Karoline Faust is an Associate Professor at KU Leuven, affiliated with the Laboratory of Molecular Bacteriology (Rega Institute) and the Faculty of Medicine . She contributes to the iSi Health and Leuven One Health institutes, and serves on senior academic councils. Her research spans microbial systems biology, focusing on community dynamics and network analysis. Education: PhD in bioinformatics (2010, KU Leuven) Affiliations: KU Leuven, ISME Journal editorial board, Belgian Society for Microbiology Her research investigates microbial community dynamics , systems biology approaches to microbiomes, and bioinformatics tool development . She specializes in modeling human gut microbiota , synthetic microbial communities , and environmental microbiomes (e.g., microplastic impacts on Daphnia microbiomes). Her work integrates metabolic modeling , network analysis , and experimental systems to understand microbial interactions. Recent publications highlight her contributions to microbial network inference , 16S rRNA sequencing protocols , microfluidics , and ecological modeling of microbiomes. She develops tools like manta , miaSim , and CoNet to analyze community structures. Teaching: Karoline co-teaches courses in microbiology, bioinformatics, and network analysis at KU Leuven, and has contributed to international workshops on microbial network inference. Scientific Engagement: She serves as Senior Editor at ISME Journal and Secretary of the Belgian Society for Microbiology .
Dr. Aaron Logan is a Clinical Associate Professor of Medicine at the University of California, San Francisco (UCSF). He specializes in the clinical management of acute leukemias, myelodysplastic syndromes, aplastic anemia, and hemophagocytic lymphohistiocytosis. Additionally, he directs a research laboratory focused on immune repertoire profiling following hematopoietic cell transplantation. MD and PhD in Molecular Microbiology and Immunology from Keck School of Medicine (2006) MPhil in History of Medicine from University of Cambridge (2005) Internal Medicine Residency and Hematology Fellowship at Stanford University Dr. Logan's research explores clonotypic diversity in B and T lymphocyte repertoires, utilizing techniques like TREC/KREC quantification, high-throughput sequencing, and mixed lymphocyte reactions. His work has significant applications in tracking immune responses post-transplantation and quantifying measurable residual disease in lymphoid cancers. Notable scientific contributions include advancements in CAR T-cell therapy and immune profiling for blood malignancies. His publications cover topics in B-cell ALL , AML , and measurable residual disease monitoring. 2020 - UCSF Hematology-Oncology Fellowship Teaching Award 2011 - ASH Abstract Award and Research Training Award 2003 - Keck School of Medicine Outstanding Teaching Award As director of the UCSF Hematologic Malignancies Tissue Bank, Dr. Logan provides deidentified patient samples to support collaborative research on blood cancers and post-transplantation immune dynamics.
Jered Haun is an Associate Professor at the Samueli School of Engineering , University of California, Irvine , with joint appointments in Biomedical Engineering , Chemical and Biomolecular Engineering , and Materials Science and Engineering . Based in 3107 Natural Sciences II , his research focuses on developing nanoengineering and molecular medicine technologies to improve disease diagnosis and treatment. Email: jered.haun@uci.edu Phone: (949) 824-1243 Research Interests include: Nanomaterial Probes for molecular profiling and disease detection Microfabricated Platforms for cell analysis and tissue processing Targeted Delivery Carriers that interact with unique disease molecules Technologies employed in his lab encompass: Fluorescence imaging and MRI enhancements Bioorthogonal chemistry and nanosensor development Micro-NMR for tumor analysis Quantum dot-based detection systems Awards include: NIH National Cancer Institute's Innovative Molecular Analysis Technologies Funding The Haun Laboratory actively recruits graduate and undergraduate students for projects related to nanoengineering, molecular medicine, and microfluidic device development.
