Publications - The Gaykalova Lab

Ling X, Bazyar S, Ferris M, Molitoris J, Allor E, Thomas H, Arons D, Schumaker L, Krc R, Mendes WS, Tran PT, Sawant A, Mehra R, Gaykalova DA, Ren L. Identification of CT based radiomic biomarkers for progression free survival in head and neck squamous cell carcinoma. Sci Rep. 2025 Jan 8;15(1):1279. doi: 10.1038/s41598-025-85498-x. PMID: 39779914; PMCID: PMC11711663.
Baretti M, Danilova L, Durham JN, Betts CB, Cope L, Sidiropoulos DN, Tandurella JA, Charmsaz S, Gross N, Hernandez A, Ho WJ, Thoburn C, Walker R, Leatherman J, Mitchell S, Christmas B, Saeed A, Gaykalova DA, Yegnasubramanian S, Fertig EJ, Coussens LM, Yarchoan M, Jaffee E, Azad NS. Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial. Nat Commun. 2024 Nov 12;15(1):9801. doi: 10.1038/s41467-024-52528-7. PubMed PMID: 39532835; PubMed Central PMCID: PMC11557583.
Palmer T, Kessler MD, Shao XM, Balan A, Yarchoan M, Zaidi N, Lopez-Vidal TY, Saeed AM, Gore J, Azad NS, Jaffee EM, Favorov AV, Anagnostou V, Karchin R, Gaykalova DA, Fertig EJ, Danilova L. SpliceMutr enables pan-cancer analysis of splicing-derived neoantigen burden in tumors. Cancer Res Commun. 2024 Oct 29. doi: 10.1158/2767-9764.CRC-23-0309. Epub ahead of print. PMID: 39470352.
Gupta I, Gaykalova DA. Unveiling the role of PIK3R1 in cancer: A comprehensive review of regulatory signaling and therapeutic implications. Semin Cancer Biol. 2024 Aug 26;106-107:58-86. doi: 10.1016/j.semcancer.2024.08.004. Epub ahead of print. PMID: 39197810.
Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res. 2024 Aug 21;43(1):239. doi: 10.1186/s13046-024-03141-5. PMID: 39169426; PMCID: PMC11337877.
Rodriguez I, Rossi NM, Keskus AG, Xie Y, Ahmad T, Bryant A, Lou H, Paredes JG, Milano R, Rao N, Tulsyan S, Boland JF, Luo W, Liu J, O’Hanlon T, Bess J, Mukhina V, Gaykalova D, Yuki Y, Malik L, Billingsley KJ, Blauwendraat C, Carrington M, Yeager M, Mirabello L, Kolmogorov M, Dean M. Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing. Am J Hum Genet. 2024 Mar 7;111(3):544-561. doi: 10.1016/j.ajhg.2024.01.002. Epub 2024 Feb 1. PubMed PMID: 38307027; PubMed Central PMCID: PMC10940022.
Guo T, Zamuner F, Ting S, Chen L, Rooper L, Tamayo P, Fakhry C, Gaykalova D, Mehra R. Clinical and genomic characterization of chemoradiation-resistant HPV-positive oropharyngeal squamous cell carcinoma. Front Oncol. 2024;14:1336577. doi: 10.3389/fonc.2024.1336577. eCollection 2024. PubMed PMID: 38505587; PubMed Central PMCID: PMC10949886.
Ren L, Ling X, Alexander G, Molitoris J, Choi J, Schumaker L, Mehra R, Gaykalova D. Radiomic Biomarkers of Locoregional Recurrence: Prognostic Insights from Oral Cavity Squamous Cell Carcinoma preoperative CT scans. Res Sq. 2024 Jan 22;. doi: 10.21203/rs.3.rs-3857391/v1. PubMed PMID: 38343846; PubMed Central PMCID: PMC10854303.
