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Hauke SmidtView profile

Professor

• Microbiology
• Environmental Microbiology
• Gut Microbiota
• +4 more

Hauke Smidt is a Personal Professor at Wageningen University & Research, affiliated with the Molecular Ecology group within the Faculty of Veterinary Medicine and Animal Sciences. His research focuses on microbial ecology, particularly gut microbiota dynamics, antibiotic resistance, environmental microbiology, and the One Health framework. Smidt has supervised over 50 PhD students and contributed to 519 publications, including studies on microbiome resilience, fermented food impacts, and bioremediation strategies. Education and affiliations include leadership roles in projects addressing antimicrobial resistance, pig health, and drinking water microbiology. His work spans collaborations across Europe and Asia, with notable contributions to understanding microbial community responses to environmental stressors and dietary interventions. Smidt is actively involved in public outreach, as seen in media contributions discussing microbiome research and health benefits. Key projects include aquifer treatment for drinking water, microbiome simulation models, and combating plant pathogens. His awards and recognition are not explicitly listed, but his extensive publication record and project leadership highlight significant academic impact.

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.

Alexis BattleView profile

Associate Professor

• Genomics
• Machine Learning
• Computational Biology
• +3 more

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 .

Itsik Pe'erView profile

Professor

• Human Genetics
• Computational Biology
• Genomics
• +3 more

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.

Lourdes Pena-CastilloView profile

Professor

• Bioinformatics
• Genomics
• Machine Learning
• +5 more

Dr. Lourdes Pena-Castillo is a Professor jointly appointed in the Departments of Computer Science and Biology at Memorial University of Newfoundland's Faculty of Science. Her research focuses on applying machine learning and bioinformatics to study bacterial gene regulation, with emphasis on transcriptomics, gene expression pathways, and microbiology. She leads the Bioinformatics Lab at MUN, developing computational tools like Promotech for promoter prediction and sRNARFTarget for sRNA target identification. Education: BSc in Information Systems Engineering, ITESM-Mexico MSc in Computer Science, University of Alberta PhD in Computer Science (Doktoringenieurin), Otto-von-Guericke Universität Magdeburg Postdoc in Bioinformatics, University of Toronto Research Interests: Bioinformatics, Genomics, Machine Learning, Artificial Intelligence, Transcriptomics, Gene Regulation, Microbiology Her work integrates computational methods with biological data to address challenges in molecular biology, including analyzing bacterial sRNA functions, promoter recognition, and disease diagnostics using machine learning. She has advised numerous graduate students, including PhD candidates Purvikalyan Pallegar and Bonita McCuaig, and MSc students like Ruben Chevez-Guardado and Kratika Naskulwar. Her lab focuses on translational research with applications in both basic science and clinical contexts. Publications span computational methods for bacterial gene regulation, bioinformatics tool development, and interdisciplinary projects in VR and healthcare informatics. Her research has contributed to understanding symbiotic relationships in marine organisms, inflammatory bowel disease diagnostics, and clavulanic acid production in Streptomyces. Grants & Collaborations: Works with interdisciplinary teams across computer science and biology, supported by grants enabling projects in bacterial genomics and computational tool development. Labs & Teams: Leads the Bioinformatics Lab at MUN, fostering collaborations with researchers in microbiology, computer science, and healthcare.

• Human Evolutionary Genetics
• Population Genetics
• Ancestry Analysis
• +3 more

Aylwyn Scally is a researcher at the Department of Genetics, University of Cambridge, specializing in human evolutionary genetics and ancestry. His work focuses on computational and mathematical models of genome evolution, leveraging population-scale datasets and archeogenetic evidence to explore ancient human populations and their spatial dynamics. University: University of Cambridge Department: Department of Genetics Fields of Interest: Human Evolutionary Genetics, Population Genetics, Ancestry Analysis, Paleobiology, Environmental Genomics, Genome Evolution Scally's research integrates spatial dynamics into genetic models, offering insights into demographic, social, and cultural factors in ancient populations. His methodologies have broader applications for studying other species as genomic data becomes available. Recent publications highlight his work on mutation rate analysis, historical migration patterns, and ancestral population structures. These studies often employ computational simulations and large-scale genomic datasets to address evolutionary questions. He is associated with the Cambridge NERC Doctoral Landscape Awards (CREATES) and C-CLEAR DTP, contributing to training and collaborative research in genetics and environmental genomics.

