Overview
Publication Portfolio
Peer-reviewed publications in biostatistics, clinical trials, machine learning, cancer genomics, and precision oncology. Research in AI, adaptive trial design, RNA-seq, and tumor subtyping.
Work spans clinical trials, genomics, machine learning, and epigenomics, with service on the Nature Medicine Statistical Advisory Panel (2024–) and as Associate Editor for Annals of Applied Statistics (2023–) and Statistical Methods in Medical Research.
Featured Publications
The ADAPT learning cancer treatment system: ARPA-H's initiative to revolutionize cancer therapy
Cancer Cell (2026)
Describes the ARPA-H ADAPT platform trial infrastructure for metastatic breast cancer, integrating adaptive Bayesian designs, real-time biomarker monitoring, and AI-driven decision support across multiple cancer centers.
Efficient computation of high-dimensional penalized piecewise constant hazard random effects models
Statistics in Medicine (2025)
Developed scalable methods for survival analysis with high-dimensional random effects, enabling multi-center clinical studies with complex correlation structures.
DNA mutational profiling in colorectal cancer reveals racial disparities
Journal of Clinical Oncology (2024)
Profiled clinically-relevant mutations in CRC patients receiving standard-of-care therapies in CALGB 80405, uncovering outcome differences and racial disparities in mutation distributions.
Deeply-learned generalized linear models with missing data
Journal of Computational and Graphical Statistics (2024)
Co-led with David Lim to adapt deep learning for incomplete EHRs, informing ARPA-H ADAPT eligibility and toxicity modeling.
Publications by Theme
Use the search box below to find publications by keyword, or browse by research theme.
Research Themes
Clinical Trials
2026
- The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapyCancer Cell, 2026
2024
- DNA mutational profiling in patients with colorectal cancer treated with standard of care reveals differences in outcome and racial distribution of mutationsJournal of Clinical Oncology, 2024
- Purity independent subtyping of tumors (PurIST) pancreatic cancer classifier: analytic validation of a 16-RNA expression signature distinguishing basal and classical subtypesThe Journal of Molecular Diagnostics, 2024
- ETHAN: A phase II study comparing different endocrine therapies for male breast cancer.2024
2022
- Purity independent subtyping of tumors (purist), a platform and sample type independent single sample classifier for treatment decision making in pancreatic cancer2022
2021
- Abstract PO-055: Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancerCancer Research, 2021
- Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancer.CANCER RESEARCH, 2021
2020
- Purity independent subtyping of tumors (PurIST), a clinically robust, single-sample classifier for tumor subtyping in pancreatic cancerClinical Cancer Research, 2020
Penalized Mixed Models & High-Dimensional Inference
2025
- Efficient Computation of High‐Dimensional Penalized Piecewise Constant Hazard Random Effects ModelsStatistics in Medicine, 2025
2024
- glmmpen: High dimensional penalized generalized linear mixed modelsThe R journal, 2024
- Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effectsBiometrics, 2024
- Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modelingBiostatistics, 2024
2023
- Estimating cell type composition using isoform expression one gene at a timeBiometrics, 2023
2020
- Modeling between-study heterogeneity for improved replicability in gene signature selection and clinical predictionJournal of the American Statistical Association, 2020
- Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modelingbioRxiv, 2020
2019
- Improved detection of epigenomic marks with mixed-effects hidden markov modelsBiometrics, 2019
- Supplemental Material for “Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction”2019
2017
- A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing dataThe annals of applied statistics, 2017
2014
- Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observationsJournal of the American Statistical Association, 2014
Cancer Genomics & Multi-Omic Integration
2025
- Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapyCommunications Medicine, 2025
- Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approachesCancer discovery, 2025
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)Annals of Oncology, 2025
- Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methodsNPJ Precision Oncology, 2025
- Defining the MYC-regulated transcriptome and kinome that support KRAS-and ERK-dependent growth of pancreatic cancerScience Signaling, 2025
