جستجوی استاد راهنمای دانشگاهی

• Machine Learning
• Explainable AI
• Neural Networks
• +۳ مورد دیگر

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

Cathy Wuمشاهده پروفایل

استاد

• Computational Biology
• Bioinformatics
• Data Science
• +۸ مورد دیگر

Cathy Wu is a distinguished academic holding the Unidel Edward G. Jefferson Chair in Engineering and Computer Science at the University of Delaware. She serves as Director of the Center for Bioinformatics & Computational Biology (CBCB), Data Science Institute (DSI), and Protein Information Resource (PIR). Her roles include professorships in the Departments of Computer & Information Sciences and Biological Sciences. Education: BS in Plant Pathology (National Taiwan University, 1978), MS and PhD in Plant Pathology (Purdue University, 1982–1984), and a second MS in Computer Science (University of Texas at Tyler, 1989). She completed postdoctoral training in Molecular Biology at Michigan State University (1985–1986). Research interests focus on computational biology, bioinformatics, and data science with emphasis on protein informatics, biological text mining, ontology development, gene-disease-drug networks, and machine learning applications. She leads initiatives in integrating FAIR principles into biological databases like UniProt and InterPro. Her work bridges computational methods with biomedical challenges, including cancer genomics, epigenetic regulation, and proteomic analyses. She has spearheaded educational programs such as the Online Graduate Certificates in Applied Bioinformatics and Biomedical Informatics and Data Science. Her contributions include over 290 peer-reviewed publications (48,000+ citations, h-index 71) and authored/co-authored four books on bioinformatics. She directs multidisciplinary research teams and collaborates internationally on projects like the HALO study on ovarian cancer genetics. Awards and recognition are implied through her leadership roles and academic appointments, though specific prizes are not listed here. Her grants and funding support large-scale initiatives in bioinformatics infrastructure and translational research.

Christina Leslieمشاهده پروفایل

استاد پژوهش

• Computational Biology
• Systems Biology
• Machine Learning
• +۷ مورد دیگر

Dr. Christina Leslie is a Research Professor and Member of the Computational & Systems Biology Program at Memorial Sloan Kettering Cancer Center (MSK). She leads an active research laboratory focused on developing computational approaches to understand complex biological systems. Dr. Leslie earned her PhD from the University of California, Berkeley and has established herself as a leading computational biologist in cancer research and immunology. Computational & Systems Biology Program, Memorial Sloan Kettering Cancer Center Gerstner Sloan Kettering Graduate School of Biomedical Sciences Dr. Leslie's research focuses on developing novel computational methods to study cellular biological systems from a global and data-driven perspective. Her lab exploits diverse high-throughput functional and genomic data to understand molecular networks underlying fundamental cellular processes, including transcription regulation, pre-mRNA processing, signaling, and post-transcriptional gene silencing. Her algorithmic methods draw heavily on machine learning to build accurate predictive models from noisy and high-dimensional biological data. Key areas of interest include modeling cell-type specific transcriptional programs and dissecting co- and post-transcriptional regulation, particularly microRNA-mediated gene regulation. Analysis of Dr. Leslie's publication record over the last five years reveals a strong focus on computational approaches to cancer genomics, immunology, and epigenetics. Her work bridges multiple disciplines, with a particular emphasis on developing machine learning methods to interpret complex biological data. The publications demonstrate increasing sophistication in integrating multiple data types (genomic, transcriptomic, epigenomic) to understand cancer biology and immune responses. Recent work shows a growing emphasis on single-cell technologies and spatial analysis of tumor microenvironments. Introduction of string kernel methodology for SVM classification of biological sequences Development of algorithms for predictive modeling of gene regulation First systems-level analyses of competition between microRNAs and between target transcripts Dr. Leslie actively mentors numerous graduate students and research associates, with current lab members including Vianne Gao, Alireza Karbalaghareh, Erik Ladewig, and several others. Her lab has received significant research funding to support their work on computational approaches to cancer biology and immunology. The Leslie Lab maintains close collaborations with multiple experimental groups at MSK, facilitating the translation of computational insights into biological understanding. The Leslie Lab operates within the Computational & Systems Biology Program at MSK, with strong ties to both the research and clinical missions of the institution. The lab maintains state-of-the-art computational infrastructure for analyzing large-scale genomic and proteomic datasets and collaborates extensively with wet-lab researchers to validate computational predictions experimentally.

