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Title
Quantitative proteome responses to oncolytic reovirus in GM-CSF- and M-CSF-differentiated bone marrow-derived cells
Source
Journal of Proteome Research
Date
2020
Author
Giacomantonio, Michael A.; Sterea, Andra M.; Kim, Youra; Paulo, Joao A.; Clements, Derek R.; Kennedy, Barry E.; Bydoun, Moamen J.; Shi, Ge; Waisman, David M.; Gygi, Steven P.; Giacomantonio, Carman A.; Murphy, J. Patrick; Gujar, Shashi
Genre
Journal Article
Abstract
The efficacy of oncolytic viruses (OVs), such as reovirus, is dictated by host immune responses, including those mediated by the pro- versus anti...
Volume
19
Issue
2
Start Page
708
DOI
10.1021/acs.jproteome.9b00583
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Title
Improving MHC-I ligand identification by incorporating targeted searches of mass spectrometry data
Source
Bioinformatics for cancer immunotherapy
Date
2020
Author
Prathyusha, Konda; Murphy, J Patrick; Gujar, Shashi
Genre
Book, Section
Abstract
Effective immunotherapies rely on specific activation of immune cells. Class I major histocompatibility complex (MHC-I) bound peptide ligands play...
Start Page
161
DOI
10.1007/978-1-0716-0327-7_11
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Title
Multiplexed relative quantitation with isobaric tagging mass spectrometry reveals class I major histocompatibility complex ligand dynamics in response to doxorubicin
Source
Analytical Chemistry
Date
2019
Author
Murphy, J. Patrick; Yu, Qijia; Konda, Prathyusha; Paulo, Joao A.; Jedrychowski, Mark P.; Kowalewski, Daniel J.; Schuster, Heiko; Kim, Youra; Clements, Derek; Jain, Aditya; Stevanovic, Stefan; Gygi, Steven P.; Mancias, Joseph D.; Gujar, Shashi
Genre
Journal Article
Abstract
MHC-I peptides are intracellular-cleaved peptides, usually 8–11 amino acids in length, which are presented on the cell surface and facilitate CD8+...
Volume
91
Issue
8
Start Page
5106
DOI
10.1021/acs.analchem.8b05616
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Title
TAp73 modifies metabolism and positively regulates growth of cancer stem–like cells in a redox-sensitive manner
Source
Clinical Cancer Research
Date
2019
Author
Sharif, Tanveer; Dai, Cathleen; Martell, Emma; Ghassemi-Rad, Mohammad Saleh; Hanes, Mark Robert; Murphy, Patrick J.; Kennedy, Barry E.; Venugopal, Chitra; Subapanditha, Minomi; Giacomantonio, Carman A.; Marcato, Paola; Singh, Sheila K.; Gujar, Shashi
Genre
Journal Article
Abstract
Purpose: Stem-like cancer cells, with characteristic self-renewal abilities, remain highly refractory to various clinical interventions. As such,...
Volume
25
Issue
6
Start Page
2001
DOI
10.1158/1078-0432.CCR-17-3177
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Title
Enhancing mass spectrometry-based MHC-I peptide identification through a targeted database search approach
Source
Immunoproteomics
Date
2019
Author
Prathyusha, Konda; Murphy, J. Patrick; Nielsen, Morten; Gujar, Shashi
Genre
Book, Section
Abstract
MHC-bound peptide ligands dictate the activation and specificity of CD8+ T- cells-based and thus are important for devising T-cell immunotherapies....
Start Page
301
DOI
10.1007/978-1-4939-9597-4_19
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Title
Unraveling metabolite function with disruptive new tools in metabolomics and proteomics
Date
2019
Author
Murphy, JP
Genre
Invited talk
Publisher
University of Prince Edward Island Faculty of Science Environmental and Human Biology Seminar Series
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Title
HDAC6 differentially regulates autophagy in stem-like versus differentiated cancer cells
Source
Autophagy
Date
2019
Author
Sharif, Tanveer; Martell, Emma; Dai, Cathleen; Ghassemi-Rad, Mohammad Saleh; Hanes, Mark Robert; Murphy, Patrick J.; Margam, Nandini N.; Parmar, Hirendrasinh B.; Giacomantonio, Carman A.; Duncan, Roy; Lee, Patrick W.K.; Gujar, Shashi
Genre
Journal Article
Abstract
Cancer stem-like cells (CSCs), a small population of pluripotent cells residing within heterogeneous tumor mass, remain highly resistant to various...