Karoline FaustView profile

Associate Professor

• Microbial community dynamics
• Microbial systems biology
• Bioinformatics
• +6 more

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 .

Deniz TasdemirView profile

Professor

• Marine Natural Products Chemistry
• Marine Ecology
• Biodiscovery
• +2 more

Prof. Dr. Deniz Tasdemir is a Full Professor (W3) of Marine Natural Products Chemistry at GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel and serves as Director of the GEOMAR-Biotech center and Head of the Marine Natural Product Chemistry Research Unit. Her career spans institutions including the National University of Ireland Galway and UCL School of Pharmacy. PhD in Pharmacy, ETH Zurich (1997) Post-doctoral work, University of Utah (2001) Dr. Helmut Legerlotz Fellowship, University of Zurich (2002-2025) Her research focuses on marine chemical ecology , metabolomics , and bioprospecting for bioactive compounds from sponges, algae, and marine microbiomes. Recent work explores seagrass pathogen reduction, microbiome interactions, and aquafeed applications. Scientific awards include: Waters Award for Natural Products Innovation (2016) Egon Stahl Silver Medal (2005) Pierre Fabre Prize (2004) ETH Zurich Medal (1997) She leads collaborative projects on ocean sustainability and marine drug discovery, with editorial roles in Marine Drugs , Planta Medica , and Phytochemistry Letters .

• Parasitology
• Molecular Biology
• Phylogenetics
• +5 more

David Blair is a Professor at James Cook University, specializing in parasitic flatworms, molecular systematics, and evolutionary biology. His research focuses on understanding the genetic diversity, phylogeography, and host-parasite interactions of species such as Schistosoma, Paragonimus, and Opisthorchis. He has contributed extensively to studies on the molecular evolution of parasitic organisms and their implications for human and wildlife health. Key research areas include: molecular taxonomy of trematodes, phylogenetic analysis of parasitic flatworms, and genomic studies of host-parasite coevolution. Collaborations span global institutions, addressing public health challenges like paragonimiasis and fasciolosis. His work integrates field studies, lab-based molecular techniques, and computational biology to unravel evolutionary dynamics and ecological adaptations. Recent studies focus on the genetic diversity of Daphnia species, dugong population genetics, and drug-resistant Mycobacterium tuberculosis. His publications in journals like *Parasitology*, *Molecular Phylogenetics and Evolution*, and *Scientific Reports* highlight interdisciplinary approaches to parasitology and conservation biology.

Lucas PaoliView profile

Researcher

• Microbiome Research
• Microbial Immunity
• Ecological Genomics
• +4 more

Lucas Paoli is a Researcher and Course Instructor at École Polytechnique Fédérale de Lausanne (EPFL), Switzerland. He leads the Paoli Lab (Microbiome Immunity and Ecology) within the Global Health Institute (GHI) under the School of Life Sciences (SV). His roles include scientific collaboration and teaching responsibilities in life sciences engineering. Paoli holds a PhD in Microbiome Research from ETH Zürich (2018-2023), an M.Phil. in Environmental Policy from the University of Cambridge (2017-2018), and an M.Sc. in Ecology and Evolution from École normale supérieure (2015-2017). Research Focus: His work bridges microbial immunity and ecology, investigating how microbes defend against viral infections across ecosystems like oceans and human microbiomes. Techniques include global-scale metagenomics and functional genomics to study immune strategies and ecological interactions. Key themes involve microbial community dynamics, viral defense mechanisms, and the impact of environmental factors on microbial immunity. Lab & Education: The Paoli Lab explores microbiome-immunity interactions with a focus on ecological contexts. Paoli supervises PhD students in Life Sciences Engineering. His research outputs span microbial ecology, metagenomic tool development, and marine microbiome studies. Contact: lucas.paoli@epfl.ch, AAB 1 39, +41 21 693 16 99.

