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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 .

• Genomics
• Malaria Research
• Parasitology
• +3 more

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.

Peter A. JonesView profile

Professor

• Epigenetics
• DNA methylation
• Cancer epigenetics
• +7 more

Peter A. Jones is President and Chief Scientific Officer at the Van Andel Institute (VAI) in Grand Rapids, Michigan, where he leads the Department of Epigenetics. He previously served as Director of the USC Norris Comprehensive Cancer Center from 1993 to 2011 and has been a central figure in advancing epigenetics research, particularly in cancer. His laboratory investigates DNA methylation, chromatin dynamics, and epigenetic therapies. Research Interests: Dr. Jones's work centers on epigenetic mechanisms in cancer, including DNA methylation, histone modifications, nucleosome positioning, and the therapeutic potential of epigenetic drugs. His research has pioneered the use of DNA methylation inhibitors like 5-azacytidine and explored viral mimicry as a mechanism for immune activation in cancer. He also studies transposable elements and their role in gene regulation and immune response. Publication Trends: His recent publications (2021–2024) reveal a strong focus on the interplay between epigenetics and immunotherapy, particularly how DNA methyltransferase inhibitors (DNMTi) induce viral mimicry, enhance immune recognition, and improve responses to checkpoint blockade. Studies span hematological malignancies, solid tumors, and T cell biology, with frequent collaboration with Stephen Baylin and others. Scientific Awards: Member, National Academy of Sciences Member, National Academy of Medicine Fellow, AACR Academy Fellow, AAAS Fellow, American Academy of Arts and Sciences Kirk A. Landon Award for Basic Cancer Research (2009) Medal of Honor, American Cancer Society (2011) Outstanding Investigator Grant, NCI Harvey Prize (2024) Advising and Grants: Dr. Jones mentors multiple postdoctoral fellows, graduate students, and research scientists. His lab is supported by major grants, including the VAI-SU2C Epigenetics Dream Team, which has launched 15 clinical trials. He has received sustained funding from the National Cancer Institute and collaborates with institutions worldwide to advance epigenetic therapies. Labs and Teams: He leads the Peter Jones Laboratory at VAI, a multidisciplinary team investigating epigenetic regulation in cancer. The lab includes computational biologists, clinical researchers, and molecular biologists, working on both basic mechanisms and translational applications. The team is part of larger collaborative initiatives such as the VAI-SU2C Epigenetics Dream Team and the International Linked Clinical Trials Program.

• 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.

Montserrat AngueraView profile

Associate Professor

• Epigenetics
• X-Chromosome Inactivation
• Long Noncoding RNAs
• +6 more

Montserrat Anguera, Ph.D. is an Associate Professor in the Department of Biomedical Sciences at the University of Pennsylvania's School of Veterinary Medicine. Her research focuses on epigenetic mechanisms of gene regulation underlying sex differences in development and disease, with particular emphasis on X-chromosome inactivation (XCI) and its implications for female-biased autoimmune disorders. Dr. Anguera investigates how gene expression from the X-chromosome is regulated to ensure dosage compensation between males and females, and how these mechanisms become altered in diseases exhibiting sex-bias. Her laboratory has established novel epigenetic pathways involving the X-chromosome that impact human development, immune responses, and lymphocyte function. She employs advanced techniques including RNA/DNA fluorescence in situ hybridization, immunofluorescence, and allele-specific RNA sequencing to achieve single-cell resolution of epigenetic characteristics of the inactive X chromosome. Her research reveals a consistent focus on the intersection of X-chromosome biology and immunology, particularly regarding sex-biased autoimmune diseases like systemic lupus erythematosus. Key findings include the discovery that lymphocytes maintain X-chromosome inactivation differently than other somatic cells, with the inactive X exhibiting euchromatic features in female lymphocytes that may underlie female bias in autoimmune disorders. She coined the term 'dynamic XCI maintenance' to describe how T and B cells relocalize Xist RNA and heterochromatic marks to the inactive X chromosome following antigen-mediated stimulation. Dr. Anguera's laboratory includes postdocs Katherine Forsyth and Nikhil Jiwrajka, research specialist Zowie Searcy, graduate students Isabel Sierra and Natalie Toothacre, postdoctoral researcher Nuriban Valero-Pacheco, and PhD student Emma Welter. Together, they investigate epigenetic regulation of X-linked genes in development and disease contexts. She is an active member of multiple prestigious research institutes at Penn, including the Epigenetics Institute, Institute for Immunology, Center for Research on Reproduction & Women's Health, and Institute for Regenerative Medicine. Her work bridges epigenetics, immunology, and developmental biology, providing novel insights into mechanisms underlying female-biased autoimmune disorders.

