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PACR Publications

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PACR Supported Publications

2009

Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res. 2009 Jan 1;69:300-9. PMID: 19118015

Keshamouni VG, Jagtap P, Michailidis G, Strahler JR, Kuick R, Reka AK, Papoulias P, Krishnapuram R, Srirangam A, Standiford TJ, Andrews PC, Omenn GS. Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-Induced epithelial-mesenchymal transition.  J Proteome Res. 2009 Jan;8:35-47. PMID: 19118450

Wu YM, Nowack D, Omenn G, Haab B. Mucin glycosylation is altered by pro-inflammatory signaling in pancreatic-cancer cells. J. Proteome Res., 2009, 8, pp 1876–1886 PMID: 19166357

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457:910-4. PMID: 19212411

Hung KE, Faca V, Song K, Sarracino DA, Richard LG, Krastins B, Forrester S, Porter A, Kunin A, Mahmood U, Haab BB, Hanash SM, Kucherlapati R. Comprehensive proteome analysis of an Apc mouse model uncovers proteins associated with intestinal tumorigenesis. Cancer Prev Res (Phila Pa). 2009 Mar;2:224-33. Epub 2009 Feb 24. PMID: 19240248

Keshamouni VG, Jagtap P, Michailidis G, Strahler JR, Kuick R, Reka AK, Papoulias P, Krishnapuram R, Srirangam A, Standiford TJ, Andrews PC, Omenn GS. Temporal quantitative proteomics by iTRAQ 2D-LC-MS/MS and corresponding mRNA expression analysis identify post-transcriptional modulation of actin-cytoskeleton regulators during TGF-beta-induced epithelial-mesenchymal transition. J Proteome Res 2009; 8:35-47. PMID: 19118450.

McClelland M, Zhao L, Carskadon S, Arenberg D. Expression of CD74, the receptor for macrophage migration inhibitory factor, in non-small cell lung cancer. Am J Pathol 2009; 174:638-646. PMID: 19131591.

Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM. Metabolic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 2009; 457:910-914. PMID: 19212411.

Menon R, Zhang Q, Zhang Y, Fermin D, Bardeesy N, DePinho RA, Lu C, Hanash SM, Omenn GS, States DJ. Identification of novel alternative splice isoforms of circulating proteins in a mouse model of human pancreatic cancer. Cancer Res 2009; 69:300-309. PMID: 19118015

2008

Omenn GS, Aebersold R, Paik YK. 7th World Congress of Proteomics: Launching the second phase of the HUPO Plasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands. Proteomics 2009; 9:4-6. PMID: 19053147.

Leichert LI, Gehrke F, Gudiseva HV, Blackwell T, Ilbert M, Walker AK, Strahler JR, Andrews PC, Jakob U. Quantifying changes in the thiol redox proteome upon oxidative stress in vivo. Proc Natl Acad Sci USA 2008; 105:8197-8202. PMID: 18287020.

Gonzalez RM, Seurynck-Servoss SL, Crowley SA, Brown M, Omenn GS, Hayes DF, Zanger RC.
Development and validation of sandwich ELISA microarrays with minimal assay interference. J Proteome Res 2008; 7:2406-2414. PMID:  18422355.

Mo F, Hong X, Gao F, Du L, Wang J, Omenn GS, Lin B. A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data. BMC Bioinformatics 2008; 9:537  PMID: 19087293.

Yocum AK, Gratsch TE, Leff N, Strahler JR, Hunter CL, Walker AK,  Michailidis G, Omenn GS, O’Shea KS, Andrews PC. Coupled global and targeted proteomics of human embryonic stem cells during induced differentiation. Mol Cell Proteomics 2008; 7:750-767.  PMID: 18304949

Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics 2008; 7: 600-611. PMID: 18077443. 

2007

Omenn GS, Menon R, Adamski M, Blackwell T, Haab BB, Gao W, States DJ. The human plasma and serum proteome. In V. Thongboonkerd (ed), Proteomics of Human Body Fluids: Principles, Methods, and Applications. Humana Press, Totowa, NJ, USA, 2007, pp. 195-224.

Falkner JA, Kachman M, Veine DM, Walker A, Strahler JR, Andrews PC. Validated MALDI-TOF/TOF mass spectra for protein standards. J Am Soc Mass Spectrom 2007; 18: 850-855. PMID: 17329120.

