Selected Recent Publications

Boston University School of Medicine Cardiovascular Proteomics Center

Oxidative posttranslational modifications mediate decreased SERCA activity and myocyte dysfunction in Galphaq-overexpressing mice. Lancel S, Qin F, Lennon SL, Zhang J, Tong X, Mazzini MJ, Kang YJ, Siwik DA, Cohen RA, Colucci WS. Circ Res. 2010; 107:228-32.

Peptides presented by HLA-DR molecules in synovia of patients with Rheumatoid Arthritis or Antibiotic-refractory Lyme Arthritis. Seward RJ, Drouin EE, Steere AC, Costello CE. Mol Cell Proteomics. 2011; 10(3):M110.002477.

Relations of biomarkers of extracellular matrix remodeling to incident cardiovascular events and mortality. Velagaleti RS, Gona P, Sunström J, Larson MG, Siwik D, Colucci WS, Benjamin EJ, Vasan RS. Arterioscler Thromb Vasc Biol. 2010; 30:2283-8.

Redox regulation of sirtuin-1 is mediated by S-glutathiolation. Zee RS, Yoo CB, Pimentel DR, Perlman DH, Burgoyne JR, Hou X, McComb ME, Costello CE, Cohen RA, Bachschmid MM. Antioxidants & Redox Signaling. 2010; 13:1023-1032.

 

Johns Hopkins University Proteomics Innovation Center in Heart Failure

Crosstalk Between O-GlcNAcylation and Phosphorylation: Roles in Signaling, Transcription and Chronic Disease. Hart GW, Slawson C, Ramirez-Correa G and Lagerlof O. Ann Rev Biochem. 2011; 80:825-58

Glycomics hits the big time. Hart GW and Copeland  RJ. Cell. 2010; 143: 672-676.

Alterations in O-GlcNAc Signaling: Implications for Cancer Cell Biology. Slawson C and Hart GW. Nat Rev Cancer. 2011; 11(9):678-84

Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, Cole RN, Pandey A and Semenza GL. Cell. 2011; 145, 732-744.

Oxygen sensing, homeostasis, and disease. Semenza GL. N Engl J Med. 2011; 365: 537-547.

 

Harvard Broad Proteomics Center

Development and Application of a Biomarker Discovery through Verification Pipeline of Cardiovascular Disease. Terri A. Addona, Xu Shi, Hasmik Keshishian, DR Mani, Michael Burgess, Michael A. Gillette, Karl Clauser, Dongxiao Shen, Gregory D. Lewis, Laurie A. Farrell, Michael A. Fifer, Marc S. Sabatine, Robert E. Gerszten and Steven A. Carr. Nat Biotechnology. 2011; Jun 19.

Myocardial Ischemia Induced by Rapid Atrial Pacing Causes Troponin T Release Detectable by a High-Sensitivity Assay: Insights from a Coronary Sinus Sampling Study. Turer AT, Addo TA, Martin JL, Sabatine MS, Lewis GD, Gerszten RE, Keeley EC, Cigarroa JE, Lange RA, Hillis LD, de Lemos JA. J Am Coll Cardiol. 2011; 57(24):2398 405.

C/EBPβ controls exercise-induced cardiac growth and protects against pathological cardiac remodeling. Boström P, Mann N, Wu J, Quintero PA, Plovie ER, Panáková D, Gupta RK, Xiao C, MacRae CA, Rosenzweig A, Spiegelman BM. Cell. 2010; 143(7):1072-83

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA. Nat Biotechnol. 2011; 29(7):635-43.

Metabolite profiles and the risk of developing diabetes. Wang TJ, Larson MG, Vasan RS, Cheng S, Rhee EP, McCabe E, Lewis GD, Fox CS, Jacques PF, Fernandez C, O'Donnell CJ, Carr SA, Mootha VK, Florez JC, Souza A, Melander O, Clish CB, Gerszten RE.  Nat Med. 2011; 17(4):448-53. 

 

Stanford University Proteomics Center

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Bendall SC, Simonds EF, Qiu P, Amir el-AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP. Science. 2011; 332(6030):687-96.

Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE. Qui P, Simonds EF, Bendall SC, Gibbs KD Bruggner RV, Linderman MD, Sachs K, Nolan  GP,  Plevritis SK. Nat Biotechnol. 2011Oct 2;in press.