- Abstract B100: Spatial relationships between tumor subtypes and tumor-promoting CAFs with clinical implicationsCancer Research, 2025
- Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasetsNPJ Breast Cancer, 2025
- Baseline and adaptive activated kinome profiling identifies PTK6 as a mediator of resistance to vemurafenib and dabrafenib but not encorafenib in BRAFV600-mutant metastatic melanomaCancer Research, 2025
- Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer2025
- Targeting pancreatic cancer stroma with vitamin D normalizes survival between fibroblast subtypesHPB, 2025
2024
- Tumor intrinsic subtypes and gene expression signatures in early-stage ERBB2/HER2-positive breast cancer: a pooled analysis of CALGB 40601, NeoALTTO, and NSABP B-41 trialsJAMA oncology, 2024
- DNA mutational profiling in patients with colorectal cancer treated with standard of care reveals differences in outcome and racial distribution of mutationsJournal of Clinical Oncology, 2024
- Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypesbioRxiv, 2024
- Purity independent subtyping of tumors (PurIST) pancreatic cancer classifier: analytic validation of a 16-RNA expression signature distinguishing basal and classical subtypesThe Journal of Molecular Diagnostics, 2024
- Tumor-intrinsic and cancer-associated fibroblast subtypes independently predict outcomes in pancreatic cancerAnnals of surgery, 2024
- Baseline pancreatic cancer CAF subtype determines response to neoadjuvant chemotherapyPANCREAS, 2024
- Development of DeCAF for CAF subtyping in patient tumorsPANCREAS, 2024
- Abstract A042: Clinical classification of cancer-associated fibroblast subtypes predicts prognosis and treatment responseCancer Research, 2024
- Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell linesPeerJ, 2024
- Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer2024
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in HER2+ early-breast cancer (EBC)CANCER RESEARCH, 2024
- Combination of tumor and CAF subtypes better predict response to neoadjuvant therapy in pancreatic cancerANNALS OF SURGICAL ONCOLOGY, 2024
- Molecular subtyping of pancreatic cancers using commercial sequencing platforms-a cautionary taleHPB, 2024
2023
- Prognostic and predictive value of immune-related gene expression signatures vs tumor-infiltrating lymphocytes in early-stage ERBB2/HER2-positive breast cancer: a correlative analysis of the CALGB 40601 and PAMELA trialsJAMA oncology, 2023
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencingBioinformatics, 2023
- Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype modelCommunications Biology, 2023
- Association of PIK3CA mutation with pathologic complete response and outcome by hormone receptor status and intrinsic subtype in early-stage ERBB2/HER2-positive breast cancerJAMA Network Open, 2023
- RHOAL57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signalingScience signaling, 2023
- Abstract PD18-04: Prognostic implications of PIK3CA mutation by hormone receptor status and intrinsic subtype in early stage HER2-positive breast cancer: a correlative analysis from CALGB 40601Cancer Research, 2023
- Impact of race and age on intrinsic subtype distribution and treatment decisions in metastatic breast cancer: Preliminary analysis of HARMONY (LCCC1829).2023
2022
- Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunityCell reports Medicine, 2022
- Functional and biological heterogeneity of KRASQ61 mutationsScience signaling, 2022
- Tumor immunogenomic features determine outcomes in patients with metastatic colorectal cancer treated with standard-of-care combinations of bevacizumab and cetuximabClinical Cancer Research, 2022
- Validation of cancer-type-dependent benefit from immune checkpoint blockade in TMB-H tumors identified by the FoundationOne CDx assayAnnals of Oncology, 2022
- Prognostic and predictive implications of the intrinsic subtypes and gene expression signatures in early-stage HER2+ breast cancer: A pooled analysis of CALGB 40601, NeoALTTO, and NSABP B-41 trials.2022
- Methods and compositions for prognostic and/or diagnostic subtyping of pancreatic cancer2022
- Efficient detection and classification of epigenomic changes under multiple conditionsBiometrics, 2022
- Purity independent subtyping of tumors (purist), a platform and sample type independent single sample classifier for treatment decision making in pancreatic cancer2022
2021
- High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer typesAnnals of Oncology, 2021
