthetic organisms. Ph.D., University of Kaiserslautern, Germany Her lab investigates photosynthetic performance through multi-omics analysis of chromatin structure, transcriptomes, proteomes, and metabolomes in Chlamydomonas reinhardtii . Key areas include environmental acclimation, histone modification mapping (GreENCODE project), and regulatory RNA characterization. Recent publications emphasize computational modeling of photosynthetic protein interactions, metal homeostasis under stress, and chloroplast protein import mechanisms. Articles span 2025-2010, with 15 most recent from 2025-2022. Her work integrates genome-wide datasets to decode algal regulatory programs under climate change-relevant stressors. She teaches BS 161: Cells and Molecules and maintains a lab at 106 Plant Biology Lab. Contact: strenke2@msu.edu .
Brian D. Gregory is a Professor of Biology at the University of Pennsylvania's School of Arts & Sciences. His research focuses on RNA modifications, computational biology, and plant genetics, particularly studying how RNA modifications regulate gene expression in plants and animals. He holds a Ph.D. from Harvard University (2005) and a B.S.A. from the University of Arizona (2000). Research Interests: RNA epitranscriptomics (e.g., m6A, NAD+ caps) RNA secondary structure and protein interactions Genomic approaches to study plant stress responses Development of high-throughput sequencing tools like PIP-seq Recent Work Highlights: Recent studies include analyzing pathogen-induced RNA modifications' role in plant immunity (Plant Cell 2023), global RNA structure/protein interaction mapping, and epitranscriptomic dynamics in drought tolerance. His lab's work bridges computational methods with molecular genetics to uncover post-transcriptional regulatory mechanisms. Lab & Collaborations: The Gregory Lab uses Arabidopsis thaliana as a primary model organism but also explores animal systems. They collaborate with institutions like Cornell University and have developed protocols published in Current Protocols in Molecular Biology. Teaching: BIOL 4231: Genome Sciences and Genomic Medicine BIOL 6010: Communication for Biologists
Timothee Lionnet is an Associate Professor in the Department of Cell Biology at NYU Grossman School of Medicine. He holds a PhD from the University of Paris and completed postdoctoral training at Albert Einstein College of Medicine in Robert H Singer's lab. His research focuses on understanding how cells regulate gene expression through single-molecule imaging, bridging molecular-scale observations with cellular and tissue-level processes. Education: PhD in Paris, Postdoc at Einstein College of Medicine His work integrates live-cell imaging technologies, computational modeling, and systems genetics to investigate transcriptional dynamics, epigenetic regulation, and cellular responses to environmental cues. The Lionnet Lab develops novel tools to visualize gene activity in real time, aiming to uncover principles of robust gene expression programs and their role in diseases like cancer and viral reactivation. Recent research highlights include studies on chromatin landscape evolution in acute lymphoblastic leukemia, transcriptional stochasticity, and therapeutic resistance mechanisms in cancer cells. The lab collaborates on projects involving zinc finger design for genome editing and systems-level analysis of melanoma genetics. Lab activities emphasize interdisciplinary approaches, combining quantitative biology with clinical insights to advance regenerative medicine and cancer therapy strategies.
Ram Samudrala is a Professor and Chief of the Division of Bioinformatics at the University at Buffalo Jacobs School of Medicine and Biomedical Sciences . His research focuses on multiscale computational biology , integrating protein structure prediction , drug discovery , and translational science to address medical challenges. He leads the development of the CANDO platform for therapeutic drug discovery and co-directs the Informatics Core at the Clinical and Translational Sciences Institute. PhD in Computational Biology (University of Maryland, 1997) BA in Computing Science and Genetics (Ohio Wesleyan University, 1993) Postdoctoral Fellowship in Protein Folding (Stanford University, 1997-2001) His work spans structural biology , genomics , and computational drug design , with applications in dentistry , infectious diseases , and cancer . He has received prestigious awards including the NIH Director's Pioneer Award (2010) and multiple Wiki Science Prizes . Samudrala's group collaborates globally, emphasizing in silico methods followed by in vitro and in vivo validation. Key grants include $1.22M NIH NCATS ASPIRE Reduction-to-Practice Award and $4.5M NIH/NLM BRIGHT Training Grant . 2023 Finalist, Clinical and Translational Sciences Institute Clinical Research Achievement Awards 2016 MacArthur Foundation 100&Change Top 50 2008 Alberta Heritage Foundation Visiting Scientist Award 2005 NSF CAREER Award He directs the BRIGHT Short-Term Training Program and serves on multiple editorial boards and review panels. Samudrala's group maintains a Protinfo web server for structural predictions and the Bioverse framework for systems-level analyses.
