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Romain LopezView profile

Assistant Professor

• Single-cell omics
• Spatial transcriptomics
• Deep generative models
• +5 more

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.

• Machine Learning
• Explainable AI
• Neural Networks
• +3 more

Jonas Fischer is the head of the Explainable Machine Learning group at the Max Planck Institute for Informatics, Department of Computer Vision and Machine Learning. His research focuses on interpreting complex machine learning models, particularly in genomics and healthcare, aiming to enhance robustness and alignment with human decision-making. Prior to his role at MPI, he was a postdoctoral fellow at Harvard University's Department of Biostatistics, where he worked on interpretable models for gene regulatory systems in cancer. Education: PhD in Computer Science from Saarland University (2022), with a thesis titled More than the sum of its parts , exploring the intersection of pattern mining and deep learning. He has contributed to advancing methods in neural network pruning, federated learning, and low-dimensional embeddings (e.g., dtSNE, Mercat). His work bridges computational biology, data mining, and machine learning, with applications in DNA methylation analysis, graph-based differential networks, and biomedical informatics. Key research areas include: (1) Explainable AI and neural network interpretability, (2) Biomedical applications of machine learning (e.g., gene regulatory networks, cancer genomics), (3) Low-dimensional embeddings and visualization techniques, (4) Federated learning for privacy-preserving collaborative models, and (5) Pattern mining for error analysis in NLP and classification tasks. Publications span top venues like NeurIPS, ICLR, Bioinformatics, and Genome Biology. His group develops tools such as BONOBO for omics data integration and node2vec2rank for scalable graph analysis. He actively collaborates with biomedical researchers to address challenges in data-driven healthcare and precision medicine.

Jimeng SunView profile

Professor

• Artificial Intelligence
• Healthcare Analytics
• Drug Discovery
• +5 more

Dr. Jimeng Sun is a Health Innovation Professor at the Siebel School of Computing and Data Science and Carle Illinois College of Medicine at the University of Illinois Urbana-Champaign. Co-founder of Keiji AI , he leads groundbreaking research at the intersection of artificial intelligence and healthcare, actively deploying clinical AI systems and developing frameworks like PyHealth and Therapeutics Data Commons . His research spans four major areas: Clinical AI Systems : Developing interpretable models (e.g., RETAIN) for patient similarity, temporal event prediction, medication recommendation, and clinical outcome forecasting Drug Discovery : Creating molecular optimization frameworks, drug-target interaction models, and AI-driven platforms Clinical Trials : Pioneering patient-trial matching, outcome prediction, and optimization frameworks using deep learning and graph neural networks Biosignal Analysis : Advancing sleep staging, seizure classification, and automated EEG/Cardiac monitoring systems With over 500 top-tier publications (including in Nature , NEJM AI , and leading AI conferences) and an h-index of 99, his work has been recognized with the Top 100 AI Leaders in Drug Discovery and Advanced Healthcare award. He maintains active collaborations with institutions like Massachusetts General Hospital , Medidata Solutions , and OSF Healthcare . His recent publications reveal a strong focus on: Reinforcement learning applications in medical data analysis Large language model adaptation for clinical tasks Knowledge graph integration with AI systems Synthetic data generation for healthcare Multi-modal learning in clinical contexts Explainable AI for medical applications Dr. Sun's lab ( Sunlab ) emphasizes practical impact over theoretical work, actively collaborating with hospitals and healthtech companies. He welcomes contributions from clinicians, researchers, and industry partners through initiatives like his AI for Health webinar series .

Florentina BuneaView profile

Professor

• Statistical machine learning theory
• High-dimensional statistical inference
• Optimal transport
• +6 more