Volume
15
Issue
4
Start Page
686
DOI
10.1080/15548627.2018.1548547
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Title
Therapy-induced MHC I ligands shape neo-antitumor CD8 T cell responses during oncolytic virus-based cancer immunotherapy
Source
Journal of Proteome Research
Date
2019
Author
Murphy, J. Patrick; Kim, Youra; Clements, Derek R.; Konda, Prathyusha; Schuster, Heiko; Kowalewski, Daniel J.; Paulo, Joao A.; Cohen, Alejandro M.; Stevanovic, Stefan; Gygi, Steven P.; Gujar, Shashi
Genre
Journal Article
Abstract
Oncolytic viruses (OVs), known for their cancer-killing characteristics, also overturn tumor-associated defects in antigen presentation through the...
Volume
18
Issue
6
Start Page
2666
DOI
10.1021/acs.jproteome.9b00173
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Title
Inhibition of pyruvate dehydrogenase kinase enhances the antitumor efficacy of oncolytic reovirus
Source
Cancer Research
Date
2019
Author
Kennedy, Barry E.; Murphy, John Patrick; Clements, Derek R.; Konda, Prathyusha; Holay, Namit; Kim, Youra; Pathak, Gopal P.; Giacomantonio, Michael A.; Hiani, Yassine El; Gujar, Shashi
Genre
Journal Article
Abstract
Oncolytic viruses (OV) such as reovirus preferentially infect and kill cancer cells. Thus, the mechanisms that dictate the susceptibility of cancer...
Volume
79
Issue
15
Start Page
3824
DOI
10.1158/0008-5472.CAN-18-2414
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Bookmarks:
Title
Improving MHC-I ligand identifications from LC-MS/MS data by incorporating allelic peptide motifs
Source
PROTEOMICS
Date
2019
Author
Konda, Prathyusha; Murphy, J. Patrick; Gujar, Shashi
Genre
Journal Article
Abstract
MHC class I (MHC-I)-bound ligands play a pivotal role in CD8 T cell immunity and are hence of major interest in understanding and designing...
Volume
19
Issue
5
Start Page
1800458
DOI
10.1002/pmic.201800458
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Title
Integrated proteome and HLA peptidome quantitation with tandem mass tags
Date
2018
Author
Murphy, JP; Konda, P; Paulo, JA; Schuster, H; Kowalewski, DJ; Kim, Y; Celements, D; Giacomantonio, M; Stevanovic, S; Gygi, SP; Gujar, S
Genre
Poster presentation
Publisher
66th Conference on Mass Spectrometry and Allied Topics
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Bookmarks:
Title
Integrated proteome and HLA peptidome quantitation with tandem mass tags
Date
2018
Author
Murphy, JP; Konda, P; Paulo, JA; Schuster, H; Kowalewski, DJ; Kim, Y; Clements, D; Giacomantonio, M; Stevanovic, S; Gygi, SP
Genre
Invited talk
Publisher
17th Human Proteome Organization World Congress
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Bookmarks:
Title
Little fish, big pond, or little fish, small pond
Subtitle
Postdoctoral experiences across different laboratories and institutions
Date
2018
Author
Murphy, JP
Genre
Invited talk
Publisher
Beatrice Hunter Cancer Research Institute Annual Workshop
Full Text
Bookmarks:
Title
The NAD+ salvage pathway supports PHGDH-driven serine biosynthesis
Source
Cell Reports
Date
2018
Author
Murphy, J. Patrick; Giacomantonio, Michael A.; Paulo, Joao A.; Everley, Robert A.; Kennedy, Barry E.; Pathak, Gopal P.; Clements, Derek R.; Kim, Youra; Dai, Cathleen; Sharif, Tanveer; Gygi, Steven P.; Gujar, Shashi
Genre
Journal Article
Abstract
NAD+ is a key metabolic redox cofactor that is regenerated from nicotinamide through the NAD+ salvage pathway. Here, we find that inhibiting the...
