جست‌وجوی استاد و پژوهشگر

Romain Lopezمشاهده پروفایل

استادیار

• Single-cell omics
• Spatial transcriptomics
• Deep generative models
• +۵ مورد دیگر

Romain Lopez is an Assistant Professor of Computer Science and Biology at New York University, with a joint appointment in the Courant Institute of Mathematical Sciences and the Department of Biology. He will be joining NYU in September 2025, bringing expertise at the intersection of machine learning and computational biology. Prior to joining NYU, he was a Postdoctoral Fellow at Genentech and Stanford Medicine from 2021 to 2025, working with Jonathan Pritchard and Aviv Regev. Dr. Lopez received his educational training at prestigious institutions: PhD in Computer Science (2021) from the University of California, Berkeley, advised by Mike Jordan and Nir Yosef M.S. in Applied Mathematics (2016) from École polytechnique, Palaiseau, France Dr. Lopez's research focuses on developing machine learning methods to understand biological systems at the cellular level. His work bridges computational techniques with biological applications, particularly in single-cell and spatial omics analysis. He pioneered probabilistic approaches for single-cell analysis with scVI and co-developed scvi-tools, now widely adopted tools in the field. His research spans deep generative models, causal inference, perturbation modeling, and representation learning for biological data. His publication record demonstrates a consistent trajectory of innovation in computational biology, with recent work focusing on spatial biology, disentangled representations of cellular perturbations, and causal modeling of cellular responses. He has made significant contributions to the field of single-cell analysis, developing methods that help scientists interpret complex cellular data and predict how cells respond to various perturbations. Dr. Lopez has received numerous honors and awards for his research: Best Paper Award from the ICML Workshop on AI for Science (2024) Best Paper Award Honorable Mention from the AAAI Conference on Artificial Intelligence (2021) Best Student Poster Award from the ICML Workshop on Computational Biology (2019) UC Berkeley EECS Departmental Graduate Fellowship (2016) Carnot Foundation Fellowship (2016) Monahan Foundation Fellowship (2016) French National Defence Medal, Bronze Echelon (2014) At NYU, Dr. Lopez will lead the Biological Machine Learning group, which develops probabilistic machine learning methods to uncover biological mechanisms governing cellular behavior and disease. His lab focuses on creating tools that transform complex cellular data into biological insights, with applications in understanding cancer, immune responses, and fundamental cellular processes. His work has significant implications for precision medicine and drug discovery.

John Oakeyمشاهده پروفایل

استاد

• Microfluidics
• Microscale transport phenomena
• Tissue engineering and regenerative medicine
• +۴ مورد دیگر

John Oakey is a Professor and Graduate Coordinator in the Department of Chemical and Biomedical Engineering at the University of Wyoming, with additional affiliations to the INBRE Program, Molecular and Cellular Life Sciences Program, and Materials Science and Engineering Program. Education Postdoctoral Fellow, Center for Engineering in Medicine, Massachusetts General Hospital & Harvard Medical School (2007–2010) Ph.D. Chemical Engineering, Colorado School of Mines (2003) M.S. Chemical Engineering, Colorado School of Mines (1999) B.S. Chemical Engineering, Penn State University (1997) Research Interests Oakey’s laboratory integrates fluid dynamics, colloidal science and materials science to understand how biological systems behave under flow, on surfaces and within complex 3-D geometries. A unifying theme is the use of microfabrication and microfluidics to create new diagnostic, prognostic and therapeutic platforms. Current thrusts include: Heterogeneous biomaterials: self-assembled particulate tissue scaffolds whose mechanical and transport properties can be temporally programmed. Inertial microfluidics: exploiting lift forces for membrane-free particle sorting, enrichment and diagnostics. Multi-temporal analysis by flow cytometry: development of closed-loop, high-throughput microfluidic cytometers for longitudinal single-cell studies. Publication Trends From 2025 back to 2010, Oakey’s articles reveal a consistent trajectory that marries fundamental physics (microtubule mechanics, inertial focusing) with translational applications (cell encapsulation, tissue scaffolds, drug delivery). Recent work (2023-2025) increasingly targets injectable granular hydrogels, single-cell therapeutic delivery and sustainable carbon-sequestering living materials, demonstrating an evolution from microscale transport phenomena to macroscopic biomedical and environmental impact. Scientific Awards No named awards are listed in the supplied text. Advising & Coordination Roles As Graduate Coordinator for the Department of Chemical and Biomedical Engineering, Professor Oakey oversees graduate program development and student mentoring. While no individual students are named, his role implies active supervision of M.S. and Ph.D. advisees in chemical and biomedical engineering. Laboratory & Teams The Oakey Research Group operates from the Energy and Environmental Research Building (EERB 435A) at the University of Wyoming. The lab enjoys R1-level research infrastructure and collaborates broadly with the Wyoming INBRE network, the Molecular and Cellular Life Sciences Program, and the Materials Science and Engineering Program.

