MaxDIA enables library-based and library-free data-independent acquisition proteomics

Autor: Jürgen Cox, Favio Salinas Soto, Sean J. Humphrey, Frank McCarthy, Hamid Hamzeiy, Şule Yılmaz, Stefan Tenzer, Daniel N. Itzhak, Christoph Wichmann, Yasset Perez-Riverol, Martin Steger, Nikita Prianichnikov, Uli Ohmayer, Stephanie Kaspar-Schoenefeld, Pavel Sinitcyn, Nagarjuna Nagaraj, Jan Daniel Rudolph, Ute Distler

Publikováno v: Nature Biotechnology

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f09aaa492244f8c70ffdcbd517e75113

Sleep-wake cycles drive daily dynamics of synaptic phosphorylation

Autor: Jürgen Cox, Shiva K. Tyagarajan, Maria S. Robles, Steven A. Brown, Sara B. Noya, Matthias Mann, Franziska Brüning, Tanja Bange, Stella Koutsouli, Jan Daniel Rudolph

Publikováno v: Brüning, F, Noya, S B, Bange, T, Koutsouli, S, Rudolph, J D, Tyagarajan, S K, Cox, J, Mann, M, Brown, S A & Robles, M S 2019, ' Sleep-wake cycles drive daily dynamics of synaptic phosphorylation ', Science (New York, N.Y.), vol. 366, no. 6462, eaav3617 . https://doi.org/10.1126/science.aav3617

Sleep-wake cycles at mouse synapses Analysis of the transcriptome, proteome, and phosphoproteome at synapses in the mouse brain during daily sleep-wake cycles reveals large dynamic changes (see the Perspective by Cirelli and Tononi). Noya et al. foun

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::57e749fc7bc98cffeb1dee949f3908e3
https://www.zora.uzh.ch/id/eprint/176021/

System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis

Autor: Iris Barshack, Cecilia Lindskog, Tamar Geiger, Nora Balint-Lahat, Rotem Katzir, Fredrik Pontén, Jan Daniel Rudolph, Camilla Avivi, Yair Pozniak, Eytan Ruppin

Publikováno v: Cell Systems. 2(3):172-184

The genomic and transcriptomic landscapes of breast cancer have been extensively studied, but the proteomes of breast tumors are far less characterized. Here, we use high-resolution, high-accuracy mass spectrometry to perform a deep analysis of lumin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4b13fdfd80e454cf791891b102fc4e4b

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Autor: Sebastian Fröhlich, Andreas Dräger, Alex Thomas, Alexander Diamantikos, Clemens Wrzodek, Jakob Matthes, Bernhard O. Palsson, Roland Keller, Chris J. Myers, Nathan E. Lewis, Finja Wrzodek, Johannes Eichner, Eugen Netz, Michael Hucka, Harold F. Gómez, Leandro Watanabe, Florian Mittag, Jan Daniel Rudolph, Victor Kofia, Nicolas Rodriguez, Ibrahim Vazirabad, Nicolas Le Novère

Publikováno v: Rodriguez, N, Thomas, A, Watanabe, L, Vazirabad, I Y, Kofia, V, Gómez, H F, Mittag, F, Matthes, J, Rudolph, J, Wrzodek, F, Netz, E, Diamantikos, A, Eichner, J, Keller, R, Wrzodek, C, Fröhlich, S, Lewis, N, Myers, C J, Le Novère, N, Palsson, B, Hucka, M & Dräger, A 2015, ' JSBML 1.0: providing a smorgasbord of options to encode systems biology models ', Bioinformatics, vol. 31, no. 20, pp. 3383-6 . https://doi.org/10.1093/bioinformatics/btv341
Bioinformatics (Oxford, England), vol 31, iss 20
Bioinformatics

Summary: JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via ex

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f03d40eaec84d0ef3c2596076384c245
https://orbit.dtu.dk/en/publications/139c6c8a-b634-4f79-a667-1e92fd79adc1

Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data

Autor: Pavel Sinitcyn, Jürgen Cox, Jan Daniel Rudolph

Publikováno v: Annual Review of Biomedical Data Science

Computational proteomics is the data science concerned with the identification and quantification of proteins from high-throughput data and the biological interpretation of their concentration changes, posttranslational modifications, interactions, a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a2b3c5b54ee5e9b3e567e0da90658739