Konstantinos Anastassiadis is a Professor at the Center for Molecular and Cellular Bioengineering (CMCB) of Dresden University of Technology , leading the Stem Cell Engineering group at the Biotechnology Center (BIOTEC) . His research focuses on unraveling molecular pathways regulating stem cell self-renewal and lineage commitment, with a strong emphasis on genetic engineering tool development and epigenetic mechanisms during cellular reprogramming. The lab utilizes mouse and human embryonic stem cells, neural stem cells, mesenchymal stromal cells, and induced pluripotent stem cells (iPSCs) in their investigations. Core Research Areas: Molecular regulation of stem cell fate Epigenetic mechanisms (e.g., UTX/UTY histone demethylases) Genetic engineering tool development (Flp, Dre, Vika recombinases, CRISPR protocols) Conditional immortalization systems for rare cell expansion Publications highlight his contributions to understanding: Role of histone methyltransferases (MLL1, MLL2, Setd1b) in hematopoiesis and cancer Epigenetic regulation during mouse development and spermatogenesis Genetic tools for protein tagging, transposon-mediated BAC transgenesis Interactions between stem cells and niche microenvironments Transcriptional and mechanical markers during reprogramming Collaborations span immunology , developmental biology , and bioinformatics . The lab actively participates in teaching activities at CMCB and maintains a focus on translational applications of stem cell research.
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 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.
Sunitha Nagrath is a Professor of Chemical Engineering at the University of Michigan, leading the Nagrath Lab. Her research focuses on developing microfluidic and nanotechnology-based tools to isolate and analyze circulating tumor cells (CTCs) and extracellular vesicles (EVs) for cancer diagnostics and personalized medicine. She holds an AIMBE Fellowship and has pioneered technologies like the Graphene Oxide Chip and Microfluidic Labyrinth. Education PhD in Mechanical Engineering, Rensselaer Polytechnic Institute (2004) MS in Nuclear Engineering, Rensselaer Polytechnic Institute (2000) B.Tech in Chemical Engineering, Sri Venkateswara University (1992) Research Interests Her lab integrates engineering, biology, and clinical expertise to study CTCs' role in metastasis, develop high-throughput isolation methods, and leverage exosomes as liquid biopsy biomarkers. Key projects include: CTC-based monitoring of therapy response in lung and pancreatic cancers Microfluidic devices for simultaneous CTC and exosome analysis Functional studies of CTC-derived organoids for drug sensitivity testing Notable Achievements AIMBE Fellow (Junior Faculty, Harvard Medical School/MGH, 2008-2010) Over 150 peer-reviewed publications and patents on CTC/exosome technologies Recipient of the 2021-22 Chemical Engineering Staff Incentive Award (via lab member Mina Zeinali) Labs & Collaborations The Nagrath Lab collaborates with clinicians and engineers to translate technologies like the OncoBean Chip and EVOD chip into clinical settings. Current work emphasizes real-time CTC monitoring and exosome-based immuno-oncology strategies.
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.
Kenneth Hoehn is an Assistant Professor in the Department of Biomedical Data Science at the Geisel School of Medicine, Dartmouth College. As a computational immunologist with expertise in evolutionary biology, he develops computational evolutionary approaches to trace cellular lineages, particularly B cells, in contexts such as infection, vaccination, cancer, and autoimmune diseases. His research focuses on understanding adaptive immunity in conditions like COVID-19 Food allergies Myasthenia gravis through collaborations with experimental teams. Key projects include: Phylogenetic modeling of B cell responses Evolutionary signatures in immune repertoires Tracking B cell dissemination in autoimmune diseases Epigenetic regulation of memory B cells Recent publications highlight trends in single-cell immunology , phylogenetic inference , and computational tools for analyzing B cell dynamics. His lab at Dartmouth integrates evolutionary genetics with high-resolution immune profiling.
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.
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 .
