Metatranscriptomics Professors and Supervisors

Marc Chevretteمشاهده پروفایل

استادیار

University of Wisconsin-MadisonUnited States

Marc Chevrette is an Assistant Professor at the University of Wisconsin-Madison conducting interdisciplinary research at the nexus of microbial genomics, evolutionary biology, and natural product discovery. His work integrates computational and experimental approaches to decipher secondary metabolism in microbial communities with applications in antibiotic development and microbiome engineering. Dr. Chevrette's educational background includes: PhD in Genetics from the University of Wisconsin-Madison MSc in Genetics from the University of Wisconsin-Madison MSc in Biotechnology (Bioengineering) from Harvard University Extension BSc in Molecular Biology & Bioinformatics from Rensselaer Polytechnic Institute The Chevrette Lab investigates secondary metabolism across evolutionary, ecological, and synthetic systems. Core research areas encompass genome mining of biosynthetic gene clusters (BGCs), evolutionary dynamics of biosynthetic enzymes, microbiome-derived natural products from host-associated systems (amphibian skin, insect exoskeleton, rhizosphere) and soil bacteria, and genetic regulation of metabolite production in synthetic communities using metatranscriptomics and metametabolomics. The lab develops computational tools for BGC prediction and characterization while exploring enzyme specificity and promiscuity. Recent publications (2023-2025) reveal dominant themes in methodological innovation for genome mining (antiSMASH 8.0, GATOR-GC), biosynthetic gene cluster curation (MIBiG 4.0), and machine learning applications for enzyme specificity prediction. Research spans natural product discovery from Actinobacteria and host-associated microbiomes, evolutionary analysis of biosynthetic pathways, and experimental validation of microbial community interactions. Key interdisciplinary connections include computational biology, microbial ecology, and drug discovery. The Chevrette Lab maintains active collaborations with the Tiny Earth initiative for soil bacteria research and participates in interdisciplinary networks focused on natural product discovery. The lab's integrative approach combines computational genomics, evolutionary analysis, and experimental microbiology to explore the ecological and biomedical significance of microbial secondary metabolism.

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Asela Wijeratneمشاهده پروفایل

دانشیار

Arkansas State UniversityUnited States

Dr. Asela Wijeratne is an Associate Professor of Bioinformatics at Arkansas State University's Beck College of Sciences & Mathematics, Department of Biological Sciences. He leads the Wijeratne Lab, focusing on plant-microbe interactions and sustainable agriculture solutions. PhD in Bioinformatics (2007) - Pennsylvania State University BS in Biological Sciences (2000) - University of Peradeniya, Sri Lanka Research interests center on soybean-Phytophthora sojae interactions, gene regulatory networks, and bioinformatics applications in plant pathology. The lab develops novel strategies to combat crop losses through microbiome engineering and molecular analysis. Teaching portfolio includes bioinformatics, molecular biology, and biotechniques courses. Recent publications analyze rhizosphere microbiomes, Striga germination mechanisms, and avian ectosymbiont diversity. The lab also provides extensive mentoring opportunities for undergraduate and graduate researchers. USDA Research Funding Recipient Kays Foundation Grant Lab alumni have transitioned to roles at St. Jude Children's Research Hospital, AgriGro Inc., and doctoral programs at SUNY-Buffalo and Purdue University. The lab maintains active collaborations with institutions like University of Memphis and Ohio State University.