Florentina Bunea is a Professor in the Department of Statistics and Data Science at Cornell University’s Bowers College of Computing and Information Science, and an active member of the Graduate Fields of Statistics, Applied Mathematics, and Computer Science. She also serves on the Diversity and Inclusion Council of her college, championing workforce diversity in data-science disciplines. Education & Institutional Roles Professor, Department of Statistics and Data Science, Cornell University Member, Graduate Fields of Statistics, Applied Mathematics, Computer Science Member, Diversity and Inclusion Council, Bowers College of Computing and Information Science Research Interests Professor Bunea’s research lies at the intersection of statistical machine-learning theory and high-dimensional inference. She develops rigorous methodology supported by sharp theoretical guarantees to tackle core problems in modern data science. Recent themes include: Soft-max mixtures for understanding large-language-model/AI algorithms Optimal transport for high-dimensional mixture distributions Wasserstein-distance inference for sparse mixing measures in topic models Latent-space clustering and cluster-based inference in high dimensions Network modeling and hidden-structure inference Applications spanning genetics, systems immunology, neuroscience, sociology, and economics Research Funding & Awards Her work is supported by grants from the National Science Foundation (NSF-DMS). She is a Fellow of the Institute of Mathematical Statistics and a recipient of the IMS Medallion Award. Editorial & Service Contributions Associate Editor: Annals of Statistics, Bernoulli, JASA, JRSS-B, EJS, Annals of Applied Statistics Co-Editor: Chapman & Hall/CRC Statistics and Applied Probability Monograph Series Advising & Collaboration Professor Bunea has mentored numerous doctoral and post-doctoral researchers, including Xin Bing, Shuyu Liu, Seth Strimas-Mackey, and Yang Ning, among others. Collaborative projects extend across Cornell and external institutions, producing widely-used software packages and high-impact publications. Contact Office: 1184 Comstock Hall, Cornell University Email: fb238@cornell.edu Phone: (607) 255-8449

• Data Science
• Machine Learning
• Computational Harmonic Analysis
• +6 more

Pierre Vandergheynst is a Full Professor at the Swiss Federal Institute of Technology Lausanne (EPFL) in the Department of Electrical Engineering, with a courtesy appointment in Computer and Communication Sciences. He serves as EPFL’s Vice-Provost for Education since 2015 and leads the Signal Processing Laboratory 2 (LTS2). His research spans harmonic analysis, sparse approximations, mathematical data processing, and applications in signal/image processing, computer vision, machine learning, and graph-based data analysis. PhD in Mathematical Physics (1998), Université catholique de Louvain Postdoctoral Researcher at EPFL (1998-2001) Assistant Professor at EPFL (2002-2007) His research explores geometry/symmetry in high-dimensional data, redundant dictionaries for dimensionality reduction, and computational harmonic analysis on manifolds. Recent work focuses on protein structure modeling, geometric deep learning, and graph-based signal processing. Key article trends include graph neural networks for protein analysis, geometric deep learning in neuroscience, and structured knowledge priors in neural models. His 2023-2025 publications emphasize interpretable AI, long-range dependencies in graphs, and molecular representation learning. Scientific Awards: IEEE Signal Processing Magazine Best Paper Award (2023) Signal Processing Society Best Paper Award (2022) Apple ARTS Award (2007) De Boelpaepe Prize, Royal Academy of Sciences of Belgium (2009-2010) He has supervised over 30 PhD theses and contributed to foundational work in graph signal processing, compressive sensing, and geometric deep learning. His lab develops tools for data science on non-Euclidean structures, with applications in medicine, astronomy, and wireless systems.

Martin T. WellsView profile

Professor

• Applied Statistics
• Theoretical Statistics
• Bayesian Statistics
• +7 more

Martin T. Wells is the Charles A. Alexander Professor of Statistical Sciences at Cornell University, with joint appointments in the Department of Statistical Science, Department of Biological Statistics and Computational Biology, Department of Social Statistics, and as Professor of Clinical Epidemiology and Health Services Research at Weill Medical School. He serves as Editor-in-Chief of the ASA-SIAM Book Series and Co-Editor of the Journal of Empirical Legal Studies. Cornell University, Ithaca, NY Weill Cornell Medical College Research Interests span applied and theoretical statistics, Bayesian methods, biostatistics, clinical epidemiology, and computational biology. His work bridges disciplines like finance, legal studies, and health services research. Article Trends highlight advancements in Bayesian modeling, quantum cognition machine learning, tensor analysis, and misclassification correction, with applications in genomics, finance, and public health. Fellow of the American Statistical Association Fellow of the Royal Statistical Society Contributions include developing statistical software (e.g., rTensor), methodological innovations in clinical trials, and empirical legal studies on civil rights and the death penalty.