Hurník P, Režnarová J, Chyra Z, Motyka O, Putnová BM, Čermáková Z, Blažek T, Fománek M, Gaykalova D, Buchtová M, Ševčíková T, Štembírek J. Enhancing oral squamous cell carcinoma prediction: the prognostic power of the worst pattern of invasion and the limited impact of molecular resection margins. Front Oncol. 2023;13:1287650. doi: 10.3389/fonc.2023.1287650. eCollection 2023. PubMed PMID: 38188288; PubMed Central PMCID: PMC10766711.
Ling X, Alexander GS, Molitoris J, Choi J, Schumaker L, Mehra R, Gaykalova DA, Ren L. Identification of CT-based non-invasive radiomic biomarkers for overall survival prediction in oral cavity squamous cell carcinoma. Sci Rep. 2023 Dec 8;13(1):21774. doi: 10.1038/s41598-023-48048-x. PubMed PMID: 38066047; PubMed Central PMCID: PMC10709435.
Yang Z, Liao J, Schumaker L, Carter-Cooper B, Lapidus RG, Fan X, Gaykalova DA, Mehra R, Cullen KJ, Dan H. Simultaneously targeting ErbB family kinases and PI3K in HPV-positive head and neck squamous cell carcinoma. Oral Oncol. 2022 Aug;131:105939. doi: 10.1016/j.oraloncology.2022.105939. Epub 2022 Jun 3. PubMed PMID: 35667295.
Sidiropoulos DN, Rafie CI, Jang JK, Castanon S, Baugh AG, Gonzalez E, Christmas BJ, Narumi VH, Davis-Marcisak EF, Sharma G, Bigelow E, Vaghasia A, Gupta A, Skaist A, Considine M, Wheelan SJ, Ganesan SK, Yu M, Yegnasubramanian S, Stearns V, Connolly RM, Gaykalova DA, Kagohara LT, Jaffee EM, Fertig EJ, Roussos Torres ET. Entinostat Decreases Immune Suppression to Promote Antitumor Responses in a HER2+ Breast Tumor Microenvironment. Cancer Immunol Res. 2022 May 3;10(5):656-669. doi: 10.1158/2326-6066.CIR-21-0170. PubMed PMID: 35201318; PubMed Central PMCID: PMC9064912.
Hurník P, Chyra Z, Ševčíková T, Štembírek J, Trtková KS, Gaykalova DA, Buchtová M, Hrubá E. Epigenetic Regulations of Perineural Invasion in Head and Neck Squamous Cell Carcinoma. Front Genet. 2022;13:848557. doi: 10.3389/fgene.2022.848557. eCollection 2022. Review. PubMed PMID: 35571032; PubMed Central PMCID: PMC9091179.
Erbe R, Gore J, Gemmill K, Gaykalova DA, Fertig EJ. The use of machine learning to discover regulatory networks controlling biological systems. Mol Cell. 2022 Jan 20;82(2):260-273. doi: 10.1016/j.molcel.2021.12.011. Epub 2022 Jan 10. Review. PubMed PMID: 35016036; PubMed Central PMCID: PMC8905511.
Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A. Correction: Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor. Oncoscience. 2021;8:108-109. doi: 10.18632/oncoscience.546. eCollection 2021. PubMed PMID: 34589558; PubMed Central PMCID: PMC8460121.
Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Correction: Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. Br J Cancer. 2020 Nov;123(10):1582-1583. doi: 10.1038/s41416-020-0998-0. PubMed PMID: 32694696; PubMed Central PMCID: PMC7652830.
Ren S, Gaykalova DA, Guo T, Favorov AV, Fertig EJ, Tamayo P, Callejas-Valera JL, Allevato M, Gilardi M, Santos J, Fukusumi T, Sakai A, Ando M, Sadat S, Liu C, Xu G, Fisch KM, Wang Z, Molinolo AA, Gutkind JS, Ideker T, Koch WM, Califano JA. HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers. Oncogene. 2020 Oct;39(40):6327-6339. doi: 10.1038/s41388-020-01431-8. Epub 2020 Aug 26. PubMed PMID: 32848210; PubMed Central PMCID: PMC7529583.
