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Items: 1 to 50 of 81

1.

Mechanistically detailed systems biology modeling of the HGF/Met pathway in hepatocellular carcinoma.

Jafarnejad M, Sové RJ, Danilova L, Mirando AC, Zhang Y, Yarchoan M, Tran PT, Pandey NB, Fertig EJ, Popel AS.

NPJ Syst Biol Appl. 2019 Aug 16;5:29. doi: 10.1038/s41540-019-0107-2. eCollection 2019.

2.

A preliminary analysis of interleukin-1 ligands as potential predictive biomarkers of response to cetuximab.

Espinosa-Cotton M, Fertig EJ, Stabile LP, Gaither-Davis A, Bauman JE, Schmitz S, Gibson-Corley KN, Cheng Y, Jensen IJ, Badovinac VP, Laux D, Simons AL.

Biomark Res. 2019 Jul 16;7:14. doi: 10.1186/s40364-019-0164-0. eCollection 2019.

3.

Differential Variation Analysis Enables Detection of Tumor Heterogeneity Using Single-Cell RNA-Sequencing Data.

Davis-Marcisak EF, Sherman TD, Orugunta P, Stein-O'Brien GL, Puram SV, Roussos Torres ET, Hopkins AC, Jaffee EM, Favorov AV, Afsari B, Goff LA, Fertig EJ.

Cancer Res. 2019 Oct 1;79(19):5102-5112. doi: 10.1158/0008-5472.CAN-18-3882. Epub 2019 Jul 23.

PMID:
31337651
4.

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

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.

Nat Commun. 2019 May 29;10(1):2415. doi: 10.1038/s41467-019-10557-7.

5.

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification.

Clark BS, Stein-O'Brien GL, Shiau F, Cannon GH, Davis-Marcisak E, Sherman T, Santiago CP, Hoang TV, Rajaii F, James-Esposito RE, Gronostajski RM, Fertig EJ, Goff LA, Blackshaw S.

Neuron. 2019 Jun 19;102(6):1111-1126.e5. doi: 10.1016/j.neuron.2019.04.010. Epub 2019 May 22.

PMID:
31128945
6.

Asporin Restricts Mesenchymal Stromal Cell Differentiation, Alters the Tumor Microenvironment, and Drives Metastatic Progression.

Hughes RM, Simons BW, Khan H, Miller R, Kugler V, Torquato S, Theodros D, Haffner MC, Lotan T, Huang J, Davicioni E, An SS, Riddle RC, Thorek DLJ, Garraway IP, Fertig EJ, Isaacs JT, Brennen WN, Park BH, Hurley PJ.

Cancer Res. 2019 Jul 15;79(14):3636-3650. doi: 10.1158/0008-5472.CAN-18-2931. Epub 2019 May 23.

PMID:
31123087
7.

Decomposing Cell Identity for Transfer Learning across Cellular Measurements, Platforms, Tissues, and Species.

Stein-O'Brien GL, Clark BS, Sherman T, Zibetti C, Hu Q, Sealfon R, Liu S, Qian J, Colantuoni C, Blackshaw S, Goff LA, Fertig EJ.

Cell Syst. 2019 May 22;8(5):395-411.e8. doi: 10.1016/j.cels.2019.04.004.

8.

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.

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.

Nat Commun. 2019 May 16;10(1):2188. doi: 10.1038/s41467-019-09937-w. Erratum in: Nat Commun. 2019 May 29;10(1):2415.

9.

Programmed Cell Death Ligand-1 (PD-L1) and CD8 Expression Profiling Identify an Immunologic Subtype of Pancreatic Ductal Adenocarcinomas with Favorable Survival.

Danilova L, Ho WJ, Zhu Q, Vithayathil T, De Jesus-Acosta A, Azad NS, Laheru DA, Fertig EJ, Anders R, Jaffee EM, Yarchoan M.

Cancer Immunol Res. 2019 Jun;7(6):886-895. doi: 10.1158/2326-6066.CIR-18-0822. Epub 2019 May 1.

PMID:
31043417
10.

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.

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.

PLoS Comput Biol. 2019 Apr 19;14(4):e1006935. doi: 10.1371/journal.pcbi.1006935. eCollection 2018 Jun.

11.

Aging-like Spontaneous Epigenetic Silencing Facilitates Wnt Activation, Stemness, and BrafV600E-Induced Tumorigenesis.

