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.

Alexis Battleمشاهده پروفایل

دانشیار

• Genomics
• Machine Learning
• Computational Biology
• +۳ مورد دیگر

Alexis Battle is an Associate Professor at Johns Hopkins University with appointments in Biomedical Engineering , Computer Science , and Genetic Medicine (secondary). She directs the Malone Center for Engineering in Healthcare and serves as Deputy Director of the Data Science and AI Institute . Educated at Stanford University (PhD in Computer Science, 2013), Battle transitioned to academia after leadership roles at Google. Research Focus: Battle’s work bridges genomics and machine learning , emphasizing the impact of genetic variation on human health. Her lab develops tools like Watershed to predict functional effects of rare variants, aiming to enhance rare disease diagnosis. Key themes include non-coding DNA analysis , personalized genomics , and systems biology , with applications in cardiovascular disease and neurodegenerative disorders . Publications & Awards: Over 60 peer-reviewed articles in journals like Nature , Science , and Genome Biology , with recent emphasis on single-cell transcriptomics , multiomics integration , and telomere biology . Recipient of the President’s Frontier Award (2022), Microsoft Investigator Fellowship (2019), and Searle Scholar (2016). Scientific Awards: 2022 President’s Frontier Award 2019 Microsoft Investigator Fellowship 2019 Johns Hopkins Discovery Award 2017 Johns Hopkins Catalyst Award 2016 Searle Scholar Advising & Funding: Mentors 11 PhD students, 3 undergraduates, and postdoctoral fellows. Her research is funded by NIH, Searle Scholars, and institutional grants. The Battle Lab collaborates on projects like the GTEx Consortium , focusing on gene regulation and clinical genomics .

Wengong Jinمشاهده پروفایل

استادیار

• AI for drug discovery
• Generative AI models
• Geometric deep learning
• +۵ مورد دیگر

Wengong Jin is an Assistant Professor at the Khoury College of Computer Sciences, Northeastern University, and a visiting research scientist at the Eric and Wendy Schmidt Center at the Broad Institute. He holds a PhD from MIT CSAIL, advised by Prof. Regina Barzilay and Prof. Tommi Jaakkola. Research Interests: His work focuses on geometric and generative AI models for drug discovery, biology, and chemical engineering. Key areas include equivariant neural networks (e.g., FAFormer), diffusion models for binding energy prediction, antibody/enzyme design (RefineGNN, SurfPro), and molecular design through graph neural networks (Junction Tree VAE). He also explores domain generalization and systems for autonomous molecular discovery. Publications: His research has been published in top venues like NeurIPS, ICLR, ICML, Nature, Science, and Cell. Recent breakthroughs include discovering novel antibiotics using explainable AI and designing synergistic drug combinations for cancer treatment. Awards: He has received the BroadIgnite Award, Dimitris N. Chorafas Prize, and MIT EECS Outstanding Thesis Award for his contributions to computational biology and AI-driven drug discovery. Teaching: Currently teaches a PhD seminar on AI for Science, focusing on integrating machine learning into scientific discovery processes.

• 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.

Daiwei Zhangمشاهده پروفایل

استادیار

• Artificial Intelligence
• Machine Learning
• Spatial Omics
• +۳ مورد دیگر

Daiwei (David) Zhang, PhD, is an Assistant Professor (tenure-track) in the Department of Biostatistics at the University of North Carolina at Chapel Hill School of Medicine, with a joint appointment in the Department of Genetics. His research focuses on developing AI frameworks for analyzing high-dimensional biomedical data, particularly in spatial omics, computational pathology, and medical imaging. Education: MS (Biostatistics) and PhD (Biostatistics and Scientific Computing) from the University of Michigan. Postdoctoral Training: University of Pennsylvania. Research interests include applying machine learning to address biomedical challenges such as tumor heterogeneity, immune interactions, and tissue architecture. His work spans computational methods for spatial transcriptomics, proteomics, and histology integration. Recent publications emphasize spatial multi-omics analysis of cancer ecosystems, tertiary lymphoid structures, and metabolic coordination. These studies leverage advanced machine learning algorithms and interdisciplinary approaches to advance precision medicine. No scientific awards are explicitly mentioned, but his work reflects significant contributions to biomedical AI research. Grants and advising details are not provided in the text.

