Alternative splicing patterns Professors and Supervisors | ApplySharif

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Rotem KarniView profile

Associate Professor

University of PennsylvaniaUnited States

Rotem Karni, PhD, is an Associate Professor of Genetics at the Perelman School of Medicine, University of Pennsylvania, Philadelphia. He leads a research lab focused on understanding how alternative RNA splicing contributes to cancer and genetic diseases, with a strong emphasis on translating these findings into RNA-based therapies. Karni's lab develops decoy oligonucleotides, small molecules, and splice-switching technologies to modulate splicing factors and enhance immunotherapy. Education BSc in Biological Chemistry from The Hebrew University of Jerusalem (1997) PhD in Biological Chemistry from The Hebrew University of Jerusalem, Israel (2002) Postdoctoral Fellowship at Cold Spring Harbor Laboratory, NY (2002-2007) Karni's research explores the deregulation of alternative splicing in oncogenesis, particularly how splicing factors like RBFOX2 and S6K1 influence metastasis, DNA repair, and immune checkpoint modulation. His team investigates m6A RNA modifications for stabilizing mutant genes, with applications in Duchenne Muscular Dystrophy and pancreatic cancer. The lab's work is commercialized through biotech companies: SKIP Therapeutics, Andlit Therapeutics, and RNAble. Selected Research Trends RNA mis-splicing and neoantigen generation (2025) Splicing factor inhibition for tumor suppression (2023) Metastatic splicing signatures in pancreatic cancer (2023) Immune checkpoint splicing in cancer immunotherapy (2021) m6A modulation for mRNA stabilization (2023) Advising & Collaborations Karni has mentored numerous PhD and postdoctoral researchers, many of whom now hold leadership roles in academia, biotech, and medical institutions globally. His lab collaborates extensively on projects involving RNA innovation, including partnerships with the Institute for RNA Innovation. Contact Department of Genetics & Institute for RNA Innovation, One uCity Square, Room 4018, Philadelphia, PA 19104 Phone: 215-898-5072 Email: Rotem.Karni@Upenn.edu

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Philippe CampeauView profile

Associate Clinical Professor

University of MontrealCanada

Dr. Philippe Campeau is an Associate Clinical Professor in the Department of Pediatrics at the Faculty of Medicine, Université de Montréal. He is affiliated with CHU Sainte-Justine, a major pediatric hospital in Montreal, Quebec, where he works in the Medical Genetics Service. His clinical and research work focuses on genetic disorders affecting children, particularly in the areas of skeletal development and neurogenetics. Dr. Campeau obtained his Doctorate in Medicine from Laval University in Quebec (1998-2003) followed by specialty training in medical genetics at McGill University (2003-2008). He completed postdoctoral training at Baylor College of Medicine (2008-2013), which further developed his expertise in genetic research methodologies. His primary research interests include bone dysplasias , skeletal dysplasias , epilepsy , and epigenetic diseases . Dr. Campeau's laboratory identifies disease-causing genes, deciphers disease pathophysiology, and works to improve the management of children affected by these conditions. His work encompasses exome analysis , functional studies with cell lines and mouse models , and investigations into urea cycle abnormalities . He has made significant contributions to understanding genetic causes of conditions such as Genitopatellar syndrome (KAT6B), osteopetrosis, dysosteosclerosis (SLC29A3), osteogenesis imperfecta, early-onset osteoporosis (WNT1), Yunis-Varón syndrome (FIG4), and DOORS syndrome (TBC1D24). Dr. Campeau's publication record demonstrates a strong trajectory in medical genetics research, with numerous high-impact publications spanning from fundamental genetic discovery to translational research. His work spans skeletal disorders, neurodevelopmental conditions, and epigenetic mechanisms. Recent publications indicate an expanding focus on chromatin modifiers, DNA methylation patterns, and spliceosome function in neurodevelopmental conditions, reflecting the evolution of his research interests toward more complex molecular mechanisms. Dr. Campeau has received several research grants in recent years (6 starting in 2014) from organizations including the Fonds de la recherche en santé du Québec, Canadian Institutes of Health Research, and Fondation Grand Défi Pierre Lavoie. While specific students are not mentioned in the available information, as a clinical professor, he mentors medical students, residents, and research trainees in the Department of Pediatrics. His research is conducted as part of the 'Musculoskeletal Diseases and Rehabilitation' axis at CHU Sainte-Justine Research Center, where he collaborates with international research teams to identify disease-causing genes and develop better management strategies for children with genetic disorders.

