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Fengzhu SunView profile

Professor

• Computational Biology
• Bioinformatics
• Statistical Genetics
• +6 more

Dr. Fengzhu Sun is a Professor of Quantitative and Computational Biology and Mathematics at the University of Southern California. His research spans computational biology, bioinformatics, statistical genetics, and mathematical modeling, with a focus on metagenomics, protein interaction networks, and genome sequence analysis. Dr. Sun earned his Bachelors in Mathematics from Shandong University, Masters in Probability and Statistics from Peking University, and PhD in Applied Mathematics from USC. He returned to USC in 2000 as an associate professor after serving at Emory University (1995-2000), becoming a full professor in 2006. His research interests encompass protein interaction networks, gene expression, SNPs, linkage disequilibrium, and their applications in predicting protein functions, gene regulation networks, and disease gene identification. He pioneered alignment-free methods for genome and metagenome sequence comparison, with recent work focusing on virus-host interactions in metagenomic data. His publication record shows consistent innovation, with recent work (2023-2025) emphasizing deep learning approaches (DeepMicroClass, DeepDecon, DeepLINK) and novel statistical methods. His research demonstrates strong interdisciplinary integration of computational methods with biological applications. Fellow of American Association for the Advancement of Sciences (AAAS, 2012) Fellow of American Statistical Association (ASA, 2015) Fellow of Institute of Mathematical Statistics (IMS, 2023) Fellow of International Society for Computational Biology (ISCB, 2024) Fellow of Asia-Pacific Artificial Intelligence Association (AAIA, 2025) Member of International Statistical Institute (ISI, 2012) USC Mellon Mentoring award for faculty mentoring (2012) USC Dornsife College senior Raubenheimer Outstanding Faculty Award (2017) Dr. Sun has mentored numerous successful students and postdocs, many now in academic positions or at leading tech and biotech companies. His research group develops computational methods for complex biological data analysis, with current focus on advanced deep learning for metagenomic classification, cancer cell fraction estimation, and virus-host interaction analysis. He has created influential software tools including DeepMicroClass, ImputeCC, DeepDecon, and ViralCC that have become standard resources in computational biology.

Ben RaphaelView profile

Professor

• Bioinformatics
• Computational Biology
• Cancer Genomics
• +6 more

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.

Susan BrooksView profile

Professor

• Cancer Biology
• Glycobiology
• Cell Signaling
• +4 more

Professor Susan Brooks is a faculty member at Oxford Brookes University in the School of Biological and Medical Sciences . Her research focuses on glycobiology , cancer progression , and the role of extracellular vesicles in metastasis. Professor of Cell Biology Director of Researcher Development Focus on breast and ovarian cancer Specialized in glycosylation mechanisms Research Interests : Dr. Brooks' work explores how aberrant glycosylation of proteins and glycans influences cancer cell behavior, including metastasis and drug resistance . Her recent studies examine extracellular vesicles as diagnostic tools and therapeutic targets. Article Trends : Over 25 years, Dr. Brooks has published 15+ articles on glycosylation patterns in breast and ovarian cancer. Key areas include lectin binding , miRNA regulation , and radiation-induced metastatic changes . Her work bridges cell biology and clinical applications .

Maria HondeleView profile

Assistant Professor

• Membraneless Organelles
• Biomolecular Condensates
• Liquid-Liquid Phase Separation
• +7 more

Maria Hondele is a Tenure-track Assistant Professor at the Biozentrum, University of Basel, Switzerland, where she leads a research group dedicated to understanding the formation, regulation, and function of membraneless organelles, particularly those associated with RNA processing. Her interdisciplinary work bridges biochemistry, biophysics, and cell biology to dissect how RNA-protein condensates influence gene expression. Her research focuses on liquid-liquid phase separation and the role of DEAD-box ATPases as master regulators of biomolecular condensates. She investigates how these dynamic structures control RNA flux, processing, and localization within cells. Her lab employs a multidisciplinary approach including biochemical reconstitution, biophysical measurements, high-throughput screening, and advanced imaging techniques to uncover the molecular mechanisms underlying condensate formation and function. The recent publications of her group reveal a strong thematic focus on RNA-protein interactions, phase separation, stress granules, and the enzymatic regulation of condensates by ATPases. These studies span model systems from synthetic coacervates to human cells, reflecting a comprehensive strategy to understand both fundamental principles and biological implications of membraneless organelles. ERC Starting Grant (2020) SNSF Eccellenza Professorship (2019) HFSP Long-Term Postdoctoral Fellowship (2015–2018) ETH and EMBO Postdoctoral Fellowship (2015) PhD Prize, University of Munich (2014) Boehringer Ingelheim PhD Fellowship (2008–2011) Dr. Hondele advises a vibrant team of postdoctoral fellows, PhD students, and master’s students, indicating an active and expanding research program. She has secured competitive grants and leads a productive research group contributing significantly to the field of RNA biology and cellular organization. She is also an Associate Member of the National Center of Competence in Research (NCCR) RNA & Disease, reflecting her integration into major national research initiatives. Her research group is embedded within the Biozentrum, a leading interdisciplinary research center at the University of Basel, providing access to state-of-the-art facilities and collaborative networks in molecular and cellular biology.