• Microbiology
• Infectious Diseases
• Cell Biology
• +۷ مورد دیگر

Manuel R. Amieva is a Professor at Stanford University School of Medicine , holding joint appointments in Pediatrics - Infectious Diseases and Microbiology & Immunology . He is also a member of the Maternal & Child Health Research Institute (MCHRI) . His clinical practice at Stanford Medicine Children's Health focuses on pediatric infectious diseases. Education: Medical Education: Stanford University School of Medicine (1997) Fellowship: Stanford University Pediatric Infectious Disease Fellowship (2004) Internship & Residency: Stanford Health Care at Lucile Packard Children's Hospital (1998-1999) Dr. Amieva's research investigates host-pathogen interactions at epithelial barriers, with specific expertise in Helicobacter pylori , Listeria monocytogenes , Salmonella enterica , and Staphylococcus aureus . His lab develops innovative organoid culture systems with controlled polarity to study microbial colonization and oncogenic mechanisms. Key discoveries include: H. pylori's manipulation of epithelial junctions via the CagA protein Listeria's exploitation of cell extrusion sites for invasion Staphylococcus toxin interactions with adherens junctions Gastric stem cell activation by pathogens Recent publication trends show continued leadership in infectious disease mechanisms (2020-2025), with a focus on: Pathogen-specific epithelial breach strategies Organoid modeling of viral/bacterial interactions Redox-dependent host factor regulation Single-cell spatial transcriptomic analyses Multi-institutional educational frameworks His scientific collaborations span disciplines including: Gastric cancer genomics initiatives COVID-19 lung infection models Stem cell-microbe interactions Medical education reform projects Dr. Amieva maintains active clinical research while mentoring students in both the Microbiology & Immunology and Pediatrics programs. His lab at Stanford employs advanced 3D confocal microscopy and organ-on-a-chip technologies to visualize epithelial colonization dynamics.

Knut Drescherمشاهده پروفایل

دانشیار

• Bacterial Biofilms
• Microbial Multicellularity
• Biophysics
• +۵ مورد دیگر

Prof. Knut Drescher is an Associate Professor at the Biozentrum, University of Basel , leading a research group focused on bacterial biofilms , swarming , and microbial multicellularity . Previously, he served as a Professor of Biophysics and Max Planck Research Group Leader at Philipps-Universität Marburg (2015-2021) and conducted postdoctoral research at Princeton University. Research Interests: Physical and biological mechanisms of biofilm formation Cell-cell interactions in microbial communities Antibiotic resistance in biofilms Hydrodynamics of bacterial swarms Evolution of cooperation in multispecies biofilms Development of bioimaging software (BiofilmQ, BacStalk) Scientific Awards: 2023: SNSF Consolidator Grant 2019: Heinz Maier-Leibnitz Prize (DFG), VAAM Research Prize, IUPAP Young Scientist Prize 2016: ERC Starting Grant Advising & Grants: Advises PhD and Master's students in microbiology, biophysics, and bioinformatics Secured major grants from ERC , HFSP , and DFG

Long Caiمشاهده پروفایل

استاد

• Spatial Genomics
• Cellular Biology
• Developmental Biology
• +۴ مورد دیگر

Long Cai is a Professor at the California Institute of Technology, affiliated with the Biology and Biological Engineering department. He pioneered the field of spatial genomics and co-developed transformative technologies such as seqFISH and MEMOIR. Research Interests: His work focuses on decoding biological systems through spatial genomics, integrating molecular imaging with computational analysis to uncover cellular organization in tissues. Key areas include developmental biology, neuroscience, kidney regeneration, and cancer biology. Publications: Recent studies highlight applications of spatial transcriptomics in kidney disease, brain nuclear architecture, and multi-omics tissue mapping. His research emphasizes creating high-resolution atlases of cellular dynamics. Scientific Awards: NIH Director’s Pioneer Award (2022) Labs & Collaborations: He leads the Cai Lab, which develops cutting-edge imaging tools in collaboration with the Elowitz Lab and other interdisciplinary teams.

