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Kadir C. AkdemirView profile

Assistant Professor

• Cancer Genomics
• Computational Biology
• Chromatin Organization
• +4 more

Dr. Kadir C. Akdemir is an Assistant Professor in the Department of Neurosurgery at The University of Texas MD Anderson Cancer Center. His research focuses on integrating computational analyses and multi-omics data to understand chromatin organization and genomic alterations in brain tumors. He leads the Akdemir Lab, which collaborates with global initiatives like the NIH’s 4Dnucleome project and the Break Through Cancer Foundation’s GBM program. Education: Ph.D. in Genetics and Epigenetics from the UTHealth Houston Graduate School (2013), postdoctoral training at MD Anderson’s Genomic Medicine Department. His work combines computer science and genetics to develop tools for analyzing cancer genomes. Research interests include chromatin folding dynamics, somatic rearrangements, and computational methods for genomic data integration. His lab studies glioblastoma and chordoma, focusing on tumor evolution and microenvironment interactions. Notable achievements include identifying ERBB2 alterations in esophageal adenocarcinoma brain metastases and elucidating the role of KDM5D in colon cancer sex differences. He holds grants from NCI, Break Through Cancer, and the UT Rising Stars Award. Lab membership includes PhD/Master’s students and postdocs working on projects like spatial transcriptomics and ecDNA dynamics. Collaborations span institutions like the Brain Cancer SPORE team and the GBM Moonshot initiative.

Wu TuoqiView profile

Assistant Professor

• Immunology
• Cancer Immunotherapy
• T-cell Biology
• +3 more

Tuoqi Wu is an Assistant Professor in the Department of Immunology at UT Southwestern Medical Center, Dallas, TX. He is also a member of the Harold C. Simmons Comprehensive Cancer Center. Previously, he held an Assistant Professor position in the Department of Immunology and Microbiology at the University of Colorado School of Medicine (2019-2021), alongside memberships in the Human Immunology and Immunotherapy Initiative and University of Colorado Cancer Center. His expertise bridges immunology and molecular biology with a focus on T-cell functionality in chronic infections and cancer. Dr. Wu earned a dual Bachelor of Science degree in Biotechnology and Computer Science from Peking University in 2007. He completed his Ph.D. in Biological and Biomedical Sciences at Emory University (2013) under Dr. Rafi Ahmed in the Department of Microbiology and Immunology. Postdoctoral training at NIH (2013-2019) further refined his research skills in immunological mechanisms. His research investigates molecular pathways governing CD8+ T-cell differentiation, exhaustion, and stemness using cutting-edge techniques like single-cell transcriptomics and epigenomics. Key areas include STING signaling, KEAP1/NRF2 redox regulation, and BACH2/FOXP1 transcriptional control. Applications span antiviral immunity, cancer immunotherapy (CAR T cells), and immune checkpoint blockade efficacy in melanoma. Recent publications highlight T-cell immune landscapes in cancer patients, aging effects on cytotoxic T-cells, and computational tools like Benisse for B-cell analysis. His work emphasizes translating molecular insights into clinical immunotherapies to improve treatment outcomes. No scientific awards were mentioned in the provided text. His advising includes PhD students Ziang Zhu (focused on T-cell immunology) and Safuwra Wizzard (clinically oriented research). Postdoctoral researchers Ying Luo and Taidou Hu contribute expertise in T-cell exhaustion and epigenetic regulation. Grant funding details are not included here, though institutional memberships suggest active research support. Dr. Wu leads the Wu Lab at UTSW, a multidisciplinary team exploring T-cell biology, CAR T-cell engineering, and immune dysfunction in chronic diseases. The lab’s work integrates experimental immunology with bioinformatics to address unresolved challenges in antitumor and antiviral immunity.