Maria ChikinaView profile

Assistant Professor

• Computational Biology
• Genomics
• Machine Learning
• +7 more

Maria Chikina is an Assistant Professor at the University of Pittsburgh School of Medicine's Department of Computational and Systems Biology. She holds a PhD in Molecular Biology from Princeton University. Her research focuses on developing computational methods to analyze large-scale genomic datasets, bridging statistical rigor with biological insights to overcome experimental biases. Key research areas include latent variable modeling (e.g., PLIER, CellCODE), interpretable neural networks for sequence-to-function modeling, evolutionary rate analysis (RERconverge), and applications in tumor immunology, exercise genomics, and infectious disease (e.g., SARS-CoV-2). Her lab has developed tools like InstaPrism, NIFA, and L0 segmentation for data-driven biological discovery. Her work spans collaborations with institutions like UPMC (on tumor microenvironment) and the Molecular Transducers of Physical Activity Consortium (MoTraPAC). Notable projects include analyzing convergent evolution in marine mammals and subterranean species, and developing epigenetic biomarkers for disease states through the ECHO program. Lab members include PhD students (Rezwan Hosseini, Tugrul Balci) and postdocs (Tina Subic, Anish Sevekari). Past students Wynn Meyer now leads a group at Lehigh University. Her group emphasizes open-source tools (GitHub repository ChikinaLab) and interdisciplinary approaches to systems biology challenges.

• Genomic Medicine
• Translational Medicine
• Immunogenetics
• +4 more

Julian Knight is a Professor of Genomic Medicine at the University of Oxford, with affiliations including the Centre for Human Genetics , Merton College , and leadership roles in the NIHR Oxford Biomedical Research Centre and Central and South NHS Genomic Medicine Service . His work bridges clinical practice and research, focusing on translational genomics. Principal Investigator Deputy Director, Centre for Human Genetics Honorary Consultant Physician Tutor and Fellow, Merton College Director, Medical Sciences Division Graduate School Genomic Medicine Theme Lead, NIHR Oxford BRC Research interests include mechanisms of dysregulated immune responses in sepsis , autoimmune disease , and infection . Key contributions involve RNA signature stratification for sepsis outcomes and HLA allele associations in COVID-19 immunogenicity. Current work explores genetic/epigenetic modulators of innate immunity and causal relationships in multi-omic datasets. Recent publications highlight diverse applications of his group’s work: from pleural infection endotyping (2025) to TLR7 variants in severe COVID-19 (2024), with methodological advancements in single-cell demultiplexing (2024) and pathway analysis (2025). Keywords span genomic medicine , immunology , and multi-omic integration . Knight’s leadership extends to clinical implementation of genomics, education (DPhil/MSc programs), and public engagement. Collaborations span institutions including Imperial College , Wellcome Sanger Institute , and Queen Mary University of London .

