Non-Coding RNAs Professors and Supervisors | ApplySharif

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Igor JurisicaView profile

Professor

University of TorontoCanada

Igor Jurisica is a Professor at the University of Toronto and a Senior Scientist at the Krembil Research Institute’s Data Science Discovery Centre for Chronic Diseases. He also serves as Visiting Scientist at IBM CAS, Scientific Director of the World Community Grid, and Chief Scientist at the Creative Destruction Lab (Rotman School of Management). His research focuses on integrative computational biology, data mining, and AI-driven models for cancer mechanisms, drug discovery, and chronic disease management. Key affiliations include the Osteoarthritis Research Program, Schroeder Arthritis Institute, and leadership roles in open science initiatives like the World Community Grid, a global distributed computing platform with 810,000+ volunteers. Jurisica’s work bridges computational tools (e.g., NAViGaTOR visualization platform, MirDIP databases) and clinical applications, emphasizing explainable AI in healthcare. Research interests span proteomics, microRNA regulation, systems vaccinology, and multi-omics integration for disease stratification. Notable contributions include identifying prognostic signatures in cancer and osteoarthritis, machine learning models for drug repurposing, and sportomics analyses of athletic biomarkers. He has been recognized as a Thomson Reuters Highly Cited Researcher (2014-2016) and ranked among the Top 100 AI Leaders in Oncology (2023). His labs develop open-access tools like PathDIP, OsteoDIP, and miRAnno to advance translational research.

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Susanne FoitzikView profile

Professor

University of MainzGermany

Prof. Dr. Susanne Foitzik is a Professor of Evolutionary Biology at Johannes Gutenberg University Mainz since 2010, where she leads the Evolution & Behavioral Ecology of Ants research group at the Institute of Organismic and Molecular Evolution (IOME). Previously, she was Professor in Behavioral Ecology at LMU Munich (2004-2010) and Assistant Professor in Zoology at the University of Regensburg (2000-2004). She earned her PhD in Biology from Julius Maximilian University, Würzburg in 1998. Her research integrates approaches from behavioral ecology through genomics to epigenetics, focusing on ants as model organisms to study complex social behaviors. Host-parasite coevolution and social parasitism in ants Molecular mechanisms underlying division of labor Reversal of the fecundity-longevity trade-off in social insects Gene regulation in phenotypic plasticity Evolution of chemical communication systems Analysis of her recent publications (2022-2025) reveals a strong focus on molecular mechanisms of social behavior, with particular emphasis on host-parasite interactions, epigenetic regulation of behavior, and genomic adaptations in social insects. Her work increasingly combines transcriptomic, proteomic, and functional genomic approaches to understand the molecular basis of social evolution. Among her notable scientific achievements: Speaker of Research Training Group 2626 GenEvo: Gene Regulation in Evolution (2019-present) Speaker of EES Master Program funded by VW foundation (2007-2010) DAAD Fellow at State University of New York (1992-93) Prof. Foitzik has supervised numerous PhD students and postdocs, including Maide Macit, Tom Sistermans, and Marcel Caminer. Her research is supported by multiple DFG-funded projects investigating host-parasite coevolution, the role of gene regulation in division of labor, and parasite interference in host gene expression. She serves as Handling Editor for Biology Letters and previously served on the editorial board of Insectes Sociaux. Her research group operates within the Institute of Organismic and Molecular Evolution (IOME) at Mainz, with laboratory facilities at the Biozentrum I. The group collaborates extensively with researchers across Germany and internationally, including partnerships with institutions in Frankfurt, Freiburg, Bristol, and Tel Aviv.

