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Proteomic Analysis of CSF from Patients with Leptomeningeal Melanoma Metastases Identifies Signatures Associated with Disease Progression and Therapeutic Resistance.

Smalley I, Law V, Wyatt C, Evernden B, Fang B, Koomen JM, Welsh EA, Macaulay RJB, Forsyth PA, Smalley KSM.

Clin Cancer Res. 2020 Jan 10. doi: 10.1158/1078-0432.CCR-19-2840. [Epub ahead of print]


Intrinsic radiosensitivity, genomic-based radiation dose and patterns of failure of penile cancer in response to adjuvant radiation therapy.

Yuan Z, Grass GD, Azizi M, Ahmed KA, Yoder GSJ, Welsh EA, Fulp WJ, Dhillon J, Torres-Roca JF, Giuliano AR, Spiess PE, Johnstone PA.

Rep Pract Oncol Radiother. 2019 Nov-Dec;24(6):593-599. doi: 10.1016/j.rpor.2019.09.006. Epub 2019 Nov 1.


Proteogenomic landscape of squamous cell lung cancer.

Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB.

Nat Commun. 2019 Aug 8;10(1):3578. doi: 10.1038/s41467-019-11452-x.


Divergent Polypharmacology-Driven Cellular Activity of Structurally Similar Multi-Kinase Inhibitors through Cumulative Effects on Individual Targets.

Sumi NJ, Ctortecka C, Hu Q, Bryant AT, Fang B, Remsing Rix LL, Ayaz M, Kinose F, Welsh EA, Eschrich SA, Lawrence HR, Koomen JM, Haura EB, Rix U.

Cell Chem Biol. 2019 Sep 19;26(9):1240-1252.e11. doi: 10.1016/j.chembiol.2019.06.003. Epub 2019 Jun 27.


Proteometabolomics of Melphalan Resistance in Multiple Myeloma.

Koomen DC, Guingab-Cagmat JD, Oliveira PS, Fang B, Liu M, Welsh EA, Meads MB, Nguyen T, Meke L, Eschrich SA, Shain KH, Garrett TJ, Koomen JM.

Methods Mol Biol. 2019;1996:273-296. doi: 10.1007/978-1-4939-9488-5_21.


Transforming growth factor β-induced epithelial-to-mesenchymal signature predicts metastasis-free survival in non-small cell lung cancer.

Gordian E, Welsh EA, Gimbrone N, Siegel EM, Shibata D, Creelan BC, Cress WD, Eschrich SA, Haura EB, Muñoz-Antonia T.

Oncotarget. 2019 Jan 25;10(8):810-824. doi: 10.18632/oncotarget.26574. eCollection 2019 Jan 25.


Radiosensitivity of Lung Metastases by Primary Histology and Implications for Stereotactic Body Radiation Therapy Using the Genomically Adjusted Radiation Dose.

Ahmed KA, Scott JG, Arrington JA, Naghavi AO, Grass GD, Perez BA, Caudell JJ, Berglund AE, Welsh EA, Eschrich SA, Dilling TJ, Torres-Roca JF.

J Thorac Oncol. 2018 Aug;13(8):1121-1127. doi: 10.1016/j.jtho.2018.04.027. Epub 2018 May 5.


Cell-surface marker discovery for lung cancer.

Cohen AS, Khalil FK, Welsh EA, Schabath MB, Enkemann SA, Davis A, Zhou JM, Boulware DC, Kim J, Haura EB, Morse DL.

Oncotarget. 2017 Dec 7;8(69):113373-113402. doi: 10.18632/oncotarget.23009. eCollection 2017 Dec 26.


Escape Excel: A tool for preventing gene symbol and accession conversion errors.

Welsh EA, Stewart PA, Kuenzi BM, Eschrich JA.

PLoS One. 2017 Sep 27;12(9):e0185207. doi: 10.1371/journal.pone.0185207. eCollection 2017.


Somatic Mutations and Ancestry Markers in Hispanic Lung Cancer Patients.

Gimbrone NT, Sarcar B, Gordian ER, Rivera JI, Lopez C, Yoder SJ, Teer JK, Welsh EA, Chiappori AA, Schabath MB, Reuther GW, Dutil J, Garcia M, Ventosilla-Villanueva R, Vera-Valdivia L, Yabar-Berrocal A, Motta-Guerrero R, Santiago-Cardona PG, Muñoz-Antonia T, Cress WD.

