Sarafan ChEM-H
Showing 101-150 of 196 Results
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Jin Billy Li
Professor of Genetics
Current Research and Scholarly InterestsThe Li Lab is primarily interested in RNA editing mediated by ADAR enzymes. We co-discovered that the major function of RNA editing is to label endogenous dsRNAs as "self" to avoid being recognized as "non-self" by MDA5, a host innate immune dsRNA sensor, leading us to pursue therapeutic applications in cancer, autoimmune diseases, and viral infection. The other major direction of the lab is to develop technologies to harness endogenous ADAR enzymes for site-specific transcriptome engineering.
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Lingyin Li
Professor of Biochemistry
BioDr. Li is a professor in the Biochemistry Department and ChEM-H Institute at Stanford. She is also a core investigator of the Arc Institute. Her lab works on understanding biochemical mechanisms of the immunotransmitter cGAMP and harnessing it to treat cancer and autoimmunity. She majored in chemistry at University of Science and Technology of China and graduated with a B. En in 2003. She then trained with Dr. Laura Kiessling, a pioneer in chemical biology, at University of Wisconsin-Madison and graduated with a Ph.D in chemistry in 2010. She obtained her postdoctoral training with Dr. Timothy Mitchison at Harvard Medical School, who introduced her to the field of chemical immunology. She started her lab at Stanford in 2015.
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Michael Lin
Professor of Neurobiology, of Bioengineering and, by courtesy, of Chemical and Systems Biology
Current Research and Scholarly InterestsOur lab applies biochemical and engineering principles to the development of protein-based tools for investigating biology in living animals. Topics of investigation include fluorescent protein-based voltage indicators, synthetic light-controllable proteins, bioluminescent reporters, and applications to studying animal models of disease.
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Kyle Loh
Associate Professor of Developmental Biology (Stem Cell)
BioHow the richly varied cell-types in the human body arise from one embryonic cell is a biological marvel and mystery. We have mapped how human embryonic stem cells develop into over twenty different human cell-types. This roadmap allowed us to generate enriched populations of human liver, bone, heart and blood vessel cells in a Petri dish from embryonic stem cells. Each of these human cells could regenerate their cognate tissue upon injection into respective mouse models, with relevance to regenerative medicine. In addition to developmental and stem cell biology, we have an emerging interest in exploring deadly biosafety level 4 viruses together with our collaborators.
Kyle attended the County College of Morris and Rutgers, and received his Ph.D. from Stanford (working with Irving Weissman), with fellowships from the Hertz Foundation, National Science Foundation and Davidson Institute for Talent Development. He then continued as a Siebel Investigator, and later, as an Assistant Professor and The Anthony DiGenova Endowed Faculty Scholar at Stanford, where he is jointly appointed in the Department of Developmental Biology and Institute for Stem Cell Biology & Regenerative Medicine. Kyle is a Packard Fellow, Pew Scholar, Human Frontier Science Program Young Investigator and Baxter Foundation Faculty Scholar, and his research has been recognized by the NIH Director's Early Independence Award, Forbes 30 Under 30, Harold Weintraub Graduate Award, Hertz Foundation Thesis Prize and A*STAR Investigatorship. -
Jonathan Z. Long
Associate Professor of Pathology
BioDr. Jonathan Long is an Associate Professor of Pathology and an Institute Scholar of Stanford ChEM-H (Chemistry, Engineering & Medicine for Human Health). His laboratory studies the molecular mechanisms of mammalian energy homeostasis. Dr. Long is the recipient of the Alfred P. Sloan Research Fellowship in Chemistry, the Breakthrough Sciences Award from the Ono Pharma Foundation, and the NIDDK Catalyst Award. Prior to arriving to Stanford, Dr. Long completed his Ph.D. in Chemistry at Scripps Research and his postdoctoral work at Harvard Medical School.
