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Accurate Prediction of Personalized Olfactory Perception from Large-Scale Chemoinformatic Features.

Li H, Panwar B, Omenn GS, Guan Y.

Gigascience. 2017 Dec 15. doi: 10.1093/gigascience/gix127. [Epub ahead of print]


Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW.

Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y.


Progress and Future Direction of Chromosome-Centric Human Proteome Project.

Paik YK, Overall CM, Deutsch EW, Van Eyk JE, Omenn GS.

J Proteome Res. 2017 Dec 1;16(12):4253-4258. doi: 10.1021/acs.jproteome.7b00734.


Rapid molecular assays to study human centromere genomics.

Contreras-Galindo R, Fischer S, Saha AK, Lundy JD, Cervantes PW, Mourad M, Wang C, Qian B, Dai M, Meng F, Chinnaiyan A, Omenn GS, Kaplan MH, Markovitz DM.

Genome Res. 2017 Dec;27(12):2040-2049. doi: 10.1101/gr.219709.116. Epub 2017 Nov 15.


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.


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.


The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW.

J Proteome Res. 2017 Dec 1;16(12):4299-4310. doi: 10.1021/acs.jproteome.7b00467. Epub 2017 Oct 10.


Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.

Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW.

J Proteome Res. 2017 Dec 1;16(12):4281-4287. doi: 10.1021/acs.jproteome.7b00375. Epub 2017 Oct 9.


A wellness study of 108 individuals using personal, dense, dynamic data clouds.

Price ND, Magis AT, Earls JC, Glusman G, Levy R, Lausted C, McDonald DT, Kusebauch U, Moss CL, Zhou Y, Qin S, Moritz RL, Brogaard K, Omenn GS, Lovejoy JC, Hood L.

Nat Biotechnol. 2017 Aug;35(8):747-756. doi: 10.1038/nbt.3870. Epub 2017 Jul 17.


Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas.

Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ.

Proc Natl Acad Sci U S A. 2017 Jun 20;114(25):6581-6586. doi: 10.1073/pnas.1701263114. Epub 2017 Jun 12.


Nucleome Analysis Reveals Structure-Function Relationships for Colon Cancer.

Seaman L, Chen H, Brown M, Wangsa D, Patterson G, Camps J, Omenn GS, Ried T, Rajapakse I.

Mol Cancer Res. 2017 Jul;15(7):821-830. doi: 10.1158/1541-7786.MCR-16-0374. Epub 2017 Mar 3.


Annotation of Alternatively Spliced Proteins and Transcripts with Protein-Folding Algorithms and Isoform-Level Functional Networks.

Li H, Zhang Y, Guan Y, Menon R, Omenn GS.

Methods Mol Biol. 2017;1558:415-436. doi: 10.1007/978-1-4939-6783-4_20.


miRmine: a database of human miRNA expression profiles.

Panwar B, Omenn GS, Guan Y.

Bioinformatics. 2017 May 15;33(10):1554-1560. doi: 10.1093/bioinformatics/btx019.


Advances of the HUPO Human Proteome Project with broad applications for life sciences research.

Omenn GS.

Expert Rev Proteomics. 2017 Feb;14(2):109-111. doi: 10.1080/14789450.2017.1270763. Epub 2016 Dec 22. No abstract available.


The proteomes of the human eye, a highly compartmentalized organ.

Omenn GS.

Proteomics. 2017 Jan;17(1-2). doi: 10.1002/pmic.201600340. Epub 2016 Dec 21.


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.


Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL.

J Proteome Res. 2016 Nov 4;15(11):4091-4100. Epub 2016 Sep 12.


Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016.

Van Eyk JE, Corrales FJ, Aebersold R, Cerciello F, Deutsch EW, Roncada P, Sanchez JC, Yamamoto T, Yang P, Zhang H, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3979-3987. Epub 2016 Sep 20.


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.


Metrics for the Human Proteome Project 2016: Progress on Identifying and Characterizing the Human Proteome, Including Post-Translational Modifications.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Overall CM, Deutsch EW.

J Proteome Res. 2016 Nov 4;15(11):3951-3960. Epub 2016 Sep 20.


Strategies for Genomic and Proteomic Profiling of Cancers.

Omenn GS.

Stat Biosci. 2016 Jun;8(1):1-7. Epub 2014 Mar 11.


Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients.

Qin S, Zhou Y, Gray L, Kusebauch U, McEvoy L, Antoine DJ, Hampson L, Park KB, Campbell D, Caballero J, Glusman G, Yan X, Kim TK, Yuan Y, Wang K, Rowen L, Moritz RL, Omenn GS, Pirmohamed M, Hood L.

J Proteome Res. 2016 Oct 7;15(10):3724-3740. Epub 2016 Sep 19.


Genome-Wide Functional Annotation of Human Protein-Coding Splice Variants Using Multiple Instance Learning.

Panwar B, Menon R, Eksi R, Li HD, Omenn GS, Guan Y.

J Proteome Res. 2016 Jun 3;15(6):1747-53. doi: 10.1021/acs.jproteome.5b00883. Epub 2016 May 9.


