ProteoWizard: open source software for rapid proteomics tools development

by Kessner, Darren, Chambers, Matt, Burke, Robert, Agus, David, Mallick, Parag
Published 2008

Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach

by Strong, Michael, Mallick, Parag, Pellegrini, Matteo, Thompson, Michael J, Eisenberg, David
Published 2003

Simulation of the Protein-Shedding Kinetics of a Fully Vascularized Tumor

by Frieboes, Hermann B., Curtis, Louis T., Wu, Min, Kani, Kian, Mallick, Parag
Published 2015

Evolutionary Modeling of Combination Treatment Strategies To Overcome Resistance to Tyrosine Kinase Inhibitors in Non-Small Cell Lung Cancer

by Mumenthaler, Shannon M., Foo, Jasmine, Leder, Kevin, Choi, Nathan C., Agus, David B., Pao, William, Mallick, Parag, Michor, Franziska
Published 2011

Single cell dynamic phenotyping

by Patsch, Katherin, Chiu, Chi-Li, Engeln, Mark, Agus, David B., Mallick, Parag, Mumenthaler, Shannon M., Ruderman, Daniel
Published 2016

Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments

by Bemis, Kyle D., Harry, April, Eberlin, Livia S., Ferreira, Christina, van de Ven, Stephanie M., Mallick, Parag, Stolowitz, Mark, Vitek, Olga
Published 2015

Impact of Protein Stability, Cellular Localization, and Abundance on Proteomic Detection of Tumor-Derived Proteins in Plasma

by Fang, Qiaojun, Kani, Kian, Faca, Vitor M., Zhang, Wenxuan, Zhang, Qing, Jain, Anjali, Hanash, Sam, Agus, David B., McIntosh, Martin W., Mallick, Parag
Published 2011

The PeptideAtlas project

by Desiere, Frank, Deutsch, Eric W., King, Nichole L., Nesvizhskii, Alexey I., Mallick, Parag, Eng, Jimmy, Chen, Sharon, Eddes, James, Loevenich, Sandra N., Aebersold, Ruedi
Published 2006

Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma

by Flinders, Colin, Lam, Larry, Rubbi, Liudmilla, Ferrari, Roberto, Fitz-Gibbon, Sorel, Chen, Pao-Yang, Thompson, Michael, Christofk, Heather, B Agus, David, Ruderman, Daniel, Mallick, Parag, Pellegrini, Matteo
Published 2016

Probabilistic Segmentation of Mass Spectrometry (MS) Images Helps Select Important Ions and Characterize Confidence in the Resulting Segments*

by Bemis, Kyle D., Harry, April, Eberlin, Livia S., Ferreira, Christina R., van de Ven, Stephanie M., Mallick, Parag, Stolowitz, Mark, Vitek, Olga
Published 2016

The Impact of Microenvironmental Heterogeneity on the Evolution of Drug Resistance in Cancer Cells

by Mumenthaler, Shannon M, Foo, Jasmine, Choi, Nathan C, Heise, Nicholas, Leder, Kevin, Agus, David B, Pao, William, Michor, Franziska, Mallick, Parag
Published 2015

A high-content image-based method for quantitatively studying context-dependent cell population dynamics

by Garvey, Colleen M., Spiller, Erin, Lindsay, Danika, Chiang, Chun-Te, Choi, Nathan C., Agus, David B., Mallick, Parag, Foo, Jasmine, Mumenthaler, Shannon M.
Published 2016

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

by King, Nichole L, Deutsch, Eric W, Ranish, Jeffrey A, Nesvizhskii, Alexey I, Eddes, James S, Mallick, Parag, Eng, Jimmy, Desiere, Frank, Flory, Mark, Martin, Daniel B, Kim, Bong, Lee, Hookeun, Raught, Brian, Aebersold, Ruedi
Published 2006

Predictive Modeling of Drug Response in Non-Hodgkin’s Lymphoma

by Frieboes, Hermann B., Smith, Bryan R., Wang, Zhihui, Kotsuma, Masakatsu, Ito, Ken, Day, Armin, Cahill, Benjamin, Flinders, Colin, Mumenthaler, Shannon M., Mallick, Parag, Simbawa, Eman, AL-Fhaid, A. S., Mahmoud, S. R., Gambhir, Sanjiv S., Cristini, Vittorio
Published 2015

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

by Desiere, Frank, Deutsch, Eric W, Nesvizhskii, Alexey I, Mallick, Parag, King, Nichole L, Eng, Jimmy K, Aderem, Alan, Boyle, Rose, Brunner, Erich, Donohoe, Samuel, Fausto, Nelson, Hafen, Ernst, Hood, Lee, Katze, Michael G, Kennedy, Kathleen A, Kregenow, Floyd, Lee, Hookeun, Lin, Biaoyang, Martin, Dan, Ranish, Jeffrey A, Rawlings, David J, Samelson, Lawrence E, Shiio, Yuzuru, Watts, Julian D, Wollscheid, Bernd, Wright, Michael E, Yan, Wei, Yang, Lihong, Yi, Eugene C, Zhang, Hui, Aebersold, Ruedi
Published 2005

A Cross-platform Toolkit for Mass Spectrometry and Proteomics

by Chambers, Matthew C., Maclean, Brendan, Burke, Robert, Amodei, Dario, Ruderman, Daniel L, Neumann, Steffen, Gatto, Laurent, Fischer, Bernd, Pratt, Brian, Egertson, Jarrett, Hoff, Katherine, Kessner, Darren, Tasman, Natalie, Shulman, Nicholas, Frewen, Barbara, Baker, Tahmina A., Brusniak, Mi-Youn, Paulse, Christopher, Creasy, David, Flashner, Lisa, Kani, Kian, Moulding, Chris, Seymour, Sean L., Nuwaysir, Lydia M., Lefebvre, Brent, Kuhlmann, Frank, Roark, Joe, Rainer, Paape, Detlev, Suckau, Hemenway, Tina, Huhmer, Andreas, Langridge, James, Connolly, Brian, Chadick, Trey, Holly, Krisztina, Eckels, Josh, Deutsch, Eric W., Moritz, Robert L, Katz, Jonathan E., Agus, David B., MacCoss, Michael, Tabb, David L., Mallick, Parag
Published 2012