Ken Chen
Department of Bioinformatics and Computational Biology, Division of Discovery Science
About Dr. Ken Chen
Dr. Chen received his B.E. from Tsinghua University (Beijing), Ph.D. from University of Illinois at Urbana-Champaign, and postdoctoral training from University of California at San Diego. From 2005 to 2011, he worked for Washington University School of Medicine in St. Louis as a senior scientist and a research faculty. Having a background in machine learning, statistical signal processing, and cancer genomics, his primary interest is to develop computational tools to analyze and interpret human omics and clinical data towards the realization of evidence-based medicine. Dr. Chen has designed, developed, and co-developed a suite of computational tools such as BreakDancer, VarScan, Monovar and METAFlux that have been widely applied to characterize individual and population genomics in large-scale, high-throughput profiling studies such as those in the Cancer Genome Atlas (TCGA) and the 1000 Genomes Project. He is particularly interested in comprehensively and accurately constructing the genomes, transcriptomes, proteomes and metabolomes of various cancer cell populations towards understanding the heterogeneity, spatial-temporal evolution and therapeutic resistance of cancer as a consequence of genetics, pathogens, carcinogens and tumor microenvironment. He is also interested in developing systems-biological (including AI-based and math/physics/chemistry-grounded) approaches to identify molecular-cellular biomarkers from tissue, single-cell and spatial omics data for cancer diagnosis, therapy assessment and clinical decision support. His lab has been active in developing New Approach Methodologies (NAM) that integrate human knowledge, patient derived models, multimodal omics data, and computational mechanistic models to predict therapeutic responses at patient and cellular levels, particularly for adoptive cell therapies.
Dr. Chen has published over 220 journal articles with over 93,000 citations and a h-index of 87.
As the PI, he has obtained 1 NCI R01, 1 NCI U01, 1 CPRIT IIRA, 1 CZI grants; as a MPI, 2 NHGRI U24/U41, 1 NCI U24, 1 ARPR-H, 1 NCI UM1, 1 CPRIT IIRA, and 2 CZI network grants.
His lab has graduated over 30 trainees (>10 postdocs). Eight have continued as principal investigators at research/educational institutions world-wide. Others work as scientists in Genentech, Pfizer, Amazon, Natera, Danaher, Gilead, etc.
More Information about his research lab is available https://www.mdanderson.org/research/departments-labs-institutes/labs/ken-chen-laboratory.html.
Present Title & Affiliation
Primary Appointment
Co-Director Quantitative Science in Graduate School of Biomedical Science, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Professor (Joint appointment), Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Adjunct Faculty Member, Computer Science, Rice University, Houston, TX
Regular Member, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX
Dual/Joint/Adjunct Appointment
Professor, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
Adjunct Faculty Member, Computer Science, Rice University, Houston, TX
Regular Member, Graduate School of Biomedical Sciences, University of Texas Health Science Center, Houston, TX
Education & Training
Degree-Granting Education
| 2004 | University of Illinois, Urbana-Champaign, Illinois, US, Electrical and Computer Engineering, Ph.D |
| 1996 | Tsinghua University, Beijing, CN, Precision Instruments, BE |
Postgraduate Training
| 2004-2005 | Research Fellowship, Biochemistry and Biophysics, University of California, San Diego, California |
Experience & Service
Faculty Academic Appointments
Associate Professor, Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 2016 - 2021
Assistant Professor, Quantitative Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, 2011 - 2016
Research Instructor, Genetics, Washington University, St. Louis, MO, 2009 - 2011
Administrative Appointments/Responsibilities
GSBS representative at UTHealth’s School of Biomedical Informatics Appointment, Promotion and Tenure Committee, The University of Texas MD Anderson Cancer Center, Houston, TX, 2022 - Present
Other Professional Positions
Chair, Gulf Coast Single Cell & Spatial Omics Consortium, Houston, TX, 2024 - Present
Co-chair, Single Cell Cluster Gulf Coast Consortia, Houston, TX, 2023 - Present
Member, Scientific Advisory Board CPRIT MDA Single Cell Genomics Core, Houston, TX, 2019 - Present
Steering Committee Member, Gulf Coast Consortia Single-Cell Omics, Houston, TX, 2019 - Present
Scientific Advisory Board Single Cell Genomics Core, Baylor College of Medicine, Houston, TX, 2017
Scientific Advisory, Ignyta Inc, San Diego, 2016 - 2016
Reviewer, MD Anderson Odyssey Program Advisory Committee, Houston, TX, 2015 - 2018
Director of Bioinformatics, Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, Houston, TX, 2013 - 2018
Senior Scientist, The Genome Institute at Washington University School of Medicine, St. Louis, MO, 2005 - 2011
Intern, Microsoft Research Asia, Beijing, 2001 - 2001
Intramural Institutional Committee Activities
Member, Search Committee for The Department Chair of General Oncology, The University of Texas MD Anderson Cancer Center, 2025 - Present
Representative of Department of Bioinformatics and Computational Biology, Faculty Senate, The University of Texas MD Anderson Cancer Center, 2024 - 2025
Extramural Institutional Committee Activities
member, Promotion and Tenure Committee-Research (PTC-R), The University of Texas MD Anderson Cancer Center, 2026 - Present
Member, MDA 2024-05-01 Investigation Committee, The University of Texas MD Anderson Cancer Center, 2026 - Present
Faculty member, Executive Research Compliance Committee (ERCC), The University of Texas MD Anderson Cancer Center, 2026 - Present
Member, General Oncology Chair search committee, The University of Texas MD Anderson Cancer Center, 2025 - Present
Member, Faculty Search Committee, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, 2022
Member, Faculty Search Committee Dept. Genetics, The University of Texas MD Anderson Cancer Center, 2017 - 2018
member, Operational Priority Committee #2: Decisive Discoveries, The University of Texas MD Anderson Cancer Center, 2017 - 2018
Member, Faculty Search Committee, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 2016 - Present
Editorial Activities
Guest editor, Frontiers in immunology, 2026 - Present
Editorial Board member, Genome Medicine, 2025 - Present
Guest editor, Frontiers in Immunology, 2025 - Present
Editorial Board Member, Genomics, Proteomics & Bioinformatics (GPB), 2024 - Present
Guest editor, Frontiers in Oncology, 2022 - 2023
Associate Editor, Frontiers Immunology, 2022
Editor, Emerging Topics in Life Sciences, 2021
Honors & Awards
| 2025 - Present | Elected Fellow, Asia-Pacific Artificial Intelligence Association (AAIA) |
| 2025 - Present | Elected Fellow, American Institute of Medical and Biological Engineering (AIMBE) |
| 2024 | MD Anderson Celebration of Faculty Excellence in Research Excellence, MD Anderson Cancer Center |
| 2024 | Mentor’s Choice Award, Biomedical Data Science Innovation Lab |
| 2024 | 2024 NIH Common Fund Complement-ARIE (Complement Animal Research In Experimentation) award, NIH |
| 2024 | 1st place in subtask 2 of international AI chemotimeline reconstruction challenge from clinical narratives, NIH |
| 2023 | Highest Commendation, University of Texas Graduate School of Biomedical Science |
| 2023 | Robert M. Chamberlain Distinguished Mentor Award, MD Anderson Cancer Centre Postdoctoral Association |
| 2023 | "Wall of Science" Publication Gallery, The University of Texas MD Anderson Cancer Center |
| 2021 | President’s Recognition of Faculty Excellence, MD Anderson Cancer Center |
| 2020 | Highly Cited Researcher 2020, Clarivate |
| 2016 - 2018 | Andrew Sabin Family Fellow |
| 2016 | Nominee, Robert M. Chamberlain Distinguished Mentor Award, MD Anderson Cancer Center |
| 2014 | Best performer in ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge, dreamchallenge.org |
| 2009 - Present | Senior Member, Institute of Electrical and Electronics Engineers |
| 2009 | Sigma Xi |
| 2003 | Phi Kappa Phi, University of Illinois at Urbana-Champaign |
| 1990 | 1st place in high school software competition, The science and technology society, Sichuan Province, China |
Professional Memberships
Selected Presentations & Talks
Local Presentations
- 2025. Uncovering Spatial Niches and Molecular Signatures in Pathomics Data Using AI and Machine Learning. Invited. Annual Retreat. Houston, Texas, US.
Regional Presentations
- 2022. Single-cell multiomics. Conference. Single Cell Omics Workshop, US.
National Presentations
- 2026. From Data to Understanding to Decisions. Invited. Birmingham, Alabama, US.
- 2026. Spatial-omics Data Intelligence, a bridge for discovery and translational cancer medicine. Invited. Tampa, Florida, US.
- 2026. Phase 1/2 trial of ATR inhibitor berzosertib plus immune checkpoint inhibitor avelumab in patients with advanced cancers with DNA damage response (DDR) gene alterations: Correlative data reveal tumor microenvironment mediated pathways of resistance, US.
- 2026. TROP2 as an actionable biomarker for anal cancer, US.