Xiaoyu Cai is an Assistant Professor at the Department of Medicine, Loyola University Chicago, specializing in lung regeneration, aging biology, and stem cell plasticity. Her research focuses on the molecular mechanisms governing alveolar type 2 (AT2) stem cell dynamics during aging and chronic lung diseases. Education: Bachelor of Medicine (Peking University, 2012), Master of Science (Peking University, 2015), PhD in Biology of Aging (USC & Buck Institute, 2021) Key Research Areas: Lung regeneration, inflammation resolution, stem cell aging, 3D organoid cultures Methodologies: Single-cell multiome, mouse genetics, multicellular organoid systems Collaborations: Translational partnerships with clinical teams for bench-to-bedside applications Dr. Cai's recent work explores lineage plasticity in aged lung stem cells, ferroptosis suppression via CRISPR screens, and cellular aging atlases across species. She previously held a postdoctoral position at Genentech Inc. and maintains a professional lab website. Contact: xcai2@luc.edu | Office: CTRE 123
Dana Pe'er is a Professor and Chair of the Computational and Systems Biology Program at the Sloan Kettering Institute (SKI) of Memorial Sloan Kettering Cancer Center. She is also an Investigator of the Howard Hughes Medical Institute and holds the Alan and Sandra Gerry Endowed Chair. Dr. Pe'er leads an interdisciplinary research group that combines advanced genomics approaches with machine learning to address fundamental questions in biomedical science, with particular focus on cancer biology, developmental biology, and immunology. Dr. Pe'er earned her PhD from Hebrew University in Jerusalem, Israel. Her academic journey includes a postdoctoral fellowship with George Church at Harvard Medical School. Before joining Memorial Sloan Kettering Cancer Center in 2016, she held faculty positions at Columbia University. Dr. Pe'er's research focuses on understanding cellular plasticity, the consequences of intra-tumor heterogeneity, cancer evolution and metastasis, and the mechanisms by which regulatory circuits go awry in disease. Her lab combines single-cell and spatial profiling technologies with machine learning approaches to investigate gene regulation, cellular plasticity, and cell-cell communication in the contexts of cancer, immunity, and development. They are particularly interested in how organisms develop from a single cell to generate diverse cell types, how epigenetic control rewires during development, and how cells communicate to execute multicellular responses. Analysis of Dr. Pe'er's recent publications reveals a strong focus on developing computational methods for single-cell and spatial genomics data analysis. Her work spans cancer types including pancreatic, prostate, colorectal, and breast cancer, with emphasis on tumor heterogeneity, metastasis mechanisms, and cellular plasticity. A significant portion of her research involves creating novel algorithms and tools like CellRank, REUNION, and SEACells that enable researchers to extract meaningful biological insights from complex genomic datasets. 2023 Class of 2023 Inductee - American Academy of Cancer Research (AACR) Academy 2023 Innovator Award - International Society for Computational Biology (ISCB) 2021 Fellow - International Society for Computational Biology (ISCB) Howard Hughes Medical Institute Investigator (2021) 2019 Ernst W. Bertner Memorial Award - University of Texas MD Anderson Cancer Center 2016 Lenfest Distinguished Faculty Award - Columbia University 2014 Director's Pioneer Award - National Institutes of Health 2014 Overton Prize - International Society for Computational Biology (ISCB) Dr. Pe'er is known for her dedicated mentorship approach, describing herself as "a mama bear" who cares deeply about her trainees while expecting independence, innovation, and hard work. She mentors numerous PhD students and postdocs in her lab. Her HHMI Investigator award provides approximately $9 million over seven years, enabling ambitious research directions. She also collaborates extensively with the Single-cell Analytics and Innovation Lab (SAIL) at MSK to generate new data from emerging technologies, working closely with wet-lab collaborators at MSK and beyond to apply computational methods to cutting-edge datasets across multiple disease areas. The Pe'er Lab is an interdisciplinary group of computational biologists with diverse backgrounds ranging from pure mathematics to clinical medicine. They work closely with wet-lab collaborators to apply their computational methods to cutting-edge datasets across cancer, immunology, and developmental biology. The lab is described as open, supportive, collaborative, and fun, with access to world-class facilities at the Sloan Kettering Institute. Dr. Pe'er's work continues to push the boundaries of computational biology and cancer research, with the ultimate goal of developing more effective, personalized therapies for cancer patients.