Guanghao QiView profile

Assistant Professor

• Statistical Genetics
• Genomics
• Single-cell RNA Sequencing Analysis
• +3 more

Guanghao Qi is an Assistant Professor in the Department of Biostatistics at the University of Washington. His research focuses on developing statistical and machine learning methods for multi-omics approaches in genetic studies, particularly integrating single-cell RNA-seq, GWAS, and functional genomic data. Key areas include single-cell eQTL analysis, Mendelian randomization, and multi-trait genetic association analyses. Education: PhD in Biostatistics from Johns Hopkins Bloomberg School of Public Health (2020), BS in Mathematics from Fudan University (2015). Research interests emphasize high-dimensional data analysis, allele-specific expression in single cells, and causal inference using genetic variants. Notable achievements include a 2025 NIH K01 award for developing methods to integrate single-cell eQTL and GWAS data, and the development of the TWiST method for single-cell transcriptome-wide association studies. Recent work highlights advancements in computational tools like SURGE for context-specific genetic regulation analysis, and evaluations of Mendelian randomization methods in studies of type 2 diabetes and cardiovascular disease. His work often bridges computational biology and statistical theory to address challenges in interpreting large-scale genomic datasets. Awards: NIH K01 Award (2025) Key Contributions: TWiST method (2025), SURGE framework (2024), HIPO power optimization (2018) Labs/Teams: Active collaborations in genomic epidemiology and statistical genetics, with a focus on single-cell multi-omics integration and causal inference methodologies.

• Plant Biochemistry
• Specialized Metabolism
• Solanaceae Family
• +4 more

Cornelius Barry is an Associate Professor in the Department of Horticulture at Michigan State University, with affiliations to the Plant Breeding, Genetics and Biotechnology program, AgBioResearch, and the Molecular Plant Sciences Graduate Program. He joined MSU in July 2007 with a 75% research and 25% teaching appointment. Education: PhD and BSc from the University of Nottingham and University College of Wales Current roles: Director of NSF REU Site: Plant Genomics @ MSU His research focuses on the evolution of biochemical diversity within the Solanaceae family , particularly specialized metabolites like terpenoids, flavonoids, and alkaloids. He investigates their roles in plant defense, pollinator attraction, and human applications through genomics, metabolite profiling, and synthetic biology. Recent publications show expertise in alkaloid biosynthesis , trichome chemistry , and metabolic pathway engineering . Key collaborations include teams at Boyce Thompson Institute, Texas A&M, and University of Nottingham. He advises graduate students in Genetics , Biochemistry & Molecular Biology , and Molecular Plant Sciences programs.

Zhandong LiuView profile

Associate Professor

• Bioinformatics
• Big Data analysis
• Machine Learning
• +5 more

Zhandong Liu is an Associate Professor at Baylor College of Medicine with joint appointments in the Department of Pediatrics and Department of Neurology . He serves as Chief of Computational Sciences at Texas Children's Hospital and co-directs the Quantitative & Computational Biosciences Graduate Program at Baylor. Education: B.S. in Computer Science, Nankai University (2001) M.S. in Computer Science, Wayne State University (2003) Ph.D. in Genomics and Computational Biology, University of Pennsylvania (2010) Dr. Liu's research integrates genomics , machine learning , and bioinformatics to advance understanding of neurological diseases. His work focuses on: Multi-omics data integration for disease mechanism discovery Development of cloud-based CRISPR analysis tools like CRISPRcloud Augmented reality platforms for biomedical data visualization Identification of disease genes through computational models Alternative splicing analysis in cancer and neurodegeneration Single-cell and spatial transcriptomics algorithms His recent publications emphasize Alzheimer's disease , MECP2 syndromes , and computational therapy prediction across multiple domains. Scientific awards include the 2018 Outstanding Service Award from the International Association for Intelligent Biology and Medicine. He has secured major grants from NIH, CPRIT, and NSF for projects including: NSF grant #199977 (2018-2020): Augmented reality therapy platforms CPRIT grant #RP170387 (2016-2019): Network-guided cancer analysis NIH #1R01AG057339 (2017-2022): Alzheimer's disease networks As head of the Liu Lab , he leads teams developing tools like: MARRVEL : Human-model organism gene variant integration CRISPRcloud : Secure CRISPR screen analysis platform CrypSplice : Cryptic splicing detection algorithm

