جست‌وجوی استاد و پژوهشگر

Stephen Leveneمشاهده پروفایل

استاد

• DNA topology
• protein-DNA interactions
• nucleic acid structure
• +۵ مورد دیگر

Stephen Levene is a Professor of Bioengineering at The University of Texas at Dallas (UT Dallas), affiliated with the Erik Jonsson School of Engineering and Computer Science. His research focuses on the physical and functional genomics of DNA structure, protein-DNA interactions, and DNA topology in biological systems. He holds a PhD from Yale University (1985) and an AB from Columbia University (1979). Levene’s laboratory investigates genome organization, chromatin dynamics, and the role of circular DNA (eccDNA) in health and disease. His work employs advanced biophysical techniques, including hydroxyl radical probing, gel electrophoresis, and single-molecule analysis. Key areas include DNA supercoiling, topoisomerase function, and the interplay between DNA structure and cellular processes. His research has led to innovations in DNA topology simplification, Cre recombination kinetics, and methodologies for analyzing circular DNA populations in organisms like C. elegans and humans. Levene’s lab also develops tools for genomic studies, such as shallow-learning models for DNA fragmentation analysis and unmasking hidden topological activities in recombination systems. Levene’s contributions span over 40 years, with publications addressing DNA looping, knotting, and the thermodynamics of nucleoprotein assemblies. His work bridges biophysics, molecular biology, and engineering, emphasizing interdisciplinary approaches to genomic challenges.

Jonathan Doyeمشاهده پروفایل

استاد

• DNA Biophysics
• DNA Nanotechnology
• Liquid Crystals
• +۶ مورد دیگر

Jonathan Doye is a Professor of Theoretical Chemistry at the University of Oxford, affiliated with Queens College. He holds positions in the Department of Chemistry and collaborates with the Brandeis Bioinspired Soft Materials MRSEC. His research focuses on theoretical and computational studies of soft matter and biomolecular systems, including DNA biophysics, DNA nanotechnology, liquid crystals, and quasicrystals. He co-developed the oxDNA coarse-grained model for DNA simulations, widely used in nanotechnology research. Education: Bachelor’s and PhD in Theoretical Chemistry from the University of Cambridge Postdoctoral research at FOM Institute in Amsterdam (1996–1998) Research Interests: Coarse-grained modeling of DNA and RNA Patchy-particle self-assembly (including quasicrystals) Prokaryotic S-layer structural analysis Liquid crystal phase behavior of DNA origami rods Key Achievements: Discovery of one-component icosahedral quasicrystals via patchy particles Development of oxDNA model for DNA origami simulations Structural elucidation of S-layers across prokaryotes Awards: Royal Society of Chemistry Harrison Memorial Prize (2000) Labs/Teams: Jonathan Doye's Research Group focuses on computational studies of soft matter systems, with experimental collaborations in DNA nanotechnology and materials science.

Enoch Yeungمشاهده پروفایل

دانشیار

• Systems Biology
• Control Systems
• Machine Learning
• +۷ مورد دیگر

Enoch Yeung is an Associate Professor in the Department of Mechanical Engineering at the University of California, Santa Barbara (UCSB). His research focuses on systems biology, control systems, machine learning, and data mining, with a particular emphasis on understanding how mechanical forces in DNA regulate gene dynamics and cell fate. He leads projects on distributed biological computing, data-driven control architectures, and synthetic biological systems design, supported by funding from DARPA, NSF, and the U.S. Army. Yeung holds a PhD in Control and Dynamical Systems from the California Institute of Technology and a BS in Mathematics from Brigham Young University. His work integrates methods from DNA biophysics, synthetic biology, microfluidics, and control theory to study genome organization and cellular decision-making. Recent projects include the DARPA Living Foundries program, the NSF Molecular Programming Project, and the AFOSR Biological Research Initiative. He has received numerous awards, including the NSF Early CAREER Award and Young Investigator Award from the U.S. Army. His lab conducts interdisciplinary research, including a 2024 Summer Synthetic Biology Workshop for high school students. Key research themes include DNA supercoiling dynamics, biophysical feedback control in cells, and scalable Koopman operator methods for analyzing complex biological systems. Lab Focus: Biological Control Lab explores DNA mechanics, synthetic biology, and data-driven modeling. Grants & Collaborations: PI on multi-institutional programs involving PNNL, DARPA, and NSF. Advisory Roles: Served on panels for DARPA, NIST, and the National Defense University.

