جست‌وجوی استاد و پژوهشگر

• Bioinformatics
• Machine Learning
• Deep Learning
• +۵ مورد دیگر

Ole Winther is Professor in High dimensional biological data analysis/Machine learning at the Department of Biology, University of Copenhagen and Professor in Data science and complexity at DTU Compute, Technical University of Denmark. He serves as CRO and co-founder of raffle.ai, CTO and co-founder of FindZebra, Head of ELLIS Unit Copenhagen, and co-PI of the Machine Learning for Life Science Center. His research spans Bioinformatics , Machine Learning , and AI for Science , focusing on applying deep learning to biological sequence analysis, latent variable models, and medical NLP. Winther's work develops predictive and generative models for bioinformatics, with significant contributions to protein localization tools (SignalP, DeepLoc, DeepTMHMM), single-cell genomics, and novel deep learning architectures like variational autoencoders and diffusion models. Analysis of Winther's recent publications (2023-2025) reveals a strong trend toward integrating protein language models with traditional bioinformatics approaches and applying diffusion models to scientific problems. His work bridges theoretical machine learning advancements with practical applications in biology and medicine, particularly in protein sequence analysis, medical search engines, and scientific simulation acceleration. Winther currently supervises a diverse research group including Panagiotis Antoniadis, Rachael M. DeVries, Jun Wang, Beatrix M. G. Nielsen, Felix G. Teufel, Irene R. Rodriguez, Anders Christensen, and Christopher Heje Grønbech. His former students have established successful careers at institutions including Google, Apple, and various startups, with notable alumni like Casper Sønderby (Google Brain) and Søren Sønderby (Apple). He leads significant research initiatives including the ELLIS Unit Copenhagen and the Machine Learning for Life Science Center, while maintaining active industry partnerships through his co-founded companies raffle.ai (enterprise search using NLP) and FindZebra (search engine for rare diseases). His teaching includes Deep Learning courses at both DTU (02456) and University of Copenhagen (NDAK24002U).

• Evolutionary Biology
• Marine Biology
• Taxonomy
• +۵ مورد دیگر

Mikael Thollesson is a Senior Lecturer at Uppsala University, affiliated with the Department of Organismal Biology; Systematic Biology and Klubban’s Biological Station. His research focuses on evolutionary biology, phylogenetics, taxonomy, and molecular biology, particularly in marine and freshwater sponges (Porifera), bacterial pathogens, and computational methods in evolutionary analysis. Evolutionary Biology Marine Biology Taxonomy His recent publications highlight trends in sponge biodiversity, phylogeography, bacterial horizontal gene transfer, and mitochondrial gene evolution. Key articles include studies on Swedish demosponge faunas, Silene sect. Arenosae systematics, and computational tools like SPRIT for detecting gene transfers. No explicit awards or grants are mentioned.

Mihai Popمشاهده پروفایل

استاد

• Bioinformatics
• Genomics
• Computational Biology
• +۳ مورد دیگر

Dr. Mihai Pop is a Professor of Computer Science and Director of the University of Maryland Institute for Advanced Computer Studies (UMIACS). He holds appointments in the Department of Computer Science, UMIACS, and the Center for Bioinformatics and Computational Biology (CBCB). His research focuses on computational biology, metagenomics, and algorithm development for genomic data analysis. He received a Ph.D. in Computer Science from Johns Hopkins University (2000), followed by work at The Institute for Genomic Research (TIGR) developing genome assembly algorithms. Education: Ph.D., Computer Science, Johns Hopkins University, 2000. Research Interests: Bioinformatics, genomics, metagenomics, computational geometry, software testing. His lab develops tools for analyzing microbial communities and has pioneered methods for metagenomic assembly and analysis. Notable tools include the AMOS genome assembly toolkit. Recent Article Trends: Recent work emphasizes long-read sequencing, metagenomic profiling (e.g., TIPP3), and strain-level analysis (e.g., Strainy). He addresses challenges in scaling sequence-based searches and improving taxonomic resolution in large datasets. Awards: ACM Fellow (2019), ISCB Fellow (2022), UMD Excellence in Teaching Award (2015). Grants & Leadership: Co-leader of the Human Microbiome Project data analysis group. Active in diversity initiatives to promote inclusivity in computational fields. Labs/Teams: Pop Lab (pop-lab.org) focuses on computational methods for microbial genomics and metagenomics.

