The Arabidopsis leaf quantitative atlas: a cellular and subcellular mapping through unified data integration

Autor: Dimitri Tolleter, Edward N. Smith, Clémence Dupont-Thibert, Clarisse Uwizeye, Denis Vile, Pauline Gloaguen, Denis Falconet, Giovanni Finazzi, Yves Vandenbrouck, Gilles Curien

Publikováno v: Quantitative Plant Biology, Vol 5 (2024)

Quantitative analyses and models are required to connect a plant’s cellular organisation with its metabolism. However, quantitative data are often scattered over multiple studies, and finding such data and converting them into useful information is

Externí odkaz: https://doaj.org/article/ebd134d786b846b9879196671656edf8

A high-stringency blueprint of the human proteome

Autor: Subash Adhikari, Edouard C. Nice, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn, Stephen R. Pennington, Young-Ki Paik, Christopher M. Overall, Fernando J. Corrales, Ileana M. Cristea, Jennifer E. Van Eyk, Mathias Uhlén, Cecilia Lindskog, Daniel W. Chan, Amos Bairoch, James C. Waddington, Joshua L. Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah L. Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio C. S. Nogueira, Gilberto B. Domont, Yves Vandenbrouck, Maggie P. Y. Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen M. Schwenk, Emma Lundberg, Nuno Bandeira, Gyorgy Marko-Varga, Susan T. Weintraub, Charles Pineau, Ulrike Kusebauch, Robert L. Moritz, Seong Beom Ahn, Magnus Palmblad, Michael P. Snyder, Ruedi Aebersold, Mark S. Baker

Publikováno v: Nature Communications, Vol 11, Iss 1, Pp 1-16 (2020)

The Human Proteome Project (HPP) was launched in 2010 to enhance accurate annotation of the genome-encoded proteome. Ten years later, the HPP releases its first blueprint of the human proteome, annotating 90% of all known proteins at high-stringency

Externí odkaz: https://doaj.org/article/bb037a5bb053476e9a3946b7578e5277

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Autor: Afgan, Enis, Nekrutenko, Anton, Grüning, Bjórn, Blankenberg, Daniel, Goecks, Jeremy, Schatz, Michael, Ostrovsky, Alexander, Mahmoud, Alexandru, Lonie, Andrew, Syme, Anna, Fouilloux, Anne, Bretaudeau, Anthony, Kumar, Anup, Eschenlauer, Arthur, Desanto, Assunta, Guerler, Aysam, Serrano-Solano, Beatriz, Batut, Bérénice, Grüning, Björn, Langhorst, Bradley, Carr, Bridget, Raubenolt, Bryan, Hyde, Cameron, Bromhead, Catherine, Barnett, Christopher, Royaux, Coline, Gallardo, Cristóbal, Fornika, Daniel, Baker, Dannon, Bouvier, Dave, Clements, Dave, de Lima Morais, David, Tabernero, David Lopez, Lariviere, Delphine, Nasr, Engy, Zambelli, Federico, Heyl, Florian, Psomopoulos, Fotis, Coppens, Frederik, Price, Gareth, Cuccuru, Gianmauro, Corguillé, Gildas Le, von Kuster, Greg, Akbulut, Gulsum Gudukbay, Rasche, Helena, Hotz, Hans-Rudolf, Eguinoa, Ignacio, Makunin, Igor, Ranawaka, Isuru, Taylor, James, Joshi, Jayadev, Hillman-Jackson, Jennifer, Chilton, John, Kamali, Kaivan, Suderman, Keith, Poterlowicz, Krzysztof, Yvan, Le Bras, Lopez-Delisle, Lucille, Sargent, Luke, Bassetti, Madeline, Tangaro, Marco Antonio, van den Beek, Marius, Čech, Martin, Bernt, Matthias, Fahrner, Matthias, Tekman, Mehmet, Föll, Melanie, Crusoe, Michael, Roncoroni, Miguel, Kucher, Natalie, Coraor, Nate, Stoler, Nicholas, Rhodes, Nick, Soranzo, Nicola, Pinter, Niko, Goonasekera, Nuwan, Moreno, Pablo, Videm, Pavankumar, Melanie, Petera, Mandreoli, Pietro, Jagtap, Pratik, Gu, Qiang, Weber, Ralf, Lazarus, Ross, Vorderman, Ruben, Hiltemann, Saskia, Golitsynskiy, Sergey, Garg, Shilpa, Bray, Simon, Gladman, Simon, Leo, Simone, Mehta, Subina, Griffin, Timothy, Jalili, Vahid, Yves, Vandenbrouck, Wen, Victor, Nagampalli, Vijay, Bacon, Wendi, de Koning, Willem, Maier, Wolfgang, Briggs, Peter

