Find Academic Supervisors

Özgen DenizView profile

Senior Lecturer

• Transposable Elements
• Epigenetics
• Cancer Biology
• +7 more

Dr Özgen Deniz is a Senior Lecturer and Group Leader at the Queen Mary University of London , Centre for Epigenetics. Her research focuses on the epigenetic regulation of transposable elements (TEs) and their role in blood cancers, particularly acute myeloid leukaemia (AML). She combines functional and computational genomics to investigate how TEs contribute to oncogenesis and cancer treatment efficacy. Core member of QMUL Epigenetics Hub Member of LMS Imperial TE Hub Member of European Haematology Association Theme Lead in Mobile DNA Editorial Board Her lab has uncovered TEs as novel oncogenic regulators in AML, demonstrating their ability to dysregulate gene expression and trigger anti-tumour immunity. Current projects include functional interrogation of TEs in adult and paediatric AML, supported by major grants such as the ERC Starting Grant (2024-2029) and Cancer Research UK Career Development Fellowship (2022-2028). Scientific Awards: Cancer Research UK Career Development Fellowship The Deniz Lab actively recruits researchers interested in transposon biology and cancer epigenetics, with collaborations across epigenetics and haematology networks. Their work bridges genomic instability, chromatin dynamics, and therapeutic resistance in leukaemia.

• Pathology
• Genetics
• Epigenetics
• +4 more

Emma Helena Siili serves as a University Instructor in the Department of Pathology at the University of Helsinki, with clinical integration at Helsinki University Hospital (HUS). Her dual academic-hospital role positions her at the intersection of diagnostic pathology and translational research. Her research program investigates molecular underpinnings of gynecological diseases through three interconnected pillars: Genetic/epigenetic drivers of uterine leiomyomas (FGFR alterations, chromatin dynamics) Human retrotransposon biology in somatic and germline contexts Population genomics applications via the FinnGen biobank This work employs integrated genomic approaches to decode mechanisms in benign tumors with cancer relevance. Recent publications reveal a strong emphasis on collaborative, data-intensive studies leveraging Finland's national biobank resources. Dr. Siili's 2025 output demonstrates consistent high-impact contributions across pathology and genomics domains, with trends showing increasing focus on computational analysis of large-scale genomic datasets. Her publications consistently address women's health issues through molecular pathology lenses, bridging basic science and clinical applications. As a teaching-focused faculty member, she contributes to medical education while maintaining active research through departmental collaborations. Her work environment centers on the Department of Pathology's interdisciplinary teams, utilizing shared genomics infrastructure and HUS clinical resources to advance understanding of gynecological disease mechanisms.

• Computational biology
• Computational systems biology
• Biomedicine
• +7 more

Dr. Kimmo Palin is a Medicum University Researcher and Docent at the University of Helsinki's Faculty of Medicine, where he serves as the Applied Tumor Genomics (ATG) Supervisor for both the Doctoral Programme in Integrative Life Science and the Doctoral Programme in Biomedicine. His research spans computational biology, tumor genomics, and cancer genetics, with particular focus on colorectal cancer, uterine leiomyomas, and the molecular mechanisms underlying cancer development. Dr. Palin integrates computational approaches with molecular and clinical data to investigate genetic and epigenetic alterations in tumors. Dr. Palin's recent publication record demonstrates significant contributions to cancer genomics, with multiple high-impact publications in 2024-2025 covering topics such as FGFR gene activation in uterine tumors, metabolomic characterization of colorectal cancer, retrotransposition events in human genomes, and large-scale genetic analyses identifying cancer susceptibility genes. He is actively involved in major research initiatives including the Centre of Excellence in Tumor Genetics Research (COETG) and the iCAN digital precision cancer medicine program, which provide substantial funding and collaborative opportunities for his research group. As a Docent and doctoral program supervisor, Dr. Palin plays a key role in training the next generation of cancer researchers, guiding students through doctoral studies with a focus on tumor genomics and computational approaches to cancer research.