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Cynthia Silveiraمشاهده پروفایل

استادیار

University of MiamiUnited States

Cynthia Silveira serves as an Assistant Professor in the Biology Department within the College of Arts and Sciences at the University of Miami. Her research bridges microbiology, virology, and marine ecology with significant contributions to understanding coral reef ecosystems, microbiome dynamics, and viral ecology across diverse environments including marine, soil, and human systems. Dr. Silveira's research focuses on the intricate relationships between microorganisms and their environments. Her work spans coral reef microbiology, viral ecology across ecosystems, and medical microbiome research. She employs multi-omics approaches including metagenomics, metabolomics, and metatranscriptomics to investigate microbial community dynamics, host-pathogen interactions, and biogeochemical cycling. Her research has important implications for understanding climate change impacts on coral reefs, microbial contributions to nutrient cycling, and microbiome influences on human health conditions including cystic fibrosis and COVID-19. Analysis of Dr. Silveira's recent publications reveals a strong interdisciplinary approach connecting marine microbiology with medical applications. Her work consistently examines how microbial communities function across different scales - from coral reef ecosystems to human respiratory tracts. A recurring theme is the investigation of viral roles in microbial communities and their broader ecological impacts. Her research methodology frequently combines spatial analysis with molecular techniques to understand microbial interactions in complex environments. Dr. Silveira has collaborated extensively with researchers across multiple institutions, as evidenced by her numerous multi-authored publications. Her work on coral reef systems has been particularly impactful, with several publications appearing in high-impact journals. Her research on the nasopharyngeal microbiome during the COVID-19 pandemic demonstrates her ability to address timely health challenges through microbiome research. Dr. Silveira's laboratory likely focuses on microbial ecology across diverse environments, with particular emphasis on coral reef systems and human microbiomes. Her research group probably employs advanced molecular techniques including multi-omics approaches to study microbial community structure and function. The interdisciplinary nature of her publications suggests collaboration between marine biology, medical research, and computational biology teams.

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Nimalan Jeganathanمشاهده پروفایل

دانشیار

Pennsylvania State UniversityUnited States

Nimalan Jeganathan, MD, is an Associate Professor in the Department of Surgery, specializing in gastrointestinal diseases and surgical outcomes. His research focuses on diverticulitis, colorectal cancer, and inflammatory bowel disease (IBD), with notable contributions to understanding surgical risks and microbial roles in complicated conditions. He has published extensively in prestigious journals like Annals of Surgery and Microbiology Spectrum . Research Interests Development of patient distress indices for surgical syndromes Metatranscriptomic analysis of gut microbial consortia Prognostic factors in colon adenocarcinoma and liver metastasis Contemporary management of diverticulitis and IBD Scientific Awards Dean's Award for Excellence in Teaching (2021) Recent publications highlight his expertise in surgical validation studies, gastrointestinal microbiome dynamics, and cancer prognosis. Collaborations span multidisciplinary teams, contributing to UN Sustainable Development Goals in health and well-being.

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Laura Hugمشاهده پروفایل

دانشیار

University of WaterlooCanada

Laura Hug serves as Associate Professor and Canada Research Chair in Environmental Microbiology at the University of Waterloo, where she leads the Hug Research Group and acts as Associate Director of the Waterloo Centre for Microbial Research. Her work bridges fundamental microbial ecology with practical environmental solutions for contaminated sites. Her academic foundation includes: Ph.D. in Cell and Systems Biology, University of Toronto (2012) M.Sc. in Biochemistry and Molecular Biology, Dalhousie University (2007) B.Sc. in Molecular Biology and Genetics, University of Guelph (2005) Dr. Hug's research pioneers the application of meta-omic technologies (metagenomics, metatranscriptomics, proteomics) to characterize microbial communities in municipal landfills and other contaminated environments. Her lab integrates enrichment culturing with genome-enabled metabolic modeling to develop bioremediation tools targeting methane emissions and water/soil contamination, while exploring fundamental questions about microbial adaptation and evolution of degradation pathways for anthropogenic compounds. Her scientific excellence is evidenced by significant recognition: Canada Research Chair in Environmental Microbiology (2019) Kavli Fellow, National Academy of Sciences (2015) NSERC Post-Doctoral Fellowship (2013) Governor General’s Gold Medal, Dalhousie University (2008) Multiple NSERC Scholarships and University of Toronto Fellowships Dr. Hug actively contributes to academic service as a reviewer for high-impact journals including Nature and The ISME Journal, while teaching advanced courses in microbial ecology. Her research group maintains strong industry and governmental partnerships focused on environmental remediation challenges, supported by prestigious fellowships and awards that fund their innovative approaches to microbial community analysis. She demonstrates leadership through roles as Associate Director of the Waterloo Centre for Microbial Research and Section Chair for the Canadian Society for Microbiologists, with her 2015 discovery of novel microbial lineages featured in Scientific American and Quanta Magazine.