- The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancerJournal of Biological Chemistry, 2021
- FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036NPJ breast cancer, 2021
- Gene-expression based subtyping of pancreatic ductal adenocarcinoma2021
- Compression of quantification uncertainty for scRNA-seq countsBioinformatics, 2021
- Clinical application of next-generation sequencing in recurrent glioblastomaOnco, 2021
- Abstract PO-055: Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancerCancer Research, 2021
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-cell Silhouettes (SCISSORS) in Single-Cell SequencingbioRxiv, 2021
- Reply to:‘Real-world prevalence across 159 872 patients with cancer supports the clinical utility of TMB-H to define metastatic solid tumors for treatment with pembrolizumab.’by D. Fabrizio et al.Annals of Oncology, 2021
- Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell linesBioRxiv, 2021
- 120MO Prognostic value of immune gene-expression signatures (iGES) vs tumor-infiltrating lymphocytes (TILs) in early-stage HER2+ breast cancer: A combined analysis of CALGB 40601 (C40601) and PAMELA trialsAnnals of Oncology, 2021
- Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancer.CANCER RESEARCH, 2021
- Defining the KRAS-regulated kinome in KRAS-mutant pancreatic cancerbioRxiv, 2021
- Metadata record for the manuscript: FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036(No Title), 2021
2020
- Purity independent subtyping of tumors (PurIST), a clinically robust, single-sample classifier for tumor subtyping in pancreatic cancerClinical Cancer Research, 2020
- B cell–Derived IL35 Drives STAT3-Dependent CD8+ T-cell Exclusion in Pancreatic CancerCancer immunology research, 2020
- A P53-independent DNA damage response suppresses oncogenic proliferation and genome instabilityCell reports, 2020
- Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapyJCI insight, 2020
- INNV-17. NEXT GENERATION SEQUENCING IMPACTS OUTCOMES IN RECURRENT PRIMARY GLIOBLASTOMA: A SINGLE-CENTER RETROSPECTIVE ANALYSISNeuro-Oncology, 2020
- Epigrahmm–epigenomic r-based analysis with hidden Markov modelsF1000Research, 2020
2019
- Genetic determinants of cellular addiction to DNA polymerase thetaNature communications, 2019
- GSK2801, a BAZ2/BRD9 bromodomain inhibitor, synergizes with BET inhibitors to induce apoptosis in triple-negative breast cancerMolecular Cancer Research, 2019
- Next-generation sequencing (NGS) in metastatic colorectal cancer (mCRC): Novel mutated genes and their effect on response to therapy (Alliance)Annals of Oncology, 2019
- Multi-omic dissection of oncogenically active epiproteomes identifies drivers of proliferative and invasive breast tumorsIScience, 2019
- Improved detection of epigenomic marks with mixed-effects hidden markov modelsBiometrics, 2019
2018
- KRAS suppression-induced degradation of MYC is antagonized by a MEK5-ERK5 compensatory mechanismCancer cell, 2018
- Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissuesIn Proceedings of the National Academy of Sciences, 2018
- Stromal content is correlated with tissue site, contrast retention, and survival in pancreatic adenocarcinomaJCO precision oncology, 2018
- Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancer.MOLECULAR CANCER RESEARCH, 2018
- Abstract B34: Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancerMolecular Cancer Research, 2018
- Relationship between body mass index (BMI) and gene expression profiles of cervical cancer in the cancer genome atlas (TCGA) projectGynecologic Oncology, 2018
2017
- Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complexCancer discovery, 2017
- Combined kinase inhibitors of MEK1/2 and either PI3K or PDGFR are efficacious in intracranial triple-negative breast cancerNeuro-oncology, 2017
- Kinome profiling identifies druggable targets for novel human cytomegalovirus (HCMV) antiviralsMolecular & Cellular Proteomics, 2017
- A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing dataThe annals of applied statistics, 2017
2016
- Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent mannerIn Proceedings of the National Academy of Sciences, 2016
- Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammationMolecular metabolism, 2016
- Targeting IL-17A in multiple myeloma: a potential novel therapeutic approach in myelomaLeukemia, 2016
- Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas ProjectGynecologic oncology, 2016
2015
- Virtual microdissection identifies distinct tumor-and stroma-specific subtypes of pancreatic ductal adenocarcinomaNature genetics, 2015
- Functional and clinical impact of splicing factor dysregulation in multiple myelomaBlood, 2015
