2025

1. Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

   Yi Xu, Xianlu L Peng, Michael P East, Ian C McCabe, Grace C Stroman, Madison R Jenner, Priscilla S Chan, Ashley B Morrison, Emily C Shen, Silvia G Hererra, and  others

   Cancer Discovery, 2025
2. Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy

   Akram Yazdani, Heinz-Josef Lenz, Gianluigi Pillonetto, Raul Mendez-Giraldez, Azam Yazdani, Hanna Sanoff, Reza Hadi, Esmat Samiei, Alan P Venook, Mark J Ratain, and  others

   Communications Medicine, 2025
3. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)☆

   Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

   Annals of Oncology, 2025
4. Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets

   Brooke M Felsheim, Aranzazu Fernandez-Martinez, Cheng Fan, Adam D Pfefferle, Michele C Hayward, Katherine A Hoadley, Naim U Rashid, Sara M Tolaney, George Somlo, Lisa A Carey, and  others

   NPJ Breast Cancer, 2025

2024

1. 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 Trials

   Aranzazu Fernandez-Martinez, Mattia Rediti, Gong Tang, Tomás Pascual, Katherine A Hoadley, David Venet, N.U. Rashid, Patricia A Spears, Md N Islam, Sarra El-Abed, and  others

   JAMA Oncology, 2024
2. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2+ early breast cancer (EBC)

   Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

   Annals of Oncology, 2024
3. Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer

   Jen Jen Yeh, Richard Moffitt, and Naim Ur Rashid

   Jun 2024

   US Patent 12,000,003

2023

1. 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 Trials

   Aranzazu Fernandez-Martinez, Tomás Pascual, Baljit Singh, Paolo Nuciforo, N.U. Rashid, Karla V Ballman, Jordan D Campbell, Katherine A Hoadley, Patricia A Spears, Laia Pare, and  others

   JAMA Oncology, Jun 2023
2. Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model

   Luke A Torre-Healy, Ryan R Kawalerski, Ki Oh, Lucie Chrastecka, Xianlu L Peng, Andrew J Aguirre, N.U. Rashid, Jen Jen Yeh, and Richard A Moffitt

   Communications Biology, Jun 2023

2021

1. FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

   Steven P Angus, Timothy J Stuhlmiller, Gaurav Mehta, Samantha M Bevill, Daniel R Goulet, J Felix Olivares-Quintero, Michael P East, Maki Tanioka, Jon S Zawistowski, Darshan Singh, and  others

   NPJ breast cancer, Jun 2021
2. 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.

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, NT Ueno, and  others

   Annals of Oncology, Jun 2021
3. The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer

   J Nathaniel Diehl, Jennifer E Klomp, Kayla R Snare, Priya S Hibshman, Devon R Blake, Zane D Kaiser, Thomas SK Gilbert, Elisa Baldelli, Mariaelena Pierobon, Björn Papke, and  others

   Journal of Biological Chemistry, Jun 2021

2016

1. Targeting IL-17A in multiple myeloma: a potential novel therapeutic approach in myeloma

   Rao H Prabhala, Mariateresa Fulciniti, Dheeraj Pelluru, N.U. Rashid, Andreea Nigroiu, Puru Nanjappa, Christine Pai, Saem Lee, Nithya S Prabhala, Rajya Lakshmi Bandi, and  others

   Leukemia, Jun 2016
2. Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas Project

   Dario R Roque, Liza Makowski, Ting-Huei Chen, N.U. Rashid, D Neil Hayes, and Victoria Bae-Jump

   Gynecologic oncology, Jun 2016

2015

1. Radiation therapy for unresectable pancreatic adenocarcinoma: population-based trends in utilization and survival rates in the United States

   Mia Shapiro, N.U. Rashid, Qin Huang, Shira L Galper, Valia A Boosalis, Edward E Whang, and Jason S Gold

   JAMA surgery, Jun 2015

2025

1. Efficient computation of high-dimensional penalized piecewise constant hazard random effects survival models

   Hillary M Heiling^*, N.U. Rashid, Quefeng Li, Xianlu L Peng, Jen Jen Yeh, and Joseph G Ibrahim

   Statistics in Medicine, Accepted, In Press, 2025

2024

1. Biostat

   Differential Transcript Usage Analysis Incorporating Quantification Uncertainty Via Compositional Measurement Error Regression Modeling

   Amber Marie Young^*, S. Van Buren^*, and N.U. Rashid

   Biostatistics, 2024
2. glmmPen: high dimensional penalized generalized linear mixed models

   Hillary M Heiling, Naim U Rashid, Quefeng Li, and Joseph G Ibrahim

   The R journal, 2024
3. Biometr

   Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effects

   Hillary M Heiling^*, N.U. Rashid, Quefeng Li, Xianlu L Peng, Jen Jen Yeh, and Joseph G Ibrahim

   Biometrics, 2024
4. Purity Independent Subtyping of Tumors (PurIST) Pancreatic Cancer Classifier: Analytic Validation of a 16-RNA Expression Signature Distinguishing Basal and Classical Subtypes

   Yan Li, Jason D Merker, Rachana Kshatriya, Dimitri G Trembath, Ashley B Morrison, Peyton C Kuhlers, Naim U Rashid, Jen Jen Yeh, and Margaret L Gulley

   The Journal of Molecular Diagnostics, 2024

2023

1. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in Single-Cell RNA-Sequencing

   Jack Leary, Yi Xu, Ashley B Morrison, Chong Jin, Emily Shen, Peyton C Kuhlers, Ye Su, N.U. Rashid, Jen Jen Yeh, and Peng Xianlu

   Bioinformatics, 2023
2. Estimating cell type composition using isoform expression one gene at a time

   Hillary M Heiling^*, Douglas R Wilson, N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Biometrics, 2023

2022

1. Efficient detection and classification of epigenomic changes under multiple conditions

   Pedro L. Baldoni^*, N.U. Rashid, and Joseph G. Ibrahim

   Biometrics, 2022

   Abs

   Abstract Epigenomics, the study of the human genome and its interactions with proteins and other cellular elements, has become of significant interest in recent years. Such interactions have been shown to regulate essential cellular functions and are associated with multiple complex diseases. Therefore, understanding how these interactions may change across conditions is central in biomedical research. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is one of several techniques to detect local changes in epigenomic activity (peaks). However, existing methods for differential peak calling are not optimized for the diversity in ChIP-seq signal profiles, are limited to the analysis of two conditions, or cannot classify specific patterns of differential change when multiple patterns exist. To address these limitations, we present a flexible and efficient method for the detection of differential epigenomic activity across multiple conditions. We utilize data from the ENCODE Consortium and show that the presented method, epigraHMM, exhibits superior performance to current tools and it is among the fastest algorithms available, while allowing the classification of combinatorial patterns of differential epigenomic activity and the characterization of chromatin regulatory states.