Tao Y, Kang B, Petkovich DA, Bhandari YR, In J, Stein-O'Brien G, Kong X, Xie W, Zachos N, Maegawa S, Vaidya H, Brown S, Chiu Yen RW, Shao X, Thakor J, Lu Z, Cai Y, Zhang Y, Mallona I, Peinado MA, Zahnow CA, Ahuja N, Fertig E, Issa JP, Baylin SB, Easwaran H.

Cancer Cell. 2019 Feb 11;35(2):315-328.e6. doi: 10.1016/j.ccell.2019.01.005.

12.

Exosomal Expression of CXCR4 Targets Cardioprotective Vesicles to Myocardial Infarction and Improves Outcome after Systemic Administration.

Ciullo A, Biemmi V, Milano G, Bolis S, Cervio E, Fertig ET, Gherghiceanu M, Moccetti T, Camici GG, Vassalli G, Barile L.

Int J Mol Sci. 2019 Jan 22;20(3). pii: E468. doi: 10.3390/ijms20030468.

13.

A Mechanism of Resistance to Antibody-Targeted Immune Attack.

Aldeghaither DS, Zahavi DJ, Murray JC, Fertig EJ, Graham GT, Zhang YW, O'Connell A, Ma J, Jablonski SA, Weiner LM.

Cancer Immunol Res. 2019 Feb;7(2):230-243. doi: 10.1158/2326-6066.CIR-18-0266. Epub 2018 Dec 18.

PMID:
30563830
14.

Enter the Matrix: Factorization Uncovers Knowledge from Omics.

Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ.

Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Review.

15.

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma.

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.

Transl Res. 2018 Dec;202:109-119. doi: 10.1016/j.trsl.2018.07.007. Epub 2018 Jul 26.

PMID:
30118659
16.

Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma.

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.

Int J Cancer. 2018 Nov 15;143(10):2425-2436. doi: 10.1002/ijc.31778. Epub 2018 Sep 21.

PMID:
30070359
17.

Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes.

Ye IC, Fertig EJ, DiGiacomo JW, Considine M, Godet I, Gilkes DM.

Mol Cancer Res. 2018 Dec;16(12):1889-1901. doi: 10.1158/1541-7786.MCR-18-0345. Epub 2018 Jul 23.

PMID:
30037853
18.

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.

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.

Genome Med. 2018 May 23;10(1):37. doi: 10.1186/s13073-018-0545-2.

19.

Digitizing omics profiles by divergence from a baseline.

Dinalankara W, Ke Q, Xu Y, Ji L, Pagane N, Lien A, Matam T, Fertig EJ, Price ND, Younes L, Marchionni L, Geman D.

Proc Natl Acad Sci U S A. 2018 May 1;115(18):4545-4552. doi: 10.1073/pnas.1721628115. Epub 2018 Apr 16.

20.

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.

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.

Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004.

21.

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma.

Finegersh A, Kulich S, Guo T, Favorov AV, Fertig EJ, Danilova LV, Gaykalova DA, Califano JA, Duvvuri U.

Sci Rep. 2017 Nov 9;7(1):15173. doi: 10.1038/s41598-017-15634-9.

22.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

Stavrovskaya ED, Niranjan T, Fertig EJ, Wheelan SJ, Favorov AV, Mironov AA.

Bioinformatics. 2017 Oct 15;33(20):3158-3165. doi: 10.1093/bioinformatics/btx379.

23.

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.

Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ.

Brief Funct Genomics. 2018 Jan 1;17(1):49-63. doi: 10.1093/bfgp/elx018.

24.

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.

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.

Cancer Res. 2017 Dec 1;77(23):6538-6550. doi: 10.1158/0008-5472.CAN-17-0833. Epub 2017 Sep 25.

25.

An unbiased in vivo functional genomics screening approach in mice identifies novel tumor cell-based regulators of immune rejection.

Shuptrine CW, Ajina R, Fertig EJ, Jablonski SA, Kim Lyerly H, Hartman ZC, Weiner LM.

Cancer Immunol Immunother. 2017 Dec;66(12):1529-1544. doi: 10.1007/s00262-017-2047-2. Epub 2017 Aug 2.

26.

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.

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.

Cancer Res. 2017 Oct 1;77(19):5248-5258. doi: 10.1158/0008-5472.CAN-16-3106. Epub 2017 Jul 21.

27.