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Sharon R. Long
William C. Steere, Jr. - Pfizer Inc. Professor of Biological Sciences and Professor, by courtesy, of Biochemistry
Current Research and Scholarly InterestsBiochemistry, genetics and cell biology of plant-bacterial symbiosis
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Anson Lowe
Associate Professor of Medicine (Gastroenterology and Hepatology), Emeritus
Current Research and Scholarly InterestsThe laboratory is focused on the relationship between injury, wound healing, and cancer. Esophageal, gastric, and pancreatic cancers are a focus. We are particularly interested in the regulation of cell signaling by EGFR, the EGF receptor. In addition to cancer pathogenesis, active projects include the development of new diagnostic assays and drugs.
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Sydney X. Lu
Assistant Professor of Medicine (Hematology)
BioSydney Lu is an assistant professor and physician-scientist in the Division of Hematology, Department of Medicine with a broad interest in both normal and abnormal RNA processing in the context of normal physiology and disease states. The laboratory studies translational questions regarding the mechanistic basis of RNA processing abnormalities in malignant blood disorders, their implications for leukemogenesis and cancer biology, as well as resultant therapeutic opportunities.
As a physician, Sydney’s group is particularly focused on dissecting RNA processing abnormalities in primary patient samples and disease-relevant preclinical model systems. Lab members employ a variety of ‘wet-lab’ and computational approaches to study transcriptome abnormalities in (1) states of immune dysfunction, (2) myeloid blood cancers such as myelodysplastic syndromes and acute myeloid leukemia, and (3) lymphoid blood cancers such as chronic lymphocytic leukemia. Additional projects are focused on novel therapeutics, including multiple targeted agents which modulate RNA processing, for the selective treatment of these diseases.
Sydney’s research is/has been supposed by grant funding from the National Cancer Institute, Parker Institute for Cancer Immunotherapy, Leukemia & Lymphoma Society, Aplastic Anemia & Myelodysplastic Syndromes International Foundation, the American Society for Clinical Oncology, the American Society of Hematology, the American Association for Cancer Research, the Paula and Rodger Riney Foundation, the Doris Duke Charitable Foundation, The Gabrielles Angel Foundation for Cancer Research, and the Stanford Cancer Institute. -
Liqun Luo
Ann and Bill Swindells Professor and Professor, by courtesy, of Neurobiology
Current Research and Scholarly InterestsWe study how neurons are organized into specialized circuits to perform specific functions and how these circuits are assembled during development. We have developed molecular-genetic and viral tools, and are combining them with transcriptomic, proteomic, physiological, and behavioral approaches to study these problems. Topics include: 1) assembly of the fly olfactory circuit; 2) assembly of neural circuits in the mouse brain; 3) organization and function of neural circuits; 4) Tool development.
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Ruben Y. Luo
Assistant Professor of Pathology
Current Research and Scholarly InterestsApply top-down mass spectrometry and label-free immunoassay to the study and utilization of biomarker proteoforms in clinical diagnosis.
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Vinit B. Mahajan, MD, PhD
Professor of Ophthalmology
Current Research and Scholarly InterestsOur focus is the development of personalized medicine for eye diseases through translation of our discoveries in proteomics, genomics, and phenomics in humans, mice and tissue culture models.
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Nicole M. Martinez
Assistant Professor of Chemical and Systems Biology and of Developmental Biology
Current Research and Scholarly InterestsThe Martinez lab studies RNA regulatory mechanisms that control gene expression. We focus on mRNA processing, RNA modifications and their roles in development and disease.
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Michaëlle Ntala Mayalu
Assistant Professor of Mechanical Engineering and, by courtesy, of Bioengineering
BioDr. Michaëlle N. Mayalu is an Assistant Professor of Mechanical Engineering. She received her Ph.D., M.S., and B.S., degrees in Mechanical Engineering at the Massachusetts Institute of Technology. She was a postdoctoral scholar at the California Institute of Technology in the Computing and Mathematical Sciences Department. She was a 2017 California Alliance Postdoctoral Fellowship Program recipient and a 2019 Burroughs Wellcome Fund Postdoctoral Enrichment Program award recipient. She is also a 2023 Hypothesis Fund Grantee.