- 2026. DNA damage response (DDR)-Basket of Basket (D-BOB) Trial: Tumor immune microenvironment-mediated resistance to the combination of ATR inhibitor berzosertib plus immune checkpoint inhibitor avelumab in DDR-altered advanced cancers. ASCO, US.
- 2026. Modeling CAF-driven cAMP-mediated immunosuppressive signaling in CAR-T cells for solid tumors. SITC spring, US.
- 2026. T-CELL DYSFUNCTION IN THE PATHOGENESIS OF PARKINSON’S DISEASE. Asheville, North Carolina, US.
- 2026. Acquisition of a FOXP3-positive regulatory-like state by malignant TFH cells in relapsed TFH lymphoma. 23rd Meeting of the European Association for Haematopathology.
- 2026. Somatic variants detection in donor tissue samples using single-cell omics data.
- 2025. Cellular Modeling for Studying Cancer Dynamics in Tumor Immune Microenvironment. Invited. New York City, US.
- 2025. Powering cancer research with data intelligence. Invited. College Station, TX, US.
- 2025. Virtual cell modeling of CAR-NK cell therapy. Invited. CZI Annual Meeting. Chicago, IL, US.
- 2025. Revealing cellular-molecular features associated with cancer development and treatment. Invited. Charlottesville, Virginia, US.
- 2025. Spatial Whole Transcriptomic Analysis Reveals Differential Gene Expression in Epithelial and Mesenchymal Components of Primary Cutaneous Carcinosarcomas. Conference. USCAP, US.
- 2025. Tumor microenvironment changes after treatment with avelumab combinations in patients with advanced solid tumors. SITC, US.
- 2025. Ultrasensitive ctDNA-based MRD monitoring anticipates relapse in postoperative HR+ inflammatory breast cancer. SABCS, US.
- 2025. Digital Spatial Immune Profiling of Colorectal Liver Macro-metastases and Micro-metastases. Conference. USCAP, US.
- 2025. “Rudimentary” Germinal Center Like-Areas Seem to Contribute to the Pathobiology of Angioimmunoblastic T Cell Lymphoma through Enhanced CD40:CD40L Interactions. Conference. USCAP, US.
- 2024. Single-nucleotide variant calling in single-cell sequencing data with Monopogen. Invited. Digital data science seminar series Boston Children's Hospital and Harvard Medical School, US.
- 2024. Computational modeling in cancer evolution, metabolism, pathology and immunotherapy. Invited. New York City, New York, US.
- 2024. Computations in cancer evolution, metabolism, pathology and immunotherapy. Invited. Memphis, TN, US.
- 2024. Comparison of Spatial Transcriptomic Platforms in FFPE TMA Samples. Conference. GCC SCSOS, US.
- 2024. Agent-based Modeling of Tumor Microenvironment Dynamics in Adoptive Cell Therapy. Conference. GCC SCSOS, US.
- 2024. Advanced Spatial Data Analysis of mIF and CODEX Images in FFPE Slides: Integrating Phenotyping, Noise Reduction, and Network Analysis for Insightful Biological Interpretation. Conference. GCC SCSOS 5th annual symposium, US.
- 2024. LSGI: Interpretable Spatial Gradient Analysis for Spatial Transcriptomics Data. Conference. GCC SCSOS, US.
- 2024. Comparison of Spatial transcriptomic platforms in FFPE TMA samples. Conference. Spatial Biology Summit. Palo Alto, US.
- 2024. Characterizing Cancer/Immune Metabolism From Bulk and Single-cell RNA-seq Data Using METAFlux. Invited. 13TH ANNUAL METABOLISM IN CANCER SYMPOSIUM, US.
- 2024. LSGI: Interpretable Spatial Gradient Analysis for Spatial Transcriptomics Data. Conference. Spatial Biology Summit. Palo Alto, CA, US.
- 2024. Computational Modeling & Simulations for Cardiovascular Architecture and Regeneration. Invited. 8th Annual NIH PCTC CARDIOVASCULAR BIOENGINEERING Symposium. Houston, US.
- 2024. Impact of Bintrafusp alpha and Radiotherapy in Intrahepatic Cholangiocarcinoma: Proteomic and Transcriptomic Analysis. Conference. European Society of Medical Oncology, US.
- 2024. Targeting MYC by Degradation Rewires Metabolomics and Induces Cell Kill in TP53 Mutant Acute Myeloid Leukemias. Conference. Annual congress of EHA, US.
- 2024. Decoding the tumor immune microenvironment to unleash effective immunotherapy avenues for epithelioid malignant pleural mesothelioma. Conference. ESMO Lung Cancer conference, US.
- 2024. Spatial Single-Cell Immune Microenvironment Analysis Reveals the Transition from Innate to Adaptive Immune Response during Early Lung Adenocarcinoma Carcinogenesis. Conference. AACR, US.
- 2024. The Allelic Imbalance of Genetic Variants in Single Cell Sequencing Data. Conference. GCC SCSOS 5th annual symposium. Houston, US.
- 2024. “Guided” Unsupervised Multiplexed Cytof Analysis Enhances Detection of Minimal/Measurable Residual Disease in Acute Myeloid Leukemia. Conference. ASH, US.
- 2024. Single-Cell Multiomics Unveils Venetoclax-Resistant Monocytic Differentiation and Immune Evasion in TP53 Mutant AML Clones. Conference. ASH, US.
- 2024. Elucidating Transcriptional Heterogeneity in Venetoclax Resistant AMLs. Conference. ASH, US.
- 2024. A Multi-Site Break through Cancer Trial: Phase II Study Investigating Dual Inhibition of BCL2 and Menin in AML MRD Using the Combination of Venetoclax and Revumenib (Trial In Progress). Conference. ASH, US.
- 2024. Single-Cell Multiomics Unveils Venetoclax-Resistant Monocytic Differentiation and Immune Evasion in TP53 Mutant AML Clones. Conference. ASH, US.
- 2024. “Guided” Unsupervised Multiplexed CyTOF Analysis Enhances Detection of Minimal/Measurable Residual Disease in Acute Myeloid Leukemia. Conference. ASH, US.
- 2024. Title: Elucidating transcriptional heterogeneity in venetoclax resistant AMLs. Conference. ASH, US.
- 2024. Neoantigen Cancer Vaccines and Different Immune Checkpoint Therapies Each Utilize Both Converging and Distinct Mechanisms. Conference. SITC. Houston, US.
- 2024. An integrated tumor, immune and genetic landscape of pleural mesothelioma to unleash effective immunotherapy avenues. Conference. SITC. Houston, US.
- 2024. Depletion of effector regulatory T cells drives major response to induction dual immune checkpoint blockade (ICB) in patients with oropharyngeal carcinoma (OPC). Conference. SITC. Houston, US.
- 2024. Predictive Molecular Signatures of Tumor Reactivity from reactive tumor infiltrating lymphocytes (TILs) in HPV-Positive Oropharyngeal Carcinoma (OPC). Conference. SITC. Houston, US.
- 2024. Impact of Bintrafusp alpha and Radiotherapy in Intrahepatic Cholangiocarcinoma: Proteomic and Transcriptomic Analysis. Conference. SITC. Houston, US.
- 2024. Transcriptionally distinct subset of TP53 mutant AMLs characterized by sensitivity to JAK inhibition and an inflamed tumor microenvironment. Conference. SITC. Houston, US.
- 2024. Characterization of transcriptional programs with translational implications in Natural Killer (NK) cells via single-cell data factorization and knowledge graph integration. Conference. SITC. Houston, US.
- 2024. Analysis of PD1+ T Cells and LS Presence in Pleural Mesothelioma Using Spatial and Machine Learning Approaches. Conference. SITC. Houston, US.
- 2024. Comparison of Spatial transcriptomic platforms in FFPE TMA samples. Conference. SITC. Houston, US.
- 2024. Granulocyte-mediated immune suppression in epithelioid malignant pleural mesothelioma related to chronic obstructive pulmonary disease. Conference. Division of Pathology and Laboratory Medicine Annual Research Day 2024, US.
- 2023. Modeling cancer evolution and TME from single-cell data. Invited. Cold Spring Harbor Asia. Suzhou, Jiangsu, US.
- 2023. Genetic Ancestry Inference from Single-Cell Data. Invited. Chan-Zuckerberg Initiative, CA, US.
- 2023. Immune “Hallmarks” construction via non-negative matrix factorization with data-driven functional validations and translational implications. Conference. SITC, CA, US.
- 2023. Explainable AI in Integrative Models of Rare Cancers. Conference. AI in Healthcare. Houston, US.
- 2023. Genetic ancestry mapping from patient single-cell sequencing data. Invited. HTAN. Boston, US.
- 2023. Stem-Cell Enriched Cellular Hierarchy of TP53 Mutant Acute Myeloid Leukemia Is Vulnerable to Targeted Protein Degradation of c-MYC. Conference. ASH, US.
- 2023. Generation and Screening of Various CD70 CAR NK Cells Identify the Most Effective Construct Against Hematologic Malignancies. Conference. ASH, US.
