Publications

An up to date list of publications can be found at my google scholar page.

Methodology (* indicates student)

  1. S. Van Buren* and N.U. Rashid. Differential transcript usage analysis incorporating quantification uncertainty via compositional measurement error regression modeling. Annals of Applied Statistics, Under Review, 2020. bioarxiv

  2. S. Van Buren*, H. Sarkar, A. Srivastava, N.U. Rashid, R. Patro, and M. I. Love. Compression of quanti cation uncertainty for scrna-seq counts. Bioinformatics, Under Review, 2020. bioarxiv

  3. P. L. Baldoni*, N.U. Rashid, and J. G. Ibrahim. Efficient detection and classification of epigenomic changes under multiple conditions. Biometrics, Revision Invited, 2019. bioRxiv

  4. D. K. Lim*, N.U. Rashid, and J. G. Ibrahim. Model-based feature selection and clustering of rna-seq data for unsupervised subtype discovery. Annals of Applied Statistics, Accepted, In Press, 2020. bioarxiv

  5. N.U. Rashid, D. J. Luckett, J. Chen, M. T. Lawson, L. Wang, Y. Zhang, E. B. Laber, Y. Liu, J. J. Yeh, D. Zeng, and M. R. Kosorok.k. High dimensional precision medicine from patient-derived xenografts. Journal of the American Statistical Association, Accepted, In Press, 2019. arxiv link

  6. N.U. Rashid, X. L. Peng, C. Jin, R. A. Moffitt, K. E. Volmar, B. A. Belt, R. Z. Panni, T. M. Nywening, S. G. Herrera1, K. J. Moore1, S. G. Hennessey, A. B. Morrison, R. Kawalerski, A. Nayyar, A. E. Chang, B. Schmidt, H. J. Kim, D. C. Linehan, and J. J. Yeh. Purity independent subtyping of tumors (PurIST), a clinically robust, single-sample classifier for tumor subtyping in pancreatic cancer. Clinical Cancer Research, 26(1):82-92, 2020. PDF. PurIST Github. Media: Lineberger, Gillings SPH, ABC 11 news, PANCAN. PDF

  7. N.U. Rashid, Q. Li, J. J. Yeh, and J. G. Ibrahim. Modeling between-study heterogeneity for improved reproducibility in gene signature selection and clinical prediction. Journal of the American Statistical Association, 115(531):1125{1138, 2020. PDF. Lineberger Press Release

  8. P. L. Baldoni*, N.U. Rashid, and J. G. Ibrahim. Improved detection of epigenomic marks with mixed effects hidden markov models. Biometrics, 75(4):1401-1413, 2019

  9. N.U. Rashid, W. Sun, and J. G. Ibrahim. A statistical model to assess (allele-specific) associations between gene expression and epigenetic features using sequencing data. The Annals of Applied Statistics, 10(4):2254, 2016

  10. N.U. Rashid, A. S. Sperling, N. Bolli, D. C. Wedge, P. Van Loo, Y.-T. Tai, M. A. Shammas, M. Fulciniti, M. K. Samur, P. G. Richardson, et al. Differential and limited expression of mutant alleles in multiple myeloma. Blood, 124(20):3110-3117, 2014

  11. N.U. Rashid, W. Sun, and J. G. Ibrahim. Some statistical strategies for dae-seq data analysis: variable selection and modeling dependencies among observations. Journal of the American Statistical Association, 109(505):78-94, 2014

  12. N.U. Rashid, P. G. Giresi, J. G. Ibrahim, W. Sun, and J. D. Lieb. Zinba integrates local covariates with dna-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome biology, 12(7):R67, 2011

Collaborative - Genomics and Cancer

  1. M. B. Lipner, X. L. Peng, C. Jin, Y. Xu, Y. Gao, M. P. East, N.U. Rashid, R. A. Mott, S. G. Herrera-Loeza, A. B. Morrison, B. T. Golitz, C. Vaziri, L. M. Graves, G. L. Johnson, and J. J. Yeh. Irreversible JNK1-JUN inhibition by JNK-IN-8 sensitizes pancreatic cancer to 5-FU/FOLFOX chemotherapy. JCI Insight, 5(8), apr 2020