Donna HarrisView profile

Assistant Professor

• Plant Breeding
• Genetics
• Crop Science
• +3 more

Dr. Donna Harris is an Assistant Professor in the Department of Plant Sciences at the University of Wyoming, based at the Sheridan Research & Extension Center. Her academic career includes roles as Senior Scientist at BASF Vegetable Seeds (2015–2020), Research Professional III at the University of Georgia (2007–2015), and prior industry experience with Monsanto and Pioneer Hi-Bred International. She holds a PhD (2014) and MS (2001) in Crop Science from the University of Georgia, alongside a BS (1998) in the same field. Her research focuses on plant breeding and genetics, addressing crop needs for Wyoming producers and consumers. Key areas include soybean rust resistance, quantitative trait loci (QTL) analysis, and germplasm evaluation for disease resistance. She has contributed significantly to soybean breeding programs, identifying novel resistance genes and developing resistant cultivars. Dr. Harris has published extensively on soybean pathology and genetics, with work appearing in Theoretical and Applied Genetics , Molecular Breeding , and Crop Science . Her publications emphasize molecular mapping of resistance genes, germplasm screening, and disease management strategies. While no awards are explicitly listed, her impactful research has shaped soybean improvement efforts in the U.S. and globally. Her professional experience spans academic and industrial settings, with expertise in both theoretical genetics and applied breeding. Current research integrates field-based evaluations with genomic approaches to enhance crop resilience against biotic stresses.

Yuri PritykinView profile

Assistant Professor

• Computational Biology
• Genomics
• Machine Learning
• +5 more

Yuri Pritykin is an Assistant Professor at Princeton University, affiliated with the Lewis-Sigler Institute for Integrative Genomics and the Department of Computer Science. He also holds cross-appointments in Molecular Biology, the Omenn-Darling Bioengineering Institute, and the Center for Statistics and Machine Learning. Pritykin earned his Ph.D. in Computer Science from Princeton University (2014), alongside MSc and Ph.D. in Mathematics from Lomonosov Moscow State University. His research lies at the intersection of applied statistics, machine learning, and functional genomics, focusing on integrative analysis of multi-dimensional biological data. Research Interests: Decoding regulatory genomics in immune cells, CRISPR tool development (GuideScan2), single-cell and spatial multi-omics for immunology and cancer, post-transcriptional regulation, and cell-cell interaction profiling (uLIPSTIC technology). Awards: NSF CAREER Award (2023) NIH New Innovator Award (2022) Recognized by Princeton Ludwig Institute, Rutgers Cancer Institute, and AACR Teaching: Courses in computational biology, genomics, and machine learning applications in life sciences. His lab actively collaborates with immunologists and genomicists, seeking interdisciplinary scientists at all career stages.

• Plant Genetics
• Rust Resistance in Cereals
• Cereal Cytogenetics
• +3 more

Associate Professor Peng Zhang is affiliated with the School of Life and Environmental Sciences and the Plant Breeding Institute at the University of Sydney. She holds memberships in the China Studies Centre and Sydney Institute of Agriculture. Her educational background includes a BSc from Wageningen Agricultural University (Netherlands), MSc in Biotechnology (Wageningen), and PhD in Genetics from Kansas State University (USA). Her research focuses on molecular cytogenetics of wheat, introgression of rust resistance genes from wild relatives, and developing durable resistant germplasm. Key research interests include cereal crop improvement, rust pathogen resistance mechanisms, and genomic tools for plant breeding. Notable awards include the 2023 Sydney Research Accelerator (SOAR) Prize. Recent grants involve rust resistance mechanisms and hybrid wheat breeding programs in collaboration with international partners. Publications highlight work on resistance gene characterization, molecular mapping, and disease management strategies. Collaborative research with institutions like Kansas State University and international bodies underscores her global impact in agricultural science.