- 2023. Spatial Profiling of immune biomarkers in resected treatment-naive early stage lung adenocarcinoma. Conference. Spatial Profiling of immune biomarkers in resected treatment-naive early stage lung adenocarcinoma, US.
- 2023. Deciphering dysfunctional heterogeneity of tumor-infiltrating lymphocytes from malignant pleural mesothelioma. Conference. iMIG2023, US.
- 2023. Diversity of Tumor Immune Microenvironment landscape of epithelioid Malignant Pleural Mesothelioma in patients with primary surgically resected tumors. Conference. iMIG2023, US.
- 2023. Single-Cell Genomics and Proteomics Reveals Venetoclax-Resistant Monocytic Differentiation of TP53 LOH Clones in TP53 Mutant AML. Conference. ASH, US.
- 2022. Batch-Corrected Distance Mitigates Temporal and Spatial Variability for Clustering and Visualization of Single-Cell Gene Expression Data. Conference. RECOMB CCB. San Diego, CA, US.
- 2022. Deep Learning Modeling of the Relationship of Protein and RNA Levels with Manifold-Preserving Regularization. Conference. RECOMB CCB. San Diego, CA, US.
- 2022. Cell states identification and characterizing based on gene higher-order interactions. Conference. RECOMB CCB. San Diego, CA, US.
- 2022. Characterizing metabolism from bulk and single-cell RNA-seq data using METAFlux. Conference. RECOMB CCB. San Diego, CA, US.
- 2022. BHLHE40 orchestrates remodeling of the intratumoral immune cell populations in response to immune checkpoint therapy. Conference. AACR. New Orleans, TX, US.
- 2022. Spatial charting of single cell transcriptomes in tissues. Conference. AACR. New Orleans, US.
- 2022. Spatially resolved transcriptomics to understand mechanisms of response to neoadjuvant chemotherapy. Conference. AACR. New Orleans, US.
- 2022. novoBreak-rna: local assembly for novel splice junction detection from RNA-seq data. Conference. HitSeq ISMB 2022, US.
- 2022. Single Region Sampling Does Not Capture the Intra-Tumoral Immune Heterogeneity of Sarcomatoid Renal Cell Carcinoma. Conference. USCAP, US.
- 2022. Spatially resolved transcriptomics to understand mechanisms of response to neoadjuvant chemotherapy. Conference. AACR, US.
- 2022. Spatially resolved transcriptomics to understand mechanisms of response to neoadjuvant chemotherapy. Conference. AACR, US.
- 2022. Clinical and Molecular Characteristics of HER2-Low/Zero, Early Stage Triple-Negative Breast Cancer. Conference. SABCS, US.
- 2022. Single-cell tumor-infiltrating T cell landscape and dynamics in human papillomavirus positive oropharyngeal squamous cell carcinoma (HPV-OPSCC) before and during induction CTLA-4 and PD-1 immune checkpoint blockade (ICB). Conference. SITC, US.
- 2022. Polyploidy is necessary for apoptotic cell death in TP53-mut AML in response to Polo-Like-Kinase 4 (PLK4) Inhibition and results in Caspase 3 cleavage. Conference. ASH, US.
- 2022. Somatic Mutations in TP53 identified in T-cells of Patients with TP53 Mutated AML. Conference. ASH, US.
- 2022. Single Sample Gene Set Enrichment Analysis (ssGSEA) to Identify Dysregulated Pathways in a Biomarker Matched Pilot Study of Mantle Cell Lymphoma. Conference. ASHG, US.
- 2022. Characterization of Dysregulated Transcription in TP53-Mutated AML Subpopulations. Conference. ASH, US.
- 2022. Monopogene: variant calling and genetic ancestry inference from single cell sequencing. Conference. GCC single-cell symposium, US.
- 2022. Robust Pathway Analysis for scRNA-seq and Spatial Transcriptomics Data. Conference. GCC single-cell symposium, US.
- 2022. Intra-Tumoral Heterogeneity of Immune Microenvironment Biomarkers in Sarcomatoid Renal Cell Carcinoma. Conference. USCAP, US.
- 2022. Why are thromboembolic events so common in ovarian cancer? An investigation of tumor-mediated molecular markers. Conference. SGO 2022 Annual Meeting, US.
- 2021. Stratified Test Alleviates Batch Effects in Single-cell Data. Conference. AICoB 2020 & 2021, US.
- 2021. Bifurcation Cells Identification and Characterization Using Higher-order Interactions. Conference. MDA Leading Edge Symposium, US.
- 2021. Tumor and TME metabolic reaction flux framework from bulk and single cell gene expression data. Conference. MDA Leading Edge Symposium, US.
- 2021. Signal from evolutionary conservation among homologous sequences to predict mutation effect. Conference. MDA, US.
- 2021. Bifurcation Cells Identification and Characterization Using Higher-order Interactions. Conference. GCC SCOC, US.
- 2021. Integration of single-cell multiomics data. Conference. Single-Cell BIology 2021 Annual Meeting. virtual, US.
- 2021. Tumor and TME metabolic reaction flux framework from bulk and single cell gene expression data. Conference. GCC SCOC, US.
- 2021. Targeting Polo-Like Kinase 4 Triggers Polyploidy and Apoptotic Cell Death in TP53-Mutant Acute Myeloid Leukemia. Conference. ASH, US.
- 2021. Bi-order integration of single-cell and spatial transcriptomics data with partially overlapping features. Conference. GCC SCOC, US.
- 2021. Bi-order integration of single-cell and spatial transcriptomics data with partially overlapping features. Conference. MDA Leading Edge Symposium, US.
- 2021. Correlation of clinical response of patients with ERBB2 mutations treated with anti-HER2 therapies with in-vitro and in-silico actionability data. Conference. JCA-AACR2021, US.
- 2021. Single-cell manifold-preserving feature selection (SCMER) for detecting rare molecular programs. Conference. Cell-NCI Symposium: Beyond Cancer Genomics Toward Precision Oncology, US.
- 2021. Interpretable deep learning method enables precision MHC peptide presentation prediction and neoantigen discovery. Conference. Leading Edge of Cancer Research Symposium, US.
- 2021. Targeting uncoupling of gene expression from copy number in aneuploid cancers. Conference. Cell-NCI Symposium: Beyond Cancer Genomics Toward Precision Oncology, US.
- 2020. Unbiased integration of single cell multi-omics data. Conference. CZI seednetwork meeting, US.
- 2020. Single cell copy number lineage tracing and gene discovery. Conference. Gulf coast single-cell consortia, US.
- 2020. Latent periodic process inference from single-cell RNA-seq data. Conference. ISMB, US.
- 2020. Single-cell copy number lineage tracing enabling gene discovery. Conference. ISMB, US.
- 2020. A spatially resolved single cell atlas of the human breast. Conference. AACR, US.
- 2020. Overcoming PARP inhibitor resistance with molecularly guided rational combinations in triple-negative breast cancer patient-derived xenograft models. Conference. AACR, US.
- 2020. A spatially resolved single cell atlas of the human breast. Conference. AACR, US.
- 2020. Utility of Assessing HER2 RNA expression for precision medicine. Conference. AACR, US.
- 2020. Identifying novel therapeutic targets in cancers by elucidating the regulatory mechanics of genes insensitive to gene dosage changes. Conference. AACR, US.
- 2020. Elucidating Transcriptomic signatures in Leukemia Stem Cells and Minimal Residual Disease Following Treatment of Adverse Risk AMLs:. Conference. AACR, US.
- 2020. Modeling cancer-immune co-evolution from single-cell RNA-seq data. Conference. AACR, US.
- 2020. Mapping the Architecture of Adverse Risk AML using Single-Cell RNA Sequencing. Conference. ASH, US.
- 2019. Response to Immune Checkpoint Therapy and Clinical Outcome is Not Related to Proportion of Sarcomatous Component in Sarcomatoid Renal Cell Carcinoma. Conference. USCAP, US.
- 2019. Oxidative Phosphorylation is a Metabolic Vulnerability in Chemotherapy Resistant Triple Negative Breast Cancer. Conference. AACR/NCI/EORTC meeting, US.
- 2019. Ab initio Spillover Compensation in CyTOF Data. Conference. RECOMB-CCB, US.
- 2019. Integrated Transcriptomic-Genomic tool Texomer profiles cancer tissues. Conference. RECOMB-CCB. Washington DC, US.
- 2019. Latent periodic process inference from single-cell RNA-seq data. Conference. RECOMB-CCB. DC, US.
- 2019. Tracing tumor cellular evolution through copy number alterations. Conference. RECOMB-CCB. DC, US.
- 2019. The Concordance Between Manual and Sequence Based Tumor Estimation in Specimens with Low Tumor Fraction in Molecular Testing. Conference. USCAP 2019, US.
- 2019. Clinical outcome for gastrointestinal cancers with polymerase epsilon (POLE) mutations treated with immunotherapy. Conference. GI ASCO, US.
- 2019. Megabase length hypermutation accompanies human structural variation at 17p11.2. Conference. GSP meeting, US.