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.

Claire Donnatمشاهده پروفایل

استادیار

• Statistics
• Machine Learning
• Graph Neural Networks (GNNs)
• +۷ مورد دیگر

Claire Donnat is an Assistant Professor in the Department of Statistics at the University of Chicago, specializing in statistical and machine learning methods for graph-structured and high-dimensional data. Her work bridges theoretical innovation with applications in biomedical research, environmental science, and public health. Education: B.S. and M.S. in Applied Mathematics from Ecole Polytechnique; Ph.D. in Statistics from Stanford University (2020). Her research focuses on three methodological directions: (1) statistical foundations for graph neural networks (GNNs), (2) structured estimation with graph constraints, and (3) multimodal data integration with uncertainty quantification. Key applications include thermotolerance in photosynthetic microbes, family network analysis for child welfare, and spatial transcriptomics. The 15 most recent publications highlight her work in GNNs, CCA, tensor modeling, and epidemic analysis, with keywords spanning statistics, machine learning, and network science. Her methodological contributions address challenges in sparsity, graph topology, and heterogeneous data fusion. Scientific Awards: Facebook Research Award (2021), C3.AI COVID Grand Challenge winner (2020), Lumiata hackathon winner (2020), Stanford Centennial Award (2019), and others. Claire's research group actively recruits postdocs and students for projects involving graph-based modeling, data integration, and biomedical applications. She also provides research consulting in statistical methodology and graph modeling for life sciences.

Rex Yingمشاهده پروفایل

استادیار

• Graph Neural Networks
• Geometric Representation Learning
• Explainable AI
• +۳ مورد دیگر

Rex Ying is an Assistant Professor in the Department of Computer Science at Yale University's School of Engineering & Applied Science. He leads research in graph neural networks, geometric representation learning, and explainable AI, with applications spanning physical simulations, biology, knowledge graphs, and recommender systems. His lab actively recruits PhD students interested in geometric deep learning, graph neural networks, and trustworthy AI. Dr. Ying received his PhD in Computer Science from Stanford University under Jure Leskovec, with a thesis titled "Towards Expressive and Scalable Deep Representation Learning for Graphs." Prior to that, he graduated from Duke University in 2016 with highest distinction, majoring in Computer Science and Mathematics. His research focuses on three interconnected areas: advancing graph neural network architectures for improved expressiveness, scalability, and interpretability; innovating in geometric representation learning for data with diverse characteristics; and developing real-world applications across scientific domains. He has pioneered influential algorithms including GraphSAGE, PinSAGE, and GNNExplainer, and developed the first billion-scale graph embedding services at Pinterest as well as graph-based anomaly detection algorithms at Amazon. His recent publication trends show a strong focus on hyperbolic geometry for foundation models, non-Euclidean representation learning, and multimodal applications in computational biology. The research demonstrates increasing integration of geometric deep learning with large language models and foundation model architectures. KDD 2022 Dissertation Award 2019 Baidu Scholarship in Artificial Intelligence Dr. Ying actively serves the research community as a committee member for major conferences including AAAI, ICML, NeurIPS, ICLR, KDD, and WebConf for over seven years, and as area chair for LoG 2022. He co-leads the open-source PyTorch Geometric project and has organized numerous workshops on graph learning. His industry collaborations include Pinterest, Amazon, Facebook AI Research, DeepMind, Siemens, SLAC National Accelerator Laboratory, and Saudi Aramco. He teaches "Deep Learning for Graph-Structured Data" at Yale and mentors students in developing cutting-edge graph learning algorithms. His research lab collaborates with both academic institutions and industry partners to advance the state-of-the-art in graph representation learning, with particular emphasis on geometric deep learning and its applications to scientific discovery and real-world systems.

