Prospector Heads: Generalized Feature Attribution for Large Models & DataGautam Machiraju, Alexander Derry, Arjun Desai, Neel Guha, Amir-Hossein Karimi, James Zou … Gautam Machiraju, Alexander Derry, Arjun Desai, Neel Guha, Amir-Hossein Karimi, James Zou, Russ B Altman, Christopher Ré, Parag Mallick ICML'24: Proceedings of the 41st International Conference on Machine Learning; 2024; 34115 - 34144
Building trans-omics evidence: using imaging and 'omics' to characterize cancer profilesArunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu MachirajuPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing; 2018; 23; 377-387
A cross-platform toolkit for mass spectrometry and proteomicsMatthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann … Matthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian Pratt, Jarrett Egertson, Katherine Hoff, Darren Kessner, Natalie Tasman, Nicholas Shulman, Barbara Frewen, Tahmina A Baker, Mi-Youn Brusniak, Christopher Paulse, David Creasy, Lisa Flashner, Kian Kani, Chris Moulding, Sean L Seymour, Lydia M Nuwaysir, Brent Lefebvre, Frank Kuhlmann, Joe Roark, Paape Rainer, Suckau Detlev, Tina Hemenway, Andreas Huhmer, James Langridge, Brian Connolly, Trey Chadick, Krisztina Holly, Josh Eckels, Eric W Deutsch, Robert L Moritz, Jonathan E Katz, David B Agus, Michael MacCoss, David L Tabb, Parag Mallick Nature biotechnology; 2012; 30(10); 918-20
Large-scale analysis of intact single molecule proteoforms of TauIn PressZ. Zhang, J. Joly, V. Budamagunta, B. Norman, M. Jouzi, R. Wang … Z. Zhang, J. Joly, V. Budamagunta, B. Norman, M. Jouzi, R. Wang, S. Guha, J. Sahota, S. Tan, P. Brereton, S. Temple, T. Bertucci, S. Lotz, D. Arnott, J. Lipka, N.J. Pandya, T. Wiederhold, D. Kirkpatrick, A. Rohou, J.E. Schwarz, A. Forton, E.R. Sartori, A. Huhmer, G. Kapp, J. Blanchard, K. Juneau, Parag Mallick Nature Methods; 2026
A straightforward, robust protocol for in-solution digest for bottom-up proteomicsIn PressMichelle Hori, Parag MallickMethods in Molecular Biology; 2026
Using containerized ProteoWizard for data conversionIn PressRavali Adusumilli, Parag MallickMethods in Molecular Biology; 2026
▼20253 papers
A needed nomenclature for nucleosomesMichael-Christopher Keogh, Genevieve Almouzni, Andrew J Andrews, Karim-Jean Armache, Cheryl H Arrowsmith, Sung Hee Baek … Michael-Christopher Keogh, Genevieve Almouzni, Andrew J Andrews, Karim-Jean Armache, Cheryl H Arrowsmith, Sung Hee Baek, Mark T Bedford, Emily Bernstein, Jacques Côté, Yael David, John M Denu, Beat Fierz, Benjamin A Garcia, Karen C Glass, Or Gozani, Kristian Helin, Steven Henikoff, Ole N Jensen, Steven Z Josefowicz, Neil L Kelleher, Tatiana G Kutateladze, Herbert H Lindner, Chao Lu, Karolin Luger, Parag Mallick, Catherine A Musselman, Tom W Muir, Ljiljana Paša-Tolić, Robert Schneider, Xiaobing Shi, Yang Shi, Simone Sidoli, Lloyd M Smith, Jessica K Tyler, Cynthia Wolberger, Jerry L Workman, Brian D Strahl, Nicolas L Young Molecular cell; 2025; 85(19); 3554-3561
Annotation-Free Prediction of Cancer Cells and Glands and Spatial Analysis of Immune CellsPreprintKyeong Joo Jung, Soumya Ghose, Sanghee Cho, Elizabeth McDonough, Chrystal Chadwick, Robert West … Kyeong Joo Jung, Soumya Ghose, Sanghee Cho, Elizabeth McDonough, Chrystal Chadwick, Robert West, James D Brooks, Dongjun Chung, Fiona Ginty, Raghu Machiraju, Parag Mallick bioRxiv : the preprint server for biology; 2025
