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Paul FrankenView profile

Associate Professor

• Sleep Homeostasis
• Circadian Rhythms
• Genetics (QTL Analysis)
• +5 more

Paul Franken is an Associate Professor at the Center for Integrative Genomics (CIG), University of Lausanne. His research focuses on the molecular mechanisms underlying sleep homeostasis and circadian rhythms, with emphasis on genetic and systems-level approaches. Franken received his PhD from the University of Groningen (1993) and conducted postdoctoral work at Stanford University and the University of Geneva. His lab investigates how sleep-wake states interact with circadian processes, using mouse models to study clock gene regulation, miRNA functions, and the genetic basis of EEG traits. Key projects include systems genetics of sleep deprivation and the role of NPAS2 in linking clock genes to metabolic state. Education: PhD in Neurobiology, University of Groningen (1993) Postdoctoral Training: Stanford University (1993–2000), University of Geneva (1996–2000) Affiliations: Member of the CIG since 2005; Group Leader with postdocs, PhD students, and technical staff Research Interests: The lab employs QTL mapping, molecular genetics, and in vivo imaging to unravel how sleep homeostasis and circadian rhythms are intertwined. Current projects explore: Genetic determinants of sleep traits using BXD and Collaborative Cross mouse populations Mechanisms linking clock gene expression (e.g., PER1/PER2) to wakefulness duration Role of miRNAs like miR-709 in sleep EEG regulation Systems biology approaches to integrate genomic, metabolomic, and behavioral data Grants & Collaborations: Supported by Swiss National Science Foundation and EU grants. Collaborates with neuroscientists, bioinformaticians, and clinicians to advance sleep medicine. Labs/Teams: Franken leads a multidisciplinary team at CIG, including studies on vestibular stimulation effects (rocking and sleep) and peripheral clock interactions.

Janne LehtiöView profile

Professor

• Proteogenomics
• Cancer Proteomics
• Precision Medicine
• +3 more

Professor Janne Lehtiö leads the Cancer Proteogenomics Group at the Department of Oncology-Pathology , Karolinska Institutet. His research focuses on integrating genomics and proteomics to understand cancer mechanisms in leukaemias, lung cancer , and breast cancer , with clinical translation via decision support systems. Education: MSc in Biochemistry, University of Helsinki PhD in Biotechnology, Royal Institute of Technology (KTH) Postdoctoral training in cancer research, KI Research interests: Lehtiö’s group develops cutting-edge mass spectrometry methods (e.g., HiRIEF , SubCellBarCode ) and bioinformatics pipelines to map cancer proteogenomics, identify immunotherapy targets, and refine treatment selection through proteome-wide analysis. Article trends: His team’s publications emphasize spatial proteomics , precision oncology , and clinical decision systems , with methodological innovations like SubCellBarCode enabling protein localization studies and DEqMS improving statistical rigor in proteomics. Scientific recognition: Board of Directors, Cancer Core Europe (2023) Scientific Director, Science for Life Laboratory (2018-2023) Swedish Mass Spectrometry Society medal (2015) Collaborations and grants: Lehtiö’s group secures major funding (e.g., Vinnova grants ) and collaborates globally. They also organize doctoral courses like Proteomics by Mass Spectrometry and Omics Data Analysis .

Yardena SamuelsView profile

Professor

• Cancer Immunogenomics
• Immunopeptidomics
• Melanoma
• +7 more

Prof. Yardena Samuels is a leading researcher in cancer immunogenomics at the Department of Molecular Cell Biology, Weizmann Institute of Science, Faculty of Biological Sciences. Her lab focuses on deciphering the immunopeptidome in melanoma to identify targetable neoantigens and develop personalized immunotherapies. She is actively engaged in high-impact research, frequently publishing in top-tier journals and presenting at major conferences such as AACR. Research Interests: Her work spans melanoma biology, tumor heterogeneity, neoantigen discovery, immunopeptidomics, and biomarker identification for immunotherapy. She investigates how translational dysregulation, post-translational modifications, and genomic instability contribute to antigen presentation and immune evasion. The most recent publications highlight a strong trend in computational and functional genomics approaches to predict and validate immunogenic neoantigens, understand immune evasion mechanisms, and explore the role of the microbiome and intratumoral bacteria in shaping anti-tumor immunity. Her research increasingly integrates multi-omics data to build comprehensive models of tumor-immune interactions. Invited Plenary Speaker, AACR Annual Meeting 2025 Prof. Samuels leads a vibrant research group, mentoring students and postdocs, and securing major grants from the ERC, ISF, MRA, and other international foundations. Her lab utilizes a combination of experimental models, peptidomics, CRISPR screens, and computational tools to advance melanoma immunotherapy. She is involved in collaborative efforts to create a comprehensive atlas of cancer-specific antigens.