A Software Application for Mining and Presenting Relevant Cancer Clinical Trials per Cancer Mutation.

Gandy LM, Gumm J, Blackford AL, Fertig EJ, Diaz LA Jr.

Cancer Inform. 2017 Jun 22;16:1176935117711940. doi: 10.1177/1176935117711940. eCollection 2017.

28.

SMAD4 Loss Is Associated with Cetuximab Resistance and Induction of MAPK/JNK Activation in Head and Neck Cancer Cells.

Ozawa H, Ranaweera RS, Izumchenko E, Makarev E, Zhavoronkov A, Fertig EJ, Howard JD, Markovic A, Bedi A, Ravi R, Perez J, Le QT, Kong CS, Jordan RC, Wang H, Kang H, Quon H, Sidransky D, Chung CH.

Clin Cancer Res. 2017 Sep 1;23(17):5162-5175. doi: 10.1158/1078-0432.CCR-16-1686. Epub 2017 May 18.

29.

Synthesizer: Expediting synthesis studies from context-free data with information retrieval techniques.

Gandy LM, Gumm J, Fertig B, Thessen A, Kennish MJ, Chavan S, Marchionni L, Xia X, Shankrit S, Fertig EJ.

PLoS One. 2017 Apr 24;12(4):e0175860. doi: 10.1371/journal.pone.0175860. eCollection 2017.

30.

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.

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.

Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058.

31.

Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.

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.

Oncotarget. 2017 Feb 28;8(9):15349-15363. doi: 10.18632/oncotarget.14856.

32.

Comparative mutational landscape analysis of patient-derived tumour xenografts.

Brait M, Izumchenko E, Kagohara LT, Long S, Wysocki PT, Faherty B, Fertig EJ, Khor TO, Bruckheimer E, Baia G, Ciznadija D, Sloma I, Ben-Zvi I, Paz K, Sidransky D.

Br J Cancer. 2017 Feb 14;116(4):515-523. doi: 10.1038/bjc.2016.450. Epub 2017 Jan 24.

33.

Systems Approaches to Cancer Biology.

Archer TC, Fertig EJ, Gosline SJ, Hafner M, Hughes SK, Joughin BA, Meyer AS, Piccolo SR, Shajahan-Haq AN.

Cancer Res. 2016 Dec 1;76(23):6774-6777. Epub 2016 Nov 18.

34.

Diagnostic Yield of Epilepsy Panels in Children With Medication-Refractory Epilepsy.

Segal E, Pedro H, Valdez-Gonzalez K, Parisotto S, Gliksman F, Thompson S, Sabri J, Fertig E.

Pediatr Neurol. 2016 Nov;64:66-71. doi: 10.1016/j.pediatrneurol.2016.06.019. Epub 2016 Jul 1.

PMID:
27726903
35.

CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.

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.

Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075.

36.

The effects of lacosamide on cognition, quality-of-life measures, and quality of life in patients with refractory partial epilepsy.

Lancman ME, Fertig EJ, Trobliger RW, Perrine K, Myers L, Iyengar SS, Malik M.

Epilepsy Behav. 2016 Aug;61:27-33. doi: 10.1016/j.yebeh.2016.04.049. Epub 2016 Jun 14.

37.

Identification of methylated genes in salivary gland adenoid cystic carcinoma xenografts using global demethylation and methylation microarray screening.

Ling S, Rettig EM, Tan M, Chang X, Wang Z, Brait M, Bishop JA, Fertig EJ, Considine M, Wick MJ, Ha PK.

Int J Oncol. 2016 Jul;49(1):225-34. doi: 10.3892/ijo.2016.3532. Epub 2016 May 18.

38.

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.

Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA.

Int J Cancer. 2016 Jul 15;139(2):373-82. doi: 10.1002/ijc.30081. Epub 2016 Mar 30.

39.

Development and Feasibility Testing of a Critical Care EEG Monitoring Database for Standardized Clinical Reporting and Multicenter Collaborative Research.

Lee JW, LaRoche S, Choi H, Rodriguez Ruiz AA, Fertig E, Politsky JM, Herman ST, Loddenkemper T, Sansevere AJ, Korb PJ, Abend NS, Goldstein JL, Sinha SR, Dombrowski KE, Ritzl EK, Westover MB, Gavvala JR, Gerard EE, Schmitt SE, Szaflarski JP, Ding K, Haas KF, Buchsbaum R, Hirsch LJ, Wusthoff CJ, Hopp JL, Hahn CD; Critical Care EEG Monitoring Research Consortium (CCEMRC).

