Journal articles

  1. Cellular interactions within the immune microenvironment underpins resistance to cell cycle inhibition in breast cancers. Griffiths JI, Cosgrove PA, Medina EF, Nath A, Chen J, Adler FR, Chang JT, Khan QJ, Bild AH. Nat Commun. 2025 Mar 3;16(1):2132. doi: 10.1038/s41467-025-56279-x.PMID: 40032842

  2. The Hallmarks of Predictive Oncology. Singhal A, Zhao X, Wall P, So E, Calderini G, Partin A, Koussa N, Vasanthakumari P, Narykov O, Zhu Y, Jones SE, Abbas-Aghababazadeh F, Kadambat Nair S, Bélisle-Pipon JC, Jayaram A, Parker BA, Yeung KT, Griffiths JI, Weil R, Nath A, Haibe-Kains B, Ideker T. Cancer Discov. 2025 Jan 6:OF1-OF15. doi: 10.1158/2159-8290.CD-24-0760.PMID: 39760657

  3. Single-Cell Transcriptomics Sheds Light on Tumor Evolution: Perspectives from City of Hope's Clinical Trial Teams. Cosgrove PA, Bild AH, Dellinger TH, Badie B, Portnow J, Nath A. J Clin Med. 2024 Dec 10;13(24):7507. doi: 10.3390/jcm13247507.PMID: 39768430

  4. Paradoxical cancer cell proliferation after FGFR inhibition through decreased p21 signaling in FGFR1-amplified breast cancer cells. Chi F, Griffiths JI, Nath A, Bild AH. Breast Cancer Res. 2024 Mar 29;26(1):54. doi: 10.1186/s13058-024-01808-7.PMID: 38553760

  5. Unveiling the potential of gene editing techniques in revolutionizing Cancer treatment: A comprehensive overview. Garg P, Singhal G, Pareek S, Kulkarni P, Horne D, Nath A, Salgia R, Singhal SS. Biochim Biophys Acta Rev Cancer. 2024 Dec 3;1880(1):189233. doi: 10.1016/j.bbcan.2024.189233.

  6. ONC201/TIC10 enhances durability of mTOR inhibitor everolimus in metastatic ER+ breast cancer. Farmaki E, Nath A, Emond R, Karimi KL, Grolmusz VK, Cosgrove PA, Bild AH. Elife. 2023 Sep 29;12:e85898. doi: 10.7554/eLife.85898.PMID: 37772709

  7. Cell facilitation promotes growth and survival under drug pressure in breast cancer. Emond R, Griffiths JI, Grolmusz VK, Nath A, Chen J, Medina EF, Sousa RS, Synold T, Adler FR, Bild AH. Nat Commun. 2023 Jun 29;14(1):3851. doi: 10.1038/s41467-023-39242-6.PMID: 37386030

  8. A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types. Bishara I, Chen J, Griffiths JI, Bild AH, Nath A. Front Genet. 2022 Nov 25;13:982019. doi: 10.3389/fgene.2022.982019. eCollection 2022.PMID: 36506328

  9. Predicting clinical response to everolimus in ER+ breast cancers using machine-learning. Nath A, Cosgrove PA, Chang JT, Bild AH. Front Mol Biosci. 2022 Oct 11;9:981962. doi: 10.3389/fmolb.2022.981962. eCollection 2022.PMID: 36304922

  10. Unraveling phenotypic plasticity and evolution in small cell lung cancer. Nath A. Cell Syst. 2022 Sep 21;13(9):687-689. doi: 10.1016/j.cels.2022.08.005.PMID: 36137510

  11. ENDORSE: a prognostic model for endocrine therapy in estrogen-receptor-positive breast cancers. Nath A, Cohen AL, Bild AH. Mol Syst Biol. 2022 Jun;18(6):e10558. doi: 10.15252/msb.202110558.PMID: 35671075