2014
- Heterogeneity of genomic evolution and mutational profiles in multiple myelomaNature communications, 2014
- Differential and limited expression of mutant alleles in multiple myelomaBlood, The Journal of the American Society of Hematology, 2014
- Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observationsJournal of the American Statistical Association, 2014
- Alternative splicing is a frequent event and impacts clinical outcome in myeloma: a large RNA-seq data analysis of newly-diagnosed myeloma patientsBlood, 2014
- Frequent Igh fusion transcripts with clinical impact in multiple myelomaBlood, 2014
- Functional and Clinical Relevance of Splicing Factor SRSF1 in Multiple Myeloma (MM)Blood, 2014
- Ongoing spontaneous DNA damage and the role of aberrant epigenome in multiple myelomaBlood, 2014
2013
- Bone marrow microenvironment affects the pathogenesis of multiple myeloma through downregulation of alternative splicing factor FOX2 in myeloma cellsBlood, 2013
2012
- An integrated encyclopedia of DNA elements in the human genome.Nature, 2012
2011
- ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regionsGenome biology, 2011
Machine Learning for Precision Oncology
2026
- The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapyCancer Cell, 2026
2025
- Unsupervised Imputation of Non-Ignorably Missing Data Using Importance-Weighted AutoencodersStatistics in Biopharmaceutical Research, 2025
2024
- Deeply learned generalized linear models with missing dataJournal of Computational and Graphical Statistics, 2024
- Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell linesPeerJ, 2024
- Supplementary Materials for Unsupervised Imputation of Non-ignorably Missing Data Using Importance-Weighted Autoencoders2024
2023
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencingBioinformatics, 2023
- Supporting Information for Deeply-Learned Generalized Linear Models with Missing Data2023
2021
- High-dimensional precision medicine from patient-derived xenograftsJournal of the American Statistical Association, 2021
- Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discoveryThe annals of applied statistics, 2021
- Compression of quantification uncertainty for scRNA-seq countsBioinformatics, 2021
- Handling non-ignorably missing features in electronic health records data using importance-weighted autoencodersarXiv preprint arXiv:2101.07357, 2021
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-cell Silhouettes (SCISSORS) in Single-Cell SequencingbioRxiv, 2021
- Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell linesBioRxiv, 2021
2020
- Supporting Information for Model-based Feature Selection and Clustering of RNA-seq Data for Unsupervised Subtype Discovery2020
2019
- High dimensional precision medicine from patient-derived xenograftsarXiv preprint arXiv:1912.06667, 2019
Epigenomics & Regulatory Genomics
2022
- Efficient detection and classification of epigenomic changes under multiple conditionsBiometrics, 2022
2020
- Epigrahmm–epigenomic r-based analysis with hidden Markov modelsF1000Research, 2020
2019
- GSK2801, a BAZ2/BRD9 bromodomain inhibitor, synergizes with BET inhibitors to induce apoptosis in triple-negative breast cancerMolecular Cancer Research, 2019
- Multi-omic dissection of oncogenically active epiproteomes identifies drivers of proliferative and invasive breast tumorsIScience, 2019
- Improved detection of epigenomic marks with mixed-effects hidden markov modelsBiometrics, 2019
2018
- Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissuesIn Proceedings of the National Academy of Sciences, 2018
- Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancer.MOLECULAR CANCER RESEARCH, 2018
- Abstract B34: Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancerMolecular Cancer Research, 2018
2017
- Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complexCancer discovery, 2017
- A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing dataThe annals of applied statistics, 2017
2016
- Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent mannerIn Proceedings of the National Academy of Sciences, 2016
2014
- Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observationsJournal of the American Statistical Association, 2014
- Ongoing spontaneous DNA damage and the role of aberrant epigenome in multiple myelomaBlood, 2014
2012
- An integrated encyclopedia of DNA elements in the human genome.Nature, 2012
2011
- ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regionsGenome biology, 2011
All Publications (Chronological)
2026
- The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapyCancer Cell, 2026