2021

1. Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discovery

   David K Lim^*, N.U. Rashid, and Joseph G Ibrahim

   Annals of Applied Statistics, 2021
2. Compression of quantification uncertainty for scRNA-seq counts

   Scott Van Buren^*, Hirak Sarkar, Avi Srivastava, N.U. Rashid, Rob Patro, and Michael I Love

   Bioinformatics, 2021

2020

1. JASA

   Modeling Between-Study Heterogeneity for Improved Reproducibility in Gene Signature Selection and Clinical Prediction

   N.U. Rashid, Quefeng Li, Jen Jen Yeh, and Joseph G Ibrahim

   Journal of the American Statistical Association, 2020
2. JASA

   High-Dimensional Precision Medicine From Patient-Derived Xenografts

   N.U. Rashid, Daniel J Luckett, Jingxiang Chen, Michael T Lawson, Longshaokan Wang, Yunshu Zhang, Eric B Laber, Yufeng Liu, Jen Jen Yeh, Donglin Zeng, and  others

   Journal of the American Statistical Association, 2020
3. CCR

   Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer

   N.U. Rashid, Xianlu L Peng, Chong Jin, Richard A Moffitt, Keith E Volmar, Brian A Belt, Roheena Z Panni, Timothy M Nywening, Silvia G Herrera, Kristin J Moore, and  others

   Clinical Cancer Research, 2020

2019

1. Improved detection of epigenomic marks with mixed-effects hidden Markov models

   Pedro L Baldoni^*, N.U. Rashid, and Joseph G Ibrahim

   Biometrics, 2019

2017

1. Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex

   Jon S Zawistowski, Samantha M Bevill, Daniel R Goulet, Timothy J Stuhlmiller, Adriana S Beltran, Jose F Olivares-Quintero, Darshan Singh, Noah Sciaky, Joel S Parker, N.U. Rashid, and  others

   Cancer discovery, 2017

2016

1. A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing data

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Annals of Applied Statistics, 2016

2015

1. Trends and predictors of resection of the primary tumor for patients with stage IV colorectal cancer

   Mia Shapiro, N.U. Rashid, Edward E Whang, Valia A Boosalis, Qin Huang, Charles Yoon, Mandeep S Saund, and Jason S Gold

   Journal of surgical oncology, 2015

2014

1. Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observations

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Journal of the American Statistical Association, 2014

2025

1. Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

   Yi Xu, Xianlu L Peng, Michael P East, Ian C McCabe, Grace C Stroman, Madison R Jenner, Priscilla S Chan, Ashley B Morrison, Emily C Shen, Silvia G Hererra, and  others

   Cancer Discovery, 2025
2. Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy

   Akram Yazdani, Heinz-Josef Lenz, Gianluigi Pillonetto, Raul Mendez-Giraldez, Azam Yazdani, Hanna Sanoff, Reza Hadi, Esmat Samiei, Alan P Venook, Mark J Ratain, and  others

   Communications Medicine, 2025
3. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)☆

   Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

   Annals of Oncology, 2025
4. Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets

   Brooke M Felsheim, Aranzazu Fernandez-Martinez, Cheng Fan, Adam D Pfefferle, Michele C Hayward, Katherine A Hoadley, Naim U Rashid, Sara M Tolaney, George Somlo, Lisa A Carey, and  others

   NPJ Breast Cancer, 2025

2024

1. Biostat

   Differential Transcript Usage Analysis Incorporating Quantification Uncertainty Via Compositional Measurement Error Regression Modeling

   Amber Marie Young^*, S. Van Buren^*, and N.U. Rashid

   Biostatistics, 2024
2. JCGS

   Deeply Learned Generalized Linear Models with Missing Data

   David K Lim, Naim U Rashid, Junier B Oliva, and Joseph G Ibrahim

   Journal of Computational and Graphical Statistics, 2024
3. glmmPen: high dimensional penalized generalized linear mixed models

   Hillary M Heiling, Naim U Rashid, Quefeng Li, and Joseph G Ibrahim

   The R journal, 2024
4. 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 Trials

   Aranzazu Fernandez-Martinez, Mattia Rediti, Gong Tang, Tomás Pascual, Katherine A Hoadley, David Venet, N.U. Rashid, Patricia A Spears, Md N Islam, Sarra El-Abed, and  others

   JAMA Oncology, 2024
5. JCO

   DNA mutational profiling in patients with colorectal cancer treated with standard of care reveals differences in outcome and racial distribution of mutations

   Federico Innocenti, Wancen Mu, Xueping Qu, Fang-Shu Ou, Omar Kabbarah, Charles David Blanke, Alan P Venook, Heinz-Josef Lenz, and N.U. Rashid

   Journal of Clinical Oncology, 2024
6. Purity Independent Subtyping of Tumors (PurIST) Pancreatic Cancer Classifier: Analytic Validation of a 16-RNA Expression Signature Distinguishing Basal and Classical Subtypes

   Yan Li, Jason D Merker, Rachana Kshatriya, Dimitri G Trembath, Ashley B Morrison, Peyton C Kuhlers, Naim U Rashid, Jen Jen Yeh, and Margaret L Gulley

   The Journal of Molecular Diagnostics, 2024
7. Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines

   Matthew E Berginski, Madison R Jenner, Chinmaya U Joisa, Gabriela Herrera Loeza, Brian T Golitz, Matthew B Lipner, Jack R Leary, Naim Rashid, Gary L Johnson, Jen Jen Yeh, and  others

   PeerJ, 2024
8. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2+ early breast cancer (EBC)

   Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

   Annals of Oncology, 2024
9. Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer

   Jen Jen Yeh, Richard Moffitt, and Naim Ur Rashid

   Jun 2024

   US Patent 12,000,003

2023

1. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in Single-Cell RNA-Sequencing

   Jack Leary, Yi Xu, Ashley B Morrison, Chong Jin, Emily Shen, Peyton C Kuhlers, Ye Su, N.U. Rashid, Jen Jen Yeh, and Peng Xianlu

   Bioinformatics, Jun 2023
2. 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 Trials

   Aranzazu Fernandez-Martinez, Tomás Pascual, Baljit Singh, Paolo Nuciforo, N.U. Rashid, Karla V Ballman, Jordan D Campbell, Katherine A Hoadley, Patricia A Spears, Laia Pare, and  others

   JAMA Oncology, Jun 2023
3. Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model

   Luke A Torre-Healy, Ryan R Kawalerski, Ki Oh, Lucie Chrastecka, Xianlu L Peng, Andrew J Aguirre, N.U. Rashid, Jen Jen Yeh, and Richard A Moffitt

   Communications Biology, Jun 2023
4. RHOAL57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signaling

   Antje Schaefer, Richard G Hodge, Haisheng Zhang, G Aaron Hobbs, Julien Dilly, Minh V Huynh, Craig M Goodwin, Feifei Zhang, J Nathaniel Diehl, Mariaelena Pierobon, and  others

   Science signaling, Jun 2023
5. Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer

   Paola Zagami, Aranzazu Fernandez-Martinez, N.U. Rashid, Katherine A Hoadley, Patricia A Spears, Giuseppe Curigliano, Charles M Perou, and Lisa A Carey

   JAMA Network Open, Jun 2023

2022

1. Efficient detection and classification of epigenomic changes under multiple conditions

   Pedro L. Baldoni^*, N.U. Rashid, and Joseph G. Ibrahim

   Biometrics, Jun 2022

   Abs

   Abstract Epigenomics, the study of the human genome and its interactions with proteins and other cellular elements, has become of significant interest in recent years. Such interactions have been shown to regulate essential cellular functions and are associated with multiple complex diseases. Therefore, understanding how these interactions may change across conditions is central in biomedical research. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is one of several techniques to detect local changes in epigenomic activity (peaks). However, existing methods for differential peak calling are not optimized for the diversity in ChIP-seq signal profiles, are limited to the analysis of two conditions, or cannot classify specific patterns of differential change when multiple patterns exist. To address these limitations, we present a flexible and efficient method for the detection of differential epigenomic activity across multiple conditions. We utilize data from the ENCODE Consortium and show that the presented method, epigraHMM, exhibits superior performance to current tools and it is among the fastest algorithms available, while allowing the classification of combinatorial patterns of differential epigenomic activity and the characterization of chromatin regulatory states.

2. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab

   Federico Innocenti, Akram Yazdani, N.U. Rashid, Xueping Qu, Fang-Shu Ou, Scott Van Buren, Monica M. Bertagnolli, Omar Kabbarah, Charles David Blanke, Alan P. Venook, Heinz-Josef Lenz, and Benjamin G. Vincent

   Clinical Cancer Research, Apr 2022

   Abs

   CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS).Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured.Increased M2 macrophage score [HR, 6.30; 95\% confidence interval (CI), 3.0–12.15] and TGFβ signature expression (HR, 1.35; 95\% CI, 1.05–1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95\% CI, 0.38–0.87) and activated memory CD4+ T cells (HR, 0.34; 95\% CI, 0.16–0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0–1 beneficial features associated with longer OS, and the median (95\% CI) OS decreased from 42.5 (35.8–47.8) to 31.0 (28.8–34.4), 25.2 (20.6–27.9), and 17.7 (13.5–20.4) months respectively (P = 3.48e–11).New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.

3. Methods and compositions for prognostic and/or diagnostic subtyping of pancreatic cancer

   Richard Moffitt, Jen Jen Yeh, and Naim Ur Rashid

   Apr 2022

   US Patent App. 17/336,600
4. Validation of cancer-type-dependent benefit from immune checkpoint blockade in TMB-H tumors identified by the FoundationOne CDx assay

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, NT Ueno, and  others

   Annals of Oncology, Apr 2022
5. Functional and biological heterogeneity of KRASQ61 mutations

   Minh V Huynh, G Aaron Hobbs, Antje Schaefer, Mariaelena Pierobon, Leiah M Carey, J Nathaniel Diehl, Jonathan M DeLiberty, Ryan D Thurman, Adelaide R Cooke, Craig M Goodwin, and  others

   Science Signaling, Apr 2022
6. Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunity

   Bhalchandra Mirlekar, Yan Wang, Sirui Li, Mi Zhou, Sarah Entwistle, Tristan De Buysscher, Ashley Morrison, Gabriela Herrera, Cameron Harris, Benjamin G Vincent, and  others

   Cell Reports Medicine, Apr 2022

2021

1. Gene-expression based subtyping of pancreatic ductal adenocarcinoma

   Richard Moffitt, Jen Jen Yeh, and Naim Ur Rashid

   Jul 2021

   US Patent 11,053,550
2. Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discovery

   David K Lim^*, N.U. Rashid, and Joseph G Ibrahim

   Annals of Applied Statistics, Jul 2021
3. High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, B Lim, and  others

   Annals of Oncology, Jul 2021
4. FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

   Steven P Angus, Timothy J Stuhlmiller, Gaurav Mehta, Samantha M Bevill, Daniel R Goulet, J Felix Olivares-Quintero, Michael P East, Maki Tanioka, Jon S Zawistowski, Darshan Singh, and  others

   NPJ breast cancer, Jul 2021
5. Compression of quantification uncertainty for scRNA-seq counts

   Scott Van Buren^*, Hirak Sarkar, Avi Srivastava, N.U. Rashid, Rob Patro, and Michael I Love

   Bioinformatics, Jul 2021
6. 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.

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, NT Ueno, and  others

   Annals of Oncology, Jul 2021
7. Clinical Application of Next-Generation Sequencing in Recurrent Glioblastoma

   Daniel Zeitouni, Michael P Catalino, Jordan Wise, Sean McCabe, Kathryn Pietrosimone, N.U. Rashid, and Simon Khagi

   Onco, Jul 2021
8. The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer

   J Nathaniel Diehl, Jennifer E Klomp, Kayla R Snare, Priya S Hibshman, Devon R Blake, Zane D Kaiser, Thomas SK Gilbert, Elisa Baldelli, Mariaelena Pierobon, Björn Papke, and  others

   Journal of Biological Chemistry, Jul 2021

2020

1. JASA

   Modeling Between-Study Heterogeneity for Improved Reproducibility in Gene Signature Selection and Clinical Prediction

   N.U. Rashid, Quefeng Li, Jen Jen Yeh, and Joseph G Ibrahim

   Journal of the American Statistical Association, Jul 2020
2. JASA

   High-Dimensional Precision Medicine From Patient-Derived Xenografts

   N.U. Rashid, Daniel J Luckett, Jingxiang Chen, Michael T Lawson, Longshaokan Wang, Yunshu Zhang, Eric B Laber, Yufeng Liu, Jen Jen Yeh, Donglin Zeng, and  others

   Journal of the American Statistical Association, Jul 2020
3. A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability

   Katerina D Fagan-Solis, Dennis A Simpson, Rashmi J Kumar, Luciano G Martelotto, Lisle E Mose, N.U. Rashid, Alice Y Ho, Simon N Powell, Y Hannah Wen, Joel S Parker, and  others

   Cell Reports, Jul 2020
4. CCR

   Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer

   N.U. Rashid, Xianlu L Peng, Chong Jin, Richard A Moffitt, Keith E Volmar, Brian A Belt, Roheena Z Panni, Timothy M Nywening, Silvia G Herrera, Kristin J Moore, and  others

   Clinical Cancer Research, Jul 2020
5. B cell–Derived IL35 Drives STAT3-Dependent CD8+ T-cell Exclusion in Pancreatic Cancer

   Bhalchandra Mirlekar, Daniel Michaud, Samuel J. Lee, Nancy P. Kren, Cameron Harris, Kevin Greene, Emily C. Goldman, Gaorav P. Gupta, Ryan C. Fields, William G. Hawkins, David G. DeNardo, N.U. Rashid, Jen Jen Yeh, Autumn J. McRee, Benjamin G. Vincent, Dario A.A. Vignali, and Yuliya Pylayeva-Gupta

   Cancer immunology research, Jul 2020
6. Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapy

   M. B. Lipner, X. L. Peng, C. Jin, Y. Xu, Y. Gao, M. P. East, N.U. Rashid, R. A. Moffitt, S. G. Herrera-Loeza, A. B. Morrison, B. T. Golitz, C. Vaziri, L. M. Graves, G. L. Johnson, and J. J. Yeh

   JCI Insight, Apr 2020

2019

1. GSK2801, A BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer

   Samantha M Bevill, Jose F Olivares-Quintero, Noah Sciaky, Brian T Golitz, Darshan Singh, Adriana S Beltran, N.U. Rashid, Timothy J Stuhlmiller, Andrew Hale, Nathaniel J Moorman, and  others