J Clin Neurophysiol. 2016 Apr;33(2):133-40. doi: 10.1097/WNP.0000000000000230.

40.

Inferring causal molecular networks: empirical assessment through a community-based effort.

Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, Danilova LV, Favorov AV, Lee WS, Taylor D, Hu CW, Long BL, Noren DP, Bisberg AJ; HPN-DREAM Consortium, Mills GB, Gray JW, Kellen M, Norman T, Friend S, Qutub AA, Fertig EJ, Guan Y, Song M, Stuart JM, Spellman PT, Koeppl H, Stolovitzky G, Saez-Rodriguez J, Mukherjee S.

Nat Methods. 2016 Apr;13(4):310-8. doi: 10.1038/nmeth.3773. Epub 2016 Feb 22.

41.

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.

Stansfield JC, Rusay M, Shan R, Kelton C, Gaykalova DA, Fertig EJ, Califano JA, Ochs MF.

Cancer Inform. 2016 Feb 10;15:15-21. doi: 10.4137/CIN.S32468. eCollection 2016.

42.

Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma.

Rettig EM, Talbot CC Jr, Sausen M, Jones S, Bishop JA, Wood LD, Tokheim C, Niknafs N, Karchin R, Fertig EJ, Wheelan SJ, Marchionni L, Considine M, Ling S, Fakhry C, Papadopoulos N, Kinzler KW, Vogelstein B, Ha PK, Agrawal N.

Cancer Prev Res (Phila). 2016 Apr;9(4):265-74. doi: 10.1158/1940-6207.CAPR-15-0316. Epub 2016 Feb 9. Erratum in: Cancer Prev Res (Phila). 2018 Apr;11(4):249.

43.

Reaching out: junctions between cardiac telocytes and cardiac stem cells in culture.

Popescu LM, Fertig ET, Gherghiceanu M.

J Cell Mol Med. 2016 Feb;20(2):370-80. doi: 10.1111/jcmm.12719. Epub 2015 Nov 5.

44.

Epigenetic screening of salivary gland mucoepidermoid carcinoma identifies hypomethylation of CLIC3 as a common alteration.

Wang Z, Ling S, Rettig E, Sobel R, Tan M, Fertig EJ, Considine M, El-Naggar AK, Brait M, Fakhry C, Ha PK.

Oral Oncol. 2015 Dec;51(12):1120-5. doi: 10.1016/j.oraloncology.2015.09.010. Epub 2015 Oct 17.

45.

Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.

Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D.

Nat Commun. 2015 Sep 16;6:8258. doi: 10.1038/ncomms9258.

46.

Analysis of gene expression of secreted factors associated with breast cancer metastases in breast cancer subtypes.

Fertig EJ, Lee E, Pandey NB, Popel AS.

Sci Rep. 2015 Jul 15;5:12133. doi: 10.1038/srep12133.

47.

Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.

Cheng H, Fertig EJ, Ozawa H, Hatakeyama H, Howard JD, Perez J, Considine M, Thakar M, Ranaweera R, Krigsfeld G, Chung CH.

Cancer Biol Ther. 2015;16(8):1252-8. doi: 10.1080/15384047.2015.1056418. Epub 2015 Jun 5.

48.

NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.

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.

Int J Cancer. 2015 Oct 15;137(8):1879-89. doi: 10.1002/ijc.29558. Epub 2015 Jun 23.

49.

Structure-function studies of the bHLH phosphorylation domain of TWIST1 in prostate cancer cells.

Gajula RP, Chettiar ST, Williams RD, Nugent K, Kato Y, Wang H, Malek R, Taparra K, Cades J, Annadanam A, Yoon AR, Fertig E, Firulli BA, Mazzacurati L, Burns TF, Firulli AB, An SS, Tran PT.

Neoplasia. 2015 Jan;17(1):16-31. doi: 10.1016/j.neo.2014.10.009.

50.

AGA: Interactive pipeline for reproducible genomics analyses.

Considine M, Parker H, Wei Y, Xia X, Cope L, Ochs M, Fertig E.

Version 2. F1000Res. 2015 Jan 28 [revised 2015 Jan 1];4:28. doi: 10.12688/f1000research.6030.1. eCollection 2015.

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