• Acute Respiratory Distress Syndrome (ARDS)
• Sepsis
• Critical Care Medicine
• +3 more

Carolyn Calfee, MD, MAS is a Professor in Residence of Medicine and Anesthesia at the University of California, San Francisco (UCSF). She attends at Moffitt-Long Hospital's intensive care units and leads research on ARDS, sepsis, and lung injury mechanisms. Her roles include Principal Investigator for multiple NIH grants and memberships in UCSF’s Center for Tobacco Control Research and Education, the Cardiovascular Research Institute (CVRI), and the UCSF Cancer Center. Education and Training: Carolyn Calfee earned her MD from the University of Pennsylvania School of Medicine and completed residency and chief residency in Internal Medicine at UCSF, followed by a Pulmonary/Critical Care fellowship and a MAS in Clinical Research at UCSF. She has undergone specialized training in Diversity, Equity, and Inclusion (2021). Research Interests: Her work focuses on molecular phenotyping of ARDS and sepsis for precision medicine, cigarette smoke exposure effects, and novel treatments for critical respiratory conditions. She employs multi-omic approaches, machine learning, and clinical trials (e.g., I-SPY COVID, COMET Consortium) to advance diagnostic and therapeutic strategies. Scientific Awards: None explicitly listed in the provided text. However, her leadership roles and research contributions reflect significant recognition in her field. Advising and Grants: As Principal Investigator, she leads grants such as NIH/NHLBI R35177135 (2025–2032) and NIH U01HL168415 (2023–2029). Her research also involves collaborations with institutions like the Cardiovascular Research Institute and teams like the COMET Consortium focused on critical illness subphenotypes. Labs and Teams: She directs the Calfee Lab, which investigates ARDS and sepsis biology. Active collaborations include the UCSF COMET Consortium, IMPACC Network, and I-SPY COVID adaptive platform trial. Her work integrates multi-omic data and clinical informatics for precision medicine applications.

Philipp ZerbeView profile

Assistant Professor

• Plant specialized metabolism
• Terpenoid biosynthesis
• Metabolic engineering
• +5 more

Philipp Zerbe is an Assistant Professor in the Department of Plant Biology at the University of California, Davis. His research focuses on the discovery, characterization, and engineering of specialized metabolic pathways in medicinal, bioenergy, and food plants, with particular emphasis on terpenoids and their roles in plant adaptation and biomanufacturing.

Michael BoehnkeView profile

Professor

• Biostatistics
• Genetics
• Genomics
• +3 more

Michael Boehnke is the Richard G. Cornell Distinguished University Professor of Biostatistics at the University of Michigan School of Public Health. He has been on the faculty since 1984 and directs the University of Michigan Center for Statistical Genetics and the Genome Science Training Program. His research focuses on statistical methods for human genetics, particularly in type 2 diabetes and genome-wide association studies (GWAS). He leads major consortia such as DIAGRAM and MAGIC, and has published over 400 peer-reviewed articles. He has trained 36 doctoral students and post-doctoral fellows, many of whom hold academic positions at major research institutions. Education PhD in Biomathematics, University of California, Los Angeles (1983) BA in Mathematics, University of Oregon (1977) Research Boehnke develops statistical tools for analyzing genetic data and investigates genetic contributors to type 2 diabetes, lipid traits, and anthropometric measures. His work emphasizes collaborative consortia to aggregate large-scale genetic datasets. Recent projects include the Accelerating Medicines Partnership (AMP) to integrate genomic data for metabolic disease research. Publications His most recent work addresses pleiotropy in genetic variants, sex-specific gene expression in skeletal muscle, and causal mechanisms of complex traits using multi-omics approaches. These studies highlight the utility of integrative genomics and population-scale data. Awards Member, National Academy of Medicine Fellow, American Statistical Association Fellow, American Association for the Advancement of Science Grants & Advising He oversees NIH-funded projects (e.g., R01 HG009976, U01 DK062370) and has trained 24 doctoral students and 12 postdocs. His lab collaborates globally through initiatives like the Finland-United States Investigation of NIDDM (FUSION) study. Labs & Teams He leads the Center for Statistical Genetics, a hub for interdisciplinary research in computational genetics and statistical methodology.

