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Liver disease-associated keratin 8 and 18 mutations modulate keratin acetylation and methylation.

Jang KH, Yoon HN, Lee J, Yi H, Park SY, Lee SY, Lim Y, Lee HJ, Cho JW, Paik YK, Hancock WS, Ku NO.

FASEB J. 2019 Jun 14:fj201800263RR. doi: 10.1096/fj.201800263RR. [Epub ahead of print]


On-demand manufacturing of clinical-quality biopharmaceuticals.

Crowell LE, Lu AE, Love KR, Stockdale A, Timmick SM, Wu D, Wang YA, Doherty W, Bonnyman A, Vecchiarello N, Goodwine C, Bradbury L, Brady JR, Clark JJ, Colant NA, Cvetkovic A, Dalvie NC, Liu D, Liu Y, Mascarenhas CA, Matthews CB, Mozdzierz NJ, Shah KA, Wu SL, Hancock WS, Braatz RD, Cramer SM, Love JC.

Nat Biotechnol. 2018 Oct 1. doi: 10.1038/nbt.4262. [Epub ahead of print]


Integrated Bottom-Up and Top-Down Liquid Chromatography-Mass Spectrometry for Characterization of Recombinant Human Growth Hormone Degradation Products.

Wang YA, Wu D, Auclair JR, Salisbury JP, Sarin R, Tang Y, Mozdzierz NJ, Shah K, Zhang AF, Wu SL, Agar JN, Love JC, Love KR, Hancock WS.

Anal Chem. 2017 Dec 5;89(23):12771-12777. doi: 10.1021/acs.analchem.7b03026. Epub 2017 Nov 21.


Advances in the Chromosome-Centric Human Proteome Project: looking to the future.

Paik YK, Omenn GS, Hancock WS, Lane L, Overall CM.

Expert Rev Proteomics. 2017 Dec;14(12):1059-1071. doi: 10.1080/14789450.2017.1394189. Epub 2017 Nov 10. Review.


Systematic Proteogenomic Approach To Exploring a Novel Function for NHERF1 in Human Reproductive Disorder: Lessons for Exploring Missing Proteins.

Na K, Shin H, Cho JY, Jung SH, Lim J, Lim JS, Kim EA, Kim HS, Kang AR, Kim JH, Shin JM, Jeong SK, Kim CY, Park JY, Chung HM, Omenn GS, Hancock WS, Paik YK.

J Proteome Res. 2017 Dec 1;16(12):4455-4467. doi: 10.1021/acs.jproteome.7b00146. Epub 2017 Nov 1.


Characterization of Site-Specific Glycosylation in Influenza A Virus Hemagglutinin Produced by Spodoptera frugiperda Insect Cell Line.

Liu YJ, Wu SL, Love KR, Hancock WS.

Anal Chem. 2017 Oct 17;89(20):11036-11043. doi: 10.1021/acs.analchem.7b03025. Epub 2017 Oct 4.


Integrated Proteomic and Transcriptomic-Based Approaches to Identifying Signature Biomarkers and Pathways for Elucidation of Daoy and UW228 Subtypes.

Higdon R, Kala J, Wilkins D, Yan JF, Sethi MK, Lin L, Liu S, Montague E, Janko I, Choiniere J, Kolker N, Hancock WS, Kolker E, Fanayan S.

Proteomes. 2017 Feb 3;5(1). pii: E5. doi: 10.3390/proteomes5010005.


Progress in the Chromosome-Centric Human Proteome Project as Highlighted in the Annual Special Issue IV.

Paik YK, Overall CM, Deutsch EW, Hancock WS, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3945-3950. No abstract available.


Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3961-3970. Epub 2016 Aug 24.


Identifying N-Glycan Biomarkers in Colorectal Cancer by Mass Spectrometry.

Sethi MK, Hancock WS, Fanayan S.

Acc Chem Res. 2016 Oct 18;49(10):2099-2106. Epub 2016 Sep 21. Review.


Microfluidic Platform for Assessment of Therapeutic Proteins Using Molecular Charge Modulation Enhanced Electrokinetic Concentration Assays.

Ouyang W, Ko SH, Wu D, Wang AY, Barone PW, Hancock WS, Han J.

Anal Chem. 2016 Oct 4;88(19):9669-9677. Epub 2016 Sep 23.


Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans.

Kim S, Lee HJ, Hahm JH, Jeong SK, Park DH, Hancock WS, Paik YK.

J Proteome Res. 2016 Feb 5;15(2):531-9. doi: 10.1021/acs.jproteome.5b00884. Epub 2016 Jan 21.


Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS.

J Proteome Res. 2016 Feb 5;15(2):339-59. doi: 10.1021/acs.jproteome.5b00769. Epub 2016 Jan 12. Review.


Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.

Yan JF, Kim H, Jeong SK, Lee HJ, Sethi MK, Lee LY, Beavis RC, Im H, Snyder MP, Hofree M, Ideker T, Wu SL, Paik YK, Fanayan S, Hancock WS.

J Proteome Res. 2015 Dec 4;14(12):4995-5006. doi: 10.1021/acs.jproteome.5b00827. Epub 2015 Oct 20.


Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light.

Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS.

J Proteome Res. 2015 Sep 4;14(9):3409-14. doi: 10.1021/acs.jproteome.5b00785. No abstract available.


Combination of Multiple Spectral Libraries Improves the Current Search Methods Used to Identify Missing Proteins in the Chromosome-Centric Human Proteome Project.

Cho JY, Lee HJ, Jeong SK, Kim KY, Kwon KH, Yoo JS, Omenn GS, Baker MS, Hancock WS, Paik YK.

J Proteome Res. 2015 Dec 4;14(12):4959-66. doi: 10.1021/acs.jproteome.5b00578. Epub 2015 Sep 14.


GenomewidePDB 2.0: A Newly Upgraded Versatile Proteogenomic Database for the Chromosome-Centric Human Proteome Project.

Jeong SK, Hancock WS, Paik YK.

J Proteome Res. 2015 Sep 4;14(9):3710-9. doi: 10.1021/acs.jproteome.5b00541. Epub 2015 Aug 19.


In-depth N-glycome profiling of paired colorectal cancer and non-tumorigenic tissues reveals cancer-, stage- and EGFR-specific protein N-glycosylation.

Sethi MK, Kim H, Park CK, Baker MS, Paik YK, Packer NH, Hancock WS, Fanayan S, Thaysen-Andersen M.

Glycobiology. 2015 Oct;25(10):1064-78. doi: 10.1093/glycob/cwv042. Epub 2015 Jun 17.


Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Horvatovich P, Lundberg EK, Chen YJ, Sung TY, He F, Nice EC, Goode RJ, Yu S, Ranganathan S, Baker MS, Domont GB, Velasquez E, Li D, Liu S, Wang Q, He QY, Menon R, Guan Y, Corrales FJ, Segura V, Casal JI, Pascual-Montano A, Albar JP, Fuentes M, Gonzalez-Gonzalez M, Diez P, Ibarrola N, Degano RM, Mohammed Y, Borchers CH, Urbani A, Soggiu A, Yamamoto T, Salekdeh GH, Archakov A, Ponomarenko E, Lisitsa A, Lichti CF, Mostovenko E, Kroes RA, Rezeli M, Végvári Á, Fehniger TE, Bischoff R, Vizcaíno JA, Deutsch EW, Lane L, Nilsson CL, Marko-Varga G, Omenn GS, Jeong SK, Lim JS, Paik YK, Hancock WS.

J Proteome Res. 2015 Sep 4;14(9):3415-31. doi: 10.1021/pr5013009. Epub 2015 Jul 23.


Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis.

Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S.

J Proteomics. 2015 Aug 3;126:54-67. doi: 10.1016/j.jprot.2015.05.037. Epub 2015 Jun 6.


Clusterin glycopeptide variant characterization reveals significant site-specific glycan changes in the plasma of clear cell renal cell carcinoma.

Gbormittah FO, Bones J, Hincapie M, Tousi F, Hancock WS, Iliopoulos O.

J Proteome Res. 2015 Jun 5;14(6):2425-36. doi: 10.1021/pr501104j. Epub 2015 May 11.


Use of ENCODE resources to characterize novel proteoforms and missing proteins in the human proteome.

Nilsson CL, Mostovenko E, Lichti CF, Ruggles K, Fenyö D, Rosenbloom KR, Hancock WS, Paik YK, Omenn GS, LaBaer J, Kroes RA, Uhlén M, Hober S, Végvári Á, Andrén PE, Sulman EP, Lang FF, Fuentes M, Carlsohn E, Emmett MR, Moskal JR, Berven FS, Fehniger TE, Marko-Varga G.

J Proteome Res. 2015 Feb 6;14(2):603-8. doi: 10.1021/pr500564q. Epub 2014 Nov 26.


Identification of novel glycans with disialylated structures in α3 integrin from mouse kidney cells with the phenotype of polycystic kidney disease.

Zhang AF, Wu SL, Jung Y, Qin S, Hancock WS, Kreidberg JA.

