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Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events
TLDR
We present a major update to TopFIND, version 3, which includes a 70% increase in the underlying data to now cover a 90 696 proteins, 165 044 N- termini, 130 182 C-termini, 14 382 cleavage sites and 33 209 substrate cleavages in H. sapiens, M. musculus, A. thaliana, S. cerevisiae and E. coli. Expand
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The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space
Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet little is known about the role of the epigenome in glioblastoma disease progression. Here, we presentExpand
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Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web
Network modeling of interactions between proteases and their inhibitors reveals a network of new protein connections and cascades in the protease web.
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Chromatin mapping and single-cell immune profiling define the temporal dynamics of ibrutinib response in CLL
The Bruton tyrosine kinase (BTK) inhibitor ibrutinib provides effective treatment for patients with chronic lymphocytic leukemia (CLL), despite extensive heterogeneity in this disease. To define theExpand
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The path of no return—Truncated protein N‐termini and current ignorance of their genesis
Almost all regulatory processes in biology ultimately lead to or originate from modifications of protein function. However, it is unclear to which extent each mechanism of regulation actually affectsExpand
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Interactome disassembly during apoptosis occurs independent of caspase cleavage
Protein–protein interaction networks (interactomes) define the functionality of all biological systems. In apoptosis, proteolysis by caspases is thought to initiate disassembly of protein complexesExpand
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Can we predict protein from mRNA levels?
Prediction of protein levels from mRNA levels has long been fraught with unreliability and a lack of precision. However, Wilhelm et al.1 claimed that using estimated gene-specific translation ratesExpand
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Single-cell transcriptomics combined with interstitial fluid proteomics defines cell-type-specific immune regulation in atopic dermatitis.
BACKGROUND Atopic dermatitis (AD) is the most common chronic inflammatory skin disease, but its complex pathogenesis is only insufficiently understood, resulting in still limited treatment options.Expand
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Uncovering a Dual Regulatory Role for Caspases During Endoplasmic Reticulum Stress-induced Cell Death
Many diseases are associated with endoplasmic reticulum (ER) stress, which results from an accumulation of misfolded proteins. This triggers an adaptive response called the “unfolded proteinExpand
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Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data
TLDR
We demonstrate deep learning on biological networks, where every node has a molecular equivalent (such as a protein or gene) and every edge has a mechanistic interpretation. Expand
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