Forrester S, Qiu J, Mangold L, Partin A, Misek D, Phinney B, Whitten D, Andrews P, Diamandis E, Omenn GS, Hanash S, Haab B. An experimental strategy for quantitative analysis of the humoral immune response to prostate cancer antigens using natural protein microarrays. Proteomics-Clinical Applications 2007, 1: 494-505.

Forrester S, Hung K, Kuick R, Kucherlapati R, Haab BB. Low-volume, high–throughput sandwich immunoassays for profiling plasma proteins in mice: identification of early-stage systemic inflammation in a mouse model of intestinal cancer. Molecular Oncology 2007 1:216-225. 

Tian Y, McEachin RC, Santos C, States DJ, Patel JM. SAGA: A subgraph matching tool for biological graphs. Bioinformatics 2007; 23: 232-239. PMID: 17110368.

2006

Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. 2006;7:R35. PMID: 16646984.

Haab BB. Applications of antibody array platforms. Curr Opin Biotechnol. 2006;17:415-421. PMID: 16837184.

Haab BB, Lizardi PM. RCA-enhanced protein detection arrays. Methods Mol Biol. 2006;328:15-29. PMID: 16785639.

Keshamouni VG, Michailidis G, Grasso CS, Anthwal S, Strahler JR, Walker A, Arenberg DA, Reddy RC, Akulapalli S, Thannickal VJ, Standiford TJ, Andrews PC, Omenn GS. Differential protein expression profiling by iTRAQ-2DLC1MS/MS of lung cancer cells undergoing epithelial-mesenchymal transition reveals a migratory/invasive phenotype. J Proteome Research. 2006;5:1143-54; PMID: 16674103.

Kim YJ, Patel JM. A framework for protein structure classification and identification of novel protein structures. BMC Bioinformatics 2006; 7:456. PMID: 17042958.

Omenn GS. Strategies for plasma proteomic profiling of cancers. Proteomics. 2006; 6:5662-5673. PMID: 16991194.

Ulintz PJ, Zhu J, Qin ZS, Andrews PC. Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol Cell Proteomics 2006; 5: 497-509. PMID: 16321970.

States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, Hanash SM. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006; 24: 333-338. PMID: 16525410

2005

Omenn GS. Plasma protein biomarker discovery. European Pharm Rev 2005;10:26-33.

Kim YJ, Boyd A, Athey BD, Patel JM. miBLAST: Scalable evaluation of a batch of nucleotide sequence queries with BLAST. Nucleic Acids Res 2005; 33: 4335-4344. PMID: 156040401.

Santos C, Blake J, States DJ. Supplementary data need to be kept in public repositories. Nature 2005;438: 738. PMID: 16340990.

PACR-Related Publications

2009

Hung KE, Faca V, Song K, Sarracino DA, Richard LG, Krastins B, Forrester S, Porter A, Kunin A, Mahmood U, Haab BB, Hanash SM, Kucherlapati R. Comprehensive proteome analysis of an Apc mouse model uncovers proteins associated with intestinal tumorigenesis. Cancer Prev Res 2009; 2:224-233. PMID:19240248. 

Ivanov SV, Miller J, Lucito R, Tang C, Ivanova AV, Pei J, Carbone M, Cruz C, Beck A, Webb C, Nonaka D, Testa JR, Pass HI. Genomic events associated with progression of pleural malignant mesothelioma. Int J Cancer 2009; 124:589-599. PMID: 18973227

Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-Only, MSA, and MS(2)/MS(3) Methodologies for Phosphopeptide Identification. J Proteome Res 2009; 8:887-899. PMID: 19072539.

2008

Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics 2008; 7: 71-87. PMID: 17872894.

Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ. Cytoscape ESP: Simple search of complex biological networks. Bioinformatics 2008; 24:1465-1566. PMID: 18445605.

Bujold E, Romero R, Kusanovic JP, Erez O, Gotsch F, Chaiworapongsa T, Gomez R, Espinoza J, Vaisbuch E, Mee Kim Y, Edwin S, Pisano M, Allen B, Podust VN, Dalmasso EA, Rutherford J, Rogers W, Moser A, Yoon BH, Barder T. Proteomic profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry. J Matern Fetal Neonatal Med 2008; 21:697-713. PMID: 19012186.