J Proteome Res. 2014 Nov 7;13(11):4901-9. doi: 10.1021/pr5009702. Epub 2014 Oct 15.


Comprehensive N-glycome profiling of cultured human epithelial breast cells identifies unique secretome N-glycosylation signatures enabling tumorigenic subtype classification.

Lee LY, Thaysen-Andersen M, Baker MS, Packer NH, Hancock WS, Fanayan S.

J Proteome Res. 2014 Nov 7;13(11):4783-95. doi: 10.1021/pr500331m. Epub 2014 Sep 11.


Comparative studies of the proteome, glycoproteome, and N-glycome of clear cell renal cell carcinoma plasma before and after curative nephrectomy.

Gbormittah FO, Lee LY, Taylor K, Hancock WS, Iliopoulos O.

J Proteome Res. 2014 Nov 7;13(11):4889-900. doi: 10.1021/pr500591e. Epub 2014 Sep 10.


Identification of human complement factor B as a novel biomarker candidate for pancreatic ductal adenocarcinoma.

Lee MJ, Na K, Jeong SK, Lim JS, Kim SA, Lee MJ, Song SY, Kim H, Hancock WS, Paik YK.

J Proteome Res. 2014 Nov 7;13(11):4878-88. doi: 10.1021/pr5002719. Epub 2014 Aug 8.


Functional annotation of proteome encoded by human chromosome 22.

Pinto SM, Manda SS, Kim MS, Taylor K, Selvan LD, Balakrishnan L, Subbannayya T, Yan F, Prasad TS, Gowda H, Lee C, Hancock WS, Pandey A.

J Proteome Res. 2014 Jun 6;13(6):2749-60. doi: 10.1021/pr401169d. Epub 2014 Apr 29.


Abundance-ratio-based semiquantitative analysis of site-specific N-linked glycopeptides present in the plasma of hepatocellular carcinoma patients.

Lee HJ, Cha HJ, Lim JS, Lee SH, Song SY, Kim H, Hancock WS, Yoo JS, Paik YK.

J Proteome Res. 2014 May 2;13(5):2328-38. doi: 10.1021/pr4011519. Epub 2014 Apr 4.


Genome-wide proteomics, Chromosome-Centric Human Proteome Project (C-HPP), part II.

Paik YK, Omenn GS, Thongboonkerd V, Marko-Varga G, Hancock WS.

J Proteome Res. 2014 Jan 3;13(1):1-4. doi: 10.1021/pr4011958. Epub 2013 Dec 16. No abstract available.


Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome.

Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S.

J Proteome Res. 2014 Jan 3;13(1):76-83. doi: 10.1021/pr400794x. Epub 2013 Dec 13.


Characterization of glycoproteins in pancreatic cyst fluid using a high-performance multiple lectin affinity chromatography platform.

Gbormittah FO, Haab BB, Partyka K, Garcia-Ott C, Hancapie M, Hancock WS.

J Proteome Res. 2014 Jan 3;13(1):289-99. doi: 10.1021/pr400813u. Epub 2013 Dec 13.


Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines.

Sethi MK, Thaysen-Andersen M, Smith JT, Baker MS, Packer NH, Hancock WS, Fanayan S.

J Proteome Res. 2014 Jan 3;13(1):277-88. doi: 10.1021/pr400861m. Epub 2013 Dec 2.


Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes.

Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS.

J Proteome Res. 2014 Jan 3;13(1):212-27. doi: 10.1021/pr400773v. Epub 2013 Nov 7.


Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.

Zhang EY, Cristofanilli M, Robertson F, Reuben JM, Mu Z, Beavis RC, Im H, Snyder M, Hofree M, Ideker T, Omenn GS, Fanayan S, Jeong SK, Paik YK, Zhang AF, Wu SL, Hancock WS.

J Proteome Res. 2013 Jun 7;12(6):2805-17. doi: 10.1021/pr4001527. Epub 2013 May 22.


Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.

Fanayan S, Smith JT, Lee LY, Yan F, Snyder M, Hancock WS, Nice E.

J Proteome Res. 2013 Apr 5;12(4):1732-42. doi: 10.1021/pr3010869. Epub 2013 Mar 13.


Identification of potential glycan cancer markers with sialic acid attached to sialic acid and up-regulated fucosylated galactose structures in epidermal growth factor receptor secreted from A431 cell line.

Wu SL, Taylor AD, Lu Q, Hanash SM, Im H, Snyder M, Hancock WS.