Sangjin Kimمشاهده پروفایل

استادیار

• Biophysics
• Microbiology
• Computational Biology
• +۵ مورد دیگر

Sangjin Kim is an Assistant Professor in the Department of Physics at the University of Illinois, focusing on biomedical and translational sciences. After earning a B.S. in chemistry from Seoul National University and a Ph.D. from Harvard University under Sunney Xie, Kim conducted postdoctoral research in microbiology at Yale University under Christine Jacobs-Wagner. Their work combines single-molecule biophysics, microbiology, and computational modeling to study cellular complexity at the single-molecule and single-cell levels. Education: B.S., Chemistry, Seoul National University Ph.D., Harvard University (2010), thesis on single-molecule biophysics Research Interests: Kim investigates physical principles governing molecular interactions in cells, particularly how gene expression machinery operates collectively. Key areas include DNA supercoiling, mRNA degradation, transcription-translation coordination, and bacterial cellular organization. Their lab develops interdisciplinary methodologies integrating molecular biology, optics, and computational analysis. Article Trends: Kim’s publications highlight single-molecule imaging, gene regulatory mechanisms, and bacterial systems biology, with a focus on Escherichia coli. Research spans DNA mechanics, RNA dynamics, and intracellular organization, often using hybrid experimental-computational approaches. Scientific Awards: NIH Maximizing Investigators' Research Award (2021) Searle Scholar, Kinship Foundation (2020) Kavli Fellow, National Academy of Sciences (2022) University of Illinois CAS Fellow (2022-2023) Teaching: Kim has taught courses in physics, including College Physics: Mechanics & Heat (PHYS 101), University Physics: Mechanics (PHYS 211), University Physics: Electricity & Magnetism (PHYS 212), Experimental Biophysics (PHYS 407), and Special Topics in Physics (PHYS 498 EBP). Labs & Teams: The Kim Lab at UIUC focuses on solving many-body problems in biology at the single-molecule level, seeking energetic and curious graduate students and postdocs with backgrounds in physics, chemistry, or biology.

• Polymer Dynamics
• Liquid-Liquid Phase Separation
• Electrochromism
• +۴ مورد دیگر

Yuecheng Zhou is an Assistant Professor at the University of Illinois, affiliated with the departments of Materials Science and Engineering, Bioengineering, the Materials Research Lab, and the Beckman Institute for Advanced Science and Technology. His research focuses on polymer dynamics, liquid-liquid phase separation, and electrochromic materials for biomedical applications. Zhou’s work bridges fundamental polymer science with practical applications in biomedicine and material design. His research interests include studying single polymer dynamics under various flow conditions, developing optical recording techniques for bioelectric potentials using electrochromic materials, and investigating the rheological behavior of complex polymer solutions. He has contributed significantly to understanding the dynamics of ring-linear polymer blends and the role of molecular architecture in non-equilibrium systems. Zhou’s recent publications highlight advancements in label-free optical detection of cellular signals, liquid-liquid phase separation in synthetic biosystems, and theoretical insights into viscoelastic hysteresis using fluctuation theorems. These studies underscore his interdisciplinary approach, combining experimental and computational methods to address challenges in materials science and biophysics. His work is supported by affiliations with leading research institutes at the University of Illinois, enabling collaborative projects across engineering, physics, and biology. Zhou’s research has implications for developing novel materials for biomedical diagnostics, energy storage, and advanced sensor technologies.