The Impact of Alternative Payment Models on Oncology Innovation and Patient Care.

Miller AM, Omenn GS, Kean MA.

Clin Cancer Res. 2016 May 15;22(10):2335-41. doi: 10.1158/1078-0432.CCR-16-0892. Epub 2016 Apr 17.


A Network of Splice Isoforms for the Mouse.

Li HD, Menon R, Eksi R, Guerler A, Zhang Y, Omenn GS, Guan Y.

Sci Rep. 2016 Apr 15;6:24507. doi: 10.1038/srep24507.


Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.

Sarntivijai S, Zhang S, Jagannathan DG, Zaman S, Burkhart KK, Omenn GS, He Y, Athey BD, Abernethy DR.

Drug Saf. 2016 Jul;39(7):697-707. doi: 10.1007/s40264-016-0414-0.


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.


Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.

Li HD, Menon R, Govindarajoo B, Panwar B, Zhang Y, Omenn GS, Guan Y.

J Proteome Res. 2015 Sep 4;14(9):3484-91. doi: 10.1021/acs.jproteome.5b00494. Epub 2015 Aug 11.


MI-PVT: A Tool for Visualizing the Chromosome-Centric Human Proteome.

Panwar B, Menon R, Eksi R, Omenn GS, Guan Y.

J Proteome Res. 2015 Sep 4;14(9):3762-7. doi: 10.1021/acs.jproteome.5b00525. Epub 2015 Aug 3.


Structural Bioinformatics Inspection of neXtProt PE5 Proteins in the Human Proteome.

Dong Q, Menon R, Omenn GS, Zhang Y.

J Proteome Res. 2015 Sep 4;14(9):3750-61. doi: 10.1021/acs.jproteome.5b00516. Epub 2015 Jul 30.


Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.

J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.


Computational Inferences of the Functions of Alternative/Noncanonical Splice Isoforms Specific to HER2+/ER-/PR- Breast Cancers, a Chromosome 17 C-HPP Study.

Menon R, Panwar B, Eksi R, Kleer C, Guan Y, Omenn GS.

J Proteome Res. 2015 Sep 4;14(9):3519-29. doi: 10.1021/acs.jproteome.5b00498. Epub 2015 Jul 23.


State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.

Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS, Moritz RL.

J Proteome Res. 2015 Sep 4;14(9):3461-73. doi: 10.1021/acs.jproteome.5b00500. Epub 2015 Jul 24.


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.


MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse.

Li HD, Omenn GS, Guan Y.

Database (Oxford). 2015 May 7;2015:bav045. doi: 10.1093/database/bav045. Print 2015.


Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences.

Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM.

J Virol. 2015 Jul;89(14):7187-201. doi: 10.1128/JVI.00544-15. Epub 2015 Apr 29.


Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans.

Zahn J, Kaplan MH, Fischer S, Dai M, Meng F, Saha AK, Cervantes P, Chan SM, Dube D, Omenn GS, Markovitz DM, Contreras-Galindo R.

Genome Biol. 2015 Apr 12;16:74. doi: 10.1186/s13059-015-0641-1.


Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc. 2015 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28. Review.


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.


Revisiting the identification of canonical splice isoforms through integration of functional genomics and proteomics evidence.

Li HD, Menon R, Omenn GS, Guan Y.

Proteomics. 2014 Dec;14(23-24):2709-18. doi: 10.1002/pmic.201400170. Epub 2014 Nov 17.


Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.

Bai Y, Hassler J, Ziyar A, Li P, Wright Z, Menon R, Omenn GS, Cavalcoli JD, Kaufman RJ, Sartor MA.

PLoS One. 2014 Jul 3;9(7):e100864. doi: 10.1371/journal.pone.0100864. eCollection 2014.


The emerging era of genomic data integration for analyzing splice isoform function.

Li HD, Menon R, Omenn GS, Guan Y.

Trends Genet. 2014 Aug;30(8):340-7. doi: 10.1016/j.tig.2014.05.005. Epub 2014 Jun 17. Review.


Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein.

Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM.

J Virol. 2014 Aug;88(16):8924-35. doi: 10.1128/JVI.00556-14. Epub 2014 May 28.


A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines.

Omenn GS, Guan Y, Menon R.

J Proteomics. 2014 Jul 31;107:103-12. doi: 10.1016/j.jprot.2014.04.012. Epub 2014 May 5. Review.


ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.


MetDisease--connecting metabolites to diseases via literature.

Duren W, Weymouth T, Hull T, Omenn GS, Athey B, Burant C, Karnovsky A.

Bioinformatics. 2014 Aug 1;30(15):2239-41. doi: 10.1093/bioinformatics/btu179. Epub 2014 Apr 8.


Epigenetics: relevance and implications for public health.

Rozek LS, Dolinoy DC, Sartor MA, Omenn GS.

Annu Rev Public Health. 2014;35:105-22. doi: 10.1146/annurev-publhealth-032013-182513. Review.


Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan.

Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS.

Proteomics. 2014 May;14(9):975-88. doi: 10.1002/pmic.201400041.

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