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Carlos León Sobrinoمشاهده پروفایل

پژوهشگر

Technical University of DenmarkDenmark

Carlos León Sobrino is a Post-doctoral Researcher at the DTU Biosustain (The Novo Nordisk Foundation Center for Biosustainability) under the SEM group at the Technical University of Denmark. Formerly, he worked at the Centre for Microbial Ecology and Genomics at the University of Pretoria (South Africa) and obtained his PhD from the Danish Archaea Centre at the University of Copenhagen. Education: MSc in Biology (University of Oviedo, Spain), PhD in Molecular Biology (University of Copenhagen, Denmark) His research focuses on leveraging CRISPR-Cas systems for genome engineering in Pseudomonas to enhance bioproduction strains. This builds on his prior work studying natural CRISPR-Cas immunity in hyperthermophilic archaea ( Sulfolobus islandicus ) and metatranscriptomics of arid soil microbiomes in the Namib Desert. Carlos has been recognized with the Villum Foundation Experiment Grant in 2019 to support his work at DTU. His technical expertise spans microbial genetics, bioinformatics, and ecological systems analysis.

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Josef P Werneمشاهده پروفایل

استاد

University of PittsburghUnited States

Josef P Werne serves as Professor and Chair of the Department of Geology and Environmental Science at the University of Pittsburgh's Dietrich School of Arts and Sciences. His research group employs organic biomarkers and stable isotopes in lake and ocean sediments to reconstruct Earth's climate history and biogeochemical processes across geological timescales. His educational foundation includes a BS in Geology from Denison University, MS/PhD in Geological Sciences from Northwestern University, and postdoctoral research at the Royal Netherlands Institute for Sea Research. Dr. Werne's work centers on paleoclimatology and biogeochemistry , utilizing molecular fossils to decode past climate conditions through sulfur isotope systematics, carbon cycling, and microbial community analysis. Current projects investigate Precambrian ocean analogs in sulfidic lakes, Pleistocene climate-human interactions across the Americas and Africa, and development of GDGT-based temperature proxies. Recent publications reveal strong trends in limnological climate proxies (70% of works), sulfur biogeochemistry (20%), and methodological innovations (10%), with field sites concentrated in the Americas, East Africa, and hypersaline rift lakes. His research group has secured significant NSF funding for projects including the Titicaca Basin human-biomarker study and MexiDrill's 1km Lake Chalco core recovery. Mentees like Dervla Kumar and Molly O'Beirne have earned NSF, GSA, and Mellon fellowships for paleoclimate proxy development. The Werne Lab maintains active collaborations with archaeologists, microbiologists, and international drilling programs, operating specialized facilities for lipid and isotope analysis to support ongoing investigations into Earth's climate evolution.

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Margaret Wengمشاهده پروفایل

پژوهشگر ارشد

Stanford UniversityUnited States

Margaret "Maggie" Weng is a NASA Postdoctoral Fellow at Stanford University, affiliated with the Earth System Science department. She employs cutting-edge techniques like metagenomics, metatranscriptomics, and stable isotope probing to study microbial communities in extreme environments, focusing on molybdenum dynamics at deep-sea methane seeps and microbial adaptation in hypersaline/polluted sites. PhD in Microbial Ecology (2024), Georgetown University BSc in Environmental Science (2019), Washington University in St. Louis Her research explores microbial persistence at environmental extremes, linking community behavior to bioremediation potential and ecosystem stability. Fieldwork experiences span the Atacama Desert, Iceland's Kerlingarfjöll, Western Australia, and industrial settings like San Diego salt factories. Scientific recognition: NASA Postdoctoral Fellowship Active in science communication through publications in The Los Angeles Review and Northern Woodlands magazine, Weng combines field research with narrative storytelling about microbial ecosystems.