Mol Cell Proteomics. 2013 May;12(5):1239-49. doi: 10.1074/mcp.M112.024554. Epub 2013 Jan 31.


Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project.

Lee HJ, Jeong SK, Na K, Lee MJ, Lee SH, Lim JS, Cha HJ, Cho JY, Kwon JY, Kim H, Song SY, Yoo JS, Park YM, Kim H, Hancock WS, Paik YK.

J Proteome Res. 2013 Jun 7;12(6):2458-66. doi: 10.1021/pr301040g. Epub 2013 Feb 14.


Development of a method to quantitate nematode pheromone for study of small-molecule metabolism in Caenorhabditis elegans.

Kim KY, Joo HJ, Kwon HW, Kim H, Hancock WS, Paik YK.

Anal Chem. 2013 Mar 5;85(5):2681-8. doi: 10.1021/ac4001964. Epub 2013 Feb 14.


Chromosome 11-centric human proteome analysis of human brain hippocampus tissue.

Kwon KH, Kim JY, Kim SY, Min HK, Lee HJ, Ji IJ, Kang T, Park GW, An HJ, Lee B, Ravid R, Ferrer I, Chung CK, Paik YK, Hancock WS, Park YM, Yoo JS.

J Proteome Res. 2013 Jan 4;12(1):97-105. doi: 10.1021/pr3008368.


Modulation of glycan detection on specific glycoproteins by lectin multimerization.

Cao Z, Partyka K, McDonald M, Brouhard E, Hincapie M, Brand RE, Hancock WS, Haab BB.

Anal Chem. 2013 Feb 5;85(3):1689-98. doi: 10.1021/ac302826a. Epub 2013 Jan 16.


A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

Liu S, Im H, Bairoch A, Cristofanilli M, Chen R, Deutsch EW, Dalton S, Fenyo D, Fanayan S, Gates C, Gaudet P, Hincapie M, Hanash S, Kim H, Jeong SK, Lundberg E, Mias G, Menon R, Mu Z, Nice E, Paik YK, Uhlen M, Wells L, Wu SL, Yan F, Zhang F, Zhang Y, Snyder M, Omenn GS, Beavis RC, Hancock WS.

J Proteome Res. 2013 Jan 4;12(1):45-57. doi: 10.1021/pr300985j. Epub 2012 Dec 21.


A first step toward completion of a genome-wide characterization of the human proteome.

Marko-Varga G, Omenn GS, Paik YK, Hancock WS.

J Proteome Res. 2013 Jan 4;12(1):1-5. doi: 10.1021/pr301183a. Epub 2012 Dec 20. No abstract available.


GenomewidePDB, a proteomic database exploring the comprehensive protein parts list and transcriptome landscape in human chromosomes.

Jeong SK, Lee HJ, Na K, Cho JY, Lee MJ, Kwon JY, Kim H, Park YM, Yoo JS, Hancock WS, Paik YK.

J Proteome Res. 2013 Jan 4;12(1):106-11. doi: 10.1021/pr3009447. Epub 2012 Dec 19.


Chromosome 7-centric analysis of proteomics data from a panel of human colon carcinoma cell lines.

Fanayan S, Smith JT, Sethi MK, Cantor D, Goode R, Simpson RJ, Baker MS, Hancock WS, Nice E.

J Proteome Res. 2013 Jan 4;12(1):89-96. doi: 10.1021/pr300906y. Epub 2012 Dec 18.


The proteome browser web portal.

Goode RJ, Yu S, Kannan A, Christiansen JH, Beitz A, Hancock WS, Nice E, Smith AI.

J Proteome Res. 2013 Jan 4;12(1):172-8. doi: 10.1021/pr3010056. Epub 2012 Dec 5.


Uniting ENCODE with genome-wide proteomics.

Paik YK, Hancock WS.

Nat Biotechnol. 2012 Nov;30(11):1065-7. doi: 10.1038/nbt.2416. No abstract available.


An optimized approach for enrichment of glycoproteins from cell culture lysates using native multi-lectin affinity chromatography.

Lee LY, Hincapie M, Packer N, Baker MS, Hancock WS, Fanayan S.

J Sep Sci. 2012 Sep;35(18):2445-52. doi: 10.1002/jssc.201200049.


Multidimensional liquid chromatography platform for profiling alterations of clusterin N-glycosylation in the plasma of patients with renal cell carcinoma.

Tousi F, Bones J, Iliopoulos O, Hancock WS, Hincapie M.

J Chromatogr A. 2012 Sep 21;1256:121-8. doi: 10.1016/j.chroma.2012.07.066. Epub 2012 Jul 28.

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