- 2019. Identification of Gene Expression Signatures in Leukemia Stem Cells and Minimal Residual Disease Following Treatment of Adverse Risk Acute Myeloid Leukemia. Conference. ASH, US.
- 2019. Towards A Human Breast Cell Atlas of Normal Cell Types. Conference. CSHL Asia, US.
- 2019. TP53 and PTEN Mutational Status and Outcome Prediction in Aggressive Chromophobe Renal Cell Carcinoma. Conference. USCAP 2019, US.
- 2018. Exploration of markers of synergistic lethality of PARP and PI3K-Akt-mTOR inhibitors in women’s cancer. Conference. SGO Annual meeting on Women's cancer. Honolulu, US.
- 2018. Hybrid Oncocytic Renal Tumors Display A Molecular Profile Intermediate Between Oncocytoma And Chromophobe RCC. Conference. USCAP, US.
- 2018. NanoString 3D Biology™ Technology: Simultaneous Digital Counting of DNA, RNA and Protein. Conference. AACR, US.
- 2018. Identifying the unknown primary site of metastatic tumors using support vector machines: an exploration of different dimension reduction models. Conference. Rice Data Science, US.
- 2018. Mixed-type Kernel Gaussian Process Latent Variable Kernel (mGPLVM) Helps Delineate Complex Biological Processes. Conference. Rice Data Science. Houston, US.
- 2017. SiFit: A method for inferring tumor trees from single-cell sequencing data under finite-site models. Conference. ASHG, FL, US.
- 2017. SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models. Conference. RECOMB-CCB. Los Angelos, US.
- 2017. CLIA-certified cancer gene panel-based machine learning method to predict sensitivity of anticancer drugs for precision oncology. Conference. ISMB 2020 HitSeq, US.
- 2017. High Depth Hybrid Capture Exome Sequencing Of Somatic Mutations For Personalized Cancer Therapy. Conference. the 12th Annual Academic Surgical Congress, US.
- 2016. Tumor phylogeny inference from single-cell DNA sequencing data. Invited. ICIBM 2016, US.
- 2016. Integrating genome and transcriptome data to predict functional driver mutation in breast cancer. Conference. Biostatistics. Houston, US.
- 2016. Integrating genome and transcriptome data to predict functional driver mutation in breast cancer. Conference. VarI-SIG. Orlando, US.
- 2016. An assembly approach utilizing next and third generation sequencing data for powerful structural variant detection. Conference. HiTSeq. Orlando, US.
- 2016. An Integrative Approach Utilizing Illumina and Pacbio Sequences for Powerful Structural Variant Detection. Conference. Southeast Texas Evolutionary Genetics and Genomics (STEGG) Symposium. Houston, US.
- 2016. Computational oncology in the era of precision medicine. Invited. BBSB. Houston, US.
- 2016. Human Genome Structural Variation Consortium. Invited. Human Genome Structural Variation Consortium. Cold Spring Harbor, US.
- 2016. Correlative biomarkers of clinical activity of the BCL-2 inhibitor, venetoclax (ABT-199/ GDC-0199), in acute myeloid leukemia patients. Conference. AACR, US.
- 2016. Patient Derived Xenografts to Test Emerging Therapies for Triple Negative Breast Cancer. Conference. AACR, US.
- 2015. Computational approaches for advancing cancer genomic medicine. Invited. Festival of Genomics. San Francisco, CA, US.
- 2015. TransVar: a multilevel variant annotator for precision medicine. Conference. TCGA network, US.
- 2015. Somatic Mutations In Young-Onset Colorectal Cancer Unrelated To Hereditary Syndromes: A Comparative Study Using High-Depth Targeted Exome Sequencing. Conference. 2015 Gastrointestinal Cancers Symposium, US.
- 2015. Multiple independent methods fail to confirm MET amplification rate reported in literature for metastatic colorectal cancer (mCRC). Conference. 2015 Gastrointestinal Cancers Symposium, US.
- 2014. ConvertHER: Evolution of Genomic Alterations from Primary to Metastatic Breast Cancer. Conference. 2014 San Antonio Breast Cancer Symposium. San Antonio, US.
- 2014. novoBreak: robust characterization of structural breakpoints in cancer genomes. Invited. dreamchallenges.org. San Diego, CA, US.
- 2014. ClinSeK: targeted clinical variant identification from high-throughput sequencing data. Conference. ASHG, US.
- 2014. Development and validation of a ultra-high depth FFPE targeted exome sequencing platform for routine cancer patient care. Conference. ASHG. San Diego, US.
- 2014. novoBreak: comprehensively characterizing somatic structural breakpoints in cancer genomes. Conference. ASHG. San Diego, US.
- 2014. Oncogenic driver hotspot identification through large-scale clinical genomics and functional screening programs. Conference. VariSig, US.
- 2014. Developing and validating a targeted exome sequencing platform for routine cancer patient care. Conference. HITSeq. Boston, US.
- 2014. ClinSeK: targeted clinical variant identification from high-throughput sequencing data. Conference. HITSeq. Boston, US.
- 2014. 1000 Genome Phase III Small indel genotyping and analysis of PCR-free genomes. Invited. 1000 Genome Phase III Small indel genotyping and analysis of PCR-free genomes. Cold Spring Harbor Lab, NY, US.
- 2013. Integrated Genotyping of Structural Variation. Invited. 2013 IEEE GlobalSIP Symposium on Bioinformatics and Systems Biology. Austin, TX, US.
- 2013. Preliminary molecular features of adult patients with gangliogliomas. Conference. Society for Neuro-Oncology. San Francisco, CA, US.
- 2013. Optimization of Targeted Sequencing Data Analysis in Cancer Clinics. Conference. Symposia on Cancer Research. Houston, US.
- 2013. T200: an integrated platform for personalized cancer therapy. Conference. Symposia on Cancer Research. Houston, US.
- 2013. CanDrA: Cancer-specific driver missense mutation annotation with optimized features. Conference. AACR, MD, US.
- 2012. OutBreak: identification of viral and retroposon insertions in cancer genomes. Conference. The Cancer Genome Atlas' 2nd Annual Scientific Symposium. Washington DC, MD, US.
- 2012. CanDrA: Cancer-Specific Driver Missense Mutation Annotation with Optimized Features. Conference. The Cancer Genome Atlas' 2nd Annual Scientific Symposium. Washington DC, MD, US.
- 2012. A unified framework for structural variant discovery from next generation sequencing data. Conference. Pacific BioScience. Marco Island, FL, US.
- 2011. BreakFusion: accurate profiling of tumor transcriptomes from NGS RNA-seq data. Conference. The Cancer Genome Atlas' 1st Annual Scientific Symposium. National Harbor, MD, US.
- Neoadjuvant and adjuvant tiragolumab plus atezolizumab in PD-L1-positive oral cavity squamous cell carcinoma. Hamburg, Hamburg, DE.
- AI‑Spatial Assistant (AISA): An Agentic AI Framework for Automated Pathology Data Review and Spatial–Molecular Functional Niche Discovery in Translational Cancer Science. AI in Health Conference. Houston, Texas, US.
- Lite3D: Lightweight 3D Tissue Reconstruction from Sparse Spatial Transcriptomics and Histology Images. AI in Health Conference. Houston, Texas, US.
- LitePath: a lightweight vision-language assistant for histopathological image chatting. AI in Health Conference. Houston, Texas, US.
- A phase II trial of adjuvant PD-1 blockade with endocrine therapy in hormone receptor positive inflammatory breast cancer: Circulating biomarkers and molecular correlates of clinical outcomes, US.
International Presentations
- 2026. Bhlhe40 Shapes Distinct T cell Reponses to anti-PD-1 and anti-CTLA-4 Immune Checkpoint Therapy, US.
- 2026. Oncolytic viruses induce sustained anti-tumor cytotoxicity in NK cells through AP-1 and IRF pathways activation, US.
- 2026. Phase I Trial of Cryoablation and Immunotherapy in Patients with Adaptive Immunotherapy Resistance, the CEDAR Trial: Cryoablation Challenge Evaluated in Adaptive-Immune Resistance. SIR 2026, US.
- 2026. Engineering CAR-T cell resistance to CAF-derived paracrine cAMP-mediated immunosuppression. SITC. Milwaukee, US.
- 2026. High-Dimensional CyTOF Profiling of Pleural Mesothelioma TIL 3.0 Products Reveals a Consistent CXCR3⁺ Effector-Memory CD8⁺ T cell Signature. 2026 CYTO, US.
- 2025. Agent-based modeling of cellular dynamics in adoptive cell therapy. Invited. Global Cancer Research Conference 2025 (G-CARE), US.
- 2025. INVESTIGATING THE EFFICACY OF PLEURAL MESOTHELIOMA ORGANOID CULTURE IN RECONSTITUTING EX VIVO TUMORIGENIC PHENOTYPE FROM TRADITIONAL 2D CULTURE, US.
- 2025. Integrative profiling of t-follicular helper cells heterogeneity and tumor microenvironment signatures in angioimmunoblastic T cell lymphoma. Conference, US.