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Philipp NeumannView profile

Professor

Helmut Schmidt UniversityGermany

Philipp Neumann is a Professor and Chair of High-Performance Computing at Helmut Schmidt University since 2019. Previously, he held roles including Senior Researcher at the German Climate Computing Center (2016–2019), Postdoc at the University of Hamburg (2017–2019), and completed his Habilitation in Scientific Computing at TU Munich (2019). He transitioned to DESY/Universität Hamburg in May 2024. Education : PhD (Dr. rer. nat.) in Scientific Computing at TU Munich (2008–2013) Habilitation in Scientific Computing at TU Munich (2019) Studies in Technomathematics at Friedrich-Alexander University Erlangen-Nuremberg (2003–2008) Research Interests focus on high-performance computing, parallel and distributed systems, computational science, and applications in climate modeling. His work bridges computational methods with medical challenges, including surgical simulation training, wound healing mechanisms, and gastrointestinal pathology. Professional Activities include leadership roles in major conferences such as steering committee member for ISPDC (since 2021) and program committee roles in IPDPS, ICCS, and IEEE Cluster. He also managed the DFG priority program SPPEXA (2013–2016). Labs/Teams include the Chair for High-Performance Computing at Helmut Schmidt University and collaborations with the German Climate Computing Center. His current work at DESY/Universität Hamburg likely expands these computational efforts into interdisciplinary research.

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Brent FogelView profile

Professor

University of California, Los AngelesUnited States

Dr. Brent Fogel is a Professor in the Departments of Neurology and Human Genetics at the David Geffen School of Medicine, UCLA. He directs the Neurogenetics Clinic and the UCLA Clinical Neurogenomics Research Center , focusing on diagnosing and managing genetic neurological disorders such as cerebellar ataxia , ataxia with oculomotor apraxia , spastic paraplegia , and leukodystrophies . His research integrates genomics , bioinformatics , and neuroimaging to improve precision medicine in prenatal counseling and rare disease diagnosis. Education: MD, PhD from Medical College of Wisconsin (2003) PhD in Genetics (2001) Internship in Internal Medicine (Northwestern University, 2004) Residency in Neurology (UCLA, 2007) Fellowship in Neurogenetics (UCLA, 2009) Board Certified in Neurology (2009) Research Focus: Dr. Fogel’s work spans neurogenetics , spinocerebellar ataxia , leukodystrophy , and genomic technologies . He has pioneered gene discovery in hereditary ataxias, developed transcriptional biomarkers , and contributed to diagnostic guidelines for rare disorders. His studies on lysosomal genes in Parkinson’s disease and exome sequencing disparities address critical gaps in neurogenetic research. Key Collaborations: He leads multicenter studies with the Ataxia Global Initiative , Undiagnosed Diseases Network , and Genomics England Research Consortium . His lab ( FogelLab ) develops tools like multiWGCNA for gene network analysis.

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Franz Lennard RicklefsView profile

Professor

University Medical Center Hamburg-EppendorfGermany

Prof. Dr. med. Franz Lennard Ricklefs is a Senior Physician and Head of the Working Group at the Department of Neurosurgery, University of Hamburg Faculty of Medicine. He is a Medical Specialist in Neurosurgery with cross-disciplinary expertise in neuro-oncology, molecular pathology, and extracellular vesicle research. Affiliations: University Medical Center Hamburg-Eppendorf (UKE), European Liquid Biopsy Society (ELBS), International Consortium on Meningiomas (ICOM) Research Interests: His work focuses on neurosurgical oncology, particularly glioblastoma and meningioma pathobiology. He investigates DNA methylation patterns, extracellular vesicle biomarkers, and liquid biopsy implementation in clinical neuro-oncology. Additional interests include surgical outcomes for epilepsy and aneurysm management. Article Trends: Over the last decade, Dr. Ricklefs has published extensively on: Extracellular vesicle applications as liquid biopsy markers DNA methylation subclasses for glioblastoma and meningioma Multicenter surgical outcome benchmarking Immune evasion mechanisms in neuro-oncology Technological innovations in neurosurgical visualization Molecular characterization of rare CNS tumors Professional Contributions: He co-authored the MISEV2023 guidelines for extracellular vesicle studies and participates in international consensus reviews for meningioma classification. His collaborations span institutions across Europe and North America.

