RNA-seq Analysis Professors and Supervisors | ApplySharif

جست‌وجوی استاد و پژوهشگر

استاد راهنما، استاد دانشگاه یا پژوهشگر مناسب برای مسیر پژوهشی‌تان را پیدا کنید و با او ارتباط بگیرید.

نمایش ۷۰۶-۷۲۰ از ۱٬۷۲۷ استاد راهنما

اطلاعات این پروفایل‌ها از صفحات عمومی دانشگاه‌ها جمع‌آوری شده و ممکن است به‌روز نباشد.

Fernando Camargoمشاهده پروفایل

استاد

Harvard UniversityUnited States

Fernando Camargo, Ph.D. , is a Professor of Stem Cell and Regenerative Biology at Harvard University and a Principal Faculty member of the Harvard Stem Cell Institute . His lab is based at Children’s Hospital Boston , where he investigates fundamental mechanisms of adult stem cell biology , organ size regulation , and cancer pathogenesis . Education: Ph.D., Baylor College of Medicine (2004) Prior Positions: Whitehead Fellow, Whitehead Institute for Biomedical Research (2004-2009) Research Interests include: YAP/TAZ signaling in organ growth and regeneration Single-cell lineage tracing to map hematopoietic and intestinal stem cell dynamics Epigenetic barriers to cellular reprogramming Mechanotransduction in intestinal stem cells Crosstalk between Hippo and metabolic pathways (e.g., glutamine/nucleotide synthesis) Stem cell aging and tumor suppression via transcriptional regulators Recent Articles reveal expertise in: 2025: Epigenetic regulation in liver reprogramming 2023: Multimodal single-cell profiling and mechanotransduction in gut stem cells 2022: Aging-dependent transcriptional control in hematopoiesis 2020: In vivo stem cell imaging and Hippo-metabolism integration 2018: Hippo pathway genomic analysis in cancer Scientific Awards: 2009 V Foundation Scholar NIH Director’s New Innovator Award Lab Members include researchers developing innovative technologies for live-cell imaging and CRISPR-based lineage tracing , with clinical translation efforts in bone marrow transplantation and liver disease therapies.

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Elissa Hallemمشاهده پروفایل

استاد

University of California, Los AngelesUnited States

Elissa Hallem is a Professor at the University of California, Los Angeles (UCLA) School of Medicine, affiliated with the Department of Microbiology, Immunology, and Molecular Genetics. Her research integrates neurobiology and parasitology to investigate sensory-driven behaviors in parasitic nematodes and the free-living model Caenorhabditis elegans . Williams College, BA in Biology and Chemistry (1999) Yale University, PhD in Neuroscience (2005) Caltech, Postdoc in Biology (2010) Hallem's work focuses on sensory neural circuits , host-seeking behaviors , and chemosensory valence in parasitic nematodes like Strongyloides stercoralis . She explores how sensory circuits evolve to enable parasitism and generate flexible behavioral outputs. Her publications highlight advancements in genetic tools for parasitic nematodes, thermosensation in host invasion, and olfactory mechanisms shaping host-parasite interactions. Key journals include Proc Natl Acad Sci USA , Curr Biol , and Mol Biochem Parasitol . 2023 UCLA Life Sciences Excellence in Research Award 2020 UCLA Faculty Mentor Award 2016 HHMI Faculty Scholar Award 2015 Burroughs-Wellcome Fund Investigators in the Pathogenesis of Disease Award 2014 NIH Director's New Innovator Award 2012 MacArthur Fellowship 2011 Alfred P. Sloan Research Fellowship The Hallem Lab develops tools like the Strongyloides RNA-seq Browser and Wild Worm Codon Adapter to advance functional genomics in parasitic nematodes. They emphasize diversity and inclusion in scientific training.

