Nath A, Cosgrove PA, Mirsafian H, Christie EL, Pflieger L, Copeland B, Majumdar S, Cristea MC, Han ES, Lee SJ, Wang EW, Fereday S, Traficante N, Salgia R, Werner T, Cohen AL, Moos P, Chang JT, Bowtell DDL, Bild AH. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. Nat Commun. 2021 May 24;12(1):3039. doi: 10.1038/s41467-021-23171-3. PubMed PMID: 34031395; PubMed Central PMCID: PMC8144406.
Nath A, Oak A, Chen KY, Li I, Splichal RC, Portis J, Foster S, Walton SP, Chan C. Palmitate-Induced IRE1-XBP1-ZEB Signaling Represses Desmoplakin Expression and Promotes Cancer Cell Migration. Mol Cancer Res. 2021 Feb;19(2):240-248. doi: 10.1158/1541-7786.MCR-19-0480. Epub 2020 Oct 26. PubMed PMID: 33106375; PubMed Central PMCID: PMC7864864.
Lee AM, Ferdjallah A, Moore E, Kim DC, Nath A, Greengard E, Huang RS. Long Non-Coding RNA ANRIL as a Potential Biomarker of Chemosensitivity and Clinical Outcomes in Osteosarcoma. Int J Mol Sci. 2021 Oct 16;22(20). doi: 10.3390/ijms222011168. PubMed PMID: 34681828; PubMed Central PMCID: PMC8538287.
Chi F, Liu J, Brady SW, Cosgrove PA, Nath A, McQuerry JA, Majumdar S, Moos PJ, Chang JT, Kahn M, Bild AH. A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer. Transl Oncol. 2021 Jan;14(1):100946. doi: 10.1016/j.tranon.2020.100946. Epub 2020 Nov 19. PubMed PMID: 33221681; PubMed Central PMCID: PMC7689336.
Grolmusz VK, Chen J, Emond R, Cosgrove PA, Pflieger L, Nath A, Moos PJ, Bild AH. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Cancer Cell Int. 2020;20:253. doi: 10.1186/s12935-020-01337-1. eCollection 2020. PubMed PMID: 32565737; PubMed Central PMCID: PMC7301982.
O'Donnell PH, Trubetskoy V, Nurhussein-Patterson A, Hall JP, Nath A, Huo D, Fleming GF, Ingle JN, Abramson VG, Morrow PK, Storniolo AM, Forero A, Van Poznak C, Liu MC, Chang JC, Merkel DE, Peppercorn JM, Rugo HS, Dees EC, Hahn OM, Hoffman PC, Rosner GL, Huang RS, Ratain MJ, Cox N, Olopade OI, Wolff AC, Dolan ME, Nanda R. Clinical evaluation of germline polymorphisms associated with capecitabine toxicity in breast cancer: TBCRC-015. Breast Cancer Res Treat. 2020 Jun;181(3):623-633. doi: 10.1007/s10549-020-05603-8. Epub 2020 May 6. PubMed PMID: 32378051.
Nath A, Chang J, Huang RS. iMIRAGE: an R package to impute microRNA expression using protein-coding genes. Bioinformatics. 2020 Apr 15;36(8):2608-2610. doi: 10.1093/bioinformatics/btz939. PubMed PMID: 31860075; PubMed Central PMCID: PMC7828470.
Nath A, Geeleher P, Huang RS. Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. Brief Bioinform. 2020 Mar 23;21(2):637-648. doi: 10.1093/bib/bby129. PubMed PMID: 30657858; PubMed Central PMCID: PMC7299297.
Nath A, Lau EYT, Lee AM, Geeleher P, Cho WCS, Huang RS. Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes. Proc Natl Acad Sci U S A. 2019 Oct 29;116(44):22020-22029. doi: 10.1073/pnas.1909998116. Epub 2019 Sep 23. PubMed PMID: 31548386; PubMed Central PMCID: PMC6825320.
