Genome structural evolution Professors and Supervisors | ApplySharif

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Varsha S. PathareView profile

Visiting Assistant Professor

Cornell UniversityUnited States

Varsha S. Pathare is a Visiting Assistant Professor at Cornell University's School of Integrative Plant Science (Soil and Crop Sciences Section), joining as a tenure-track Assistant Professor in July 2025. She holds a PhD from Western Sydney University and has held postdoctoral positions at Washington State University and the University of Illinois. Her research focuses on plant ecophysiology, particularly optimizing photosynthesis and water-use efficiency in grasses under climate change. She investigates leaf anatomy, CO2/water fluxes, and C3/C4 photosynthetic pathways using field and controlled experiments. Education includes a PhD in Biological Sciences (2018, Western Sydney University), MSc (Botany, 2009, Savitribai Phule Pune University), and BSc (Botany, 2007, Sir Parshurambhau College). Awards include a Carl Woese Fellowship and recognition for her PhD work. She has mentored over 20 students across institutions and co-authored over 20 peer-reviewed papers. Her work bridges plant physiology and ecology, addressing climate resilience in crops and grasslands. Key projects include redesigning leaf cell walls for optimized gas exchange and integrating plant-atmosphere CO2-water fluxes into Earth system models. She collaborates with the RIPE project and serves on DEI committees, promoting STEM education at K-12 levels through PlantingScience. Affiliations: Cornell University, University of Illinois, Western Sydney University Grants: Over $370,000 in funding from institutions like the Carl Woese Institute Outreach: K-12 mentorship, public science engagement, and DEI advocacy

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Mary StoddardView profile

Professor

Princeton UniversityUnited States

Mary Stoddard is Professor in Princeton University's Department of Ecology and Evolutionary Biology. Her research explores animal coloration, avian vision, and evolutionary processes using multidisciplinary approaches combining computer science, optics, physiology, and genomics. Fieldwork is conducted at the Rocky Mountain Biological Laboratory (Colorado) and Mountain Lake Biological Station (Virginia). Research investigates visual communication, color perception in hummingbirds, pattern recognition in eggshells, and the biomechanics of structural coloration. Develops open-source optical tools and software for quantifying animal coloration. Leads the Princeton Better for Birds Project to reduce bird-window collisions through community engagement and architectural solutions.

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Tom BrownView profile

Professor

University of OxfordUnited Kingdom

Tom Brown is a Professor of Nucleic Acid Chemistry at the University of Oxford's Department of Chemistry. His research focuses on designing and synthesizing chemically modified DNA and RNA for diagnostic and therapeutic applications, including CRISPR systems for genome editing. He has developed Scorpion primers and HyBeacons, used in personalized medicine and rapid forensic analysis. His work has led to the creation of biotech companies like ATDBio and Primer Design, contributing significantly to COVID-19 diagnostics. Research Interests: Brown's group explores nucleic acid modifications, DNA structure-function relationships, and the application of click chemistry for gene assembly. They use techniques like X-ray crystallography and NMR to study DNA interactions with repair enzymes and mutagenic lesions. Key Contributions: Contributions include rapid mutation identification methods, oligonucleotide delivery platforms, and spherical nucleic acids for stem cell isolation. His work bridges chemistry and medicine, with applications in diagnostics, therapeutics, and biotechnology. Awards: While no specific awards are listed, his impactful research has driven industry collaboration and innovation in nucleic acid-based technologies. Labs/Teams: Leads the Nucleic Acids Research Group and the Brown Group, focusing on interdisciplinary projects in chemistry, biology, and medicine.