2025
- Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapyCommunications Medicine, 2025
- Unsupervised Imputation of Non-Ignorably Missing Data Using Importance-Weighted AutoencodersStatistics in Biopharmaceutical Research, 2025
- Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approachesCancer discovery, 2025
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)Annals of Oncology, 2025
- Efficient Computation of High‐Dimensional Penalized Piecewise Constant Hazard Random Effects ModelsStatistics in Medicine, 2025
- Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methodsNPJ Precision Oncology, 2025
- Defining the MYC-regulated transcriptome and kinome that support KRAS-and ERK-dependent growth of pancreatic cancerScience Signaling, 2025
- Abstract B100: Spatial relationships between tumor subtypes and tumor-promoting CAFs with clinical implicationsCancer Research, 2025
- Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasetsNPJ Breast Cancer, 2025
- Baseline and adaptive activated kinome profiling identifies PTK6 as a mediator of resistance to vemurafenib and dabrafenib but not encorafenib in BRAFV600-mutant metastatic melanomaCancer Research, 2025
- Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer2025
- Targeting pancreatic cancer stroma with vitamin D normalizes survival between fibroblast subtypesHPB, 2025
2024
- Tumor intrinsic subtypes and gene expression signatures in early-stage ERBB2/HER2-positive breast cancer: a pooled analysis of CALGB 40601, NeoALTTO, and NSABP B-41 trialsJAMA oncology, 2024
- DNA mutational profiling in patients with colorectal cancer treated with standard of care reveals differences in outcome and racial distribution of mutationsJournal of Clinical Oncology, 2024
- glmmpen: High dimensional penalized generalized linear mixed modelsThe R journal, 2024
- Determination of permissive and restraining cancer-associated fibroblast (DeCAF) subtypesbioRxiv, 2024
- Purity independent subtyping of tumors (PurIST) pancreatic cancer classifier: analytic validation of a 16-RNA expression signature distinguishing basal and classical subtypesThe Journal of Molecular Diagnostics, 2024
- Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effectsBiometrics, 2024
- ETHAN: A phase II study comparing different endocrine therapies for male breast cancer.2024
- Tumor-intrinsic and cancer-associated fibroblast subtypes independently predict outcomes in pancreatic cancerAnnals of surgery, 2024
- Deeply learned generalized linear models with missing dataJournal of Computational and Graphical Statistics, 2024
- Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modelingBiostatistics, 2024
- Baseline pancreatic cancer CAF subtype determines response to neoadjuvant chemotherapyPANCREAS, 2024
- Development of DeCAF for CAF subtyping in patient tumorsPANCREAS, 2024
- Abstract A042: Clinical classification of cancer-associated fibroblast subtypes predicts prognosis and treatment responseCancer Research, 2024
- Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell linesPeerJ, 2024
- Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer2024
- Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in HER2+ early-breast cancer (EBC)CANCER RESEARCH, 2024
- Supplementary Materials for Unsupervised Imputation of Non-ignorably Missing Data Using Importance-Weighted Autoencoders2024
- Combination of tumor and CAF subtypes better predict response to neoadjuvant therapy in pancreatic cancerANNALS OF SURGICAL ONCOLOGY, 2024
- Molecular subtyping of pancreatic cancers using commercial sequencing platforms-a cautionary taleHPB, 2024
2023
- Prognostic and predictive value of immune-related gene expression signatures vs tumor-infiltrating lymphocytes in early-stage ERBB2/HER2-positive breast cancer: a correlative analysis of the CALGB 40601 and PAMELA trialsJAMA oncology, 2023
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencingBioinformatics, 2023
- Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype modelCommunications Biology, 2023
- Association of PIK3CA mutation with pathologic complete response and outcome by hormone receptor status and intrinsic subtype in early-stage ERBB2/HER2-positive breast cancerJAMA Network Open, 2023
- RHOAL57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signalingScience signaling, 2023
- Estimating cell type composition using isoform expression one gene at a timeBiometrics, 2023
- Abstract PD18-04: Prognostic implications of PIK3CA mutation by hormone receptor status and intrinsic subtype in early stage HER2-positive breast cancer: a correlative analysis from CALGB 40601Cancer Research, 2023