Jeremy Wangمشاهده پروفایل

استادیار

• Computational Biology
• Genomics
• Microbiome Research
• +۷ مورد دیگر

Jeremy Wang, PhD is an Assistant Professor in the Department of Genetics at the UNC School of Medicine . His research focuses on applying high-performance computational methods and machine learning to analyze high-throughput sequence data using long-read technologies (e.g., Oxford Nanopore) to advance precision personalized medicine . Key disease areas include Inflammatory Bowel Diseases (IBD) Respiratory Infectious Diseases His lab specializes in microbiome analysis , host-pathogen interactions , and computational genomics , working with collaborators in clinical, translational, and computational domains. His publications demonstrate expertise in long-read sequencing applications for Pediatric cancer classification SARS-CoV-2 genomic epidemiology Microbiome spatiotemporal dynamics Murine disease models Drosophilid genome assemblies Metagenomic bias analysis Collaborations span UNC and global institutions, with current work extending to clinical laboratory partnerships for pathogen sequencing and oral microbiome sampling methodology.

Max Alekseyevمشاهده پروفایل

دانشیار

• Computational Graph Theory
• Enumerative Combinatorics
• Computational/Algorithmic Biology
• +۱ مورد دیگر

Max Alekseyev is an Associate Professor in the Mathematics Department and Computational Biology Institute. His research spans computational graph theory, enumerative combinatorics, computational/algorithmic biology, and comparative genomics. He focuses on interdisciplinary problems, blending mathematics with biological applications, particularly in genome assembly and analysis. His work includes advancements in genome scaffolding algorithms, combinatorial sequence analysis, and mathematical biology. Notable contributions involve genome assembly tools like CAMSA and studies on ancestral genome reconstruction. He also explores theoretical topics such as Bernoulli series generalizations and modular data classification. His research trends highlight a blend of pure mathematics (e.g., number theory, graph theory) and applied computational methods, addressing challenges in genomics and evolutionary biology. He secured an NSF Student Travel Grant in 2018 for computational molecular biology.

• Cancer Genomics
• Liquid Biopsies
• Machine Learning in Oncology
• +۷ مورد دیگر

Ash A. Alizadeh is the Moghadam Family Professor of Medicine, Oncology, and Hematology (by courtesy) at Stanford University, where he serves as leader of the Cancer Genomics Program at Stanford Cancer Institute. He holds multiple academic appointments including Professor in Medicine - Oncology, and membership in Bio-X, the Institute for Stem Cell Biology and Regenerative Medicine, and the Maternal & Child Health Research Institute (MCHRI). Dr. Alizadeh received his BS in Biochemistry from UCLA (1994), MD from Stanford Medical School, and PhD in Biophysics from Stanford. He completed additional training at the National Cancer Institute (NCI), the National Institutes of Health (NIH), and the Howard Hughes Medical Institute (HHMI). His primary research focuses on developing and applying genome technologies and computing (machine learning & data science) to problems in human disease, with special emphasis on cancer detection, classification, monitoring, and tumor immunology. His laboratory pioneers noninvasive cancer genomic techniques including CAPP-Seq, PhasED-Seq, and EPIC-Seq for "liquid biopsies" that analyze circulating nucleic acids for early cancer detection and monitoring therapeutic response. Using machine learning approaches, his group studies how cellular compositional variation impacts cancer behavior and therapeutic response, including anti-tumor immunity. His work spans molecular, cellular, organism and population levels of tumor behavior analysis. Dr. Alizadeh has received numerous prestigious awards including the Scholar Award from the American Society of Hematology (ASH), the Leukemia & Lymphoma Society (LLS), the V-Foundation, as well as awards from the American Red Cross, Damon Runyon Cancer Research Foundation, and Doris Duke Charitable Research Foundation. He is an elected member of the American Society for Clinical Investigation (ASCI) and serves on the Scientific Advisory Board of the Lymphoma Research Foundation (LRF). As an educator and mentor, Dr. Alizadeh advises numerous doctoral students, postdoctoral fellows, and medical scholars. He teaches in the Department of Medicine and Immunology and serves on various admissions panels at Stanford. His laboratory, the Alizadeh Lab, is a hub for interdisciplinary cancer genomics research that combines computational biology, molecular genetics, and clinical oncology to develop novel cancer diagnostics and therapeutics.