Qianwen WangView profile

Assistant Professor

• Interactive Visualization
• Interpretable Machine Learning
• Human-AI Collaboration
• +5 more

Qianwen Wang is a tenure-track Assistant Professor in the Computer Science department at the University of Minnesota, Twin Cities. Her research combines interactive visualization with interpretable machine learning to foster intuitive, efficient, and reliable Human-AI collaboration. She actively seeks motivated students, research assistants, and interns to join her dynamic research team at UMN CS. Dr. Wang's research focuses on three primary themes: Human-AI Collaboration, where she designs tools to facilitate Human-AI interaction; Automatic & Intelligent Visualization, where she develops techniques to make visualizations accurately interpreted and easily used; and VIS+(X)AI in Biomed/Healthcare, where she studies how visualization and explainable AI can promote scientific discoveries in biomedicine and healthcare. Her work has made significant contributions to visualization, human-computer interaction, and bioinformatics, with particular applications in biomedical knowledge graphs and single-cell omics analysis. Her recent publications demonstrate a strong trend toward integrating visualization with large language models and graph neural networks for biomedical applications. She has published extensively at top venues including IEEE VIS, ACM CHI, and Nature Medicine, with a focus on making AI systems more interpretable and useful for domain experts, particularly in healthcare contexts. Her work often bridges theoretical advances in visualization with practical applications in genomics and healthcare. Two IEEE VIS Honorable Mention Awards (2022, 2024) Best Paper Award from IMLH@ICML 2021 Two Best Abstract Awards from BioVis ISMB (2021, 2022) HDSI Postdoctoral Research Fund Award Research covered by MIT News and Nature Technology Features Dr. Wang actively contributes to the academic community through service roles including General Chair for ISMB BioVis, VisNotes and Poster Chair for IEEE PacificVis, and Program Committee member for IEEE VIS, ACM CHI, and ACM IUI. Her research has been supported by various grants that enable her team to develop innovative visualization techniques and explore their practical applications in biomedical domains. Her research group maintains an active presence in the visualization and HCI communities, with members participating in major conferences and workshops. The lab focuses on creating tools that bridge the gap between complex AI models and human understanding, with particular emphasis on making these technologies accessible and useful for domain experts in biomedical research.

Laura EloView profile

Professor

• Computational Biomedicine
• Medical Bioinformatics
• Data Science
• +7 more

Laura Elo serves as Professor of Computational Medicine and Head of the Medical Bioinformatics Centre at the University of Turku, Finland. She concurrently holds the position of Research Director at Turku Bioscience Centre and acts as InFLAMES Flagship Contact, driving interdisciplinary biomedical research initiatives. Her academic foundation includes a PhD in Applied Mathematics (2007) and Adjunct Professorship in Biomathematics (2011), establishing her quantitative expertise before transitioning into biomedical applications. Her research program focuses on transforming molecular and clinical datasets through statistical modeling and advanced machine learning . Key thrusts include robust computational tools for proteome/epigenome analysis, AI-driven digital health diagnostics, and computational systems immunology for immune-mediated diseases. This work directly addresses challenges in reproducibility and scalability of high-throughput biotechnology data. Analysis of her recent publications reveals dominant themes in type 1 diabetes biomarker discovery , multi-omics integration , and immune system modeling , with strong emphasis on clinical translation through collaborations with experimental and medical teams. Her scientific recognition includes: JDRF Career Development Award Professor Elo actively trains MSc/PhD students and postdoctoral fellows while leading major research initiatives including ERC grants. Her teaching portfolio spans Bioinformatics Journal Club, AI in Diagnostics, and Systems Biology courses. The Elo Lab (https://elolab.utu.fi) operates as a hub for computational biomedicine, developing open-source tools like CellRomeR while maintaining close ties with Turku Bioscience Centre's experimental facilities for validating computational predictions in immunology and metabolic disease contexts.