Publikováno v: Nucleic Acids Research
Nucleic Acids Research, 2022, 50 (W1), pp.W345-W351. ⟨10.1093/nar/gkac247⟩
Afgan, E, Nekrutenko, A, Grüning, B A, Blankenberg, D, Goecks, J, Schatz, M C, Ostrovsky, A E, Mahmoud, A, Lonie, A J, Syme, A, Fouilloux, A, Bretaudeau, A, Nekrutenko, A, Kumar, A, Eschenlauer, A C, Desanto, A D, Guerler, A, Serrano-Solano, B, Batut, B, Grüning, B A, Langhorst, B W, Carr, B, Raubenolt, B A, Hyde, C J, Bromhead, C J, Barnett, C B, Royaux, C, Gallardo, C, Blankenberg, D, Fornika, D J, Baker, D, Bouvier, D, Clements, D, De Lima Morais, D A, Tabernero, D L, Lariviere, D, Nasr, E, Afgan, E, Zambelli, F, Heyl, F, Psomopoulos, F, Coppens, F, Price, G R, Cuccuru, G, Corguillé, G L, Von Kuster, G, Akbulut, G G, Rasche, H, Hans-Rudolf, H, Eguinoa, I, Makunin, I, Ranawaka, I J, Taylor, J P, Joshi, J, Hillman-Jackson, J, Chilton, J M, Kamali, K, Suderman, K, Poterlowicz, K, Yvan, L B, Lopez-Delisle, L, Sargent, L, Bassetti, M E, Tangaro, M A, Van Den Beek, M, Cech, M, Bernt, M, Fahrner, M, Tekman, M, Föll, M C, Schatz, M C, Crusoe, M R, Roncoroni, M, Kucher, N, Coraor, N, Stoler, N, Rhodes, N, Soranzo, N, Pinter, N, Goonasekera, N A, Moreno, P A, Videm, P, Melanie, P, Mandreoli, P, Jagtap, P D, Gu, Q, Weber, R J M, Lazarus, R, Vorderman, R H P, Hiltemann, S, Golitsynskiy, S, Garg, S, Bray, S A, Gladman, S L, Leo, S, Mehta, S P, Griffin, T J, Jalili, V, Yves, V, Wen, V, Nagampalli, V K, Bacon, W A, De Koning, W, Maier, W & Briggs, P J 2022, ' The Galaxy platform for accessible, reproducible and collaborative biomedical analyses : 2022 update ', Nucleic Acids Research, vol. 50, no. W1, pp. W345-W351 . https://doi.org/10.1093/nar/gkac247
Nucleic Acids Research, 50(W1), W345-W351. Oxford University Press

Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments. A thriving global community continues to use, maintain and contribute

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c391994be394041f6d06e629a94d035a
https://hal.science/hal-04142105

Advances and Utility of the Human Plasma Proteome

Autor: Michal Maes, Natasha Letunica, Krishnan K. Palaniappan, Yves Vandenbrouck, Robert L. Moritz, Gilbert S. Omenn, Sheng-Ce Tao, Virginie Brun, Maria Pernemalm, Vera Ignjatovic, Eric W. Deutsch, Philipp E. Geyer, Xiaobo Yu, Zhi Sun, Jochen M. Schwenk

Publikováno v: Journal of Proteome Research
Journal of Proteome Research, 2021, 20 (12), pp.5241-5263. ⟨10.1021/acs.jproteome.1c00657⟩
J Proteome Res
Journal of Proteome Research, 2021, ⟨10.1021/acs.jproteome.1c00657⟩

International audience; The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::422541cf428b0c595832c8f0626fa079
https://hal.science/hal-04142088

GO Enrichment Analysis for Differential Proteomics Using ProteoRE

Autor: Florence, Combes, Valentin, Loux, Yves, Vandenbrouck

Publikováno v: Methods in molecular biology (Clifton, N.J.). 2361

With the increased simplicity of producing proteomics data, the bottleneck has now shifted to the functional analysis of large lists of proteins to translate this primary level of information into meaningful biological knowledge. Tools implementing s

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::29be5926e2d43db01b5c6d8c79a1caed
https://pubmed.ncbi.nlm.nih.gov/34236662