Alexandra Berroyerمشاهده پروفایل

استادیار

• DNA Structure
• DNA Repair
• Genomic Instability
• +۲ مورد دیگر

Alexandra Berroyer serves as an Assistant Professor in the Department of Biological Sciences at St. Mary's University, San Antonio, Texas. Her research program investigates the biological roles of non-canonical DNA structures, particularly G-quadruplexes (G4s), and their implications for genomic instability and cancer pathogenesis using human cell cultures and yeast models. Her academic credentials include: Ph.D. in Microbiology and Molecular Genetics from The University of Texas M.D. Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston M.S. in Biotechnology from Illinois State University B.S. in Biology from Millikin University Following her doctoral work, she completed a postdoctoral fellowship at the Harvard T.H. Chan School of Public Health. Dr. Berroyer's research centers on G-quadruplex DNA structures—four-stranded configurations formed in guanine-rich genomic regions. She examines how regulated G4 formation controls gene expression versus dysregulated G4s that cause DNA replication stress and genomic instability, ultimately driving carcinogenesis. Her laboratory employs molecular, genetic, and biochemical approaches to dissect interactions between G4 structures and DNA repair machinery, with particular focus on topoisomerases, nucleolin, and AP endonucleases. Analysis of her 2015-2022 publications reveals dominant themes in G-quadruplex biology across molecular genetics and cancer research. Key trends include structural characterization of G4-forming genomic regions, mechanistic studies of repair enzyme dysfunction at G4 sites, and exploration of metabolic influences on DNA repair. Her work bridges fundamental genome maintenance mechanisms with disease pathogenesis, featuring one interdisciplinary study in entomological behavior. Dr. Berroyer actively mentors undergraduate researchers, as evidenced by co-authorship patterns in her publications. Her laboratory operations are supported by institutional resources at St. Mary's University, with collaborative networks extending to Harvard and University of Texas researchers. Current projects investigate how DNA repair factors regulate cellular G4 homeostasis and the consequences of G4 dysregulation for genome integrity. Her research laboratory specializes in DNA structure-function analysis, utilizing yeast genetics and human cell models to probe G-quadruplex dynamics. The team employs chromatin immunoprecipitation, fluorescence microscopy, and in vitro reconstitution assays to characterize protein-G4 interactions and their impact on replication fidelity. Future work aims to translate mechanistic insights into therapeutic strategies for G4-associated cancers.

• statistical mechanics
• nonlinear dynamics
• geometric mechanics
• +۶ مورد دیگر

Tomohiro Yanao is a Professor at Waseda University's Faculty of Science and Engineering, School of Fundamental Science and Engineering. His academic career spans over 15 years at Waseda, having progressed from Assistant Professor (2009) to Associate Professor (2011) and finally to his current position as Professor. His research bridges the gap between microscopic molecular systems and macroscopic astronomical phenomena through the lens of nonlinear dynamics and geometric mechanics. His educational background includes: Ph.D. in Multidisciplinary Science from the Graduate School of Arts and Sciences, University of Tokyo (2003) Professor Yanao's research interests focus on the intersection of physics, mathematics, and molecular science. He specializes in statistical mechanics, nonlinear dynamics, and geometric mechanics, applying these to understand collective motions in complex systems. His work reveals how geometric phase effects and symmetry breaking drive structural transitions in both molecular and astronomical systems. He has made significant contributions to understanding the mechanics of molecular motors, DNA structure, and orbital dynamics in celestial mechanics. His publication record shows a consistent focus on geometric mechanics applied to diverse systems, from polymer chains and DNA to celestial bodies. The research demonstrates how internal shape changes can induce rotational motions without external torque, connecting phenomena from the "falling cat" problem to molecular motors like ATP synthase. His work also bridges molecular and astronomical scales through the common framework of nonlinear dynamics and three-body problems. Professor Yanao has been actively involved in several major research projects: Study on the mechanisms for collective motions of molecular and astronomical systems based the methods of many-body problems (2014-2017) Study on collective motions and functions of complex molecular systems based on the geometry of shape and rotational dynamics (2011-2014) Elucidation of the mechanisms for collective motions of complex molecular systems with hierarchical structures (2009-2010) He teaches a wide range of courses including Statistical Mechanics, Dynamics, Applied Mechanics, and Aerospace Engineering Laboratory. He also supervises graduate theses in the Graduate School of Fundamental Science and Engineering, focusing on nonequilibrium statistical mechanics and applied mathematics.

