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 .

• Biomedical Data Privacy
• Genomics
• Machine Learning
• +۳ مورد دیگر

Hyunghoon Cho is an Assistant Professor at Yale School of Medicine in the Department of Biomedical Informatics & Data Science, with a secondary appointment in the Department of Computer Science. He received his PhD in Electrical Engineering and Computer Science from MIT (2019) and MS/BS in Computer Science from Stanford University (2013). His research focuses on computational challenges in biomedical data privacy, single-cell genomics, and network biology. Assistant Professor (Primary): Biomedical Informatics & Data Science Assistant Professor (Secondary): Computer Science Appointments: Yale School of Medicine | Broad Institute (Schmidt Fellow) Research Themes: Privacy-Enhancing Technologies for genomic and health data Scalable AI/ML tools for omics data analysis Structured biological modeling for system-level discovery His work includes secure GWAS, transcriptomic privacy assessment, and sfkit - a federated genomic analysis toolkit. He received the NIH Director's Early Independence Award and leads NSF-funded projects on confidential genome analytics. Awards: NIH Director's Early Independence Award Lab Members: Haris Smajlović (Postdoc), Vincent Angelo (CBB MS), Denis Loginov (Senior Software Engineer), Lucy Zheng (CBB PhD)

Anirban Paulمشاهده پروفایل

دانشیار

• Neuroscience
• GABAergic inhibitory circuits
• Interneuron biology
• +۵ مورد دیگر

Anirban Paul is an Associate Professor in the Department of Neuroscience and Experimental Therapeutics at Pennsylvania State University, affiliated with the Penn State Neuroscience Institute. His research focuses on cellular and molecular mechanisms of GABAergic inhibitory circuits, with particular emphasis on interneuron biology and its implications in neurological disorders. Dr. Paul's research spans multiple neuroscience domains, with primary focus on GABAergic inhibitory circuits and interneuron biology. His work investigates how specific neuron subtypes, particularly Chandelier cells and cortical interneurons, contribute to brain function and dysfunction. He has made significant contributions to understanding the role of these cells in schizophrenia, Alzheimer's disease, and other neurological conditions. His research integrates molecular, cellular, and systems-level approaches to uncover fundamental mechanisms of neural circuit assembly, plasticity, and function. Key areas include RNA regulation in neuronal development, transcriptomic subtypes of inhibitory neurons, and cell-type specific vulnerabilities in neurodegenerative diseases. His research portfolio demonstrates consistent productivity with publications spanning from 2003 to 2025, showing an evolving focus from basic molecular neuroscience to translational research in neurological disorders. Recent work emphasizes single-cell analysis techniques and the role of specific interneuron populations in disease mechanisms, particularly in schizophrenia and Alzheimer's disease. His publications appear in high-impact neuroscience journals including Neuron, BMC Biology, and Frontiers in Cellular Neuroscience. Dr. Paul has received the NARSAD Young Investigator Award (2018), recognizing his promising research in neuroscience. His scientific contributions have been supported by multiple competitive grants from prestigious organizations including the National Institute on Aging (NIA) and the Brain and Behavior Research Foundation. He serves as Principal Investigator on multiple active research projects, including two major grants from the National Institute on Aging focused on cell-type specific risk and resilience in Alzheimer's disease and aging (2021-2024 and 2024-2026), as well as previous projects from the Brain and Behavior Research Foundation investigating Chandelier cells in schizophrenia. His research program demonstrates sustained funding and scientific leadership in the field of interneuron biology and its clinical implications.

John Paisleyمشاهده پروفایل

دانشیار

• Machine Learning
• Bayesian Statistics
• Data Science
• +۳ مورد دیگر

John Paisley is an Associate Professor of Electrical Engineering at Columbia University's Fu Foundation School of Engineering and Applied Science, and a member of Columbia's Data Science Institute (DSI). He holds a B.S., M.S., and Ph.D. in Electrical and Computer Engineering from Duke University (2004-2010), followed by postdoctoral research in Computer Science at Princeton University and UC Berkeley. His research focuses on Bayesian models, posterior inference techniques for Big Data, and applications in data analysis, recommendation systems, information retrieval, and compressed sensing. He has pioneered methods like Bayesian Gaussian Process ODEs and Double Normalizing Flows, with recent work emphasizing uncertainty quantification in environmental modeling and neuroimaging analysis. His collaborative workflows (e.g., bneR ) address air pollution exposure and PM2.5 concentration uncertainties, combining Bayesian nonparametric ensembles with geospatial data. He has also developed frameworks for neural network interpretability, image denoising, and compressed sensing MRI. Paisley's work bridges statistical theory and applied machine learning, with applications in healthcare, environmental science, and geophysics. His academic contributions include over 50 publications since 2016, spanning topics like deep metric learning, adversarial learning, and variational inference optimization. He maintains an active research group and serves on editorial boards for machine learning and signal processing journals.