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Erica M Hartmannمشاهده پروفایل

دانشیار

Northwestern UniversityUnited States

Erica M Hartmann is an Associate Professor at Northwestern University Feinberg School of Medicine (Department of Medicine, Pulmonary and Critical Care) and holds a secondary appointment at the McCormick School of Engineering . Her research bridges environmental microbiology, metagenomics, and public health, focusing on microbial interactions in built environments and their implications for antibiotic resistance and human health. Her work explores the microbiology of indoor spaces, chemical-microbe interactions, and the application of synthetic biology to combat pathogens. She has developed innovative protocols for metagenomic analysis, including DNA extraction, viability assays, and functional gene discovery. Her NSF CAREER Award (2021) supports research redefining antimicrobial interactions in indoor environments. The 15 most recent publications highlight her contributions to metagenomic methodologies, antibiotic resistance dynamics, phage-bacteria interactions, and microbial responses to pollutants. Her studies span diverse environments—from aircraft filters to household dust—and emphasize the intersection of human health, environmental microbiology, and engineering solutions. Scientific Awards : NSF CAREER Award (2021) Research Trends : Her recent work focuses on microbial dark matter, built environment microbiomes, and strategies to mitigate antibiotic resistance using synthetic biology and environmental interventions.

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Charles Caraguelمشاهده پروفایل

دانشیار

The University of AdelaideAustralia

Associate Professor Charles Caraguel affiliated with the School of Animal and Veterinary Science at the University of Adelaide specializes in aquatic animal health and epidemiology. After graduating from the National Veterinary School of Toulouse and obtaining a specialized diploma in aquaculture and fish pathology from Nantes, he completed a Master of Science at the Lobster Science Centre in Canada. His PhD in aquatic epidemiology at the Centre for Aquatic Health Sciences focused on infectious salmon anaemia virus diagnostics. Education : DVM (Toulouse), MSc (Canadian Lobster Science Centre), PhD (Atlantic Veterinary College) Research Areas : Aquatic epidemiology, diagnostic test validation, zoonotic disease dynamics, wildlife-livestock interface health Supervision : Eligible to supervise Masters and PhD students in animal health and disease ecology Publications : 15 most recent works address climate-disease modeling, metatranscriptomics in aquaculture, and zoonotic pathogen surveillance His field-based epidemiology research informs evidence-based health policies for aquaculture industries, emphasizing complex interactions between environmental factors, host responses, and disease management effectiveness.

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Selin DELİCEIRMAKمشاهده پروفایل

استادیار

Near East UniversityCyprus

Dr. Selin DELİCEIRMAK is an Assistant Professor in the Department of Molecular Biology and Genetics at Near East University's Faculty of Arts and Sciences, where she also directs the Molecular Ecology Research Center. She joined the university in September 2019 after earning her PhD at METU Institute of Marine Sciences. Her educational background includes: BSc in Biology, Hacettepe University MSc in Earth System Sciences, Middle East Technical University (METU) PhD in Marine Sciences, METU Institute of Marine Sciences Dr. DELİCEIRMAK's research investigates marine microbial ecology through three interconnected themes: Biogeochemical cycles : Roles of microorganisms in nitrogen/phosphorus cycling Climate resilience : Impacts of climate change on marine ecosystems Biotechnological innovation : Sustainable use of marine resources She employs cutting-edge genomic methods including metagenomics and metatranscriptomics in her work. As Director of the Molecular Ecology Research Center, she leads initiatives to study Cyprus island ecosystems and mentor researchers in molecular ecology techniques.

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