Fluorescent cell barcoding for multiplex flow cytometry. Krutzik PO, Clutter MR, Trejo A, Nolan GP.  Curr Protoc Cytom. 2011; Chapter 6:Unit 6.31.

Cloud and heterogeneous computing solutions exist today for the emerging big data problems in biology. Schadt EE, Linderman MD, Sorenson J, Lee L, Nolan GP.  Nat Rev Genet. 2011; 12(3):224.

Fishing for biomarkers with antigen mimics. Lindstrom TM, Robinson WH. Cell. 2011; 144:13-5.

Human peptidome display. Robinson WH, Steinman L. Nat Biotechnol. 2011; 29(6):500-2.

 

UTHSCSA Proteomics Center

Combining experimental and mathematical modeling to reveal mechanisms of macrophage-dependent left ventricular remodeling. Yu-Fang Jin, Hai- Chao Han, Jamie Berger, Qiuxia Dai and Merry L Lindsey.  BMC Systems Biology. 2011; 5:60.

Multi-Analyte Profiling Reveals Matrix Metalloproteinase-9 and Monocyte Chemotactic Protein-1 as Plasma Biomarkers of Cardiac Aging. Chiao YA, Dai Q, Zhang J, Lin J, Lopez EF, Ahuja SS, Chou YM, Lindsey ML, Jin YF.  Circ Cardiovasc Genet. 2011; 4:455-462.

Proteomic analysis identifies in vivo candidate matrix metalloproteinase-9 substrates in the left ventricle post-myocardial infarction. Zamilpa R, Lopez EF, Chiao YA, Dai Q, Escobar GP, Hakala K, Weintraub ST, Lindsey ML. Proteomics. 2010; 10:2214-23.

CC Chemokine Receptor 5 Deletion Impairs Macrophage Activation and Induces Adverse Remodeling Following Myocardial Infarction. Zamilpa R, Kanakia R, Cigarroa J 4th, Dai Q, Escobar GP, Martinez HM, Jimenez F, Ahuja S, Lindsey ML.  Am J Physiol Heart Circ Physiol. 2011; 300(4):H1418-26.

C mediates early extracellular matrix remodeling following myocardial infarction. McCurdy SM, Dai Q, Zhang J, Zamilpa R, Ramirez TA, Dayah T, Nguyen N, Jin YF, Bradshaw AD, Lindsey ML. Am J Physiol Heart Circ Physiol. 2011; 301(2):H497-505.

 

UTMB Proteomics Center at Galveston

Quantification of activated NF-κB/RelA complexes using ssDNA aptamer affinity-stable isotope dilution-selected reaction monitoring-mass spectrometry. Zhao Y, Widen SG, Jamaluddin M, Tian B, Wood TG, Edeh CB, and Brasier AR. Mol Cell Proteomics. 2011; 10(6):M111.008771.

Host S-nitrosylation inhibits clostridial small molecule-activated autoprocessing toxins. Savidge T, Urvil P, Oezgun N, Pinchuk I, Torres A, English R, Wiktorowicz J, Kumar R, Braun W, Stamler J, and Pothoulakis C. Nat Med. 2011; 17(9):1136-41

Quantification of activated NF-B/RelA complexes using ssDNA aptamer affinity – stable isotope dilution-selective reaction monitoring-MS. Zhao Y, Widen SG, Jamaluddin M, Tian B, Wood, TG and Brasier AR.  Mol Cell Proteomics. 2011; 10:1-16.

Viral-mediated inhibition of antioxidant enzymes contributes to the pathogenesis of severe respiratory syncytial virus bronchiolitis. Hosakote YM, Jantzi PD, Esham DL, Spratt H, Kurosky A, Casola A, and Garofalo RP.  Am J  Respir Crit Care Med. 2011; 183:1550-60.

 

UCLA Proteomics Center

Conducting the metabolic syndrome orchestra. Civelek M, Lusis AJ. Nat Genet. 2011; 43(6):506-8.

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; 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; 28(12):1248-50.

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; 10(5):M110.006122. Epub 2011 Feb 25.

Differential regulation of proteasome function in isoproterenol-induced cardiac hypertrophy. Drews O, Tsukamoto O, Liem D, Streicher J, Wang Y, Ping P. Circ Res. 2010; 107(9):1094-101. 

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. 2011; 10(2):M110.000117. Epub 2010 May 22.

A community standard format for the representation of protein affinity reagents. Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. Mol Cell Proteomics. 2010; 9(1):1-10.