Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies von Lazar, Cosmin, Gatto, Laurent, Ferro, Myriam, Bruley, Christophe, Burger, Thomas

Volltext

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation von Gatto, Laurent, Lilley, Kathryn S.

Volltext

BioContainers: an open-source and community-driven framework for software standardization von 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

Volltext

ProteomeXchange provides globally coordinated proteomics data submission and dissemination von 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

Volltext

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics von Geladaki, Aikaterini, Kočevar Britovšek, Nina, Breckels, Lisa M., Smith, Tom S., Vennard, Owen L., Mulvey, Claire M., Crook, Oliver M., Gatto, Laurent, Lilley, Kathryn S.

Volltext

A cross-platform toolkit for mass spectrometry and proteomics von 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

Volltext

A draft map of the mouse pluripotent stem cell spatial proteome von Christoforou, Andy, Mulvey, Claire M., Breckels, Lisa M., Geladaki, Aikaterini, Hurrell, Tracey, Hayward, Penelope C., Naake, Thomas, Gatto, Laurent, Viner, Rosa, Arias, Alfonso Martinez, Lilley, Kathryn S.

Volltext

Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic von Lizcano-Perret, Belén, Lardinois, Cécile, Wavreil, Fanny, Hauchamps, Philippe, Herinckx, Gaëtan, Sorgeloos, Frédéric, Vertommen, Didier, Gatto, Laurent, Michiels, Thomas

Volltext

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments von Gatto, Laurent, Aebersold, Ruedi, Cox, Juergen, Demichev, Vadim, Derks, Jason, Emmott, Edward, Franks, Alexander M., Ivanov, Alexander R., Kelly, Ryan T., Khoury, Luke, Leduc, Andrew, MacCoss, Michael J., Nemes, Peter, Perlman, David H., Petelski, Aleksandra A., Rose, Christopher M., Schoof, Erwin M., Van Eyk, Jennifer, Vanderaa, Christophe, Yates, John R., Slavov, Nikolai

Volltext

CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building and visualizing automated pre-processing pipelines for flow cytometry data von Hauchamps, Philippe, Bayat, Babak, Delandre, Simon, Hamrouni, Mehdi, Toussaint, Marie, Temmerman, Stephane, Lin, Dan, Gatto, Laurent

Volltext

Molecular networks in Network Medicine: Development and applications von Silverman, Edwin K., Schmidt, Harald H. H. W., Anastasiadou, Eleni, Altucci, Lucia, Angelini, Marco, Badimon, Lina, Balligand, Jean‐Luc, Benincasa, Giuditta, Capasso, Giovambattista, Conte, Federica, Di Costanzo, Antonella, Farina, Lorenzo, Fiscon, Giulia, Gatto, Laurent, Gentili, Michele, Loscalzo, Joseph, Marchese, Cinzia, Napoli, Claudio, Paci, Paola, Petti, Manuela, Quackenbush, John, Tieri, Paolo, Viggiano, Davide, Vilahur, Gemma, Glass, Kimberly, Baumbach, Jan

Volltext

Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism von Baers, Laura L, Breckels, Lisa M, Mills, Lauren A, Gatto, Laurent, Deery, Michael J, Stevens, Tim J, Howe, Christopher J, Lilley, Kathryn S, Lea-Smith, David J

Volltext

Ten Simple Rules for Taking Advantage of Git and GitHub von 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

Volltext

A Bayesian mixture modelling approach for spatial proteomics von Crook, Oliver M, Mulvey, Claire M, Kirk, Paul D W, Lilley, Kathryn S, Gatto, Laurent

Volltext

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line von Mulvey, Claire M., Breckels, Lisa M., Crook, Oliver M., Sanders, David J., Ribeiro, Andre L. R., Geladaki, Aikaterini, Christoforou, Andy, Britovšek, Nina Kočevar, Hurrell, Tracey, Deery, Michael J., Gatto, Laurent, Smith, Andrew M., Lilley, Kathryn S.

Volltext

Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant von Gatto, Laurent

Volltext

Exploiting the DepMap cancer dependency data using the depmap R package [version 1; peer review: 2 approved with reservations] von Killian, Theo, Gatto, Laurent

Volltext

Urine metabolomics links dysregulation of the tryptophan-kynurenine pathway to inflammation and severity of COVID-19 von Dewulf, Joseph P., Martin, Manon, Marie, Sandrine, Oguz, Fabie, Belkhir, Leila, De Greef, Julien, Yombi, Jean Cyr, Wittebole, Xavier, Laterre, Pierre-François, Jadoul, Michel, Gatto, Laurent, Bommer, Guido T., Morelle, Johann

Volltext

Post-Hypoglycemic hyperglycemia are highly relevant markers for stratification of glycemic variability and partial remission status of pediatric patients with new-onset type 1 diab... von Harvengt, Antoine A, Polle, Olivier G, Martin, Manon, van Maanen, Aline, Gatto, Laurent, Lysy, Philippe A

Volltext

Plasma proteomics in children with new-onset type 1 diabetes identifies new potential biomarkers of partial remission von Pollé, Olivier G., Pyr dit Ruys, Sébastien, Lemmer, Julie, Hubinon, Camille, Martin, Manon, Herinckx, Gaetan, Gatto, Laurent, Vertommen, Didier, Lysy, Philippe A.

Volltext