- Supporting Information for Deeply-Learned Generalized Linear Models with Missing Data2023
- Impact of race and age on intrinsic subtype distribution and treatment decisions in metastatic breast cancer: Preliminary analysis of HARMONY (LCCC1829).2023
2022
- Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunityCell reports Medicine, 2022
- Functional and biological heterogeneity of KRASQ61 mutationsScience signaling, 2022
- Tumor immunogenomic features determine outcomes in patients with metastatic colorectal cancer treated with standard-of-care combinations of bevacizumab and cetuximabClinical Cancer Research, 2022
- Validation of cancer-type-dependent benefit from immune checkpoint blockade in TMB-H tumors identified by the FoundationOne CDx assayAnnals of Oncology, 2022
- Prognostic and predictive implications of the intrinsic subtypes and gene expression signatures in early-stage HER2+ breast cancer: A pooled analysis of CALGB 40601, NeoALTTO, and NSABP B-41 trials.2022
- Methods and compositions for prognostic and/or diagnostic subtyping of pancreatic cancer2022
- Efficient detection and classification of epigenomic changes under multiple conditionsBiometrics, 2022
- Purity independent subtyping of tumors (purist), a platform and sample type independent single sample classifier for treatment decision making in pancreatic cancer2022
2021
- High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer typesAnnals of Oncology, 2021
- The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancerJournal of Biological Chemistry, 2021
- FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036NPJ breast cancer, 2021
- High-dimensional precision medicine from patient-derived xenograftsJournal of the American Statistical Association, 2021
- Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discoveryThe annals of applied statistics, 2021
- Gene-expression based subtyping of pancreatic ductal adenocarcinoma2021
- Compression of quantification uncertainty for scRNA-seq countsBioinformatics, 2021
- Handling non-ignorably missing features in electronic health records data using importance-weighted autoencodersarXiv preprint arXiv:2101.07357, 2021
- Clinical application of next-generation sequencing in recurrent glioblastomaOnco, 2021
- Abstract PO-055: Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancerCancer Research, 2021
- Sub-Cluster Identification through Semi-Supervised Optimization of Rare-cell Silhouettes (SCISSORS) in Single-Cell SequencingbioRxiv, 2021
- Reply to:‘Real-world prevalence across 159 872 patients with cancer supports the clinical utility of TMB-H to define metastatic solid tumors for treatment with pembrolizumab.’by D. Fabrizio et al.Annals of Oncology, 2021
- Kinome state is predictive of cell viability in pancreatic cancer tumor and stroma cell linesBioRxiv, 2021
- 120MO Prognostic value of immune gene-expression signatures (iGES) vs tumor-infiltrating lymphocytes (TILs) in early-stage HER2+ breast cancer: A combined analysis of CALGB 40601 (C40601) and PAMELA trialsAnnals of Oncology, 2021
- Phase II clinical trial of subtype directed neoadjuvant therapy in patients with localized pancreatic cancer.CANCER RESEARCH, 2021
- Defining the KRAS-regulated kinome in KRAS-mutant pancreatic cancerbioRxiv, 2021
- Metadata record for the manuscript: FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036(No Title), 2021
2020
- Purity independent subtyping of tumors (PurIST), a clinically robust, single-sample classifier for tumor subtyping in pancreatic cancerClinical Cancer Research, 2020
- B cell–Derived IL35 Drives STAT3-Dependent CD8+ T-cell Exclusion in Pancreatic CancerCancer immunology research, 2020
- A P53-independent DNA damage response suppresses oncogenic proliferation and genome instabilityCell reports, 2020
- Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapyJCI insight, 2020
- Modeling between-study heterogeneity for improved replicability in gene signature selection and clinical predictionJournal of the American Statistical Association, 2020
- Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modelingbioRxiv, 2020
- INNV-17. NEXT GENERATION SEQUENCING IMPACTS OUTCOMES IN RECURRENT PRIMARY GLIOBLASTOMA: A SINGLE-CENTER RETROSPECTIVE ANALYSISNeuro-Oncology, 2020
- Supporting Information for Model-based Feature Selection and Clustering of RNA-seq Data for Unsupervised Subtype Discovery2020
- Epigrahmm–epigenomic r-based analysis with hidden Markov modelsF1000Research, 2020
2019
- Genetic determinants of cellular addiction to DNA polymerase thetaNature communications, 2019