Andre Levchenkoمشاهده پروفایل

استاد

• Systems Biology
• Signal Transduction
• Cell Communication
• +۵ مورد دیگر

Andre Levchenko is the John C. Malone Professor of Biomedical Engineering at Yale University, with secondary appointments in the Department of Neurosurgery and affiliations with the Cancer Signaling Networks, Immunology, and the Yale Program in Neurodevelopment and Regeneration. His research focuses on systems biology, signal transduction, and cell-cell communication, utilizing microfluidics and computational modeling to study cancer progression, stem cell behavior, and neurological disorders. PhD, Columbia University MEng, Moscow Institute of Physics and Technology Levchenko's work explores how cells process dynamic signals to make critical decisions, particularly in glioblastoma migration, organoid development, and cardiovascular tissue engineering. His lab develops innovative microfluidic platforms and mathematical models to dissect multicellular communication and signaling networks. Recent publications highlight his contributions to understanding YAP-driven cancer invasion , NOTCH signaling in angiogenesis , and metabolic regulation of hypoxia responses . He has pioneered methods for organoid modeling and single-cell analysis , advancing precision in biological signaling studies. Scientific Awards : Computational Molecular Biology Post-Doctoral Fellowship (Burroughs Wellcome Fund) National Academies Keck Futures Conference Invitee Distinguished Guest Lecturer, University of Virginia American Asthma Foundation Early Excellence Award Fellow, American Institute for Medical and Biological Engineering Levchenko leads the Levchenko Lab at the Yale Systems Biology Institute, collaborating with institutions like Mayo Clinic and Yale Cancer Center. His research has received recognition in Faculty of 1000 and multiple journal highlights.

• Computational Neuroscience
• Computational Psychiatry
• Neuroimaging
• +۳ مورد دیگر

John D. Murray is the Gregg L. Engles Associate Professor of Psychological and Brain Sciences at Dartmouth College and an Adjunct Associate Professor of Psychiatry at Yale School of Medicine. He holds a PhD in Physics from Yale University (2013) and a BS in Physics and Mathematics from Yale (2006). His research focuses on computational neuroscience and computational psychiatry, with secondary appointments in Physics and Neuroscience at Yale until 2023. His work integrates computational modeling, neuroimaging, and systems neuroscience to study decision-making processes, cortical organization, and psychiatric disorders. Collaborators include prominent researchers like Dr. John Krystal and Dr. Anticevic. Research interests include hierarchical brain organization, neuroimaging analysis techniques, and pharmacological effects on neural circuits. His lab (Murray Lab) develops computational tools like PsychRNN for cognitive task modeling. Notable contributions include linking transcriptomic data to neuroimaging patterns and modeling LSD’s effects on brain topography. He has been featured in YaleNews and Nature Communications for innovations in mapping mental illness variability and neural circuit dynamics. Grants and collaborations span translational neuroscience, addiction, and PTSD research through partnerships with Yale’s Center for Biomedical Data Science and VA National Center for PTSD. His interdisciplinary approach bridges physics, computer science, and clinical psychiatry to advance understanding of brain function and dysfunction.

• Machine Learning
• Genomics
• Gene Regulatory Networks
• +۳ مورد دیگر

Sushmita Roy is a Professor at the University of Wisconsin–Madison, affiliated with the Department of Computer Sciences and the College of Letters and Science. Her research focuses on developing computational methods in statistical machine learning to understand gene regulatory networks in living cells, particularly under environmental, developmental, disease, and evolutionary contexts. She explores bulk and single-cell genomic data integration to study processes like cell fate specification, host-microbe interactions, and diseases such as cancer and neurodevelopmental disorders. Her work emphasizes three key areas: inference of genome-scale transcriptional networks, evolutionary analysis of regulatory networks, and 3D genome organization dynamics. Roy’s lab collaborates across disciplines, leveraging genomic data from plant and mammalian systems. She has contributed to methodologies for analyzing chromatin accessibility, single-cell profiling, and network-based models of pathogen systems. Her affiliations include Wisconsin Institutes for Discovery, and she is a leader in computational biology and systems genomics research.