Menden MP, Wang D, Mason MJ, Szalai B, Bulusu KC, Guan Y, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, Jang IS, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang EKY, Garnett MJ, Veroli GYD, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nat Commun. 2019 Jun 17;10(1):2674. doi: 10.1038/s41467-019-09799-2. PubMed PMID: 31209238; PubMed Central PMCID: PMC6572829.
Geeleher P, Nath A, Wang F, Zhang Z, Barbeira AN, Fessler J, Grossman RL, Seoighe C, Stephanie Huang R. Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Genome Biol. 2018 Sep 11;19(1):130. doi: 10.1186/s13059-018-1507-0. PubMed PMID: 30205839; PubMed Central PMCID: PMC6131897.
Wang F, Chang JT, Zhang Z, Morrison G, Nath A, Bhutra S, Huang RS. Discovering drugs to overcome chemoresistance in ovarian cancers based on the cancer genome atlas tumor transcriptome profile. Oncotarget. 2017 Dec 29;8(70):115102-115113. doi: 10.18632/oncotarget.22870. eCollection 2017 Dec 29. PubMed PMID: 29383145; PubMed Central PMCID: PMC5777757.
Geeleher P, Zhang Z, Wang F, Gruener RF, Nath A, Morrison G, Bhutra S, Grossman RL, Huang RS. Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Genome Res. 2017 Oct;27(10):1743-1751. doi: 10.1101/gr.221077.117. Epub 2017 Aug 28. PubMed PMID: 28847918; PubMed Central PMCID: PMC5630037.
Bilgin B, Nath A, Chan C, Walton SP. Characterization of transcription factor response kinetics in parallel. BMC Biotechnol. 2016 Aug 24;16(1):62. doi: 10.1186/s12896-016-0293-6. PubMed PMID: 27557669; PubMed Central PMCID: PMC4997724.
Dalgic E, Li I, Nath A, Chan C. GR-RNF43 Regulation In Colorectal Cancer. Journal of Proteomics And Genomics Research. 2016-3-; 1(4):60-66. doi: 10.14302/issn.2326-0793.jpgr-16-941.
Nath A, Chan C. Genetic alterations in fatty acid transport and metabolism genes are associated with metastatic progression and poor prognosis of human cancers. Sci Rep. 2016 Jan 4;6:18669. doi: 10.1038/srep18669. PubMed PMID: 26725848; PubMed Central PMCID: PMC4698658.
Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. J Biol Chem. 2015 Oct 30;290(44):26457-70. doi: 10.1074/jbc.M115.676635. Epub 2015 Aug 20. PubMed PMID: 26296891; PubMed Central PMCID: PMC4646304.
Nath A, Li I, Roberts LR, Chan C. Elevated free fatty acid uptake via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma. Sci Rep. 2015 Oct 1;5:14752. doi: 10.1038/srep14752. PubMed PMID: 26424075; PubMed Central PMCID: PMC4589791.
Cho H, Wu M, Zhang L, Thompson R, Nath A, Chan C. Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells. BMC Syst Biol. 2013 Jan 22;7:9. doi: 10.1186/1752-0509-7-9. PubMed PMID: 23339444; PubMed Central PMCID: PMC3557202.
Hijazi H, Wu M, Nath A, Chan C. Ensemble Classification of Cancer Types and Biomarker Identification. Drug Dev Res. 2012 Nov;73(7):414-419. doi: 10.1002/ddr.21032. PubMed PMID: 25221378; PubMed Central PMCID: PMC4162531.
Wang X, Nath A, Yang X, Portis A, Walton SP, Chan C. Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. PLoS One. 2011;6(11):e28138. doi: 10.1371/journal.pone.0028138. Epub 2011 Nov 23. PubMed PMID: 22132232; PubMed Central PMCID: PMC3223234.
Yang X, Nath A, Opperman MJ, Chan C. The double-stranded RNA-dependent protein kinase differentially regulates insulin receptor substrates 1 and 2 in HepG2 cells. Mol Biol Cell. 2010 Oct 1;21(19):3449-58. doi: 10.1091/mbc.E10-06-0481. Epub 2010 Aug 4. PubMed PMID: 20685959; PubMed Central PMCID: PMC2947480.