   Molecular Cancer Research, Apr 2019
2. Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors

   John A Wrobel, Ling Xie, Li Wang, Cui Liu, N.U. Rashid, Kristalyn K Gallagher, Yan Xiong, Kyle D Konze, Jian Jin, Michael L Gatza, and  others

   iScience, Apr 2019
3. Genetic determinants of cellular addiction to DNA polymerase theta

   Wanjuan Feng, Dennis A Simpson, Juan Carvajal-Garcia, Brandon A Price, Rashmi J Kumar, Lisle E Mose, Richard D Wood, N.U. Rashid, Jeremy E Purvis, Joel S Parker, and  others

   Nature communications, Apr 2019
4. Improved detection of epigenomic marks with mixed-effects hidden Markov models

   Pedro L Baldoni^*, N.U. Rashid, and Joseph G Ibrahim

   Biometrics, Apr 2019

2018

1. JCO

   Stromal content is correlated with tissue site, contrast retention, and survival in pancreatic adenocarcinoma

   Robert J Torphy, Zhen Wang, Aisha True-Yasaki, Keith E Volmar, N.U. Rashid, Benjamin Yeh, Julia S Johansen, Michael A Hollingsworth, Jen Jen Yeh, and Eric A Collisson

   JCO precision oncology, Apr 2018
2. Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues

   Yanyan Yang, Ogun Adebali, Gang Wu, Christopher P Selby, Yi-Ying Chiou, N.U. Rashid, Jinchuan Hu, John B Hogenesch, and Aziz Sancar

   Proceedings of the National Academy of Sciences, Apr 2018
3. Relationship between body mass index (BMI) and gene expression profiles of cervical cancer in the cancer genome atlas (TCGA) project

   AQ Tran, SA Sullivan, SD McCabe, N.U. Rashid, and VL Bae-Jump

   Gynecologic Oncology, Apr 2018
4. KRAS Suppression-induced degradation of MYC is antagonized by a MEK5-ERK5 compensatory mechanism

   Angelina V Vaseva, Devon R Blake, Thomas SK Gilbert, Serina Ng, Galen Hostetter, Salma H Azam, Irem Ozkan-Dagliyan, Prson Gautam, Kirsten L Bryant, Kenneth H Pearce, and  others

   Cancer cell, Apr 2018

2017

1. Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex

   Jon S Zawistowski, Samantha M Bevill, Daniel R Goulet, Timothy J Stuhlmiller, Adriana S Beltran, Jose F Olivares-Quintero, Darshan Singh, Noah Sciaky, Joel S Parker, N.U. Rashid, and  others

   Cancer discovery, Apr 2017
2. Kinome profiling identifies druggable targets for novel human cytomegalovirus (HCMV) antivirals

   Kyle C Arend, Erik M Lenarcic, Heather A Vincent, N.U. Rashid, Eric Lazear, Ian M McDonald, Thomas SK Gilbert, Michael P East, Laura E Herring, Gary L Johnson, and  others

   Molecular & Cellular Proteomics, Apr 2017
3. Combined kinase inhibitors of MEK1/2 and either PI3K or PDGFR are efficacious in intracranial triple-negative breast cancer

   Amanda ED Van Swearingen, Maria J Sambade, Marni B Siegel, Shivani Sud, Robert S McNeill, Samantha M Bevill, Xin Chen, Ryan E Bash, Louisa Mounsey, Brian T Golitz, and  others

   Neuro-oncology, Apr 2017

2016

1. Targeting IL-17A in multiple myeloma: a potential novel therapeutic approach in myeloma

   Rao H Prabhala, Mariateresa Fulciniti, Dheeraj Pelluru, N.U. Rashid, Andreea Nigroiu, Puru Nanjappa, Christine Pai, Saem Lee, Nithya S Prabhala, Rajya Lakshmi Bandi, and  others

   Leukemia, Apr 2016
2. Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammation

   Amy R Johnson, Yuanyuan Qin, Alyssa J Cozzo, Alex J Freemerman, Megan J Huang, Liyang Zhao, Brante P Sampey, J Justin Milner, Melinda A Beck, Blossom Damania, and  others

   Molecular metabolism, Apr 2016
3. Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner

   Yi-Ying Chiou, Yanyan Yang, N.U. Rashid, Rui Ye, Christopher P Selby, and Aziz Sancar

   Proceedings of the National Academy of Sciences, Apr 2016
4. Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas Project

   Dario R Roque, Liza Makowski, Ting-Huei Chen, N.U. Rashid, D Neil Hayes, and Victoria Bae-Jump

   Gynecologic oncology, Apr 2016
5. A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing data

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Annals of Applied Statistics, Apr 2016

2015

1. Radiation therapy for unresectable pancreatic adenocarcinoma: population-based trends in utilization and survival rates in the United States

   Mia Shapiro, N.U. Rashid, Qin Huang, Shira L Galper, Valia A Boosalis, Edward E Whang, and Jason S Gold

   JAMA surgery, Apr 2015
2. Trends and predictors of resection of the primary tumor for patients with stage IV colorectal cancer

   Mia Shapiro, N.U. Rashid, Edward E Whang, Valia A Boosalis, Qin Huang, Charles Yoon, Mandeep S Saund, and Jason S Gold

   Journal of surgical oncology, Apr 2015
3. Mu opioid splice variant MOR-1K contributes to the development of opioid-induced hyperalgesia

   Folabomi A Oladosu, Matthew S Conrad, Sandra C O’Buckley, N.U. Rashid, Gary D Slade, and Andrea G Nackley

   PloS one, Apr 2015
4. Nat Gen

   Virtual microdissection identifies distinct tumor-and stroma-specific subtypes of pancreatic ductal adenocarcinoma

   Richard A Moffitt, Raoud Marayati, Elizabeth L Flate, Keith E Volmar, S Gabriela Herrera Loeza, Katherine A Hoadley, N.U. Rashid, Lindsay A Williams, Samuel C Eaton, Alexander H Chung, and  others

   Nature genetics, Apr 2015

2014

1. Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observations

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Journal of the American Statistical Association, Apr 2014
2. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

   Niccolo Bolli, Hervé Avet-Loiseau, David C Wedge, Peter Van Loo, Ludmil B Alexandrov, Inigo Martincorena, Kevin J Dawson, Francesco Iorio, Serena Nik-Zainal, Graham R Bignell, and  others

   Nature communications, Apr 2014
3. Differential and limited expression of mutant alleles in multiple myeloma

   N.U. Rashid, Adam S Sperling, Niccolo Bolli, David C Wedge, Peter Van Loo, Yu-Tzu Tai, Masood A Shammas, Mariateresa Fulciniti, Mehmet K Samur, Paul G Richardson, and  others

   Blood, Apr 2014

2013

1. Pain modality-and sex-specific effects of COMT genetic functional variants

   Inna Belfer, Samantha K Segall, William R Lariviere, Shad B Smith, Feng Dai, Gary D Slade, N.U. Rashid, Jeffrey S Mogil, Claudia M Campbell, Robert R Edwards, and  others

   PAIN, Apr 2013

2012

1. Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase Activity

   Douglas Tsao, Jeffrey S Wieskopf, N.U. Rashid, Robert E Sorge, Rachel L Redler, Samantha K Segall, Jeffrey S Mogil, William Maixner, Q Zheng, D Fang, and  others

   Molecular Pain, Apr 2012
2. An integrated encyclopedia of DNA elements in the human genome.

