Parag Mallick
Parag Mallick
Associate Professor, Stanford University
Verified email at - Homepage
Cited by
Cited by
A cross-platform toolkit for mass spectrometry and proteomics
MC Chambers, B Maclean, R Burke, D Amodei, DL Ruderman, ...
Nature biotechnology 30 (10), 918-920, 2012
ProteoWizard: open source software for rapid proteomics tools development
D Kessner, M Chambers, R Burke, D Agus, P Mallick
Bioinformatics 24 (21), 2534-2536, 2008
The peptideatlas project
F Desiere, EW Deutsch, NL King, AI Nesvizhskii, P Mallick, J Eng, S Chen, ...
Nucleic acids research 34 (suppl_1), D655-D658, 2006
Computational prediction of proteotypic peptides for quantitative proteomics
P Mallick, M Schirle, SS Chen, MR Flory, H Lee, D Martin, J Ranish, ...
Nature biotechnology 25 (1), 125-131, 2007
How many human proteoforms are there?
R Aebersold, JN Agar, IJ Amster, MS Baker, CR Bertozzi, ES Boja, ...
Nature chemical biology 14 (3), 206-214, 2018
Neuronal activity promotes glioma growth through neuroligin-3 secretion
HS Venkatesh, TB Johung, V Caretti, A Noll, Y Tang, S Nagaraja, ...
Cell 161 (4), 803-816, 2015
Proteomics: a pragmatic perspective
P Mallick, B Kuster
Nature biotechnology 28 (7), 695-709, 2010
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlas
T Farrah, EW Deutsch, GS Omenn, DS Campbell, Z Sun, JA Bletz, ...
Molecular & cellular proteomics 10 (9), 2011
Scoring proteomes with proteotypic peptide probes
B Kuster, M Schirle, P Mallick, R Aebersold
Nature reviews Molecular cell biology 6 (7), 577-583, 2005
Data conversion with ProteoWizard msConvert
R Adusumilli, P Mallick
Proteomics: methods and protocols, 339-368, 2017
Characterizing deformability and surface friction of cancer cells
S Byun, S Son, D Amodei, N Cermak, J Shaw, JH Kang, VC Hecht, ...
Proceedings of the National Academy of Sciences 110 (19), 7580-7585, 2013
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry
F Desiere, EW Deutsch, AI Nesvizhskii, P Mallick, NL King, JK Eng, ...
Genome biology 6, 1-12, 2005
Building high-quality assay libraries for targeted analysis of SWATH MS data
OT Schubert, LC Gillet, BC Collins, P Navarro, G Rosenberger, WE Wolski, ...
Nature protocols 10 (3), 426-441, 2015
Semi-automatically mapping structured sources into the semantic web
CA Knoblock, P Szekely, JL Ambite, A Goel, S Gupta, K Lerman, ...
Extended semantic web conference, 375-390, 2012
Employing ProteoWizard to convert raw mass spectrometry data
JD Holman, DL Tabb, P Mallick
Current protocols in bioinformatics, 13.24. 1-13.24. 9, 2014
GXXXG and AXXXA: common α-helical interaction motifs in proteins, particularly in extremophiles
G Kleiger, R Grothe, P Mallick, D Eisenberg
Biochemistry 41 (19), 5990-5997, 2002
Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments
KD Bemis, A Harry, LS Eberlin, C Ferreira, SM van de Ven, P Mallick, ...
Bioinformatics 31 (14), 2418-2420, 2015
High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry
H Zhang, CY Eugene, X Li, P Mallick, KS Kelly-Spratt, CD Masselon, ...
Molecular & Cellular Proteomics 4 (2), 144-155, 2005
Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds
P Mallick, DR Boutz, D Eisenberg, TO Yeates
Proceedings of the National Academy of Sciences 99 (15), 9679-9684, 2002
The standard protein mix database: a diverse data set to assist in the production of improved peptide and protein identification software tools
J Klimek, JS Eddes, L Hohmann, J Jackson, A Peterson, S Letarte, ...
The Journal of Proteome Research 7 (01), 96-103, 2008
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