Chen X, Ulintz PJ, Simon ES, Williams JA, Andrews PC. Global topology analysis of pancreatic zymogen granule membrane proteins. Mol Cell Proteomics 2008; 7:2323-2336. PMID: 18682380.

Du X, Yang F, Manes NP, Stenoien DL, Monroe ME, Adkins JN. States DJ, Purvine SO, Camp DG 2nd, Smith RD. Linear discriminant analysis-based estimation of the false discovery rate for phosphopeptide identifications. J Proteome Res 2008; 7:2195-2203. PMID: 18422353.

Everton KL, Abbott DR, Crockett DK, Elenitoba-Johnson KS, Lim MS. Quantitative proteomic analysis of follicular lymphoma cells in response to rituximab. J Chromatogr B Analyt Technol Biomed Life Sci 2008; [Epub ahead of print]. PMID: 19010092.

Falkner JA, Falkner JW, Yocum AK, Andrews PC. A spectral clustering approach to MS/MS identification of post-translational modifications. J Proteome Res 2008; 7:4614-4622. PMID: 18800783.

Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ. Integrating and annotating the interactome using the MiMI plugin for Cytoscape. Bioinformatics 2009; 25:137-138  PMID: 18812364.

Gibson F, Anderson L, Babnigg G, Baker M, Berth M, Binz PA, Borthwick A, Cash P, Day BW, Friedman DB, Garland D, Gutstein HB, Hoogland C, Jones NA, Khan A, Klose J, Lamond AI, Lemkin PF, Lilley KS, Minden J, Morris NJ, Paton NW, Pisano MR, Prime JE, Rabilloud T, Stead DA, Taylor CF, Voshol H, Wipat A, Jones AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol 2008; 26:863-864. PMID: 18688234.

Glaros S, Cirrincione GM, Palanca A, Metzger D, Reisman D. Targeted knockout of BRG1 potentiates lung cancer development. Cancer Res 2008; 68:3689-3696. PMID: 18483251.

Lucitt MB, Yocum AK, Price TS, Pizarro A, Wu W, Seiler C, Pack MA, Blair IA, FitzGerald GA, Grosser T.  Analysis of the zebrafish proteome during embryonic development. Mol Cell Proteomics 2008; 7:981-994. PMID:  18212345.

Qiu J, Choi G, Li L, Wang H, Pitteri SJ, Pereira-Faca SR, Krasnoselsky AL, Randolph TW, Omenn GS, Edelstein C, Barnett MJ, Thornquist MD, Goodman GE, Brenner DE, Feng Z, Hanash SM. Occurrence of autoantibodies to annexin I, 14-3-3 theta and LAMR1in prediagnostic lung cancer sera. J Clin Oncol 2008; 26(31):5060-5066. PMID: 18794547.

Sarntivijai S, Ade AS, Athey BD, States DJ. A bioinformatics analysis of the cell line nomenclature. Bioinformatics 2008; 24(23):2760-2766. PMID: 18849319.

States DJ, Ade AS, Wright ZC, Bookvich AV, Athey BD. MiSearch adaptive PubMed search tool.
Bioinformatics 2008; [epub ahead of print]. PMID:  18326507.

Yocum AK, Chinnaiyan AM. Current Affairs in Quantitative Targeted Proteomics: Multiple Reaction Monitoring -- Mass Spectrometry. Briefings in Functional Genomics and Proteomics 2008. PMID: 19279071.

Varambally S, Laxman B, Mehra R, Cao Q, Dhanasekaran SM, Tomlins SA, Granger J, Vellaichamy A, Sreekumar A, Yu J, Gu W, Shen R, Ghosh D, Wright LM, Kladney RD, Kuefer R, Rubin MA, Fimmel CJ, Chinnaiyan AM. Gogli protein GOLM1 is a tissue and urine biomarker of prostate cancer. Neoplasia 2008; 10:1285-1294. PMID: 18953438.

Woods Ignatoski KM, Grewal NK, Markwart SM, Vellaichamy A, Chinnaiyan AM, Yeung K, Ray ME, Keller ET. Loss of Raf kinase inhibitory protein induces radioresistance in prostate cancer. Int J Radiat Oncol Biol Phys. 2008; 72:153-160. PMID: 18722266.

Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D, Hung KE, Kucherlapati R, Jacks T, Politi K, Aebersold R, Omenn GS, States DJ, Hanash SM. A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol  2008; 9:R93, Epub 2008 Jun 3; PMID:  18522751

Balbus JM, Maynard AD, Colvin VL, Castranova V, Daston GP, Denison RA, Dreher KL, Goering PL, Goldberg AM, Kulinowski KM, Monteiro-Riviere NA, Oberdorster G, Omenn GS, Pinkerton KE, Ramos KS, Rest KM, Sass JB, Silbergeld EK, Wong BA. Meeeting Report: Hazard assessment for nanoparticles – Report from an interdisciplinary workshop. Environ Health Perspect 2007; 115: 1654-1659. PMID: 18007999.

Chen X, Andrews PC. Purification and proteomics analysis of pancreatic zymogen granule membranes. Methods Mol Biol 2008; 432: 275-287.  PMID:  18370025.

Choi H, Ghosh D, Nesvizhskii AI. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res 2008; 7:286-292. PMID: 18078310.

Choi H, Nesvizhskii AI. False discovery rates and related statistical concepts in mass spectrometry-based products.  J Proteome Res 2008; 7:47-50. PMID:  18067251.

Choi H, Nesvizhskii AI.  Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. J Proteome Res 2008; 7:254-265. PMID:  18159924.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC,…Elinitoba-Johnson K,… Falkner J,… Lim M,… Menon R,… Omenn GS,… States DS,…Pandey A [160 coauthors]. Human Proteinpedia: A portal for sharing and integration of human protein data. Nature Biotechnol 2008; 26: 164-167. PMID: 18259167.

Omenn GS, Ping P.  The Future: Translation from Discovery to the Clinic—Roles of HUPO and Industry in Biomarker Discovery. In Van Eyk J, Dunn M (eds.) Clinical Proteomics, Weinheim: Wiley-VCH, 2008: 595-613.

Yocum AK, Ulitz PJ, Andrews PC. Use of Physiochemical Properties in Peptide and Protein Identification. In von Hagen J (ed), Sample Preparation in Proteomics. VCH Wiley, Weinheim, Germany, 2008, 453 pp.

2007

Omenn GS, Aebersold R, Paik YK. HUPO Plasma Proteome Project 2007 Workshop Report. Mol Cell Proteomics 2007; 6:2252-2253. PMID:  18070836.

Glaros S, Cirrincione GM, Muchardt C, Kleer CG, Michael CW, Reisman D. The reversible epigenetic silencing of BRM: implications for clinical targeted therapy. Oncogene 2007; 26:7058-7066. PMID: 17546055.

Kim B, Nesvizhskii A, Rani PG, Hahn S, Aebersold R, Ranish JA. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proc Natl Acad Sci USA 2007; 104:16068-16073. PMID:  17913884.

Mueller D, Bach C, Zeiseg D, Garcia-Cuellar MP, Monroe S, Sreekumar A, Zhou R, Nesvizhskii A, Chinnaiyan A, Hess JL, Slany RK. A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification. Blood 2007; 110:4445-4454. PMID:  17855633.

Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007; 4:787-797. PMID:  17901868.

Rao A, Hero III, AO, States DJ, Engel JD. Motif discovery in tissue-specific regulatory sequences using directed information. EURASIP J Bioinform Syst Biol 2007; 13853. PMID: 18340376.

Rosania GR, Crippen G, Woolf P, States D, Shedden K. A cheminformatic toolkit for mining biomedical knowledge. Pharm Res 2007; 24:1791-1802. PMID:  17385012.

Searle B, Turner M, Nesvizhskii AI. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. J Proteome Res 2008; 7:245-253. PMID: 18173222.

Schumacher JA, Crockett DK, Elenitoba-Johnson KS, Lim MS. Proteome-wide changes induced by the Hsp90 inhibitor, geldanamycin in anaplastic large cell lymphoma cells. Proteomics 2007; 7:2603-2616. PMID: 17610208.

Chen S, LaRoche T, Hamelinck D, Bergsma D, Brenner D, Simeone D, Brand R E, Haab BB. Multiplexed analysis of glycan variation on native proteins captured by antibody microarrays.
Nature Methods 2007; 4: 437-444. PMID: 17417647.

Gao W-M, Chadha MS, Berger RP, Omenn GS, Allen DL, Pisano M, Adelson PD, Clark RSB, Jenkins LW, Kochanek PM. A gel-based proteomic comparison of human cerebrospinal fluid global protein patterns between inflicted and non-inflicted pediatric traumatic brain injury. J Neurotrauma 2007; 24:43-53. PMID: 17263669.