Waldemar Kolanusمشاهده پروفایل

استاد

• Molecular Immunology
• Cell Signaling
• Signal Transduction Pathways
• +۴ مورد دیگر

Prof. Waldemar Kolanus leads the Molecular Immunology and Cell Biology department at the University of Bonn's Life & Medical Sciences Institute (LIMES) . His research bridges immunoregulation , stem cell dynamics , and metabolic stress responses in immune cells. Unit 2 member at LIMES Principal investigator in SFB 704 and ImmunoSensation Cluster Leads a multidisciplinary lab with postdocs, PhD students, and technical staff His work focuses on intracellular signaling pathways connecting immune activation to tissue homeostasis, particularly through: Cytohesin proteins in integrin-mediated adhesion and migration TRIM71 in stem cell regulation and congenital hydrocephalus High-salt environments affecting macrophage function Publication trends show expertise in immune cell migration , genetic models , and chemical inhibition , with frequent use of mice and zebrafish for in vivo studies. Key articles explore: TRIM71's dual role in auditory development and germ cell maintenance Cytohesin family's Golgi regulation and insulin signaling Ruxolitinib's off-target migration inhibition of dendritic cells Contact details: Address: LIMES Institute, Carl-Troll-Straße 31, Bonn Email: kolanus.sekretariat@uni-bonn.de Phone: +49 228 73-62788

Kevin M. Franksمشاهده پروفایل

دانشیار

• Neurobiology
• Olfactory System
• Neural Circuits
• +۳ مورد دیگر

Kevin M. Franks is an Associate Professor of Neurobiology at Duke University, where he investigates how the olfactory system forms neural representations of sensory environments. His work focuses on functional neural circuits in the olfactory bulb and piriform cortex, using techniques like in vivo recordings, optogenetics, and behavioral assays. His research explores Neural circuit dynamics and plasticity Odor coding mechanisms Role of recurrent circuitry Integration of sensory modalities Recent publications highlight his contributions to understanding cortical odor representations, developmental neural connectivity, and cross-modal interactions. Awards include the 2024 Don Tucker Finalist recognition. He teaches advanced neuroscience courses at Duke, including Neurobiology research and concepts in neuronal systems.

Xiuwei Zhangمشاهده پروفایل

استادیار

• Computational Biology
• Bioinformatics
• Single-Cell Data Analysis
• +۵ مورد دیگر

Xiuwei Zhang is the J.Z. Liang Early-Career Assistant Professor in the School of Computational Science and Engineering (SCoSE) at Georgia Institute of Technology, part of the College of Computing. Her research focuses on computational biology and bioinformatics, particularly in developing machine learning methods for analyzing single-cell omics data, including multi-modal, temporal, and spatial data integration. She leads a lab that designs tools like scDART , scMoMaT , and scMultiSim , which address challenges in multi-omics integration, lineage reconstruction, and simulation. Before joining Georgia Tech, she held postdoctoral positions at UC Berkeley (Nir Yosef’s group), the European Bioinformatics Institute (EBI), and École Polytechnique Fédérale de Lausanne (EPFL). She earned her PhD in computer science from EPFL under Bernard Moret. Her Erdős number is 3, reflecting her collaborative work across computational fields. Her research spans four key areas: multi-batch/single-cell data integration, temporal analysis of cell differentiation, spatial-temporal omics dynamics, and simulation tools for benchmarking methods. She has received prestigious awards, including the NSF CAREER Award (2022) and NIH MIRA (2021). She actively participates in conferences (RECOMB, ISMB) and serves on editorial boards (Journal of Computational Biology). Her group’s recent work includes the scMultiSim simulator (2025), which generates multi-omics spatial data, and LinRace (2023), reconstructing cell lineage histories. She mentors over 15 students and collaborates internationally on projects like the InQuBATE Workshop on Single-Cell Transcriptomics.

Markus Heinonenمشاهده پروفایل

پژوهشگر ارشد

• Machine Learning
• Probabilistic Modeling
• Bayesian Inference
• +۵ مورد دیگر

Markus Heinonen is an Academy Research Fellow at Aalto University's Department of Computer Science within the School of Science. His academic position is tied to Harri Lähdesmäki's Professorship, focusing on probabilistic machine learning. He holds a Doctoral degree in Engineering and Technology from the University of Helsinki (2013). His research integrates probabilistic modeling , deep learning , and differential equations , with applications in computational biology, drug discovery, and biophysics. Key themes include Gaussian processes, Bayesian inference, generative models, and their use in understanding complex biological systems like immune cell behavior (e.g., T cell receptor analysis in aplastic anemia) and molecular design. He leads major projects such as the Deep Learning with Differential Equations initiative (2020–2025), exploring continuous-time models and physics-informed neural networks. His work bridges theory and application, evidenced by collaborations in diffusion models , optimal transport , and single-cell analysis . Publications span over 65 peer-reviewed outputs, with recent emphases on robust neural network training, multi-target molecular prediction, and interpretable drug design frameworks. His research contributes to UN Sustainable Development Goal 3 (Good Health) through advancements in disease modeling and therapeutic development. He has undertaken visiting research roles at the University of California, San Francisco (2017) and Telecom ParisTech (2013–2014). Media highlights include recognition for work on TCR-epitope prediction and AI-driven enzyme engineering.