  2. B. Mirlekar, D. Michaud, S. J. Lee, N. P. Kren, C. Harris, K. Greene, E. C. Goldman, G. P. Gupta, R. C. Fields, W. G. Hawkins, D. G. DeNardo, N.U. Rashid, J. J. Yeh, A. J. McRee, B. G. Vincent, D. A. Vignali, and Y. Pylayeva-Gupta. B cell-derived IL35 drives stat3-dependent CD8+ t-cell exclusion in pancreatic cancer. Cancer Immunology Research, 2020

  3. K. D. Fagan-Solis, D. A. Simpson, R. J. Kumar, L. G. Martelotto, L. E. Mose, N.U. Rashid, A. Y. Ho, S. N. Powell, Y. H. Wen, J. S. Parker, et al. A p53-independent dna damage response suppresses oncogenic proliferation and genome instability. Cell Reports, 30(5):1385{1399, 2020

  4. W. Feng, D. A. Simpson, J. Carvajal-Garcia, B. A. Price, R. J. Kumar, L. E. Mose, R. D.Wood, N.U. Rashid, J. E. Purvis, J. S. Parker, et al. Genetic determinants of cellular addiction to dna polymerase theta. Nature communications, 10(1):1-13, 2019

  5. J. A. Wrobel, L. Xie, L. Wang, C. Liu, N.U. Rashid, K. K. Gallagher, Y. Xiong, K. D. Konze, J. Jin, M. L. Gatza, et al. Multi-omic dissection of oncogenically active epiproteomes identifies drivers of proliferative and invasive breast tumors. iScience, 17:359-378, 2019

  6. S. M. Bevill, J. F. Olivares-Quintero, N. Sciaky, B. T. Golitz, D. Singh, A. S. Beltran, N.U. Rashid, T. J. Stuhlmiller, A. Hale, N. J. Moorman, et al. Gsk2801, a baz2/brd9 bromodomain inhibitor, synergizes with bet inhibitors to induce apoptosis in triple-negative breast cancer. Molecular Cancer Research, 2019

  7. A. V. Vaseva, D. R. Blake, T. S. Gilbert, S. Ng, G. Hostetter, S. H. Azam, I. Ozkan-Dagliyan, P. Gautam, K. L. Bryant, K. H. Pearce, et al. Kras suppression-induced degradation of myc is antagonized by a mek5-erk5 compensatory mechanism. Cancer cell, 34(5):807-822, 2018

  8. Y. Yang, O. Adebali, G. Wu, C. P. Selby, Y.-Y. Chiou, N.U. Rashid, J. Hu, J. B. Hogenesch, and A. Sancar. Cisplatin-dna adduct repair of transcribed genes is controlled by two circadian programs in mouse tissues. Proceedings of the National Academy of Sciences, 115(21), 2018

  9. R. J. Torphy, Z. Wang, A. True-Yasaki, K. E. Volmar, N.U. Rashid, B. Yeh, J. S. Johansen, M. A. Hollingsworth, J. J. Yeh, and E. A. Collisson. Stromal content is correlated with tissue site, contrast retention, and survival in pancreatic adenocarcinoma. JCO precision oncology, 2:1-12, 2018

  10. A. E. Van Swearingen, M. J. Sambade, M. B. Siegel, S. Sud, R. S. McNeill, S. M. Bevill, X. Chen, R. E. Bash, L. Mounsey, B. T. Golitz, et al. Combined kinase inhibitors of mek1/2 and either pi3k or pdgfr are efficacious in intracranial triple-negative breast cancer. Neurooncology, 19(11):1481-1493, 2017

  11. K. C. Arend, E. M. Lenarcic, H. A. Vincent, N.U. Rashid, E. Lazear, I. M. McDonald, T. S. Gilbert, M. P. East, L. E. Herring, G. L. Johnson, et al. Kinome profiling identifies druggable targets for novel human cytomegalovirus (hcmv) antivirals. Molecular & Cellular Proteomics, 16(4 suppl 1), 2017

  12. J. S. Zawistowski, S. M. Bevill, D. R. Goulet, T. J. Stuhlmiller, A. S. Beltran, J. F. Olivares-Quintero, D. Singh, N. Sciaky, J. S. Parker, N.U. Rashid, et al. Enhancer remodeling during adaptive bypass to mek inhibition is attenuated by pharmacologic targeting of the p-tefb complex. Cancer discovery, 7(3):302-321, 2017