Jiang M, Sullivan SM, Walker AK, Strahler JR, Andrews PC, Maddock JR. Identification of novel Escherichia coli ribosome-associated proteins using isobaric tags and multidimensional protein identification techniques. J Bacteriol 2007; 189:3434-3444. PMID: 17337586.

Kuick R, Misek DE, Monsma DJ, Webb CP, Wang H, Peterson KJ, Pisano M, Omenn GS, Hanash SM. Discovery of cancer biomarkers through the use of mouse models. Cancer Letters 2007; 249:
40-48. PMID: 17320282.

McClelland MR, Carskadon SL, Zhao L, White ES, Beer DG, Orringer MB, Pickens A, Chang AC, Arenberg DA. Diversity of the angiogenic phenotype in non-small cell lung cancer. Am J Respir Cell Mol Biol. 2007; 36:343-350. PMID: 17079777.

Price TS, Lucitte MB, Wu W, Austin DJ, Pizarro A, Yocum AK, Blair IA, FitzGerald GA, Grosser T. EBP, a program for protein identification using multiple tandem mass spectrometry datasets. Mol Cell Proteomics; 6:527-536. PMID: 17164401.

Samtivijai S, Ade AS, Athey BD, States DJ. The cell line ontology and its use in tagging cell line names in biomedical text. AMIA Annu Symp Proc 2007; 11:1103. PMID: 18694200.

Wallentine JC, Kim KK, Seiler CE 3rd, Vaughn CP, Crockett DK, Tripp SR, Elenitoba-Johnson KS, Lim MS. Comprehensive identification of proteins in Hodgkin Lympohoma-derived Reed-Stemberg cells by LC-MS/MS. Lab Invest 2007; 87:1113-1124. PMID: 17876297

Yu C, Hanauer DA, Athey BD, Jagadish HV, States DJ. Simplifying access to a clinical data repository using schema Summarization. AMIA Annu Symp Proc 2007; 11:1164. PMID: 18694259.

Barker PE, Wagner PD, Stein SE, Bunk DM, Srivastava S, Omenn GS. Standards for plasma and serum proteomics in early cancer detection: a needs assessment report from the national institute of standards and technology--National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19, 2005. Clin Chem. 2006;52:1669-1674. PMID: 16840585.

Chen X, Walker AK, Strahler JR, Simon ES, Tomanicek-Volk SL, Nelson BB, Hurley MC, Ernst SA, Williams JA, Andrews PC. Organellar proteomics: Analysis of pancreatic zymogen granule membranes. Mol Cell Proteomics 2006; 5:306-312. PMID: 16278343.

Falkner JA, Falkner JW, Andrews PC. ProteomeCommons.org IO Framework: reading and writing multiple proteomics data formats. Bioinformatics 2007; 23:262-263. PMID: 17121776.

Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan molecular interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res 2007; 35 (Database issue):D566-571. PMID: 17130145.

Kozarova A, Sliskovic I, Mutus B, Vacratsis PO, Simon ES, Andrews PC. Identification of redox sensitive thiols of protein disulfide isomerase using isotope coded affinity technology and mass spectrometry. J Am Soc Mass Spectrom 2007; 18:260-269. PMID: 17074504.

Shafer MW, Mangold L, Partin AW, Haab BB. Antibody array profiling reveals serum TSP-1 as a marker to distinguish benign from malignant prostatic disease. Prostate 2007; 67:255-267. PMID: 17192876.

2006

Omenn GS, Paik YK, Speicher D. The HUPO Plasma Proteome Project: A report from the Munich congress. Proteomics 2006; 6:9-11. PMID: 16400715.

Falkner JA, Falkner JW, Andrews PC. ProteomeCommons.org JAF: reference information and tools for proteomics. ProteomeCommons.org 2006; 22:632-633. PMID: 16434446.

Garcia B, Joshi S, Thomas CE, Chitta RK, Diaz RL, Busby SA, Andrews PC, Ogorzalek Loo RR, Shabanowitz J, Kelleher NL, Mizzen CA, Allis CD, Hunt DF. Comprehensive phosphoprotein analysis of linker histone H1 from Tetrahymena thermophila. Mol Cell Proteomics 2006; 5:1593-1609. PMID: 16835217.