J Thorac Oncol. 2017 Dec;12(12):1851-1856. doi: 10.1016/j.jtho.2017.08.019. Epub 2017 Sep 11.


Evaluating somatic tumor mutation detection without matched normal samples.

Teer JK, Zhang Y, Chen L, Welsh EA, Cress WD, Eschrich SA, Berglund AE.

Hum Genomics. 2017 Sep 4;11(1):22. doi: 10.1186/s40246-017-0118-2.


The radiosensitivity of brain metastases based upon primary histology utilizing a multigene index of tumor radiosensitivity.

Ahmed KA, Berglund AE, Welsh EA, Naghavi AO, Kim Y, Yu M, Robinson TJ, Eschrich SA, Johnstone PAS, Torres-Roca JF.

Neuro Oncol. 2017 Aug 1;19(8):1145-1146. doi: 10.1093/neuonc/nox043. No abstract available.


Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures.

Berglund AE, Welsh EA, Eschrich SA.

Int J Genomics. 2017;2017:2354564. doi: 10.1155/2017/2354564. Epub 2017 Feb 6.


Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer.

Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura EB.

Proteomes. 2016 Apr 27;4(2):16. doi: 10.3390/proteomes4020016. eCollection 2016 Jun.


Early2 factor (E2F) deregulation is a prognostic and predictive biomarker in lung adenocarcinoma.

Chen L, Kurtyka CA, Welsh EA, Rivera JI, Engel BE, Muñoz-Antonia T, Yoder SJ, Eschrich SA, Creelan BC, Chiappori AA, Gray JE, Ramirez JL, Rosell R, Schabath MB, Haura EB, Chen DT, Cress WD.

Oncotarget. 2016 Dec 13;7(50):82254-82265. doi: 10.18632/oncotarget.12672.


Phosphoproteomics Reveals MAPK Inhibitors Enhance MET- and EGFR-Driven AKT Signaling in KRAS-Mutant Lung Cancer.

Kim JY, Welsh EA, Fang B, Bai Y, Kinose F, Eschrich SA, Koomen JM, Haura EB.

Mol Cancer Res. 2016 Oct;14(10):1019-1029. Epub 2016 Jul 15.


Radiosensitivity Differences Between Liver Metastases Based on Primary Histology Suggest Implications for Clinical Outcomes After Stereotactic Body Radiation Therapy.

Ahmed KA, Caudell JJ, El-Haddad G, Berglund AE, Welsh EA, Yue B, Hoffe SE, Naghavi AO, Abuodeh YA, Frakes JM, Eschrich SA, Torres-Roca JF.

Int J Radiat Oncol Biol Phys. 2016 Aug 1;95(5):1399-1404. doi: 10.1016/j.ijrobp.2016.03.050. Epub 2016 Apr 8.


Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics.

Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB.

Clin Cancer Res. 2016 Nov 15;22(22):5605-5616. doi: 10.1158/1078-0432.CCR-15-1673. Epub 2016 May 24.


A Sensitive NanoString-Based Assay to Score STK11 (LKB1) Pathway Disruption in Lung Adenocarcinoma.

Chen L, Engel BE, Welsh EA, Yoder SJ, Brantley SG, Chen DT, Beg AA, Cao C, Kaye FJ, Haura EB, Schabath MB, Cress WD.

J Thorac Oncol. 2016 Jun;11(6):838-49. doi: 10.1016/j.jtho.2016.02.009. Epub 2016 Feb 23.


Identifying Regulatory Changes to Facilitate Nitrogen Fixation in the Nondiazotroph Synechocystis sp. PCC 6803.

Mueller TJ, Welsh EA, Pakrasi HB, Maranas CD.

ACS Synth Biol. 2016 Mar 18;5(3):250-8. doi: 10.1021/acssynbio.5b00202. Epub 2016 Jan 7.


Overexpression of major CDKN3 transcripts is associated with poor survival in lung adenocarcinoma.

Fan C, Chen L, Huang Q, Shen T, Welsh EA, Teer JK, Cai J, Cress WD, Wu J.

Br J Cancer. 2015 Dec 22;113(12):1735-43. doi: 10.1038/bjc.2015.378. Epub 2015 Nov 10.


A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.

Stewart PA, Parapatics K, Welsh EA, Müller AC, Cao H, Fang B, Koomen JM, Eschrich SA, Bennett KL, Haura EB.