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Miler T. LeeView profile

Associate Professor

University of PittsburghUnited States

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.

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Hajk-Georg DrostView profile

Senior Lecturer

University of DundeeUnited Kingdom

Dr. Hajk-Georg Drost is a Senior Lecturer and Principal Investigator in the Division of Computational Biology at the University of Dundee's School of Life Sciences. He leads the Digital Biology Group, focusing on integrating machine learning and high-performance computing with biological research to advance healthcare innovation. Previously, he established a Computational Biology group at the Max Planck Institute for Biology Tübingen (2019-2024) and conducted postdoctoral research at the University of Cambridge's Sainsbury Laboratory. His research explores: Evolutionary transcriptomics and phylotranscriptomic patterns across species Machine learning applications in genomics and proteomics Development of bioinformatics tools (DIAMOND, myTAI) for tree-of-life scale analyses Gene regulatory networks and transposable element dynamics His publications demonstrate a consistent focus on evolutionary constraints in development, with recent work expanding into single-cell resolution analyses of developmental diseases. Awards include: Royal Society Wolfson Fellowship (2024) Fellow, Cambridge Philosophical Society Postdoctoral Affiliate, Trinity College Cambridge He currently supervises PhD students including Stefan Manolache and leads projects funded by the Royal Society and others, focusing on protein alignment infrastructure and developmental disease research. His lab develops open-source software for genomic analyses and maintains active collaborations across Europe.

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Claudia CrociniView profile

Researcher

Max Planck Institute for Dynamics and Self-OrganizationGermany

Claudia Crocini is a DZHK junior research group leader at the Max Rubner Center for Cardiovascular Metabolic Renal Research, Charité - Universitätsmedizin Berlin. Her work bridges cardiac physiology, epigenetics, and sex-specific medicine to address critical gaps in cardiovascular research where female hearts have been historically neglected. Her research program centers on sex-dependent differences in human cardiac cells, investigating how biological sex influences contractility, ionic currents, gene expression, and epigenetic regulation. By leveraging induced pluripotent stem cell technology, tissue engineering, and computational modeling, her lab identifies fundamental mechanisms underlying sex-specific cardiac responses to disease. This approach integrates cardiac mechanobiology with molecular analysis to uncover targets for precision medicine. Analysis of her publication record reveals a consistent trajectory toward understanding sex-dimorphic cardiac function, with recent work emphasizing sarcomere mechanics, RNA splicing, and nuclear mechanosensing. Her methodology combines voltage/calcium imaging, contractility assays, and next-generation sequencing to establish sex-specific biomarkers and therapeutic pathways. Dr. Crocini's scientific contributions have been recognized through competitive awards: First prize: Best Postdoc at the MDC (2022) Marie Skłodowska-Curie Fellowship for 'TiGER: Titin can govern epigenetic remodelling' (2021) American Heart Association Postdoc Fellowship (2020) Biophysical Society Travel Award (2020) HSFP Long-Term Fellowship (2017) As principal investigator of her DZHK-funded research group, she directs projects examining sex-dependent cardiac adaptation mechanisms while securing major grants including the Marie Skłodowska-Curie and American Heart Association fellowships. Her work directly addresses the urgent need for sex-inclusive cardiac research to improve clinical outcomes. The Crocini Lab operates within the Max Rubner Center, utilizing stem cell differentiation platforms, engineered cardiac tissues, and advanced imaging to dissect sex-specific cardiac physiology. Current projects focus on translating cellular findings into clinically relevant insights for sex-tailored cardiovascular therapies.