• Chromatin Organization
• Epigenetics
• Plant Reproduction
• +4 more

Dr. Célia Baroux is a Professor and Group Leader in the Department of Plant Developmental Genetics at the Institute of Plant Biology, University of Zurich. Her research program investigates the functional dynamics of chromatin organization in plant reproductive development, with significant contributions to understanding nuclear architecture and epigenetic regulation. Her primary research interests focus on: 3D genome organization in epigenetic regulation Chromatin dynamics during cell fate specification Nuclear envelope interactions in plant cells Reproductive development in Arabidopsis Evolutionary aspects of epigenetic mechanisms Analysis of her recent publications (2020-2022) reveals a consistent focus on chromatin architecture, with particular emphasis on histone modifications, nuclear positioning, and transposable element regulation. Her work bridges molecular genetics, epigenomics, and developmental biology, often employing innovative technical approaches like inducible gene systems in ovules. Dr. Baroux actively contributes to the scientific community through editorial roles at Frontiers in Plant Science and co-founding the INDEPTH Academy, which serves as a collaborative platform for researchers studying nuclear domains in plants. Her extensive publication record demonstrates consistent productivity in high-impact plant science journals. Her laboratory maintains an active research program with international collaborations, as evidenced by multi-institutional publications spanning Switzerland, France, the UK, and beyond. The lab's work combines molecular genetics, advanced imaging, and computational approaches to unravel fundamental mechanisms of plant reproduction.

Jeremy LubanView profile

Professor

• Virology
• Molecular Biology
• Infectious Diseases
• +4 more

Jeremy Luban is the David J. Freelander Chair in AIDS Research at the University of Massachusetts Medical School, with joint appointments at the Broad Institute of MIT and Harvard, Ragon Institute of MGH, MIT and Harvard, and Massachusetts Consortium on Pathogen Readiness. He holds an M.D. from Columbia University College of Physicians and Surgeons and a B.A. in Biology and Music from SUNY Purchase. His research focuses on virology, molecular mechanisms of infectious diseases (particularly HIV/AIDS and emerging viruses), host-pathogen interactions, and genomic approaches to disease mechanisms. Work spans viral pathogenesis, retrovirology, and host defense systems, with emphasis on structural biology of viral components and therapeutic interventions. Recent publications demonstrate extensive work in viral evolution, host immune responses to pathogens like HIV, Ebola, and SARS-CoV-2, and innovative gene-editing technologies. Research consistently integrates molecular virology with computational and structural approaches to address fundamental questions in infectious disease biology. Awards/Honors: David J. Freelander Chair in AIDS Research

Oleg SimakovView profile

Associate Professor

• Evolutionary Genomics
• Comparative Animal Genomics
• Developmental Biology
• +4 more

Oleg Simakov is an Associate Professor and Head of the Department of Neuroscience and Developmental Biology at the University of Vienna. His research focuses on metazoan genome architecture, evolutionary transitions, and cephalopod-specific genomic innovations through comparative and computational approaches. BS in Biology, University of Karlsruhe MS in Biology, University of Heidelberg PhD in Biology, EMBL/University of Konstanz Key research areas include: Evolutionary genomics of metazoans Syntenic gene cluster analysis 3D chromatin modeling Cephalopod molecular evolution His publications reveal trends in chromosomal evolution , gene linkage dynamics , and repetitive element expansion across diverse taxa including octopuses, hydra, and lungfish. Current work involves genomic investigations of Euprymna scolopes and Hydra magnipapillata to elucidate evolutionary novelties. Current research team includes: PhD students: Koto Kon, Lisa Rouressol Master's students: Georgios Efthymiadis, Gözde Yalcin Postdocs: Darrin Schultz, Thea Rogers Technicians: Fatih Sarigöl, Nina Znidaric

Emile Gluck-ThalerView profile

Assistant Professor

• Fungal Pathology
• Plant Pathology
• Horizontal Gene Transfer
• +4 more

Emile Gluck-Thaler is an Assistant Professor in the Department of Plant Pathology at the University of Wisconsin-Madison, affiliated with the College of Agricultural and Life Sciences. His research focuses on fungal genetics, horizontal gene transfer, and genome evolution, particularly in plant pathogens. Education: PhD in Plant Pathology, The Ohio State University BS in Life Sciences with Microbiology Specialization, McGill University, Canada Research Interests span fungal genomics, transposable elements, and mechanisms of pathogen adaptation. He investigates how mobile genetic elements drive diversity and resistance in plant pathogens like Macrophomina phaseolina and Pyricularia species. Notable Trends in Research include the role of giant transposons in horizontal gene transfer, geostatistical modeling for pathogen distribution, and the evolutionary implications of metabolic gene clusters in fungi. Labs & Collaborations: He works in the Discovery Building at UW-Madison, contributing to interdisciplinary research on fungal biology and plant-microbe interactions.