- GSK2801, a BAZ2/BRD9 bromodomain inhibitor, synergizes with BET inhibitors to induce apoptosis in triple-negative breast cancerMolecular Cancer Research, 2019
- Next-generation sequencing (NGS) in metastatic colorectal cancer (mCRC): Novel mutated genes and their effect on response to therapy (Alliance)Annals of Oncology, 2019
- Multi-omic dissection of oncogenically active epiproteomes identifies drivers of proliferative and invasive breast tumorsIScience, 2019
- High dimensional precision medicine from patient-derived xenograftsarXiv preprint arXiv:1912.06667, 2019
- Improved detection of epigenomic marks with mixed-effects hidden markov modelsBiometrics, 2019
- Supplemental Material for “Modeling Between-Study Heterogeneity for Improved Replicability in Gene Signature Selection and Clinical Prediction”2019
2018
- KRAS suppression-induced degradation of MYC is antagonized by a MEK5-ERK5 compensatory mechanismCancer cell, 2018
- Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissuesIn Proceedings of the National Academy of Sciences, 2018
- Stromal content is correlated with tissue site, contrast retention, and survival in pancreatic adenocarcinomaJCO precision oncology, 2018
- Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancer.MOLECULAR CANCER RESEARCH, 2018
- Abstract B34: Novel synergistic combination therapies with BET bromodomain inhibitors in triple-negative breast cancerMolecular Cancer Research, 2018
- Relationship between body mass index (BMI) and gene expression profiles of cervical cancer in the cancer genome atlas (TCGA) projectGynecologic Oncology, 2018
2017
- Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complexCancer discovery, 2017
- Combined kinase inhibitors of MEK1/2 and either PI3K or PDGFR are efficacious in intracranial triple-negative breast cancerNeuro-oncology, 2017
- Kinome profiling identifies druggable targets for novel human cytomegalovirus (HCMV) antiviralsMolecular & Cellular Proteomics, 2017
- A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing dataThe annals of applied statistics, 2017
2016
- Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent mannerIn Proceedings of the National Academy of Sciences, 2016
- Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammationMolecular metabolism, 2016
- Targeting IL-17A in multiple myeloma: a potential novel therapeutic approach in myelomaLeukemia, 2016
- Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas ProjectGynecologic oncology, 2016
2015
- Virtual microdissection identifies distinct tumor-and stroma-specific subtypes of pancreatic ductal adenocarcinomaNature genetics, 2015
- Mu opioid splice variant MOR-1K contributes to the development of opioid-induced hyperalgesiaPloS one, 2015
- Trends and predictors of resection of the primary tumor for patients with stage IV colorectal cancerJournal of surgical oncology, 2015
- Functional and clinical impact of splicing factor dysregulation in multiple myelomaBlood, 2015
- Radiation therapy for unresectable pancreatic adenocarcinoma: population-based trends in utilization and survival rates in the United StatesJAMA surgery, 2015
2014
- Heterogeneity of genomic evolution and mutational profiles in multiple myelomaNature communications, 2014
- Differential and limited expression of mutant alleles in multiple myelomaBlood, The Journal of the American Society of Hematology, 2014
- Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observationsJournal of the American Statistical Association, 2014
- Alternative splicing is a frequent event and impacts clinical outcome in myeloma: a large RNA-seq data analysis of newly-diagnosed myeloma patientsBlood, 2014
- Frequent Igh fusion transcripts with clinical impact in multiple myelomaBlood, 2014
- Functional and Clinical Relevance of Splicing Factor SRSF1 in Multiple Myeloma (MM)Blood, 2014
- Ongoing spontaneous DNA damage and the role of aberrant epigenome in multiple myelomaBlood, 2014
2013
- Pain modality-and sex-specific effects of COMT genetic functional variantsPAIN®, 2013
- Bone marrow microenvironment affects the pathogenesis of multiple myeloma through downregulation of alternative splicing factor FOX2 in myeloma cellsBlood, 2013
2012
- An integrated encyclopedia of DNA elements in the human genome.Nature, 2012
- Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase ActivityMolecular Pain, 2012
2011
- ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regionsGenome biology, 2011
- Cytokine biomarkers and chronic pain: association of genes, transcription, and circulating proteins with temporomandibular disorders and widespread palpation tendernessPain, 2011