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Bei BeiView profile

Associate Professor

Monash UniversityAustralia

Dr. Bei Bei is an Associate Professor at the School of Psychological Sciences, Monash University, and an NHMRC Emerging Leadership (EL2) Fellow. She leads the Behavioural Sleep Medicine service, research, and training at Monash University Healthy Sleep Clinic, focusing on individual differences in sleep-wake behaviors, sleep-mental health relationships, and community dissemination of evidence-based sleep interventions. Doctor of Psychology (Clinical), University of Melbourne PhD, University of Melbourne Her research spans six major areas: Sleep-wake circadian rhythm disorders Cognitive Behavioral Therapy for Insomnia (CBT-I) Psychological/behavioral aspects of sleep Sleep-mental health interactions (mood, anxiety) Adolescent sleep patterns and wellbeing Perinatal/postpartum sleep interventions for women Recent publications (2024-2025) address: Insomnia treatment mechanisms in depression comorbidity Neurodevelopmental impacts of circadian factors Pregnancy-related insomnia risk identification Adolescent sleep facilitators/barriers Integrated models for youth depression and sleep across continents She also contributes to: Antifungal drug tolerance mechanisms RNA polyadenylation dynamics Mitochondrial RNA stability in cancer 3' UTR splice variants in rare diseases Awarded the NHMRC Emerging Leadership (EL2) Fellowship and Early Career Research Grant , Dr. Bei serves on editorial boards for Sleep Medicine Reviews, Sleep, and Behavioral Sleep Medicine journals.

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Xianghong Jasmine ZhouView profile

Professor

University of California, Los AngelesUnited States

Dr. Xianghong Jasmine Zhou is a Professor in the Department of Pathology and Laboratory Medicine at the University of California, Los Angeles (UCLA) School of Medicine . Her work focuses on integrating genomic , epigenetic , and bioinformatic approaches for non-invasive cancer detection and monitoring through cell-free DNA analysis . Principal Investigator for multiple NIH grants (R01CA246329, U01CA230705, etc.) Developed software tools ( cfSNV , cfTools , CancerDetector ) for cell-free DNA mutation and methylation analysis Co-developed CancerLocator and HCC EV ECG score for tumor-of-origin prediction and hepatocellular carcinoma monitoring Research Interests: Specializes in 3D genome modeling , epigenetic regulation , and machine learning for liquid biopsy applications. Her work bridges computational biology with clinical translation , particularly in cancer diagnostics and treatment response assessment . Scientific Contributions: She has pioneered deep learning and population-based modeling approaches for cell-free DNA deconvolution , isoform-level functional annotation , and multi-omics integration . Her 2016 Cell paper on alternative splicing has been highly influential, with over 266 mentions.

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Donna SlonimView profile

Professor

Tufts UniversityUnited States

Professor Donna Slonim is a leading computational biologist at Tufts University with dual appointments in the Department of Computer Science and Department of Immunology , and membership in the Genetics, Molecular and Cellular Biology program. She holds a Ph.D. from MIT (1996) and focuses on integrating genomic data with algorithmic approaches to advance disease diagnosis and treatment. Education Ph.D., MIT, 1996 M.S., University of California, Berkeley, 1991 B.S., Yale University, 1990 Research Interests include: Algorithm development for biological network analysis Precision medicine applications in human development Pharmacogenomics and drug discovery Temporal gene expression modeling Machine learning for biomedical data Scientific Awards : Best Student-Led Paper Award at ACM-BCB 2022 Academic Leadership : Teaches courses like Computational Biology , Statistical Bioinformatics , and Biological Networks Co-leads the BCB Group at Tufts On sabbatical during 2025-26 but remains active in research

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Eduardo EyrasView profile

Professor

Australian National University (ANU)Australia

Eduardo Eyras is a Professor at the Australian National University (ANU) and EMBL Australia Group Leader, leading research in computational RNA biology and cancer genomics. He directs the Centre for Computational Biomedical Sciences and is part of the Shine-Dalgarno Centre for RNA Innovation. His work focuses on transcriptome and epitranscriptome analysis using long-read sequencing, machine learning, and computational methods to study cancer mechanisms. Eyras holds a PhD in Mathematics from the University of Groningen (1999) and previously led research at the Sanger Institute and Pompeu Fabra University. Affiliations: Director, Centre for Computational Biomedical Sciences Researcher, Shine-Dalgarno Centre for RNA Innovation Member, Division of Genome Sciences and Cancer Leader, The Eyras Group - Computational RNA Biology Research Interests: Development of algorithms for long-read sequencing Machine learning applications in RNA biology Epitranscriptomic modifications and cancer Therapeutic mRNA platform steering Key Projects: Novel algorithms for transcriptome variation analysis Predictive models of RNA modifications in disease Ribosomal DNA variation analysis Advisees & Grants: Supervises PhD students (e.g., Favour Oyelami, Stefan Prodic) and leads ARC-funded projects on mRNA diagnostics and epitranscriptomic therapies. Collaborates with global teams on forensic genomics, cancer drug resistance, and AI-driven translational research. Labs/Teams: Leads the Eyras Group, collaborating with the Hannan Group (Cancer Therapeutics) and Shirokikh Group (Protein Biosynthesis).

