Journal Articles That Used Scaffold
Scaffold is used in a wide variety of proteomics experiments by a wide variety of research labs. The following papers mention using Scaffold in their data analysis. If know of other papers citing Scaffold, we will be glad to add them to this list.
- Susan L. Kozak, Mariana Marin, Kristine M. Rose, Cory Bystrom, and David Kabat
"The Anti-HIV-1 Editing Enzyme APOBEC3G Binds HIV-1 RNA and Messenger RNAs That Shuttle between Polysomes and Stress Granules "
J. Biol. Chem., Sep 2006; 281: 29105 - 29119. - Nathaniel A. Jeske, Amol M. Patwardhan, Nikita Gamper, Theodore J. Price, Armen N. Akopian, and Kenneth M. Hargreaves
"Cannabinoid WIN 55,212-2 Regulates TRPV1 Phosphorylation in Sensory Neurons"
J. Biol. Chem., Oct 2006; 281: 32879 - 32890. -
Mark J. Sartain, Richard A. Slayden, Krishna K. Singh, Suman Laal, and John T. Belisle
"Disease State Differentiation and Identification of Tuberculosis Biomarkers via Native Antigen Array Profiling"
Mol. Cell. Proteomics, Nov 2006; 5: 2102 - 2113. - Richard M. LoPachin, David S. Barber, Brian C. Geohagen, Terrence Gavin, Deke He, and Soma Das
" Structure-Toxicity Analysis of Type-2 Alkenes: In Vitro Neurotoxicity"
Toxicol. Sci., Jan 2007; 95: 136 - 146. - Dominik Huster, Tina D. Purnat, Jason L. Burkhead, Martina Ralle, Oliver Fiehn, Franziska Stuckert, N. Erik Olson, Daniel Teupser, and Svetlana Lutsenko
" High copper selectively alters lipid metabolism and cell cycle machinery in the mouse model of Wilson disease "
J. Biol. Chem., Jan 2007; 10.1074/jbc.M607496200. - Todd M. Greco, Roberto Hodara, Ioannis Parastatidis, Harry F. G. Heijnen, Michelle K. Dennehy, Daniel C. Liebler, and Harry Ischiropoulos
" Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells"
PNAS, May 2006; 103: 7420 - 7425. - Artigues A, Iriarte A, Martinez-Carrion M.
" Identification of Hsc70 binding sites in mitochondrial aspartate aminotransferase."
Arch Biochem Biophys. 2006 Jun 1;450(1):30-8 - Jean-Paul Noben, Debora Dumont, Natalia Kwasnikowska, Peter Verhaert, Veerle Somers, Raymond Hupperts, Piet Stinissen, and Johan Robben
"Lumbar Cerebrospinal Fluid Proteome in Multiple Sclerosis: Characterization by Ultrafiltration, Liquid Chromatography, and Mass Spectrometry"
J. Proteome Res.; 2006; 5(7) pp 1647 - 1657 - Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL.
" Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility?"
J Proteome Res. 2006 Oct;5(10):2554-66. - Gravett MG, Thomas A, Schneider KA, Reddy AP, Dasari S, Jacob T, Lu X, Rodland M, Pereira L, Sadowsky DW, Roberts CT Jr, Novy MJ, Nagalla SR.
" Proteomic analysis of cervical-vaginal fluid: identification of novel biomarkers for detection of intra-amniotic infection."
J Proteome Res. 2007 Jan;6(1):89-96. - Alexander DL, Mital J, Ward GE, Bradley P, Boothroyd JC.
" Identification of the moving junction complex of Toxoplasma gondii: a collaboration between distinct secretory organelles."
PLoS Pathog. 2005 Oct;1(2):e17. Epub 2005 Oct 21. - Alexander DL, Arastu-Kapur S, Dubremetz JF, Boothroyd JC.
" Plasmodium falciparum AMA1 binds a rhoptry neck protein homologous to TgRON4, a component of the moving junction in Toxoplasma gondii."