Lopatina T, Favaro E, Danilova L, Fertig EJ, Favorov AV, Kagohara LT, Martone T, Bussolati B, Romagnoli R, Albera R, Pecorari G, Brizzi MF, Camussi G, Gaykalova DA. Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells. Front Cell Dev Biol. 2020;8:698. doi: 10.3389/fcell.2020.00698. eCollection 2020. PubMed PMID: 33015029; PubMed Central PMCID: PMC7509153.
Guo T, Zambo KDA, Zamuner FT, Ou T, Hopkins C, Kelley DZ, Wulf HA, Winkler E, Erbe R, Danilova L, Considine M, Sidransky D, Favorov A, Florea L, Fertig EJ, Gaykalova DA. Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma. Epigenetics. 2020 Sep;15(9):959-971. doi: 10.1080/15592294.2020.1741757. Epub 2020 Mar 22. PubMed PMID: 32164487; PubMed Central PMCID: PMC7518675.
Erbe R, Kessler MD, Favorov AV, Easwaran H, Gaykalova DA, Fertig EJ. Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets. Nucleic Acids Res. 2020 Jul 9;48(12):e68. doi: 10.1093/nar/gkaa349. PubMed PMID: 32392348; PubMed Central PMCID: PMC7337516.
Kagohara LT, Zamuner F, Davis-Marcisak EF, Sharma G, Considine M, Allen J, Yegnasubramanian S, Gaykalova DA, Fertig EJ. Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lines. Br J Cancer. 2020 Jul;123(1):101-113. doi: 10.1038/s41416-020-0851-5. Epub 2020 May 4. PubMed PMID: 32362655; PubMed Central PMCID: PMC7341752.
Gaykalova DA, Mambo E, Choudhary A, Houghton J, Buddavarapu K, Sanford T, Darden W, Adai A, Hadd A, Latham G, Danilova LV, Bishop J, Li RJ, Westra WH, Hennessey P, Koch WM, Ochs MF, Califano JA, Sun W. Correction: Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma. PLoS One. 2020;15(5):e0233409. doi: 10.1371/journal.pone.0233409. eCollection 2020. PubMed PMID: 32401780; PubMed Central PMCID: PMC7219749.
London NR Jr, Rooper LM, Bishop JA, Xu H, Bernhardt LJ, Ishii M, Hann CL, Taube JM, Izumchenko E, Gaykalova DA, Gallia GL. Expression of Programmed Cell Death Ligand 1 and Associated Lymphocyte Infiltration in Olfactory Neuroblastoma. World Neurosurg. 2020 Mar;135:e187-e193. doi: 10.1016/j.wneu.2019.11.112. Epub 2019 Nov 27. PubMed PMID: 31785431.
Schubert AD, Channah Broner E, Agrawal N, London N, Pearson A, Gupta A, Wali N, Seiwert TY, Wheelan S, Lingen M, Macleod K, Allen H, Chatterjee A, Vassiliki S, Gaykalova D, Hoque MO, Sidransky D, Suresh K, Izumchenko E. Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma. Cancer Lett. 2020 Feb 28;471:49-60. doi: 10.1016/j.canlet.2019.12.006. Epub 2019 Dec 10. PubMed PMID: 31830557; PubMed Central PMCID: PMC6980748.
Flam EL, Danilova L, Kelley DZ, Stavrovskaya E, Guo T, Considine M, Qian J, Califano JA, Favorov A, Fertig EJ, Gaykalova DA. Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer. Sci Rep. 2019 Oct 21;9(1):15034. doi: 10.1038/s41598-019-51018-x. PubMed PMID: 31636280; PubMed Central PMCID: PMC6803762.
Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 29;10(1):2415. doi: 10.1038/s41467-019-10557-7. PubMed PMID: 31142745; PubMed Central PMCID: PMC6541594.