PLoS One. 2015 Nov 5;10(11):e0142162. doi: 10.1371/journal.pone.0142162. eCollection 2015.


Differential association of STK11 and TP53 with KRAS mutation-associated gene expression, proliferation and immune surveillance in lung adenocarcinoma.

Schabath MB, Welsh EA, Fulp WJ, Chen L, Teer JK, Thompson ZJ, Engel BE, Xie M, Berglund AE, Creelan BC, Antonia SJ, Gray JE, Eschrich SA, Chen DT, Cress WD, Haura EB, Beg AA.

Oncogene. 2016 Jun 16;35(24):3209-16. doi: 10.1038/onc.2015.375. Epub 2015 Oct 19.


Role of LKB1-CRTC1 on glycosylated COX-2 and response to COX-2 inhibition in lung cancer.

Cao C, Gao R, Zhang M, Amelio AL, Fallahi M, Chen Z, Gu Y, Hu C, Welsh EA, Engel BE, Haura EB, Cress WD, Wu L, Zajac-Kaye M, Kaye FJ.

J Natl Cancer Inst. 2014 Dec 1;107(1):358. doi: 10.1093/jnci/dju358. Print 2015 Jan.


Dissection of TBK1 signaling via phosphoproteomics in lung cancer cells.

Kim JY, Welsh EA, Oguz U, Fang B, Bai Y, Kinose F, Bronk C, Remsing Rix LL, Beg AA, Rix U, Eschrich SA, Koomen JM, Haura EB.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12414-9. doi: 10.1073/pnas.1220674110. Epub 2013 Jul 8.


Iterative rank-order normalization of gene expression microarray data.

Welsh EA, Eschrich SA, Berglund AE, Fenstermacher DA.

BMC Bioinformatics. 2013 May 7;14:153. doi: 10.1186/1471-2105-14-153.


Aqueous-based spinning of fibers from self-assembling structural proteins.

Arcidiacono S, Welsh EA, Soares JW.

Methods Mol Biol. 2013;996:43-59. doi: 10.1007/978-1-62703-354-1_3.


Multiplex transcriptional analysis of paraffin-embedded liver needle biopsy from patients with liver fibrosis.

Staten NR, Welsh EA, Sidik K, McDonald SA, Dufield DR, Maqsodi B, Ma Y, McMaster GK, Mathews RW, Arch RH, Masferrer JL, Souberbielle BE.

Fibrogenesis Tissue Repair. 2012 Dec 27;5(1):21. doi: 10.1186/1755-1536-5-21.


The hope in her eyes: the role of children in Afghan women's resilience.

Brodsky AE, Talwar G, Welsh EA, Scheibler JE, Backer P, Portnoy GA, Carrillo A, Kline E.

Am J Orthopsychiatry. 2012 Jul;82(3):358-66. doi: 10.1111/j.1939-0025.2012.01162.x.


Dynamic proteome analysis of Cyanothece sp. ATCC 51142 under constant light.

Aryal UK, Stöckel J, Welsh EA, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB, Jacobs JM.

J Proteome Res. 2012 Feb 3;11(2):609-19. doi: 10.1021/pr200959x. Epub 2011 Dec 1.


Diurnal rhythms result in significant changes in the cellular protein complement in the cyanobacterium Cyanothece 51142.

Stöckel J, Jacobs JM, Elvitigala TR, Liberton M, Welsh EA, Polpitiya AD, Gritsenko MA, Nicora CD, Koppenaal DW, Smith RD, Pakrasi HB.

PLoS One. 2011 Feb 22;6(2):e16680. doi: 10.1371/journal.pone.0016680.


Global proteomics reveal an atypical strategy for carbon/nitrogen assimilation by a cyanobacterium under diverse environmental perturbations.

Wegener KM, Singh AK, Jacobs JM, Elvitigala T, Welsh EA, Keren N, Gritsenko MA, Ghosh BK, Camp DG 2nd, Smith RD, Pakrasi HB.

Mol Cell Proteomics. 2010 Dec;9(12):2678-89. doi: 10.1074/mcp.M110.000109. Epub 2010 Sep 21.


The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle.

Welsh EA, Liberton M, Stöckel J, Loh T, Elvitigala T, Wang C, Wollam A, Fulton RS, Clifton SW, Jacobs JM, Aurora R, Ghosh BK, Sherman LA, Smith RD, Wilson RK, Pakrasi HB.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):15094-9. doi: 10.1073/pnas.0805418105. Epub 2008 Sep 23.