• Bioinformatics
• Microbiome
• Gut Microbiota
• +7 more

Greg Caporaso is a Professor in the Department of Biological Sciences and the Pathogen & Microbiome Institute (PMI) at Northern Arizona University. His work bridges computational biology and microbiome science, with a strong focus on developing and applying bioinformatics tools for microbial community analysis. His research interests are centered on the human microbiome, particularly the oral and gut microbiomes, and their roles in health and disease. Key areas include bioinformatics , microbiome dynamics , gut and oral microbiota , cancer microbiome interactions , and multi-omics data integration . He is best known for his contributions to the QIIME (Quantitative Insights Into Microbial Ecology) platform, a foundational tool in microbiome research. The recent publications highlight a strong trend in linking microbiome profiles to diseases such as colorectal cancer, endometrial cancer, and metabolic conditions. His work increasingly involves large-scale epidemiological datasets and population-level microbiome analyses, demonstrating a shift toward translational and public health applications. Although no specific awards are listed in the provided text, his high h-index (244) and extensive publication record in top-tier journals reflect significant scholarly impact. His collaborative network spans multiple institutions and disciplines, underscoring his role as a key figure in the microbiome research community. Dr. Caporaso is actively involved in scholarly output and research leadership. While student mentorship is not explicitly detailed, his professorial role and research activity suggest active advising. He also contributes to science education, integrating microbiome data science into higher education curricula. He is a core member of the Pathogen & Microbiome Institute (PMI) at NAU, a multidisciplinary research center focused on infectious diseases and microbial ecology. This institute serves as the primary hub for his collaborative and computational research efforts.

Neil CarragherView profile

Professor

• Drug Discovery
• Phenotypic Screening
• Oncology
• +9 more

Neil Carragher is a Professor of Drug Discovery at the Institute of Genetics and Cancer , University of Edinburgh. He serves as Director of Science for Edinburgh Cancer Research and Associate Director of Cancer Research UK Scotland Centre. His work bridges industry and academia, focusing on phenotypic screening , machine learning , and oncology drug development . Education: B.Sc. in Cell and Immunobiology, University of Aberdeen (1992) Ph.D. at Yamanouchi Research Institute, Oxford (1996) Neil’s research emphasizes high-content imaging , kinetic assays , and multi-omics integration to enhance clinical predictivity in drug discovery. His articles span glioblastoma , breast cancer , and drug repurposing , leveraging AI/ML and 3D disease models . Notable scientific awards include Fellowship of the Royal Society of Edinburgh He advises PhD students such as Mungo Harvey and Prasad Palani Velu , and leads the Edinburgh Cancer Discovery Unit and Edinburgh Phenotypic Assay Centre , integrating automated robotics and novel compound libraries .

• Mathematics
• Statistics
• Computational Biology
• +2 more

Hao Huang is a Tutor at the School of Mathematics and Statistics , University of Sydney, and a recent MPhil graduate (2023) . His work focuses on computational methods in bioinformatics and machine learning. His research interests include: Computational biology Feature selection in single-cell RNA sequencing Integrative analysis of multimodal omics data Recent publications highlight his contributions to: Deep learning frameworks for feature selection Multi-task learning strategies for omics data