   BE Bernstein, E Birney, I Dunham, ED Green, C Gunter, M Snyder, and  others

   Nature, Apr 2012

2011

1. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

   N.U. Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, and Jason D Lieb

   Genome biology, Apr 2011
2. Cytokine biomarkers and chronic pain: association of genes, transcription, and circulating proteins with temporomandibular disorders and widespread palpation tenderness

   Gary D Slade, Mathew S Conrad, Luda Diatchenko, N.U. Rashid, Sheng Zhong, Shad Smith, Jesse Rhodes, Alex Medvedev, Sergei Makarov, William Maixner, and  others

   Pain, Apr 2011

2024

1. Unsupervised Imputation of Non-ignorably Missing Data Using Importance-Weighted Autoencoders

   David K Lim, Naim U Rashid, Junier B Oliva, and Joseph G Ibrahim

   Statistics in Biopharmaceutical Research, Accepted, In Press, 2024

2022

1. Efficient detection and classification of epigenomic changes under multiple conditions

   Pedro L. Baldoni^*, N.U. Rashid, and Joseph G. Ibrahim

   Biometrics, 2022

   Abs

   Abstract Epigenomics, the study of the human genome and its interactions with proteins and other cellular elements, has become of significant interest in recent years. Such interactions have been shown to regulate essential cellular functions and are associated with multiple complex diseases. Therefore, understanding how these interactions may change across conditions is central in biomedical research. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is one of several techniques to detect local changes in epigenomic activity (peaks). However, existing methods for differential peak calling are not optimized for the diversity in ChIP-seq signal profiles, are limited to the analysis of two conditions, or cannot classify specific patterns of differential change when multiple patterns exist. To address these limitations, we present a flexible and efficient method for the detection of differential epigenomic activity across multiple conditions. We utilize data from the ENCODE Consortium and show that the presented method, epigraHMM, exhibits superior performance to current tools and it is among the fastest algorithms available, while allowing the classification of combinatorial patterns of differential epigenomic activity and the characterization of chromatin regulatory states.

2. Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunity

   Bhalchandra Mirlekar, Yan Wang, Sirui Li, Mi Zhou, Sarah Entwistle, Tristan De Buysscher, Ashley Morrison, Gabriela Herrera, Cameron Harris, Benjamin G Vincent, and  others

   Cell Reports Medicine, 2022

2019

1. Improved detection of epigenomic marks with mixed-effects hidden Markov models

   Pedro L Baldoni^*, N.U. Rashid, and Joseph G Ibrahim

   Biometrics, 2019

2017

1. Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex

   Jon S Zawistowski, Samantha M Bevill, Daniel R Goulet, Timothy J Stuhlmiller, Adriana S Beltran, Jose F Olivares-Quintero, Darshan Singh, Noah Sciaky, Joel S Parker, N.U. Rashid, and  others

   Cancer discovery, 2017

2016

1. Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner

   Yi-Ying Chiou, Yanyan Yang, N.U. Rashid, Rui Ye, Christopher P Selby, and Aziz Sancar

   Proceedings of the National Academy of Sciences, 2016
2. A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing data

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Annals of Applied Statistics, 2016

2025

1. Efficient computation of high-dimensional penalized piecewise constant hazard random effects survival models

   Hillary M Heiling^*, N.U. Rashid, Quefeng Li, Xianlu L Peng, Jen Jen Yeh, and Joseph G Ibrahim

   Statistics in Medicine, Accepted, In Press, 2025
2. Tumor-intrinsic kinome landscape of pancreatic cancer reveals new therapeutic approaches

   Yi Xu, Xianlu L Peng, Michael P East, Ian C McCabe, Grace C Stroman, Madison R Jenner, Priscilla S Chan, Ashley B Morrison, Emily C Shen, Silvia G Hererra, and  others

   Cancer Discovery, 2025
3. Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy

   Akram Yazdani, Heinz-Josef Lenz, Gianluigi Pillonetto, Raul Mendez-Giraldez, Azam Yazdani, Hanna Sanoff, Reza Hadi, Esmat Samiei, Alan P Venook, Mark J Ratain, and  others

   Communications Medicine, 2025
4. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2-positive early breast cancer (EBC)☆

   Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

   Annals of Oncology, 2025
5. Prognostic and molecular multi-platform analysis of CALGB 40603 (Alliance) and public triple-negative breast cancer datasets

   Brooke M Felsheim, Aranzazu Fernandez-Martinez, Cheng Fan, Adam D Pfefferle, Michele C Hayward, Katherine A Hoadley, Naim U Rashid, Sara M Tolaney, George Somlo, Lisa A Carey, and  others

   NPJ Breast Cancer, 2025

2024

1. Biostat

   Differential Transcript Usage Analysis Incorporating Quantification Uncertainty Via Compositional Measurement Error Regression Modeling

   Amber Marie Young^*, S. Van Buren^*, and N.U. Rashid

   Biostatistics, 2024
2. Unsupervised Imputation of Non-ignorably Missing Data Using Importance-Weighted Autoencoders

   David K Lim, Naim U Rashid, Junier B Oliva, and Joseph G Ibrahim

   Statistics in Biopharmaceutical Research, Accepted, In Press, 2024
3. JCGS

   Deeply Learned Generalized Linear Models with Missing Data

   David K Lim, Naim U Rashid, Junier B Oliva, and Joseph G Ibrahim

   Journal of Computational and Graphical Statistics, 2024
4. glmmPen: high dimensional penalized generalized linear mixed models

   Hillary M Heiling, Naim U Rashid, Quefeng Li, and Joseph G Ibrahim

   The R journal, 2024
5. Biometr

   Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effects

   Hillary M Heiling^*, N.U. Rashid, Quefeng Li, Xianlu L Peng, Jen Jen Yeh, and Joseph G Ibrahim

   Biometrics, 2024
6. 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 Trials

   Aranzazu Fernandez-Martinez, Mattia Rediti, Gong Tang, Tomás Pascual, Katherine A Hoadley, David Venet, N.U. Rashid, Patricia A Spears, Md N Islam, Sarra El-Abed, and  others

   JAMA Oncology, 2024
7. JCO

   DNA mutational profiling in patients with colorectal cancer treated with standard of care reveals differences in outcome and racial distribution of mutations

   Federico Innocenti, Wancen Mu, Xueping Qu, Fang-Shu Ou, Omar Kabbarah, Charles David Blanke, Alan P Venook, Heinz-Josef Lenz, and N.U. Rashid

   Journal of Clinical Oncology, 2024
8. Purity Independent Subtyping of Tumors (PurIST) Pancreatic Cancer Classifier: Analytic Validation of a 16-RNA Expression Signature Distinguishing Basal and Classical Subtypes