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Bambarendage Pinithi Upekka Pereraمشاهده پروفایل

پژوهشگر

University of Michigan-Ann ArborUnited States

Bambarendage Pinithi Upekka Perera is a Researcher at the University of Michigan School of Public Health , affiliated with the Environmental Health Sciences department and Environmental Epigenetics and Nutrition Lab . She holds a PhD in Biological Sciences from Louisiana State University (2016) and a BS in Biological Sciences from the University of New Orleans (2011). Her research focuses on environmental epigenetics, non-coding RNA (piRNA), genomic imprinting, and developmental toxicology. PhD, Biological Sciences, Louisiana State University, 2016 BS, Biological Sciences, University of New Orleans, 2011 Dr. Perera's work explores how environmental toxicants like lead , phthalates , and bisphenol A alter epigenetic mechanisms such as DNA methylation , histone modifications , and piRNA expression , linking these changes to human health outcomes like neurodevelopmental disorders and late-onset diseases . Her recent publications highlight tissue- and sex-specific epigenetic responses to developmental exposures. She is actively involved in teaching through courses like EHS 687/688: Environmental Health Sciences Professional Development and has secured NIH funding for projects on imprinted gene regulation by lead exposure . Dr. Perera collaborates with Dr. Dolinoy's team on applying piRNA-based tools for epigenome editing in environmental health.

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Stanley Watson Jrمشاهده پروفایل

استاد پژوهشی

University of Michigan-Ann ArborUnited States

Stanley Watson Jr. is a Research Professor at the Michigan Neuroscience Institute within the University of Michigan . His research focuses on neuroscience , gene expression , and transcription factor dynamics in psychiatric disorders like schizophrenia and bipolar disorder. Recent publications highlight his work on: Cell-type specific gene expression reductions in interneurons Multiomic profiling of transcription factor binding in human brain tissue Long-term effects of early life stress on myelin-related gene expression Development of brain-specific functional gene set databases (Brain.GMT) Collaborations with Huda Akil and others have produced high-impact studies in journals like Nature Neuroscience and Genome Research . His work also explores stress resilience mechanisms and environmental enrichment effects using rodent models.

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Nicolas Vergneمشاهده پروفایل

مدرس

University of Rouen NormandyFrance

Nicolas Vergne is a University Lecturer at the University of Rouen, where he has been actively teaching mathematics, statistics, and bioinformatics courses since at least 2010. His academic affiliation centers around the Laboratoire de Mathématiques Raphaël Salem (LMRS) at the University of Rouen, where his office is located (M.2.10, 2nd floor). His educational background includes: Doctorate in Applied Mathematics (2003-2008) from University of Evry-Val-d'Essonne DEA AMIB (Application of Mathematics and Computer Science to Biology) (2002-2003) Dual Masters in Mathematics and Mathematical Engineering (2001-2002) Bachelor's degree in Mathematics (2000-2001) DEUG MIAS (Mathematics and Computer Science Applied to Science) (1998-2000) BAC S (Scientific, Specialty Mathematics) (1997-1998) Vergne's research spans the intersection of probability theory, statistics, and biological applications. His primary focus involves developing and applying Markov chain models (including regulated, drifting, and semi-Markov variants) to analyze biological sequences and genomic data. He has made significant contributions to DNA barcoding methodology, Poisson approximation techniques for rare word detection in DNA sequences, and statistical approaches for RNA sequencing data analysis. His work bridges theoretical probability with practical bioinformatics applications, particularly in the areas of reliability analysis, survival modeling, and mixture models for high-throughput genomic data. Analysis of his publication record reveals a consistent trajectory from theoretical probability foundations toward increasingly applied bioinformatics research. His earliest work focused on rigorous mathematical treatments of Markov chains and Poisson approximation theory. Over time, his research evolved to address concrete biological problems including DNA sequence analysis, DNA barcoding, microarray analysis, and RNA-Seq data processing. A notable trend is his development of specialized R packages (SMM, DRIMM'R, WebDRIMM) that translate theoretical models into practical tools for the bioinformatics community. His most recent publications demonstrate expertise across multiple domains including cancer genomics, marine microbiology (diatom research), and rheumatoid arthritis biomarker discovery. Vergne has extensive teaching experience across multiple levels of the French university system, supervising both undergraduate and graduate students. His teaching portfolio includes probability, statistics, real analysis, biostatistics, and specialized bioinformatics courses. He has served as an apprenticeship supervisor for CNRS apprentices in bioinformatics and supervised multiple third-year interns. His laboratory affiliations include the LMRS at University of Rouen, the Bioinformatics Unit 900 of the Curie Institute, and the MIA unit of INRA in Jouy-en-Josas, reflecting his interdisciplinary approach spanning mathematics, statistics, and biology.