Simon Boultonمشاهده پروفایل

استاد

• DNA Damage Response
• DNA Repair
• Genome Integrity & Repair
• +۷ مورد دیگر

Simon Boulton is a distinguished molecular biologist and cancer researcher serving as a Senior Group Leader at the Francis Crick Institute and holding an honorary Professorship at University College London. He also serves as Senior Vice President of Science Strategy at Artios Pharma Ltd, which he helped establish in 2016, where he additionally chairs the Scientific Advisory Board and serves on the Executive Board. His educational background includes: Molecular Biology studies at the University of Edinburgh PhD at the University of Cambridge with Professor Steve Jackson (Gurdon Institute) EMBO and HFSP funded postdoctoral fellowships at Harvard Medical School with Prof. Nick Dyson (MGH Cancer Centre) and Prof. Marc Vidal (Dana Farber Cancer Institute) Boulton's research focuses on understanding DNA damage response mechanisms, particularly DNA double-strand break repair in both mitotic and meiotic cells. His laboratory employs the complementary experimental strengths of C. elegans and mouse genetics, combined with cell biology and biochemistry approaches. Over his career, his lab has discovered novel DNA repair genes and provided crucial molecular insights into human diseases, especially cancer. His work bridges fundamental biological processes with potential therapeutic applications in oncology. Analysis of his recent publications reveals a consistent focus on genome integrity mechanisms, with particular emphasis on DNA repair pathways, telomere biology, replication stress responses, and the development of novel assays to study these processes. His research increasingly intersects with cancer therapeutics, particularly through his work with Artios Pharma on DNA Damage Response (DDR) target pipelines. His significant scientific contributions have been recognized with numerous prestigious awards: Member of EMBO Fellowship of the Academy of Medical Sciences Colworth Medal European Association for Cancer Research (EACR) Young Investigator Award Eppendorf/Nature Award for Young European Investigators Royal Society Wolfson Research Merit award EMBO Gold Medal Paul Marks Prize for Cancer Research Royal Society Francis Crick Prize lecture Mendel Lecture Boulton has secured substantial research funding throughout his career, including EMBO and HFSP postdoctoral fellowships, and currently leads a well-funded research group at the Crick Institute. His dual role in academia and industry through Artios Pharma demonstrates a successful translation of basic research into therapeutic development, with the company building an innovative DNA Damage Response (DDR) target pipeline aimed at transforming cancer therapy. His laboratory at the Francis Crick Institute maintains strong collaborative networks across multiple disciplines, utilizing advanced facilities including proteomics, genomics, bioinformatics, and microscopy resources. The lab's work spans from fundamental DNA repair mechanisms to potential clinical applications, with a particular focus on how failures in DNA repair contribute to cancer and other diseases.

• R-loop Biology
• Epigenetics
• DNA Methylation
• +۴ مورد دیگر

Frédéric Chédin is a Professor in the Department of Molecular and Cellular Biology at the University of California Davis, College of Biological Sciences. He has held continuous faculty positions at UC Davis since 2004, progressing from Assistant Professor (2004-2010) to Associate Professor (2010-2015), and currently serving as full Professor (2015-present). His research focuses on R-loop biology, DNA methylation, and epigenetic regulation. Chédin's laboratory investigates how RNA:DNA hybrids form, persist, and impact genome stability, with particular emphasis on their roles in transcription, chromatin organization, and disease mechanisms. His work has established foundational methodologies for R-loop detection and mapping, including critical assessments of common techniques like the S9.6 antibody. Chédin's publication record demonstrates consistent leadership in R-loop research, with numerous high-impact papers in journals like PNAS , Nature Communications , and Molecular Cell . His recent work explores protein-mediated R-loop stabilization, R-loop classification systems, and connections between R-loops and topological stress management. Director of NIH T32 Predoctoral Training Program in MCB (2020-present) Co-Director of NIH T32 Program (2019-2020) Chair of Integrative Genetics and Genomics (2015-2019) His laboratory trains numerous graduate students and postdoctoral researchers, with frequent collaborators including Stella Hartono and Lionel Sanz appearing as first authors on key publications. Chédin maintains active service roles in graduate education and program leadership at UC Davis.