   Yan Li, Jason D Merker, Rachana Kshatriya, Dimitri G Trembath, Ashley B Morrison, Peyton C Kuhlers, Naim U Rashid, Jen Jen Yeh, and Margaret L Gulley

   The Journal of Molecular Diagnostics, 2024
9. Kinome state is predictive of cell viability in pancreatic cancer tumor and cancer-associated fibroblast cell lines

   Matthew E Berginski, Madison R Jenner, Chinmaya U Joisa, Gabriela Herrera Loeza, Brian T Golitz, Matthew B Lipner, Jack R Leary, Naim Rashid, Gary L Johnson, Jen Jen Yeh, and  others

   PeerJ, 2024
10. Prognostic value of residual disease (RD) biology and gene expression changes during the neoadjuvant treatment in patients with HER2+ early breast cancer (EBC)

    Aranzazu Fernandez-Martinez, Maki Tanioka, Sung Gwe Ahn, Paola Zagami, Tomás Pascual, Mattia Rediti, Gong Tang, Katherine A Hoadley, David Venet, Naim U Rashid, and  others

    Annals of Oncology, 2024
11. Platform and sample type independent single sample classifier for treatment decision making in pancreatic ductal adenocarcinoma cancer

    Jen Jen Yeh, Richard Moffitt, and Naim Ur Rashid

    Jun 2024

    US Patent 12,000,003

2023

1. Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in Single-Cell RNA-Sequencing

   Jack Leary, Yi Xu, Ashley B Morrison, Chong Jin, Emily Shen, Peyton C Kuhlers, Ye Su, N.U. Rashid, Jen Jen Yeh, and Peng Xianlu

   Bioinformatics, Jun 2023
2. Estimating cell type composition using isoform expression one gene at a time

   Hillary M Heiling^*, Douglas R Wilson, N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Biometrics, Jun 2023
3. 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 Trials

   Aranzazu Fernandez-Martinez, Tomás Pascual, Baljit Singh, Paolo Nuciforo, N.U. Rashid, Karla V Ballman, Jordan D Campbell, Katherine A Hoadley, Patricia A Spears, Laia Pare, and  others

   JAMA Oncology, Jun 2023
4. Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model

   Luke A Torre-Healy, Ryan R Kawalerski, Ki Oh, Lucie Chrastecka, Xianlu L Peng, Andrew J Aguirre, N.U. Rashid, Jen Jen Yeh, and Richard A Moffitt

   Communications Biology, Jun 2023
5. RHOAL57V drives the development of diffuse gastric cancer through IGF1R-PAK1-YAP1 signaling

   Antje Schaefer, Richard G Hodge, Haisheng Zhang, G Aaron Hobbs, Julien Dilly, Minh V Huynh, Craig M Goodwin, Feifei Zhang, J Nathaniel Diehl, Mariaelena Pierobon, and  others

   Science signaling, Jun 2023
6. Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer

   Paola Zagami, Aranzazu Fernandez-Martinez, N.U. Rashid, Katherine A Hoadley, Patricia A Spears, Giuseppe Curigliano, Charles M Perou, and Lisa A Carey

   JAMA Network Open, Jun 2023

2022

1. Efficient detection and classification of epigenomic changes under multiple conditions

   Pedro L. Baldoni^*, N.U. Rashid, and Joseph G. Ibrahim

   Biometrics, Jun 2022

   Abs

   Abstract Epigenomics, the study of the human genome and its interactions with proteins and other cellular elements, has become of significant interest in recent years. Such interactions have been shown to regulate essential cellular functions and are associated with multiple complex diseases. Therefore, understanding how these interactions may change across conditions is central in biomedical research. Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is one of several techniques to detect local changes in epigenomic activity (peaks). However, existing methods for differential peak calling are not optimized for the diversity in ChIP-seq signal profiles, are limited to the analysis of two conditions, or cannot classify specific patterns of differential change when multiple patterns exist. To address these limitations, we present a flexible and efficient method for the detection of differential epigenomic activity across multiple conditions. We utilize data from the ENCODE Consortium and show that the presented method, epigraHMM, exhibits superior performance to current tools and it is among the fastest algorithms available, while allowing the classification of combinatorial patterns of differential epigenomic activity and the characterization of chromatin regulatory states.

2. Tumor Immunogenomic Features Determine Outcomes in Patients with Metastatic Colorectal Cancer Treated with Standard-of-Care Combinations of Bevacizumab and Cetuximab

   Federico Innocenti, Akram Yazdani, N.U. Rashid, Xueping Qu, Fang-Shu Ou, Scott Van Buren, Monica M. Bertagnolli, Omar Kabbarah, Charles David Blanke, Alan P. Venook, Heinz-Josef Lenz, and Benjamin G. Vincent

   Clinical Cancer Research, Apr 2022

   Abs

   CALGB/SWOG 80405 was a randomized phase III trial in first-line patients with metastatic colorectal cancer treated with bevacizumab, cetuximab, or both, plus chemotherapy. We tested the effect of tumor immune features on overall survival (OS).Primary tumors (N = 554) were profiled by RNA sequencing. Immune signatures of macrophages, lymphocytes, TGFβ, IFNγ, wound healing, and cytotoxicity were measured. CIBERSORTx scores of naive and memory B cells, plasma cells, CD8+ T cells, resting and activated memory CD4+ T cells, M0 and M2 macrophages, and activated mast cells were measured.Increased M2 macrophage score [HR, 6.30; 95\% confidence interval (CI), 3.0–12.15] and TGFβ signature expression (HR, 1.35; 95\% CI, 1.05–1.77) were associated with shorter OS. Increased scores of plasma cells (HR, 0.55; 95\% CI, 0.38–0.87) and activated memory CD4+ T cells (HR, 0.34; 95\% CI, 0.16–0.65) were associated with longer OS. Using optimal cutoffs from these four features, patients were categorized as having either 4, 3, 2, or 0–1 beneficial features associated with longer OS, and the median (95\% CI) OS decreased from 42.5 (35.8–47.8) to 31.0 (28.8–34.4), 25.2 (20.6–27.9), and 17.7 (13.5–20.4) months respectively (P = 3.48e–11).New immune features can be further evaluated to improve patient response. They provide the rationale for more effective immunotherapy strategies.