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Britt Anne Goodsمشاهده پروفایل

استادیار

Dartmouth CollegeUnited States

Britt Anne Goods is an Assistant Professor of Engineering at the Thayer School of Engineering , Dartmouth College. Her research focuses on the intersection of reproductive health, immunology, and biological engineering , utilizing advanced techniques such as single-cell RNA-sequencing , ex vivo models , and systems biology approaches . Education: BA in Biochemistry from Colby College (2010) BE in Chemical and Biochemical Engineering from Dartmouth (2011) PhD in Biological Engineering from MIT (2017) Her work addresses critical clinical challenges in reproductive health , including non-hormonal contraceptive discovery , uterine immunology , and lactation biology . By integrating single-cell transcriptomics with multi-omics datasets , she explores how sex hormones modulate immune cell behavior and tissue homeostasis. Dr. Goods' recent publications highlight her leadership in ovulation dynamics , macrophage biology , and human lactation studies . Her research has been recognized through prestigious awards, including the NRSA Postdoctoral Fellowship and National Science Foundation Graduate Research Fellowship . Scientific Awards: NRSA Postdoctoral Fellow (2017–2021) Seibel Scholar (2016) NSF Graduate Research Fellow (2013–2017) Howard A. Schroedel Fellow (2010–2011) Goldwater Scholarship Honorable Mention (2009) She mentors a diverse team of PhD students, postdoctoral researchers , and undergraduate trainees , contributing to collaborative initiatives like the Ovarian Contraceptive Discovery Initiative . Her lab is actively involved in open-access publishing and interdisciplinary training .

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Gordon P. Mearesمشاهده پروفایل

دانشیار

West Virginia UniversityUnited States

Gordon P. Meares is an Associate Professor at the Rockefeller Neuroscience Institute within the School of Medicine at West Virginia University. His research focuses on neuroimmunology, specifically the cellular and molecular mechanisms regulating inflammation in the central nervous system (CNS) and its role in neurological diseases such as Multiple Sclerosis. Education: PhD, University of Alabama at Birmingham, 2007 BS, Auburn University, 2001 Dr. Meares' laboratory investigates inflammatory responses in glial cells (astrocytes and microglia) to metabolic stress and injury, and their impact on other CNS cell types. His primary research areas include AMPK/LKB1 signaling in neuroinflammation for Multiple Sclerosis, PERK-dependent inflammatory pathways in ER stress, and transcriptome-wide mapping of neuroinflammatory responses using RNA-seq and bioinformatics. His work bridges molecular mechanisms with therapeutic applications for neurodegenerative conditions. Analysis of Dr. Meares' 12 publications (2011-2017) reveals a dominant focus on ER stress-induced neuroinflammation, particularly the PERK-JAK-STAT and AMPK regulatory pathways. His research consistently links molecular signaling in glial cells to disease mechanisms in Multiple Sclerosis and neurodegeneration, with strong emphasis on translational potential through conditional knockout models and primary cell cultures. Dr. Meares currently mentors graduate students in his laboratory and is accepting new trainees. His research is funded by a National Multiple Sclerosis Society (NMSS) grant investigating AMPK/LKB1 signaling in EAE models of MS. He is an active member of the Center for Neuroscience and the Center for Basic and Translational Stroke Research at West Virginia University. His laboratory employs advanced techniques including conditional knockout mice, primary glial cultures, in vivo cell-specific RNA labeling, and next-generation sequencing to dissect neuroinflammatory mechanisms.