Lucas Paoliمشاهده پروفایل

پژوهشگر

• Microbiome Research
• Microbial Immunity
• Ecological Genomics
• +۴ مورد دیگر

Lucas Paoli is a Researcher and Course Instructor at École Polytechnique Fédérale de Lausanne (EPFL), Switzerland. He leads the Paoli Lab (Microbiome Immunity and Ecology) within the Global Health Institute (GHI) under the School of Life Sciences (SV). His roles include scientific collaboration and teaching responsibilities in life sciences engineering. Paoli holds a PhD in Microbiome Research from ETH Zürich (2018-2023), an M.Phil. in Environmental Policy from the University of Cambridge (2017-2018), and an M.Sc. in Ecology and Evolution from École normale supérieure (2015-2017). Research Focus: His work bridges microbial immunity and ecology, investigating how microbes defend against viral infections across ecosystems like oceans and human microbiomes. Techniques include global-scale metagenomics and functional genomics to study immune strategies and ecological interactions. Key themes involve microbial community dynamics, viral defense mechanisms, and the impact of environmental factors on microbial immunity. Lab & Education: The Paoli Lab explores microbiome-immunity interactions with a focus on ecological contexts. Paoli supervises PhD students in Life Sciences Engineering. His research outputs span microbial ecology, metagenomic tool development, and marine microbiome studies. Contact: lucas.paoli@epfl.ch, AAB 1 39, +41 21 693 16 99.

Anja Meryandiniمشاهده پروفایل

استاد

• Microbiology
• Enzyme Technology
• Probiotics
• +۴ مورد دیگر

Prof. Dr. Anja Meryandini is a Professor in the Department of Biology at IPB University (Bogor Agricultural University), Indonesia. She leads research in microbial biotechnology with a focus on enzyme technology, probiotics, prebiotics, and fermentation processes for food and agricultural applications. Her educational journey includes a Bachelor's degree in Biology from Padjadjaran University, a Master's degree in Biology from IPB University, and a PhD in Microbiology from Albert Ludwig Universitaet, Germany. This strong academic foundation has supported her extensive research career spanning over three decades. Professor Meryandini's research interests encompass: Microbial enzyme technology (protease, mannanase, xylanase) for animal feed processing Development of probiotics and prebiotics for food and animal applications Flour production using microbial technology Fermentation processes for various agricultural products Soil microbiome analysis in relation to land use changes Biodegradation of environmental pollutants Her recent publications reveal a consistent focus on lactic acid bacteria, yeast fermentation, enzyme characterization, and biodegradation processes, often utilizing Indonesian indigenous microorganisms. She has made significant contributions to understanding cocoa fermentation microbiology, tempeh processing, and agricultural waste valorization. Professor Meryandini has been actively involved in important research projects including 'Impact of rainforest transformation on phylogenetic and functional diversity of soil prokaryotic communities in Sumatra (Indonesia)' which is part of a larger CRC 990 program. Her work demonstrates strong interdisciplinary connections between microbiology, environmental science, and food technology. With over 100 publications documented from 1994 to 2024, Professor Meryandini maintains an active research program with significant contributions to microbial biotechnology in the Indonesian context and beyond.