Gill BejeranoView profile

Professor

• Genomics
• Computational Biology
• Non-coding DNA
• +4 more

Gill Bejerano is a Professor at Stanford University with joint appointments in Developmental Biology, Computer Science, Pediatrics (Genetics), and Biomedical Data Science. His career spans mathematics, computer science, and genomics, with key contributions to understanding conserved non-coding elements, RNA splicing, and genomic disease mechanisms. Ph.D. in Computer Science (Machine Learning in Biology), Hebrew University (2004) B.Sc. Mathematics, Physics, Computer Science (summa cum laude), Hebrew University (1997) His research focuses on genomic evolution , non-coding DNA , RNA splicing , and genomic medicine . He pioneered methods like GREAT for functional enrichment analysis and tools for secure genomic data sharing. Recent publications highlight work on echolocating mammals , RNA splicing prediction , clinical variant interpretation , and genomic privacy . Collaborations span computational biologists, clinicians, and engineers. Scientific Awards : Mallinckrodt Fellowship Sloan Research Fellowship Human Frontiers Fellowship Best Paper & Tomorrow's PI Awards Okawa Foundation Award David and Lucile Packard Fellowship Microsoft & Sony Scholar Awards He advises interdisciplinary trainees and consults for start-ups/Fortune 500 companies, bridging genomics , machine learning , and clinical diagnostics .

Florent GinhouxView profile

Researcher

• Myeloid Cell Biology
• Cancer Immunology
• Tumor Microenvironment
• +4 more

Florent Ginhoux is a Researcher at Gustave Roussy 's Tumor Immunology and Cancer Immunotherapy Program (U1015). He leads the Florent Ginhoux Laboratory (ginhouxlab.com), focusing on myeloid cell biology in cancer progression and immunotherapy development. His team integrates spatial transcriptomics (Visium HD, Xenium), single-cell RNA sequencing , and MACSIMA spatial proteomics to dissect tumor-immune interactions. His research spans pediatric oncology (brain tumors, neuroblastomas, sarcomas) and adult cancers (pancreatic, head/neck carcinomas). Key projects include Developing iPSC-derived macrophages for patient-specific tumor modeling Characterizing TREM2+ multinucleated macrophages as prognostic indicators Creating MoMac-VERSE and DC-VERSE compendiums for cross-tissue myeloid cell analysis His lab collaborates with pediatric oncologists and bioinformaticians on projects funded by 2024 Fight-Kid Cancer grant ( MiMiC-Kids ) 2024 ANR Excellence Chair ( MATCH ) 2024 Horizon HIT-GLIO grant 2021 INCa PEDIAHRG High-Risk/High-Gain program

Andrew BarbourView profile

Professor

• Surgical Oncology
• Cancer Genomics
• Translational Research
• +3 more

Professor Andrew Barbour is an academic general surgeon and translational researcher at The University of Queensland , specifically affiliated with the School of Medicine under the Faculty of Health, Medicine and Behavioural Sciences . He specializes in upper gastrointestinal, pancreatic, melanoma, and sarcoma surgery , with expertise in robotic and laparoscopic procedures for conditions like oesophageal cancer and soft tissue tumours. Doctor of Philosophy, The University of Queensland Faculty of Anaesthetists, Royal Australasian College of Surgeons His research integrates genomic, epigenomic, and transcriptomic data to advance precision medicine in cancer , focusing on biomarker discovery for therapy response and recurrence prediction. Key contributions include the DOCTOR trial (first PET-guided personalized therapy for oesophageal cancer) and the GAP Trial (establishing preoperative chemotherapy for pancreatic cancer). Recent publications emphasize spatial transcriptomics for thin melanoma mortality prediction, multi-omic profiling of oesophageal adenocarcinoma, and radiomics for immune signature analysis in melanoma. His work also explores small extracellular vesicle heterogeneity and genomic catastrophes as drivers in cancer. Queensland Advancing Clinical Research Fellowship for melanoma recurrence prediction Key roles in NHMRC-funded trials and MRFF MASTERPLAN trial As Chair of the AGITG Upper GI working party , he leads national cancer research initiatives. His Surgical Oncology Lab at TRI operates the Cancer Evolution Biobank , linking tumour biology with clinical outcomes.