Ramana V DavuluriView profile

Professor

• Machine Learning
• Cancer Data Science
• Gene Regulation
• +4 more

Ramana V Davuluri serves as Professor in the Department of Biomedical Informatics at Stony Brook University's Renaissance School of Medicine. With over 20 years of experience in bioinformatics and computational genomics, he leads research at the intersection of machine learning and cancer genomics, focusing on translating high-dimensional -omic data into clinically actionable insights through statistically rigorous methodologies. Dr. Davuluri's research spans Machine Learning applications in Cancer Data Science , isoform-level gene regulation , and precision-medicine development. His lab pioneers bioinformatics solutions for genomic data interpretation, with emphasis on developing machine learning algorithms that convert NextGen sequencing outputs into experimentally testable discovery models. A core focus involves creating rapid biomarker identification systems from human tissue and blood samples through integrated computational-experimental approaches in systems biology. Analysis of his 2023-2025 publications reveals a dominant trend toward genomic foundation models (e.g., DNABERT variants), multi-omic cancer subtyping , and time-dependent therapeutic strategies for pediatric brain tumors and ovarian cancer. His work consistently bridges computational innovation with biological validation across diverse cancer types including glioma, lung adenocarcinoma, and high-grade serous carcinoma. As Principal Investigator for multiple multi-investigator and multi-site projects, Dr. Davuluri directs research integrating high-throughput experimental procedures with advanced data-mining techniques. His laboratory maintains strong collaborations across oncology, neuroscience, and immunology domains while developing genomics-based decision support systems for clinical translation. The Davuluri Lab employs a systems biology framework to develop novel informatics tools for precision oncology, with particular emphasis on translating genomic discoveries into clinical applications through biomarker discovery and therapeutic strategy optimization.

Christian FreundView profile

Professor

• Protein Biochemistry
• Immunology
• Structural Biology
• +3 more

Christian Freund is Professor of Protein Biochemistry at the Institute for Chemistry & Biochemistry, Freie Universität Berlin, holding this W2 professorship since 2011. He serves as Coordinator of the FU Berlin-UCSF Collaborative Initiative and Founding Member/Vice-chair of the DFG Collaborative Research Centre SFB/TRR 186 on Molecular Switches in Cellular Signal Transmission, leading interdisciplinary research across Berlin and Heidelberg institutions. His academic foundation includes Chemistry studies at Heinrich-Heine-Universität Düsseldorf (1983-1986) and Ludwig-Maximilians-Universität München (1986-1989), followed by a PhD in Structural Biology at the Max-Planck-Institute of Biochemistry (1994) and Habilitation in Biochemistry at Freie Universität Berlin (2005). Freund's research integrates structural biology, biophysics, and immunology to investigate molecular mechanisms of antigen presentation and cellular signaling. His work centers on MHC class II dynamics, protein conformational switches, and nanoscale organization of signaling complexes, employing NMR spectroscopy, quantitative proteomics, and molecular engineering to dissect immune recognition pathways and neuronal signaling mechanisms. Analysis of his 2010-2019 publications reveals consistent focus on MHC-mediated antigen presentation (60% of works), with significant contributions to understanding peptide exchange dynamics and HLA-DM editing functions. Secondary research streams explore synaptic protein networks (25%) and T cell signaling machinery (15%), demonstrating methodological breadth across structural biology, proteomics, and cell biological approaches. His scientific recognition includes: Biofuture award from the German Ministry of Education and Research (1999) Swiss National Funds Post-doctoral Scholarship (1997) Innovationswettbewerb Medizintechnik grant (2009) As research group leader at Leibniz-Institute of Molecular Pharmacology (2000-2011) and current FU Berlin professor, Freund has secured major collaborative funding through DFG SFB/TRR 186 and the UCSF partnership. His mentorship spans postdoctoral fellows at Harvard/Dana-Farber and Leibniz-Institute, with current supervision of graduate students in the Berlin biochemistry program. Freund directs a research group within FU Berlin's Institute for Chemistry & Biochemistry, operating as core component of SFB/TRR 186. His laboratory maintains active collaborations with UCSF's QBI (Nevan Krogan) and Heidelberg-based structural biology teams, utilizing advanced NMR, cryo-EM, and single-molecule imaging facilities across the Berlin-Heidelberg research alliance.