Heng JiView profile

Professor

• Natural Language Processing
• Data Mining
• Social Science
• +2 more

Heng Ji is a Professor at the Siebel School of Computing and Data Science , affiliated with the Department of Computer Science , Electrical and Computer Engineering Department , and multiple research labs including the Coordinated Science Laboratory and Carl R. Woese Institute for Genomic Biology at the University of Illinois Urbana-Champaign. She serves as an Amazon Scholar and Founding Director of the Amazon-Illinois Center on AI for Interactive Conversational Experiences (AICE) and CapitalOne-Illinois Center on AI Safety and Knowledge Systems (ASKS) . B.A. and M.A. in Computational Linguistics from Tsinghua University M.S. and Ph.D. in Computer Science from New York University Her research bridges Natural Language Processing with Vision-Language Models , Knowledge-Enhanced LLMs , and AI for Science (e.g., chemical language modeling). She leads major multi-institutional projects such as DARPA ECOLE MIRACLE , KAIROS RESIN , and DEFT Tinker Bell , while advising governments (U.S. Air Force Data Analytics Expert Panel) and industry (Amazon, Google, IBM). Her work on multimodal reasoning, agent-based systems, and chemical language models (e.g., mCLM ) has been supported by NSF, DARPA, and corporate partners. Recent publications (2025) focus on LLM agents , vision-language integration , and scientific knowledge acquisition . Awards include NSF CAREER , IEEE Intelligent Systems' AI's 10 to Watch , and multiple Outstanding Paper Awards at ACL/NAACL. She advises students like Chi Han (ACL/NAACL awardee) and post-docs Xiusi Chen and Yuji Zhang , and leads the BLENDER Lab , which develops frameworks like WiNELL (Wikipedia updating) and ProteinZero (protein generation). She has also served as NAACL Secretary and Program Co-Chair for ACL-IJCNLP2022. Outstanding Paper Award at ACL2024 Two Outstanding Paper Awards at NAACL2024 Young Scientist by World Laureates Association (2023-2024) AI's 10 to Watch by IEEE (2013) NSF CAREER (2009) Google/IBM/Bosch Research Awards

Colin SempleView profile

Professor

• Cancer genomics
• Structural mutations
• Molecular evolution
• +5 more

Professor Colin Semple is a leading researcher at the University of Edinburgh's Institute of Genetics and Cancer (IGC), where he serves as Group Leader and Head of Bioinformatics. His work is conducted within the MRC Human Genetics Unit, focusing on computational genomics and the analysis of structural mutations in both germline and cancer contexts. Professor Semple's research investigates the origins and impacts of structural mutations in the human genome, with particular emphasis on how these alterations affect gene function in developmental contexts and drive cancer progression. His group studies complex structural rearrangements in challenging cancer types including ovarian cancer, glioblastoma, and mesothelioma, where tumor genomes undergo dramatic reorganization. The research is guided by four key questions: What are the origins of structural mutations? How do they impact gene function? How does structural complexity drive disease progression? How do diverse mutational constellations combine to create adaptations and vulnerabilities? Analysis of Professor Semple's publications reveals a consistent focus on structural variation in cancer genomics, with particular attention to ovarian cancer mechanisms, lesion segregation in tumor evolution, and the functional consequences of genomic rearrangements. His work frequently employs whole genome sequencing approaches to uncover previously hidden layers of genomic variation that affect more of the genome than traditional short variants. Professor Semple leads a substantial research team including bioinformaticians and PhD students, and oversees the Bioinformatics Analysis Core which provides collaborative expertise to over 500 researchers at the IGC. His group maintains strong collaborations with both local researchers at the University of Edinburgh and international consortia, working closely with clinicians to translate genomic findings into potential diagnostic and therapeutic approaches. The Semple Lab is funded by major organizations including the Medical Research Council (MRC), Cancer Research UK (CRUK), and the Chief Scientist Office (CSO).

• Statistical Genomics
• Computational Immunology
• Human Genetics
• +2 more

Yang Luo is a Kennedy Trust Senior Research Fellow in Data Science at the University of Oxford's Kennedy Institute of Rheumatology. His research bridges statistical genomics and computational immunology to unravel genetic contributions to immune-mediated traits, with a focus on the major histocompatibility complex (MHC) region. His work leverages large biobank datasets (UK Biobank, Biobank Japan), gene expression resources (GTEx), and proteomic data to decode molecular mechanisms linking genetic variation to disease risk. Specific interests include tuberculosis genetics, multi-ancestry polygenic risk scores, and single-cell eQTL modeling. Recent publications highlight expertise in HLA association studies, evolutionary immunogenetics, and disease-specific cell state dynamics. Key contributions include constructing a global HLA haplotype panel and developing novel statistical methods for admixed population genetics. Scientific Awards: Kennedy Trust Senior Research Fellow in Data Science His lab integrates computational and experimental approaches to translate genetic findings into clinical applications for immune disorders.