- 2024. T-Cell Dysfunction Associated With The LRRK2 Mutation In The Pathogenesis Of Parkinson’s Disease. Conference. ASAP COSA 2024, US.
- 2024. Decoding Tumor Associated Macrophages and Metastasis in Pleural Mesothelioma. Conference. 2024 DPLM Annual Research Day, US.
- 2023. SINGLE-CELL EV PROFILING WITH TIMING™ IDENTIFIES A GENE SIGNATURE ASSOCIATED WITH METASTATIC BREAST CANCER. Conference. ISCT NA 2023. Houston, US.
- 2023. Revealing the clinical, molecular and spatial transcriptomic profile of resected treatment-naïve early stage lung adenocarcinoma. Conference. Revealing the clinical, molecular and spatial transcriptomic profile of resected treatment-naïve early stage lung adenocarcinoma, BE.
- 2023. Single-cell RNA (scRNA-seq) and T cell receptor (scTCR-seq) sequencing reveals TCR clonotype expansion and phenotypic states associated with exceptional responders (ER) after induction CTLA4 and PD-1 immune checkpoint blockade (ICB) in patients with HPV-positive head and neck squamous cell carcinoma (HNSCC). Conference. ASCO, US.
- 2023. Induction PD-1 and CTLA-4 immune checkpoint blockade induces T cell responses against HPV16 in patients with newly diagnosed HPV-positive HNSCC. Conference. ASCO, US.
- 2022. Univariate and multivariate analysis of clinical and immune features associated with overall survival (OS) in patients (pts) with melanoma brain metastases (MBMs). Conference. Society for Melanoma Research (SMR), US.
- 2021. Single-Cell Proteomics Identifies Leukemia Landscape Associated with Clinical Outcomes in R/R AML Treated with MDM2i (Milademetan) and FLT3i (Quizartinib): Putative Role of CD68 and Diversity Index. Conference. ASH, US.
- 2021. Identifying drug resistant states and their associated vulnerabilities from cell-line expression and drug-response profiles. Conference. Cell-NCI Symposium: Beyond Cancer Genomics Toward Precision Oncology, US.
- 2021. Molecular and immune features associated with of overall survival (OS) in patients (pts) with melanoma brain metastases (MBMs). Conference. SMR (Society for Melanoma Research) 2021 Conference, US.
- 2020. Keynote: Quantitative molecular dissection of cancer evolution. Invited. 2ND INTERNATIONAL SYMPOSIUM ON MATHEMATICAL AND COMPUTATIONAL ONCOLOGY (ISMCO), US.
- 2020. TP53 mutated AML is Associated with an Immune Dysfunction. Conference. European Hematology Association, DE.
- 2020. ESR1 Mutations Provide Novel Targets for Breast Cancer Immunotherapy. Conference. ASCO, US.
- 2020. Clinical Phenotyping Using Semantic Knowledge Graphs. Conference. AMIA 2020 Summit, US.
- 2018. Structural variant mutagenesis at 17p11.2 mediates increased local single nucleotide mutation rate and deamination of the genome. Conference. International Congress of Genetics in Brazil, US.
- 2017. A Feasibility Study of Returning Clinically Actionable Somatic Genomic Alterations Identified in a Research Laboratory. Conference. the Society of Surgical Oncology’s 70th Annual Cancer Symposium. Seatle, US.
- 2017. Pathogenic variants in DNA damage response genes in patients with advanced solid tumors. Conference. ASCO, US.
- 2017. Whole Exome Sequencing of Metaplastic Breast Cancer (MpBC): Mutation Status Impacts Survival. Conference. ASCO, US.
- 2017. Prevalence of incidental germline deleterious variants in hereditary cancer-related genes identified in matched tumor/normal sequencing of advanced solid tumors. Conference. ASCO, US.
- 2017. Genomic alterations driving breast cancer (BC) metastases and their relationship with the subtype switch in the GEICAM ConvertHER study. Conference. ASCO, US.
- 2016. Monovar: single-nucleotide variant detection in single cells. Conference. ASHG. Vancouver, CA.
- 2016. Integrating genome and transcriptome data to predict functional driver mutation in breast cancer. Conference. ASHG. Vancouver, CA.
- 2016. A hybrid approach combining next and third generation sequencing data for powerful structural variant detection. Conference. ASHG. Vancouver, CA.
- 2016. High Depth Hybrid Capture Exome Sequencing Of Somatic Mutations For Personalized Cancer Therapy. Conference. Society of Surgical Oncology, US.
- 2016. Validation of HER2 amplification as a negative predictive biomarker for anti-epidermal growth factor receptor antibody therapy in metastatic colorectal cancer. Conference. ASCO, US.
- 2015. Computational approaches for advancing cancer genomic medicine. Invited. Albert Einstein Hospital. San Paulo, BR.
- 2015. novoBreak: robust characterization of structural breakpoints in cancer genomes. Invited. ISMB/ECCB 2015. Dublin, IE.
- 2015. scSNV: A SNV Calling And Genotyping Method For Single-cell Sequencing Data. Conference. ISMB/ECCB 2015. Dublin, IE.
- 2015. Prevalence of Incidental Actionable Germline Mutations in 1000 Advanced Cancer Patients on a Prospective Somatic Genomic Profiling Program. Conference. ASCO, US.
- 2015. Demographics, tumor characteristics, and clinical outcomes associated with somatic mutations in 201 cancer-related genes in advanced melanoma patients (pts). Conference. ASCO, US.
- 2014. Towards Routine Molecular Profiling of Cancer Patients at MD Anderson. Invited. The 3rd World Genetics & Genomics Online Conference, US.
- 2014. Mutation and Copy Number Discordance in Primary vs. Metastatic Colorectal Cancer. Conference. ASCO, US.
- 2013. Informatics Infrastructure for Routine Personalized Medicine. Invited. AMIA. Washington DC, US.
- 2013. T200: AN INTEGRATED PLATFORM FOR PERSONALIZED CANCER THERAPY. Conference. Ken Chen. Paris, FR.
- 2013. Targeted Sequencing in Cancer Clinics. Conference. Ken Chen. Paris, FR.
- 2013. An Institution-wide Molecular Testing Program to facilitate Personalized Cancer Therapy. Conference. ASCO, US.
- 2012. Whole genome sequencing to characterize luminal-type breast cancer. Conference. ASCO, US.
- Neoadjuvant and adjuvant tiragolumab plus atezolizumab in PD-L1-positive oral cavity squamous cell carcinoma. Lugano, CH.
Formal Peers
- 2024. Revealing cellular-molecular signatures associated with cancer development and treatment. Invited. College Station, TX, US.
- 2023. Functional views of single-cell/spatial omics data. Invited, US.
- 2022. Population genetics using single-cell sequencing. Invited, US.
- 2022. Data integration/discrimination approaches for illuminating cancer immunology targets. Invited, US.
- 2021. Single-cell molecular dissection of cancer evolution. Invited, US.
- 2021. Cancer evolution and single-cell data analysis. Invited, US.
- 2020. Single-cell data analysis. Invited. Houston, TX, US.
- 2019. Single-cell copy number lineage tracing and functional analysis. Invited. Pittzburgh, OH, US.
- 2018. Single-cell omics. Invited, US.
- 2018. Single-cell omics. Invited, US.
- 2018. Computational analysis of single-cell data. Invited, US.
- 2018. Single-cell omics. Invited, US.
- 2017. Genetic underpinning and functions of allele-specific expressions in cancer. Invited, US.
- 2017. Functional integration of heterogeneous cancer genomes and transcriptomes. Invited, US.
- 2015. Computational tools for clinical genomic medicine. Invited. Sao Paulo, BR.
- 2015. novoBreak: robust characterization of structural breakpoints in cancer genomes. Invited. Dublin, IE.
- 2015. Computational Approaches for Advancing Cancer Genomic Medicine. Invited. Dallas, US.
- 2014. Targeted approaches in clinical cancer genomics. Invited. Houston, US.
- 2014. Computational approaches for cancer genomics. Invited, US.
- 2013. Identifying driver mutations in cancer genomes. Invited, US.
- 2013. Identifying driver mutations in cancer genomes. Invited, US.
- 2011. Towards comprehensive and accurate detection of structural variants in human genomes. Invited. Chapel Hill, NC, US.