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Xiaojie Qiuمشاهده پروفایل

استادیار

Stanford UniversityUnited States

Dr. Xiaojie Qiu serves as an Assistant Professor at Stanford University with dual appointments in the Department of Genetics and Department of Computer Science, as well as the BASE program. He holds additional memberships in Bio-X, the Cardiovascular Institute, the Maternal & Child Health Research Institute (MCHRI), and the Wu Tsai Neurosciences Institute, reflecting his interdisciplinary approach to biomedical research. His educational journey includes: Postdoctoral fellowship at Whitehead Institute & MIT (2023) in single cell and spatial genomics; systems biology PhD from University of Washington (2018) in Molecular & cellular biology; genome sciences Masters from East China Normal University (2012) in Bioinformatics and systems biology BS from Changchun University of Technology (2008) in Bioengineer Dr. Qiu's research integrates single-cell and spatial genomics with machine learning to unravel the complexities of heart evolution, development, and disease. His lab employs a full experimental-computational cycle, beginning with novel genomics approaches to measure single-cell states over time and space, then developing interpretable machine learning models to understand underlying gene regulatory networks. These computational models enable predictions of congenital heart diseases, aiming to identify when and where disease begins in the heart to develop preventive therapies. His scientific excellence has been recognized with several prestigious awards: NIH Director's New Innovator Award (2024) Arc Ignite Award (2023) Pathway to Independence Awards (K99/R00) (2023) Dr. Qiu mentors a diverse group of researchers including Tony Zeng (Doctoral Dissertation Reader), Sijie Chen, Naoki Konno, Nianping Liu, and Weize Xu (Postdoctoral Faculty Sponsors), and Peter Pao-Huang (Doctoral Dissertation Co-Advisor). His research program receives substantial support from the National Human Genome Research Institute, Chan Zuckerberg Institute, Impetus longevity grant, and Arc institute. The publication trends reveal his expertise spans computational biology, single-cell analysis, and cardiac development, with increasing focus on spatial transcriptomics and predictive modeling. The Qiu Lab has pioneered several influential computational tools including Monocle 2/3 (for pseudotemporal trajectory analysis), Dynamo (for RNA velocity vector field reconstruction), and Spateo (for multi-dimensional spatiotemporal modeling). Currently, the lab is developing the Aristotle ecosystem, an end-to-end predictive software framework that aims to bridge the gap between big data from single-cell and spatial genomics and quantitative predictive modeling of mammalian cell fate transitions.

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Kimberley Evasonمشاهده پروفایل

دانشیار

University of UtahUnited States

Kimberley Evason serves as Associate Professor of Anatomic Pathology in the Department of Pathology at the University of Utah School of Medicine and Adjunct Assistant Professor of Oncological Sciences. Her research program at the Huntsman Cancer Institute focuses on liver cancer mechanisms and therapeutic development, leveraging zebrafish models to address critical challenges in hepatocellular carcinoma treatment. Education: B.S. from University of Iowa M.D. and Ph.D. from Washington University School of Medicine Dr. Evason's laboratory investigates β-catenin-activated hepatocellular carcinoma (HCC), which accounts for 20-40% of human cases. Her team developed transgenic zebrafish models expressing hepatocyte-specific activated β-catenin that develop HCC, enabling chemical screening for targeted therapies. Key discoveries include JNK inhibitors and serotonergic antidepressants (notably amitriptyline) that suppress tumor growth, with amitriptyline showing efficacy in mouse models. Current research explores molecular mechanisms of drug action and identifies conserved genetic pathways through RNA-seq analysis and functional validation in zebrafish and human cell lines. Analysis of her 2015-2019 publications reveals a cohesive research trajectory centered on liver cancer biology using zebrafish models. Her work integrates chemical screening, genetic analysis, and translational validation across multiple systems (zebrafish, mouse, human cells), with strong emphasis on Wnt/β-catenin signaling pathways. Publications span molecular mechanisms, tumor microenvironment interactions, and diagnostic innovations, demonstrating consistent focus on bridging basic science discoveries to clinical applications in HCC treatment. Dr. Evason leads a multidisciplinary research team at the Huntsman Cancer Institute, utilizing core facilities for zebrafish husbandry and advanced imaging. Her collaborative network includes oncologists, geneticists, and pharmacologists across the University of Utah, facilitating translational research from bench to bedside. The laboratory's resources and institutional support enable high-throughput chemical screening and sophisticated molecular analyses central to her therapeutic discovery pipeline.