Xiao DongView profile

Assistant Professor

• Aging
• Genetics
• Cell Biology
• +4 more

Xiao Dong is an Assistant Professor at the University of Minnesota in the Genetics, Cell Biology and Development (TMED) department. Their research focuses on aging biology, somatic mutations, and cancer mechanisms, with significant contributions to understanding cellular senescence and its therapeutic implications. Research Interests: Aging and longevity mechanisms Genetic variants in age-related diseases Senolytic drug discovery Computational biology applications Recent Publications highlight advancements in: Machine learning for transcriptome analysis Somatic mutation profiling via single-cell sequencing Senomorphic microRNA identification TREM2 macrophage roles in metabolic liver disease Current collaborative projects include: Genetic variant-based drug discovery (NIH-funded) Cardiovascular regeneration with pioneer factors Exogenic organ development in gene-edited pigs

• Genomics
• Epigenetics
• Systems Biology
• +7 more

Gary Hon is an Assistant Professor at the University of Texas Southwestern Medical Center (UTSW), jointly affiliated with the Cecil H. and Ida Green Center for Reproductive Biology Sciences and the Lyda Hill Department of Bioinformatics. His research lies at the intersection of genomics, epigenetics, and systems biology, with a focus on decoding the regulatory complexity of the human genome. His research interests include: Understanding the molecular basis of cell state for applications in regenerative medicine Elucidating how non-coding genetic variants contribute to development and disease Developing integrative techniques combining gene regulation, epigenetics, genome engineering, and single-cell genomics Advancing bioinformatics tools for analyzing chromatin and transcriptional regulation The trends across his recent publications reveal a strong emphasis on enhancer biology, epigenetic modifications (especially 5mC and 5hmC), single-cell functional genomics, and the development of novel molecular tools such as in situ chromatin capture and combinatorial perturbation assays. His work frequently leverages CRISPR-based technologies and high-throughput sequencing to dissect gene regulatory networks. Dr. Hon has received significant recognition for his innovative research, including: CPRIT Scholar NIH Director’s New Innovator Award Dr. Hon leads the Hon Lab, which actively develops and applies systems-level approaches to study genome regulation. His collaborative research involves advising graduate students and postdoctoral fellows, many of whom appear as co-authors on his publications. While specific grant details are not listed, his prestigious awards suggest substantial federal and state funding support for his high-impact, interdisciplinary research program.

Sara MostafaviView profile

Associate Professor

• Computational Biology
• Machine Learning
• Artificial Intelligence
• +4 more

Sara Mostafavi is an Associate Professor at the Paul Allen School of Computer Science & Engineering at the University of Washington (UW), with a focus on Artificial Intelligence and Computational Biology. She is currently on leave (2024-2025) leading the Computational Biology and Translation Organization at Genentech. Mostafavi previously held faculty roles at the University of British Columbia (UBC) and the Vector Institute, where she received prestigious Canada Research Chair (CRC II) and Canada CIFAR Chair in AI (CIFAR-AI) awards. PhD in Computer Science, University of Toronto (2011) Postdoctoral Researcher, Stanford University Her research develops machine learning and statistical methods to study gene regulation, disease susceptibility, and molecular networks, with applications in immunology, genetics, and neuroscience. She has pioneered sequence-to-function models for understanding gene regulatory grammar and predicting disease mechanisms. Her publications highlight expertise in genomic data integration, interpretable AI, and cross-modality learning. Recent work includes analyzing mosaic chromosome loss in aging microglia, immune cell differentiation, and Alzheimer's disease networks. Scientific Awards Canada Research Chair (CRC II) in Computational Biology (2015–2020) Canada CIFAR Chair in Artificial Intelligence (CIFAR-AI) Co-founder of the Machine Learning for Computational Biology (MLCB) Conference Mostafavi has mentored numerous PhD and Master’s students, including Xinming Tu, Anna Spiro, Gherman Novakovsky (PhD 2023), and Elijah Willie (MSc 2020). Her lab collaborates with institutions like the Immunological Genome (ImmGen) Consortium and Canadian Institute for Advanced Research (CIFAR). She leads the Mostafavi Lab, which specializes in combining association evidence across genomics datasets and modeling biological pathways to disentangle spurious correlations. Her team develops tools like CEWAS, AI-TAC, and Brain xQTL web server.