Grant & Contract Support
| Date: | 2027 - 2032 |
| Title: | Macrophage Fate Remodeling to Overcome Resistance to Cancer Immunotherapy |
| Funding Source: | NCI |
| Role: | Co-I |
| ID: | R01CA325521 |
| Date: | 2027 - 2031 |
| Title: | AI‑Spatial Assistant (AISA): An Agentic AI Framework for Automated Pathology Data Review and Spatial–Molecular Functional Niche Discovery in Translational Cancer Science |
| Funding Source: | NIH |
| Role: | PI |
| ID: | 00030565 |
| Date: | 2027 - 2030 |
| Title: | AI-gUided longitUdinal modeling of Resistant Ovarian Residual disease for Adaptive therapy in Ovarian Cancer (AURORA-OC) |
| Funding Source: | Ovarian Cancer Research Alliance |
| Role: | PI |
| ID: | 00030573 |
| Date: | 2027 - 2029 |
| Title: | Defining Spatially Organized Immunosuppression and Metabolic Rewiring in MASLD-Associated Liver Cancer |
| Funding Source: | NIH |
| Role: | PI |
| ID: | 0003566 |
| Date: | 2026 - 2031 |
| Title: | AI-powered multiomic immunotherapeutic discovery of HPV peptide-TCR interactome in HPV+ cancer patients |
| Funding Source: | NIH |
| Role: | PI |
| ID: | R01CA319384 |
| Date: | 2026 - 2031 |
| Title: | Breaking the Zonation Code: Monocarboxylate Metabolism as a Driver of Liver Metabolic Disease |
| Funding Source: | NIDDK |
| Role: | MPI |
| ID: | R01DK150044 |
| Date: | 2026 - 2030 |
| Title: | OPTIMA: Oncology Precision Trials using Individualized Model Avatars |
| Funding Source: | NCI |
| Role: | MPI |
| ID: | UM1CA321705 |
| Date: | 2026 - 2029 |
| Title: | Spatial Metabolic Dissection of the CAF-Centric Niches in MASLD-Associated Hepatobiliary Cancer |
| Funding Source: | Cancer Prevention and Research Institute of Texas |
| Role: | PI |
| ID: | RP27035 |
| Date: | 2026 - 2028 |
| Title: | Discovering Biomarkers of Lymphovascular Invasion, Progression and Survival in Esophageal Adenocarcinoma Using a Multiomic Approach |
| Funding Source: | US Department of Defense |
| Role: | Co-I |
| ID: | RA251136 |
| Date: | 2026 - 2028 |
| Title: | Integrating ctDNA and Spatial Multi-Omics to Predict Relapse and Target Immune Suppression in Inflammatory Breast Cancer |
| Funding Source: | American Cancer Society |
| Role: | Co-I |
| ID: | 00027582 |
| Date: | 2026 - 2028 |
| Title: | Modulating the cAMP pathway to improve the activity of CAR-T cell therapy in kidney cancer |
| Funding Source: | US Department of Defense |
| Role: | Co-I |
| ID: | 00027524 |
| Date: | 2026 - 2031 |
| Title: | Liquid biopsy as a predictor for response to immune checkpoint inhibitors in patients with NSCLC |
| Funding Source: | Ohio State University via NIH |
| Role: | Co-I |
| ID: | 00028081 |
| Date: | 2026 - 2028 |
| Title: | Developing AI-Driven Personalized Early Detection and Clinical Decision Support for Prostate Cancer |
| Funding Source: | NATIONAL INSTITUTES OF HEALTH |
| Role: | PI |
| ID: | R21CA317878 |
| Date: | 2026 - 2028 |
| Title: | Evaluating a multimodality platform of tissue-, blood- and advanced imaging-based, predictive biomarkers to neoadjuvant immunotherapy and radiotherapy response in mucosal melanoma |
| Funding Source: | US Department of Defense |
| Role: | Co-I |
| ID: | GRANT14502937 |
| Date: | 2026 - 2027 |
| Title: | A Multiscale Structural-to-Functional Framework for Modeling TCR Cytotoxic Potency |
| Funding Source: | Duke University |
| Role: | Mentor |
| ID: | FP00029257 |
| Date: | 2026 - 2028 |
| Title: | Integrating patient-reported outcomes and T-cell receptor sequencing to predict immune-related adverse events |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | R01CA279749 |
| Date: | 2025 - 2027 |
| Title: | Metabolic rewiring of CAR-T cells to counter the hostile tumor microenvironment in ovarian cancer |
| Funding Source: | US Department of Defense |
| Role: | Co-I |
| ID: | GRANT14497316 |
| Date: | 2025 - 2026 |
| Title: | Multiplexed, Single‐cell Proteomic Assessment of Acute Myeloid Leukemia Proteomic Landscape in Patients Treated with CDK9 Inhibitor |
| Funding Source: | SELLAS Life Sciences Group |
| Role: | MPI |
| ID: | AWD0008125 |
| Date: | 2025 - 2030 |
| Title: | Advancing next-generation CAR-NK therapies targeting CD5 positive T cell malignancies to the clinic |
| Funding Source: | NIH |
| Role: | Co-I |
| ID: | R01CA303579 |
| Date: | 2025 - 2028 |
| Title: | Neoadjuvant combination anti-PD-L1 and anti-TIGIT immune checkpoint blockade in oral cavity squamous cell carcinoma |
| Funding Source: | Cancer Prevention & Research Institute of Texas |
| Role: | MPI |
| ID: | RP205201 |
| Date: | 2025 - 2028 |
| Title: | Developing Effective Cancer Vaccine-Based Combinatorial Therapies |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RP250200 |
| Date: | 2024 - 2029 |
| Title: | Dietary intervention to modulate the microbiome and immune response |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RP240557 |
| Date: | 2024 - 2026 |
| Title: | Insights into the Somatic Mutation Landscape from Single-Cell Omics |
| Funding Source: | Chan Zuckerberg Initiative |
| Role: | PI |
| ID: | DI3-0000000288 |
| Date: | 2024 - 2029 |
| Title: | The cross-talk between α-Synucleinopathies and T cell immunity in ADRD |
| Funding Source: | John Hopkins University (Subaward via NIH) |
| Role: | Principal Investigator-MDACC |
| ID: | R01AG089605 |
| Date: | 2024 - 2029 |
| Title: | Bhlhe40 Regulation of T Cell Function During Cancer Immunotherapy |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA282027 |
| Date: | 2024 - 2029 |
| Title: | TROP2-Directed CAR-NK Cells for the Immunotherapy of Pancreatic Cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA288617 |
| Date: | 2024 - 2027 |
| Title: | Multifaceted roles of AXL in shaping tumor immune microenvironment |
| Funding Source: | American Cancer Society (ACS) |
| Role: | Co-I |
| ID: | AWD00008475 |
| Date: | 2023 - 2029 |
| Title: | THOR: Targeted Hybrid Oncotherapeutic Regulation |
| Funding Source: | Advanced Research Projects Agency for Health (ARPA-H) |
| Role: | Co-I |
| ID: | AWD00008179 |
| Date: | 2023 - 2028 |
| Title: | The University of Texas MD Anderson Cancer Center SPORE in Ovarian Cancer |
| Funding Source: | NIH/NIDCR |
| Role: | Co-I |
| ID: | P50CA281701 |
| Date: | 2023 - 2028 |
| Title: | Medical Students Summer in Oncology at Anderson Research (Med Students SOAR) program |
| Funding Source: | NIH/NCI |
| Role: | Preceptor |
| ID: | R25CA265800 |
| Date: | 2023 - 2028 |
| Title: | Systematic Characterization and Targeting of Neomorph Drivers in Cancer |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | U01CA281902 |
| Date: | 2023 - 2028 |
| Title: | Next Generation Engineered NK Cells for Lymphoma Patients after CD19 CAR-T Cell Failure |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | R01CA280827 |
| Date: | 2023 - 2026 |
| Title: | Targeting Clonal Hematopoiesis (CH) to Prevent Acute Myeloid Leukemia (AML) |
| Funding Source: | Break Through Cancer |
| Role: | MPI |
| ID: | AWD00007334 |
| Date: | 2022 - 2029 |
| Title: | Partnerships for Accelerating Cancer Therapy – Statement of Work 7 |
| Funding Source: | Foundation for the National Institutes of Health |
| Role: | Co-I |
| ID: | AWD00006709 |
| Date: | 2021 - 2024 |
| Title: | Ancestry network for the human cell atlas in the eye |
| Funding Source: | Chan-Zuckerberg Initiative |
| Role: | Principal Investigator-MDACC |
| ID: | AWD00006490 |
| Date: | 2021 - 2026 |
| Title: | A Genome Data Analysis Center Focused on Batch Effect Analysis and Data Integration |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | U24CA264006 |
| Date: | 2021 - 2026 |
| Title: | Cancer Immune-Interception for Lynch Syndrome |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 R01 CA257375-02 |
| Date: | 2021 - 2024 |
| Title: | From cancer associations to altered immunity in the pathogenesis of Parkinson's disease |
| Funding Source: | Harvard Medical School |
| Role: | Co-I |
| ID: | AWD00005569 |
| Date: | 2020 - 2024 |
| Title: | Informatics for functional integration of heterogeneous cancer genome and transcriptome sequencing data |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 5 U01 CA247760-03 |