  12. RAGE Inhibitors as Alternatives to Dexamethasone for Managing Cerebral Edema Following Brain Tumor Surgery. Liu S, Song Y, Zhang IY, Zhang L, Gao H, Su Y, Yang Y, Yin S, Zheng Y, Ren L, Yin HH, Pillai R, Nath A, Medina EF, Cosgrove PA, Bild AH, Badie B. Neurotherapeutics. 2022 Mar;19(2):635-648. doi: 10.1007/s13311-022-01207-w. Epub 2022 Feb 28.PMID: 35226341

  13. Long Non-Coding RNA ANRIL as a Potential Biomarker of Chemosensitivity and Clinical Outcomes in Osteosarcoma. Lee AM, Ferdjallah A, Moore E, Kim DC, Nath A, Greengard E, Huang RS. Int J Mol Sci. 2021 Oct 16;22(20):11168. doi: 10.3390/ijms222011168.PMID: 34681828

  14. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. 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. Nat Commun. 2021 May 24;12(1):3039. doi: 10.1038/s41467-021-23171-3.PMID: 34031395

  15. Leveraging Single-Cell Approaches in Cancer Precision Medicine. Nath A, Bild AH. Trends Cancer. 2021 Apr;7(4):359-372. doi: 10.1016/j.trecan.2021.01.007. Epub 2021 Feb 6.PMID: 33563578.

  16. A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer. Chi F, Liu J, Brady SW, Cosgrove PA, Nath A, McQuerry JA, Majumdar S, Moos PJ, Chang JT, Kahn M, Bild AH. Transl Oncol. 2021 Jan;14(1):100946. doi: 10.1016/j.tranon.2020.100946. Epub 2020 Nov 19.PMID: 33221681

  17. Palmitate-Induced IRE1-XBP1-ZEB Signaling Represses Desmoplakin Expression and Promotes Cancer Cell Migration. Nath A, Oak A, Chen KY, Li I, Splichal RC, Portis J, Foster S, Walton SP, Chan C. Mol Cancer Res. 2021 Feb;19(2):240-248. doi: 10.1158/1541-7786.MCR-19-0480. Epub 2020 Oct 26.PMID: 33106375

  18. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Grolmusz VK, Chen J, Emond R, Cosgrove PA, Pflieger L, Nath A, Moos PJ, Bild AH. Cancer Cell Int. 2020 Jun 17;20:253. doi: 10.1186/s12935-020-01337-1. eCollection 2020.PMID: 32565737

  19. Clinical evaluation of germline polymorphisms associated with capecitabine toxicity in breast cancer: TBCRC-015. 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; Translational Breast Cancer Research Consortium (TBCRC). Breast Cancer Res Treat. 2020 Jun;181(3):623-633. doi: 10.1007/s10549-020-05603-8. Epub 2020 May 6.PMID: 32378051

  20. MicroRNA targeting energy metabolism in ovarian cancer: a potent contender for future therapeutics. Pareek S, Nath A, Huang RS. Ann Transl Med. 2019 Dec;7(Suppl 8):S299. doi: 10.21037/atm.2019.11.15.PMID: 32016018

  21. Emerging role of long non-coding RNAs in cancer precision medicine. Nath A, Huang RS. Mol Cell Oncol. 2019 Nov 10;7(1):1684130. doi: 10.1080/23723556.2019.1684130. eCollection 2020.PMID: 31993497

  22. iMIRAGE: an R package to impute microRNA expression using protein-coding genes. Nath A, Chang J, Huang RS. Bioinformatics. 2020 Apr 15;36(8):2608-2610. doi: 10.1093/bioinformatics/btz939.PMID: 31860075

  23. Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes. Nath A, Lau EYT, Lee AM, Geeleher P, Cho WCS, Huang RS. Proc Natl Acad Sci U S A. 2019 Oct 29;116(44):22020-22029. doi: 10.1073/pnas.1909998116. Epub 2019 Sep 23.PMID: 31548386

  24. Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes. Nath A, Geeleher P, Huang RS. Brief Bioinform. 2020 Mar 23;21(2):637-648. doi: 10.1093/bib/bby129.PMID: 30657858