Qingling DuanView profile

Associate Professor

• Bioinformatics
• Computational Biology
• Genomics
• +6 more

Qingling Duan is an Associate Professor and Queen's National Scholar in Bioinformatics at Queen's University, jointly appointed in the School of Computing and Department of Biomedical & Molecular Sciences. She leads the Computational Genomics Laboratory, focusing on genetic and epigenetic mechanisms in multifactorial diseases. PhD in Human Genetics, McGill University BSc in Biology, McGill University Her research integrates genomics, transcriptomics, and epigenomics to investigate gene-environment interactions in asthma, COPD, and drug response variability. Key areas include: Multi-Omics Data Integration Environmental Exposure Effects Pharmacogenomics Microbiota-Host Interactions Developmental Disease Trajectories Recent publications examine epigenetic aging, human milk microbiota, and prenatal exposure effects. Her work has appeared in leading journals like Nature Communications and American Journal of Respiratory and Critical Care Medicine. Queen’s National Scholar Award in Bioinformatics CIHR Grant Recipient International Collaboration with CHILD Cohort Study Dr. Duan advises numerous graduate students and postdocs in bioinformatics and biomedical research. Her lab collaborates with Kingston General Hospital, Hotel-Dieu Hospital, and the IMPACTT network.

Arnaud GaigherView profile

Researcher

• Evolutionary Immunogenomics
• Immunogenomics
• Evolutionary Biology
• +3 more

Arnaud Gaigher serves as a Postdoctoral Researcher at the University of Hamburg within the Faculty of Mathematics, Computer Science and Natural Sciences. He is formally affiliated with the Department of Biology and operates under the Institute of Animal Cell and Systems Biology (Institut für Zell- und Systembiologie der Tiere), specifically within the Evolutionary immunogenomics research group led by Prof. Dr. Tobias Lenz. His workspace is located at Martin Luther King Square 3, 20146 Hamburg. Dr. Gaigher's research centers on Evolutionary Immunogenomics , investigating genomic mechanisms driving immune system adaptation across species. This work integrates comparative genomics , population genetics , and functional immunology to decode evolutionary pressures on host defense systems. His institutional placement within Animal Cell and Systems Biology further indicates methodological expertise in cellular phenotyping and multi-omics data integration for evolutionary questions. No scientific awards or honors were documented in the source material. While the provided text does not specify student supervision activities or externally funded research grants, Dr. Gaigher's postdoctoral position implies active collaboration within Prof. Lenz's research team on ongoing immunogenomics projects. His email contact (gaigher@evolbio.mpg.de) suggests institutional linkage with the Max Planck Institute for Evolutionary Biology. He is embedded in the Evolutionary immunogenomics laboratory at the Institute of Animal Cell and Systems Biology, which maintains research infrastructure for high-throughput genomic analyses and evolutionary model systems. The group's work intersects with broader university initiatives in molecular ecology and host-microbe interactions.

Robert ClarkeView profile

Professor

• Breast Cancer
• Systems Biology
• Drug Resistance
• +5 more

Robert Clarke serves as Executive Director of The Hormel Institute and Professor in the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota's College of Biological Sciences. An internationally recognized breast cancer researcher, he leads multinational studies in collaboration with Mayo Clinic, University of Edinburgh, and Virginia Tech. His research focuses on breast cancer systems biology , specializing in endocrine responsiveness , drug resistance mechanisms , and multi-omics data integration . Clarke's laboratory employs genomic, transcriptomic, proteomic, and metabolomic approaches combined with machine learning to build predictive models of therapy resistance. Key research areas include the unfolded protein response, cell death mechanisms (apoptosis, ferroptosis, necroptosis), and signaling networks involving IRF1, NFkB, XBP1, and GRP78. His publication trends reveal sustained leadership in translational breast cancer research , with recent emphasis on radiogenomics, maternal dietary impacts, and social determinants of cancer. Early work established foundational hormone-resistant breast cancer models now widely used in the field. Fellow of the American Association for the Advancement of Science Fellow of the Royal Society of Chemistry, Medicine, and Biology NCI-Sigma Xi Distinguished Lecturer (2012-2015) Senior Editor for Cancer Research journal Former NCI Center for Cancer Systems Biology leader (2010-2016) Clarke has secured significant NCI funding including the In Silico Research Center of Excellence (2009-2014). His mentoring extends through leadership roles as Georgetown University's Associate Vice President for Research (2007-2019) and Co-Director of the Breast Cancer Program at Lombardi Comprehensive Cancer Center. Current collaborations integrate engineering, biostatistics, and clinical oncology across multiple institutions. His team maintains active laboratory facilities at The Hormel Institute focusing on translational models of endocrine resistance and tumor dormancy.