Baijian Yangمشاهده پروفایل

استاد

• Cybersecurity
• Big Data
• Applied Machine Learning
• +۴ مورد دیگر

Dr. Baijian "Justin" Yang serves as the Associate Dean for Research at Purdue Polytechnic Institute and is a Professor in the Department of Computer and Information Technology at Purdue University. He earned his Ph.D. in Computer Science from Michigan State University, with Master's and Bachelor's degrees in Automation (EECS) from Tsinghua University. Dr. Yang has established himself as a leader in multiple interdisciplinary research domains. Dr. Yang's educational background includes: PhD in Computer Science, Michigan State University (2002) MS in Automation (EECS), Tsinghua University (1998) BS in Automation (EECS), Tsinghua University (1995) His research interests span multiple cutting-edge domains with practical applications: Cybersecurity : Developing novel approaches for threat intelligence, security education, and network defense Big Data : Creating innovative algorithms for dimension reduction, regression with categorical variables, and tensor decomposition Applied Machine Learning : Implementing AI solutions in healthcare, manufacturing, and forestry applications Digital Forestry : Using UAV imagery and remote sensing for forest management and tree species classification Dr. Yang's publication record demonstrates significant impact across multiple disciplines, with recent work focusing on spatial transcriptomics analysis (SiGra), delirium detection using limited-lead EEG, and visual localization technologies. His research bridges theoretical advances with practical applications in healthcare, manufacturing quality control, and environmental monitoring. The interdisciplinary nature of his work is evident in collaborations spanning computer science, healthcare, forestry, and manufacturing domains. His scientific achievements have been recognized with numerous awards: 2023 HRSA Building Bridges to Better Health Competition Winner (Phase 1) and 2nd place ($100,000 prize) in Phase 3 2023 Outstanding Faculty Award in Engagement, Department of Computer and Information Technology, Purdue University 2021 Leadership in Manufacturing Award, Manufacturing Times Digital (MxD) 2021 Good to Great Award, Purdue Polytechnic 2020 Outstanding Faculty Award in Discovery, Department of Computer and Information Technology 2019 University Faculty Scholars, Purdue University As an educator and mentor, Dr. Yang has advised numerous graduate students through their PhD and Master's research. His leadership extends to significant service roles including serving as Faculty Champion for the Holistic Safety and Security research impact area at Purdue Polytechnic from 2018 to 2021, board membership with ATMAE (2014-2016), and participation in the IEEE Cybersecurity Initiative Steering Committee (2015-2017). He holds valuable industry certifications including CISSP, MCSE, and Six Sigma Black Belt, demonstrating his commitment to bridging academic research with industry practice. Dr. Yang leads multiple research projects including "Digital Forestry" for developing tools to quantify forest function, "CHEESE" (Cyber Human Ecosystem of Engaged Security Education), and "CICI" (Supporting Controlled Unclassified Information with a Campus Awareness and Risk Management Framework). His work on "Applied Machine Learning" focuses on solving real-world problems, while his "Dimension Reduction and Memory Amnestic Big Data Regression" project innovates computational algorithms for large-scale data analysis.

