Single Cell Transcriptomics and Epigenomics Professors and Supervisors

Joshua Mark Brickmanمشاهده پروفایل

استاد

University of CopenhagenDenmark

Joshua Mark Brickman is a Professor in the Department of Biomedical Sciences at the University of Copenhagen's Faculty of Health and Medical Sciences. He leads the Brickman Group at reNEW (Novo Nordisk Foundation Center for Stem Cell Medicine), a global research center focused on stem cell medicine. His laboratory, the Brickman Lab, is located at Blegdamsvej 3B, 2200 København N, Denmark. Professor Brickman earned his B.A. in Chemistry & Philosophy from the University of Vermont in 1985, followed by a Ph.D. in Biochemistry and Molecular Biology from Harvard University in 1996. After completing his doctoral studies focusing on transcription, he pursued post-doctoral training in developmental biology, working with early mouse development and embryonic stem cells as models for understanding developmental processes. Brickman's research focuses on understanding how transcription factors regulate cell fate choice in embryonic stem cells and early embryos. His group investigates transcriptional priming and commitment in stem cells, particularly in the specification of the endoderm lineage. They aim to understand how these priming events relate to stem and progenitor cell potency. The Brickman Group explores three main research themes: the molecular biology of enhancer function, transcription factors and metabolic influence in stem cell competence, and transcriptional regulation in the endoderm lineage. Their work has led to significant innovations including the development of human hypoblast stem cells, drugs for improved organ differentiation, and new approaches to IVF culture. Professor Brickman's laboratory has received funding from prestigious sources including the European Research Council, Novo Nordisk Foundation, Danmarks Frie Forskningsfond, Lundbeck Foundation, and the BRIDGE - Translational Excellence Program. His research on FGF/ERK signaling has proposed a new paradigm for understanding transcription factor function as enablers of signaling response rather than determinants of transcription itself. The Brickman Group consists of a diverse team of approximately 28 researchers including postdocs, PhD students, research assistants, and visiting scientists. Current members include Assistant Professor Molly Lowndes, Researcher Rita S. Monteiro, Postdocs Joji Marie Yap Teves and S M Nazmus Salehin, Master Students Hanna Kreilgaard McNamara and Sarah Sølling Brendstrup, and several others working collaboratively on various aspects of stem cell biology and developmental regulation.

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Zachary Smithمشاهده پروفایل

استادیار

Max Planck Institute of Molecular Cell Biology and GeneticsGermany

Zachary Smith is an Assistant Professor (Adjunct) in the Department of Genetics at Yale School of Medicine, with additional affiliations at the Yale Stem Cell Center, Center for RNA Science and Medicine, and the Genomics, Genetics, and Epigenetics program. His research focuses on epigenetic regulation during mammalian development. Dr. Smith received his B.S. in Biology from M.I.T. in 2008 and his Ph.D. in Biology from Harvard University in 2019. His doctoral work focused on applying cutting-edge genomic technologies to understand chromatin dynamics during mammalian development. He joined the Yale Stem Cell Center and Department of Genetics as an Assistant Professor in September 2020. Dr. Smith's research program investigates three critical developmental processes: fertilization, implantation, and gastrulation. His lab seeks to understand how the genome is reconstructed after fertilization, how distinct epigenetic states are established in embryonic versus extraembryonic lineages, and how chromatin regulators orchestrate the complex process of gastrulation. They employ advanced genomic techniques including single-cell sequencing, Cas9-mediated genome editing, and novel molecular recording technologies. His recent publications highlight significant contributions to understanding DNA methylation dynamics in development and disease, X-chromosome biology, and the development of innovative genomic technologies. Dr. Smith's work bridges fundamental developmental biology with potential applications to understanding developmental disorders and cancer. Epigenetic regulation of mammalian development Chromatin dynamics during embryogenesis DNA methylation reprogramming Single-cell genomic analysis Novel molecular recording technologies Dr. Smith's lab collaborates extensively with researchers at Yale and other institutions, including Michael Caplan, Berna Sozen, and Biff Forbush. His interdisciplinary approach combines expertise in genetics, developmental biology, and technology development to address fundamental questions about how epigenetic mechanisms shape development. Students and postdocs in Dr. Smith's lab have opportunities to work at the forefront of developmental epigenetics, gaining expertise in both experimental and computational approaches to studying genome regulation during development.