Sahand Hormozمشاهده پروفایل

استادیار

• Systems Biology
• Computational Biology
• Single-Cell Analysis
• +۹ مورد دیگر

Sahand Hormoz is an Assistant Professor at Harvard Medical School and a faculty member in the Department of Data Science at Dana-Farber Cancer Institute. His research focuses on controlling biological systems to understand cell state transitions and develop technologies for single-cell analysis, synthetic biology, and organoid modeling. PhD in Applied Physics from Harvard University (advised by Michael Brenner) Postdoctoral work at Kavli Institute for Theoretical Physics (UCSB) and Elowitz Lab at Caltech Research Interests His lab combines high-throughput single-cell measurements with differential geometry and machine learning to analyze complex biological data. They engineer cells for lineage tracing, develop organoid systems, and aim to automate biological modeling to overcome human cognitive limitations in understanding life systems. Publication Trends Key areas in his recent work include: Computational methods for single-cell and lineage analysis Cancer evolution in myeloproliferative neoplasms Synthetic biology tools for DNA-based cellular memory Integration of machine learning with biological dynamics Applications in stem cell biology and microbial systems Development of microfluidic platforms Labs & Teams Hormoz Lab at Harvard Medical School collaborates with Dana-Farber's Data Science Department to advance quantitative biology approaches.

Christoph George Baumannمشاهده پروفایل

مدرس

• Molecular Biophysics
• Biophysics
• Biochemistry
• +۳ مورد دیگر

Dr. Christoph George Baumann is a Lecturer in Molecular Biophysics at the Department of Biology , University of York. His research focuses on the interplay between DNA topology and molecular motor proteins, utilizing advanced single-molecule techniques like optical tweezers and total internal reflection fluorescence microscopy. Current role: Lecturer in Molecular Biophysics Former roles: Lecturer, Research Fellow in Biology Research Interests: Dr. Baumann investigates how motor proteins drive DNA strand separation, unwinding, and translocation, leading to supercoiling. His work bridges structural biology, biophysics, and biochemistry to understand the molecular mechanisms underlying mechanical work in cellular processes such as transcription, replication, and recombination. Recent Publications: His recent articles highlight advancements in glyco-engineering bacterial surfaces, molecular adsorption techniques, and bacterial virulence protein analysis, reflecting collaborations in biophysics and biochemical tool development. Grants and Projects: Dr. Baumann co-investigates projects funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and Medical Research Council (MRC), including the C-Trap and Refeyn Mass Photometer initiatives. Labs and Teams: He contributes to the Technology Facility at the University of York, specializing in protein and complex molecular weight analysis.

Eugene Kimمشاهده پروفایل

استاد پژوهشی

• Chromosome Structure
• DNA Organization
• Single-Molecule Microscopy
• +۱ مورد دیگر

Dr. Eugene Kim is a Research Professor and group leader at the Max Planck Institute of Biophysics, where she investigates the structural organization and dynamics of chromosomes. Her research focuses on DNA packaging mechanisms in cell nuclei using high-resolution microscopy, with implications for understanding developmental disorders and cancer. She holds a PhD from Friedrich Alexander University and was a postdoctoral fellow at the Kavli Institute of Nanoscience. Kim's work explores how proteins organize DNA throughout the cell cycle, particularly through loop extrusion by SMC complexes. Her recent publications reveal patterns in chromosome condensation mechanics and DNA topology. She has received prestigious awards including an ERC Starting Grant (2022) and Marie Skłodovska-Curie Fellowship. Kim leads the 'Structure and Dynamics of Chromosomes' group and secured €1.5 million in ERC funding to support her research on genomic architecture.

Andre Sanches Ribeiroمشاهده پروفایل

استاد

• Computational Systems Biology
• Gene Expression Dynamics
• Gene Regulatory Networks
• +۱۲ مورد دیگر

Andre Sanches Ribeiro is a tenured Professor in the Faculty of Medicine and Health Technology at Tampere University, Finland, where he also leads the Laboratory of Biosystem Dynamics (LBD). His research lies at the intersection of computational modeling, single-cell biology, and synthetic biology, with a focus on understanding bacterial gene regulatory networks under stress conditions. He is affiliated with the Biosciences department and conducts interdisciplinary research combining experimental and computational approaches. His primary research interests include Gene Expression Dynamics , Gene Regulatory Networks , Single-Cell Biology , Systems Microbiology , and Synthetic Biology . He applies methods from stochastic modeling, network theory, and signal processing to decode transcriptional programs and regulatory mechanisms in bacteria. His lab uses live single-cell microscopy, RNA-seq, flow cytometry, and synthetic gene engineering to study how gene circuits function in vivo, particularly under antibiotic stress. The recent publications demonstrate a strong trend in understanding transcriptional regulation at multiple scales—from single promoters to entire regulatory networks. His work integrates empirical data with dynamic models, focusing on phenomena such as transcription attenuation, bimodal expression, and genome-wide stress responses. The lab has developed valuable genetic tools, including a widely accessible library of fluorescent reporters for global regulators in E. coli, distributed through AddGene. Andre S. Ribeiro has mentored several PhD students to completion, including Ines Baptista and Suchintak Dash, and continues to train the next generation of systems biologists. His lab actively collaborates with researchers internationally, as seen in joint publications with experts like Barry Sanders. Though no specific grants are listed, the sustained output and infrastructure suggest active funding support. The Laboratory of Biosystem Dynamics, founded in 2009, has evolved from a purely computational group into a multidisciplinary team with wet-lab capabilities. The lab maintains a strong online presence through its website , Twitter , YouTube , and repositories like AddGene , promoting open science and collaboration.