• Bioinformatics
• Biostatistics
• Genomics
• +7 more

H. Robert Frost is an Associate Professor of Biomedical Data Science and Molecular and Systems Biology at the Geisel School of Medicine, Dartmouth College. He serves as Associate Director of the Quantitative Biomedical Sciences Graduate Program, contributing to academic leadership and graduate education. Education: PhD from Dartmouth College (2014), MS (1995) and BS (1993) from Stanford University Dr. Frost's research focuses on developing bioinformatics and biostatistics methods for high-dimensional genomic data. Key areas include dimensionality reduction (e.g., PCA), hypothesis aggregation (e.g., gene set testing), penalized estimation (e.g., LASSO regression), cell signaling analysis, tissue-specific gene activity, tumor immunology, and computational approaches to cancer prognosis prediction. Recent work emphasizes spatial transcriptomics data analysis, single-cell RNA sequencing methods, and chromatin accessibility integration. His research is supported by NIH grants R35GM146586 and R21CA253408, with publications spanning cancer transcriptomics, pathogen immunology, and spatial data algorithms. The 2025 publications highlight methodological innovations in gene set optimization and spatial transcriptomics analysis, while 2024 work includes pathogen-host interactions and multi-omics tool development. Key Collaborations: Involvement in tumor immunology, germinal center dynamics, and pathogen-specific immunity research

• Cancer Genomics
• Epigenetics
• Bioinformatics
• +2 more

Timothy J Triche is Professor of Pathology at the Keck School of Medicine, University of Southern California. He directs research in cancer genomics, epigenetics, and bioinformatics, with emphasis on pediatric malignancies. His laboratory develops computational tools for genomic analysis and focuses on translating molecular discoveries into clinical diagnostics. Research spans pediatric acute myeloid leukemia, prostate cancer, and sarcoma biology, integrating multi-omics approaches. Key interests include liquid biopsy development, epigenetic dysregulation, and gene fusion mechanisms in oncogenesis. Publications demonstrate consistent focus on molecular diagnostics and bioinformatic innovation, with recent work advancing single-cell analysis methodologies and non-invasive cancer profiling. Earlier foundational studies established mechanisms of fusion oncoproteins in sarcomas.

Huy DinhView profile

Assistant Professor

• Cancer Immunology
• Single-Cell and Spatial Omics
• Neutrophil Heterogeneity
• +5 more

Huy Dinh is an **Assistant Professor** at the University of Wisconsin-Madison, with a joint appointment in the **Department of Biostatistics and Medical Informatics** and the **McArdle Laboratory for Cancer Research** (School of Medicine and Public Health). His research focuses on **computational analysis of single-cell and spatial omics data** to understand cancer immunology, neutrophil heterogeneity, and tumor microenvironment dynamics. He leads the Dinh Lab, which employs interdisciplinary approaches combining experimental and computational methods. **Education & Career**: Ph.D. in Bioinformatics (University of Vienna), postdoctoral training at USC/Cedars Sinai Medical Center and La Jolla Institute for Immunology. Joined UW-Madison as a **Human Precision Medicine Cluster Hire** in 2020. **Research Interests**: Anti-tumoral neutrophil phenotypes and their roles in immunotherapy response Neutrophil activation in burn injury and wound healing High-dimensional data integration (single-cell RNA-Seq, spatial transcriptomics) **Key Achievements**: NIH MIRA R35 Award (2023) Over 30 peer-reviewed publications, including work in Nature Genetics , Immunity , and Clinical Cancer Research Lab has pioneered methods to identify neutrophil subpopulations in cancer and inflammation **Lab Members**: Mentors ~20 trainees across PhD, MD, and undergraduate programs. Notable advisees include Athena Golfinos-Owens (PhD, 2025) and Parth Khatri (PhD candidate). **Grants & Collaborations**: Leads projects on neutrophil heterogeneity in burns (NIH-funded) and collaborates with institutions like Stanford and the NIH.