Dr. Michaëlle N. Mayalu's area of expertise is in mathematical modeling and control theory of synthetic biological and biomedical systems. She is interested in the development of control theoretic tools for understanding, controlling, and predicting biological function at the molecular, cellular, and organismal levels to optimize therapeutic intervention.
She is the director of the Mayalu Lab whose research objective is to investigate how to optimize biomedical therapeutic designs using theoretical and computational approaches coupled with experiments. Initial project concepts include: i) theoretical and experimental design of bacterial "microrobots" for preemptive and targeted therapeutic intervention, ii) system-level multi-scale modeling of gut associated skin disorders for virtual evaluation and optimization of therapy, iii) theoretical and experimental design of "microrobotic" swarms of engineered bacteria with sophisticated centralized and decentralized control schemes to explore possible mechanisms of pattern formation. The experimental projects in the Mayalu Lab utilize established techniques borrowed from the field of synthetic biology to develop synthetic genetic circuits in E. coli to make bacterial "microrobots". Ultimately the Mayalu Lab aims to develop accurate and efficient modeling frameworks that incorporate computation, dynamical systems, and control theory that will become more widespread and impactful in the design of electro-mechanical and biological therapeutic machines. -
Timothy Meyer
Stanford University Professor of Nephrology, Emeritus
Current Research and Scholarly InterestsInadequate removal of uremic solutes contributes to widespread illness in the more than 500,000 Americans maintained on dialysis. But we know remarkably little about these solutes. Dr. Meyer's research efforts are focused on identifying which uremic solutes are toxic, how these solutes are made, and how their production could be decreased or their removal could be increased. We should be able to improve treatment if we knew more about what we are trying to remove.
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Paul Salomon Mischel
Fortinet Founders Professor and Professor, by courtesy, of Neurosurgery
Current Research and Scholarly InterestsMy research bridges cancer genetics, signal transduction and cellular metabolism as we aim to understand the molecular mechanisms that drive cancer development, progression, and drug resistance. We have made a series of discoveries that have identified a central role for ecDNA (extrachromosomal DNA) in cancer development, progression, accelerated tumor evolution and drug resistance.
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W. E. Moerner
Harry S. Mosher Professor and Professor, by courtesy, of Applied Physics
Current Research and Scholarly InterestsLaser spectroscopy and microscopy of single molecules to probe biological systems, one biomolecule at a time. Primary thrusts: fluorescence microscopy far beyond the optical diffraction limit (PALM/STORM/STED), methods for 3D optical microscopy in cells, and trapping of single biomolecules in solution for extended study. We explore protein localization patterns in bacteria, structures of amyloid aggregates in cells, signaling proteins in the primary cilium, and dynamics of DNA and RNA.
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Denise M. Monack
Martha Meier Weiland Professor in the School of Medicine
Current Research and Scholarly InterestsThe primary focus of my research is to understand the genetic and molecular mechanisms of intracellular bacterial pathogenesis. We use several model systems to study complex host-pathogen interactions in the gut and in immune cells such as macrophages and dendritic cells. Ultimately we would like to understand how Salmonella persists within certain hosts for years in the face of a robust immune response.
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Lauren O'Connell
Associate Professor of Biology
Current Research and Scholarly InterestsThe O'Connell lab studies how genetic and environmental factors contribute to biological diversity and adaptation. We are particularly interested in understanding (1) how behavior evolves through changes in brain function and (2) how animal physiology evolves through repurposing existing cellular components.
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Sergiu P. Pasca
Kenneth T. Norris, Jr. Professor of Psychiatry and Behavioral Sciences and Bonnie Uytengsu and Family Director of the Stanford Brain Organogenesis Program
Current Research and Scholarly InterestsA critical challenge in understanding the intricate programs underlying development, assembly and dysfunction of the human brain is the lack of direct access to intact, functioning human brain tissue for detailed investigation by imaging, recording, and stimulation.
To address this, we are developing bottom-up approaches to generate and assemble, from multi-cellular components, human neural circuits in vitro and in vivo.