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Maria EricssonView profile

Researcher

Harvard UniversityUnited States

Maria Ericsson, B.S., is the Director of the Harvard Medical School (HMS) Electron Microscopy Core within the Cell Biology Department. She joined HMS in 1995 to establish the Electron Microscopy Facility, following her B.Sc. in Chemistry from Uppsala University (Sweden) and specialization in electron microscopy at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. Her work focuses on advancing ultrastructural studies, providing expertise in sample preparation (TEM/SEM), high-pressure freezing, immunogold labeling, and imaging support for researchers. Ericsson collaborates extensively on projects involving Parkinson’s disease, Alzheimer’s disease, and viral pathogenesis (e.g., SARS-CoV-2). Her publications highlight contributions to neurodegenerative mechanisms, mitochondrial function, and microscopy techniques. Ongoing research emphasizes the role of electron microscopy in understanding cellular processes, protein aggregation, and immune responses. As Core Director, she supports over 89 publications, including studies on α-synuclein in Parkinson’s, amyloid-β in Alzheimer’s, and SARS-CoV-2 lung pathology. Her facility bridges technical expertise with cutting-edge research, aiding advancements in structural biology and disease modeling.

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Joanna MelonekView profile

Research Fellow

The University of Western AustraliaAustralia

Dr Joanna Melonek is an Adjunct Research Fellow at The University of Western Australia's School of Molecular Sciences. She holds a PhD from Kiel University (2011) and completed postdoctoral research at UWA's Plant Energy Biology Centre. Her work focuses on plant mitochondrial biology, particularly Restorer-of-Fertility-like (RFL) proteins critical for hybrid crop development. Melonek collaborates with institutions like the Leibniz Institute (Germany) and companies such as Groupe Limagrain to advance wheat fertility restoration and genomics. She has contributed to the International Wheat Genome Sequencing Consortium and pioneered volatile biomarker detection for honeybee health. Awards include the Peter Goldacre Medal (2021) and Western Australian Young Tall Poppy Science Award (2021). Education: MSc (August Cieszkowski Agricultural University), PhD (Kiel University) Research Themes: Cytoplasmic Male Sterility, RNA Processing, Plant Genetics Recent projects include genomic analysis of Triticeae plants and development of non-invasive pathogen detection methods. Melonek leads grants totaling over AUD million, with active projects on hybrid wheat breeding and fertility restoration mechanisms.

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Ian LidburyView profile

Research Fellow

University of SheffieldUnited Kingdom

Dr Ian Lidbury is a Royal Society University Research Fellow and MMBD Comms Lead at the University of Sheffield's School of Biosciences. His research focuses on microbial ecophysiology, particularly linking microbial activity to ecosystem services such as food security and climate change mitigation. He holds a BBSRC Discovery Fellowship and previously served as a Postdoctoral Research Fellow at the University of Warwick. Education: PhD in Marine Microbiology (University of Warwick, 2011-2015) MRes in Marine Microbiology (Marine Biological Association & Plymouth University, 2010-2011) Research Interests: Organic phosphorus cycling in plant-associated bacteria Soil polysaccharide degradation by Bacteroidetes Microbial interactions at the root-soil interface Meta-omics approaches to study soil microbiome function Publications: Recent work includes studies on phosphatase enzymes in marine cyanobacteria, nitrogen-phosphorus dynamics in soil, and bacterial adaptations to nutrient-poor environments. His lab employs multi-layered omics techniques combined with bacterial genetics to explore microbial ecophysiology. Awards: Royal Society University Research Fellowship BBSRC Discovery Fellowship Teaching & Mentorship: Teaches courses on microbial genetics and environmental microbiology Supervises PhD students in topics such as rhizosphere microbiology and biogeochemical cycles Lab Collaborations: Collaborates with Dr. Ellie Harrison (phage-rhizobia-legume interactions) and Prof. Tim Daniell (agroecosystem nitrogen cycling) at the Arthur Willis Environmental Centre.