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Aaron Quinlanمشاهده پروفایل

استاد

University of UtahUnited States

Aaron Quinlan is a Professor and Chair of Human Genetics at the University of Utah's School of Medicine. His research integrates genetics, genomics, computer science, and machine learning to address critical problems in genome biology and the genetic basis of diseases. He focuses on genome variation analysis, chromosome evolution, and mining genetic variation for insights into human disease. B.S., College of William and Mary Ph.D., Boston College Quinlan's work emphasizes practical approaches to understanding genome mutation mechanisms, rare disease genetics, and computational genomics. His lab develops tools like STRchive and Vcfexpress for tandem repeat analysis and variant filtering, contributing to diagnostic advancements in genomic medicine. Recent research trends highlight his expertise in: De novo mutation rate estimation Tandem repeat expansion disorders Male infertility genetics Genome-wide variant discovery Structural variant detection Computational genomics tools Quinlan leads the Utah Center for Genetic Discovery and participates in the Undiagnosed Diseases Network. His collaborative projects span neonatal genomic diagnostics, equity in rare disease research, and multidisciplinary approaches to complex genetic disorders.

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Qi Chenمشاهده پروفایل

دانشیار مدعو

University of UtahUnited States

Dr. Qi Chen is an Adjunct Associate Professor at the University of California, Riverside and joined the University of Utah School of Medicine in 2023. His research bridges molecular biology and epigenetic inheritance , focusing on how paternal health influences offspring via sperm RNA modifications . Education : MD (Chongqing Medical University), PhD (Institute of Zoology, Chinese Academy of Sciences) Dr. Chen pioneered the discovery of tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs) as epigenetic carriers in intergenerational disease transmission . His work demonstrates how paternal diet, toxin exposure, and metabolic conditions alter RNA profiles to affect offspring health via RNA structural modifications . Recent publications (2025-2023) highlight his innovations in PANDORA-seq and MLC-seq technologies for RNA analysis, revealing novel roles for mitochondrial tsRNAs in Alzheimer's, RNA-TLR interactions in inflammation, and RNA decapping enzymes in immune signaling. Scientific Awards Keynote Lecture at EMGS 2024 George E. Seidel Jr. Keynote (IETS 2023) Highly Cited Researcher (2019) Chinese Academy of Sciences Fellowship (2013) His lab develops tools like SPORTS1.0 and PANDORA-seq to decode the 'sperm RNA code' and explore RNA structural memory propagation through biomolecular condensates . Current NIH/NICHD R01 funding supports ongoing investigations into RNA modification-mediated epigenetic inheritance .

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Omid Faridaniمشاهده پروفایل

پژوهشگر

University of New South WalesAustralia

Dr. Omid Faridani is a group leader at the School of Medical Sciences and a visiting group leader at the Garvan Institute of Medical Research . His work focuses on advancing single-cell technologies for precision oncology applications, particularly in pancreatic and other solid tumors. He has pioneered methods like Smart-seq2 , Small-seq , and Smart-seq3 for single-cell RNA sequencing, alongside developing a microfluidics platform for blood-based liquid biopsy and a culture system for solid biopsies. Research Highlights: Keywords: single-cell analysis, next-generation sequencing, circulating tumor cells, RNA splicing, biomarker discovery Grants: Cancer Council NSW, Cellular Genomics Futures Institute grant, CAG Cancer grant Scientific Awards: 2019 Pathfinders Award for CTC enrichment device innovation Supervision & Collaboration: Dr. Faridani seeks HDR students with molecular biology or biochemistry backgrounds for projects validating novel single-cell RNA sequencing technologies that profile both mRNAs and miRNAs.

