Proteomic profiling dataset of chemical perturbations in multiple biological backgrounds

Autor: Deborah O. Dele-Oni, Karen E. Christianson, Shawn B. Egri, Alvaro Sebastian Vaca Jacome, Katherine C. DeRuff, James Mullahoo, Vagisha Sharma, Desiree Davison, Tak Ko, Michael Bula, Joel Blanchard, Jennie Z. Young, Lev Litichevskiy, Xiaodong Lu, Daniel Lam, Jacob K. Asiedu, Caidin Toder, Adam Officer, Ryan Peckner, Michael J. MacCoss, Li-Huei Tsai, Steven A. Carr, Malvina Papanastasiou, Jacob D. Jaffe

Publikováno v: Scientific Data, Vol 8, Iss 1, Pp 1-10 (2021)

Measurement(s) drug perturbation response Technology Type(s) proteomic profiling Factor Type(s) cell line • drug Sample Characteristic - Organism Homo sapiens Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9

Externí odkaz: https://doaj.org/article/b86900b2f9b8425aac6d9c1d14f49b98

Sensitive, high-throughput HLA-I and HLA-II immunopeptidomics using parallel accumulation-serial fragmentation mass spectrometry

Autor: Kshiti Meera Phulphagar, Claudia Ctortecka, Alvaro Sebastian Vaca Jacome, Susan Klaeger, Eva K. Verzani, Gabrielle M. Hernandez, Namrata D. Udeshi, Karl R. Clauser, Jennifer G. Abelin, Steven A. Carr

Publikováno v: bioRxiv

Comprehensive, in-depth identification of the human leukocyte antigen HLA-I and HLA-II tumor immunopeptidome can inform the development of cancer immunotherapies. Mass spectrometry (MS) is powerful technology for direct identification of HLA peptides

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3f313274303cd151b25fcb6257107086
https://europepmc.org/articles/PMC10054976/

Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks

Autor: Ilse Delint-Ramirez, Lahiri Konada, Lance Heady, Richard Rueda, Alvaro Sebastian Vaca Jacome, Eric Marlin, Charlotte Marchioni, Amir Segev, Oleg Kritskiy, Satoko Yamakawa, Andrew H. Reiter, Li-Huei Tsai, Ram Madabhushi

Publikováno v: Molecular cell. 82(20)

Neuronal activity induces topoisomerase IIβ (Top2B) to generate DNA double-strand breaks (DSBs) within the promoters of neuronal early response genes (ERGs) and facilitate their transcription, and yet, the mechanisms that control Top2B-mediated DSB

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0440e1bdcc2bbfa319de6c055fcaddd
https://pubmed.ncbi.nlm.nih.gov/36206766

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

Autor: Sarah Cianférani, Charlotte Macron, Sebastian Alvaro Vaca-Jacome, Catherine Aude-Garcia, Christine Carapito, Joanna Bons, Magali Rompais, Thierry Rabilloud

Publikováno v: Molecular and Cellular Proteomics
Molecular and Cellular Proteomics, American Society for Biochemistry and Molecular Biology, 2019, 18 (6), pp.1085-1095. ⟨10.1074/mcp.RA118.001269⟩
Molecular and Cellular Proteomics, 2019, 18 (6), pp.1085-1095. ⟨10.1074/mcp.RA118.001269⟩
Mol Cell Proteomics

International audience; All but thirteen mammalian mitochondrial proteins are encoded by the nuclear genome, translated in the cytosol and then imported into the mitochondria. For a significant proportion of the mitochondrial proteins, import is coup

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd0fc04c60e43343b2dff6cbbc77f676
https://doi.org/10.1074/mcp.ra118.001269

Molecular data meet pathway knowledge

Autor: Funda Durupinar, Chris Sander, Anil Korkut, Karen E. Christianson, Joseph E. Aslan, Emek Demir, Ryan Peckner, Özgün Babur, Jacob D. Jaffe, Augustin Luna, Metin Can Siper, Ugur Dogrusoz, Paul T. Spellman, Alvaro Sebastian Vaca Jacome

Publikováno v: Patterns
Patterns, Vol 2, Iss 6, Pp 100257-(2021)

Summary We present a computational method to infer causal mechanisms in cell biology by analyzing changes in high-throughput proteomic profiles on the background of prior knowledge captured in biochemical reaction knowledge bases. The method mimics a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5de403fdce77c49680f8f3ad40b1a58f
https://aperta.ulakbim.gov.tr/record/230538