Saud Alhusainiمشاهده پروفایل

استادیار

• Neurology
• Movement Disorders
• Parkinson's Disease
• +۴ مورد دیگر

Saud Alhusaini MD PhD is an Assistant Professor of Neurology at the Warren Alpert Medical School of Brown University and serves as a Neurologist/Movement Disorders Specialist at Rhode Island Hospital. His research integrates imaging genomics and multimodal brain imaging approaches to investigate neurological disorders including Parkinson's disease, essential tremor, and epilepsy. He is affiliated with the Carney Institute for Brain Science and collaborates extensively with clinicians, geneticists, electrophysiologists, MRI specialists, neuropsychologists, and data scientists. Education: PhD from the Royal College of Surgeons in Ireland (RCSI) MSc in Neuroscience from Trinity College Dublin MD from University of Dublin, School of Medicine Adult neurology residency at McGill University/Montreal Neurological Institute Clinical research fellowship at Yale School of Medicine Clinical fellowship at Stanford University Medical Center Dr. Alhusaini's research focuses on identifying key endophenotypes and subclinical biomarkers to elucidate the underlying mechanisms of complex neurological conditions. His work spans multiple areas including movement disorders, epilepsy, and brain structure genetics. He has made significant contributions to understanding the genetic architecture of brain structures through his involvement with the ENIGMA consortium, which conducts large-scale collaborative analyses of neuroimaging and genetic data across institutions worldwide. An analysis of his publication record reveals a consistent pattern of high-impact research at the intersection of neurology, genetics, and advanced imaging techniques. His recent work demonstrates particular expertise in Parkinson's disease genetics, epilepsy network analysis, and movement disorder diagnostics. The breadth of his research, spanning from basic genetic mechanisms to clinical applications, highlights his comprehensive approach to understanding neurological disorders. Dr. Alhusaini has received funding from the Rhode Island Research Foundation, Brown Physicians, Inc., and Advance RI-CTR to support his research initiatives. His collaborative approach is evident through his numerous multi-institutional projects and extensive co-author network across Brown University departments including Neurology, Neurosurgery, and Pathology and Laboratory Medicine.