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Xihong LinView profile

Professor

Harvard UniversityUnited States

Xihong Lin is a Professor of Statistics at Harvard University and a Professor of Biostatistics at the Harvard T.H. Chan School of Public Health. She is a distinguished academic, holding membership in both the National Academy of Sciences and the National Academy of Medicine. Her research focuses on scalable statistical inference for big data, statistical machine learning, causal inference, and integrative data analysis, with applications in genomics, public health, and precision medicine. Lin’s work addresses challenges in analyzing large-scale genomic and multi-ancestry data, including methods for rare variant association testing, ancestry-adjusted sample analysis, and scalable computing frameworks. Her contributions span biobank studies (e.g., UK Biobank, TOPMed) and clinical applications in lung cancer, cardiovascular health, and smoking cessation. Her scientific awards reflect her leadership in statistical genetics and public health. Key research trends include leveraging single-cell sequencing for functional genomics, developing ensemble machine learning methods for health subtyping, and enhancing polygenic risk prediction across diverse populations. Lin’s methodologies prioritize interpretability and scalability, enabling impactful analyses of complex observational and genomic datasets. Awards: Member, National Academy of Sciences; Member, National Academy of Medicine Her grants and advising efforts focus on interdisciplinary collaborations, bridging statistics, AI, and domain sciences. Lin leads initiatives to improve genomic data management and ethical use of federated data (e.g., FADI framework). She is affiliated with labs advancing statistical genetics and cloud-based workflows (e.g., STAAR workflow).

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Sven PankeView profile

Professor

ETH ZurichSwitzerland

Prof. Dr. Sven Panke is a Full Professor and Head of the Department of Biosystems Science and Engineering at ETH Zürich. His research focuses on bioprocess engineering, synthetic biology, and enzymatic process development. Key areas include miniaturized bioreactor systems, microbial engineering for novel metabolite production, and high-throughput screening methodologies. Education: Studied Biotechnology at TU Braunschweig, with postgraduate research at the German National Research Center for Biotechnology and ETH Zurich. Transitioned from industry (DSM) to academia in 2001 as an Assistant Professor, progressing to Associate Professor (2007-2009) before leading the BSS department. Research interests emphasize directed evolution of enzymes, metabolic pathway engineering, and systems biology approaches to optimize microbial production systems. Current projects include bio-indigo synthesis, antimicrobial peptide discovery, and synthetic biology tools for cellular engineering. Labs/Teams: Leads the Bioprocess Engineering Lab at ETH Zurich, collaborating on projects like the E. coli import system design and γ-glutamyltransferase engineering. Active in developing microfluidics platforms for parallel reaction analysis. Grants/Advising: Funded by initiatives in sustainable biomanufacturing and synthetic biology. Supervises graduate students in bioprocess design and microbial systems engineering.

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Andrew BassettView profile

Researcher

Leibniz Institute for Zoo and Wildlife ResearchGermany

Dr. Andrew Bassett serves as Head of the Cellular and Gene Editing Research group at the Wellcome Sanger Institute, where he develops cutting-edge genome engineering techniques using human pluripotent stem cells to investigate neurodegenerative diseases including Alzheimer's and Parkinson's. His work focuses on scaling genetic screening approaches and improving CRISPR specificity for modeling complex disease mechanisms. His academic training includes: PhD at the MRC Laboratory of Molecular Biology (MRC-LMB) with Andrew Travers on chromatin remodelling in heterochromatin formation Postdoctoral research with David Baulcombe at the University of Cambridge studying small RNA roles in chromatin modification Additional postdoctoral work with Chris Ponting at the MRC Functional Genomics Unit (MRC-FGU) in Oxford, where he pioneered CRISPR applications in Drosophila Bassett's research program centers on developing advanced genome engineering methodologies for precise modulation of gene expression networks during development and neurodegeneration. His group specializes in creating complex editing events (SNPs, paired knockouts, enhancer perturbations) within iPSC-derived models, with particular emphasis on epigenetic regulation and transcriptional control. Current projects integrate single-cell 'omics and phenotypic assays to decode genetic causes of neurodegenerative disorders through the OpenTargets consortium. Analysis of his 15 most recent publications reveals dominant trends in CRISPR technology development (35%), neurodegenerative disease modeling (30%), and single-cell functional genomics (25%). His work consistently bridges methodological innovation with disease mechanism studies, increasingly incorporating multi-omics approaches and expanding into cancer immunology and infectious disease applications since 2022. As group leader, Bassett mentors postdoctoral researchers and PhD students while securing major funding for genome engineering initiatives. His team operates within the Sanger Institute's Cellular Operations division and maintains critical partnerships with the OpenTargets consortium for therapeutic target validation. The laboratory specializes in high-throughput screening platforms using iPSC-derived neural and microglial models, with recent methodological advances including scSNV-seq and ONE-STEP tagging systems that significantly enhance precision genome editing capabilities.

