Search Results - "Eric Deutsch"

GHOST: Graph-based higher-order similarity transformation for classification by Battistella, Enzo, Vakalopoulou, Maria, Paragios, Nikos, Deutsch, Éric

“…Exploring and identifying a good feature representation to describe high-dimensional datasets is a challenge of prime importance. However, plenty of feature…”
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Optimising efficacy and reducing toxicity of anticancer radioimmunotherapy by Deutsch, Eric, Prof, Chargari, Cyrus, Prof, Galluzzi, Lorenzo, PhD, Kroemer, Guido, Prof

“…SummaryImmunotherapy is radically changing the clinical management of patients affected by an increasingly wide array of tumours. However, not all patients…”
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File Formats Commonly Used in Mass Spectrometry Proteomics by Deutsch, Eric W.

“…The application of mass spectrometry (MS) to the analysis of proteomes has enabled the high-throughput identification and abundance measurement of hundreds to…”
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Radiotherapy–immunotherapy combinations – perspectives and challenges by Mondini, Michele, Levy, Antonin, Meziani, Lydia, Milliat, Fabien, Deutsch, Eric

“…Ionizing radiation has historically been used to treat cancer by killing tumour cells, in particular by inducing DNA damage. This view of radiotherapy (RT) as…”
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The ProteomeXchange consortium in 2020: enabling ‘big data’ approaches in proteomics by Deutsch, Eric W, Bandeira, Nuno, Sharma, Vagisha, Perez-Riverol, Yasset, Carver, Jeremy J, Kundu, Deepti J, García-Seisdedos, David, Jarnuczak, Andrew F, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, Hermjakob, Henning, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan A

“…Abstract The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) has standardized data submission and dissemination of…”
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The ProteomeXchange consortium at 10 years: 2023 update by Deutsch, Eric W, Bandeira, Nuno, Perez-Riverol, Yasset, Sharma, Vagisha, Carver, Jeremy J, Mendoza, Luis, Kundu, Deepti J, Wang, Shengbo, Bandla, Chakradhar, Kamatchinathan, Selvakumar, Hewapathirana, Suresh, Pullman, Benjamin S, Wertz, Julie, Sun, Zhi, Kawano, Shin, Okuda, Shujiro, Watanabe, Yu, MacLean, Brendan, MacCoss, Michael J, Zhu, Yunping, Ishihama, Yasushi, Vizcaíno, Juan Antonio

“…Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources…”
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The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition by Deutsch, Eric W, Csordas, Attila, Sun, Zhi, Jarnuczak, Andrew, Perez-Riverol, Yasset, Ternent, Tobias, Campbell, David S, Bernal-Llinares, Manuel, Okuda, Shujiro, Kawano, Shin, Moritz, Robert L, Carver, Jeremy J, Wang, Mingxun, Ishihama, Yasushi, Bandeira, Nuno, Hermjakob, Henning, Vizcaíno, Juan Antonio

“…The ProteomeXchange (PX) Consortium of proteomics resources (http://www.proteomexchange.org) was formally started in 2011 to standardize data submission and…”
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PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows by Deutsch, Eric W, Lam, Henry, Aebersold, Ruedi

“…A crucial part of a successful systems biology experiment is an assay that provides reliable, quantitative measurements for each of the components in the…”
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The PeptideAtlas Project by Deutsch, Eric W

“…PeptideAtlas is a multi-species compendium of peptides observed with tandem mass spectrometry methods. Raw mass spectrometer output files are collected from…”
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ProteomeXchange provides globally coordinated proteomics data submission and dissemination by Vizcaíno, Juan A, Deutsch, Eric W, Wang, Rui, Csordas, Attila, Reisinger, Florian, Ríos, Daniel, Dianes, José A, Sun, Zhi, Farrah, Terry, Bandeira, Nuno, Binz, Pierre-Alain, Xenarios, Ioannis, Eisenacher, Martin, Mayer, Gerhard, Gatto, Laurent, Campos, Alex, Chalkley, Robert J, Kraus, Hans-Joachim, Albar, Juan Pablo, Martinez-Bartolomé, Salvador, Apweiler, Rolf, Omenn, Gilbert S, Martens, Lennart, Jones, Andrew R, Hermjakob, Henning

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Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics by Deutsch, Eric W., Mendoza, Luis, Shteynberg, David, Slagel, Joseph, Sun, Zhi, Moritz, Robert L.