David Serre is a Professor in the Department of Microbiology and Immunology at the University of Maryland School of Medicine, with an additional appointment at the Institute for Genome Sciences. His research focuses on developing genomic approaches to study eukaryotic pathogens, particularly Plasmodium vivax, the leading cause of malaria outside Africa. His laboratory investigates parasite responses to antimalarial drugs, host immune responses, and mosquito vector biology using genomic and transcriptomic techniques. Education 1997–2000: Engineering degree in Chemistry, École Nationale Supérieure de Chimie, Montpellier, France 2000–2004: PhD in Biology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 2004–2007: Postdoctoral fellowship, McGill University and Genome Quebec Innovation Centre, Montreal, Canada Research Focus Dr. Serre’s work integrates genomics to study Plasmodium vivax’s drug resistance, relapse mechanisms, and interactions with hosts and vectors. Key areas include: Genomic assays to characterize parasite drug responses Transcriptomic analysis of host immune responses Genomic studies of Anopheles mosquitoes as malaria vectors Recent Trends in Publications Recent work highlights genomic and transcriptomic approaches to dissect Plasmodium vivax biology, including: Single-cell RNA sequencing to resolve transcript isoforms and stage-specific expression Analysis of relapse dynamics and drug resistance mechanisms Microbiome studies in mosquitoes and environmental contexts Grants & Advising No explicit grants or advisee names are listed in the provided text. Collaborators include institutions like the Max Planck Institute, McGill University, and the Institute for Genome Sciences. Labs & Teams His lab is affiliated with the University of Maryland School of Medicine and the Institute for Genome Sciences, focusing on genomic and molecular approaches to infectious diseases.
Lisa Westerberg is a Professor of Experimental Immunology at the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet. Her research focuses on understanding how compromised immune systems lead to immunodeficiency, autoimmunity, and hematological cancers, particularly studying the role of actin regulators in immune cell function. She leads the 'Immunodeficiency Diseases – Lisa Westerberg Group' and collaborates internationally with institutions like Harvard Medical School and the University College London. Education: PhD in Cell and Molecular Biology from Karolinska Institutet (2003), postdoc at Harvard Medical School (2009). Affiliations: Department of Microbiology, Tumor and Cell Biology; WASPSTINGS network (STINT-funded); Swedish Society for Immunology (Treasurer). Research Interests: Immunodeficiency diseases, actin cytoskeleton dynamics in immune cells, cancer immunology, and space immunology. Her lab investigates how genetic mutations in actin regulators affect immune cell communication, migration, and genomic stability. Recent projects include studying immune system adaptation in microgravity and developing therapies targeting actin regulators in cancer. Articles Trends: Recent work highlights immune cell adaptations in space environments, therapeutic modulation of actin pathways, and clonal evolution in lymphomas. Over 15 articles since 2020 explore mechanisms linking immune dysfunction to cancer and immunodeficiency. Awards: Ragnar Söderberg Fellowship, ERC Starting Grant (2019), Wallenberg Academy Fellow. Funding: Swedish Research Council, Knut och Alice Wallenberg Foundation, EU grants. Advising & Grants: Supervised over 40 students (PhD, Master’s, undergrad) since 2010. Active in training programs like the Amgen Scholars initiative. Collaborates with global teams on projects funded by VR, NIH, and international partnerships. Labs/Teams: Leads the core Immunodeficiency Diseases Group and collaborates with the Dosenovic Lab (focusing on B cell vaccine development). The group uses CRISPR, high-resolution microscopy, and single-cell sequencing to study immune mechanisms.
.png)