Integrated Plasma and Tumor Proteomics of Nasopharyngeal Carcinoma in a Moroccan CohortAyman Reffai, Michelle Hori, Ravali Adusumilli, Abel Bermudez, Houssam Haddad, Nezha Tawfiq … Ayman Reffai, Michelle Hori, Ravali Adusumilli, Abel Bermudez, Houssam Haddad, Nezha Tawfiq, Sharon Pitteri, Mohcine Bennani Mechita, Parag Mallick International journal of molecular sciences; 2025; 26(12)
AZGP1 deficiency promotes angiogenesis in prostate cancerRu M Wen, Zhengyuan Qiu, G Edward W Marti, Eric E Peterson, Fernando Jose Garcia Marques, Abel Bermudez … Ru M Wen, Zhengyuan Qiu, G Edward W Marti, Eric E Peterson, Fernando Jose Garcia Marques, Abel Bermudez, Yi Wei, Rosalie Nolley, Nathan Lam, Alex LaPat Polasko, Chun-Lung Chiu, Dalin Zhang, Sanghee Cho, Grigorios Marios Karageorgos, Elizabeth McDonough, Chrystal Chadwick, Fiona Ginty, Kyeong Joo Jung, Raghu Machiraju, Parag Mallick, Laura Crowley, Jonathan R Pollack, Hongjuan Zhao, Sharon J Pitteri, James D Brooks Journal of translational medicine; 2024; 22(1); 383
Prospector Heads: Generalized Feature Attribution for Large Models & Data★ SelectedGautam Machiraju, Alexander Derry, Arjun Desai, Neel Guha, Amir-Hossein Karimi, James Zou … Gautam Machiraju, Alexander Derry, Arjun Desai, Neel Guha, Amir-Hossein Karimi, James Zou, Russ B Altman, Christopher Ré, Parag Mallick ICML'24: Proceedings of the 41st International Conference on Machine Learning; 2024; 34115 - 34144
Prospectors: Leveraging Short Contexts to Mine Salient Objects in High-Dimensional ImageryGautam Machiraju, Arjun Desai, James Zou, Christopher Ré, Parag MallickICML 3rd Workshop on Interpretable Machine Learning in Healthcare (IMLH); 2023
A flexible electronic strain sensor for the real-time monitoring of tumor regressionAlex Abramson, Carmel T Chan, Yasser Khan, Alana Mermin-Bunnell, Naoji Matsuhisa, Robyn Fong … Alex Abramson, Carmel T Chan, Yasser Khan, Alana Mermin-Bunnell, Naoji Matsuhisa, Robyn Fong, Rohan Shad, William Hiesinger, Parag Mallick, Sanjiv Sam Gambhir, Zhenan Bao Science advances; 2022; 8(37); eabn6550
High-density and scalable protein arrays for single-molecule proteomic studiesPreprintTural Aksel, Hongji Qian, Pengyu Hao, Pierre F Indermuhle, Christina Inman, Shubhodeep Paul … Tural Aksel, Hongji Qian, Pengyu Hao, Pierre F Indermuhle, Christina Inman, Shubhodeep Paul, Kevin Chen, Ryan Seghers, Julia K Robinson, Mercedes De Garate, Brittany Nortman, Jiongyi Tan, Steven Hendricks, Subra Sankar, Parag Mallick bioRxiv; 2022
Modular fluorescent nanoparticle DNA probes for detection of peptides and proteinsCassandra M Stawicki, Torri E Rinker, Markus Burns, Sonal S Tonapi, Rachel P Galimidi, Deepthi Anumala … Cassandra M Stawicki, Torri E Rinker, Markus Burns, Sonal S Tonapi, Rachel P Galimidi, Deepthi Anumala, Julia K Robinson, Joshua S Klein, Parag Mallick Scientific reports; 2021; 11(1); 19921
PTR Explorer: An approach to identify and explore Post Transcriptional Regulatory mechanisms using proteogenomicsArunima Srivastava, Michael Sharpnack, Kun Huang, Parag Mallick, Raghu MachirajuPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing; 2020; 25; 475-486
