Search Results - "Leprevost, Felipe da Veiga"

Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors by Djomehri, Sabra I., Gonzalez, Maria E., da Veiga Leprevost, Felipe, Tekula, Shilpa R., Chang, Hui-Yin, White, Marissa J., Cimino-Mathews, Ashley, Burman, Boris, Basrur, Venkatesha, Argani, Pedram, Nesvizhskii, Alexey I., Kleer, Celina G.

“…Metaplastic breast carcinoma (MBC) is a highly aggressive form of triple-negative cancer (TNBC), defined by the presence of metaplastic components of spindle,…”
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BioContainers: an open-source and community-driven framework for software standardization by da Veiga Leprevost, Felipe, Grüning, Björn A, Alves Aflitos, Saulo, Röst, Hannes L, Uszkoreit, Julian, Barsnes, Harald, Vaudel, Marc, Moreno, Pablo, Gatto, Laurent, Weber, Jonas, Bai, Mingze, Jimenez, Rafael C, Sachsenberg, Timo, Pfeuffer, Julianus, Vera Alvarez, Roberto, Griss, Johannes, Nesvizhskii, Alexey I, Perez-Riverol, Yasset

“…BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for…”
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Statistical Detection of Differentially Abundant Proteins in Experiments with Repeated Measures Designs and Isobaric Labeling by Huang, Ting, Staniak, Mateusz, Veiga Leprevost, Felipe da, Figueroa-Navedo, Amanda M., Ivanov, Alexander R., Nesvizhskii, Alexey I., Choi, Meena, Vitek, Olga

“…Repeated measures experimental designs, which quantify proteins in biological subjects repeatedly over multiple experimental conditions or times, are commonly…”
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The Ewing Sarcoma Secretome and Its Response to Activation of Wnt/beta-catenin Signaling by Hawkins, Allegra G., Basrur, Venkatesha, da Veiga Leprevost, Felipe, Pedersen, Elisabeth, Sperring, Colin, Nesvizhskii, Alexey I., Lawlor, Elizabeth R.

“…Tumor: tumor microenvironment (TME) interactions are critical for tumor progression and the composition and structure of the local extracellular matrix (ECM)…”
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Unraveling the glycosylated immunopeptidome with HLA-Glyco by Bedran, Georges, Polasky, Daniel A., Hsiao, Yi, Yu, Fengchao, da Veiga Leprevost, Felipe, Alfaro, Javier A., Cieslik, Marcin, Nesvizhskii, Alexey I.

“…Recent interest in targeted therapies has been sparked by the study of MHC-associated peptides (MAPs) that undergo post-translational modifications (PTMs),…”
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The Intrinsically Disordered N Terminus in Atg12 from Yeast Is Necessary for the Functional Structure of the Protein by Popelka, Hana, Lahiri, Vikramjit, Hawkins, Wayne D, da Veiga Leprevost, Felipe, Nesvizhskii, Alexey I, Klionsky, Daniel J

“…The Atg12 protein in yeast is an indispensable polypeptide in the highly conserved ubiquitin-like conjugation system operating in the macroautophagy/autophagy…”
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Differences in Extracellular Vesicle Protein Cargo Are Dependent on Head and Neck Squamous Cell Carcinoma Cell of Origin and Human Papillomavirus Status by Goudsmit, Christine, da Veiga Leprevost, Felipe, Basrur, Venkatesha, Peters, Lila, Nesvizhskii, Alexey, Walline, Heather

“…To identify potential extracellular vesicle (EV) biomarkers in head and neck squamous cell carcinoma (HNSCC), we evaluated EV protein cargo and whole cell…”
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A validated analysis pipeline for mass spectrometry-based vitreous proteomics: new insights into proliferative diabetic retinopathy by Weber, Sarah R, Zhao, Yuanjun, Ma, Jingqun, Gates, Christopher, da Veiga Leprevost, Felipe, Basrur, Venkatesha, Nesvizhskii, Alexey I, Gardner, Thomas W, Sundstrom, Jeffrey M

“…Vitreous is an accessible, information-rich biofluid that has recently been studied as a source of retinal disease-related proteins and pathways. However, the…”
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Recommendations for the packaging and containerizing of bioinformatics software [version 2; peer review: 2 approved, 1 approved with reservations] by Gruening, Bjorn, Sallou, Olivier, Moreno, Pablo, da Veiga Leprevost, Felipe, Ménager, Hervé, Søndergaard, Dan, Röst, Hannes, Sachsenberg, Timo, O'Connor, Brian, Madeira, Fábio, Dominguez Del Angel, Victoria, Crusoe, Michael R, Varma, Susheel, Blankenberg, Daniel, Jimenez, Rafael C, Perez-Riverol, Yasset

“…Software Containers are changing the way scientists and researchers develop, deploy and exchange scientific software. They allow labs of all sizes to easily…”
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Philosopher: a versatile toolkit for shotgun proteomics data analysis by da Veiga Leprevost, Felipe, Haynes, Sarah E., Avtonomov, Dmitry M., Chang, Hui-Yin, Shanmugam, Avinash K., Mellacheruvu, Dattatreya, Kong, Andy T., Nesvizhskii, Alexey I.

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PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results by Geiszler, Daniel J., Kong, Andy T., Avtonomov, Dmitry M., Yu, Fengchao, Leprevost, Felipe da Veiga, Nesvizhskii, Alexey I.