Volume
24
Issue
9
Start Page
2381
DOI
10.1016/j.celrep.2018.07.086
Publication Status
PUBLISHED
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Title
RTN4 knockdown dysregulates the AKT pathway, destabilizes the cytoskeleton, and enhances paclitaxel-induced cytotoxicity in cancers
Source
Molecular Therapy
Date
2018
Author
Pathak, Gopal P.; Shah, Rashmi; Kennedy, Barry E.; Murphy, J. Patrick; Clements, Derek; Konda, Prathyusha; Giacomantonio, Michael; Xu, Zhaolin; Schlaepfer, Isabel R.; Gujar, Shashi
Genre
Journal Article
Abstract
Reticulon-4 (RTN4), commonly known as a neurite outgrowth inhibitor (Nogo), is emerging as an important player in human cancers. Clinically, we...
Volume
26
Issue
8
Start Page
2019
DOI
10.1016/j.ymthe.2018.05.026
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Title
The Warburg Effect and mass spectrometry-based proteomic analysis
Source
Cancer Genomics & Proteomics
Date
2017
Author
Murphy, J.P.; Côté, P.D.
Genre
Journal Article
Abstract
Compared to normal cells, cancer cells have a unique metabolism by performing lactic acid fermentation in the presence of oxygen, also known as the...
Volume
14
Issue
4
Start Page
211
DOI
10.21873/cgp.20032
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Bookmarks:
Title
MHC-I ligand discovery using targeted database searches of mass spectrometry data
Subtitle
Implications for T-cell immunotherapies
Source
Journal of Proteome Research
Date
2017
Author
Murphy, J. Patrick; Konda, Prathyusha; Kowalewski, Daniel J.; Schuster, Heiko; Clements, Derek; Kim, Youra; Cohen, Alejandro M.; Sharif, Tanveer; Nielsen, Morten; Stevanovic, Stefan; Lee, Patrick W.; Gujar, Shashi
Genre
Journal Article
Abstract
Class I major histocompatibility complex (MHC-I)-bound peptide ligands dictate the activation and specificity of CD8+ T cells and thus are...
Volume
16
Issue
4
Start Page
1806
DOI
10.1021/acs.jproteome.6b00971
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Bookmarks:
Title
Autophagic homeostasis is required for the pluripotency of cancer stem cells
Source
Autophagy
Date
2017
Author
Sharif, Tanveer; Martell, Emma; Dai, Cathleen; Kennedy, Barry E.; Murphy, Patrick; Clements, Derek R.; Kim, Youra; Lee, Patrick W. K.; Gujar, Shashi A.
Genre
Journal Article
Abstract
Pluripotency is an important feature of cancer stem cells (CSCs) that contributes to self-renewal and chemoresistance. The maintenance of...
Volume
13
Issue
2
Start Page
264
DOI
10.1080/15548627.2016.1260808
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Bookmarks:
Title
Quantitative temporal in vivo proteomics deciphers the transition of virus-driven myeloid cells into M2 macrophages
Source
Journal of Proteome Research
Date
2017
Author
Clements, Derek R.; Murphy, John Patrick; Sterea, Andra; Kennedy, Barry E.; Kim, Youra; Helson, Erin; Almasi, Shekoufeh; Holay, Namit; Konda, Prathyusha; Paulo, Joao A.; Sharif, Tanveer; Lee, Patrick W.; Weekes, Michael P.; Gygi, Steven P.; Gujar, Shashi
Genre
Journal Article
Abstract
Myeloid cells play a central role in the context of viral eradication, yet precisely how these cells differentiate throughout the course of acute...
Volume
16
Issue
9
Start Page
3391
DOI
10.1021/acs.jproteome.7b00425
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Title
Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1
Source
Oncotarget
Date
2016
Author
Coyle, Krysta M.; Murphy, J. Patrick; Vidovic, Dejan; Vaghar-Kashani, Ahmad; Dean, Cheryl A.; Sultan, Mohammad; Clements, Derek; Wallace, Melissa; Thomas, Margaret L.; Hundert, Amos; Giacomantonio, Carman A.; Helyer, Lucy; Gujar, Shashi A.; Lee, Patrick W.K.; Weaver, Ian C.G.; Marcato, Paola
Genre
Journal Article
Abstract
Breast cancer subtyping, based on the expression of hormone receptors and other genes, can determine patient prognosis and potential options for...
Volume
7
Issue
28
Start Page
44096
DOI
10.18632/oncotarget.9858

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