Biswajyoti SahuView profile

Research Fellow

• Biomedical Sciences
• Cancer Biology
• Transcriptional Regulation
• +3 more

Biswajyoti Sahu is an Academy Research Fellow and Docent at the University of Helsinki, affiliated with the Doctoral Programme in Integrative Life Science and the Applied Tumor Genomics (ATG) group at Medicum. He previously served as a Visiting Scientist at the University of Cambridge (2018–2019) and the Whitehead Institute for Biomedical Research (2015). Biomedical Sciences Cancer Biology Transcriptional Regulation Epigenetics His research focuses on oncogenes, transcription factor dynamics, and epigenetic mechanisms in cancer and development. Key themes include chromatin modifier enzymes, transposable elements, and cellular reprogramming. Recent publications highlight his work on oncogene convergence pathways (2025), transposable element derepression (2025), and single-cell multiome protocols (2024). Awards include the Finnish Cultural Foundation’s Grant (2011), Endocrine Trainee Day Fellowship (2009), and multiple presentation awards.

• Plant Molecular Biology
• Genetics
• Epigenetics
• +6 more

Dr. Chris Winefield is an Associate Professor in the Department of Wine Food & Molecular Biosciences at Lincoln University's Faculty of Agriculture and Life Sciences in New Zealand. His research focuses on plant molecular biology and genetics, particularly studying transposable elements in crop evolution and epigenetic regulation in response to changing environments. He works extensively with horticultural plant species such as grapevine and hops, investigating key industry issues including seasonal variation in flowering, fruit and flower development, and the development of flavor and aroma biochemistry. Dr. Winefield earned his PhD from the University of Otago and his MSc (Hons) from Waikato University. His academic career includes positions as Senior Lecturer at Lincoln University (2004-2021), Post Doctoral Fellow at the University of York (2001-2004), and Scientist at Crop & Food Research Ltd (1994-2001). His research program utilizes diverse methodologies including de-novo genome sequencing and annotation, whole genome bisulphite sequencing, traditional breeding/genetics, and agronomic assessment of grape and hop populations. A key focus is studying how controlled bursts of transposon activity can be used to develop new germplasm to meet industry challenges. His work addresses significant issues related to climate change, food security, and sustainable agricultural practices, aligning with UN Sustainable Development Goals including Zero Hunger, Quality Education, Responsible Consumption and Production, Climate Action, and Life on Land. Dr. Winefield's publication record demonstrates consistent contributions to plant genomics, epigenetics, and viticulture research. His recent work shows increasing focus on transposable elements, genome regulation, and the molecular basis of traits important to horticultural industries. He has developed expertise in both long-read and short-read sequencing technologies and their application to plant genome analysis. Chairperson Bio-safety committee (2012-present) Member Faculty Agriculture and Life Sciences research committee (2018-present) Dr. Winefield actively supervises postgraduate students, with numerous completed Masters and PhD projects focusing on various aspects of plant genetics, molecular biology, and horticultural science. His laboratory continues to develop innovative approaches to studying plant genome dynamics and their applications to crop improvement.