• Immunology
• Genomics
• Multiomics Analysis
• +3 more

Calliope Dendrou is an Associate Professor in Clinical Pathology and Inflammation at the Kennedy Institute of Rheumatology (KIR), University of Oxford, leading the Immune Disease Multiomics Laboratory. She previously held a Wellcome & Royal Society Sir Henry Dale Fellowship at the University of Oxford’s Centre for Human Genetics before joining KIR in 2023. Her research focuses on immune disease mechanisms using multiomics approaches, including genomic profiling to identify therapeutic targets across tissues and immune-mediated diseases. She co-leads large-scale projects like the Oxford-J&J Cartography Consortium and the Chan Zuckerberg Initiative’s LEGACY Network, and teaches on the MSc in Genomic Medicine program. Educational Background: BSc (Biology, Imperial College London, 2005; Forbes Memorial Medal Winner); PhD in Infection & Immunity (University of Cambridge, 2010). Postdoctoral training at the Weatherall Institute of Molecular Medicine under Prof. Lars Fugger. Research interests include immunogenetics, cytokine signaling pathways, drug repositioning, and cross-disease pathophysiology. Her work integrates single-cell and spatial transcriptomics to dissect immune-cell interactions in diseases like rheumatoid arthritis, inflammatory bowel disease, and celiac disease. Recent articles highlight her contributions to understanding vaccine adjuvant responses, Th17 cell roles in spondyloarthritis, and immune-epithelial networks in celiac disease. Collaborations emphasize multi-omic data analysis (e.g., Panpipes pipeline) and translational studies toward precision medicine. Awards: Forbes Memorial Medal (BSc), Wellcome & Royal Society Sir Henry Dale Fellowship. Leadership roles include Equality, Diversity, and Inclusion Champion and 'Single-Cell & Spatial Omics for Precision Medicine' Module Lead. Lab & Teams: Immune Disease Multiomics Lab at KIR. Active in collaborative initiatives such as the LEGACY Network, focusing on large-scale immune profiling in ancestrally diverse populations.

Knut ReinertView profile

Professor

• Algorithmic Bioinformatics
• Genomic Sequence Analysis
• Proteomics
• +7 more

Professor Knut Reinert is a leading figure in algorithmic bioinformatics at the Free University of Berlin, where he holds a professorship in the Department of Mathematics and Computer Science. He also maintains a significant affiliation with the Max Planck Institute for Molecular Genetics in Berlin, where he leads the Efficient Algorithms for Omics Data group. His research spans both institutions through the Reinert Lab, which focuses on developing novel computational approaches for biological data analysis. Reinert's educational background includes a Diploma in Computer Science (1994) and a Doctorate (Dr. Ing./Ph.D., 1999, with honors) from the Max-Planck-Institut for Computer Science and Universität des Saarlandes in Saarbrücken. Prior to his professorship, he worked as a computer scientist under Prof. Gene Myers at Celera Genomics in Rockville, USA (1999-2002). His primary research interests center on algorithmic bioinformatics with specific focus on developing novel algorithms and data structures for biomedical mass data analysis. This includes creating mathematical models for genomic sequence analysis and algorithms for mass spectrometry data to detect differential protein expression between normal and diseased samples. His work bridges the gap between computational tool development and practical biological applications, with particular emphasis on NGS and proteomics data. The publications and projects led by Prof. Reinert demonstrate a consistent focus on advancing computational methods in bioinformatics. His research spans genomic sequence analysis, RNA research (particularly long non-coding RNAs), parallel computing applications, and GPU acceleration for biological data processing. The work shows increasing sophistication in handling large-scale biological datasets through innovative algorithmic approaches. Intel® Parallel Computing Center designation for his lab CUDA Research Center status DFG funding of 530 thousand Euros for RNA research de.NBI funding of 2 million Euros BMBF funded projects 'LIVE-DREAM' and 'EssBar' Prof. Reinert leads multiple significant research projects and has established strong collaborations with international partners including Texas A&M, Kings College London, Eberhardt-Karls Universität Tübingen, Robert-Koch-Institute, and various Turkish institutions. His lab receives funding from major organizations including DFG, BMBF, and Intel. The Reinert Lab maintains active teaching responsibilities at FU Berlin, offering courses at BSc, MSc, and PhD levels using both traditional and innovative learning concepts like e-learning and inverted classrooms. The Reinert Lab consists of two interconnected research groups that work closely with experimental biologists and medical researchers to develop practical computational solutions for real-world biological problems. The lab has established itself as a key player in the German and international bioinformatics community through its development of the widely-used SeqAn library and participation in national infrastructure initiatives.