Katherine E. Varleyمشاهده پروفایل

دانشیار

• Breast Cancer
• Epigenetics
• Gene Expression Regulation
• +۵ مورد دیگر

Katherine E. Varley, PhD is a Huntsman Cancer Institute Investigator and Associate Professor in the Department of Oncological Sciences at the University of Utah. She leads the Varley Lab and is a member of the Nuclear Control of Cell Growth and Differentiation Program, focusing on breast cancer genomics, epigenetics, and biomarker discovery. Her work bridges computational biology with clinical applications to improve breast cancer diagnosis and treatment. Dr. Varley earned her BS in Biology with a concentration in Computational Biology from Cornell University in 2003, followed by a PhD in Computational Biology from Washington University School of Medicine in 2009 under Dr. Robi Mitra. Her postdoctoral training was conducted in Dr. Richard M. Myers' laboratory at the HudsonAlpha Institute for Biotechnology, where she participated in the ENCODE Project Consortium. Her research focuses on using next-generation sequencing and computational analysis to study gene expression, transcription factor binding, and DNA methylation patterns in breast cancer. The Varley Lab investigates epigenetic gene regulation, develops novel molecular methods and bioinformatics approaches, and translates discoveries into clinical tools. Key research areas include Clinical Trial Genomics, Epigenome Engineering, Detecting Circulating Tumor DNA, and identifying Transcription Factors Driving Metastasis, with particular emphasis on triple-negative breast cancer. Analysis of Dr. Varley's publications reveals a consistent trajectory from fundamental genomic mechanisms to clinical translation, with recent work emphasizing biomarker discovery, tumor heterogeneity, and the development of genomic tools for precision oncology. Her research spans cancer biology, genomics, and computational analysis to address critical challenges in breast cancer treatment. Dr. Varley holds multiple patents related to cancer diagnostics and genomic technologies, including targeted sequencing methods, multigene assays for recurrence risk, and biomarkers for triple-negative breast cancer. These inventions reflect her commitment to translating basic research into clinical applications. She actively collaborates with clinical investigators in breast cancer trials and works closely with the Breast and Gynecologic Cancers Disease Center at Huntsman Cancer Institute. Her lab maintains four main research thrusts that collectively address breast cancer from molecular mechanisms to clinical applications, demonstrating a comprehensive approach to improving patient outcomes through genomic technologies.

G. Petur Nielsenمشاهده پروفایل

استاد

• Bone and Soft Tissue Pathology
• Molecular Genetics of Bone Tumors
• Chordoma Research
• +۵ مورد دیگر

G. Petur Nielsen, MD is a Professor of Pathology at Harvard Medical School and serves as Subspecialty Head, Bone and Soft Tissue Pathology at Massachusetts General Hospital . With a clinical focus on bone and soft tissue tumors, his expertise spans diagnostic pathology, molecular genetics of neoplasms, and ancillary testing applications. Research interests center on Pathology and biology of bone/soft tissue tumors Molecular genetics of bone and soft tissue neoplasms Chordoma and sarcoma research Epithelioid vascular tumor differentiation Mesenchymal tumors of the female genital tract His work includes landmark studies on tumor misdiagnosis rates, immunohistochemical profiling, and genomic analysis of chordomas. Scientific contributions appear in leading journals like Nature and American Journal of Surgical Pathology , with major emphasis on Molecular tumor classification Mutational signature analysis Translational oncology Diagnostic accuracy improvement Genomic instability mechanisms

David R. Raleighمشاهده پروفایل

استادیار

• Neuro-oncology
• Radiation Oncology
• Molecular Mechanisms of Brain Tumors
• +۳ مورد دیگر

David R. Raleigh, MD, PhD, is an Assistant Professor in the Departments of Radiation Oncology and Neurological Surgery at the University of California San Francisco (UCSF). He serves as a Principal Investigator at the Brain Tumor Center and Director of the Preclinical Therapeutics Core. Education: BA in Molecular and Cell Biology and Cognitive Science (UC Berkeley, 2004), MD and PhD in Pathology (University of Chicago, 2012), Residency in Radiation Oncology (UCSF, 2017) His research focuses on the molecular mechanisms of brain tumor growth, particularly meningiomas, integrating developmental biology with oncology to identify novel treatments. Methodologies include biochemistry, mouse genetics, genomics, and pharmacology. Dr. Raleigh's recent publications highlight molecular classification of meningiomas, genomics, and targeted therapies. Awards include Phi Beta Kappa, multiple travel grants, and the Robert and Ruth Halperin Endowed Chair in Meningioma Research.