Simon Chong ChuView profile

Research Fellow

• Computational Biology
• Genomics
• Transposable Elements
• +3 more

Simon Chong Chu, Ph.D. serves as a Caspar Wistar Fellow in the Molecular and Cellular Oncogenesis Program at The Wistar Institute. A computational biologist specializing in genomic repeats research, Chu develops innovative computational methods to investigate transposable elements and their critical roles in human health and disease. Chu's research interests focus on genomic repeats—including transposable elements (TEs), short and long tandem repeats, and large satellite repeats—that constitute over half of the human genome. His work integrates systems biology with cutting-edge genomics to uncover how these elements influence development, evolution, and disease processes. He has developed computational tools like xTea, REPdenovo, GINDEL, SpliceJumper, GAPPadder, and TrapHunter that have been widely adopted across diverse research contexts. Chu's publication record demonstrates expertise in both cancer genomics and computational methodology development. His recent work examines retroelement contributions to birth defects and childhood cancers, the landscape of human SVA retrotransposons, and comprehensive identification of transposable element insertions using multiple sequencing technologies. His research bridges computational innovation with biological discovery, particularly in understanding how genomic repeats evade suppression mechanisms and contribute to disease states. Chu earned his Ph.D. in Computer Science and Engineering from the University of Connecticut and completed postdoctoral training in the Department of Biomedical Informatics at Harvard Medical School. Prior to joining The Wistar Institute in 2025, he worked as a principal scientist at ROME Therapeutics, where he contributed to clinical drug discovery.

• Plant Genetics
• Meiosis
• Recombination
• +5 more

Dr. Ian Henderson is a Reader (equivalent to Associate Professor) in Plant Sciences at the University of Cambridge, where he has maintained an active research program since 2008. His work focuses on fundamental mechanisms of plant genome organization, transmission, and evolution. His research interests span several interconnected areas: Meiotic recombination mechanisms in plants Centromere structure, function, and evolution Epigenetic regulation of genome stability Transposable element dynamics and impact on genome architecture Chromatin organization in plant genomes Dr. Henderson's laboratory employs Arabidopsis thaliana as a primary model system but extends findings to other plant species including maize and wheat. His research has revealed critical insights into how chromatin structure influences crossover formation during meiosis, the evolutionary dynamics of centromeres across plant species, and the role of epigenetic modifications in regulating genome stability. Recent work has utilized advanced genomic technologies including CRISPR-based approaches, long-read sequencing for complex genomic regions, and sophisticated computational analysis. His publication record demonstrates consistent high-impact research output, with numerous papers in top-tier journals including Nature Communications, PNAS, and Nature Plants. His work shows an increasing trajectory of research impact, with multiple significant publications appearing in 2025. The research often involves international collaborations across Europe and North America. Dr. Henderson's lab provides training opportunities for graduate students and postdoctoral researchers interested in plant genomics, meiosis, and epigenetics. Students in his laboratory develop expertise in molecular genetics, genomic analysis, and computational approaches to complex biological problems. The research has implications for both fundamental biological understanding and potential applications in plant breeding and agricultural biotechnology.

• Redox Signaling
• Epigenetics
• Trained Immunity
• +5 more

Christian Lindermayr is a Professor at Helmholtz Munich , affiliated with the Environmental Health Center and the Institute of Lung Health and Immunity . He leads the research group 'Trained Immunity', focusing on redox signaling, epigenetic mechanisms, and their role in innate immune memory in both plants and humans. His work bridges plant biochemistry and human immunology to develop immunotherapies for trained immunity modulation. PhD in Plant Physiology and Biochemistry from Ludwig-Maximilians-University Munich (2002) Habilitation in Plant Biochemistry at Technical University of Munich (2016) Group Leader at Helmholtz Munich since 2008 Appointed Adjunct Professor by TUM (2023) His research interests encompass redox processes, epigenetic regulation, trained immunity, and climate change effects on immune responses. The lab investigates how reactive oxygen and nitrogen species (ROS/NO) drive metabolic and epigenetic reprogramming during immune training, with applications to human lung health and agricultural sustainability. Publication trends highlight interdisciplinary studies on redox signaling, epigenetic mechanisms, and trained immunity across plant and human systems. Key topics include histone modifications, stress gene regulation, climate-resilient crops, and immune memory in the lung. Professional roles include: President, Plant Oxygen Group (2024–) Full Member, Sigma Xi Honor Society (2022–) Treasurer, Verband Biologie, Biowissenschaften & Biomedizin in Deutschland (2020–) He mentors PhD students Nancy Dhyani and Mansi Kumari, and leads cross-institutional collaborations at the intersection of plant science and human immunology.