Kathryn RoederView profile

Professor

• Statistical Genetics
• Genomics
• Biostatistics
• +5 more

Kathryn Roeder is the UPMC University Professor of Statistics and Life Sciences at Carnegie Mellon University (CMU), affiliated with the Dietrich College of Humanities and Social Sciences and the Departments of Statistics & Data Science and Computational Biology. Her research focuses on developing statistical methods for genetic and genomic data, particularly in identifying autism risk genes and analyzing single-cell multi-omic data. She earned her Ph.D. in Statistics from Penn State University and has been at CMU since 1994, previously serving as Vice Provost for Faculty (2015–2019). Education: Ph.D. in Statistics, Penn State University (1988) B.S. in Wildlife Resources, University of Idaho (1982) Research Interests: Her work integrates modern statistical techniques (high-dimensional statistics, machine learning, networks) to study complex diseases like autism and schizophrenia. Recent efforts include tools for analyzing single-cell RNA-seq and proteomic data, such as UNICORN, DAWN, and SCEPTRE. Key Awards: COPSS Distinguished Achievement Award (2020) National Academy of Sciences Member (2019) COPSS Presidents’ Award (1997) AAAS Fellow (2020) Advising & Grants: She has advised over 20 Ph.D. students, many contributing to landmark studies in autism genetics. Her grants include NIH funding for projects like the Autism Sequencing Consortium. Current research teams focus on computational biology and statistical genetics. Labs & Collaborations: Her lab develops software tools (e.g., TADA, MIND) and collaborates with the Autism Sequencing Consortium and iPSYCH-BROAD Consortium on large-scale genomic studies.

Kelly ArnoldView profile

Associate Professor

• Biomedical Computation and Modeling
• Drug Delivery and Therapeutics
• Systems Immunology
• +5 more

Kelly Arnold is an Associate Professor in the Department of Biomedical Engineering at the University of Michigan. Her research integrates systems engineering principles with immunology to investigate variability in immune responses across infection, vaccination, and injury, with a focus on computational modeling and clinical translation. Research Focus Systems-level immune response modeling Vaccination and antibody functionality Vaginal microbiome-host interactions Chronic lung disease progression Computational serology and proteomics Recent Work Her 2025 studies examine SARS-CoV-2 vaccination responses in cancer patients and computational frameworks for vaginal probiotics. Earlier works (2024-2007) span COPD progression, lupus fibrosis, HIV susceptibility, and tissue engineering for fertility preservation. Methodologies include proteomic profiling, network modeling, and microfluidic systems.

• Machine Learning
• Genomics
• Gene Regulatory Networks
• +3 more

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 ZhangView profile

Assistant Professor

• Artificial Intelligence
• Machine Learning
• Spatial Omics
• +3 more

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.

Farnoush Banaei-KashaniView profile

Associate Professor

• Data Management
• Big Data
• Decision Support Systems
• +4 more

Farnoush Banaei-Kashani is an Associate Professor (Tenured) in the Department of Computer Science and Engineering at the University of Colorado Denver. She also holds an Adjunct Associate Professor position in the Department of Mathematical and Statistical Sciences. As the founder and director of the Big Data Management and Mining Lab (BDLab), she leads multiple GAANN Fellowship Programs, including BDSE (Big Data Science and Engineering), DDC (Data-Driven Cybersecurity), and II (Infrastructure Informatics). She directs the 'Data Science in Biomedicine' MS Track and focuses on data-driven decision systems (DDSs), integrating machine learning and big data analytics into healthcare, energy, transportation, and environmental applications. Education: Details not explicitly provided in the text. Her research spans data management cycles for DDSs, addressing challenges like big data volume, velocity, and variety. Key projects include iWatch (crime surveillance), POCM (mobility monitoring), and GeoSIM (urban texture documentation). She teaches courses such as Machine Learning Systems, Big Data Science, and Data Mining. Publications highlight advancements in sea ice classification, federated learning, proteomic networks, and privacy-preserving AI. Her work is funded by NSF, NIH, DOT, and industry partners like Google and IBM. She has advised numerous students and contributes to academic leadership as editor, conference chair (ACM SIGSPATIAL 2018/2019), and program committee member for venues like SIGMOD and KDD.