Using information about the influence of nutrient diffusion on tumor evolution to enhance learning of patient trajectoriesHunter Boyce, Parag MallickProceedings of the AAAI Fall 2020 Symposium on Physics-Guided AI to Accelerate Scientific Discovery; 2020
Improving Precursor Selectivity in Data-Independent Acquisition Using Overlapping WindowsDario Amodei, Jarrett Egertson, Brendan X MacLean, Richard Johnson, Gennifer E Merrihew, Austin Keller … Dario Amodei, Jarrett Egertson, Brendan X MacLean, Richard Johnson, Gennifer E Merrihew, Austin Keller, Don Marsh, Olga Vitek, Parag Mallick, Michael J MacCoss Journal of the American Society for Mass Spectrometry; 2019; 30(4); 669-684
Loss of ER retention motif of AGR2 can impact mTORC signaling and promote cancer metastasisKatrin Tiemann, Carolina Garri, Sang Bok Lee, Paymaneh D Malihi, Mincheol Park, Ruth M Alvarez … Katrin Tiemann, Carolina Garri, Sang Bok Lee, Paymaneh D Malihi, Mincheol Park, Ruth M Alvarez, Li Peng Yap, Parag Mallick, Jonathan E Katz, Mitchell E Gross, Kian Kani Oncogene; 2019; 38(16); 3003-3018
A blood biomarker for monitoring response to anti-EGFR therapyNicholas P Hughes, Lingyun Xu, Carsten H Nielsen, Edwin Chang, Sharon S Hori, Arutselvan Natarajan … Nicholas P Hughes, Lingyun Xu, Carsten H Nielsen, Edwin Chang, Sharon S Hori, Arutselvan Natarajan, Samantha Lee, Andreas Kjær, Kian Kani, Shan X Wang, Parag Mallick, Sanjiv Sam Gambhir Cancer biomarkers : section A of Disease markers; 2018; 22(2); 333-344
Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles★ SelectedArunima Srivastava, Chaitanya Kulkarni, Parag Mallick, Kun Huang, Raghu MachirajuPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing; 2018; 23; 377-387
How many human proteoforms are there?Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi, Emily S Boja … Ruedi Aebersold, Jeffrey N Agar, I Jonathan Amster, Mark S Baker, Carolyn R Bertozzi, Emily S Boja, Catherine E Costello, Benjamin F Cravatt, Catherine Fenselau, Benjamin A Garcia, Ying Ge, Jeremy Gunawardena, Ronald C Hendrickson, Paul J Hergenrother, Christian G Huber, Alexander R Ivanov, Ole N Jensen, Michael C Jewett, Neil L Kelleher, Laura L Kiessling, Nevan J Krogan, Martin R Larsen, Joseph A Loo, Rachel R Ogorzalek Loo, Emma Lundberg, Michael J MacCoss, Parag Mallick, Vamsi K Mootha, Milan Mrksich, Tom W Muir, Steven M Patrie, James J Pesavento, Sharon J Pitteri, Henry Rodriguez, Alan Saghatelian, Wendy Sandoval, Hartmut Schlüter, Salvatore Sechi, Sarah A Slavoff, Lloyd M Smith, Michael P Snyder, Paul M Thomas, Mathias Uhlén, Jennifer E Van Eyk, Marc Vidal, David R Walt, Forest M White, Evan R Williams, Therese Wohlschlager, Vicki H Wysocki, Nathan A Yates, Nicolas L Young, Bing Zhang Nature chemical biology; 2018; 14(3); 206-214
Proteogenomic Analysis of Surgically Resected Lung AdenocarcinomaMichael F Sharpnack, Nilini Ranbaduge, Arunima Srivastava, Ferdinando Cerciello, Simona G Codreanu, Daniel C Liebler … Michael F Sharpnack, Nilini Ranbaduge, Arunima Srivastava, Ferdinando Cerciello, Simona G Codreanu, Daniel C Liebler, Celine Mascaux, Wayne O Miles, Robert Morris, Jason E McDermott, James L Sharpnack, Joseph Amann, Christopher A Maher, Raghu Machiraju, Vicki H Wysocki, Ramaswami Govindan, Parag Mallick, Kevin R Coombes, Kun Huang, David P Carbone Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer; 2018; 13(10); 1519-1529