Eduardo Rochaمشاهده پروفایل

استاد

• Microbial Evolutionary Genomics
• Genome Organization
• Mobile Genetic Elements
• +۱۳ مورد دیگر

Eduardo Rocha is a Professor and Head of the Microbial Evolutionary Genomics laboratory at the Institut Pasteur, within the Department of Genomes and Genetics. His research integrates bioinformatics, molecular evolution, and genomics to understand bacterial genome organization and dynamics, particularly focusing on mobile genetic elements and their role in adaptation and antibiotic resistance. His research interests include microbial evolutionary genomics, genome organization, horizontal gene transfer, mobile genetic elements (plasmids, phages, integrons), bacterial pathogen evolution, and computational biology. His work lies at the intersection of molecular evolution, population genetics, and molecular epidemiology, with strong translational implications for understanding antimicrobial resistance and infectious disease emergence. The recent publications highlight a consistent focus on mobile genetic elements, genome plasticity, and bacterial adaptation. Key themes include the role of integrons and CRISPR-Cas systems in bacterial immunity, plasmid-mediated spread of antibiotic resistance, phage-plasmid interactions, and the development of bioinformatics tools for microbial genomics. These works frequently appear in high-impact journals such as Science , Nature Microbiology , and PLoS Biology , reflecting significant contributions to the field. Eduardo Rocha leads multiple funded research projects, including ERC-2011-StG EVOMOBILOME, ANR Magisbac, and ANR SHAPE. He has developed and maintains several widely used bioinformatics software tools: IntegronFinder, MacSyFinder, PanACoTA, SatelliteFinder, CapsuleFinder, TXSScan, and others. He mentors a large team of PhD students, postdoctoral researchers, and engineers, and has supervised numerous former students who now hold independent research positions worldwide. Eduardo Rocha has received research funding from major agencies including the European Research Council (ERC) and the French National Research Agency (ANR). His work is central to the LabEx IBEID and the INCEPTION convergence program, where he serves on the steering committee, promoting interdisciplinary research in infectious disease emergence. His laboratory, part of the Genomes and Genetics department, actively contributes to microbial evolutionary genomics through both methodological development and biological discovery. The team participates in networks such as Phages.fr, GDR BIM, and GDR AIEM, reinforcing its collaborative and integrative approach.

Jacques Archambaultمشاهده پروفایل

استاد

• Human Papillomavirus (HPV)
• Polyomavirus
• Viral DNA Replication
• +۴ مورد دیگر

Dr. Jacques Archambault is a Professor in the Department of Microbiology and Immunology at McGill University , and an associate member of the Division of Experimental Medicine since 2016. His research focuses on the molecular biology and pathogenesis of human papillomaviruses (HPVs) and polyomaviruses (HPyVs), with an emphasis on their replication mechanisms as episomes in host cells. The Archambault laboratory employs functional genomics, proteomics, and chemical biology approaches to identify cellular pathways exploited by these viruses and develop high-throughput assays for screening small molecule inhibitors of viral replication. Analysis of his recent publications reveals a strong focus on HPV and HPyV replication machinery, including studies on the E1 helicase, UAF1-USP1 interactions, and structural characterization of viral proteins involved in DNA replication. His work bridges virology, oncology, and drug discovery, particularly targeting oncogenic HPV types implicated in anogenital and oropharyngeal cancers, as well as HPyVs like BKPyV and JCPyV that cause pathologies in immunosuppressed patients. Current efforts in the lab aim to elucidate the molecular mechanisms by which HPVs and HPyVs replicate their genomes and to develop antiviral therapies targeting these processes. Techniques such as fluorescence anisotropy, NMR spectroscopy, and crystallography are frequently employed to study protein-DNA and protein-protein interactions critical to viral replication.

Bingzhang Chenمشاهده پروفایل

مدرس ارشد

• Biological oceanography
• Theoretical Ecology
• Ecosystem modeling
• +۹ مورد دیگر