Norbert O. ReichView profile

Professor

• Materials Chemistry
• Biochemistry & Biophysics
• Biomedical Sciences
• +5 more

Norbert O. Reich is a Distinguished Professor in the Department of Chemistry & Biochemistry at the University of California, Santa Barbara (UCSB), affiliated with the College of Letters and Science. He joined UCSB in 1987 after completing his Ph.D. at UCSF in 1984 and an NIH postdoctoral fellowship there. His research focuses on enzyme mechanisms, particularly DNA methylation and telomerase, with applications in antibiotic and cancer therapy design. He also develops innovative chemical biology tools, including gold nanoshell-based drug delivery systems and fluorescence-based protein tracking methods. Education: Ph.D. in Chemistry from UCSF (1984). Awards: Regent's Junior Faculty Fellowship (1987), American Cancer Society Faculty Research Award (1991), UC President's Award for Excellence in Undergraduate Research (1994). Research Interests: Epigenetic regulation via DNA methylation in bacteria and mammals Enzyme mechanisms of DNA methyltransferases (e.g., DNMT3A, CcrM) Design of therapeutic inhibitors targeting epigenetic enzymes Light-controlled delivery of proteins/RNA via gold nanoshells Protein-DNA interaction analysis using microfluidic arrays Awards and Recognition: His honors reflect contributions to both research and education, emphasizing his dual impact in science and teaching. Lab and Collaborations: Leads the Reich Lab, collaborating with researchers like Tom Pettus (UCSB) and Erkki Ruoslahti. Projects include antibiotic development, cancer epigenetics, and nanotechnology-driven drug delivery. Future Work: Expanding applications of nanoshell technology for targeted gene silencing and exploring allosteric inhibitors of DNMT3A for cancer treatment.

Daniela StrenkertView profile

Assistant Professor

• Plant Biology
• Systems Biology
• Molecular Biology
• +12 more

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 .

Jonathan WeissmanView profile

Professor

• Protein Folding
• Systems Biology
• Genomics
• +6 more

Jonathan Weissman is a Professor of Biology at the Massachusetts Institute of Technology (MIT) and a Member of the Whitehead Institute. He is also an Investigator of the Howard Hughes Medical Institute and the Landon T. Clay Professor of Biology. His research spans protein folding mechanisms, ribosome profiling, CRISPR-based tools (CRISPRi/a), and genetic interaction mapping. Whitehead Institute Member MIT Professor HHMI Investigator Co-founder, Maze Therapeutics & KSQ Therapeutics Research Interests focus on: Protein folding in cellular contexts Endoplasmic reticulum (ER) function and stress responses Genome-wide CRISPR screening for gene regulation High-density genetic interaction maps in mammals Mitochondrial protein targeting and quality control Epigenomic engineering with synthetic tools Scientific Awards include: Protein Society Irving Sigal Young Investigator Award (2004) Raymond & Beverly Sackler Prize (2008) National Academy of Sciences election (2009) NAS Award for Scientific Discovery (2015) Genetics Society of America Ira Herskowitz Award (2020) Labs & Collaborations : Leads the Weissman Lab at MIT/Whitehead Institute, co-leads the Laboratory for Genomic Research with GlaxoSmithKline, and chairs the Stowers Institute Scientific Advisory Board.