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Lukas Steuernagelمشاهده پروفایل

پژوهشگر

Max Planck Institute for Metabolism ResearchGermany

Lukas Steuernagel leads the Neurogenomics Research Group at the Max Planck Institute for Metabolism Research in Cologne, Germany. His laboratory focuses on developing and applying computational biology methods to understand the brain's role in regulating metabolism and energy balance. His research program explores the full spectrum of neuronal cell types in the hypothalamus and hindbrain, moving beyond established models of Agrp and Pomc neurons. The group studies neurons at transcriptomic, epigenomic, metabolomic, and spatial levels to understand how genetic and environmental factors influence metabolism-regulating cell types. Dr. Steuernagel's recent publications demonstrate expertise in creating comprehensive cellular maps of the hypothalamus, with work appearing in top-tier journals including Nature and Nature Metabolism. His research addresses three main areas: mapping cell type architecture of metabolic brain regions, effects of genetics and environment on metabolism-regulating cells, and interpretation of large-scale OMICS data. He maintains active collaborations with other research groups at the institute to translate computational findings into biological mechanisms.

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Korbinian Schneebergerمشاهده پروفایل

استاد پژوهش

Max Planck Institute for Plant Breeding ResearchGermany

Prof. Dr. Korbinian Schneeberger is a Research Professor and Group Leader at the Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research in Cologne, Germany. His research focuses on genome plasticity and computational genetics, developing cutting-edge technologies to explore genome evolution. He leads a multidisciplinary team consisting of bioinformaticians, biologists, and biotechnologists driven by curiosity and passion for new genomic technologies. Dr. Schneeberger's research group pioneers genomic biotechnology for crop biology, addressing real-world problems in genomics-assisted science and breeding using Arabidopsis, potato, and fruit trees as model systems. They study genomic differences, how to find and describe them, and their relevance to phenotype. The group specializes in single-cell sequencing technologies to understand controlled (recombination) and uncontrolled (mutations) events that drive genomic diversity. His research spans four main areas: Optimizing Plant Performance by Mapping the Interface between Development and Metabolism, Plant Microbiota Metabolic Networks and Edaphic Adaptation, Synthetic and Reconstruction Biology, and Theoretical Plant Biology and Data Science. The group has developed several important bioinformatics tools including SyRI for finding genomic rearrangements, plotsr for visualization, SHOREmap for mapping-by-sequencing, and findGSE for genome size estimation. Genome Assembly: Developing new methods for genome assembly, particularly using long-read sequencing data Genomic Variation: Studying mutation accumulation and its role in evolution and adaptation Computational Genetics: Bridging genotype and phenotype using next-generation sequencing Association Studies: Creating methods that associate morphological differences to genomic differences Dr. Schneeberger's recent publications focus on somatic mutations in fruit trees, pan-genome analysis of Arabidopsis, and chromosome-scale genome assembly of potato. His work has significant implications for understanding plant evolution and improving crop breeding strategies. He mentors several PhD students and postdocs, with alumni who have gone on to successful careers in academia and industry. His laboratory maintains the Plant Metabolism and Metabolomics Facility and an Imaging Platform.

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Franziska Turckمشاهده پروفایل

استاد

Max Planck Institute for Plant Breeding ResearchGermany

Dr. Franziska Turck is a Professor and Research Group Leader in the Department of Plant Developmental Biology at the Max Planck Institute for Plant Breeding Research in Cologne, Germany. Her laboratory focuses on epigenetic mechanisms that regulate plant development, particularly how plants form transcriptional memories based on past experiences through chromatin modifications. Dr. Turck's research centers on epigenetic pathways, particularly Polycomb Group (PcG) protein complexes that establish chromatin compaction leading to gene repression. Her group investigates mechanisms that recruit and stabilize epigenetic repression and how distal enhancers can overcome epigenetic gene repression. Key projects include studying Polycomb Group Proteins in Plant Development and the Regulation of FLOWERING LOCUS T by distal enhancers and epigenetic repressors. Her work has revealed how TELOMERE REPEAT BINDING FACTORs recruit Polycomb Repressive Complex 2 to target regions and how chromatin accessibility at the FLOWERING LOCUS T locus is regulated by distal enhancers within PcG-repressed chromatin. Analysis of Dr. Turck's recent publications shows a consistent focus on plant epigenetics, chromatin structure, and flowering time regulation. Her work bridges molecular mechanisms with developmental outcomes, particularly in how plants integrate environmental cues through epigenetic memory systems. Many publications appear in high-impact journals including Nature Genetics, Nature Plants, and PNAS, with several receiving Faculty of 1000 recommendations. Faculty of 1000 Recommendation for Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana (2019) Faculty of 1000 Recommendation for Telobox motifs recruit CLF/SWN–PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis (2018) Faculty of 1000 Recommendation for H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity (2017) Dr. Turck mentors several PhD students including Juanjuan Wang (recently defended), Nicole Ivanov, Maik Mendler, Prathamesh Sannak, and Haoran Zhou. Her lab consists of postdocs, PhD students, and technical staff working on various aspects of plant epigenetics. Current projects include investigating TRB proteins' role in coordinating expression of translational machinery genes and floral organ identity genes, and exploring induced gametophytic embryogenesis through single-cell transcriptomics and epigenomics (EpiHAP project). The Turck lab maintains active collaborations and participates in multiple research initiatives focused on understanding how epigenetic mechanisms control plant development and adaptation. The group utilizes advanced genomic, molecular, and imaging techniques to investigate chromatin dynamics at both whole-genome and locus-specific levels.