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Nicola NadeauView profile

Senior Lecturer

University of SheffieldUnited Kingdom

Dr Nicola Nadeau is a Senior Lecturer in the School of Biosciences at the University of Sheffield. Her research focuses on the evolution and genetics of color pattern variation, structural coloration in animals, speciation, and adaptation to environmental pressures. She holds a BSc in Zoology from the University of Newcastle-upon-Tyne and a PhD in Zoology from the University of Cambridge. Prior to her current role, she was a NERC Independent Research Fellow (2014–2019) and has held postdoctoral positions at the University of Cambridge and the University of Sheffield. Her teaching responsibilities include coordinating modules such as BIS320 (Topics in Zoology) and BIS4101 (The Scientific Cycle), and she supervises undergraduate and postgraduate research projects in evolutionary biology, ecology, and genomics. She is a Senior Fellow of the Higher Education Academy and actively engages in professional activities, including editorial roles and committee memberships. Dr Nadeau’s research has led to significant contributions in understanding genetic and developmental mechanisms underlying structural coloration, as well as the role of altitude in shaping butterfly adaptations. Her work frequently involves interdisciplinary approaches, combining genomic analysis, field studies, and experimental methods. Research Highlights: Evolution of iridescent colors in Heliconius butterflies, genomic basis of speciation, and adaptation to high-altitude environments. Awards: NERC Independent Research Fellowship, Fellow of the Royal Entomological Society. Labs/Teams: Active in the School of Biosciences, collaborating with international research networks.

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Michael BeerView profile

Professor

Johns Hopkins UniversityUnited States

Michael Beer is a Professor of Biomedical Engineering and Genetic Medicine at Johns Hopkins University, affiliated with the McKusick-Nathans Institute of Genetic Medicine and the Department of Biomedical Engineering. His research focuses on computational regulatory genomics, leveraging AI/ML to decode DNA sequence-based gene regulation and its role in development and disease. He holds a PhD from Princeton University and has received awards including the Searle Scholars Award and the Simon Ramo Award. Education: PhD in Astrophysical Sciences, Princeton University, 1995 MA in Astrophysical Sciences, Princeton University, 1991 BSE in Engineering, University of Michigan, 1989 Research Interests: Beer's lab develops computational models to understand enhancer activity, CRISPR-based perturbation, and gene regulatory networks in cancer and disease. They use functional genomics data (ATAC-seq, ChIP-seq, Hi-C) to study regulatory mutations and therapeutic strategies. Key Contributions: Pioneered methods like gkm-SVM for regulatory variant prediction and led ENCODE Consortium efforts. His work bridges machine learning and genomics to model dynamic regulatory networks. Awards: Simon Ramo Award (Thesis in Plasma Physics) DOE Fusion Energy Postdoctoral Fellowship National Science Foundation Graduate Fellowship Searle Scholars Award Johns Hopkins Teaching Excellence Award Lab & Collaborations: Located in the McKusick-Nathans Institute, the lab collaborates with the Ph.D. program in Human Genetics and Genomics. Recent projects include CRISPRi screens and ENCODE grant-funded research on regulatory elements.

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Per PalsbollView profile

Professor

University of GroningenNetherlands

Prof. Per Palsboll is a Professor of Marine Evolution and Conservation at the University of Groningen’s Faculty of Science and Engineering, affiliated with the Groningen Institute for Evolutionary Life Sciences. He holds an adjunct scientist position at the Center for Coastal Studies (USA) and serves as an Associate Editor for Marine Ecology Progress Series and Animal Biodiversity and Conservation . His expertise spans population genetics, conservation genetics, and marine mammal research. Education: PhD in Evolutionary Genetics (University of Copenhagen, 1993) and Cand. scient (equivalent to MSc, 1989). Previous academic roles include professorships at Stockholm University, UC Berkeley, and Harvard University. He coordinates MSc courses on population genetics and computational biology and teaches in conservation biology and polar ecology programs. Research focuses on marine mammal genomics, including studies on humpback whales, minke whales, and fin whales. His work addresses trophic dynamics, genetic diversity, and conservation strategies. Awards include the 2024 Open Research Award and 2021 UG Open Research Award for promoting open science.