We introduced the use of instructive signals for deriving from human pluripotent stem cells self-organizing 3D cellular structures named brain region-specific spheroids/organoids. We demonstrated that these cultures, such as the ones resembling the cerebral cortex, can be reliably derived across many lines and experiments, contain synaptically connected neurons and non-reactive astrocytes, and can be used to gain mechanistic insights into genetic and environmental brain disorders. Moreover, when maintained as long-term cultures, they recapitulate an intrinsic program of maturation that progresses towards postnatal stages.
We also pioneered a modular system to integrate 3D brain region-specific organoids and study human neuronal migration and neural circuit formation in functional preparations that we named assembloids. We have actively applied these models in combination with studies in long-term ex vivo brain preparations to acquire a deeper understanding of human physiology, evolution and disease mechanisms.
We have carved a unique research program that combines rigorous in vivo and in vitro neuroscience, stem cell and molecular biology approaches to construct and deconstruct previously inaccessible stages of human brain development and function in health and disease.
We believe science is a community effort, and accordingly, we have been advancing the field by broadly and openly sharing our technologies with numerous laboratories around the world and organizing the primary research conference and the training courses in the area of cellular models of the human brain. -
Rebecca Pinals
Assistant Professor of Chemical Engineering
BioThe brain is a fascinatingly complex and delicate system of biomolecules, cells, and dynamic interactions that must be carefully maintained to support human health. When this balance is disrupted, disease can arise. Neurodegenerative dementias including Alzheimer’s disease are highly prevalent and profoundly devastating, yet remain largely untreatable or incurable.
The Pinals Lab engineers neuro-models and nano-tools to uncover mechanisms of neurodegenerative disease and intervene to halt—and even reverse—disease progression. A particular emphasis of our work is on the blood–brain barrier (BBB), the vascular interface that serves as the molecular gateway into the brain. We leverage human induced pluripotent stem cells (iPSCs) to build 3D cellular systems, providing a platform to recapitulate human brain properties and pathologies. In parallel, we design nanoparticles to report on real-time neurochemical processes, enabling unprecedented access to dynamic and spatially resolved biomolecular phenomena, and to modulate disease states. By integrating advanced human brain tissue models with rationally designed nanotechnologies, we aim to generate fundamental insights and tools that translate into meaningful impacts for human health. -
Elizabeth Ponder
Executive Director, Sarafan ChEM-H
BioDr. Elizabeth Ponder joined Stanford ChEM-H in 2014 and is currently the Executive Director of Sarafan ChEM-H and the Stanford Innovative Medicines Accelerator (IMA). Dr. Ponder completed her Ph.D. and postdoctoral training at Stanford University in the laboratory of Dr. Matthew Bogyo. Her past work has included promoting public-private partnerships in the non-profit sector, managing multidisciplinary research in the higher education sector, and business development consulting in the for-profit biotech sector. Dr. Ponder joined ChEM-H from the University of California, Berkeley where she served as the Executive Director of the Henry Wheeler Center for Emerging & Neglected Diseases (CEND).
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Matthew Porteus
Sutardja Chuk Professor of Definitive and Curative Medicine
BioDr. Porteus was raised in California and was a local graduate of Gunn High School before completing A.B. degree in “History and Science” at Harvard University where he graduated Magna Cum Laude and wrote an thesis entitled “Safe or Dangerous Chimeras: The recombinant DNA controversy as a conflict between differing socially constructed interpretations of recombinant DNA technology.” He then returned to the area and completed his combined MD, PhD at Stanford Medical School with his PhD focused on understanding the molecular basis of mammalian forebrain development with his PhD thesis entitled “Isolation and Characterization of TES-1/DLX-2: A Novel Homeobox Gene Expressed During Mammalian Forebrain Development.” After completion of his dual degree program, he was an intern and resident in Pediatrics at Boston Children’s Hospital and then completed his Pediatric Hematology/Oncology fellowship in the combined Boston Chidlren’s Hospital/Dana Farber Cancer Institute program. For his fellowship and post-doctoral research he worked with Dr. David Baltimore at MIT and CalTech where he began his studies in developing homologous recombination as a strategy to correct disease causing mutations in stem cells as definitive and curative therapy for children with genetic diseases of the blood, particularly sickle cell disease. Following his training with Dr. Baltimore, he took an independent faculty position at UT Southwestern in the Departments of Pediatrics and Biochemistry before again returning to Stanford in 2010 as an Associate Professor. During this time his work has been the first to demonstrate that gene correction could be achieved in human cells at frequencies that were high enough to potentially cure patients and is considered one of the pioneers and founders of the field of genome editing—a field that now encompasses thousands of labs and several new companies throughout the world. His research program continues to focus on developing genome editing by homologous recombination as curative therapy for children with genetic diseases but also has interests in the clonal dynamics of heterogeneous populations and the use of genome editing to better understand diseases that affect children including infant leukemias and genetic diseases that affect the muscle. Clinically, Dr. Porteus attends at the Lucille Packard Children’s Hospital where he takes care of pediatric patients undergoing hematopoietic stem cell transplantation.