  13. D. R. Roque, L. Makowski, T.-H. Chen, N.U. Rashid, D. N. Hayes, and V. Bae-Jump. Asso- ciation between differential gene expression and body mass index among endometrial cancers from the cancer genome atlas project. Gynecologic oncology, 142(2):317-322, 2016

  14. Y.-Y. Chiou, Y. Yang, N.U. Rashid, R. Ye, C. P. Selby, and A. Sancar. Mammalian period represses and de-represses transcription by displacing clock-bmal1 from promoters in a cryptochrome-dependent manner. Proceedings of the National Academy of Sciences, 113(41):E6072-E6079, 2016

  15. A. R. Johnson, Y. Qin, A. J. Cozzo, A. J. Freemerman, M. J. Huang, L. Zhao, B. P. Sampey, J. J. Milner, M. A. Beck, B. Damania, et al. Metabolic reprogramming through fatty acid transport protein 1 (fatp1) regulates macrophage inammatory potential and adipose inflammation. Molecular metabolism, 5(7):506-526, 2016

  16. R. H. Prabhala, M. Fulciniti, D. Pelluru, N.U. Rashid, A. Nigroiu, P. Nanjappa, C. Pai, S. Lee, N. S. Prabhala, R. L. Bandi, et al. Targeting il-17a in multiple myeloma: a potential novel therapeutic approach in myeloma. Leukemia, 30(2):379, 2016

  17. R. A. Moffitt, R. Marayati, E. L. Flate, K. E. Volmar, S. G. H. Loeza, K. A. Hoadley, N.U. Rashid, L. A. Williams, S. C. Eaton, A. H. Chung, et al. Virtual microdissection identifies distinct tumor-and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nature genetics, 47(10):1168, 2015

  18. M. Shapiro, N.U. Rashid, E. E. Whang, V. A. Boosalis, Q. Huang, C. Yoon, M. S. Saund, and J. S. Gold. Trends and predictors of resection of the primary tumor for patients with stage iv colorectal cancer. Journal of surgical oncology, 111(7):911-916, 2015

  19. M. Shapiro, N.U. Rashid, Q. Huang, S. L. Galper, V. A. Boosalis, E. E. Whang, and J. S. Gold. Radiation therapy for unresectable pancreatic adenocarcinoma: population-based trends in utilization and survival rates in the united states. JAMA surgery, 150(3):274-277, 2015

  20. N. Bolli, H. Avet-Loiseau, D. C. Wedge, P. Van Loo, L. B. Alexandrov, I. Martincorena, K. J. Dawson, F. Iorio, S. Nik-Zainal, G. R. Bignell, et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nature communications, 5:2997, 2014

  21. B. Bernstein, E. Birney, I. Dunham, E. Green, C. Gunter, M. Snyder, et al. An integrated encyclopedia of dna elements in the human genome. Nature, 489(7414):57, 2012

Collaborative - Other

  1. F. A. Oladosu, M. S. Conrad, S. C. O’Buckley, N.U. Rashid, G. D. Slade, and A. G. Nackley. Mu opioid splice variant mor-1k contributes to the development of opioid-induced hyperalgesia. PloS one, 10(8):e0135711, 2015

  2. I. Belfer, S. K. Segall, W. R. Lariviere, S. B. Smith, F. Dai, G. D. Slade, N.U. Rashid, J. S. Mogil, C. M. Campbell, R. R. Edwards, et al. Pain modality-and sex-specific effects of comt genetic functional variants. PAIN, 154(8):1368-1376, 2013

  3. D. Tsao, J. S. Wieskopf, N.U. Rashid, R. E. Sorge, R. L. Redler, S. K. Segall, J. S. Mogil, W. Maixner, Q. Zheng, D. Fang, et al. Serotonin-induced hypersensitivity via inhibition of catechol o-methyltransferase activity. Molecular Pain, 8(1):25, 2012

  4. G. D. Slade, M. S. Conrad, L. Diatchenko, N.U. Rashid, S. Zhong, S. Smith, J. Rhodes, A. Medvedev, S. Makarov, W. Maixner, et al. Cytokine biomarkers and chronic pain: associ- ation of genes, transcription, and circulating proteins with temporomandibular disorders and widespread palpation tenderness. Pain, 152(12):2802-2812, 2011