|Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles|
A Subramanian, P Tamayo, VK Mootha, S Mukherjee, BL Ebert, ...
Proceedings of the National Academy of Sciences 102 (43), 15545-15550, 2005
|Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma|
TA Addona, SE Abbatiello, B Schilling, SJ Skates, DR Mani, DM Bunk, ...
Nature biotechnology 27 (7), 633, 2009
|When checkpoints fail|
AG Paulovich, DP Toczyski, LH Hartwell
Cell 88 (3), 315-321, 1997
|A checkpoint regulates the rate of progression through S phase in S. cerevisiae in response to DNA damage|
AG Paulovich, LH Hartwell
Cell 82 (5), 841-847, 1995
|Proteogenomics connects somatic mutations to signalling in breast cancer|
P Mertins, DR Mani, KV Ruggles, MA Gillette, KR Clauser, P Wang, ...
Nature 534 (7605), 55, 2016
|Repeatability and reproducibility in proteomic identifications by liquid chromatography− tandem mass spectrometry|
DL Tabb, L Vega-Montoto, PA Rudnick, AM Variyath, AJL Ham, DM Bunk, ...
Journal of proteome research 9 (2), 761-776, 2009
|Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach|
SA Carr, SE Abbatiello, BL Ackermann, C Borchers, B Domon, ...
Molecular & Cellular Proteomics 13 (3), 907-917, 2014
|Integrated proteogenomic characterization of human high-grade serous ovarian cancer|
H Zhang, T Liu, Z Zhang, SH Payne, B Zhang, JE McDermott, JY Zhou, ...
Cell 166 (3), 755-765, 2016
|An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein …|
JR Whiteaker, L Zhao, L Anderson, AG Paulovich
Molecular & Cellular Proteomics 9 (1), 184-196, 2010
|A targeted proteomics–based pipeline for verification of biomarkers in plasma|
JR Whiteaker, C Lin, J Kennedy, L Hou, M Trute, I Sokal, P Yan, ...
Nature biotechnology 29 (7), 625, 2011
|A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS|
M Bellew, M Coram, M Fitzgibbon, M Igra, T Randolph, P Wang, D May, ...
Bioinformatics 22 (15), 1902-1909, 2006
|Antibody-based enrichment of peptides on magnetic beads for mass-spectrometry-based quantification of serum biomarkers|
JR Whiteaker, L Zhao, HY Zhang, LC Feng, BD Piening, L Anderson, ...
Analytical biochemistry 362 (1), 44-54, 2007
|RAD9, RAD17, and RAD24 Are Required for S Phase Regulation in Saccharomyces cerevisiae in Response to DNA Damage|
AG Paulovich, RU Margulies, BM Garvik, LH Hartwell
Genetics 145 (1), 45-62, 1997
|A human proteome detection and quantitation project|
NL Anderson, NG Anderson, TW Pearson, CH Borchers, AG Paulovich, ...
Molecular & Cellular Proteomics 8 (5), 883-886, 2009
|The interface between biomarker discovery and clinical validation: the tar pit of the protein biomarker pipeline|
AG Paulovich, JR Whiteaker, AN Hoofnagle, P Wang
PROTEOMICS–Clinical Applications 2 (10‐11), 1386-1402, 2008
|Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer|
JR Whiteaker, H Zhang, L Zhao, P Wang, KS Kelly-Spratt, RG Ivey, ...
Journal of proteome research 6 (10), 3962-3975, 2007
|Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry|
B MacLean, DM Tomazela, SE Abbatiello, S Zhang, JR Whiteaker, ...
Analytical chemistry 82 (24), 10116-10124, 2010
|Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments|
A Rauch, M Bellew, J Eng, M Fitzgibbon, T Holzman, P Hussey, M Igra, ...
Journal of proteome research 5 (1), 112-121, 2006
|Pancreatic tumor pathogenesis reflects the causative genetic lesion|
EP Sandgren, CJ Quaife, AG Paulovich, RD Palmiter, RL Brinster
Proceedings of the National Academy of Sciences 88 (1), 93-97, 1991
|Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels|
P Mertins, F Yang, T Liu, DR Mani, VA Petyuk, MA Gillette, KR Clauser, ...
Molecular & cellular proteomics 13 (7), 1690-1704, 2014