NHLBI Proteomics
Administrative and
Coordination Center

National, Heart,
Lung and
Blood Institute

National Institutes
of Health

Nucleic Acid programmable protein arrays: versatile tools for array-based functional protein studies.

Miersch S, LaBaer J.

Curr Protoc Protein Sci. 2011 Apr;Chapter 27:Unit27.2.


 Immunoprofiling using NAPPA protein microarrays.

Sibani S, LaBaer J.

Methods Mol Biol. 2011;723:149-61.


 PSI:Biology-materials repository: a biologist's resource for protein expression plasmids.

Cormier CY, Park JG, Fiacco M, Steel J, Hunter P, Kramer J, Singla R, Labaer J.

J Struct Funct Genomics. 2011 Jul;12(2):55-62. Epub 2011 Mar 1.


 High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy.

Gonzalez-Malerva L, Park J, Zou L, Hu Y, Moradpour Z, Pearlberg J, Sawyer J, Stevens H, Harlow E, LaBaer J.

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2058-63. Epub 2011 Jan 13.


 Protein microarray signature of autoantibody biomarkers for the early detection of breast cancer.

Anderson KS, Sibani S, Wallstrom G, Qiu J, Mendoza EA, Raphael J, Hainsworth E, Montor WR, Wong J, Park JG, Lokko N, Logvinenko T, Ramachandran N, Godwin AK, Marks J, Engstrom P, Labaer J.

J Proteome Res. 2011 Jan 7;10(1):85-96. Epub 2010 Nov 23.


 Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community.

Cormier CY, Mohr SE, Zuo D, Hu Y, Rolfs A, Kramer J, Taycher E, Kelley F, Fiacco M, Turnbull G, LaBaer J.

Nucleic Acids Res. 2010 Jan;38(Database issue):D743-9. Epub 2009 Nov 11.


 Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, Matic I, Geiger T, Cox J, Algenäs C, Lundeberg J, Mann M, Uhlen M.

Mol Syst Biol. 2010 Dec 21;6:450.


 Towards a knowledge-based Human Protein Atlas.

Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, Forsberg M, Zwahlen M, Kampf C, Wester K, Hober S, Wernerus H, Björling L, Ponten F.

Nat Biotechnol. 2010 Dec;28(12):1248-50. No abstract available.


 Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.

Schwenk JM, Igel U, Neiman M, Langen H, Becker C, Bjartell A, Ponten F, Wiklund F, Grönberg H, Nilsson P, Uhlen M.

Mol Cell Proteomics. 2010 Nov;9(11):2497-507. Epub 2010 Aug 3.


 A guide to UniProt for protein scientists.

O'Donovan C, Apweiler R.

Methods Mol Biol. 2011;694:25-35.


 Ongoing and future developments at the Universal Protein Resource.

UniProt Consortium.

Nucleic Acids Res. 2011 Jan;39(Database issue):D214-9. Epub 2010 Nov 4.


A large-scale protein-function database.

Apweiler R, Armstrong R, Bairoch A, Cornish-Bowden A, Halling PJ, Hofmeyr JH, Kettner C, Leyh TS, Rohwer J, Schomburg D, Steinbeck C, Tipton K.

Nat Chem Biol. 2010 Nov;6(11):785. No abstract available.


 The renal gene ontology annotation initiative.

Alam-Faruque Y, Dimmer EC, Huntley RP, O'Donovan C, Scambler P, Apweiler R.

Organogenesis. 2010 Apr;6(2):71-5.


QuickGO: a user tutorial for the web-based Gene Ontology browser.

Huntley RP, Binns D, Dimmer E, Barrell D, O'Donovan C, Apweiler R.

Database (Oxford). 2009;2009:bap010. Epub 2009 Sep 29.


 On the importance of comprehensible classification models for protein function prediction.

Freitas AA, Wieser DC, Apweiler R.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Jan-Mar;7(1):172-82.


 From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.

Hinz U; UniProt Consortium.

Cell Mol Life Sci. 2010 Apr;67(7):1049-64. Epub 2009 Dec 31. Review.


 The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. Epub 2009 Nov 17.


 QuickGO: a web-based tool for Gene Ontology searching.

Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.

Bioinformatics. 2009 Nov 15;25(22):3045-6. Epub 2009 Sep 10.


Approaching clinical proteomics: current state and future fields of application in cellular proteomics.

Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G.

Cytometry A. 2009 Oct;75(10):816-32. Review.


 A cell cycle phosphoproteome of the yeast centrosome.

Keck JM, Jones MH, Wong CC, Binkley J, Chen D, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates JR 3rd, Winey M.

Science. 2011 Jun 24;332(6037):1557-61.