| Date: | 2020 - 2022 |
| Title: | Developing single-cell RNAseq-based genetics screens to identify novels targets for cancer immunotherapy |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Co-I |
| ID: | RP200520 |
| Date: | 2020 - 2024 |
| Title: | SPORE in Brain Cancer |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| ID: | 5 P50 CA127001-15 |
| Date: | 2020 - 2024 |
| Title: | Multifaceted Roles of AXL in shaping tumor immune microenvironment |
| Funding Source: | American Cancer Society (ACS) |
| Role: | Collaborator |
| Date: | 2020 - 2023 |
| Title: | Tumor-TAMs crosswalk enables bypass of oncogenic KRAS dependency in pancreatic cancer |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| Date: | 2020 - 2023 |
| Title: | Integrating single cell genomic and spatial information to delineate tumor heterogeneity and microenvironment interactions in inflammatory breast cancer |
| Funding Source: | Damon Runyon Cancer Research Foundation |
| Role: | Dry Lab Mentor |
| Date: | 2020 - 2023 |
| Title: | Texas Experimental Cancer Therapeutics Network - TEX CTN |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 UM1 CA 186688 - 03 |
| Date: | 2019 - 2023 |
| Title: | Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human Genomes |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 U24 HG007497-04 |
| Date: | 2019 - 2024 |
| Title: | Cancer Center Support (Core) Grant |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | P30CA016672 |
| Date: | 2019 - 2023 |
| Title: | Human Breast Cell Atlas Seed Network |
| Funding Source: | Chan Zuckerberg Initiative |
| Role: | PI |
| ID: | CZF2019-002432 |
| Date: | 2019 - 2022 |
| Title: | The Human Breast Cell Atlas (HBCA) Seed Network |
| Funding Source: | Chan Zuckerberg Institute |
| Role: | Co-PI |
| ID: | CZF2019-002432 |
| Date: | 2019 - 2020 |
| Title: | Novel mechanisms of emergence of hypervirulent group A Streptococcus |
| Funding Source: | NIH/NIAID |
| Role: | Other Significant Contributor |
| ID: | 1R21AI132920-01A1 |
| Date: | 2019 - 2023 |
| Title: | Partnerships for Accelerating Cancer Therapy – Statement of Work 3 |
| Funding Source: | Foundation for the National Institutes of Health |
| Role: | Co-I |
| ID: | AWD00004586 |
| Date: | 2018 - 2023 |
| Title: | Integrated Single Cell Genomics Core Facility |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | Collaborator |
| ID: | RP180684 |
| Date: | 2018 - 2023 |
| Title: | Integrative bioinformatics and functional characterization on oncogenic driver aberrations in cancer |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 U01 CA217842-04 |
| Date: | 2018 - 2022 |
| Title: | National Clinical Laboratory |
| Funding Source: | Leidos Biomedical Research, Inc |
| Role: | Co-I |
| ID: | HHSN261201500003I |
| Date: | 2018 - 2023 |
| Title: | Characterizing cancer genome instability and translational impact using new sequencing technologies |
| Funding Source: | Cancer Prevention & Research Institute of Texas (CPRIT) |
| Role: | PI |
| ID: | RP180248 |
| Date: | 2018 - 2019 |
| Title: | Pan-omics single-cell data integration for joint cell-type identification |
| Funding Source: | Chan Zuckerberg Initiative |
| Role: | PI |
| ID: | 2018-182735 |
| Date: | 2017 - 2028 |
| Title: | MD Anderson Cancer Immune Monitoring and Analysis Center MDA-CIMAC |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | U24CA224285 |
| Date: | 2017 - 2023 |
| Title: | MD Anderson Cancer Immune Monitoring and Analysis Center MDA-CIMAC |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1 U24 CA224285-01 |
| Date: | 2017 - 2023 |
| Title: | Translational Cancer Immune Monitoring and Analysis Center (TCIMAC) |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 1U24CA224285-01 |
| Date: | 2016 - 2021 |
| Title: | Deep Discovery and Clinical Interpretation of Germline and Somatic Cancer Drivers |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 U24 CA211006-05 |
| Date: | 2016 - 2019 |
| Title: | NO TITLE PROVIDED |
| Funding Source: | Andrew Sabin Family Foundation |
| Role: | PI |
| Date: | 2014 - 2018 |
| Title: | Virus Discovery and Characterization in Large-Scale Cancer Sequencing Data |
| Funding Source: | Washington University/NCI |
| Role: | Co-I |
| ID: | 5R01CA178383 |
| Date: | 2014 - 2020 |
| Title: | Southwest Early Clinical Trials Consortium |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 UM1 CA186688-03 |
| Date: | 2013 - 2016 |
| Title: | Informatics to Enable Routine Personalized Cancer Therapy |
| Funding Source: | NIH/NCI (Subcontract from the University of Texas Health Science Center) |
| Role: | Co-I |
| ID: | 1U01CA180964-01 |
| Date: | 2013 - 2019 |
| Title: | An Integrative Analysis of Structural Variation for the 1000 Genomes Project (U41) |
| Funding Source: | NIH/NCI (Subaward with The Jackson Laboratory) |
| Role: | Principal Investigator-MDACC |
| ID: | U41 HG007497 |
| Date: | 2013 - 2019 |
| Title: | Delineating Heterogeneous Structural Complexity in Cancer Genomes |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01 CA172652-03S1 |
| Date: | 2013 - 2019 |
| Title: | Applying the Cloud Computing resources to efficiently and comprehensively accomplish genomic analysis of TCGA/ICGC samples (R01 supplement) |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | R01 CA172652-03S1 |
| Date: | 2013 - 2019 |
| Title: | Delineating Heterogeneous Structural Complexity in Cancer Genomes |
| Funding Source: | NIH/NCI |
| Role: | PI |
| ID: | 4 R01 CA172652-04 |
| Date: | 2012 - 2017 |
| Title: | Center for Clinical and Translational Research (PP-2) |
| Funding Source: | NIH/NCI |
| Role: | Collaborator |
| ID: | UL1TR000371 |
| Date: | 2011 - 2023 |
| Title: | Novel Cord Blood-Derived Cellular Therapies |
| Funding Source: | NIH/NCI |
| Role: | Co-I |
| ID: | 5 P01 CA148600-12 |
Selected Publications
Peer-Reviewed Articles
- Cobb LP, Dai Y, Molina Ayala M, Ozirmak Lermi N, Hernandez SD, Davis J, Lee S, Lawson BC, Hajek RA, Celestino J, Liu J, Wang L, Soto LMS, Haymaker C, Chen K, Jiang M, Lu W, Sanchez-Espiridion B, Dang M, Hull S, Vining D, Fellman B, Yuan Y, Sood AK, Westin SN, Taylor J, Bevers M, Shafer A, Fleming ND, Lu KH, Gershenson DM, Jazaeri AA. A pilot translational study of neoadjuvant fulvestrant plus abemaciclib in women with advanced low-grade serous carcinoma. Nat Commun, 2026. e-Pub 2026. PMID: 42374029.
- Wang Y, Casarin S, Daher M, Mohanty V, Dede M, Shanley M, Dondossola E, La Posta L, Basar R, Rezvani K, Chen K. Agent-based modeling of cellular dynamics in adoptive cell therapy. Commun Biol 9(1), 2026. e-Pub 2026. PMID: 41673469.
- Zhu B, Aminu M, Chen P, Li JR, Dong C, Li C, Tian Y, Lu SW, Chen H, Ma C, Hu X, Ye J, Liu AY, Huang B, Rojas FR, Roger PCE, Shi O, Nilsson MB, Poteete A, Khan KB, Lu W, Solis Soto LM, Fujimoto J, Haymaker C, Wistuba II, Wei Z, Wang L, Gibbons DL, Chen K, Reuben A, Schenke JM, Heymach JV, Cheng C, Wu J, Zhang J. Spatial Profiling Reveals Distinct Molecular and Immune Evolution of Mouse Lung Adenocarcinoma Precancers with or Without Carcinogen Exposure. Adv Sci (Weinh):e12597, 2026. e-Pub 2026. PMID: 41580978.
- He S, Tan Y, Ye Q, M Gubin M, Dede M, Rafei H, Peng W, Rezvani K, Mohanty V, Chen K. AI-powered Immune Cell Knowledge Graph (ICKG) with granular immune contexts enables immune program interpretation. NPJ Artif Intell 2(1):13, 2026. e-Pub 2026. PMID: 41614120.
- Jaffery R, Zhao Y, Ahmed S, Schumacher JG, Ahn J, Shi L, Wang Y, Tan Y, Zhang J, Chen K, Tawbi H, Wang J, Schwarzschild MA, Peng W, Chen X. Soluble immune factor profiles in blood and CSF associated with LRRK2 mutations and Parkinson's disease. NPJ Parkinsons Dis, 2025. e-Pub 2025. PMID: 41309625.
- Liu Y, Hill HA, Li Y, McIntosh J, Jiang V, Yan F, Yao Y, Fei Y, Zhang J, Qu L, Yao J, Jain P, Chen K, Wang M. Integrative profiling strategies to guide personalized therapy in mantle cell lymphoma: a pilot study. NPJ Precis Oncol 9(1):373, 2025. e-Pub 2025. PMID: 41272086.