Allen W. Cowley, Jr.View profile

Professor

• Cardiovascular Physiology
• Genetics and Genomics
• Renal Physiology
• +4 more

Allen W. Cowley, Jr. is the Harry & Gertrude Hack Term Professor and Chair of the Department of Physiology at the Medical College of Wisconsin since 1980. He holds a PhD in Physiology from Hahnemann Medical University (1968) and a BA in Economics from Trinity College (1961). His research focuses on cardiovascular and renal physiology, hypertension mechanisms, and physiological genomics, with over 325 peer-reviewed publications and continuous NIH funding since 1971. **Research Interests**: Dr. Cowley pioneered studies on baroreceptor reflexes, renin-angiotensin system, renal medullary circulation, and hypertension genetics. His work demonstrated how reduced renal medullary blood flow contributes to chronic hypertension, and he advanced the field of physiological genomics by linking genetic variants to complex diseases. He leads two NIH-funded programs: one on kidney-based blood pressure control and another on salt-sensitive hypertension genetics. **Awards & Leadership**: He served as APS President, IUPS President, and AHA Council Chair. His honors include the Walter Cannon, Ernest Starling, and Carl Wiggers Awards (APS), Novartis Award, and AHA Distinguished Scientist Award. **Advising & Grants**: He has mentored over 50 trainees and directs NIH program projects. His lab explores oxidative stress in hypertension, renal injury mechanisms, and metabolic responses to high salt intake. **Labs/Teams**: His laboratory integrates systems biology, genomics, and experimental physiology to uncover genetic and molecular bases of hypertension and renal dysfunction.

Hao WuView profile

Associate Professor

• Epigenomics
• DNA methylation and demethylation
• Transcriptional control
• +4 more

Hao Wu, PhD is an Associate Professor of Genetics at the University of Pennsylvania's Perelman School of Medicine. He is a Core member of the Penn Epigenetics Institute, Member of the Penn Cardiovascular Institute (CVI), Member of the Penn Institute of Regenerative Medicine (IRM), and Member of the CHOP Center for Mitochondrial and Epigenomic Medicine (CMEM). His educational background includes: B.S. in Biological Sciences and Biotechnology from Tsinghua University (2002) Ph.D. in Epigenetic regulation of neural stem cell differentiation from University of California Los Angeles (2009) Dr. Wu's research focuses on understanding how epigenetic processes regulate gene expression to establish diverse cell types and respond to environmental signals. His lab combines experimental approaches with bioinformatics to study cell-type specification and maturation from mammalian stem cells, particularly in cardiovascular and neural lineages. The Wu lab investigates molecular mechanisms regulating the interaction between environment and epigenome, and how extrinsic signals modify epigenetic marks to influence development or disease. Their long-term goal is to quantitatively analyze and engineer cell-type specific epigenomes to inform therapeutic approaches for human diseases. Analysis of Dr. Wu's recent publications reveals a strong focus on single-cell and spatial multiomic technologies to investigate epigenetic regulation. His work spans cardiovascular biology, neuroscience, and stem cell biology, with emphasis on DNA methylation/demethylation, transcriptional control, and development of novel genomic sequencing methods. Recent publications highlight advances in single-cell epigenomic profiling, time-resolved RNA sequencing, and their application to neural development, cardiac maturation, and disease mechanisms. As a mentor, Dr. Wu oversees a diverse research group including postdoctoral fellows, graduate students, research specialists, and undergraduates. His lab members work on various projects related to epigenomic profiling, epigenome editing, and single-cell technologies. Dr. Wu's research is supported by grants enabling the development of innovative genomic technologies and their application to understand fundamental biological processes. The Wu Lab maintains a collaborative environment focused on developing high-precision single-cell epigenomic profiling methods, novel epigenome editing tools, and time-resolved single-cell RNA sequencing approaches. Current projects investigate neural development, cardiac lineage specification, and the environment-epigenome interaction, bridging fundamental epigenetic mechanisms with translational applications.