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Petra PjevacView profile

Researcher

University of ViennaAustria

Dr. Petra Pjevac is a Senior Scientist and Group Leader at the Joint Microbiome Facility within the University of Vienna's Centre for Microbiology and Environmental Systems Science . Her work focuses on microbial community dynamics, particularly chemolithoautotrophic microorganisms in soils and sediments, and their roles in nitrogen, sulfur, and metal cycling. She employs sequencing-based methods, physiological experiments, and biogeochemical analyses to study environmental and clinical microbiome systems. Research Interests: Her key areas include microbial niche differentiation, anaerobic metabolism, and the impact of environmental stressors (e.g., salinization) on microbial communities. She also investigates microbiome interactions in human health contexts, such as gut-brain axis effects and post-COVID syndrome. Recent Trends in Publications: Recent work highlights microbiome shifts in response to dietary interventions, post-viral gut dysbiosis, and the role of microbial communities in environmental biogeochemistry. Collaborations span environmental science, clinical research, and systems biology. Labs/Teams: Leads a dynamic team at the Joint Microbiome Facility, supporting researchers across study design, sequencing, and data interpretation. Current projects include optimizing nitrification inhibitors for sustainable agriculture and exploring microbial diversity in nitrite-oxidizing bacteria.

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Willem WilderingView profile

Associate Professor

University of CalgaryCanada

Willem Wildering is an Associate Professor in the Department of Biological Sciences at the University of Calgary’s Faculty of Science, and a Full Member of the Hotchkiss Brain Institute. He holds a B.S. in Biological Sciences (University of Groningen, 1982), an M.S. in Pharmacology and Behavioral Physiology (University of Groningen, 1986), and a Ph.D. in Physiology/Neurobiology (Free University of Amsterdam, 1992). His research focuses on Cellular and molecular mechanisms of neuronal aging and neurodegeneration, Neurotoxicology of aquatic pollutants, Neuronal plasticity and memory impairment in aging models. He uses gastropod models like Lymnaea stagnalis to investigate aging-related changes in neuronal excitability, redox balance, and synaptic function. Wildering’s publications (15 most recent highlighted) span mechanisms of axonal regeneration, neuroinflammation, and epigenetic regulation. His work bridges molecular neurobiology with behavioral studies, emphasizing translational relevance to human neurodegenerative diseases. He teaches ZOOL 595: Evolutionary Perspectives in Neurobiology and collaborates on projects exploring neurotrophic factors and environmental toxin impacts. No scientific awards are listed, but his extensive grant-funded research has advanced understanding of nervous system aging. Wildering’s lab at the Hotchkiss Brain Institute integrates electrophysiology, transcriptomics, and behavioral assays to dissect age-related neural decline. His team studies how environmental pollutants and molecular pathways (e.g., PLA2, EGF) influence nervous system resilience across lifespans.

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Ronald BreakerView profile

Professor

Yale UniversityUnited States

Ronald Breaker is a Sterling Professor of Molecular, Cellular, and Developmental Biology, and Professor of Molecular Biophysics and Biochemistry at Yale University. He serves as Chair of the Department of Molecular Biophysics and Biochemistry and is an Investigator at the Howard Hughes Medical Institute. His research focuses on nucleic acid functions, including riboswitch discovery, RNA engineering, and molecular switch technology. Breaker earned his PhD in Biology/Biochemistry from Purdue University (1992) and BS in Biology/Chemistry from the University of Wisconsin-Stevens Point (1987). Breaker’s research has identified over 30 riboswitch classes and pioneered the use of in vitro evolution for creating functional RNAs and deoxyribozymes. His work on riboswitches revealed their role in metabolite sensing and gene regulation, with applications in antibiotic development. He has co-founded two biotech companies, Archemix and BioRelix, and holds editorial roles at journals like RNA Biology and Cell Chemical Biology. His awards include the National Academy of Sciences’ Molecular Biology Award, the Merck Award (ASBMB), and election to the National Academy of Sciences (2014) and American Academy of Arts and Sciences (2021). Breaker’s lab employs bioinformatics, genetics, and biochemistry to explore RNA’s functional potential across diverse bacterial species.