Allyn Schoefflerمشاهده پروفایل

استادیار

• Biophysical Chemistry
• Structural Biology
• Biochemistry
• +۴ مورد دیگر

Dr. Allyn Schoeffler is an Assistant Professor in the Department of Chemistry at Loyola University New Orleans. Prior to her current position, she was an assistant professor at Spring Hill College and spent five years in early discovery research at Genentech. She holds a Ph.D. from U.C. Berkeley. Education: Ph.D. from University of California, Berkeley Dr. Schoeffler's research focuses on understanding the structural and biophysical determinants of protein function, particularly enzyme specialization. She employs a multidisciplinary approach combining structural biology, biochemistry, bioinformatics, and biophysics to study clinically and biophysically relevant enzyme classes. Her work has been published in high-impact journals including Science, Nature, and PNAS, reflecting her contributions to the fields of biophysical chemistry and structural biology. Her recent publications demonstrate a consistent theme in protein structure-function relationships, with particular emphasis on enzyme mechanisms and conformational dynamics. The research spans areas from protein ubiquitination and apoptosis regulation to DNA topology and chromosome dynamics, highlighting the breadth of her expertise in biophysical chemistry. Scientific Awards: No scientific awards were mentioned in the provided text. Dr. Schoeffler is actively involved in mentoring students in her laboratory and through classroom instruction. She maintains collaborative research efforts with colleagues at Louisiana State University and the University of Alabama, Tuscaloosa, fostering interdisciplinary research networks. While specific grant funding is not detailed, her ongoing research program and publications indicate active research support. She operates a research laboratory at Loyola University New Orleans and collaborates extensively with researchers at Louisiana State University and the University of Alabama, creating a dynamic research environment that bridges multiple institutions.

Sabrina Leslieمشاهده پروفایل

دانشیار

• Single-Molecule Biophysics
• Biomedical Imaging
• Nanotechnology
• +۳ مورد دیگر

Sabrina Leslie is an Associate Professor at the University of British Columbia (UBC) in the Michael Smith Laboratories and Department of Physics. Her research focuses on developing single-molecule microscopy tools to study biomolecular interactions in biologically relevant environments. She leads the Leslie Lab, which bridges physics, engineering, and biology to advance genetic medicines and vaccines. Education BSc (Honours Physics and Mathematics), University of British Columbia (2002) PhD in Optical and Atomic Physics, UC Berkeley (2008) Postdoctoral Fellowship, Harvard University (2009–2011) Research Interests Dr. Leslie pioneers the Convex Lens-induced Confinement (CLiC) imaging platform to visualize single molecules (DNA, RNA, proteins) and lipid nanoparticles in realistic cellular conditions. Her lab investigates nucleic acid dynamics, nanoparticle formulation for drug delivery, and single-cell analysis. Applications include improving mRNA vaccines and oligonucleotide therapeutics. Key Awards Member of Royal Society of Canada’s College of New Scholars (2020) NSERC Accelerator Award (2017–2020) Young Investigator Award, Canadian Biophysical Society (2019) Advising & Collaborations Her lab has trained over 50 students and postdocs. Collaborators include industry partners in biotechnology and nanotechnology. She co-founded ScopeSys to commercialize CLiC technology. Labs & Teams Based at UBC’s Michael Smith Laboratories, the Leslie Lab integrates interdisciplinary expertise. Ongoing projects include lipid nanoparticle characterization, single-molecule RNA studies, and CLiC-based diagnostics.