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Claudio R. AlarcónView profile

Associate Professor

Yale UniversityUnited States

Claudio R. Alarcón is an Associate Professor in Pharmacology at Yale University School of Medicine. His research focuses on RNA metabolism's role in development, health, and disease, particularly RNA modifications and non-coding RNAs. He joined Yale in 2017 after postdoctoral training at The Rockefeller University and holds a PhD from Cornell University (2009) and a BSc from Pontificia Universidad Católica de Chile (1999). Research Interests: Functional roles of m6A RNA modifications MicroRNA biogenesis and cancer progression Non-coding RNA regulation in metastasis Key Appointments: Primary Faculty, Yale Cancer Biology Institute Member, Yale Cancer Center Faculty, Yale Combined Program in Biological and Biomedical Sciences His lab integrates bioinformatics, molecular, and cellular approaches to study cancer metastasis mechanisms, including miRNA processing disruptions and SOX4/TMEM2 pathways linked to clinical outcomes.

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Michael BoutrosView profile

Professor

German Cancer Research CenterGermany

Michael Boutros is a Full Professor at Heidelberg University and Head of Division at the German Cancer Research Center (DKFZ). He currently serves as Dean of the Medical Faculty at Heidelberg University (since 2023) and Director of the Marsilius Kolleg (since 2020). He has held leadership roles including Coordinator of the Functional and Structural Genomics Program at DKFZ (2014–2023) and Acting Scientific Director (2015–2016). His academic base is within the Medical Faculty, focusing on molecular oncology and functional genomics. PhD, Witten/Herdecke University (1993–1996) Postdoctoral Research, Harvard Medical School (1999–2003) MPA, John F. Kennedy School of Government, Harvard University (1999–2001) Additional training: Cold Spring Harbor Laboratory, SUNY Stony Brook His research centers on Wnt signaling, functional genomics, and cancer pathways. He leads major research initiatives such as CRC 1324 on Wnt signaling and the ERC Synergy Grant DECODE. His work integrates high-throughput screening, CRISPR, and systems biology to dissect signaling networks in cancer and development. He has pioneered genome-wide RNAi and CRISPR screens to identify novel regulators of Wnt signaling across models. The 15 most recent articles reflect a strong focus on Wnt pathway regulation using functional genomics in both Drosophila and mammalian systems. Themes include high-throughput screening, CRISPR-based validation, cross-species conservation, and therapeutic targeting. Keywords span Cancer Biology, Systems Biology, and Signal Transduction, with subfields like RNAi, ubiquitination, stem cell regulation, and machine learning in image analysis. Michael Boutros has received numerous scientific honors: Elected member, Leopoldina National Academy of Sciences (2022) Elected member, Heidelberg Academy of Sciences (2022) EMBO Member (2013) ERC Advanced Grant (2012) Johann-Georg Zimmermann Research Award (2007) EMBO Young Investigator (2005) Member, 'Die Junge Akademie' (2003) He has been a recipient of the Emmy-Noether Program, McCloy Fellowship, Boehringer Ingelheim PhD Fellowship, Studienstiftung Fellowship, and Fulbright Fellowship. As a mentor and research leader, he has supervised numerous early-career scientists and coordinated large collaborative grants including the FP7 'CancerPathways' project. He currently serves as Speaker of the Research and Strategy Commission at Heidelberg University and Managing Director of the Health and Life Science Alliance Heidelberg Mannheim. He leads the CRC 1324 on Wnt signaling and is Coordinating PI of the ERC Synergy Grant DECODE. He is also Spokesperson of DFG Research Group 1036 and Coordinator of the former FP7 Coordinated Project 'CancerPathways'. His lab employs cutting-edge functional genomics tools to decode signaling networks in cancer and development.