3. Methods and compositions for prognostic and/or diagnostic subtyping of pancreatic cancer

   Richard Moffitt, Jen Jen Yeh, and Naim Ur Rashid

   Apr 2022

   US Patent App. 17/336,600
4. Validation of cancer-type-dependent benefit from immune checkpoint blockade in TMB-H tumors identified by the FoundationOne CDx assay

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, NT Ueno, and  others

   Annals of Oncology, Apr 2022
5. Functional and biological heterogeneity of KRASQ61 mutations

   Minh V Huynh, G Aaron Hobbs, Antje Schaefer, Mariaelena Pierobon, Leiah M Carey, J Nathaniel Diehl, Jonathan M DeLiberty, Ryan D Thurman, Adelaide R Cooke, Craig M Goodwin, and  others

   Science Signaling, Apr 2022
6. Balance between immunoregulatory B cells and plasma cells drives pancreatic tumor immunity

   Bhalchandra Mirlekar, Yan Wang, Sirui Li, Mi Zhou, Sarah Entwistle, Tristan De Buysscher, Ashley Morrison, Gabriela Herrera, Cameron Harris, Benjamin G Vincent, and  others

   Cell Reports Medicine, Apr 2022

2021

1. Gene-expression based subtyping of pancreatic ductal adenocarcinoma

   Richard Moffitt, Jen Jen Yeh, and Naim Ur Rashid

   Jul 2021

   US Patent 11,053,550
2. Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discovery

   David K Lim^*, N.U. Rashid, and Joseph G Ibrahim

   Annals of Applied Statistics, Jul 2021
3. High tumor mutation burden fails to predict immune checkpoint blockade response across all cancer types

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, B Lim, and  others

   Annals of Oncology, Jul 2021
4. FOXA1 and adaptive response determinants to HER2 targeted therapy in TBCRC 036

   Steven P Angus, Timothy J Stuhlmiller, Gaurav Mehta, Samantha M Bevill, Daniel R Goulet, J Felix Olivares-Quintero, Michael P East, Maki Tanioka, Jon S Zawistowski, Darshan Singh, and  others

   NPJ breast cancer, Jul 2021
5. Compression of quantification uncertainty for scRNA-seq counts

   Scott Van Buren^*, Hirak Sarkar, Avi Srivastava, N.U. Rashid, Rob Patro, and Michael I Love

   Bioinformatics, Jul 2021
6. 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.

   DJ McGrail, PG Pilié, N.U. Rashid, L Voorwerk, M Slagter, M Kok, E Jonasch, M Khasraw, AB Heimberger, NT Ueno, and  others

   Annals of Oncology, Jul 2021
7. Clinical Application of Next-Generation Sequencing in Recurrent Glioblastoma

   Daniel Zeitouni, Michael P Catalino, Jordan Wise, Sean McCabe, Kathryn Pietrosimone, N.U. Rashid, and Simon Khagi

   Onco, Jul 2021
8. The KRAS-regulated kinome identifies WEE1 and ERK coinhibition as a potential therapeutic strategy in KRAS-mutant pancreatic cancer

   J Nathaniel Diehl, Jennifer E Klomp, Kayla R Snare, Priya S Hibshman, Devon R Blake, Zane D Kaiser, Thomas SK Gilbert, Elisa Baldelli, Mariaelena Pierobon, Björn Papke, and  others

   Journal of Biological Chemistry, Jul 2021

2020

1. JASA

   Modeling Between-Study Heterogeneity for Improved Reproducibility in Gene Signature Selection and Clinical Prediction

   N.U. Rashid, Quefeng Li, Jen Jen Yeh, and Joseph G Ibrahim

   Journal of the American Statistical Association, Jul 2020
2. JASA

   High-Dimensional Precision Medicine From Patient-Derived Xenografts

   N.U. Rashid, Daniel J Luckett, Jingxiang Chen, Michael T Lawson, Longshaokan Wang, Yunshu Zhang, Eric B Laber, Yufeng Liu, Jen Jen Yeh, Donglin Zeng, and  others

   Journal of the American Statistical Association, Jul 2020
3. A P53-Independent DNA Damage Response Suppresses Oncogenic Proliferation and Genome Instability

   Katerina D Fagan-Solis, Dennis A Simpson, Rashmi J Kumar, Luciano G Martelotto, Lisle E Mose, N.U. Rashid, Alice Y Ho, Simon N Powell, Y Hannah Wen, Joel S Parker, and  others

   Cell Reports, Jul 2020
4. CCR

   Purity Independent Subtyping of Tumors (PurIST), A Clinically Robust, Single-sample Classifier for Tumor Subtyping in Pancreatic Cancer

   N.U. Rashid, Xianlu L Peng, Chong Jin, Richard A Moffitt, Keith E Volmar, Brian A Belt, Roheena Z Panni, Timothy M Nywening, Silvia G Herrera, Kristin J Moore, and  others

   Clinical Cancer Research, Jul 2020
5. B cell–Derived IL35 Drives STAT3-Dependent CD8+ T-cell Exclusion in Pancreatic Cancer

   Bhalchandra Mirlekar, Daniel Michaud, Samuel J. Lee, Nancy P. Kren, Cameron Harris, Kevin Greene, Emily C. Goldman, Gaorav P. Gupta, Ryan C. Fields, William G. Hawkins, David G. DeNardo, N.U. Rashid, Jen Jen Yeh, Autumn J. McRee, Benjamin G. Vincent, Dario A.A. Vignali, and Yuliya Pylayeva-Gupta

   Cancer immunology research, Jul 2020
6. Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapy

   M. B. Lipner, X. L. Peng, C. Jin, Y. Xu, Y. Gao, M. P. East, N.U. Rashid, R. A. Moffitt, S. G. Herrera-Loeza, A. B. Morrison, B. T. Golitz, C. Vaziri, L. M. Graves, G. L. Johnson, and J. J. Yeh

   JCI Insight, Apr 2020

2019

1. GSK2801, A BAZ2/BRD9 Bromodomain Inhibitor, Synergizes with BET Inhibitors to Induce Apoptosis in Triple-Negative Breast Cancer

   Samantha M Bevill, Jose F Olivares-Quintero, Noah Sciaky, Brian T Golitz, Darshan Singh, Adriana S Beltran, N.U. Rashid, Timothy J Stuhlmiller, Andrew Hale, Nathaniel J Moorman, and  others

   Molecular Cancer Research, Apr 2019
2. Multi-omic Dissection of Oncogenically Active Epiproteomes Identifies Drivers of Proliferative and Invasive Breast Tumors

   John A Wrobel, Ling Xie, Li Wang, Cui Liu, N.U. Rashid, Kristalyn K Gallagher, Yan Xiong, Kyle D Konze, Jian Jin, Michael L Gatza, and  others

   iScience, Apr 2019
3. Genetic determinants of cellular addiction to DNA polymerase theta

   Wanjuan Feng, Dennis A Simpson, Juan Carvajal-Garcia, Brandon A Price, Rashmi J Kumar, Lisle E Mose, Richard D Wood, N.U. Rashid, Jeremy E Purvis, Joel S Parker, and  others

   Nature communications, Apr 2019
4. Improved detection of epigenomic marks with mixed-effects hidden Markov models

   Pedro L Baldoni^*, N.U. Rashid, and Joseph G Ibrahim

   Biometrics, Apr 2019

2018

1. JCO

   Stromal content is correlated with tissue site, contrast retention, and survival in pancreatic adenocarcinoma

   Robert J Torphy, Zhen Wang, Aisha True-Yasaki, Keith E Volmar, N.U. Rashid, Benjamin Yeh, Julia S Johansen, Michael A Hollingsworth, Jen Jen Yeh, and Eric A Collisson

   JCO precision oncology, Apr 2018
2. Cisplatin-DNA adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues

   Yanyan Yang, Ogun Adebali, Gang Wu, Christopher P Selby, Yi-Ying Chiou, N.U. Rashid, Jinchuan Hu, John B Hogenesch, and Aziz Sancar