Nath A, Bild AH. Leveraging Single-Cell Approaches in Cancer Precision Medicine. Trends Cancer. 2021 Apr;7(4):359-372. doi: 10.1016/j.trecan.2021.01.007. Epub 2021 Feb 6. Review. PubMed PMID: 33563578; PubMed Central PMCID: PMC7969443.
Nath A, Huang RS. Emerging role of long non-coding RNAs in cancer precision medicine. Mol Cell Oncol. 2020;7(1):1684130. doi: 10.1080/23723556.2019.1684130. eCollection 2020. PubMed PMID: 31993497; PubMed Central PMCID: PMC6961685.
Pareek S, Nath A, Huang RS. MicroRNA targeting energy metabolism in ovarian cancer: a potent contender for future therapeutics. Ann Transl Med. 2019 Dec;7(Suppl 8):S299. doi: 10.21037/atm.2019.11.15. PubMed PMID: 32016018; PubMed Central PMCID: PMC6976402.
Nath A, Wang J, Stephanie Huang R. Pharmacogenetics and Pharmacogenomics of Targeted Therapeutics in Chronic Myeloid Leukemia. Mol Diagn Ther. 2017 Dec;21(6):621-631. doi: 10.1007/s40291-017-0292-x. Review. PubMed PMID: 28698977; PubMed Central PMCID: PMC5693681.
Geeleher P, Nath A, Huang RS. Institutional Profile: Pharmacogenomic research in R Stephanie Huang Laboratory. Pharmacogenomics. 2017 Apr;18(6):519-522. doi: 10.2217/pgs-2017-0031. Epub 2017 Mar 14. PubMed PMID: 28290771.
Nath A, Chan C. Relevance of Network Hierarchy in Cancer Drug-Target Selection. In: Azmi A, editor. Systems Biology in Cancer Research and Drug Discovery [Internet] Dordrecht: Springer Netherlands; 2012. Chapter Chapter 15; 339-362p. Available from: http://link.springer.com/10.1007/978-94-007-4819-4_15.
Nath A, Huang R. Abstract 3897: Pharmacogenomic landscape of long non-coding RNAs in human cancers. Experimental and Molecular Therapeutics. Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL; ; American Association for Cancer Research; c2018.
Nath A, Geeleher P, Huang R. Abstract 3481: Leveraging protein coding gene expression profiles to accurately impute lncRNA transcriptome of cancer cells. Molecular and Cellular Biology, Genetics. Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC; ; American Association for Cancer Research; c2017.
Geeleher P, Zhang Z, Wang F, Nath A, Bhutra S, Grossman R, Huang R. Abstract 5035: IDWAS: Imputing drug response in large cohorts of cancer patients to discover novel predictive biomarkers. Experimental and Molecular Therapeutics. Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC; ; American Association for Cancer Research; c2017.
Nath A, Wang F, Lenkala D, LaCroix B, Glavin N, Kipping-Johnson K, Geeleher P, Thirman M, Godley L, Raca G, Larson R, Huang. R. Abstract 2039: Exploring the longitudinal transcriptomic landscape of tyrosine kinase inhibitor treatment response in chronic myeloid leukemia patients. Experimental and Molecular Therapeutics. Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA; ; American Association for Cancer Research; c2016.
Nath A, Chan C. Abstract A1-58: Revisiting cancer energetics: Establishing a link between altered fatty-acid metabolism and metastasis. Patient Stratification: Biomarker/Genomic Approaches. Abstracts: AACR Special Conference: Translation of the Cancer Genome; February 7-9, 2015; San Francisco, CA; ; American Association for Cancer Research; c2015.
Nath A, Li I, Chan C. Abstract 5157: Elevated uptake of free fatty acids via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma. Tumor Biology. Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA; ; American Association for Cancer Research; c2015.
Nath A, Chan C. Abstract C29: Free fatty acid induced epithelial to mesenchymal transition (EMT) in hepatocellular carcinoma cells. Metastasis. Abstracts: Third AACR International Conference on Frontiers in Basic Cancer Research - September 18-22, 2013; National Harbor, MD; ; American Association for Cancer Research; c2014.