• Membrane Biology
• Cellular Stress Response
• Lysosomal Function
• +2 more

Dr. Phyllis I. Hanson is the Minor J. Coon Professor and Chair of Biological Chemistry at the University of Michigan Medical School. She also holds secondary appointments in Neurology and Cell and Developmental Biology, with affiliations to the Rogel Cancer Center and Precision Health Initiative. Research Interests: Her lab investigates mechanisms of cellular membrane stress sensing and repair, focusing on lysosomes and the ESCRT pathway. Her work integrates biochemical, cell biological, and advanced imaging techniques to study organelle membrane dynamics in health and disease. Recent Publications highlight her contributions to understanding ESCRT function in endolysosomal trafficking, membrane resilience under osmotic stress, and protein degradation pathways. These studies intersect with neurodegeneration, cancer biology, and infectious disease. Scientific Awards: AAAS Fellow Keck Scholar Searle Scholar Sloan Scholar McKnight Scholar Grants from NIH and disease-focused foundations since 2018 support her work on ESCRT pathway analysis, HSC70 AMPylation, and signal relay during cell migration. Leadership: She co-chairs Michigan Medicine’s Endowment for the Basic Sciences and chaired the 2024 Gordon Research Conference on Lysosomes & Endocytosis. She serves as Associate Editor of the Journal of Biological Chemistry .

• Developmental Neurobiology
• RNA Modification
• Post-transcriptional Regulation
• +4 more

Dr. Sheng-Jian Ji is a Tenured Associate Professor at the School of Life Sciences, Department of Neuroscience at Southern University of Science and Technology (SUSTech) in Shenzhen, China. He also serves as the Academic Vice President of Shude Academy and was previously the first Deputy Director of Research and Graduate Affairs in the Department of Biology at SUSTech (2016-2018). As a leading neuroscientist specializing in RNA modification and neural development, Dr. Ji has established an internationally recognized research program. Dr. Ji's educational background includes: 2003-2007: Postdoctoral Fellow, Johns Hopkins University School of Medicine, Neurobiology 1998-2003: PhD in Biochemistry and Molecular Biology, Peking University School of Life Sciences 1994-1998: Bachelor's Degree in Biochemistry, Yantai University Department of Biochemistry Dr. Ji's research primarily focuses on developmental neurobiology, with particular emphasis on post-transcriptional regulation mechanisms including RNA modification and local translation of mRNA in axons. His laboratory is recognized as one of the leading international groups studying how mRNA modification (particularly m6A and m5C) regulates neural development and function. Through innovative approaches combining molecular biology, cell biology, and microfluidic technologies, his team has revealed important insights into axon growth, dendrite maintenance, cortical neurogenesis, and retinal development. His publication record shows a clear trajectory from fundamental mechanisms of RNA modification to applications in understanding neurological disorders and aging. Recent work has expanded into aging-related neural decline, cognitive functions, and potential therapeutic targets for neurological conditions. Dr. Ji has received numerous prestigious awards: 2020, 2016: SUSTech Excellent College Mentor 2020: SUSTech Biology Department Outstanding Service Award 2019: Guangdong Province Talent Youyue Card A 2017: Guangdong Provincial Professor of Neurobiology 2013: Jiangsu Distinguished Professor (Nanjing University) 2011: National Natural Science Award Second Prize (third contributor) As an educator, Dr. Ji teaches undergraduate Neurobiology and graduate Cellular and Molecular Neurobiology courses. He actively mentors students, with recent master's graduates including Yuan Jiaxin and Zhang Pingrui. His laboratory recruits postdoctoral fellows (with salaries of 335,000+ RMB annually), research assistants, and graduate students, providing comprehensive training in molecular techniques, neuronal cell culture, microfluidics, and omics approaches. Dr. Ji leads a vibrant research team that collaborates both within SUSTech and internationally. His work continues to advance understanding of RNA modification in neural development, function, and aging, with recent progress highlighted in June 2025.

Debswapna BhattacharyaView profile

Associate Professor

• Computational Biology
• Bioinformatics
• Machine Learning
• +5 more

Debswapna Bhattacharya is an Associate Professor in the Department of Computer Science at Virginia Tech. Her research focuses on computational biology, bioinformatics, and machine learning with applications in structural biology. She holds a Ph.D. from the University of Missouri-Columbia (2016) and previously served as an Assistant Professor at Auburn University (2017–2021). Her work develops AI-driven methods for biomolecular modeling, including RNA and protein structure prediction, quality assessment, and refinement. Notable contributions include software tools like lociPARSE, RNAbpFlow, and EquiPNAS. She has received prestigious awards such as the NSF CAREER Award (2020) and NIH MIRA Award (2020). Teaching includes courses on machine learning and AI in molecular modeling. Her lab collaborates on NIH-funded projects (R35GM138146) and NSF initiatives (DBI2208679). Recent work emphasizes equivariant neural networks and transformer-based models for biomolecular analysis.