Vessela N. KristensenView profile

Professor

• Genetics
• Genomics
• Breast Cancer Research
• +3 more

Vessela N. Kristensen is a Professor at the Department of Medical Genetics , Institute of Clinical Medicine, Oslo University Hospital. Her research focuses on inherited genetic variation in breast and ovarian cancers, particularly how single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) influence tumor susceptibility, clinical presentation, treatment response, and gene regulation. Leadership: Head of the Kristensen Research Group at Oslo University Hospital Key collaborations: BRIDGES sequencing dataset, international consortia Research interests span: Cancer Genetics: Identifying germline variants affecting tumor biology and drug response Epigenetics: Mechanisms linking enhancer methylation to transcriptional networks Functional Genomics: Exploring gene-environment interactions in cancer risk Clinical Applications: Developing polygenic risk scores for personalized prevention Recent publications highlight her work on: BRCA1/2 variant classification using large-scale case-control data Tumor immunogenomics (CTLA4 expression as a prognostic biomarker) Computational models for predicting treatment outcomes in Luminal B cancer Epigenetic drivers of hormone-dependent breast cancer phenotypes Spatial transcriptomics applications in tumor heterogeneity analysis Key contributions include integrating multi-omics approaches to understand cancer progression and developing tools for molecular risk stratification in clinical settings.

Jonathan StokesView profile

Assistant Professor

• Machine Learning
• Antibiotic Discovery
• Computational Biology
• +3 more

Jonathan Stokes is an Assistant Professor at McMaster University in the Department of Biochemistry & Biomedical Sciences , where he leads the Stokes Lab and serves as a member of the Michael G. DeGroote Institute for Infectious Disease Research . He also co-founded the AI drug discovery startup Stoked Bio , which commercializes his research breakthroughs. Stoked Bio CEO Jeff Skinner Co-founder Chris Sinclair Research Interests : Stokes specializes in machine learning applications for antibiotic discovery , targeting drug-resistant pathogens like Acinetobacter baumannii . His work combines computational biology , bacterial metabolism , and deep learning to identify novel antimicrobial compounds and synergistic drug combinations. Scientific Contributions : His 15 most recent publications focus on AI-guided antibiotic design , metabolism-driven drug lethality , and explainable deep learning frameworks . Articles highlight trends in generative AI for synthesizable antibiotics, fitness cost exploitation in resistance mechanisms, and multi-omics integration for target identification. Teaching & Mentorship : Stokes teaches graduate courses in Artificial Intelligence in Healthcare and Antibiotic Discovery , while mentoring students like Autumn Arnold , Denise Catacutan , and Gary Liu in both academic and industrial contexts at Stoked Bio.

• Rheumatology
• Immunology
• Genetics
• +3 more

Professor Liye Chen serves as a Career Development Fellow funded by Versus Arthritis and Principal Investigator at the Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Science (NDORMS), University of Oxford. He leads the Chen group focused on Human Immunology in Inflammation, collaborating with Professor Paul Bowness and Professor Richard Williams. His medical training was completed at HuaZhong University of Science and Technology, followed by a Versus Arthritis-funded PhD (2009-2013) at the University of Oxford under Paul Bowness. Chen's research centers on immunogenetics of rheumatic diseases, particularly Ankylosing Spondylitis (AS). His seminal work elucidated HLA-B*27/ERAP1 interactions in antigen presentation, identified novel Th17-regulating microRNAs and epigenetic regulators (BRPF1/2), and defined unique T-cell phenotypes in AS patients. He pioneers genetics-led immunological interrogation to discover therapeutic targets for immune-mediated diseases, integrating molecular immunology with translational approaches. His publication portfolio demonstrates consistent focus on spondyloarthritis pathogenesis, HLA immunobiology, and therapeutic target validation, with increasing integration of computational methods for drug discovery across immune disorders. Key scientific recognition includes: Versus Arthritis PhD Fellowship Versus Arthritis Career Development Fellowship As Principal Investigator, Chen directs Versus Arthritis-funded research programs investigating genetic mechanisms of inflammatory arthritis. His group leverages human immunology approaches to translate genetic associations into biological mechanisms and therapeutic opportunities, with emphasis on T-cell immunology and antigen presentation pathways. The Chen group operates within NDORMS' Human Immunology in Inflammation research theme, maintaining active collaboration with the Kennedy Institute of Rheumatology and utilizing resources from the ULTRA-DD consortium for target validation in spondyloarthritis.