Bingzhang Chen is a Senior Lecturer in the Department of Mathematics and Statistics at the University of Strathclyde, Faculty of Science. He previously held positions as a Chancellor’s Fellow at the same institution, a researcher at the Japan Agency of Marine-Earth Science and Technology (JAMSTEC), and was affiliated with Xiamen University and Mount Allison University. His academic journey began with a PhD from the Hong Kong University of Science and Technology. Education: PhD in Trophic interactions within the microbial food web, Hong Kong University of Science and Technology (Awarded 2009) His primary research interests lie at the intersection of biological oceanography and theoretical ecology, with a strong focus on ecosystem modeling. He investigates how biodiversity, particularly of phytoplankton, influences marine ecosystem functioning such as primary production and the biological carbon pump. A central theme in his work is understanding the differential temperature sensitivity between autotrophs and heterotrophs, a question that bridges statistical analysis, metabolic theory, and Earth system science. His recent publications highlight a consistent trend in developing and applying individual-based models (e.g., PIBM 1.0), analyzing large datasets on plankton thermal responses, and studying the impacts of climate change and anthropogenic activities (like nutrient input) on marine microbial communities across diverse regions from the South China Sea to the North Pacific and Scottish coastal waters. His work often combines modeling with observational data to address fundamental ecological questions. Scientific Awards: David Cushing Prize (2015) from the Journal of Plankton Research New Century Excellent Talent (2012) from the Ministry of Education of China Dr. Chen is actively involved in research supervision, currently guiding five PhD students. He has been the Principal Investigator on multiple research projects funded by organizations such as the Leverhulme Trust, FILAMO, and the National Science Foundation. His expertise in programming (R, Fortran, MATLAB) underpins his methodological approach. He also contributes to the scientific community as an Associate Editor for the prestigious journal Limnology and Oceanography . His work is associated with efforts to understand and model invasive species dynamics, such as the spread of Sargassum muticum in Scottish waters, and he is involved with external advisory groups like the MASTS Marine Artificial Intelligence Forum.

Katherine J. Franzمشاهده پروفایل

استاد

• Bioinorganic Chemistry
• Metal Homeostasis
• Antimicrobial Agents
• +۴ مورد دیگر

Katherine J. Franz is a Professor of Chemistry at Duke University, affiliated with the Trinity College of Arts & Sciences and the Duke Cancer Institute. She holds a Ph.D. from MIT (2000) and a B.A. from Wellesley College (1995). Her research focuses on bioinorganic chemistry, particularly metal ion coordination in biological systems, with applications in antimicrobial therapies, cancer metallomics, and neurodegenerative diseases. Key projects include developing prochelators targeting fungal and bacterial pathogens, studying copper's role in antifungal drug efficacy, and designing light-activated metal complexes for controlled drug release. Dr. Franz has received numerous awards including the Camille Dreyfus Teacher-Scholar Award (2009), Sloan Research Fellowship (2008), and the NSF CAREER Award (2005). She leads a lab with 6 current students/mentees and has secured grants from NIH, NSF, and the US-Israel Binational Science Foundation. Her lab's work spans from fundamental metalloprotein studies to translational drug development, emphasizing interdisciplinary approaches in chemistry and biology. Education: Ph.D. in Chemistry, MIT, 2000 B.A. in Chemistry, Wellesley College, 1995 Research Interests: Metal homeostasis in pathogens, copper's role in antifungal resistance, prodrug design for targeted therapy, and mechanistic studies of metalloproteins. Grants: Tri-Institutional Molecular Mycology Training Program (NIH, 2024–2029) Duke PREP Biomedical Sciences Program (NIGMS, 2022–2027) Copper-Mucin Interaction Study (BSF, 2022–2026) Her lab's publications (n=15+ since 2020) highlight breakthroughs in prodrug selectivity, copper-induced protein toxicity, and histatin antifungal mechanisms. The Franz Lab actively collaborates with clinicians and computational scientists to advance therapeutic strategies addressing unmet medical needs in infectious diseases and cancer.

