Ken Chen

Associate Professor Professor

The University of Texas MD Anderson Cancer Center

Affiliations

Metabolomics Core Facility

Department Of Bioinformatics And Computational Biology

Department Of Pathology And Translational Molecular Pathology

Department Of Systems Biology

Institute for Data Science in Oncology

The University of Texas MD Anderson Cancer Center

Ken Chen is a Professor at The University of Texas MD Anderson Cancer Center, where his research integrates cancer genomics, immunology, and spatial transcriptomics. His recent work includes developing a visual-omics foundation model bridging histopathology with spatial transcriptomics (Nature Methods, 2025) and identifying CREM as a regulatory checkpoint in CAR and IL-15 signaling in NK cells (Nature, 2025). He has also employed genome-wide CRISPR screens to enhance CAR-NK cell antitumor potency (Cancer Cell, 2025) and characterized TIM-3 as a target for lung adenocarcinoma precancer interception. His contributions span spatial multiomics analysis and large cell atlases, advancing precision oncology.

Honors

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Education

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Ken Chen

The University of Texas MD Anderson Cancer Center

Associate Professor Professor

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Notable Scholarly Works

Notable Federal Grants

Collaborators

1283 “Rudimentary” Germinal Center Like-Areas Seem to Contribute to the Pathobiology of Angioimmunoblastic T Cell Lymphoma Through Enhanced Cd40: Cd40l Interactions. Laboratory Investigation (2025)

Vishal SahuKun Hee KimTania SainzNicholas DcunhaYuchen PanJuan DonosoAniruddha MundhadaHideaki MinzunoClaudia KettlunAkshay BasiJavier GomezArrate ZuberoMichael GreenJared HendersonJared BurksDeepa SampathMichael AndreeffVakul MohantyKen ChenFrancisco Vega

immunologylymphoid neoplasialaboratory investigation

191 Tumor Microenvironment Changes After Treatment With Avelumab Combinations in Patients With Advanced Solid Tumors. Regular and Young Investigator Award Abstracts (2025)

jama oncologycancer treatmentradiation oncologyavelumab combinationsadvanced solid tumorstumor microenvironment changesoncologycancer cellspathologymetronomic therapytumor microenvironmentcancer letter

Abstract 3651: AI-Derived Immune Cell Knowledge Graphs to Advance Immunotherapy. Cancer Research (2025)

immunotherapyimmune responsesclinical immunologyimmunomodulationsystems biologycell researchcancer immunotherapybiomedical informaticsimmunological computingsystem immunologyknowledge-based systemsabstract 3651immunologyknowledge graphs

Abstract 6396: Crem is a Regulatory Checkpoint of Car and Il-15 Signaling in Nk Cells. Cancer Research (2025)

Hind RafeiRafet BasarSunil AcharyaYu-Sung HsuPinghua LiuDeqiang ZhangQingnan LiangVakul MohantyRanjan UpadhyayPing LiPravin PhadatareMerve DedeDonghai XiongCorry JonesMay DaherAna Karen Nunez CortesMayra ShanleyBin LiuSadie M. MoseleyPatrick ZhangDexing FangPinaki BanerjeeNadima UpretyYe LiRejeena ShresthaXinhai WanHong ShenVernikka WoodsApril GilbertSeema RawalJinzhuang DouYukun TanJeong-Min ParkFrancia Reyes SilvaAlexander BiederstädtMecit KaplanXin Ru JiangInci BiederstädtSilvia TibertiMadison MooreJingling JinLuis Muniz-FelicianoPaul LinGary M. DeyterNatalie W. FowlkesAbhinav JainDavid MarinKen ChenElizabeth ShpallKatayoun Rezvani

cancer researchcancer biologyregulatory checkpointnk cells

Abstract B040: Literature-Scaled Immunological Gene Set Annotation Using AI-Powered Immune Cell Knowledge Graph (Ickg). Clinical Cancer Research (2025)

immunological biomarkersknowledge discoveryimmunity (medicine)omicsimmune responsestranslational bioinformaticsmolecular informaticssystems biologycell researchimmunological computingbiomedical informaticscellular therapysystem immunologyabstract b040immunologyliterature-scaled immunological geneknowledge graphs

Agent-Based Modeling of Cellular Dynamics in Adoptive Cell Therapy. bioRxiv (Cold Spring Harbor Laboratory) (2025)

adoptive cell therapybiomedical modelingcell transplantationcellular therapycell engineeringcell biologytheoretical biology

A Visual–Omics Foundation Model to Bridge Histopathology Image With Transcriptomics. Research Square (2025)

Guangyu WangWeiqing ChenPengzhi ZhangTu TranYiwei XiaoShengyu LiVrutant ShahKristopher BrannanKeith YoukerLi LaiLonghou FangYu YangNhat-Tu LeJun-Ichi AbeShu-Hsia ChenQin MaKen ChenQianqian SongJohn CookeHao Cheng

visual-omics foundation modelomics integrationomicssystems biologyhistopathologyhistopathology image

A Visual–Omics Foundation Model to Bridge Histopathology With Spatial Transcriptomics. Nature Methods (2025)

molecular cell biologyomicsbiological imagingvisual sciencespatial omicssystems biologymolecular and cellular biologybiomedical data analysiscell biologybioinformaticsmulti-omics studiesmolecular biologybioimage analysisbiological network visualizationtranscriptomevisual–omics foundation model

Bhlhe40 Governs T Cell Effector Differentiation With Distinct Requirements in Cd4 and Cd8 T Cells for Anti-Pd-1 and Anti-Ctla-4 Efficacy. bioRxiv (Cold Spring Harbor Laboratory) (2025)

immunotherapylymphocyte developmentcellular immune responsesimmune responsescell researchcell biologyimmunology

Coco-St Detects Global and Local Biological Structures in Spatial Transcriptomics Datasets. Nature Cell Biology (2025)

genome biologygeneticsbiological network visualizationspatial transcriptomics datasetslocal biological structurescomputational genomicsspatial omicssystems biologycomputational biologycoco-st detectsbiomedical informaticsbioinformaticsmolecular biologytranscription (biology)transcriptometranscriptomics technologygene expression