Mehdi DamaghiView profile

Assistant Professor

• Cancer Evolution
• Tumor Microenvironment
• Metabolic Reprogramming
• +7 more

Mehdi Damaghi, PhD is an Assistant Professor in the Department of Pathology at the Renaissance School of Medicine, Stony Brook University, and a faculty member at the Stony Brook Cancer Center. His research focuses on understanding cancer through ecological-evolutionary principles, with particular emphasis on breast and ovarian cancers. Dr. Damaghi received his BSc in Cell & Molecular Biology-Genetics from Chamran University in Iran (1998-2002), his MSc in Biochemistry from Tarbiat Modares University in Iran (2002-2005), and his PhD in Cell Biology and Genetics from the Max Planck Institute in Dresden, Germany (2008-2012). He completed postdoctoral training at the Moffitt Cancer Center (2012-2017) and served as a Research Scientist (2017-2021) and Instructor (2021) there before joining Stony Brook University. Dr. Damaghi's research applies ecological and evolutionary principles to understand cancer initiation, progression, and metastasis. His lab investigates how tumor cells adapt to variable microenvironments, leading to metabolic reprogramming linked to epigenetics and transcription factors. He studies the interplay between tumor cells and their microenvironment, which drives genotypic heterogeneity and phenotypic plasticity. His work integrates single-cell multi-omics approaches (genome, epigenome, transcriptome, proteome, and metabolome) with pathomics analysis to capture cancer cell heterogeneity in their natural context. An analysis of Dr. Damaghi's recent publications reveals a strong focus on cancer metabolism, particularly how tumor acidosis and hypoxia influence cancer progression and treatment resistance. His work bridges evolutionary biology with cancer research, examining how selective pressures in the tumor microenvironment drive adaptive changes in cancer cells. Key themes include metabolic reprogramming, lysosomal function in acidic environments, and the application of ecological principles to improve cancer treatment strategies, especially for breast and ovarian cancers. NIH/NCI U01CA261841-01 as PI: "Ecology and Evolution of Breast Cancer" (2021-2026) NIH/NCI R01CA249016-01 as Co-PI: "Radiomics and Pathomics to Predict Progress of DCIS Lesion" (2021-2026) Dr. Damaghi actively mentors students and researchers, with openings available for MSc, PhD, MD/PhD, and postdoctoral positions in his lab. His lab, the Damaghi Research Lab, focuses on four main projects: 1) Ecology and Evolution of Breast Carcinogenesis, 2) Metabolic phenotypes in DCIS to stratify disease progression, 3) Co-evolution of tumor and stroma in breast cancer, and 4) Evolution of resistant phenotype to PARPi in ovarian cancer.

James KoltesView profile

Associate Professor

• Bioinformatics
• Genetics & Genomics
• Phenomics
• +3 more

James Koltes is an Associate Professor in the Department of Animal Science at Iowa State University. His research focuses on leveraging genetics, genomics, and bioinformatics to address challenges in livestock production, particularly improving feed efficiency and sustainability in dairy and swine systems. He holds a PhD in Genetics (with a Statistics minor) from Iowa State University and a BS in Dairy Science and Genetics from the University of Wisconsin-Madison. Dr. Koltes leads projects such as the Farm Animal Genotype-Tissue Expression (FarmGTEx) initiative and the Resilient Dairy Genome Project, aiming to enhance understanding of genomic and phenotypic relationships in livestock. His work integrates multi-omics data, including transcriptomics and epigenomics, to identify genes and pathways influencing feed efficiency, methane emissions, and other critical traits. Collaborative efforts involve international teams through initiatives like the ruminant telomere-to-telomere (rt2t) consortium and the FAANG (Functional Annotation of Animal Genomes) project. Key areas of research include analyzing dietary fatty acid impacts on animal physiology, developing FAIR-compliant data ecosystems for agricultural genomics, and applying high-throughput phenotyping technologies. His lab emphasizes translational research, with applied outcomes like improving dairy cattle breeding decisions and mitigating environmental impacts. Education and outreach activities include student internships (e.g., summer feed efficiency genetics programs) and creating educational resources on animal genetics via YouTube. Research Themes: Functional genomics, feed efficiency, precision livestock farming Key Tools: Single-cell transcriptomics, genomic selection models, sensor-based phenotyping Collaborations: USDA-NIFA, NRSP8, international dairy and beef cattle networks His publications highlight advancements in genomic annotation, microbiome associations with feed efficiency, and epigenetic regulation of livestock traits. Current projects aim to bridge gaps between basic genetic research and agricultural industry applications, fostering sustainable livestock systems.