  25. Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Geeleher P, Nath A, Wang F, Zhang Z, Barbeira AN, Fessler J, Grossman RL, Seoighe C, Stephanie Huang R. Genome Biol. 2018 Sep 11;19(1):130. doi: 10.1186/s13059-018-1507-0.PMID: 30205839

  26. Discovering drugs to overcome chemoresistance in ovarian cancers based on the cancer genome atlas tumor transcriptome profile. Wang F, Chang JT, Zhang Z, Morrison G, Nath A, Bhutra S, Huang RS. Oncotarget. 2017 Dec 4;8(70):115102-115113. doi: 10.18632/oncotarget.22870. eCollection 2017 Dec 29.PMID: 29383145

  27. Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies. Geeleher P, Zhang Z, Wang F, Gruener RF, Nath A, Morrison G, Bhutra S, Grossman RL, Huang RS. Genome Res. 2017 Oct;27(10):1743-1751. doi: 10.1101/gr.221077.117. Epub 2017 Aug 28.PMID: 28847918

  28. Pharmacogenetics and Pharmacogenomics of Targeted Therapeutics in Chronic Myeloid Leukemia. Nath A, Wang J, Stephanie Huang R. Mol Diagn Ther. 2017 Dec;21(6):621-631. doi: 10.1007/s40291-017-0292-x.PMID: 28698977.

  29. Institutional Profile: Pharmacogenomic research in R Stephanie Huang Laboratory. Geeleher P, Nath A, Huang RS. Pharmacogenomics. 2017 Apr;18(6):519-522. doi: 10.2217/pgs-2017-0031. Epub 2017 Mar 14.PMID: 28290771

  30. Characterization of transcription factor response kinetics in parallel. Bilgin B, Nath A, Chan C, Walton SP. BMC Biotechnol. 2016 Aug 24;16(1):62. doi: 10.1186/s12896-016-0293-6.PMID: 27557669

  31. Genetic alterations in fatty acid transport and metabolism genes are associated with metastatic progression and poor prognosis of human cancers. Nath A, Chan C. Sci Rep. 2016 Jan 4;6:18669. doi: 10.1038/srep18669.PMID: 26725848

  32. Elevated free fatty acid uptake via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma. Nath A, Li I, Roberts LR, Chan C. Sci Rep. 2015 Oct 1;5:14752. doi: 10.1038/srep14752.PMID: 26424075

  33. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing. Kowalsky CA, Faber MS, Nath A, Dann HE, Kelly VW, Liu L, Shanker P, Wagner EK, Maynard JA, Chan C, Whitehead TA. J Biol Chem. 2015 Oct 30;290(44):26457-70. doi: 10.1074/jbc.M115.676635. Epub 2015 Aug 20.PMID: 26296891

  34. Signaling dynamics of palmitate-induced ER stress responses mediated by ATF4 in HepG2 cells. Cho H, Wu M, Zhang L, Thompson R, Nath A, Chan C. BMC Syst Biol. 2013 Jan 22;7:9. doi: 10.1186/1752-0509-7-9.PMID: 23339444

  35. Ensemble Classification of Cancer Types and Biomarker Identification. Hijazi H, Wu M, Nath A, Chan C. Drug Dev Res. 2012 Nov;73(7):414-419. doi: 10.1002/ddr.21032.PMID: 25221378

  36. Synergy analysis reveals association between insulin signaling and desmoplakin expression in palmitate treated HepG2 cells. Wang X, Nath A, Yang X, Portis A, Walton SP, Chan C. PLoS One. 2011;6(11):e28138. doi: 10.1371/journal.pone.0028138. Epub 2011 Nov 23.PMID: 22132232

  37. The double-stranded RNA-dependent protein kinase differentially regulates insulin receptor substrates 1 and 2 in HepG2 cells. Yang X, Nath A, Opperman MJ, Chan C. Mol Biol Cell. 2010 Oct 1;21(19):3449-58. doi: 10.1091/mbc.E10-06-0481. Epub 2010 Aug 4.PMID: 20685959