Silvia Santosمشاهده پروفایل

پژوهشگر

• Developmental Biology
• Cell Biology
• Cell Cycle & Chromosomes
• +۳ مورد دیگر

Silvia Santos is a Group Leader at the Francis Crick Institute, leading the Quantitative Stem Cell Biology Lab since January 2018. Her research focuses on understanding cell decision-making during transitions, specifically cell division and differentiation in early development using human embryonic stem cells. She combines experimental techniques with theoretical approaches, including advanced microscopy, genomics, and computational modeling. Education and Career: PhD in Molecular and Cell Biology from EMBL-Heidelberg (2008), followed by postdoctoral training at Stanford University (2009-2014). She held an MRC Career Development Award at Imperial College London (2014-2017) before joining the Crick. Her work emphasizes interdisciplinary methods to study cellular processes in health and disease. Research Interests: Spatial-temporal control in cell decisions, stem cell differentiation, cell cycle regulation, and modeling embryonic development. She advocates for women in science and mentorship programs for early-career researchers. Key Achievements: Recipient of Marie Curie E-Star, EMBO, and HFSP fellowships. Recognized with the BioModels’ Model of the Year 2023 for contributions to systems biology. Her lab develops models like gastruloids to study embryonic development. Grants and Mentorship: Supported by MRC and other grants. Committed to fostering excellence in training and mentorship, previously chairing mentorship initiatives at Imperial College London. Labs and Teams: Quantitative Stem Cell Biology Lab at the Crick, collaborating with interdisciplinary teams on projects involving proteomics, genomics, and high-throughput screening.

• Immunology
• Virology
• Inflammation
• +۵ مورد دیگر

Santiago F. González is a Group Leader at the Institute for Research in Biomedicine (IRB) in Bellinzona, Switzerland, and an extraordinary professor at the University of Italian Switzerland (USI). He earned dual PhDs in microbiology (University of Santiago de Compostela, Spain) and immunology (University of Copenhagen, Denmark), followed by postdoctoral work (2007–2011) at Harvard Medical School's Immune Disease Institute under Michael Carroll. PhD in Microbiology, University of Santiago de Compostela PhD in Immunology, University of Copenhagen His research focuses on immune system dynamics during respiratory viral infections, vaccination, and cancer metastasis. Key areas include influenza recognition , lymph node inflammation , and immune cell behavior in vivo. He pioneered studies on C-type lectin receptors (e.g., SIGN-R1) in viral immunity and epigenetic modulators for inflammation. Recent publications highlight his work in epigenetic drug development , nanovaccines , and computational tools for immune cell tracking. His group uses two-photon intravital microscopy and spatial-temporal modeling to dissect immune responses. Scientific awards include three EU Marie Curie Fellowships (2004–2013), enabling his transition to independent research. His collaborations span Harvard, USI, and European institutions, with grants from the EU and Swiss research bodies. His lab at IRB, established via the 2013 Marie Curie Career Integration Grant , develops novel imaging approaches and therapeutic strategies for infectious and immune-mediated diseases.

Yang Songمشاهده پروفایل

دانشیار

• Computer Vision
• Deep Learning
• Multimodal AI
• +۷ مورد دیگر

Yang Song is an ARC Future Fellow and Scientia Associate Professor at the School of Computer Science and Engineering , University of New South Wales (UNSW) . She serves as Associate Head of School (Research) and Co-Director of iCinema , focusing on AI and Computer Vision applications for social good. Education: BEng in Computer Engineering (Nanyang Technological University, Singapore), PhD in Computer Science (UNSW, 2013) Research Areas: Biomedical image analysis, human-centred AI, graph data modeling, neuro-symbolic learning, and AI trustworthiness. Her work develops domain-specific deep learning models for radiological segmentation, histopathology cancer analysis, and 3D reconstruction. Recent projects address explainability in LLMs, fairness in AI, and human-robot interaction frameworks. With over 200 peer-reviewed publications in top venues like CVPR , MICCAI , and NeurIPS , her research spans biomedical imaging, robotics, and general multimodal AI. Scientific Awards include: 2024: ARC Industrial Transformation Research Hub for Human-Robot Teaming 2023: Google Inclusion Research Award 2022: NHMRC Ideas Grant for computational brain imaging 2021: UNSW Engineering Research Excellence Award 2020: Scientia Fellowship (UNSW) 2019: ARC Future Fellowship She supervises 24 current PhD/MPhil students and has graduated 15 advisees, including placements at Harvard University and Siemens Healthineers. Her grants include collaborations with Surf Life Saving Australia and industry partnerships for AI-driven solutions.