The Predictive Value of Inflammation-Related Peripheral Blood Measurements in Cancer Staging and PrognosisJoanna L Sylman, Annachiara Mitrugno, Michelle Atallah, Garth W Tormoen, Joseph J Shatzel, Samuel Tassi Yunga … Joanna L Sylman, Annachiara Mitrugno, Michelle Atallah, Garth W Tormoen, Joseph J Shatzel, Samuel Tassi Yunga, Todd H Wagner, John T Leppert, Parag Mallick, Owen J T McCarty Frontiers in oncology; 2018; 8; 78
AshwaMAX and Withaferin A inhibits gliomas in cellular and murine orthotopic modelsEdwin Chang, Christoph Pohling, Arutselvan Natarajan, Timothy H Witney, Jasdeep Kaur, Lingyun Xu … Edwin Chang, Christoph Pohling, Arutselvan Natarajan, Timothy H Witney, Jasdeep Kaur, Lingyun Xu, Gayatri Gowrishankar, Aloma L D'Souza, Surya Murty, Sophie Schick, Liyin Chen, Nicholas Wu, Phoo Khaw, Paul Mischel, Taher Abbasi, Shahabuddin Usmani, Parag Mallick, Sanjiv S Gambhir Journal of neuro-oncology; 2016; 126(2); 253-64
Automated Hypothesis Testing with Large Scientific Data RepositoriesYolanda Gil, Daniel Garijo, Varun Ratnakar, Rajiv Mayani, Ravali Adusumilli, Hunter Boyce … Yolanda Gil, Daniel Garijo, Varun Ratnakar, Rajiv Mayani, Ravali Adusumilli, Hunter Boyce, Parag Mallick Proceedings of the Fourth Annual Conference on Advances in Cognitive Systems; 2016
Dual transcript and protein quantification in a massive single cell arraySeung-Min Park, Jae Young Lee, Soongweon Hong, Sang Hun Lee, Ivan K Dimov, Hojae Lee … Seung-Min Park, Jae Young Lee, Soongweon Hong, Sang Hun Lee, Ivan K Dimov, Hojae Lee, Susie Suh, Qiong Pan, Keyu Li, Anna M Wu, Shannon M Mumenthaler, Parag Mallick, Luke P Lee Lab on a chip; 2016; 16(19); 3682-8
Single cell dynamic phenotypingKatherin Patsch, Chi-Li Chiu, Mark Engeln, David B Agus, Parag Mallick, Shannon M Mumenthaler … Katherin Patsch, Chi-Li Chiu, Mark Engeln, David B Agus, Parag Mallick, Shannon M Mumenthaler, Daniel Ruderman Scientific reports; 2016; 6; 34785
A fully human scFv phage display library for rapid antibody fragment reformattingKeyu Li, Kirstin A Zettlitz, Julia Lipianskaya, Yu Zhou, James D Marks, Parag Mallick … Keyu Li, Kirstin A Zettlitz, Julia Lipianskaya, Yu Zhou, James D Marks, Parag Mallick, Robert E Reiter, Anna M Wu Protein engineering, design & selection : PEDS; 2015; 28(10); 307-16
Building high-quality assay libraries for targeted analysis of SWATH MS dataOlga T Schubert, Ludovic C Gillet, Ben C Collins, Pedro Navarro, George Rosenberger, Witold E Wolski … Olga T Schubert, Ludovic C Gillet, Ben C Collins, Pedro Navarro, George Rosenberger, Witold E Wolski, Henry Lam, Dario Amodei, Parag Mallick, Brendan MacLean, Ruedi Aebersold Nature protocols; 2015; 10(3); 426-41
Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experimentsKyle D Bemis, April Harry, Livia S Eberlin, Christina Ferreira, Stephanie M van de Ven, Parag Mallick … Kyle D Bemis, April Harry, Livia S Eberlin, Christina Ferreira, Stephanie M van de Ven, Parag Mallick, Mark Stolowitz, Olga Vitek Bioinformatics (Oxford, England); 2015; 31(14); 2418-20