Britt Adamsonمشاهده پروفایل

دانشیار

• Stress Response Networks
• DNA Damage Response
• Genome Editing
• +۳ مورد دیگر

Britt Adamson is an Associate Professor in the Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics at Princeton University, where she serves as Director of the Undergraduate Program in Quantitative and Computational Biology. Her lab investigates molecular networks in human cells with focus on stress response mechanisms and genome editing technologies. She received her B.S. in Biology from the Massachusetts Institute of Technology (2005) and Ph.D. in Genetics and Genomics from Harvard University (2012), followed by postdoctoral training at UCSF under Jonathan Weissman supported by a Damon Runyon Cancer Research Foundation Fellowship. Adamson's research centers on how cells organize stress response networks during DNA damage and endoplasmic reticulum stress, developing CRISPR-based functional genomics and single-cell sequencing tools to map molecular behaviors. Her work bridges fundamental cell biology with therapeutic applications in genome editing. Analysis of her 15 most recent publications reveals dominant themes in precision genome editing (prime/base editing optimization) and systematic dissection of DNA repair pathways through combinatorial CRISPR screening. Her lab consistently integrates computational approaches with high-resolution experimental techniques to uncover context-dependent cellular behaviors. Her scientific recognitions include: Damon Runyon Cancer Research Foundation Postdoctoral Fellowship Princeton IP Accelerator Award (2025) STAT Who to Know: 10 Scientists leading a new generation of gene editors (2024) Adamson actively mentors eight graduate students (including alumni Ann Cirincione and Jun Hussmann) and two postdocs, with research funded through institutional awards and collaborative grants. Her lab's technological developments have enabled projects spanning virology, immunology, and developmental biology. The Adamson Lab operates within Princeton's Lewis-Sigler Institute for Integrative Genomics, fostering an interdisciplinary environment that merges cell biology, genomics, and computational science. Current projects focus on improving prime editing efficiency and understanding stress response adaptation in disease contexts.

Hyun Kooمشاهده پروفایل

استاد

• Biofilms
• Oral Infectious Diseases
• Nanotechnology
• +۳ مورد دیگر

Hyun (Michel) Koo is a Professor at the University of Pennsylvania School of Dental Medicine , with affiliations in the Department of Orthodontics , Division of Community Oral Health , and Division of Pediatric Dentistry . As Co-Founder and Co-Director of the Center for Innovation & Precision Dentistry (CiPD) , he leads interdisciplinary efforts merging bioengineering, nanotechnology, and oral health research. Education : DDS and PhD Research Focus : Biofilms, bacterial-fungal interactions, and nanotechnology for oral disease prevention Leadership : Co-Director of CiPD; key roles in training programs like NIDCR-sponsored R90 and T90/R90 Dr. Koo’s research explores biofilm mechanisms in oral infectious diseases, particularly childhood caries, through engineering methods and microrobotics . His team developed micron-scale robots for automated biofilm eradication and FDA-approved nanoparticles for caries prevention. Collaborations with Penn Engineering, including Dr. Daeyeon Lee and Dr. Kacy Cullen, emphasize translational approaches. The 15 most recent publications highlight his work in nanorobotics , interkingdom biofilms , and precision diagnostics . Articles span 2025–2024 and address topics like adaptive micromotors , biofilm matrix degradation , and single-cell microbial interactions . These emphasize his focus on targeted therapies and biofilm microenvironment engineering . Key Awards : Elected Fellow, American Association for the Advancement of Science (AAAS) IADR Distinguished Scientist Award for innovative dental research Dr. Koo trains next-generation researchers through the CiPD NIDCR T90/R90 Postdoctoral Training Program , mentoring fellows like Smruti Nair (ACE2 Chewing Gum development) and Zhi Ren (K99 awardee). His work intersects with Penn Health-Tech, CT3N , and Penn Institute for Biomedical Informatics , fostering transdisciplinary innovation.