Vikas Singhمشاهده پروفایل

استاد

• Image Analysis
• Machine Learning
• Computer Vision
• +۳ مورد دیگر

Vikas Singh is a Professor in the Department of Biostatistics at the University of Wisconsin-Madison, with appointments in Computer Sciences and Statistics. He also serves as a part-time Faculty Researcher at Google DeepMind. His research focuses on image analysis, machine learning, and medical imaging applications, particularly in neuroimaging and Alzheimer's disease studies. Singh holds a Ph.D. in Computer Science from SUNY Buffalo and has taught courses such as BMI/CS 767 (Medical Image Analysis) and CS 766 (Computer Vision). Affiliations: UW Computer Vision Group, Wisconsin Alzheimer's Disease Research Center (W-ADRC), Machine Learning@UW. Research: Develops algorithms for medical image analysis, including tools for neuroimaging and longitudinal biomarker studies. Grants: Collaborates on grants related to Alzheimer's progression modeling and imaging techniques. His work emphasizes interdisciplinary applications, bridging statistics, geometry, and optimization to solve real-world problems in healthcare and engineering.

• Machine Learning
• Computer Vision
• Medical Image Analysis
• +۷ مورد دیگر

Professor Arcot Sowmya is a distinguished academic at the University of New South Wales, serving as Professor in the School of Computer Science and Engineering. With a strong background in both computer science and mathematics, she has established herself as a leading researcher in machine learning and computer vision applications, particularly in medical imaging and diagnostics. Dr. Sowmya earned her PhD in Computer Science from the Indian Institute of Technology, Bombay, along with an MTech in Computer Science, MSc in Mathematics, and BSc in Mathematics from the same institution. Her academic journey has positioned her at the intersection of theoretical computer science and practical medical applications. Her research interests span multiple domains with a primary focus on Machine Learning for Computer Vision . She has made significant contributions to learning object models, feature extraction, segmentation, and recognition techniques. Her work extends into medical image analysis, computer-aided diagnostics, high-resolution remote sensing, and biomedical informatics. More recently, she has applied similar techniques to social sciences domains, developing improved forecasting models for genocide and politicide. Her earlier work also includes contributions to real-time, concurrent, and embedded systems. Analyzing her recent publications reveals a strong trend toward medical applications of computer vision and deep learning. Her work spans from OCT-based glaucoma diagnosis to tumor segmentation, lung disease detection, and breast cancer prognosis. She has successfully bridged computer science with clinical medicine, developing practical tools for disease diagnosis and prediction that incorporate explainable AI approaches. Professor Sowmya's collaborative approach is evident in her extensive publication record across multiple journals and conferences. She has worked with researchers from diverse fields including ophthalmology, oncology, neurology, and public health, demonstrating the interdisciplinary nature of her research. Her laboratory work focuses on developing robust deep learning architectures for medical image analysis, with particular attention to segmentation networks, transformer models, and multimodal data fusion techniques. Her team has developed specialized networks for lung segmentation, tumor detection, and disease classification that address specific challenges in medical imaging.

Istvan Albertمشاهده پروفایل

استاد پژوهشی

• Bioinformatics
• Genomics
• Computational Biology
• +۵ مورد دیگر

Istvan Albert is a Research Professor of Bioinformatics at Pennsylvania State University , affiliated with the Department of Biochemistry and Molecular Biology . He leads the Bioinformatics Consulting Center and teaches BMMB 852: Applied Bioinformatics . Research Interests: Specializing in bioinformatics, large-scale biological data analysis, microarray and sequence analysis, scientific programming, algorithm development, and database-driven web development. His work spans gene ontology visualization , RNA-Seq analysis , and coronavirus research . Software Development: Created GeneScape for gene function visualization and bio for bioinformatics workflows. Maintains the Biostar Handbook series and the Biostars Q&A Forum , a leading bioinformatics resource.