Matloob KhushiView profile

Senior Lecturer

• Artificial Intelligence
• Machine Learning
• Natural Language Processing
• +7 more

Dr. Matloob Khushi serves as a Senior Lecturer in Computer Science at Brunel University London's College of Engineering, Design and Physical Sciences. With over 25 years of combined academic and industry experience, his work bridges theoretical AI advancements with practical applications in finance, healthcare, and public health domains. His research has established significant collaborations with international banks, healthcare institutions, and technology startups. Dr. Khushi earned his PhD in AI and Data Science from the University of Sydney, developing novel algorithms for genomic data analysis. His postdoctoral research at the Children's Medical Research Institute (2014-2017) pioneered AI-based diagnostic tools for medical condition detection. More recently, he developed bioinformatics tools for environmental assessment under a UKRI NEC grant. Research Focus FinTech Innovation : Creator of the SS Ratio (incorporating volatility and drawdown sensitivities), advanced portfolio optimization models, and synthetic data generation techniques for fraud detection and credit risk assessment Bioinformatics Leadership : Developer of AI tools for genomic analysis and early cancer detection, featured in SBS News and The Daily Telegraph Public Health NLP : Architect of systems for vaccine misinformation detection, mental health monitoring, and health surveillance on social media His publication portfolio shows consistent growth from foundational bioinformatics work to current multimodal AI applications, with increasing interdisciplinary collaboration across finance and healthcare sectors. Awards and Recognition Ranked among Stanford/Elsevier's top 2% of global AI scientists Recipient of Best Paper Awards from IEEE Transactions on Computational Social Systems and PeerJ Media recognition for cancer detection research by major news outlets Mentorship and Teaching Dr. Khushi has supervised six PhD candidates to completion and over 100 postgraduate dissertations. He teaches CS3002 Artificial Intelligence and mentors students in Final Year Projects. His supervision focuses on Deep Learning/NLP for FinTech prediction and Public Health Surveillance applications, emphasizing practical implementation of theoretical concepts.

• Microbiomics
• Genomics
• Complex Diseases
• +4 more

Elin Org is a Professor of Microbiomics at the University of Tartu's Institute of Genomics, where she also serves as Head of the Estonian Genome Centre and Vice Director of the Institute. Her academic career spans over two decades with significant contributions to microbiome and genomic research. Education: PhD in Genetics, University of Tartu (2006) Master's Degree in Molecular Biotechnology and Biomedicine, University of Tartu (2000) Bachelor's Degree, University of Tartu (1997) Classical Singing, Heino Eller Tartu Music School (1996) Professor Org's research primarily focuses on the intricate relationships between host and gut microbiota and their influence on metabolism and common complex diseases. Her work bridges microbiomics, genomics, and complex disease research, with particular emphasis on understanding how gut microbiome composition affects human health. She has pioneered research connecting long-term antibiotic usage with microbiota-dependent effects and has made significant contributions to understanding the role of gut microbiome in conditions such as gestational diabetes, endometriosis, and polycystic ovary syndrome. Her approach integrates advanced computational methods with comprehensive health data to uncover causal relationships in microbiome research. Her recent publications demonstrate a strong trend toward integrating microbiome data with extensive digital health metrics, using machine learning approaches to identify microbial predictors of health outcomes. This work is increasingly focused on translating microbiome research into clinical applications for disease prediction and personalized medicine approaches, particularly in the context of the Estonian Biobank initiative. Major Scientific Recognition: 2025 National Science Award in medical and health sciences 2023 and 2022: Recognized among the world's top 1% most cited researchers by Clarivate Analytics 2020: Member of AcademiaNet, a portal for top female researchers 2017: EMBO Installation grant 2013: Marie Curie International Outgoing Fellowship Professor Org has secured substantial research funding as principal investigator for multiple significant projects, including 'DISCERN - Discovering the causes of three poorly understood cancers in Europe' (€245,466, European Commission) and 'Improving colorectal cancer screening and prediction using microbiome-based biomarkers' (€760,450, Estonian Research Council). She has served as an opponent for numerous PhD theses across European institutions, contributing to the development of emerging researchers in her field. As Head of the Estonian Genome Centre, Professor Org leads a multidisciplinary research team that plays a crucial role in Estonia's transition from biobanking to personalized medicine applications. She is actively involved in international collaborations through COST networks including INFOGUT (focused on in vitro colon models) and ML4Microbiome (statistical and machine learning techniques in human microbiome studies), positioning her at the forefront of global microbiome research initiatives.