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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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Brian D. GregoryView profile

Professor

University of PennsylvaniaUnited States

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

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Amin ArdestaniView profile

Senior Lecturer

University of HullUnited Kingdom

Dr Amin Ardestani , Senior Lecturer in Metabolic Signaling at the Biomedical Institute for Multimorbidity (BIM), Hull York Medical School (HYMS) , specializes in unraveling molecular mechanisms of pancreatic β-cell failure in diabetes. His research program identifies novel therapeutic targets through signal transduction studies in metabolic disorders. Bachelor's in Biology, Tarbiat Moalem University (2004) Master's in Biochemistry, Institute of Biochemistry and Biophysics (2007) PhD in Biology, University of Bremen (2013) Junior Group Leader at University of Bremen (2014-2023) Research focuses on Hippo and mTOR signaling pathways in β-cell biology, autoimmunity, and regeneration. His work bridges mechanistic biology with drug discovery for diabetes, with significant findings on PHLPP1/2 phosphatases and MST1/2 kinases. Recent publications highlight therapeutic strategies for β-cell protection , including small molecule inhibitors (e.g., MST1/2 inhibitors) and metabolic enzyme modulation (LDHA). Collaborative studies explore SARS-CoV-2 interactions with pancreatic cells and cross-talk between acinar and β-cells in diabetes. 2019 JDRF Advanced Postdoctoral Fellowship 2018 Impulse grant & Career Advancement Award 2017 Early Investigators awards (Endocrine Society, EFSD/Lilly Programme) 2014 Albert Renold Fellowship & Bremer Studienpreis Professional roles include Editorial Board Member at Scientific Reports and Associate Editor at Frontiers in Endocrinology . He reviews grants for DFG, Diabetes UK, and ISF, and evaluates manuscripts for top-tier journals like Cell Metabolism and Nature Communications.

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Katherine E. VarleyView profile

Associate Professor

University of UtahUnited States

Katherine E. Varley, PhD is a Huntsman Cancer Institute Investigator and Associate Professor in the Department of Oncological Sciences at the University of Utah. She leads the Varley Lab and is a member of the Nuclear Control of Cell Growth and Differentiation Program, focusing on breast cancer genomics, epigenetics, and biomarker discovery. Her work bridges computational biology with clinical applications to improve breast cancer diagnosis and treatment. Dr. Varley earned her BS in Biology with a concentration in Computational Biology from Cornell University in 2003, followed by a PhD in Computational Biology from Washington University School of Medicine in 2009 under Dr. Robi Mitra. Her postdoctoral training was conducted in Dr. Richard M. Myers' laboratory at the HudsonAlpha Institute for Biotechnology, where she participated in the ENCODE Project Consortium. Her research focuses on using next-generation sequencing and computational analysis to study gene expression, transcription factor binding, and DNA methylation patterns in breast cancer. The Varley Lab investigates epigenetic gene regulation, develops novel molecular methods and bioinformatics approaches, and translates discoveries into clinical tools. Key research areas include Clinical Trial Genomics, Epigenome Engineering, Detecting Circulating Tumor DNA, and identifying Transcription Factors Driving Metastasis, with particular emphasis on triple-negative breast cancer. Analysis of Dr. Varley's publications reveals a consistent trajectory from fundamental genomic mechanisms to clinical translation, with recent work emphasizing biomarker discovery, tumor heterogeneity, and the development of genomic tools for precision oncology. Her research spans cancer biology, genomics, and computational analysis to address critical challenges in breast cancer treatment. Dr. Varley holds multiple patents related to cancer diagnostics and genomic technologies, including targeted sequencing methods, multigene assays for recurrence risk, and biomarkers for triple-negative breast cancer. These inventions reflect her commitment to translating basic research into clinical applications. She actively collaborates with clinical investigators in breast cancer trials and works closely with the Breast and Gynecologic Cancers Disease Center at Huntsman Cancer Institute. Her lab maintains four main research thrusts that collectively address breast cancer from molecular mechanisms to clinical applications, demonstrating a comprehensive approach to improving patient outcomes through genomic technologies.

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Ben RaphaelView profile

Professor

Princeton UniversityUnited States

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.

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