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Joachim L. Schultzeمشاهده پروفایل

استاد

Helmholtz Association of German Research CentersGermany

Prof. Dr. Joachim L. Schultze is Director of Systems Medicine at the German Center for Neurodegenerative Diseases (DZNE) and leads the Genomics & Immunoregulation group at the University of Bonn's LIMES Institute. His research integrates immunology, neurobiology, genomics, and artificial intelligence, with a focus on single-cell technologies and systems medicine approaches. Key research areas include: Swarm Learning : Development of decentralized AI frameworks for medical research NEUROCOV : Investigation of neurological complications in COVID-19 PRECISE Platform : Single-cell genomics and epigenomics technology development Systems immunology approaches for chronic inflammatory diseases Myeloid cell biology and trained immunity mechanisms His recent publications (2019-2022) demonstrate strong focus on: COVID-19 immunopathology and myeloid cell dysregulation Neuroimmunology and neurodegenerative disorders AI/blockchain applications in healthcare Single-cell transcriptomics in inflammation Metabolic regulation of immune cells Prof. Schultze coordinates multiple international consortia including the DFG-funded NGS Competence Network and Immunosensation2 Cluster of Excellence. His laboratory combines experimental genomics with computational biology at the PRECISE joint platform between DZNE and University of Bonn.

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Lars Maegdefesselمشاهده پروفایل

استاد

Max Planck Institute for Dynamics and Self-OrganizationGermany

Lars Maegdefessel is a Professor of Molecular Vascular Medicine at the Technical University Munich (TUM), School of Medicine and Health. He leads the Experimental Vascular Medicine unit at Klinikum rechts der Isar and serves as a DZHK Junior Group Leader. His research focuses on the therapeutic and biomarker potential of non-coding RNAs in vascular diseases including atherosclerosis, aortic aneurysm, and related vascular pathologies. Dr. Maegdefessel's research interests center on the role of non-coding RNAs in vascular diseases, with particular focus on the vulnerability of atherosclerotic vascular lesions and the progression and rupture of abdominal aortic aneurysms. His laboratory utilizes unique human biobank materials and various pre-clinical experimental models to investigate novel molecular approaches for combating cardiovascular diseases. His work spans from basic research on microRNAs, long non-coding RNAs, and circular RNAs to translational applications in vascular medicine. Analysis of Dr. Maegdefessel's publication record reveals a strong focus on non-coding RNA mechanisms in vascular pathology, with particular emphasis on atherosclerosis stabilization, aneurysm development, and vascular inflammation. His research has evolved from basic miRNA characterization to sophisticated therapeutic applications including targeted delivery systems and novel biomarker discovery. The publications demonstrate a consistent trajectory toward clinical translation of RNA-based vascular therapeutics. ERC Consolidator Grant (2023) Russel Ross Award from American Heart Association (2023) Heisenberg Professorship of German Research Foundation (2016) Werner Risau Award of American Heart Association (2016) ERC Starting Grant (2015) Prince Daniel Research Award of Swedish Heart and Lung Foundation (2014) Ragnar Söderberg Fellowship in Medicine (2014) Dr. Maegdefessel's research program includes extensive collaboration with international teams and utilizes advanced methodologies including RNA sequencing, microarrays, proteomics, and epigenomic analyses. His laboratory investigates ncRNA function in human vascular tissues and pre-clinical models, with recent work focusing on artery-on-a-chip technology and novel therapeutic delivery systems for vascular applications.