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- Link DC, Schuettpelz LG, Shen D, Wang J, Walter MJ, Kulkarni S, Payton JE, Ivanovich J, Goodfellow PJ, Le Beau M, Koboldt DC, Dooling DJ, Fulton RS, Bender RH, Fulton LL, Delehaunty KD, Fronick CC, Appelbaum EL, Schmidt H, Abbott R, O'Laughlin M, Chen K, McLellan MD, Varghese N, Nagarajan R, Heath S, Graubert TA, Ding L, Ley TJ, Zambetti GP, Wilson RK, Mardis ER. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. JAMA 305(15):1568-76, 2011. e-Pub 2011. PMID: 21505135.
- Welch JS, Westervelt P, Ding L, Larson DE, Klco JM, Kulkarni S, Wallis J, Chen K, Payton JE, Fulton RS, Veizer J, Schmidt H, Vickery TL, Heath S, Watson MA, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Ley TJ, Wilson RK. Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. JAMA 305(15):1577-84, 2011. e-Pub 2011. PMID: 21505136.
- Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, Project G. Mapping copy number variation by population-scale genome sequencing. Nature 470(7332):59-65, 2011. e-Pub 2011. PMID: 21293372.
- Wang J, Mullighan CG, Easton J, Roberts S, Heatley SL, Ma J, Rusch MC, Chen K, Harris CC, Ding L, Holmfeldt L, Payne-Turner D, Fan X, Wei L, Zhao D, Obenauer JC, Naeve C, Mardis ER, Wilson RK, Downing JR, Zhang J. CREST maps somatic structural variation in cancer genomes with base-pair resolution. Nat Methods 8(8):652-4, 2011. e-Pub 2011. PMID: 21666668.
- Consortium GP. A map of human genome variation from population-scale sequencing. Nature 467(7319):1061-73, 2010. e-Pub 2010. PMID: 20981092.
- Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 464(7291):999-1005, 2010. e-Pub 2010. PMID: 20393555.
- Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677-81, 2009. e-Pub 2009. PMID: 19668202.
- Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, Meyer RJ, Schindler JK, Pohl CS, Wallis JW, Shi X, Lin L, Schmidt H, Tang Y, Haipek C, Wiechert ME, Ivy JV, Kalicki J, Elliott G, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson MA, Baty J, Heath S, Shannon WD, Nagarajan R, Link DC, Walter MJ, Graubert TA, DiPersio JF, Wilson RK, Ley TJ. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 361(11):1058-66, 2009. e-Pub 2009. PMID: 19657110.
- Ley TJ, Mardis ER, Ding L, Fulton B, McLellan MD, Chen K, Dooling D, Dunford-Shore BH, McGrath S, Hickenbotham M, Cook L, Abbott R, Larson DE, Koboldt DC, Pohl C, Smith S, Hawkins A, Abbott S, Locke D, Hillier LW, Miner T, Fulton L, Magrini V, Wylie T, Glasscock J, Conyers J, Sander N, Shi X, Osborne JR, Minx P, Gordon D, Chinwalla A, Zhao Y, Ries RE, Payton JE, Westervelt P, Tomasson MH, Watson M, Baty J, Ivanovich J, Heath S, Shannon WD, Nagarajan R, Walter MJ, Link DC, Graubert TA, DiPersio JF, Wilson RK. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456(7218):66-72, 2008. e-Pub 2008. PMID: 18987736.
- Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, Larson DE, Chen K, Dooling DJ, Sabo A, Hawes AC, Shen H, Jhangiani SN, Lewis LR, Hall O, Zhu Y, Mathew T, Ren Y, Yao J, Scherer SE, Clerc K, Metcalf GA, Ng B, Milosavljevic A, Gonzalez-Garay ML, Osborne JR, Meyer R, Shi X, Tang Y, Koboldt DC, Lin L, Abbott R, Miner TL, Pohl C, Fewell G, Haipek C, Schmidt H, Dunford-Shore BH, Kraja A, Crosby SD, Sawyer CS, Vickery T, Sander S, Robinson J, Winckler W, Baldwin J, Chirieac LR, Dutt A, Fennell T, Hanna M, Johnson BE, Onofrio RC, Thomas RK, Tonon G, Weir BA, Zhao X, Ziaugra L, Zody MC, Giordano T, Orringer MB, Roth JA, Spitz MR, Wistuba II, Ozenberger B, Good PJ, Chang AC, Beer DG, Watson MA, Ladanyi M, Broderick S, Yoshizawa A, Travis WD, Pao W, Province MA, Weinstock GM, Varmus HE, Gabriel SB, Lander ES, Gibbs RA, Meyerson M, Wilson RK. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455(7216):1069-75, 2008. e-Pub 2008. PMID: 18948947.
- Research Network CGA. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 2008. e-Pub 2008. PMID: 18772890.
- Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res 17(5):659-66, 2007. e-Pub 2007. PMID: 17416743.
- Chen K, Hasegawa-Johnson M, Cohen A, Borys S, Kim S, Cole J, Choi JY. Prosody dependent speech recognition on radio news corpus of American English. IEEE Transactions on Speech and Audio Processing 14(1):232-245, 2006. e-Pub 2006.
- Kim S, Hasegawa-Johnson M, Chen K. Automatic recognition of pitch movements using time-delayed recurrent neural network. IEEE Signal Processing Letter, 2004. e-Pub 2004.
- Lermi N, Chen K, Naing A. Impact of avelumab and immune-stimulating agent combinations on the tumor microenvironment in patients with advanced solid tumors.
- Michael Wang et al. Interrogation of Signaling Dysregulation and Drug Efficacy for Precision Medicine in Mantle Cell Lymphoma. Haematologica.
- Bing Z. Carter et al. Acquired resistance of AML to menin inhibition is mediated by targetable alterations in.
- Martin Hemberg et al. Insights, opportunities and challenges provided by large cell atlases. Genome Biology.
- Kanishicar Sircar RREA. Genomic and Epigenomic Signatures Can Risk-Stratify Renal Oncocytic Tumors from Clinical-Grade Samples.
Invited Articles
- Zafar H, Navi N, Nakhleh L, Chen K. Computational approaches for inferring tumor evolution from single-cell genomic data. Current Opinion on Systems Biology 7:16-25, 2018. e-Pub 2018.
- Navin NE, Chen K. Genotyping tumor clones from single-cell data. Nat Methods 13(7):555-6, 2016. e-Pub 2016. PMID: 27355792.
- Chen K, Meric-Bernstam F. Whole genome sequencing in cancer clinics. EBioMedicine 2(1):15-6, 2015. e-Pub 2015. PMID: 26137530.
- Fan X, Abbott TE, Larson D, Chen K. BreakDancer: Identification of Genomic Structural Variation from Paired-End Read Mapping. Curr Protoc Bioinformatics 2014, 2014. e-Pub 2014. PMID: 25152801.
Review Articles
- Johnson A, Shen Y, Zheng X, Su F, Zeng J, Uzunparmak B, Breuer EK, Holla V, Kahle M, Kim SH, Vu T, Mills Shaw KR, Dumbrava EI, Yap TA, Rodon J, Routbort M, Patel K, Kulkarni S, Hansel D, Bryan J, Korkut A, Chen K, Meric-Bernstam F. The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology. Nat Rev Clin Oncol, 2026. e-Pub 2026. PMID: 41492079.
- Hemberg M, Marini F, Ghazanfar S, Al Ajami A, Abassi N, Anchang B, Benayoun BA, Cao Y, Chen K, Cuesta-Astroz Y, DeBruine Z, Dendrou CA, De Vlaminck I, Imkeller K, Korsunsky I, Lederer AR, Li JJ, Meysman P, Miller CL, Mullan KA, Ohler U, Panwar P, Patikas N, Schuck J, Siu JHY, Triche TJ Jr, Tsankov A, van der Laan SW, Yajima M, Yang J, Zanini F, Jelic I. Insights, opportunities, and challenges provided by large cell atlases. Genome Biol 26(1):358, 2025. e-Pub 2025. PMID: 41116172.
Other Articles
- Luo R, Chen K Somatic variant detection in normal tissues from single-cell sequencing data. Cell Genomics.
Abstracts
- Kopetz S, Overman MJ, Chen K, Lucio-Eterovic AK, Kee BK, Fogelman DR, Dasari A, Raghav KP, Sanchez EV, Phillips J, Shureigi I, Garrett CR, Wolff RA, Patel K, Aldape KD, Luthra R, Routbort M, Maru DM, Meric-Bernstam F, Eng C. Mutation and copy number discordance in primary versus metastatic colorectal cancer (mCRC). Journal of Clinical Oncology(32:15_suppl):3509-3509, 2014. e-Pub 2014.
Book Chapters
- Pan Y, Huang Y, Mohanty V, Chen K. Inferring Metabolic Flux from Gene Expression Data Using METAFlux. In: Methods in Molecular Biology. Humana Press Inc, 187-202, 2025.
- Chen K, Hasegawa-Johnson M, Cole J. A Factored Language Model for Prosody-Dependent Speech Recognition. In: Speech Synthesis and Recognition, Advanced Robotic Systems, 2007.
Patient Reviews
CV information above last modified September 05, 2026