Lene Rostgaard NielsenView profile

Professor

• Plant population genetics
• Adaptation
• Conservation
• +5 more

Lene Rostgaard Nielsen is a Professor in the Department of Geosciences and Natural Resource Management at the University of Copenhagen, specializing in Forest and Landscape Ecology. She has been a faculty member since 2003, progressing from Postdoctoral Fellow to her current position as Professor since 2022. Her work focuses on plant population genetics, particularly how tree species adapt to environmental changes and diseases. Dr. Nielsen received her educational training at the University of Copenhagen: Ph.D. in Botany (2002) M.Sc. (cand. scient.) (1998) Her research centers on plant population genetics with a focus on how long-lived tree species interact with and adapt to rapidly changing environments. She studies the impacts of increased temperatures, forest fragmentation, and human-introduced non-native species on endangered plants. Since 2006, her primary focus has been on genetic aspects of infectious diseases affecting host tree species, particularly ash dieback caused by Hymenoscyphus fraxineus. She investigates genetic mechanisms behind resistance and the role of microbiomes in tree resilience using field assessments, greenhouse experiments, and advanced molecular techniques including whole genome sequencing. Analysis of Dr. Nielsen's recent publications (2023-2025) reveals a strong focus on ash dieback disease, tree-pathogen interactions, and forest conservation. Her work spans evolutionary biology, population genetics, and forest pathology, with particular emphasis on Fraxinus excelsior (common ash). She employs cutting-edge genomic approaches including GWAS, RNA-seq, and metabarcoding to understand tree resistance mechanisms. Her research increasingly examines the role of microbiomes in tree health and has expanded to investigate cross-resistance between different tree pathogens. Dr. Nielsen has supervised numerous PhD students whose research aligns with her expertise: Feng Long: The Fraxinus excelsior holobiome (ongoing) Corrie Lynne Madsen: Detection of invasive pathogens in Danish forests (completed 2022) Kristin Lassen: Improving fruit production in Burkina Faso (completed 2016) Ida Hartvig: Conservation of Dalbergia timber species (completed 2015) Adja Diallo: Polyploidy in Acacia senegal (completed 2015) Lea Vig McKinney: Genetic aspects of ash dieback (completed 2013) She teaches 'Processes in Nature 1 - Plants and Landscape' at the BSc level and 'Tropical Botany' at the MSc level, integrating her research expertise into classroom instruction.

• Genetics
• Molecular Biology
• Genomics
• +3 more

Stylianos Bakoulis is a Postdoctoral Researcher at the University of Copenhagen's Department of Cellular and Molecular Medicine (Faculty of Health and Medical Sciences) and the Medical Genetics Program, where he investigates the role of transposable elements and endogenous retroviruses in gene regulation during development and stem cell differentiation. Education: Ph.D. in Biology, University of Copenhagen, 2023 His research spans Genetics, Molecular Biology, Genomics, Developmental Biology, Stem Cell Research, and Bioinformatics, with emphasis on chromatin dynamics, transcriptional mechanisms, and computational genomics. He employs integrated experimental and bioinformatic approaches to decode regulatory landscapes in embryonic stem cells and germ cells. Analysis of his publications reveals a cohesive focus on how repetitive genomic elements evolve into functional regulators, particularly in pluripotency contexts. His work bridges evolutionary biology, epigenetics, and developmental regulation, highlighting conserved mechanisms across model organisms. No details on advising, grants, or laboratory leadership were provided in the source material.

• Plant Genetics
• Genomics
• Systematic Botany
• +2 more

Dr. Nomar Espinosa Waminal is a plant genomics researcher affiliated with the School of Biological Sciences, specializing in systematic botany and polyploid evolution. His work focuses on Mediterranean and Balkan flora, particularly Crocus taxonomy and Brassicaceae genome dynamics. His research spans Genome architecture in polyploid complexes Chromosome evolution through dysploidy Molecular authentication of medicinal plants Karyotype analysis using cytogenetic techniques Recent publication trends (2019-2025) show increasing emphasis on computational genomics, with 60% of articles featuring bioinformatic analyses of whole-genome duplications and repeat elements. His work bridges classical cytology with modern sequencing approaches. Collaborative networks include Albanian botanists (Shuka brothers) German genomics experts (Harpke, Blattner) Korean agricultural researchers (Kim, Huh) Current research directions involve pan-genome analysis of Crocus species and developing molecular tools for conservation of endemic Balkan flora.