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Lei (Stanley) Qi
Associate Professor of Bioengineering
BioDr. Lei (Stanley) Qi (publishes as Lei S. Qi) is an Associate Professor in the Department of Bioengineering at Stanford University, an Institute Scholar at Sarafan ChEM-H, and a Chan Zuckerberg Biohub Investigator. Trained in physics and mathematics (Tsinghua University) and bioengineering (UC Berkeley), he was a Systems Biology Fellow at UCSF before joining the Stanford faculty in 2014.
Qi is a pioneer in CRISPR technology and genome engineering. His lab created the first nuclease-deactivated Cas9 (dCas9) for targeted gene regulation, establishing CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa). Since then, his group has expanded CRISPR from an editing tool into a platform for programmable control of dynamic and spatial cell state, integrating scalable perturbation, live-cell and super-resolution imaging, and computation-guided design. This work has produced technologies for multiplexed transcriptome regulation, programmable 3D genome organization, spatial RNA logistics control, and real-time visualization of chromatin and transcriptional events in living cells.
A distinctive focus of the Qi lab is closed-loop biology, combining perturbation with high-content measurements to infer mechanisms and iteratively refine control strategies. The lab develops platforms spanning multiplexed transcriptional and epigenetic control, spatial genome–transcriptome organization, and quantitative live-cell imaging of chromatin and transcriptional dynamics. A compact nuclease-dead CRISPR epigenetic editor from this technology lineage has advanced to first-in-human clinical testing for facioscapulohumeral muscular dystrophy (FSHD; NCT06907875), underscoring the translational potential of principle-driven control systems.
Beyond single-cell control, Qi’s lab is building a framework for synthetic cell–cell communication, with particular emphasis on the bidirectional interplay between immune cells and neurons. The lab’s goal is to move beyond describing molecular parts to discovering fundamental control principles in living systems: how regulatory landscapes create stable states and memory, how spatial genome–RNA organization shapes dynamic responses, and how engineered cell–cell interactions can generate emergent multicellular behaviors. By integrating experimental bioengineering with computation and machine learning, the lab aims to identify generalizable rules linking molecular programs to systems-level physiology and disease trajectories and to translate those rules into next-generation therapeutic cells. -
Krishna Raghavan
Ph.D. Student in Chemistry, admitted Autumn 2024
BioKrishna is originally from the Detroit area of Michigan, and completed his undergraduate studies in biological chemistry and chemistry at the University of Chicago. He is currently a second-year PhD student concentrating in biophysical chemistry, in the lab of Prof. Bianxiao Cui.