Ando M, Saito Y, Xu G, Bui NQ, Medetgul-Ernar K, Pu M, Fisch K, Ren S, Sakai A, Fukusumi T, Liu C, Haft S, Pang J, Mark A, Gaykalova DA, Guo T, Favorov AV, Yegnasubramanian S, Fertig EJ, Ha P, Tamayo P, Yamasoba T, Ideker T, Messer K, Califano JA. Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers. Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. PubMed PMID: 31097695; PubMed Central PMCID: PMC6522544.
Sherman TD, Kagohara LT, Cao R, Cheng R, Satriano M, Considine M, Krigsfeld G, Ranaweera R, Tang Y, Jablonski SA, Stein-O’Brien G, Gaykalova DA, Weiner LM, Chung CH, Fertig EJ. CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. PLoS Comput Biol. 2018 Jun;14(4):e1006935. doi: 10.1371/journal.pcbi.1006935. eCollection 2018 Jun. PubMed PMID: 31002670; PubMed Central PMCID: PMC6504085.
Lopatina T, Favaro E, Grange C, Cedrino M, Ranghino A, Occhipinti S, Fallo S, Buffolo F, Gaykalova DA, Zanone MM, Romagnoli R, Camussi G. PDGF enhances the protective effect of adipose stem cell-derived extracellular vesicles in a model of acute hindlimb ischemia. Sci Rep. 2018 Dec 4;8(1):17458. doi: 10.1038/s41598-018-36143-3. PubMed PMID: 30514962; PubMed Central PMCID: PMC6279818.
Kelley DZ, Flam EL, Guo T, Danilova LV, Zamuner FT, Bohrson C, Considine M, Windsor EJ, Bishop JA, Zhang C, Koch WM, Sidransky D, Westra WH, Chung CH, Califano JA, Wheelan S, Favorov AV, Florea L, Fertig EJ, Gaykalova DA. Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma. Transl Res. 2018 Dec;202:109-119. doi: 10.1016/j.trsl.2018.07.007. Epub 2018 Jul 26. PubMed PMID: 30118659; PubMed Central PMCID: PMC6218276.
Ren S, Gaykalova D, Wang J, Guo T, Danilova L, Favorov A, Fertig E, Bishop J, Khan Z, Flam E, Wysocki PT, DeJong P, Ando M, Liu C, Sakai A, Fukusumi T, Haft S, Sadat S, Califano JA. Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma. Int J Cancer. 2018 Nov 15;143(10):2425-2436. doi: 10.1002/ijc.31778. Epub 2018 Sep 21. PubMed PMID: 30070359.
Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nat Protoc. 2018 Nov;13(11):2535-2556. doi: 10.1038/s41596-018-0048-z. PubMed PMID: 30341436; PubMed Central PMCID: PMC6322412.
Rettig EM, Bishop JA, Agrawal N, Chung CH, Sharma R, Zamuner F, Li RJ, Koch WM, Califano JA, Guo T, Gaykalova DA, Fakhry C. HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma. Oral Oncol. 2018 Jul;82:168-175. doi: 10.1016/j.oraloncology.2018.05.017. Epub 2018 Jun 1. PubMed PMID: 29909892.
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer. Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004. PubMed PMID: 29342249; PubMed Central PMCID: PMC5972655.
Stein-O’Brien G, Kagohara LT, Li S, Thakar M, Ranaweera R, Ozawa H, Cheng H, Considine M, Schmitz S, Favorov AV, Danilova LV, Califano JA, Izumchenko E, Gaykalova DA, Chung CH, Fertig EJ. Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance. Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2. PubMed PMID: 29792227; PubMed Central PMCID: PMC5966898.
Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A. Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor. Oncoscience. 2018 Jan;5(1-2):21-38. doi: 10.18632/oncoscience.395. eCollection 2018 Jan. PubMed PMID: 29556515; PubMed Central PMCID: PMC5854290.
Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics. 2018 Jan 1;17(1):49-63. doi: 10.1093/bfgp/elx018. PubMed PMID: 28968850; PubMed Central PMCID: PMC5860551.
Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Afsari B, Skaist AM, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan SJ, Califano JA, Favorov AV, Fertig EJ, Gaykalova DA. Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks. Cancer Res. 2017 Dec 1;77(23):6538-6550. doi: 10.1158/0008-5472.CAN-17-0833. Epub 2017 Sep 25. PubMed PMID: 28947419; PubMed Central PMCID: PMC6029614.
Finegersh A, Kulich S, Guo T, Favorov AV, Fertig EJ, Danilova LV, Gaykalova DA, Califano JA, Duvvuri U. DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma. Sci Rep. 2017 Nov 9;7(1):15173. doi: 10.1038/s41598-017-15634-9. PubMed PMID: 29123240; PubMed Central PMCID: PMC5680248.
Guo T, Sakai A, Afsari B, Considine M, Danilova L, Favorov AV, Yegnasubramanian S, Kelley DZ, Flam E, Ha PK, Khan Z, Wheelan SJ, Gutkind JS, Fertig EJ, Gaykalova DA, Califano J. A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers. Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21. PubMed PMID: 28733453; PubMed Central PMCID: PMC6042297.
Faraji F, Zaidi M, Fakhry C, Gaykalova DA. Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer. Microbes Infect. 2017 Sep-Oct;19(9-10):464-475. doi: 10.1016/j.micinf.2017.06.001. Epub 2017 Jun 12. Review. PubMed PMID: 28619685; PubMed Central PMCID: PMC5603399.
Stein-O’Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. PubMed PMID: 28174896; PubMed Central PMCID: PMC5860188.
Makarev E, Schubert AD, Kanherkar RR, London N, Teka M, Ozerov I, Lezhnina K, Bedi A, Ravi R, Mehra R, Hoque MO, Sloma I, Gaykalova DA, Csoka AB, Sidransky D, Zhavoronkov A, Izumchenko E. In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia. Cell Death Discov. 2017;3:17022. doi: 10.1038/cddiscovery.2017.22. eCollection 2017. PubMed PMID: 28580171; PubMed Central PMCID: PMC5439156.
Gaykalova DA, Zizkova V, Guo T, Tiscareno I, Wei Y, Vatapalli R, Hennessey PT, Ahn J, Danilova L, Khan Z, Bishop JA, Gutkind JS, Koch WM, Westra WH, Fertig EJ, Ochs MF, Califano JA. Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC. Oncotarget. 2017 Feb 28;8(9):15349-15363. doi: 10.18632/oncotarget.14856. PubMed PMID: 28146432; PubMed Central PMCID: PMC5362490.
Fertig EJ, Ozawa H, Thakar M, Howard JD, Kagohara LT, Krigsfeld G, Ranaweera RS, Hughes RM, Perez J, Jones S, Favorov AV, Carey J, Stein-O’Brien G, Gaykalova DA, Ochs MF, Chung CH. CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network. Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075. PubMed PMID: 27650546; PubMed Central PMCID: PMC5342018.
Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer. 2016 Jul 15;139(2):373-82. doi: 10.1002/ijc.30081. Epub 2016 Mar 30. PubMed PMID: 26949921; PubMed Central PMCID: PMC5579720.
Stansfield JC, Rusay M, Shan R, Kelton C, Gaykalova DA, Fertig EJ, Califano JA, Ochs MF. Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination. Cancer Inform. 2016;15:15-21. doi: 10.4137/CIN.S32468. eCollection 2016. PubMed PMID: 26884679; PubMed Central PMCID: PMC4750896.
Fakhry C, Qualliotine JR, Zhang Z, Agrawal N, Gaykalova DA, Bishop JA, Subramaniam RM, Koch WM, Chung CH, Eisele DW, Califano J, Viscidi RP. Serum Antibodies to HPV16 Early Proteins Warrant Investigation as Potential Biomarkers for Risk Stratification and Recurrence of HPV-Associated Oropharyngeal Cancer. Cancer Prev Res (Phila). 2016 Feb;9(2):135-41. doi: 10.1158/1940-6207.CAPR-15-0299. Epub 2015 Dec 23. PubMed PMID: 26701665; PubMed Central PMCID: PMC4811031.