Itsik Pe'erمشاهده پروفایل

استاد

• Human Genetics
• Computational Biology
• Genomics
• +۳ مورد دیگر

Itsik Pe'er is a Full Professor and Vice-Chair in the Department of Computer Science at Columbia University's Fu Foundation School of Engineering & Applied Science, and holds a joint appointment as Professor of Systems Biology at the Vagelos College of Physicians and Surgeons. His research focuses on computational methods in human genetics, including genetic variation analysis, disease association studies, and algorithm development for genomic data. He leads the Itsik Pe'er Lab of Computational Genomics, which develops tools like Xplorigin, Germline, and SEACells to address challenges in genomics and medical research. His work spans machine learning applications in healthcare, microbiome analysis, and cancer genomics. Notable contributions include studies on hypertensive disorders in pregnancy, bias correction in predictive models, and the development of non-Euclidean learning libraries like Manify. Pe'er has advised students including Vladimir Vacic, Anat Kreimer, and Arthi Ramachandran, and collaborates on grants addressing genetic epidemiology and computational biology. His lab's location is in the Computer Science Building at Columbia's Morningside Campus.

• 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.

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.

• Bioinformatics
• Genomics
• Transcriptomics
• +۶ مورد دیگر

Owen R. White is a Professor in the Department of Epidemiology & Public Health at the University of Maryland School of Medicine, serving as Associate Director of the Institute for Genome Sciences and Associate Director of Research Collaboration & Development. He leads a team of 25 scientists and engineers developing genomic annotation pipelines and data analysis tools for state-of-the-art research in microbiome and multi-omic studies. His academic background includes: BS in Biotechnology from the University of Massachusetts (1985) PhD in Molecular Biology from New Mexico State University (1992) Postdoctoral Fellowship in Genome Informatics at the Institute for Genomic Research (TIGR) (1994) Dr. White's research spans bioinformatics, genomics, transcriptomics, and metagenomics with emphasis on data management, metadata standards, ontologies, and cloud systems. His work has been foundational for large-scale initiatives like the Human Microbiome Project (HMP) and Integrative Human Microbiome Project (iHMP), generating over 50,000 datasets totaling 10 terabytes of multi-omic data. Analysis of his recent publications reveals a strong trend toward neuroscience multi-omics (BRAIN Initiative), cloud-based data infrastructure, and ethical data sharing frameworks. His work consistently bridges microbiome research with emerging fields like single-cell analysis and Alzheimer's disease biomarker discovery through integrated data platforms. Notable awards include: Benjamin Franklin Award for Open Access in the Life Sciences (2015) Kumho Science International Award in Plant Molecular Biology and Biotechnology (2001) As Principal Investigator for major NIH-funded centers, he has secured sustained support for the HMP Data Analysis and Coordination Center and iHMP Data Coordination Center. His team's work combines fee-for-service models with collaborative research funding to maintain cutting-edge genomic analysis capabilities. The Institute for Genome Sciences houses his computational team responsible for developing production annotation pipelines, database systems, and visualization tools that serve researchers across the University of Maryland School of Medicine and national consortia.

Zhe Jiمشاهده پروفایل

استادیار

• Data Science
• Computational Biology
• Functional Genomics
• +۴ مورد دیگر

Zhe Ji is an Assistant Professor in the Department of Biomedical Engineering at McCormick School of Engineering and the Department of Pharmacology at Feinberg School of Medicine, Northwestern University. His research integrates computational and experimental genomics to study gene transcription and RNA translation in cell fate commitment and oncogenic processes, aiming to develop precision medicine strategies. **Education**: Postdoctoral Fellow in Cancer Systems Biology, Harvard Medical School Postdoctoral Fellow in Computational Biology, Broad Institute of MIT and Harvard Ph.D. in Computational Genomics, Rutgers University B.S. in Biotechnology, Nanjing University, China **Research Focus**: Keywords include Data Science, Computational Biology, Functional Genomics, RNA, Cancer, Inflammation, and Machine Learning. The lab explores regulatory mechanisms underlying disease, with a focus on translational control, cancer metastasis, and inflammatory networks. **Grants & Advising**: No specific grants or student advisees listed. The lab emphasizes collaborative projects and computational-experimental approaches. **Lab Affiliations**: Zhe Ji’s lab is part of Northwestern’s interdisciplinary environment, bridging engineering and medicine to advance genomic technologies and therapeutic strategies.

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.

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.