Victoria J. Orphanمشاهده پروفایل

استاد

• Microbial Ecology
• Biogeochemistry
• Marine Microbiology
• +۲ مورد دیگر

Victoria J. Orphan is the James Irvine Professor of Environmental Science and Geobiology at Caltech, where she directs the Center for Environmental Microbial Interactions. Her research investigates microbial processes in anaerobic ecosystems including deep-sea methane seeps, hydrothermal vents, and coastal sediments using interdisciplinary approaches combining molecular biology, stable isotope techniques, and geochemistry. Her laboratory focuses on: Microbial partnerships in methane cycling Ecophysiology of uncultured archaea and bacteria Viral ecology in marine environments Biogeochemical impacts of microbial communities Blue carbon sequestration in seagrass ecosystems Professor Orphan has developed innovative methods including BONCAT-FISH and nanoSIMS for studying microbial activity in environmental samples. Her research group maintains active field programs in Monterey Canyon and hydrothermal vent systems, and develops high-pressure incubation systems for studying deep-sea microbes. She teaches courses on microbial ecology and evolution, and mentors graduate students through the Geobiology and Environmental Science programs.

Sarah Lummisمشاهده پروفایل

استاد

• Neuroscience
• Biochemistry
• Structural Biology
• +۳ مورد دیگر

Sarah Lummis is a Professor in the Department of Biochemistry at the University of Cambridge. Her research focuses on understanding the structure-function relationships of Cys-loop ligand-gated ion channels (pLGICs), which are critical for neurotransmission and targets for pharmaceuticals. Her work addresses how structural features of these receptors influence their function and drug interactions. Research interests include ion channel biology, molecular pharmacology, and structural biology. Key publications investigate residues affecting receptor activity in 5-HT3 receptors, glycine receptors, and the prokaryotic channel ELIC. Her studies contribute to drug development for neurological disorders like epilepsy and Alzheimer's disease. Contact: sl120sec@bioc.cam.ac.uk | Group accepts interns, students, and researchers. Located at the Hopkins Building, Downing Site, Cambridge.

• Molecular Genetics
• Microbiology
• Biotechnology
• +۷ مورد دیگر

Joseph Meier is an Adjunct Associate Professor in the School of Humanities and Sciences at ArtCenter College of Design, where he teaches courses such as Light & Color and Pattern Formation in Nature . With a multidisciplinary background in chemistry, mathematics, and molecular genetics, he bridges science and art through his teaching and research. His educational journey includes undergraduate degrees in Chemistry and Mathematics from Kalamazoo College, initial graduate work in cosmochemistry at UC San Diego, and a PhD in Molecular Genetics from Caltech, based on groundbreaking research on Borrelia hermsii and prokaryotic gene regulation conducted at the Rocky Mountain National Laboratory. PhD in Molecular Genetics, Caltech, 1993 Graduate Studies in Cosmochemistry, UC San Diego Bachelor's Degrees in Chemistry and Mathematics, Kalamazoo College Dr. Meier’s research interests center on molecular biology, gene regulation mechanisms, biotechnology innovation, and the scientific underpinnings of natural patterns and visual perception. His interdisciplinary curiosity extends to the Arts and Crafts movement and California plein air painting, reflecting a deep integration of scientific and artistic inquiry. His work has led to a U.S. patent for a DNA sequencing system, and he is currently involved in designing new biotechnology equipment. Though no publications are listed in the provided text, his research trajectory spans microbiology, genetics, and applied biotech, with implications across medical and technological domains. Notable recognition includes the Elder Scholarship, which supported his early marine biology research on gorgonians in the Cayman Islands. Dr. Meier has held research positions at Oak Ridge National Laboratory, the Lunar and Planetary Institute, and NASA’s Johnson Space Center, demonstrating a unique career path that integrates space science, microbiology, and technology development. He previously served as CTO at a visual effects company and returned to ArtCenter in 2018 to contribute to science education in an art and design context. He has no listed advisees in the provided text, and there is no mention of external grants. His current work emphasizes biotech design and interdisciplinary science education.