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Alonso FavelaView profile

Assistant Professor

University of ArizonaUnited States

Alonso Favela is an Assistant Professor at the University of Arizona's School of Plant Sciences, part of the College of Agriculture, Life & Environmental Sciences. He holds a B.S. in Biology from the University of Arizona (2015) and a Ph.D. in Ecology, Evolution, and Conservation Biology from the University of Illinois at Urbana-Champaign (2018). His research focuses on understanding plant-microbiome interactions in agroecosystems, with particular emphasis on microbial contributions to climate resilience, nitrogen cycling dynamics, and sustainable agriculture. Dr. Favela's work spans microbial ecology, genomic biodiversity, and ecosystem processes. He has received prestigious fellowships including an NSF Postdoctoral Fellowship in Biology (Rules of Life) and a USDA NIFA Postdoctoral Researcher position. His research integrates field experiments, genomic analyses, and computational modeling to address challenges in agroecosystem sustainability and climate adaptation. Key themes include the role of plant genetics in shaping microbiome composition, the functional impacts of microbial communities on nutrient cycling, and the application of evolutionary biology principles to sustainable crop management. His recent studies explore how crop domestication history influences rhizosphere microbiome recruitment and how plant phenotypes can be optimized to enhance soil health. Articles published since 2015 highlight advancements in understanding microbial contributions to nitrogen cycling, root microbiome assembly, and the ecological implications of crop domestication. These studies underscore the necessity of integrating microbiome science into agricultural practices to mitigate climate change impacts.

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Kristian HasselView profile

Professor

Norwegian University of Science And TechnologyNorway

Kristian Hassel is a Professor and Head of Herbarium TRH at the NTNU University Museum (Norwegian University of Science and Technology). His research focuses on Arctic bryophyte ecology, biosystematics, and conservation, particularly Sphagnum species. He leads Norway's red list assessments for bryophytes and chairs the Nordic Bryological Society. His work combines field studies in Greenland and Svalbard with genomic approaches to study speciation and climate impacts. Affiliations: NTNU University Museum, Department of Natural History Roles: Professor, Herbarium TRH Director, Nordic Bryological Society President Key Projects: Norwegian Taxonomy Initiative, MIRACLE (Mires and Climate), Nordic bryophyte conservation networks Research emphasizes Arctic ecosystems' responses to climate change through metabarcoding, fossil pollen studies, and species distribution modeling. Recent work addresses Sphagnum peatmoss genetics and conservation of carbon-sequestering mires. Publications span 2018–2025, with contributions to New Phytologist , American Journal of Botany , and bryological journals. Active in red-listing assessments and policy advising on mire protection.

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Michele LeoneView profile

Researcher

University of LausanneSwitzerland

Dr. Michele Leone is a researcher at the Department of Ecology and Evolution , University of Lausanne, affiliated with the Robinson-Rechavi Group. His work bridges biology and computational methods, with expertise in machine learning, natural language processing, and evolutionary biology. As a post-doctoral researcher, he focuses on understanding arthropod moulting evolution through the creation of MoultDB, a comprehensive data repository. His research includes developing computational tools like GeMI for genomic metadata integration using transformer models, and SMfinder for metabolomics analysis. Previously, his PhD involved creating methods to analyze genomic functional elements via Hidden Markov Models and applying sequence-to-sequence models to structure genomic data from free-text descriptions. This work incorporated active learning frameworks and user feedback mechanisms. Leone’s interdisciplinary approach combines bioinformatics with evolutionary questions, addressing challenges in data interpretation and metadata standardization. His office is located in room 3220 at Biophore, Lausanne, and he can be reached at michele.leone@unil.ch .

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