Neuronal Activity Promotes Glioma Growth through Neuroligin-3 SecretionHumsa S Venkatesh, Tessa B Johung, Viola Caretti, Alyssa Noll, Yujie Tang, Surya Nagaraja … Humsa S Venkatesh, Tessa B Johung, Viola Caretti, Alyssa Noll, Yujie Tang, Surya Nagaraja, Erin M Gibson, Christopher W Mount, Jai Polepalli, Siddhartha S Mitra, Pamelyn J Woo, Robert C Malenka, Hannes Vogel, Markus Bredel, Parag Mallick, Michelle Monje Cell; 2015; 161(4); 803-16
New Horizons in Intact Protein Analysis: Optimization of Top-Down Protein AnalysisSeema Sharma, Parag Mallick, Tanya Stoyanova, Christopher Mullen, Chad Weisbrod, Jesse Canterbury … Seema Sharma, Parag Mallick, Tanya Stoyanova, Christopher Mullen, Chad Weisbrod, Jesse Canterbury, David Horn, Vlad Zabrouskov Chemical & Engineering News; 2015; 12-14
Predictive Modeling of Drug Response in Non-Hodgkin's LymphomaHermann B Frieboes, Bryan R Smith, Zhihui Wang, Masakatsu Kotsuma, Ken Ito, Armin Day … Hermann B Frieboes, Bryan R Smith, Zhihui Wang, Masakatsu Kotsuma, Ken Ito, Armin Day, Benjamin Cahill, Colin Flinders, Shannon M Mumenthaler, Parag Mallick, Eman Simbawa, A S Al-Fhaid, S R Mahmoud, Sanjiv S Gambhir, Vittorio Cristini PloS one; 2015; 10(6); e0129433
Cancer as a Multi-scale Complex Adaptive System (Asia)Parag MallickAssessment of Physical Sciences and Engineering Advances in Life Sciences and Oncology (Aphelion) in Asia; 2014
A physical sciences network characterization of non-tumorigenic and metastatic cellsDavid B Agus, Jenolyn F Alexander, Wadih Arap, Shashanka Ashili, Joseph E Aslan, Robert H Austin … David B Agus, Jenolyn F Alexander, Wadih Arap, Shashanka Ashili, Joseph E Aslan, Robert H Austin, Vadim Backman, Kelly J Bethel, Richard Bonneau, Wei-Chiang Chen, Chira Chen-Tanyolac, Nathan C Choi, Steven A Curley, Matthew Dallas, Dhwanil Damania, Paul C W Davies, Paolo Decuzzi, Laura Dickinson, Luis Estevez-Salmeron, Veronica Estrella, Mauro Ferrari, Claudia Fischbach, Jasmine Foo, Stephanie I Fraley, Christian Frantz, Alexander Fuhrmann, Philippe Gascard, Robert A Gatenby, Yue Geng, Sharon Gerecht, Robert J Gillies, Biana Godin, William M Grady, Alex Greenfield, Courtney Hemphill, Barbara L Hempstead, Abigail Hielscher, W Daniel Hillis, Eric C Holland, Arig Ibrahim-Hashim, Tyler Jacks, Roger H Johnson, Ahyoung Joo, Jonathan E Katz, Laimonas Kelbauskas, Carl Kesselman, Michael R King, Konstantinos Konstantopoulos, Casey M Kraning-Rush, Peter Kuhn, Kevin Kung, Brian Kwee, Johnathon N Lakins, Guillaume Lambert, David Liao, Jonathan D Licht, Jan T Liphardt, Liyu Liu, Mark C Lloyd, Anna Lyubimova, Parag Mallick, John Marko, Owen J T McCarty, Deirdre R Meldrum, Franziska Michor, Shannon M Mumenthaler, Vivek Nandakumar, Thomas V O'Halloran, Steve Oh, Renata Pasqualini, Matthew J Paszek, Kevin G Philips, Christopher S Poultney, Kuldeepsinh Rana, Cynthia A Reinhart-King, Robert Ros, Gregg L Semenza, Patti Senechal, Michael L Shuler, Srimeenakshi Srinivasan, Jack R Staunton, Yolanda Stypula, Hariharan Subramanian, Thea D Tlsty, Garth W Tormoen, Yiider Tseng, Alexander van Oudenaarden, Scott S Verbridge, Jenny C Wan, Valerie M Weaver, Jonathan Widom, Christine Will, Denis Wirtz, Jonathan Wojtkowiak, Pei-Hsun Wu Scientific reports; 2013; 3; 1449