 Human common salivary protein 1 (CSP-1) promotes binding of Streptococcus mutans to experimental salivary pellicle and glucans formed on hydroxyapatite surface.

Ambatipudi KS, Hagen FK, Delahunty CM, Han X, Shafi R, Hryhorenko J, Gregoire S, Marquis RE, Melvin JE, Koo H, Yates JR 3rd.

J Proteome Res. 2010 Dec 3;9(12):6605-14. Epub 2010 Oct 22.


 Identifying components of protein complexes in C. elegans using co-immunoprecipitation and mass spectrometry.

Moresco JJ, Carvalho PC, Yates JR 3rd.

J Proteomics. 2010 Oct 10;73(11):2198-204. Epub 2010 May 28. Review.


 Proteomic survey towards the tissue-specific proteins of mouse mitochondria.

Wang Y, Sun H, Ru Y, Yin S, Yin L, Liu S.

Sci China Life Sci. 2011 Jan;54(1):3-15. Epub 2011 Jan 21.


 The nitrated proteome in heart mitochondria of the db/db mouse model: characterization of nitrated tyrosine residues in SCOT.

Wang Y, Peng F, Tong W, Sun H, Xu N, Liu S.

J Proteome Res. 2010 Aug 6;9(8):4254-63.


 Heterogeneous cardiac proteasomes: mandated by diverse substrates?

Scruggs SB, Ping P, Zong C.

Physiology (Bethesda). 2011 Apr;26(2):106-14.


Proteome dynamics and proteome function of cardiac 19S proteasomes.

Wang D, Zong C, Koag MC, Wang Y, Drews O, Fang C, Scruggs SB, Ping P.

Mol Cell Proteomics. 2011 May;10(5):M110.006122. Epub 2011 Feb 25.


 Managing the quality of life for proteins: focusing on the exit path. Introduction.

Ping P, Mayor T, Huang L.

Mol Cell Proteomics. 2011 May;10(5):O111.009969. Epub 2011 Mar 26. No abstract available.


 Advancing cardiovascular biology and medicine via proteomics: Opportunities and present challenges of cardiovascular proteomics.

Ping P, Chan DW, Srinivas P.

Circulation. 2010 Jun 1;121(21):2326-8. No abstract available.


Native capillary isoelectric focusing for the separation of protein complex isoforms and subcomplexes.

Fonslow BR, Kang SA, Gestaut DR, Graczyk B, Davis TN, Sabatini DM, Yates JR 3rd.

Anal Chem. 2010 Aug 1;82(15):6643-51.

Census for proteome quantification.

Park SK, Yates JR 3rd.

Curr Protoc Bioinformatics. 2010 Mar;Chapter 13:Unit 13.12.1-11.PMID: 20205189 [PubMed - indexed for MEDLINE]Related citations

Phosphoproteome analysis reveals regulatory sites in major pathways of cardiac mitochondria.

Deng N, Zhang J, Zong C, Wang Y, Lu H, Yang P, Wang W, Young GW, Wang Y, Korge P, Lotz C, Doran P, Liem DA, Apweiler R, Weiss JN, Duan H, Ping P.

Mol Cell Proteomics. 2010 Sep 7. [Epub ahead of print]PMID: 20495213 [PubMed - as supplied by publisher]Free Article

Creation of an antibody-based subcellular protein atlas.

Lundberg E, Uhlén M.

Proteomics. 2010 Jul 19. [Epub ahead of print]PMID: 20648481 [PubMed - as supplied by publisher

A global view of protein expression in human cells, tissues, and organs.

Pontén F, Gry M, Fagerberg L, Lundberg E, Asplund A, Berglund L, Oksvold P, Björling E, Hober S, Kampf C, Navani S, Nilsson P, Ottosson J, Persson A, Wernérus H, Wester K, Uhlén M.

Mol Syst Biol. 2009;5:337. Epub 2009 Dec 22.PMID: 20029370 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

The Universal Protein Resource (UniProt) in 2010.

UniProt Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D142-8. Epub 2009 Oct 20.PMID: 19843607 [PubMed - indexed for MEDLINE]Free PMC ArticleFree text

Genome-wide study of Pseudomonas aeruginosa outer membrane protein immunogenicity using self-assembling protein microarrays.

Montor WR, Huang J, Hu Y, Hainsworth E, Lynch S, Kronish JW, Ordonez CL, Logvinenko T, Lory S, LaBaer J.

Infect Immun. 2009 Nov;77(11):4877-86. Epub 2009 Sep 8.PMID: 19737893 [PubMed - indexed for MEDLINE]Free PMC ArticleFree text

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