High sensitivity proteomics assisted discovery of a novel operon involved in the assembly of photosystem II, a membrane protein complex.

Wegener KM, Welsh EA, Thornton LE, Keren N, Jacobs JM, Hixson KK, Monroe ME, Camp DG 2nd, Smith RD, Pakrasi HB.

J Biol Chem. 2008 Oct 10;283(41):27829-37. doi: 10.1074/jbc.M803918200. Epub 2008 Aug 8.


Global transcriptomic analysis of Cyanothece 51142 reveals robust diurnal oscillation of central metabolic processes.

Stöckel J, Welsh EA, Liberton M, Kunnvakkam R, Aurora R, Pakrasi HB.

Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):6156-61. doi: 10.1073/pnas.0711068105. Epub 2008 Apr 21.


Psb29, a conserved 22-kD protein, functions in the biogenesis of Photosystem II complexes in Synechocystis and Arabidopsis.

Keren N, Ohkawa H, Welsh EA, Liberton M, Pakrasi HB.

Plant Cell. 2005 Oct;17(10):2768-81. Epub 2005 Sep 9.


ProVal: a protein-scoring function for the selection of native and near-native folds.

Berglund A, Head RD, Welsh EA, Marshall GR.

Proteins. 2004 Feb 1;54(2):289-302.


Spider silk fibers spun from soluble recombinant silk produced in mammalian cells.

Lazaris A, Arcidiacono S, Huang Y, Zhou JF, Duguay F, Chretien N, Welsh EA, Soares JW, Karatzas CN.

Science. 2002 Jan 18;295(5554):472-6.


Successful treatment of uterine torsion in a cat with severe metabolic and haemostatic complications.

Ridyard AE, Welsh EA, Gunn-Moore DA.

J Feline Med Surg. 2000 Jun;2(2):115-9.


Extent of laminin-5 assembly and secretion effect junctional epidermolysis bullosa phenotype.

Matsui C, Pereira P, Wang CK, Nelson CF, Kutzkey T, Lanigan C, Woodley D, Morohashi M, Welsh EA, Hoeffler WK.

J Exp Med. 1998 Apr 20;187(8):1273-83.


Analysis of HLA-D locus alleles in alopecia areata patients and families.

Duvic M, Welsh EA, Jackow C, Papadopoulos E, Reveille JD, Amos C.

J Invest Dermatol. 1995 May;104(5 Suppl):5S-6S. No abstract available.


Human leukocyte antigen-DQB1*03 alleles are associated with alopecia areata.

Welsh EA, Clark HH, Epstein SZ, Reveille JD, Duvic M.

J Invest Dermatol. 1994 Dec;103(6):758-63.


Localization of the gene whose mutations underlie Hailey-Hailey disease to chromosome 3q.

Ikeda S, Welsh EA, Peluso AM, Leyden W, Duvic M, Woodley DT, Epstein EH Jr.

Hum Mol Genet. 1994 Jul;3(7):1147-50.


Hailey-Hailey disease is not allelic to Darier's disease.

Welsh EA, Ikeda S, Peluso AM, Bonifas JM, Bare JW, Woodley DT, Epstein EH Jr.

J Invest Dermatol. 1994 Jun;102(6):992-3.


Studies on the mechanism of immunologic tolerance induction by murine dendritic epidermal Thy-1+ cell lines.

Welsh EA, Love-Schimenti C, Kripke ML.

J Leukoc Biol. 1992 Oct;52(4):425-32.


Multivariate statistical analysis of electron micrographs of a mammalian transcription initiation complex.

Harauz G, Welsh EA.

J Electron Microsc (Tokyo). 1992 Aug;41(4):264-6.


Visualization of a mammalian transcription initiation complex.

Welsh EA, Zahradka P, Larson DE, Sells BH, Harauz G.

Biochem Cell Biol. 1992 May;70(5):291-300.


Murine Thy-1+ dendritic epidermal cells induce immunologic tolerance in vivo.

Welsh EA, Kripke ML.

J Immunol. 1990 Feb 1;144(3):883-91.


Why not rub it better?

Welsh EA.

Ann R Coll Surg Engl. 1988 Jul;70(4):260. No abstract available.

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