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Aristotelis Tsirigosمشاهده پروفایل

استاد

New York UniversityUnited States

Aristotelis Tsirigos is a Professor in both the Department of Medicine and Department of Pathology at New York University Grossman School of Medicine. He serves as Director of the Applied Bioinformatics Laboratories and Co-director of the Division of Precision Medicine, where he leads a multidisciplinary research team focused on computational genomics and cancer research. Dr. Tsirigos received his academic training at: PhD in Computer Science, Courant Institute of New York University, 2006 B.S., National Technical University of Athens, Greece, 1998 His research focuses on computational genomics and epigenomics, with particular emphasis on cancer genomics, 3D chromatin architecture, and pediatric acute lymphoblastic leukemia. Dr. Tsirigos' lab designs computational methods and pipelines for high-throughput genomic data analysis, developing platforms such as GenomicTools and HiC-bench. His seminal work has contributed significantly to understanding epigenetic changes in leukemia and discovering novel non-coding RNAs as potential biomarkers and therapeutic targets, with publications in high-impact journals including Nature, Nature Medicine, and Cell. Dr. Tsirigos leads the Applied Bioinformatics Laboratories, which includes numerous research scientists, postdoctoral fellows, data scientists, and PhD students working on diverse projects spanning machine learning applications in genomics, single-cell transcriptomics, 3D chromatin architecture, and cancer epigenetics. His research has been supported by various funding agencies, enabling his team to make significant contributions to the fields of computational biology and cancer genomics.

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Andrea Gallavottiمشاهده پروفایل

استاد

Rutgers, The State University of New JerseyUnited States

Andrea Gallavotti is a Professor at the Waksman Institute of Microbiology within the School of Environmental and Biological Sciences at Rutgers University. He is also a member of the Department of Plant Biology, where his research focuses on understanding the molecular mechanisms regulating plant architecture using maize as a primary model system. Gallavotti earned his PhD from the University of Milan under the supervision of Dr. Mario Enrico and completed postdoctoral training at the University of California San Diego in Dr. Robert Schmidt's laboratory and at Cold Spring Harbor Laboratory with Dr. David Jackson. His academic journey has established him as a leading researcher in plant developmental biology. His research program investigates several key pathways in maize development, particularly focusing on how the plant hormone auxin regulates meristem formation, groups of undifferentiated stem cells that form branches and flowers. His lab also explores transcriptional repression mechanisms in maize development and how mineral nutrition affects plant development and fertility. As sessile organisms, plants must constantly adapt to environmental changes, and Gallavotti's work examines how meristem number, position, and activity contribute to plant architecture variability across species. His research combines traditional forward and reverse genetics with molecular biology and genomics approaches. Analysis of Gallavotti's recent publications reveals a strong focus on transcriptional regulation in maize development, with particular emphasis on meristem organization, inflorescence architecture, and the genetic networks controlling these processes. His work spans basic molecular mechanisms through to potential agricultural applications. Gallavotti actively leads the Gallavotti Lab, which uses maize mutants affected in branch and flower formation to isolate and characterize genes affecting branching in both tassels and ears (the male and female inflorescences of maize). His research has significant implications for understanding plant developmental plasticity and its applications in crop improvement.

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Jakub Sedzinskiمشاهده پروفایل

دانشیار

University of CopenhagenDenmark

Jakub Sedzinski is an Associate Professor and Group Leader at the Department of Biomedical Sciences, University of Copenhagen, where he leads the Sedzinski Lab as part of reNEW (Novo Nordisk Foundation Center for Stem Cell Medicine). His research focuses on understanding cellular mechanisms in development and tissue regeneration, with particular emphasis on epithelial integration, multiciliated cell development, and the mechanical interplay between cells and their microenvironment. Dr. Sedzinski's research interests span developmental biology, cell biology, and biomechanics. His work investigates how cells integrate into tissues during development and regeneration, with a special focus on multiciliated cells and their role in epithelial function. He employs advanced techniques including in vivo imaging, single-cell profiling, and mechanical analysis to uncover fundamental principles of tissue organization and cell behavior. His research has significant implications for understanding developmental disorders and regenerative processes. Analysis of Dr. Sedzinski's recent publications reveals a strong focus on the mechanical aspects of cell integration and tissue morphogenesis. His work bridges developmental biology with biophysics, examining how physical forces influence cell fate decisions and tissue organization. A recurring theme is the investigation of multiciliated cells and their integration into epithelial tissues, with implications for understanding respiratory and other epithelial disorders. His research spans from molecular mechanisms to tissue-level organization, providing comprehensive insights into developmental processes. Dr. Sedzinski leads the Sedzinski Lab at reNEW, which includes postdocs, PhD fellows, and master's students working collaboratively on various aspects of cell and developmental biology. His team employs interdisciplinary approaches combining genetics, imaging, and biomechanical analysis to address fundamental questions in tissue development and regeneration. The lab's work is highly collaborative, with connections to other research groups within reNEW and internationally.

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