Andrew Godwinمشاهده پروفایل

استاد

• Molecular Oncology
• Precision Medicine
• Biomarker Discovery
• +۳ مورد دیگر

Andrew Godwin is a Professor at the University of Kansas Medical Center , where he serves as the Chancellor’s Distinguished Chair in Biomedical Sciences and Director of Molecular Oncology in the Department of Pathology and Laboratory Medicine. He is also the Deputy Director of the NCI-designated University of Kansas Cancer Center and the Founding Director of the Kansas Institute for Precision Medicine and Biospecimen Shared Resource . Dr. Godwin is a leader in translational research and precision medicine , with a focus on molecular oncology , biomarker discovery , and genomic diagnostics . His work bridges basic and clinical science to improve cancer patient care, particularly in ovarian cancer , Ewing sarcoma , and breast cancer . He has contributed over 230 ovarian cancer-related publications and pioneered studies linking the PI3K/AKT pathway to cancer treatment targets. His research program encompasses liquid biopsies using extracellular vesicles , molecular therapeutics , companion diagnostics , and clinical trial validation . He leads the Biomarker Discovery Laboratory and has secured over $250M in extramural funding , including a $11.4M NIH grant for precision medicine initiatives. His team has developed CELLSEARCH® , the first FDA-cleared test for circulating tumor cells. Notable awards include the Dolph C. Simons, Sr. Higuchi Award (2020), Outstanding Mentorship in Pathology Award (2024), and multiple mentoring accolades from KU. He has mentored over 150 trainees across career stages and leads a multidisciplinary lab with expertise in genomics , proteomics , and bioengineering . Academic Roles: Chancellor’s Distinguished Chair in Biomedical Sciences Director, Molecular Oncology, Pathology and Laboratory Medicine Deputy Director, KU Cancer Center Founding Director, Kansas Institute for Precision Medicine Adjunct Professor, Bioengineering Program, University of Kansas Scientific Awards: KUMC Achievement Award for mentoring postdocs (2014) Chancellor’s Club Award for Research (2018) Dolph C. Simons, Sr. Higuchi Award (2020) KU Excellence in Mentoring Award (2021) Outstanding Mentorship in Pathology (2024) Key Research Themes: Extracellular vesicles as liquid biopsy tools Molecular mechanisms of sarcoma and breast cancer Genomic diagnostics and precision oncology Clinical trial biomarker validation Biospecimen repository leadership

Timothy D. O'Brienمشاهده پروفایل

استاد

• Veterinary Pathology
• Comparative Pathology
• Transplantation Biology
• +۴ مورد دیگر

Timothy D. O'Brien is a Professor and Division Head of Comparative Pathology in the Department of Veterinary Population Medicine at the University of Minnesota College of Veterinary Medicine. He holds multiple affiliations including the Stem Cell Institute, Masonic Cancer Center, and Institute for Engineering in Medicine. Dr. O'Brien also serves as faculty for the Masters Program in Stem Cell Biology. Dr. O'Brien earned his BS, DVM, and PhD degrees from the University of Minnesota in 1976, 1978, and 1985 respectively. He is a Diplomate of the American College of Veterinary Pathologists (Anatomic Pathology, 1984). His research spans veterinary pathology, transplantation biology, stem cell research, and cancer biology with a focus on comparative pathology models. He has made significant contributions to understanding interspecies organogenesis, islet xenotransplantation, and animal models for human diseases. His work bridges veterinary and human medicine, exploring translational applications of findings from animal models to human conditions. Recent publications highlight innovative approaches to transplantation without long-term immunosuppression and studies on hemangiosarcoma biology. Dr. O'Brien's publication record demonstrates expertise across multiple disciplines including diabetes research using feline models, lung cancer heterogeneity, and innovative transplantation techniques. His work frequently involves interdisciplinary collaborations across veterinary medicine, engineering, and human medical specialties, reflecting the integrative nature of modern biomedical research. His research program involves extensive collaborations across the University of Minnesota and beyond, working on projects related to stem cell biology, cancer research, and transplantation medicine. As Division Head of Comparative Pathology, he oversees diagnostic pathology services while maintaining an active research program that contributes to advancing our understanding of disease mechanisms through comparative approaches.