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Dirk SchneiderView profile

Professor

University of MainzGermany

Prof. Dirk Schneider is a Full Professor (W3) of Biochemistry at Johannes Gutenberg University Mainz since 2010, with previous appointments at the University of Freiburg (2003-2009) and postdoctoral training at Yale University. His research spans membrane biochemistry, biophysics, and transmembrane protein folding/assembly, focusing on thylakoid membrane biogenesis and protein-lipid interactions in cyanobacteria and chloroplasts. Current roles: Full Professor, University Mainz Previous roles: Assistant Professor (W1), University of Freiburg Education: PhD (summa cum laude) from Ruhr-University Bochum His research interests include: Membrane protein folding and stability ESCRT-III/Vipp1/PspA family structural dynamics ABC transporter activity regulation (e.g., BmrA) Protein-lipid interaction mechanisms Thylakoid membrane remodeling Comparative membrane biology between prokaryotes and eukaryotes Development of spectroscopic and computational methods Recent publications reveal trends in bacterial membrane remodeling (SynDLP, PspA), lipid effects on transporter activity (BmrA), and IM30/Vipp1-mediated membrane fusion. His work combines structural biology, biophysics, and functional assays to elucidate membrane dynamics. Awarded the Dr. Heinrich Kost Award (2001) and Leopoldina Fellowship (2001) , he has held leadership roles including Study Section Speaker (2010-2014) , Director of Institute of Pharmacy and Biochemistry (2013-2015) , and Dean of Faculty of Chemistry (2015-2020) . His scientific advisory roles include editorial board memberships and study section leadership.

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Sven-Erik BehrensView profile

Professor

Martin Luther University Halle-WittenbergGermany

Prof. Dr. Sven-Erik Behrens serves as a Professor in the Department of Microbial Biotechnology at the Faculty of Natural Sciences I of Martin Luther University Halle-Wittenberg. He is affiliated with the Protein Research Center 'Charles Tanford' and maintains an active research program focused on RNA biology, molecular virology, and biotechnological applications. His primary research interests encompass RNA-based plant protection strategies, viral replication mechanisms (particularly for flaviviruses and plant viruses), and innovative vaccine development using Kluyveromyces lactis yeast expression systems. Behrens' work investigates fundamental RNA-protein interactions, RNA chaperone activities, and the molecular basis of antiviral defense mechanisms in plants. His laboratory explores how RNA accessibility influences viral replication and how this knowledge can be harnessed for developing novel RNA-based antiviral strategies. Analysis of his recent publications (2021-2025) reveals a clear research trajectory focused on identifying accessible RNA sites for targeted antiviral applications, optimizing yeast-based vaccine platforms for both plant and animal pathogens, and investigating the role of non-coding RNAs in plant development and stress responses. His work spans multiple disciplines including plant virology, medical virology, and microbial biotechnology, demonstrating translational research from basic molecular mechanisms to practical applications. Prof. Behrens leads research in the Department of Microbial Biotechnology, collaborating with various groups working on plant-pathogen interactions and vaccine development. His laboratory employs advanced techniques including RNA structure probing, fluorescence-based assays for RNA chaperone activity, and plant in vitro systems for studying viral replication. The research demonstrates significant potential for developing novel approaches to combat viral diseases in both agricultural and medical contexts.

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Qiang WeiView profile

Adjunct Professor

Vanderbilt UniversityUnited States

Qiang Wei, Ph.D., is an Adjunct Research Instructor in the Department of Molecular Physiology and Biophysics at Vanderbilt University School of Medicine. His research focuses on computational and systems biology approaches to study genomic and epigenomic mechanisms in cancer, drug response prediction, and disease risk gene prioritization. He has pioneered integrative frameworks combining multi-omics data (genomics, epigenomics, transcriptomics) with clinical information for precision medicine applications. Key research areas include: Developing computational tools for analyzing non-coding variants and DNA methylation patterns Characterizing tumor heterogeneity through circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs) Identifying genomic drivers of therapy resistance in metastatic cancers Integrating GWAS data with functional genomics for disease mechanism discovery His work spans multiple cancer types including breast, prostate, and hepatocellular carcinoma, with a particular emphasis on translating genomic insights into clinical diagnostics and therapeutic strategies. Ongoing projects include optimizing liquid biopsy approaches for early cancer detection and leveraging single-cell technologies to understand tumor evolution. In recent years, his lab has developed novel algorithms like TVAR for functional variant analysis and Bayesian frameworks for multi-omics integration. These methods have been applied to study schizophrenia genetics, autism risk genes, and platelet reactivity regulation.