   Proceedings of the National Academy of Sciences, Apr 2018
3. Relationship between body mass index (BMI) and gene expression profiles of cervical cancer in the cancer genome atlas (TCGA) project

   AQ Tran, SA Sullivan, SD McCabe, N.U. Rashid, and VL Bae-Jump

   Gynecologic Oncology, Apr 2018
4. KRAS Suppression-induced degradation of MYC is antagonized by a MEK5-ERK5 compensatory mechanism

   Angelina V Vaseva, Devon R Blake, Thomas SK Gilbert, Serina Ng, Galen Hostetter, Salma H Azam, Irem Ozkan-Dagliyan, Prson Gautam, Kirsten L Bryant, Kenneth H Pearce, and  others

   Cancer cell, Apr 2018

2017

1. Enhancer remodeling during adaptive bypass to MEK inhibition is attenuated by pharmacologic targeting of the P-TEFb complex

   Jon S Zawistowski, Samantha M Bevill, Daniel R Goulet, Timothy J Stuhlmiller, Adriana S Beltran, Jose F Olivares-Quintero, Darshan Singh, Noah Sciaky, Joel S Parker, N.U. Rashid, and  others

   Cancer discovery, Apr 2017
2. Kinome profiling identifies druggable targets for novel human cytomegalovirus (HCMV) antivirals

   Kyle C Arend, Erik M Lenarcic, Heather A Vincent, N.U. Rashid, Eric Lazear, Ian M McDonald, Thomas SK Gilbert, Michael P East, Laura E Herring, Gary L Johnson, and  others

   Molecular & Cellular Proteomics, Apr 2017
3. Combined kinase inhibitors of MEK1/2 and either PI3K or PDGFR are efficacious in intracranial triple-negative breast cancer

   Amanda ED Van Swearingen, Maria J Sambade, Marni B Siegel, Shivani Sud, Robert S McNeill, Samantha M Bevill, Xin Chen, Ryan E Bash, Louisa Mounsey, Brian T Golitz, and  others

   Neuro-oncology, Apr 2017

2016

1. Targeting IL-17A in multiple myeloma: a potential novel therapeutic approach in myeloma

   Rao H Prabhala, Mariateresa Fulciniti, Dheeraj Pelluru, N.U. Rashid, Andreea Nigroiu, Puru Nanjappa, Christine Pai, Saem Lee, Nithya S Prabhala, Rajya Lakshmi Bandi, and  others

   Leukemia, Apr 2016
2. Metabolic reprogramming through fatty acid transport protein 1 (FATP1) regulates macrophage inflammatory potential and adipose inflammation

   Amy R Johnson, Yuanyuan Qin, Alyssa J Cozzo, Alex J Freemerman, Megan J Huang, Liyang Zhao, Brante P Sampey, J Justin Milner, Melinda A Beck, Blossom Damania, and  others

   Molecular metabolism, Apr 2016
3. Mammalian Period represses and de-represses transcription by displacing CLOCK–BMAL1 from promoters in a Cryptochrome-dependent manner

   Yi-Ying Chiou, Yanyan Yang, N.U. Rashid, Rui Ye, Christopher P Selby, and Aziz Sancar

   Proceedings of the National Academy of Sciences, Apr 2016
4. Association between differential gene expression and body mass index among endometrial cancers from The Cancer Genome Atlas Project

   Dario R Roque, Liza Makowski, Ting-Huei Chen, N.U. Rashid, D Neil Hayes, and Victoria Bae-Jump

   Gynecologic oncology, Apr 2016
5. A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing data

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Annals of Applied Statistics, Apr 2016

2015

1. Radiation therapy for unresectable pancreatic adenocarcinoma: population-based trends in utilization and survival rates in the United States

   Mia Shapiro, N.U. Rashid, Qin Huang, Shira L Galper, Valia A Boosalis, Edward E Whang, and Jason S Gold

   JAMA surgery, Apr 2015
2. Trends and predictors of resection of the primary tumor for patients with stage IV colorectal cancer

   Mia Shapiro, N.U. Rashid, Edward E Whang, Valia A Boosalis, Qin Huang, Charles Yoon, Mandeep S Saund, and Jason S Gold

   Journal of surgical oncology, Apr 2015
3. Mu opioid splice variant MOR-1K contributes to the development of opioid-induced hyperalgesia

   Folabomi A Oladosu, Matthew S Conrad, Sandra C O’Buckley, N.U. Rashid, Gary D Slade, and Andrea G Nackley

   PloS one, Apr 2015
4. Nat Gen

   Virtual microdissection identifies distinct tumor-and stroma-specific subtypes of pancreatic ductal adenocarcinoma

   Richard A Moffitt, Raoud Marayati, Elizabeth L Flate, Keith E Volmar, S Gabriela Herrera Loeza, Katherine A Hoadley, N.U. Rashid, Lindsay A Williams, Samuel C Eaton, Alexander H Chung, and  others

   Nature genetics, Apr 2015

2014

1. Some statistical strategies for DAE-seq data analysis: variable selection and modeling dependencies among observations

   N.U. Rashid, Wei Sun, and Joseph G Ibrahim

   Journal of the American Statistical Association, Apr 2014
2. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma

   Niccolo Bolli, Hervé Avet-Loiseau, David C Wedge, Peter Van Loo, Ludmil B Alexandrov, Inigo Martincorena, Kevin J Dawson, Francesco Iorio, Serena Nik-Zainal, Graham R Bignell, and  others

   Nature communications, Apr 2014
3. Differential and limited expression of mutant alleles in multiple myeloma

   N.U. Rashid, Adam S Sperling, Niccolo Bolli, David C Wedge, Peter Van Loo, Yu-Tzu Tai, Masood A Shammas, Mariateresa Fulciniti, Mehmet K Samur, Paul G Richardson, and  others

   Blood, Apr 2014

2013

1. Pain modality-and sex-specific effects of COMT genetic functional variants

   Inna Belfer, Samantha K Segall, William R Lariviere, Shad B Smith, Feng Dai, Gary D Slade, N.U. Rashid, Jeffrey S Mogil, Claudia M Campbell, Robert R Edwards, and  others

   PAIN, Apr 2013

2012

1. Serotonin-Induced Hypersensitivity via Inhibition of Catechol O-Methyltransferase Activity

   Douglas Tsao, Jeffrey S Wieskopf, N.U. Rashid, Robert E Sorge, Rachel L Redler, Samantha K Segall, Jeffrey S Mogil, William Maixner, Q Zheng, D Fang, and  others

   Molecular Pain, Apr 2012
2. An integrated encyclopedia of DNA elements in the human genome.

   BE Bernstein, E Birney, I Dunham, ED Green, C Gunter, M Snyder, and  others

   Nature, Apr 2012

2011

1. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

   N.U. Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, and Jason D Lieb

   Genome biology, Apr 2011
2. Cytokine biomarkers and chronic pain: association of genes, transcription, and circulating proteins with temporomandibular disorders and widespread palpation tenderness

   Gary D Slade, Mathew S Conrad, Luda Diatchenko, N.U. Rashid, Sheng Zhong, Shad Smith, Jesse Rhodes, Alex Medvedev, Sergei Makarov, William Maixner, and  others

   Pain, Apr 2011