Omer Bayraktarمشاهده پروفایل

پژوهشگر

• Neural Diversity
• Spatial Transcriptomics
• Glia Biology
• +۳ مورد دیگر

Omer Bayraktar is a Group Leader at the Wellcome Sanger Institute , leading research in the Cellular Genomics Programme. His work focuses on decoding human brain cellular diversity using spatial transcriptomics , imaging , and functional screening to study neural complexity in health and disease. Bayraktar's educational background includes a PhD from HHMI under Chris Doe, investigating neural diversity development in Drosophila , followed by postdoctoral work at University of California, San Francisco and University of Cambridge as a Life Sciences Research Foundation Fellow. He developed a spatial transcriptomic pipeline during his postdoc to analyze astrocyte heterogeneity in the cerebral cortex. His research explores neural cell type mapping , glial-neuronal interactions , and cellular pathways in neurodevelopmental disorders . Recent publications emphasize 3D tissue mapping , multi-omic integration , and computational tools like Cell2fate and WebAtlas. His work bridges neurogenetics and computational biology to advance understanding of human tissue ecosystems. Bayraktar's lab collaborates with the Human Cell Atlas initiative and develops technologies such as automated histology pipelines and highly-multiplexed smFISH for molecular cell typing. His team also investigates glia-based therapies and astrocyte functional heterogeneity in neurodevelopmental contexts. Key scientific contributions include: Discovering astrocyte layer patterns independent of neuronal laminae Developing cell2location for spatial cell mapping Characterizing Drosophila neural stem cell models with human relevance Notable awards include the Life Sciences Research Foundation Fellowship during his postdoctoral training. His current group includes a PhD student , Senior Data Scientists , and Bioinformaticians .

• Behavioral Ecology
• Evolutionary Biology
• Population Ecology
• +۱۱ مورد دیگر

Prof. Dr. Oliver Krüger is a behavioral ecologist and evolutionary biologist at Bielefeld University 's Faculty of Biology , where he leads the Department of Animal Behaviour since 2013. His research spans avian and marine mammal systems, focusing on life history strategies, parasite-host interactions, and environmental adaptation. Education: Biology studies at Bielefeld University (1994-1996) MSc in Oxford (1996-1997) PhD at Bielefeld University with Fritz Trillmich and Jan Lindström (1998-2000) Research Themes: Behavioral ecology, evolutionary biology, and population dynamics across tropical and temperate ecosystems. Key projects include NC³ (Niche Choice/Construction) and studies on Galápagos sea lions, common buzzards, and pinniped species. Scientific Leadership: Spokesperson, SFB TRR 212 "NC³" (2018-2025) Advisory Board member: German Ornithologists Union, IUCN SSC pinniped group, German Primate Centre Peer review roles: Humboldt Foundation, DFG, HFSP, NSF Awards: Leopoldina Prize (2001) Niko Tinbergen Award (2008) DFG Heisenberg Professorship (2010-2015)

Brian Hieمشاهده پروفایل

استادیار

• Machine Learning
• Computational Biology
• Protein Engineering
• +۶ مورد دیگر

Brian Hie is an Assistant Professor of Chemical Engineering at Stanford University , a Dieter Schwarz Foundation Stanford Data Science Faculty Fellow , and an Innovation Investigator at Arc Institute . He leads the Laboratory of Evolutionary Design , focusing on the intersection of biology and machine learning . His prior roles include a Stanford Science Fellow in the Stanford University School of Medicine and a Visiting Researcher at Meta AI . Education: Ph.D. , Electrical Engineering and Computer Science , Massachusetts Institute of Technology (2021) Bachelor’s Degree , Stanford University Research Interests: Brian’s work bridges machine learning and computational biology , with a focus on protein engineering , single-cell RNA sequencing , and viral evolution . His Evolutionary velocity framework predicts protein evolutionary dynamics across timescales, while his Scanorama algorithm enables efficient integration of heterogeneous single-cell datasets. He also develops structure-informed language models for antibody optimization and uncertainty-aware ML for biological discovery. Publication Trends: His recent work (2023) emphasizes structure-based inverse folding for antibody evolution, evolutionary scale modeling , and unsupervised optimization . Earlier studies (2022-2021) cover evolutionary velocity , multi-modal single-cell analysis , and viral escape prediction using natural language analogies. Scientific Awards: Stanford Science Fellow (2021) National Defense Science and Engineering Graduate Fellowship (2019) Advising: He mentors doctoral students including Brandon Ameglio , Garyk Brixi , and Chang M. Yun , with a focus on biological design and computational methods . Labs & Collaborations: His lab collaborates with Bio-X and the Institute for Human-Centered Artificial Intelligence (HAI) , and he maintains affiliations with Sarafan ChEM-H and Stanford Data Science .