High-throughput identification of calcium-regulated proteins across diverse proteomes

Authors: Locke, Timothy M. ^{1, 6}, Fields, Rose ^{2, 3, 4, 6}, Gizinski, Hayden ¹, Otto, George M. ¹, MacEwen, Melissa J.S. ¹, Rusnac, Domnita-Valeria ^{1, 5}, He, Peixian ¹, Shechner, David M. ¹, McGann, Chris D. ^{2, 3, 4}, Berg, Matthew D. ², Villen, Judit ², Sancak, Yasemin ^{1, ∗}, Schweppe, Devin K. ^{2, 3, 4, 7, ∗∗}

Source: In Cell Reports 26 November 2024 43(11)

Automated Enrichment of Phosphotyrosine Peptides for High-Throughput Proteomics

Authors: Chang, Alexis, Leutert, Mario, Rodriguez-Mias, Ricard A., Villén, Judit

Source: Journal of proteome research. 22(6):1868-1880

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632774667&indx=1&recIds=ETOCRN632774667

A Python Package for the Localization of Protein Modifications in Mass Spectrometry Data

Authors: Barente, Anthony S., Villén, Judit

Source: Journal of proteome research. 22(2):501-507

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631750162&indx=1&recIds=ETOCRN631750162

Coisolation of Peptide Pairs for Peptide Identification and MS/MS-Based Quantification

Authors: Smith, Ian R., Eng, Jimmy K., Barente, Anthony S., Hogrebe, Alexander, Llovet, Ariadna, Rodriguez-Mias, Ricard A., Villén, Judit

Source: Analytical chemistry. 94(44):15198-15206

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN630656757&indx=1&recIds=ETOCRN630656757

A function of TPL/TBL1-type corepressors is to nucleate the assembly of the preinitiation complex.

Authors: Leydon, Alexander R.¹, Downing, Benjamin¹, Sanchez, Janet Solano¹, Loll-Krippleber, Raphael², Belliveau, Nathan M.¹, Rodriguez-Mias, Ricard A.³, Bauer, Andrew J.¹, Watson, Isabella J.¹, Bae, Lena¹, Villén, Judit³, Brown, Grant W.², Nemhauser, Jennifer L.¹, jn7@uw.edu

Source: Journal of Cell Biology; 2/3/2025, Vol. 224 Issue 2, p1-22, 29p

Preventing inappropriate signals pre-and post-ligand perception by a toggle switch mechanism of ERECTA.

Authors: Liangliang Chen, Maes, Michal, Cochran, Alicia M., Avila, Julian R., Derbyshire, Paul, Sklenar, Jan, Haas, Kelsey M., Villén, Judit, Menke, Frank L. H., Torii, Keiko U.

Source: Proceedings of the National Academy of Sciences of the United States of America; 1/28/2025, Vol. 122 Issue 4, p1-10, 34p

Subject Terms: PEPTIDE receptors, PEPTIDES, LIGANDS (Biochemistry), SOMATOTROPIN, KINASE inhibitors

Decoding Post-Translational Modification Crosstalk With Proteomics

Authors: Leutert, Mario, Entwisle, Samuel W., Villén, Judit

Source: In Molecular & Cellular Proteomics 2021 20

DIAmeter: matching peptides to data-independent acquisition mass spectrometry data

Authors: Lu, Yang Young, Bilmes, Jeff, Rodriguez-Mias, Ricard A, Villén, Judit, Noble, William Stafford

Source: Bioinformatics. 37(1):i434-i442

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100125776895.0x000001&indx=1&recIds=ETOCvdc_100125776895.0x000001

The fitness cost of spurious phosphorylation.

Authors: Bradley, David, Hogrebe, Alexander, Dandage, Rohan, Dubé, Alexandre K, Leutert, Mario, Dionne, Ugo, Chang, Alexis, Villén, Judit, Landry, Christian R

Source: EMBO Journal; Oct2024, Vol. 43 Issue 20, p4720-4751, 32p

Subject Terms: PROTEIN kinases, PROTEIN-tyrosine kinases, STRUCTURAL bioinformatics, PHOSPHOTYROSINE, CYTOSKELETAL proteins

Proteome and Phosphoproteome Analysis of Brown Adipocytes Reveals That RICTOR Loss Dampens Global Insulin/AKT Signaling

Authors: Entwisle, Samuel W. ^{‡, §, **}, Martinez Calejman, Camila ^{¶, **}, Valente, Anthony S. ^§, Lawrence, Robert T. ^{‡, §, ‡‡}, Hung, Chien-Min ^{¶, §§}, Guertin, David A. ^{¶, ‖}, Villén, Judit ^{‡, §, ¶¶}