Characterizing deformability and surface friction of cancer cellsSangwon Byun, Sungmin Son, Dario Amodei, Nathan Cermak, Josephine Shaw, Joon Ho Kang … Sangwon Byun, Sungmin Son, Dario Amodei, Nathan Cermak, Josephine Shaw, Joon Ho Kang, Vivian C Hecht, Monte M Winslow, Tyler Jacks, Parag Mallick, Scott R Manalis Proceedings of the National Academy of Sciences of the United States of America; 2013; 110(19); 7580-5
A cross-platform toolkit for mass spectrometry and proteomics★ SelectedMatthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann … Matthew C Chambers, Brendan Maclean, Robert Burke, Dario Amodei, Daniel L Ruderman, Steffen Neumann, Laurent Gatto, Bernd Fischer, Brian Pratt, Jarrett Egertson, Katherine Hoff, Darren Kessner, Natalie Tasman, Nicholas Shulman, Barbara Frewen, Tahmina A Baker, Mi-Youn Brusniak, Christopher Paulse, David Creasy, Lisa Flashner, Kian Kani, Chris Moulding, Sean L Seymour, Lydia M Nuwaysir, Brent Lefebvre, Frank Kuhlmann, Joe Roark, Paape Rainer, Suckau Detlev, Tina Hemenway, Andreas Huhmer, James Langridge, Brian Connolly, Trey Chadick, Krisztina Holly, Josh Eckels, Eric W Deutsch, Robert L Moritz, Jonathan E Katz, David B Agus, Michael MacCoss, David L Tabb, Parag Mallick Nature biotechnology; 2012; 30(10); 918-20
Cancer as a Multi-scale Complex Adaptive SystemParag MallickAssessment of Physical Sciences and Engineering Advances in Life Sciences and Oncology (APHELION) in Europe; 2012; 4-21
Quantitative proteomic profiling identifies protein correlates to EGFR kinase inhibitionKian Kani, Vitor M Faca, Lindsey D Hughes, Wenxuan Zhang, Qiaojun Fang, Babak Shahbaba … Kian Kani, Vitor M Faca, Lindsey D Hughes, Wenxuan Zhang, Qiaojun Fang, Babak Shahbaba, Roland Luethy, Jonathan Erde, Joanna Schmidt, Sharon J Pitteri, Qing Zhang, Jonathan E Katz, Mitchell E Gross, Sylvia K Plevritis, Martin W McIntosh, Anjali Jain, Samir Hanash, David B Agus, Parag Mallick Molecular cancer therapeutics; 2012; 11(5); 1071-81
Semi-Automatically Mapping Structured Sources into the Semantic WebCraig A. Knoblock, Pedro Szekely, Jose Luis Ambite, Aman Goel, Shubham Gupta, Maria Muslea … Craig A. Knoblock, Pedro Szekely, Jose Luis Ambite, Aman Goel, Shubham Gupta, Maria Muslea, Kristina Lerman, Parag Mallick Lecture Notes in Computer Science (The Semantic Web: Research and Applications); 2012; 7295; 375-390
A high-confidence human plasma proteome reference set with estimated concentrations in PeptideAtlasTerry Farrah, Eric W Deutsch, Gilbert S Omenn, David S Campbell, Zhi Sun, Julie A Bletz … Terry Farrah, Eric W Deutsch, Gilbert S Omenn, David S Campbell, Zhi Sun, Julie A Bletz, Parag Mallick, Jonathan E Katz, Johan Malmström, Reto Ossola, Julian D Watts, Biaoyang Lin, Hui Zhang, Robert L Moritz, Ruedi Aebersold Molecular & cellular proteomics : MCP; 2011; 10(9); M110.006353
Applying Multi-Agent Techniques to Cancer ModelingMatthew Brown, Sarah Bowring Epstein, Rajiv Maheswaran, Shannon Mumenthaler, Parag Mallick, Milind TambeProceedings of the Sixth Workshop on Multiagent Sequential Decision Making in Uncertain Domains; 2011
Installation and use of LabKey Server for proteomicsJoshua Eckels, Peter Hussey, Elizabeth K Nelson, Tamra Myers, Adam Rauch, Matthew Bellew … Joshua Eckels, Peter Hussey, Elizabeth K Nelson, Tamra Myers, Adam Rauch, Matthew Bellew, Brian Connolly, Wendy Law, Jimmy K Eng, Jonathan Katz, Martin McIntosh, Parag Mallick, Mark Igra Current protocols in bioinformatics; 2011; Chapter 13; 13.5.1-13.5.25