Marten MooreView profile

Research Fellow

• Plant Physiology
• Molecular Biology
• RNA Processing
• +4 more

Dr Marten Moore is a Research Fellow at the Division of Plant Sciences, The Australian National University. His research focuses on understanding mRNA dynamics, plant stress responses, and photosynthesis efficiency through molecular and genetic approaches. He investigates how plants adapt to environmental stresses such as light fluctuations and salinity, with a particular emphasis on retrograde signaling pathways linking chloroplasts to nuclear responses. Dr Moore’s work integrates experimental and computational methods, including the development of tools like ConCysFind for analyzing conserved protein sequences across plant species. He collaborates on projects aimed at enhancing crop resilience through improved energy use efficiency and yield stability, leveraging insights from wheat and Arabidopsis models. Key Projects: Using RNA regulation to improve energy use efficiency and boost yield in wheat (2024–2027) Regulators of protein translation reveal new pathways to plant productivity (2022–2025) Smart Plants and Solutions for Enhancing Crop Resilience and Yield (2021–2025) His research interests span mRNA fate during stress recovery, nitric oxide signaling in plant cells, and the role of glutathione peroxidases in symbiotic root nodules. Dr Moore’s contributions bridge fundamental plant biology with applied agricultural challenges, aiming to translate molecular insights into practical solutions for sustainable agriculture.

Rainer BöckmannView profile

Professor

• Computational Biology
• Theoretical Biophysics
• Membrane Biophysics
• +7 more

Rainer Böckmann is a Professor of Computational Biology in the Department of Biology at Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Germany, where he leads the Group for Theoretical and Computational Membrane Biophysics. His research integrates molecular dynamics simulations with biophysical analysis to study membrane structure, dynamics, and function. Research Interests: His work focuses on computational biophysics, particularly lipid bilayers, membrane proteins, molecular dynamics, and structural bioinformatics. He investigates how lipid composition, cholesterol, and embedded peptides influence membrane organization, curvature, and permeability, with applications in antimicrobial strategies and mRNA vaccine delivery systems. Recent Research Trends: His recent publications reflect a strong emphasis on lipid nanoparticles (LNPs), particularly their phase behavior, pH-dependent protonation, and structural transitions relevant to mRNA vaccines. He also explores antimicrobial peptides, membrane domain formation, and the role of cholesterol in modulating membrane properties. His group develops and applies advanced simulation techniques, including constant-pH MD and coarse-grained modeling. Member of Editorial Board, Biophysical Journal (2024–present) Elected Member, DFG Review Board for Biophysics (2020–present) Chairman, Molecular Biophysics Section, German Biophysical Society (2011–2012) Leadership and Service: Böckmann is actively involved in academic governance, serving on editorial boards, DFG committees, and as a guest editor for special issues in Frontiers journals. He contributes to graduate education and high-performance computing initiatives at FAU, including the NHR@FAU and Life@FAU Graduate School. He has organized major conferences and workshops in biophysics and membrane modeling. Laboratory and Collaboration: He leads a research group focused on biomembrane physics, collaborating with experimentalists and theorists. His lab develops and applies simulation tools to study membrane systems, bridging computational insights with biological function.

• Machine learning methods development
• Bioinformatics
• Biological sequence analysis
• +8 more