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Tim KacprowskiView profile

Professor

Technical University of BraunschweigGermany

Summary Prof. Tim Kacprowski is a Professor and Head of Data Science in Biomedicine at the Peter L. Reichertz Institute for Medical Informatics (PLRI), jointly affiliated with TU Braunschweig and Hannover Medical School. His research focuses on integrating computational methods with biomedical challenges, particularly in network medicine, federated learning, and alternative splicing analysis. Key projects include the development of the NeDRex platform for drug repurposing and the FeatureCloud framework for privacy-preserving federated learning in healthcare. Research Interests His work spans multiple domains: Network Medicine: Leveraging molecular networks for disease module identification and drug discovery. Data Science: Advanced analytics for biomedical data, including ECG monitoring, microbiome studies, and flow cytometry. Federated Learning: Developing decentralized AI systems to protect patient data while enabling collaborative research. Alternative Splicing: Investigating splicing patterns in diseases like cancer and kidney disorders. Publications Trends Recent publications emphasize tools for drug repurposing (NeDRex-Web), ethical AI in clinical decision-making, and microbiome dynamics in chronic diseases. His work bridges computational methods with clinical applications, addressing challenges in precision medicine and healthcare technology. Labs & Collaborations As head of the Data Science group at PLRI, he leads interdisciplinary teams advancing biomedical informatics. Collaborations span institutions in Germany and internationally, focusing on translational research and AI-driven healthcare solutions.

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Marcel WeberView profile

Professor

Graz University of TechnologyAustria

Marcel Weber is a Full Professor of Philosophy of Science at the Department of Philosophy, University of Geneva, with a focus on the philosophy of life sciences and general philosophy of science. He also teaches general epistemology and modern philosophy, particularly Kant. PhD in Philosophy (1996, University of Konstanz) Habilitation (2002, Leibniz University Hannover) Previous roles: SNSF Professor at University of Basel (2004–2009), Full Professor at University of Konstanz (2009–2011), and visiting appointments at institutions like University of California, Irvine, and Max Planck-Institute for the History of Science. His research spans the intersection of biology and philosophy, emphasizing evolvability, causality in biological systems, and the ontology of biological functions. Key projects include collaborations with the Institute of Genetics and Genomics of Geneva (iGE3), NCCR Evolving Language, and the DACH project on Inferentialism and Bayesianism. Marcel Weber's recent publications explore evolutionary developmental biology, causal specificity, and the metaphysics of biological modalities. His work often integrates experimental practices across levels of biological organization and critiques deterministic versus probabilistic interpretations in evolutionary theory. 2012: Elected to the German National Academy of Sciences Leopoldina 1996: Science Prize of the District of Constance He has edited volumes on probabilities in science, philosophical confirmation, and collective epistemology. His laboratory affiliations include interdisciplinary groups like 'What if? On Counterfactual Claims' and lgBig (Lake Geneva Biological Interest Group).

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Kristen W. LynchView profile

Professor

University of PennsylvaniaUnited States

Kristen W. Lynch, PhD, is the Benjamin Rush Professor of Biochemistry and Chair of the Department of Biochemistry and Biophysics at the Perelman School of Medicine, University of Pennsylvania. She leads research at the Lynch Lab and co-directs the Institute for RNA Innovation , focusing on RNA processing mechanisms in human immune responses. Education: Harvard University (B.A. 1990, Ph.D. 1996) Postdoctoral Training: University of California, San Francisco (1997-2001) Her work bridges RNA splicing , alternative polyadenylation , and gene regulation in immune cells and cancer. She discovered kinase pathways controlling RNA-binding protein (RBP) activity and demonstrated how antigen stimulation and viral infections reprogram splicing networks to modulate immunity. Collaborative studies with oncologists revealed splicing defects phenocopying genetic mutations in leukemias and identified therapeutic vulnerabilities in RNA processing . Her recent publications highlight TREX-2 complex in mRNA export, hnRNP L repressing cryptic exons, and DDX39B structural analysis . Collaborations span RNA-Seq , splicing codes , and epithelial cell post-transcriptional programs . She explores spliceosomal assembly mechanisms and signal-responsive RBPs in T cells and influenza pathogenesis.

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