Gaykalova DA, Vatapalli R, Wei Y, Tsai HL, Wang H, Zhang C, Hennessey PT, Guo T, Tan M, Li R, Ahn J, Khan Z, Westra WH, Bishop JA, Zaboli D, Koch WM, Khan T, Ochs MF, Califano JA. Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients. PLoS One. 2015;10(11):e0142148. doi: 10.1371/journal.pone.0142148. eCollection 2015. PubMed PMID: 26544568; PubMed Central PMCID: PMC4636259.
Gaykalova DA, Kulaeva OI, Volokh O, Shaytan AK, Hsieh FK, Kirpichnikov MP, Sokolova OS, Studitsky VM. Structural analysis of nucleosomal barrier to transcription. Proc Natl Acad Sci U S A. 2015 Oct 27;112(43):E5787-95. doi: 10.1073/pnas.1508371112. Epub 2015 Oct 12. PubMed PMID: 26460019; PubMed Central PMCID: PMC4629332.
Gaykalova DA, Manola JB, Ozawa H, Zizkova V, Morton K, Bishop JA, Sharma R, Zhang C, Michailidi C, Considine M, Tan M, Fertig EJ, Hennessey PT, Ahn J, Koch WM, Westra WH, Khan Z, Chung CH, Ochs MF, Califano JA. NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma. Int J Cancer. 2015 Oct 15;137(8):1879-89. doi: 10.1002/ijc.29558. Epub 2015 Jun 23. PubMed PMID: 25857630; PubMed Central PMCID: PMC4629062.
Rathi KS, Gaykalova DA, Hennessey P, Califano JA, Ochs MF. Correcting transcription factor gene sets for copy number and promoter methylation variations. Drug Dev Res. 2014 Sep;75(6):343-7. doi: 10.1002/ddr.21220. PubMed PMID: 25195578; PubMed Central PMCID: PMC4160810.
Li R, Ochs MF, Ahn SM, Hennessey P, Tan M, Soudry E, Gaykalova DA, Uemura M, Brait M, Shao C, Westra W, Bishop J, Fertig EJ, Califano JA. Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma. PLoS One. 2014;9(3):e91263. doi: 10.1371/journal.pone.0091263. eCollection 2014. PubMed PMID: 24675808; PubMed Central PMCID: PMC3967989.
Gaykalova DA, Mambo E, Choudhary A, Houghton J, Buddavarapu K, Sanford T, Darden W, Adai A, Hadd A, Latham G, Danilova LV, Bishop J, Li RJ, Westra WH, Hennessey P, Koch WM, Ochs MF, Califano JA, Sun W. Novel insight into mutational landscape of head and neck squamous cell carcinoma. PLoS One. 2014;9(3):e93102. doi: 10.1371/journal.pone.0093102. eCollection 2014. PubMed PMID: 24667986; PubMed Central PMCID: PMC3965530.
Sun W, Gaykalova DA, Ochs MF, Mambo E, Arnaoutakis D, Liu Y, Loyo M, Agrawal N, Howard J, Li R, Ahn S, Fertig E, Sidransky D, Houghton J, Buddavarapu K, Sanford T, Choudhary A, Darden W, Adai A, Latham G, Bishop J, Sharma R, Westra WH, Hennessey P, Chung CH, Califano JA. Activation of the NOTCH pathway in head and neck cancer. Cancer Res. 2014 Feb 15;74(4):1091-104. doi: 10.1158/0008-5472.CAN-13-1259. Epub 2013 Dec 18. PubMed PMID: 24351288; PubMed Central PMCID: PMC3944644.
Fertig EJ, Markovic A, Danilova LV, Gaykalova DA, Cope L, Chung CH, Ochs MF, Califano JA. Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis. PLoS One. 2013;8(11):e78127. doi: 10.1371/journal.pone.0078127. eCollection 2013. PubMed PMID: 24223768; PubMed Central PMCID: PMC3817178.
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