“…Open searching has proven to be an effective strategy for identifying both known and unknown modifications in shotgun proteomics experiments. Rather than being…”
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Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors by Kacen, Assaf, Javitt, Aaron, Kramer, Matthias P., Morgenstern, David, Tsaban, Tomer, Shmueli, Merav D., Teo, Guo Ci, da Veiga Leprevost, Felipe, Barnea, Eilon, Yu, Fengchao, Admon, Arie, Eisenbach, Lea, Samuels, Yardena, Schueler-Furman, Ora, Levin, Yishai, Nesvizhskii, Alexey I., Merbl, Yifat

“…Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but…”
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GRASP55 regulates the unconventional secretion and aggregation of mutant huntingtin by Ahat, Erpan, Bui, Sarah, Zhang, Jianchao, da Veiga Leprevost, Felipe, Sharkey, Lisa, Reid, Whitney, Nesvizhskii, Alexey I., Paulson, Henry L., Wang, Yanzhuang

“…Recent studies demonstrated that the Golgi reassembly stacking proteins (GRASPs), especially GRASP55, regulate Golgi-independent unconventional secretion of…”
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Discovering and linking public omics data sets using the Omics Discovery Index by Perez-Riverol, Yasset, Bai, Mingze, da Veiga Leprevost, Felipe, Squizzato, Silvano, Park, Young Mi, Haug, Kenneth, Carroll, Adam J, Spalding, Dylan, Paschall, Justin, Wang, Mingxun, del-Toro, Noemi, Ternent, Tobias, Zhang, Peng, Buso, Nicola, Bandeira, Nuno, Deutsch, Eric W, Campbell, David S, Beavis, Ronald C, Salek, Reza M, Sarkans, Ugis, Petryszak, Robert, Keays, Maria, Fahy, Eoin, Sud, Manish, Subramaniam, Shankar, Barbera, Ariana, Jiménez, Rafael C, Nesvizhskii, Alexey I, Sansone, Susanna-Assunta, Steinbeck, Christoph, Lopez, Rodrigo, Vizcaíno, Juan A, Ping, Peipei, Hermjakob, Henning

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Proteogenomic data and resources for pan-cancer analysis by Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Birger, Chet, Cao, Song, Chaudhary, Rekha, Cieslik, Marcin, Colaprico, Antonio, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Fenyö, David, Foltz, Steven M., Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Ketchum, Karen A., Klein, Robert J., Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, Nguyen, Ngoc, Oldroyd, Robert, Reva, Boris, Rudnick, Paul, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Storrs, Erik, Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Zhang, Hui, Zhang, Qing, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Robles, Ana I., Payne, Samuel H., Lazar, Alexander J., Paulovich, Amanda G., Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Hiltke, Tara, Yaron, Tomer M., Liu, Wenke, Song, Yizhe, Zhang, Zhen

“…The National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich…”
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Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates by Abbineni, Prabhodh S., Tang, Vi T., da Veiga Leprevost, Felipe, Basrur, Venkatesha, Xiang, Jie, Nesvizhskii, Alexey I., Ginsburg, David

“…Analysis of the full spectrum of secreted proteins in cell culture is complicated by leakage of intracellular proteins from damaged cells. To address this…”
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Crystal-C: A Computational Tool for Refinement of Open Search Results by Chang, Hui-Yin, Kong, Andy T, da Veiga Leprevost, Felipe, Avtonomov, Dmitry M, Haynes, Sarah E, Nesvizhskii, Alexey I

“…Shotgun proteomics using liquid chromatography coupled to mass spectrometry (LC-MS) is commonly used to identify peptides containing post-translational…”
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Integrated stress response plasticity governs normal cell adaptation to chronic stress via the PP2A-TFE3-ATF4 pathway by A Avelar, Rita, Gupta, Riya, Carvette, Grace, da Veiga Leprevost, Felipe, Jasti, Medhasri, Colina, Jose, Teitel, Jessica, Nesvizhskii, Alexey I, O'Connor, Caitlin M, Hatzoglou, Maria, Shenolikar, Shirish, Arvan, Peter, Narla, Goutham, DiFeo, Analisa

“…The integrated stress response (ISR) regulates cell fate during conditions of stress by leveraging the cell's capacity to endure sustainable and efficient…”
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Ten Simple Rules for Taking Advantage of Git and GitHub by Perez-Riverol, Yasset, Gatto, Laurent, Wang, Rui, Sachsenberg, Timo, Uszkoreit, Julian, Leprevost, Felipe da Veiga, Fufezan, Christian, Ternent, Tobias, Eglen, Stephen J, Katz, Daniel S, Pollard, Tom J, Konovalov, Alexander, Flight, Robert M, Blin, Kai, Vizcaíno, Juan Antonio

“…Funding: This study was supported by Wellcome Trust [grant number WT101477MA] (http://www.wellcome.ac.uk/), BBSRC [grant numbers BB/K01997X/1, BB/I00095X/1,…”
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Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics by Burton, Nikolas R., Polasky, Daniel A., Shikwana, Flowreen, Ofori, Samuel, Yan, Tianyang, Geiszler, Daniel J., Veiga Leprevost, Felipe da, Nesvizhskii, Alexey I., Backus, Keriann M.

“…Mass spectrometry-based chemoproteomics has emerged as an enabling technology for functional biology and drug discovery. To address limitations of established…”
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