Maureen Sartorمشاهده پروفایل

استاد

• Epigenetics
• Bioinformatics
• Cancer Research
• +۷ مورد دیگر

Maureen Sartor is a Professor in the Department of Computational Medicine and Bioinformatics at the University of Michigan Medical School. Her work bridges computational biology, epigenetics, and cancer research, with recent contributions to understanding environmental toxicant impacts on DNA methylation, HPV-associated head and neck cancers, and neurodegenerative disease mechanisms. Key research themes: Epigenetic regulation, bioinformatics modeling, environmental health Active clinical trial collaborations in immunotherapy rechallenge and neoadjuvant treatment strategies Leadership in cross-species toxicoepigenetic studies and microbiome-immune crosstalk in oral cancer Recent publications highlight her expertise in: Epigenetic age acceleration in ALS and its environmental correlates HPV integration mechanisms in oropharyngeal cancer Chemical oxidation techniques for piRNA discovery Sex-specific epigenetic responses to lead and phthalate exposure Her interdisciplinary approach connects computational methods with experimental validation across multiple disease models.

Catherine F. Clarkeمشاهده پروفایل

استاد

• Coenzyme Q Biosynthesis
• Mitochondrial Function
• Aging
• +۶ مورد دیگر

Catherine F. Clarke is Professor of Biochemistry at the University of California, Los Angeles, where she joined the Department of Chemistry and Biochemistry in 1993. She made history in June 2016 as the first woman to lead the UCLA Department of Chemistry and Biochemistry and was appointed Dean of Special Projects in the UCLA Division of Physical Sciences in 2019. Her laboratory investigates the biosynthesis and function of coenzyme Q (ubiquinone), a critical component of mitochondrial electron transport and cellular antioxidant defense. Dr. Clarke's research has fundamentally advanced our understanding of coenzyme Q biosynthesis through her work with yeast models. Her laboratory identified eight of the eleven polypeptides required for Q biosynthesis and discovered a novel Q biosynthetic pathway using para-aminobenzoic acid (pABA) as an alternative ring precursor. Her team demonstrated that human homologs of yeast Coq proteins can rescue corresponding yeast mutants, establishing critical connections between basic research and human diseases related to coenzyme Q deficiency. Analysis of her recent publications reveals consistent focus on coenzyme Q biosynthesis pathways, with particular emphasis on the regulation of the Coq protein complex, mechanisms of coenzyme Q uptake and trafficking, and therapeutic approaches for coenzyme Q deficiency disorders. Her work bridges fundamental biochemistry with clinical applications, particularly in understanding how coenzyme Q deficiencies contribute to kidney disease, neurodegenerative conditions, and aging. 2001 Ellison Medical Foundation Senior Scholar Award 2009 Hanson-Dow Award for Excellence in Teaching, UCLA 2018 WHS Hall of Fame, Whittier High School 2019 BSF Research Grant Award 2021 Career Development Award Dr. Clarke has mentored numerous graduate students, postdoctoral fellows, and undergraduate researchers who have gone on to successful careers in academia, industry, and medicine. Her laboratory collaborates extensively with clinical researchers to translate basic findings into potential therapeutic approaches, particularly for coenzyme Q deficiency-related disorders. The Clarke Lab maintains active research programs investigating coenzyme Q biosynthesis regulation, membrane contact sites in coenzyme Q production, and mechanisms of coenzyme Q uptake and trafficking in cells.

• Machine Learning
• Bioinformatics
• Medical Imaging
• +۵ مورد دیگر

Paul J. Kennedy is a Professor at the University of Technology Sydney's Centre for Artificial Intelligence. He holds a PhD from the same institution (1999). His research focuses on machine learning applications in healthcare, bioinformatics, medical imaging, and data mining. Key areas include developing algorithms for genomic data analysis, healthcare pathway modeling, and edge-cloud frameworks for omics data. Education: PhD in Artificial Intelligence (1999, UTS). Research interests span machine learning, health informatics, and data compression. Notable work includes studies on administrative health records, lung nodule detection, and virtual reality-based cancer cohort analysis. He has co-authored over 100 publications across journals like BMC Bioinformatics, IEEE Transactions, and Artificial Intelligence in Medicine. Advising: Collaborates extensively with students/researchers but no explicit student list provided. Grants and labs: Active in interdisciplinary projects involving medical and computational teams, though specific grants are not detailed here.