Eukaryot Cell. 2006 Jul;5(7):1169-73. - Yan, W, Spruce L, Rosenblatt M, Kleyman, T, Rubenstein R,
" Intracellular Trafficking of a Polymorphism in the Carboxyl Terminus of the Alpha Subunit of the Human Epithelial Sodium Channel is Modulated by Casein Kinase 1&
J Am J Physiol Renal Physiol June 27, 2007 -
Yi Z, Langlais P, De Filippis E, Luo M, Flynn C, Schroeder S, Weintraub S, Mapes R, Mandarino L
"Global Assessment of Regulation of Phosphorylation of Insulin Receptor Substrate-1 by Insulin In Vivo in Human Muscle"
J Diabetes, 56:1508-1516, 2007 -
Cho C, Shan S, Winsor E, Diamadis E
"Proteomic Analysis of human amniotic fluid"
J Mol Cell Proteomics, 2007 - Benschop J, Mohammed S, O'Flaherty M, Heck A, Slijper M, Menk F
"Quantitative phospho-proteomics of early elicitor signalling in Arabidopsis "
Molecular & Cellular Proteomics 6:1198-1214, 2007. - Scholten A, Poh, MK, van Veen, T, van Breukelen B, Vos M, Heck A
"Analysis of the cGMP/cAMP Interactome Using a Chemical Proteomics Approach in Mammalian Heart Tissue Validates Sphingosine Kinase Type 1-interacting Protein as Genuine and Highly Abundant AKAP",
J Proteome Res 2006 5, 1435-1447 - Fonovic M, Verhelst SH, Sorum MT, Bogyo M.
"Proteomics Evaluation of Chemically Cleavable Activity-based Probes"
Molecular Cellular Proteomics 6 (10), 1761-70 (01 Oct 2007) - D.J. Hobson, P. Rupa, G.J. Diaz 1, H. Zhang, M. Yang, Y. Mine, P.V. Turner and G.M. Kirby
"Proteomic analysis of ovomucoid hypersensitivity in mice by two-dimensional difference gel electrophoresis (2D-DIGE)"
Food and Chemical Toxicology Volume 45, Issue 12, December 2007, Pages 2372-2380 - David S. Barber, Stanley Stevens and Richard M. LoPach
"Proteomic Analysis of Rat Striatal Synaptosomes During Acrylamide Intoxication At a Low Dose-rate"
Toxicological Sciences - Richard M. LoPachin, David S. Barber , Brian C. Geohagen, Terrence Gavin, Deke He and Soma Das
"Structure-Toxicity Analysis of Type-2 Alkenes: In Vitro Neurotoxicity "
Toxicological Sciences 2007 95(1):136-146 - Juraj Gregan, Christian G Riedel, Mark Petronczki, Lubos Cipak, Cornelia Rumpf, Ina Poser, Frank Buchholz, Karl Mechtler & Kim Nasmyth
"Tandem affinity purification of functional TAP-tagged proteins from human cells"
Nat. Protocols 2 (5), 1145-51 (May 2007) - Lunetta JM, Simmons KA, Johnson SM, Pappagianis D.
"Molecular Cloning and Expression of a cDNA Encoding a Coccidioides posadasii Cu,Zn Superoxide Dismutase Identified by Proteomic Analysis of the Coccidioidal T27K Vaccine"
Annals of the New York Academy of Sciences 1111 (1), 181-97 - Vathany Kulasingam and Eleftherios Diamandis
"Proteomic analysis of conditioned media from three breast cancer cell lines: A mine for biomarkers and therapeutic targets"
Molecular & Cellular Proteomics 6:1997-2011, 2007. - Simone M. Lemeer, Rob Ruijtenbeek, Martijn W. H. Pinkse, Chris Jopling, Albert J. R. Heck, Jeroen den Hertog, and Monique Slijper
"Endogenous phosphotyrosine signaling in zebrafish embryos"
Molecular Cellular Proteomics, M600482-MCP200 (14 Aug 2007) - Kurt Højlund, Zhengping Yi, Hyonson Hwang, Benjamin Bowen, Natalie Lefort, Charles R. Flynn, Paul Langlais, Susan T. Weintraub, and Lawrence J. Mandarino
"Characterization of the human skeletal muscle proteome by one-dimensional Gel electrophoresis and HPLC-ESI-MS/MS"
Molecular Cellular Proteomics, M700304-MCP200 (01 Oct 2007) - Jeroen Kool, Léon Reubsaet, Feikje Wesseldijk, Raquel T. Maravilha, Martijn W. Pinkse, Clive S. D'Santos, Jacobus J. van Hilten, Freek J. Zijlstra, Albert J. R. Heck
"Suction blister fluid as potential body fluid for biomarker proteins"
Proteomics, 7(20) 3638-3650 - David O. Zamora, Michael Riviere, Dongseok Choi, Yuzhen Pan, Stephen R. Planck, James T. Rosenbaum, Larry L. David, Justine R. Smith
"Proteomic profiling of human retinal and choroidal endothelial cells reveals molecular heterogeneity related to tissue of origin"
Molecular Vision 2007; 13:2058-2065 - Huiyu Low, Yu Min Lye and Tiow-Suan Sim
"Pfnek3 functions as an atypical MAPKK in Plasmodium falciparum "
Biochemical and Biophysical Research Communications Volume 361, Issue 2, 21 September 2007, Pages 439-444
