Predicting clinical outcome of neuroblastoma patients using an integrative network-based approach
Biology Direct, 2018 Background One of the main current challenges in computational biology is to make sense of the huge amounts of multidimensional experimental data that are being produced.
Léon-Charles Tranchevent +7 more
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High-affinity SOAT1 ligands remodeled cholesterol metabolism program to inhibit tumor growth
BMC Medicine, 2022 Background Although cholesterol metabolism is a common pathway for the development of antitumor drugs, there are no specific targets and drugs for clinical use.
Zhihua Wang +10 more
doaj +1 more source
In silico Proteome Cleavage Reveals Iterative Digestion Strategy for High Sequence Coverage [PDF]
ISRN Computational Biology 2014, 2014 In the post-genome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome is digested into peptides that are identified followed by protein inference.
arxiv +1 more source
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
Cell, 2020 Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction ...
Edward L. Huttlin +27 more
semanticscholar +1 more source
Pharmacoproteomic characterisation of human colon and rectal cancer [PDF]
, 2017 Most molecular cancer therapies act on protein targets but data on the proteome status of patients and cellular models for proteome-guided pre-clinical drug sensitivity studies are only beginning to emerge.
Domingo, Enric +19 more
core +1 more source
proteomics technologies: Probing the proteome [PDF]
Nature, 2003 The completion of the human genome sequence, coupled with analytical techniques such as mass spectrometry, has fuelled interest in proteomics. Diane Gershon reports.
openaire +3 more sources
Data in Brief, 2022 In this article, we present a data dependent acquisition (DDA) dataset which was generated as a reference and ground truth quantitative dataset. While initially used to compare samples measured with DDA and data independent acquisition (DIA) (Barkovits ...
Julian Uszkoreit +6 more
doaj
Two-dimensional gel electrophoresis in proteomics: past, present and future [PDF]
Journal of proteomics (2010) epub ahead of print, 2010 Two-dimensional gel electrophoresis has been instrumental in the birth and developments of proteomics, although it is no longer the exclusive separation tool used in the field of proteomics. In this review, a historical perspective is made, starting from the days where two-dimensional gels were used and the word proteomics did not even exist.
arxiv +1 more source
Proteomic overview of hepatocellular carcinoma cell lines and generation of the spectral library
Scientific Data, 2022 Measurement(s) Proteome of hepatocellular carcinoma cell lines Technology Type(s) Liquid chromatography-tandem mass spectrometry Sample Characteristic - Organism Homo ...
Mingchao Wang +6 more
doaj +1 more source
DIA-NN: Neural networks and interference correction enable deep proteome coverage in high throughput
Nature Methods, 2019 We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments.
V. Demichev +4 more
semanticscholar +1 more source