Interactively Mapping Data Sources into the Semantic WebCA Knoblock, P Szekely, JL Ambite, S Gupta, A Goel, M Muslea … CA Knoblock, P Szekely, JL Ambite, S Gupta, A Goel, M Muslea, K Lerman, P Mallick Proceedings of the Workshop on Linked Science; 2011
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principlesHenry Rodriguez, Mike Snyder, Mathias Uhlén, Phil Andrews, Ronald Beavis, Christoph Borchers … Henry Rodriguez, Mike Snyder, Mathias Uhlén, Phil Andrews, Ronald Beavis, Christoph Borchers, Robert J Chalkley, Sang Yun Cho, Katie Cottingham, Michael Dunn, Tomasz Dylag, Ron Edgar, Peter Hare, Albert J R Heck, Roland F Hirsch, Karen Kennedy, Patrik Kolar, Hans-Joachim Kraus, Parag Mallick, Alexey Nesvizhskii, Peipei Ping, Fredrik Pontén, Liming Yang, John R Yates, Stephen E Stein, Henning Hermjakob, Christopher R Kinsinger, Rolf Apweiler Journal of proteome research; 2009; 8(7); 3689-92
Precursor-ion mass re-estimation improves peptide identification on hybrid instrumentsRoland Luethy, Darren E Kessner, Jonathan E Katz, Brendan Maclean, Robert Grothe, Kian Kani … Roland Luethy, Darren E Kessner, Jonathan E Katz, Brendan Maclean, Robert Grothe, Kian Kani, Vitor Faça, Sharon Pitteri, Samir Hanash, David B Agus, Parag Mallick Journal of proteome research; 2008; 7(9); 4031-9
Computational prediction of proteotypic peptides for quantitative proteomicsParag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin … Parag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin, Jeffrey Ranish, Brian Raught, Robert Schmitt, Thilo Werner, Bernhard Kuster, Ruedi Aebersold Nature biotechnology; 2007; 25(1); 125-31
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlasNichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick … Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold Genome biology; 2006; 7(11); R106
The PeptideAtlas projectFrank Desiere, Eric W Deutsch, Nichole L King, Alexey I Nesvizhskii, Parag Mallick, Jimmy Eng … Frank Desiere, Eric W Deutsch, Nichole L King, Alexey I Nesvizhskii, Parag Mallick, Jimmy Eng, Sharon Chen, James Eddes, Sandra N Loevenich, Ruedi Aebersold Nucleic acids research; 2006; 34(Database issue); D655-8
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometryFrank Desiere, Eric W Deutsch, Alexey I Nesvizhskii, Parag Mallick, Nichole L King, Jimmy K Eng … Frank Desiere, Eric W Deutsch, Alexey I Nesvizhskii, Parag Mallick, Nichole L King, Jimmy K Eng, Alan Aderem, Rose Boyle, Erich Brunner, Samuel Donohoe, Nelson Fausto, Ernst Hafen, Lee Hood, Michael G Katze, Kathleen A Kennedy, Floyd Kregenow, Hookeun Lee, Biaoyang Lin, Dan Martin, Jeffrey A Ranish, David J Rawlings, Lawrence E Samelson, Yuzuru Shiio, Julian D Watts, Bernd Wollscheid, Michael E Wright, Wei Yan, Lihong Yang, Eugene C Yi, Hui Zhang, Ruedi Aebersold Genome biology; 2005; 6(1); R9
Making sense of proteomics: Using bioinformatics to discover a protein's structure, functions and interactionsParag Mallick, Edward MarcotteProteins and Proteomics: A Laboratory Manual (Cold Spring Harbor Laboratory Press); 2002