Giordano TJ, Au AY, Kuick R, Thomas DG, Rhodes DR, Wilhelm KG Jr, Vinco M, Misek DE, Sanders D, Zhu Z, Ciampi R, Hanash S, Chinnaiyan A, Clifton-Bligh RJ, Robinson BG, Nikiforov YE, Koenig RJ. Delineation, functional validation, and bioinformatic evaluation of gene expression in thyroid follicular carcinomas with the PAX8-PPARG translocation. Clin Cancer Res. 2006;12:1983-1993. PMID: 16609007.

Haab BB, Paulovich AG, Anderson NL, Clark AM, Downing GJ, Hermjakob H, Labaer J, Uhlen M. A reagent resource to identify proteins and peptides of interest to the cancer community: A workshop report. Mol Cell Proteomics. 2006; 5:1996-2007. PMID: 16867976.

Hung KE, Kho AT, Sarracino D, Richard LG, Krastins B, Forrester S, Haab BB, Kohane IS, Kucherlapati R. Mass spectrometry-based study of the plasma proteome in a mouse intestinal tumor model. J Proteome Res. 2006; 5:1866-1878. PMID: 16889408.

Huo JS, McEachin RC, Cui TX, Duggal NK, Hai T, States DJ, Schwartz J. Profiles of growth hormone (GH)-regulated genes reveal time-dependent responses and identify a mechanism for regulation of activating transcription factor 3 by GH. J Biol Chem 2006; 281: 4132-4141. PMID: 16326703.

Jagtap P, Michailidis G, Zielke R, Walker AK, Patel N, Strahler JR, Driks A, Andrews PC, Maddock JR. Early events of Bacillus anthracis germination identified by time-course quantitative proteomics. Proteomics. 2006; 6:5199-5211. PMID: 16927434.

Jiang M, Datta K, Walker A, Strahler J, Bagamasbad P, Andrews PC, Maddock JR. The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly. J Bacteriol. 2006;188:6757-6770. PMID: 16980477.

Kong FM, Hayman JA, Griffith KA, Kalemkerian GP, Arenberg D, Lyons S, Turrisi A, Lichter A, Fraass B, Eisbruch A, Lawrence TS, Ten Haken RK. Final toxicity results of a radiation-dose escalation study in patients with non-small-cell lung cancer (NSCLC): predictors for radiation pneumonitis and fibrosis. Int J Radiat Oncol Biol Phys. 2006; 65:1075-1086. PMID: 16647222.

Lee AW, States DJ. Colony-stimulating factor-1 requires PI3-kinase-mediated metabolism for proliferation and survival in myeloid cells. Cell Death Differ. 2006; 13:1900-1914. PMID: 16514418.

Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whitaker J, States D, Hanash S, Paulovich A, McIntosh MW. Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J Proteome Res 2006; 5:112-121. PMID: 16396501.

Sanchez-Carbayo M, Socci ND, Lozano JJ, Haab BB, Cordon-Cardo C. Profiling bladder cancer using targeted antibody arrays. Am J Path 2006; 168:93-103. PMID: 16400012.

Tata S, Patel JM, Friedman JS, Swaroop A. Declarative querying for biological sequence databases. Proceedings of the 22nd International Conference on Data Engineering, ICDE 2006, 3-8 April 2006, Atlanta, GA.

Tomlins SA, Mehra R, Rhodes DR, Shah RB, Rubin MA, Bruening E, Makarov V, Chinnaiyan AM. Whole transcriptome amplification for gene expression profiling and development of molecular archives. Neoplasia. 2006;8:153-162. PMID: 16611408.

Ubels JL, Hoffman HM, Srikanth S, Resau JH, Webb CP. Gene expression in rat lacrimal gland duct cells collected using laser capture microdissection: evidence for K+ secretion by duct cells. Invest Ophthalmol Vis Sci. 2006 ;47:1876-1885. PMID: 16638994.

2005

Omenn, GS. Highlights of the HUPO Plasma Proteome Project: Creating a knowledge base for clinical assays. J Clin Ligand Soc 2005; 28:38-43.

Orchekowski R, Hamelinck D, Li L, Gliwa E, VanBrocklin M, Marrero JA, Vande Woude GF, Feng Z, Brand R, Haab BB. Antibody microarray profiling reveals individual and combined serum proteins associated with pancreatic cancer. Cancer Res 2005;65:11193-111202. PMID: 16322270.