Source: In Molecular & Cellular Proteomics July 2020 19(7):1104-1119

Thesaurus: quantifying phosphopeptide positional isomers

Authors: Searle, Brian, Lawrence, Robert, MacCoss, Michael, Villén, Judit

Source: Nature methods. 16(8):703-706

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100187168427.0x000001&indx=1&recIds=ETOCvdc_100187168427.0x000001

IsobaricQuant enables cross‐platform quantification, visualization, and filtering of isobarically‐labeled peptides

Authors: Hogrebe, Alexander, Hess, Kyle N., Llovet, Ariadna, Ramos, Y. Julian, Barente, Anthony S., Hernandez‐Portugues, Daniel, Smith, Ian R., Rodríguez‐Mias, Ricard A., Villén, Judit

Source: Proteomics. 22(19-20)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100163074611.0x000001&indx=1&recIds=ETOCvdc_100163074611.0x000001

Large-Scale Characterization of HeLa Cell Nuclear Phosphoproteins

Authors: Beausoleil, Sean A., Jedrychowski, Mark, Schwartz, Daniel, Elias, Joshua E., Villén, Judit, Li, Jiaxu, Cohn, Martin A., Cantley, Lewis C., Gygi, Steven P.

Source: Proceedings of the National Academy of Sciences of the United States of America, 2004 Aug . 101(33), 12130-12135.

Access URL: https://www.jstor.org/stable/3373102

The phosphatidic acid–binding, polybasic domain is responsible for the differences in the phosphoregulation of lipins 1 and 3

Authors: Boroda, Salome, Takkellapati, Sankeerth, Lawrence, Robert T., Entwisle, Samuel W., Pearson, Jennifer M., Granade, Mitchell E., Mullins, Garrett R., Eaton, James M., Villén, Judit, Harris, Thurl E.

Source: In Journal of Biological Chemistry 15 December 2017 292(50):20481-20493

Determinants and Regulation of Protein Turnover in Yeast

Authors: Martin-Perez, Miguel, Villén, Judit

Source: In Cell Systems 27 September 2017 5(3):283-294

Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT‐cell and T‐cell receptor protein.

Authors: Mallis, Robert J., Lee, Jonathan J., Berg, Arjen Van den, Brazin, Kristine N., Viennet, Thibault, Zmuda, Jonathan, Cross, Melissa, Radeva, Denitsa, Rodriguez‐Mias, Ricard, Villén, Judit, Gelev, Vladimir, Reinherz, Ellis L., Arthanari, Haribabu

Source: Protein Science: A Publication of the Protein Society; Apr2024, Vol. 33 Issue 4, p1-17, 17p

Altered CSNK1E, FABP4 and NEFH protein levels in the dorsolateral prefrontal cortex in schizophrenia

Authors: Pinacho, Raquel, Villalmanzo, Núria, Meana, J. Javier, Ferrer, Isidre, Berengueras, Adriana, Haro, Josep M., Villén, Judit, Ramos, Belén

Source: In Schizophrenia Research November 2016 177(1-3):88-97

Evolution of protein phosphorylation across 18 fungal species

Authors: Studer, Romain A., Rodriguez-Mias, Ricard A., Haas, Kelsey M., Hsu, Joanne I., Viéitez, Cristina, Solé, Carme, Swaney, Danielle L., Stanford, Lindsay B., Liachko, Ivan, Böttcher, René, Dunham, Maitreya J., de Nadal, Eulàlia, Posas, Francesc, Beltrao, Pedro, Villén, Judit

Source: Science, 2016 Oct . 354(6309), 229-232.

Access URL: https://www.jstor.org/stable/44710800

The Proteomic Landscape of Triple-Negative Breast Cancer

Authors: Lawrence, Robert T., Perez, Elizabeth M., Hernández, Daniel, Miller, Chris P., Haas, Kelsey M., Irie, Hanna Y., Lee, Su-In, Blau, C. Anthony, Villén, Judit

Source: In Cell Reports 28 April 2015 11(4):630-644

mRNA Destabilization Is the Dominant Effect of Mammalian MicroRNAs by the Time Substantial Repression Ensues

Authors: Eichhorn, Stephen W., Guo, Huili, McGeary, Sean E., Rodriguez-Mias, Ricard A., Shin, Chanseok, Baek, Daehyun, Hsu, Shu-hao, Ghoshal, Kalpana, Villén, Judit, Bartel, David P.

Source: In Molecular Cell 2 October 2014 56(1):104-115