“…Democratization of genomics technologies has enabled the rapid determination of genotypes. More recently the democratization of comprehensive proteomics…”
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Extending Comet for Global Amino Acid Variant and Post‐Translational Modification Analysis Using the PSI Extended FASTA Format by Eng, Jimmy K., Deutsch, Eric W.

“…Protein identification by tandem mass spectrometry sequence database searching is a standard practice in many proteomics laboratories. The de facto standard…”
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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

“…Mass-spectrometry-based proteomics has become an important component of biological research. Numerous proteomics methods have been developed to identify and…”
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Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors by Routy, Bertrand, Le Chatelier, Emmanuelle, Derosa, Lisa, Duong, Connie P M, Alou, Maryam Tidjani, Daillère, Romain, Fluckiger, Aurélie, Messaoudene, Meriem, Rauber, Conrad, Roberti, Maria P, Fidelle, Marine, Flament, Caroline, Poirier-Colame, Vichnou, Opolon, Paule, Klein, Christophe, Iribarren, Kristina, Mondragón, Laura, Jacquelot, Nicolas, Qu, Bo, Ferrere, Gladys, Clémenson, Céline, Mezquita, Laura, Masip, Jordi Remon, Naltet, Charles, Brosseau, Solenn, Kaderbhai, Coureche, Richard, Corentin, Rizvi, Hira, Levenez, Florence, Galleron, Nathalie, Quinquis, Benoit, Pons, Nicolas, Ryffel, Bernhard, Minard-Colin, Véronique, Gonin, Patrick, Soria, Jean-Charles, Deutsch, Eric, Loriot, Yohann, Ghiringhelli, François, Zalcman, Gérard, Goldwasser, François, Escudier, Bernard, Hellmann, Matthew D, Eggermont, Alexander, Raoult, Didier, Albiges, Laurence, Kroemer, Guido, Zitvogel, Laurence

“…Immune checkpoint inhibitors (ICIs) targeting the PD-1/PD-L1 axis induce sustained clinical responses in a sizable minority of cancer patients. We found that…”
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iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates by Shteynberg, David, Deutsch, Eric W., Lam, Henry, Eng, Jimmy K., Sun, Zhi, Tasman, Natalie, Mendoza, Luis, Moritz, Robert L., Aebersold, Ruedi, Nesvizhskii, Alexey I.

“…The combination of tandem mass spectrometry and sequence database searching is the method of choice for the identification of peptides and the mapping of…”
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Combining Results of Multiple Search Engines in Proteomics by Shteynberg, David, Nesvizhskii, Alexey I., Moritz, Robert L., Deutsch, Eric W.

“…A crucial component of the analysis of shotgun proteomics datasets is the search engine, an algorithm that attempts to identify the peptide sequence from the…”
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SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions by Zhang, Nathan H., Deutsch, Eric W.

“…Most tandem mass spectrometry fragmentation spectra have small calibration errors that can lead to suboptimal interpretation and annotation. We developed…”
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Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations by Dinov, Ivo D, Heavner, Ben, Tang, Ming, Glusman, Gustavo, Chard, Kyle, Darcy, Mike, Madduri, Ravi, Pa, Judy, Spino, Cathie, Kesselman, Carl, Foster, Ian, Deutsch, Eric W, Price, Nathan D, Van Horn, John D, Ames, Joseph, Clark, Kristi, Hood, Leroy, Hampstead, Benjamin M, Dauer, William, Toga, Arthur W

“…A unique archive of Big Data on Parkinson's Disease is collected, managed and disseminated by the Parkinson's Progression Markers Initiative (PPMI). The…”
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The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases by Vizcaíno, Juan Antonio, Kubiniok, Peter, Kovalchik, Kevin A., Ma, Qing, Duquette, Jérôme D., Mongrain, Ian, Deutsch, Eric W., Peters, Bjoern, Sette, Alessandro, Sirois, Isabelle, Caron, Etienne

“…Immunopeptidomics is a rapidly evolving field that is catalyzed by neoantigen discovery and cancer immunotherapy. Emulating the path of other omic disciplines,…”
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Brachytherapy: An overview for clinicians by Chargari, Cyrus, Deutsch, Eric, Blanchard, Pierre, Gouy, Sebastien, Martelli, Hélène, Guérin, Florent, Dumas, Isabelle, Bossi, Alberto, Morice, Philippe, Viswanathan, Akila N., Haie‐Meder, Christine

“…Brachytherapy is a specific form of radiotherapy consisting of the precise placement of radioactive sources directly into or next to the tumor. This technique…”
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