Ole Winther is a Professor at the Department of Biology, University of Copenhagen, specializing in Computational and RNA Biology. He also holds a joint appointment as Professor at DTU Compute, Technical University of Denmark. His research bridges machine learning, bioinformatics, and natural language processing with applications in biological sequence analysis, transcriptomics, and health informatics. Education: 1998: PhD in Physics, University of Copenhagen 1994: Master of Science in Physics, University of Copenhagen Winther's research focuses on developing advanced machine learning methodologies for biological applications. He has pioneered protein language models for sequence analysis (DeepLoc, SignalP, DeepTMHMM), interpretable deep learning for RNA subcellular localization, and benchmarking frameworks for DNA language models. His work spans latent variable models, variational inference, diffusion models, and novel architectures for deep generative modeling, with increasing emphasis on practical healthcare applications including rare disease diagnosis through findzebra.com and medical question answering with large language models. Scientific Recognition: ELLIS Fellow (2021) Head of ELLIS Copenhagen Unit H-index of 61 (Google Scholar, May 2023) 19,700+ citations (Google Scholar, May 2023) Winther has supervised 25+ PhD students to completion with 7 currently in progress, along with over 100 master's projects. He frequently serves as PhD opponent and committee chairman across European institutions. His research is supported by substantial funding including multiple Novo Nordisk Foundation grants totaling over 60 million DKK for the Center for Basic Machine Learning Research in Life Science and CAZAI projects, plus significant funding from the Danish Independent Research Fund. He leads an active research group developing cutting-edge machine learning approaches for bioinformatics and NLP challenges. Winther co-founded two spin-out companies: findzebra.com (2014, 2018), a search engine for rare diseases, and raffle.ai, an NLP startup for enterprise search. He initiated DTU's popular BSc in AI and Data program and teaches the highly enrolled MSc course in Deep Learning (450+ students) and PhD course in Bayesian Data Analysis.

• DNA Repair Mechanisms
• Genetics
• Pharmacology
• +7 more

Colin R Campbell is an Associate Professor in the Department of Pharmacology at the University of Minnesota Medical School . His research focuses on DNA repair mechanisms , particularly DNA-protein crosslink repair , homologous recombination , and mitochondrial DNA stability , with significant contributions to understanding cancer mechanisms and genetic toxicology . Research Themes DNA-Protein Crosslink Repair Homologous Recombination Pathways Mitochondrial DNA Maintenance Chemotherapy-Induced DNA Damage Enzymatic Processing Mechanisms Article Trends 2024-2025 work emphasizes transcription-coupled DNA repair and ubiquitin-mediated repair pathways 2020-2023 studies explore mitochondrial crosslink repair and interdisciplinary sustainability leadership 2000-2018 publications cover rad51 interactions , nitrogen mustard effects , and calpain-mediated repair enzyme degradation Grants & Projects NIH/NHLBI: Summer Research (2024-2029) NIH/NIEHS: DNA-Protein Crosslink Repair (2019-2025) NIH/NHLBI: Cellular Repair Mechanisms (2018-2024) Collaborations Natalia Tretyakova (Chemistry) Hoang D Nguyen (Microbiology) Paul B Bitterman (Medicine) Beverly S Moriarity (Genetics)

Guillaume BourqueView profile

Professor

• Bioinformatics
• Computational Genomics
• Comparative Genomics
• +5 more

Guillaume Bourque is a Professor in the Department of Human Genetics at McGill University's Faculty of Medicine. He serves as an Investigator at the Victor Phillip Dahdaleh Institute of Genomic Medicine and as the Scientific Director of the Canadian Centre for Computational Genomics (C3G). His laboratory is based at 740 Dr Penfield Ave, Room 6103, Montréal, Québec, Canada, H3A 1A4, where he leads research in computational genomics and bioinformatics. Professor Bourque's research focuses on understanding mammalian genomes using comparative genomic and epigenomic analyses. His lab investigates the evolution of regulatory sequences , the role of transposable elements in gene regulation , and the impact of genome rearrangements in evolution and cancer . His team develops computational methods and resources for the functional annotation of genomes with special emphasis on sequencing-based assays including ChIP-seq, RNA-Seq, exome- and whole-genome sequencing, and single-cell analysis. The lab's work involves examining billions of DNA base pairs to interpret how variation impacts basic biology and disease. Recent publications (2024-2025) demonstrate Bourque's leadership in pangenome graph construction , transposable element analysis , epigenomic profiling , and cancer genomics . His work spans multiple disciplines from basic genome evolution to clinical applications in cancer and infectious disease. Notable projects include the development of tools like DeepPolisher for genome assembly polishing and contributions to understanding the genomic basis of long COVID. Bourque's laboratory is actively recruiting postdocs and graduate students with backgrounds in programming or statistics. The lab emphasizes quantitative approaches to biology, requiring applicants to have experience in quantitative biology as a plus. His collaborative work extends across multiple institutions and international consortia, reflecting the interdisciplinary nature of modern genomic research.