Conference abstracts

  1. Single-cell RNA sequencing of early-stage to refractory metastatic ER+ breast cancers reveal phenotypic states underlying resistance to multiple lines of therapy. A Nath, P Cosgrove, J Griffiths, J Chang, A Cohen, A Bild. Cancer Research (2023) 83 (7_Supplement): 3129

  2. Acquired sensitivity to ONC201/TIC10 in ER+ breast cancer progressing on the mTOR inhibitor everolimus. E Farmaki, R Emond, A Nath, VK Grolmusz, PA Cosgrove, AH Bild (2023). Cancer Research 83 (7_Supplement), 388-388

  3. Cancer cell communication with macrophages prevents T cell activation during emergence of cell cycle therapy resistance. JI Griffiths, PA Cosgrove, EM Castaneda, A Nath, J Chen, FR Adler, JT Chang, QJ Khan, AH Bild (2023). Cancer Research 83 (7_Supplement), 4318-4318

  4. Cancer cells subvert fibroblast function to promote a growth factor enriched tumor microenvironment in endocrine therapy resistant ER+ breast cancer. JI Griffiths, PA Cosgrove, EM Castaneda, A Nath, J Chen, FR Adler, JT Chang, QJ Khan, AH Bild (2023) Cancer Research 83 (7_Supplement), 5693-5693

  5. Palmitate Induced Desmoplakin Loss and Enhanced Migration of Breast Cancer Cell Mediated By the IRE1α-XBP1-ZEB1 Pathway. K Chen, A Nath, A Oak, R Splichal, S Foster, SP Walton, C Chan. 2020 Virtual AIChE Annual Meeting

  6. The role of non-coding RNA ANRIL in chemosensitivity in osteosarcoma. A Ferdjallah, A Lee, E Moore, A Nath, RS Huang. PEDIATRIC BLOOD & CANCER 67, S122-S122

  7. Activation of IRE1α By Palmitate Leads to Loss of Desmoplakin in Liver and Breast Cancer Cells. A Oak, A Nath, G Jansen, C Chan. 2019 AIChE Annual Meeting

  8. Comprehensive pharmacogenomic analysis establishes lncRNAs as protein-coding independent biomarker of drug response in human cancers. A Nath, EY Lau, AM Lee, P Geeleher, WC Cho, RS Huang. Cancer Research 79 (13_Supplement), 3578-3578

  9. Pharmacogenomic landscape of long non-coding RNAs in human cancers. A Nath, RS Huang. Cancer Research 78 (13_Supplement), 3897-3897

  10. Leveraging protein coding gene expression profiles to accurately impute lncRNA transcriptome of cancer cells. A Nath, P Geeleher, RS Huang. Cancer Research 77 (13_Supplement), 3481-3481

  11. IDWAS: Imputing drug response in large cohorts of cancer patients to discover novel predictive biomarkers. P Geeleher, Z Zhang, F Wang, A Nath, S Bhutra, R Grossman, RS Huang. Cancer Research 77 (13_Supplement), 5035-5035

  12. Exploring the longitudinal transcriptomic landscape of tyrosine kinase inhibitor treatment response in chronic myeloid leukemia patients. A Nath, F Wang, D Lenkala, B LaCroix, N Glavin, K Kipping-Johnson, et al. Cancer Research 76 (14_Supplement), 2039-2039

  13. Revisiting cancer energetics: Establishing a link between altered fatty-acid metabolism and metastasis. A Nath, C Chan. Cancer Research 75 (22_Supplement_1), A1-58-A1-58

  14. Elevated uptake of free fatty acids via CD36 promotes epithelial-mesenchymal transition in hepatocellular carcinoma. A Nath, I Li, C Chan. Cancer Research 75 (15_Supplement), 5157-5157

  15. Free fatty acid induced epithelial to mesenchymal transition (EMT) in hepatocellular carcinoma cells. A Nath, C Chan. Cancer Research 73 (19_Supplement), C29-C29