Jason Micklefieldمشاهده پروفایل

استاد

• Biosynthesis
• Biocatalysis
• Antimicrobial Resistance (AMR)
• +۳ مورد دیگر

Jason Micklefield is a Professor of Chemical Biology at the University of Manchester's School of Chemistry and Manchester Institute of Biotechnology. His research focuses on sustainable bio-inspired molecular synthesis, integrating organic chemistry, enzymology, and molecular microbiology. He holds an honorary Visiting Professorship at East China University of Science and Technology. Micklefield earned his PhD in Chemistry from the University of Cambridge in 1993 and completed postdoctoral work at the University of Washington before joining Manchester in 1998. His lab specializes in biosynthesis pathway engineering, biocatalysis, and nucleic acid chemistry. Education: PhD in Chemistry (1993), University of Cambridge NATO Postdoctoral Fellowship, University of Washington, USA (1993–1995) Lecturer in Organic Chemistry, Birkbeck College, University of London (1995–1998) Research Themes: Biosynthesis of novel antibiotics to combat AMR, including pathway engineering for agrochemicals and drug discovery. Biocatalysis and integrated catalysis for sustainable synthesis of pharmaceuticals, focusing on amide ligases and halogenases. Nucleic acid therapeutics and riboswitch engineering for synthetic genetic control. Key Achievements: Discovered CfaL ligases enabling amide synthesis without protecting groups. Engineered vitamin K-dependent carboxylases for novel antibiotic pathways. Developed orthogonal riboswitches for synthetic biology applications. Awards: RSC Bader Award (2019) NPR Lecture Award Lab & Collaborations: The interdisciplinary Micklefield Lab includes chemists, biochemists, and bioinformaticians. Projects include MESNA (modified nucleic acid synthesis) and collaborations on sustainable chemical manufacturing.

Maria Fällmanمشاهده پروفایل

استاد

• Molecular microbiology
• Bacterial pathogenesis
• Infection biology
• +۷ مورد دیگر

Maria Fällman is a Professor at the Department of Molecular Biology at Umeå University, where she also serves as Deputy Head of Department. She is affiliated with Molecular Infection Medicine Sweden (MIMS), a leading research center for molecular infection medicine in Sweden. Dr. Fällman's research focuses on understanding the molecular mechanisms behind bacterial adaptation to different environments, with particular emphasis on Yersinia pseudotuberculosis and Salmonella enterica Typhimurium. Her group investigates gene regulation critical for establishing and maintaining infections, bacterial stress responses, and the molecular mechanisms of the Type Three Secretion System (T3SS). The lab has developed advanced methods for RNA extraction from complex tissue samples and performs in vivo gene expression analyses. Her publication record shows consistent contributions to understanding bacterial pathogenesis, with recent articles in high-impact journals including Nature Communications, Science, and PLOS Pathogens. Her work spans from fundamental molecular mechanisms of bacterial virulence to computational approaches for analyzing pathogen stress responses. A significant contribution is the PATHOgenex database (http://www.pathogenex.org), containing gene expression data of over 30 human pathogens exposed to different stress conditions. Dr. Fällman leads the Maria Fällman Lab, which has made important discoveries including the finding that sub-lethal doses of Yersinia result in persistent infection in mice with reprogramming of bacterial gene expression. Current projects focus on stress response modeling and deciphering heterogeneous populations of infecting bacteria using single-cell RNA-seq.

• Microbiology
• Marine Biology
• Environmental Science
• +۳ مورد دیگر

Detmer Sipkema is an Associate Professor at Wageningen University & Research, affiliated with the VLAG WIMEK faculty and the Department of Molecular Ecology. His research focuses on microbial ecology, marine biology, and biotechnology, particularly in aquaculture systems and sponge symbionts. He leads projects on metabolic modeling of marine bacteria, ecological impacts of seaweed farming, and probiotics development for aquaculture. Key research interests include microbial diversity, anaerobic digestion in aquaculture waste, and applications of artificial intelligence in microbial studies. He has supervised multiple PhD candidates exploring topics like microbial symbiosis, gut microbiota dynamics, and sustainable aquaculture practices. His work integrates multi-omics approaches, environmental microbiology, and bioprospecting for novel bioactive compounds. Sipkema has published widely on sponge microbiomes, anaerobic processes, and aquaculture sustainability. His datasets include bacterial community analyses from sponges and microalgae, contributing to understanding symbiotic relationships and biotechnological applications.