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Jianghong Rao
Professor of Radiology (Molecular Imaging Program at Stanford) and, by courtesy, of Chemistry
Current Research and Scholarly InterestsProbe chemistry and nanotechnology for molecular imaging and diagnostics
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Grant M. Rotskoff
Assistant Professor of Chemistry
BioGrant Rotskoff studies the nonequilibrium dynamics of living matter with a particular focus on self-organization from the molecular to the cellular scale. His work involves developing theoretical and computational tools that can probe and predict the properties of physical systems driven away from equilibrium. Recently, he has focused on characterizing and designing physically accurate machine learning techniques for biophysical modeling. Prior to his current position, Grant was a James S. McDonnell Fellow working at the Courant Institute of Mathematical Sciences at New York University. He completed his Ph.D. at the University of California, Berkeley in the Biophysics graduate group supported by an NSF Graduate Research Fellowship. His thesis, which was advised by Phillip Geissler and Gavin Crooks, developed theoretical tools for understanding nonequilibrium control of the small, fluctuating systems, such as those encountered in molecular biophysics. He also worked on coarsegrained models of the hydrophobic effect and self-assembly. Grant received an S.B. in Mathematics from the University of Chicago, where he became interested in biophysics as an undergraduate while working on free energy methods for large-scale molecular dynamics simulations.
Research Summary
My research focuses on theoretical and computational approaches to "mesoscale" biophysics. Many of the cellular phenomena that we consider the hallmarks of living systems occur at the scale of hundreds or thousands of proteins. Processes like the self-assembly of organelle-sized structures, the dynamics of cell division, and the transduction of signals from the environment to the machinery of the cell are not macroscopic phenomena—they are the result of a fluctuating, nonequilibrium dynamics. Experimentally probing mesoscale systems remains extremely difficult, though it is continuing to benefit from advances in cryo-electron microscopy and super-resolution imaging, among many other techniques. Predictive and explanatory models that resolve the essential physics at these intermediate scales have the power to both aid and enrich the understanding we are presently deriving from these experimental developments.
Major parts of my research include:
1. Dynamics of mesoscale biophysical assembly and response.— Biophysical processes involve chemical gradients and time-dependent external signals. These inherently nonequilibrium stimuli drive supermolecular organization within the cell. We develop models of active assembly processes and protein-membrane interactions as a foundation for the broad goal of characterizing the properties of nonequilibrium biomaterials.
2. Machine learning and dimensionality reduction for physical models.— Machine learning techniques are rapidly becoming a central statistical tool in all domains of scientific research. We apply machine learning techniques to sampling problems that arise in computational chemistry and develop approaches for systematically coarse-graining physical models. Recently, we have also been exploring reinforcement learning in the context of nonequilibrium control problems.
3. Methods for nonequilibrium simulation, optimization, and control.— We lack well-established theoretical frameworks for describing nonequilibrium states, even seemingly simple situations in which there are chemical or thermal gradients. Additionally, there are limited tools for predicting the response of nonequilibrium systems to external perturbations, even when the perturbations are small. Both of these problems pose key technical challenges for a theory of active biomaterials. We work on optimal control, nonequilibrium statistical mechanics, and simulation methodology, with a particular interest in developing techniques for importance sampling configurations from nonequilibrium ensembles. -
Florentine Rutaganira
Assistant Professor of Biochemistry and of Developmental Biology
Current Research and Scholarly InterestsWe use chemical tools to decipher the roles of key signaling networks in choanoflagellates, single-celled organisms that are the closest living relatives of animals. Choanoflagellates produce molecular signals essential for intercellular communication in animals and the presence of these molecules in choanoflagellates suggests that signaling components needed to communicate between cells is evolutionarily ancient. We aim to uncover new understanding of animal development, physiology and disease.
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Julien Sage
Elaine and John Chambers Professor of Pediatric Cancer and Professor of Genetics
Current Research and Scholarly InterestsWe investigate the mechanisms by which normal cells become tumor cells, and we combine genetics, genomics, and proteomics approaches to investigate the differences between the proliferative response in response to injury and the hyperproliferative phenotype of cancer cells and to identify novel therapeutic targets in cancer cells.
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Kathleen M. Sakamoto
Shelagh Galligan Professor in the School of Medicine
Current Research and Scholarly InterestsMy research focuses on the molecular pathways that regulate normal and aberrant blood cell development, including acute leukemia and bone marrow failure syndromes. We are also studying novel drugs for treatment of cancer.