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Erich Grotewoldمشاهده پروفایل

استاد

Michigan State UniversityUnited States

Erich Grotewold is a Professor at Michigan State University in the Department of Biochemistry & Molecular Biology , affiliated with the Molecular Plant Sciences Program and Genetics & Genome Sciences Program . Previously, he held roles at The Ohio State University , including Director of the Arabidopsis Biological Resource Center and leadership in the Center for Applied Plant Sciences . Ph.D. in Chemistry (1988), M.Sc. in Chemistry (1985) from University of Buenos Aires His research focuses on plant gene regulation , biosynthesis of flavonoids and phenolic compounds , and regulatory networks in crops like maize and camelina. The lab maintains databases AGRIS , GRASSIUS , and CamRegBase for comparative genomics. Recent publications emphasize transcription factor networks , metabolic engineering , and non-coding RNA in biofuel crops. Awards include Fellow of AAAS (2009) and OSU Dean's Award for Undergraduate Mentoring (2006) . Lab Members : Mentions multiple postdocs (Nathan Catlin, Yingni Xiao), graduate students (Ronnie Dewberry, Lina), and undergraduates (Luke Benedict) Collaborations : International partnerships including Guangdong Academy of Agricultural Sciences Technologies developed include high-throughput phenolic quantification protocols and multi-omic integration methods for gene network analysis. The lab actively participates in conferences like the International Camelina Conference and uses advanced tools such as fluorescence lifetime microscopy for anthocyanin imaging.

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Nikolay G Kolevمشاهده پروفایل

پژوهشگر

Yale UniversityUnited States

Nikolay G. Kolev is a Research Scientist in the Department of Epidemiology of Microbial Diseases at the Yale School of Public Health. He earned his PhD in Biochemistry from the University of Notre Dame and completed postdoctoral training at Yale University. His research focuses on molecular mechanisms governing the development of Trypanosoma brucei , the parasite causing African sleeping sickness. Key interests include RNA metabolism, antigenic variation, gene expression regulation, and transcriptional activation. He collaborates with Dr. Christian Tschudi to study parasite adaptation and host transmission dynamics. His recent publications highlight advancements in RNA-binding protein functions, transcriptome profiling, and mechanisms of parasitic gene regulation. Trends in his work span parasitology, molecular biology, and RNA biology, with specific subfields like VSG expression, snoRNA biogenesis, and vector-borne transmission. Scientific Awards Molecular, Cellular and Immunoparasitology Scientific Award (2009) from the American Society of Tropical Medicine and Hygiene Kolev's contributions include methodological innovations in RNA-Seq and RNAi plasmid design, alongside foundational discoveries in Trypanosoma developmental biology. His work bridges molecular parasitology and public health, targeting neglected tropical diseases through mechanistic insights.

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Aarthi Narayananمشاهده پروفایل

استاد

George Mason UniversityUnited States

Dr. Aarthi Narayanan is a Professor at George Mason University, affiliated with the Biology Department and the Center for Infectious Disease Research (CIDR). Her research focuses on host-pathogen interactions in viral infections, with emphasis on innate immune responses and translational therapeutic development. PhD in Biochemistry and Molecular Biology from the University of Georgia, Athens Postdoctoral research at Fred Hutchinson Cancer Research Center and National Institutes of Health (NIAID, NIH) Research interests include: Transcriptomic and proteomic analysis of viral pathogenesis Machine learning-based multiomic data integration Organ-on-a-chip models for clinically relevant disease studies Discovery of broad-spectrum antiviral targets Dynamic biomarker identification for disease states Therapeutic intervention evaluation in microphysiological systems Her publications demonstrate expertise in combining omic methodologies with computational approaches to prioritize host response events influencing disease progression. Studies span alphavirus pathogenesis, host defense peptide development, and organ-on-chip modeling of viral neurovirulence. Dr. Narayanan's laboratory collaborates with infectious disease research centers to bridge foundational virology with translational applications, utilizing both 2D cell cultures and complex microphysiological systems for antiviral evaluation.

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