Tellier, Michael Zaborowska, Justyna Caizzi, Livia Mohammad, Eusra Velychko, Taras Schwalb, Björn Ferrer-Vicens, Ivan Blears, Daniel Nojima, Takayuki Cramer, Patrick
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Published in
Nucleic acids research
Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphor...
Wolff, Joachim Rabbani, Leily Gilsbach, Ralf Richard, Gautier Manke, Thomas Backofen, Rolf Grüning, Björn A
Published in
Nucleic acids research
The Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data. Since the last publication, Galaxy HiCExplorer has been ...
Wang, Duolin Liu, Dongpeng Yuchi, Jiakang He, Fei Jiang, Yuexu Cai, Siteng Li, Jingyi Xu, Dong
Published in
Nucleic acids research
MusiteDeep is an online resource providing a deep-learning framework for protein post-translational modification (PTM) site prediction and visualization. The predictor only uses protein sequences as input and no complex features are needed, which results in a real-time prediction for a large number of proteins. It takes less than three minutes to p...
Malhis, Nawar Jacobson, Matthew Jones, Steven J M Gsponer, Jörg
Published in
Nucleic acids research
The separation of deleterious from benign mutations remains a key challenge in the interpretation of genomic data. Computational methods used to sort mutations based on their potential deleteriousness rely largely on conservation measures derived from sequence alignments. Here, we introduce LIST-S2, a successor to our previously developed approach ...
Passaro, Marco Martinovic, Martina Bevilacqua, Valeria Hershberg, Elliot A Rossetti, Grazisa Beliveau, Brian J Bonnal, Raoul J P Pagani, Massimiliano
Published in
Nucleic acids research
Fluorescence in situ hybridization (FISH) is a powerful single-cell technique that harnesses nucleic acid base pairing to detect the abundance and positioning of cellular RNA and DNA molecules in fixed samples. Recent technology development has paved the way to the construction of FISH probes entirely from synthetic oligonucleotides (oligos), allow...
Drew, Elliot D Janes, Robert W
Published in
Nucleic acids research
PDBMD2CD is a new web server capable of predicting circular dichroism (CD) spectra for multiple protein structures derived from molecular dynamics (MD) simulations, enabling predictions from thousands of protein atomic coordinate files (e.g. MD trajectories) and generating spectra for each of these structures provided by the user. Using MD enables ...
Banerjee, Priyanka Dunkel, Mathias Kemmler, Emanuel Preissner, Robert
Published in
Nucleic acids research
Cytochrome P450 enzymes (CYPs)-mediated drug metabolism influences drug pharmacokinetics and results in adverse outcomes in patients through drug-drug interactions (DDIs). Absorption, distribution, metabolism, excretion and toxicity (ADMET) issues are the leading causes for the failure of a drug in the clinical trials. As details on their metabolis...
Gumerov, Vadim M Zhulin, Igor B
Published in
Nucleic acids research
Key steps in a computational study of protein function involve analysis of (i) relationships between homologous proteins, (ii) protein domain architecture and (iii) gene neighborhoods the corresponding proteins are encoded in. Each of these steps requires a separate computational task and sets of tools. Currently in order to relate protein features...
Suplatov, Dmitry Sharapova, Yana Geraseva, Elizaveta Švedas, Vytas
Published in
Nucleic acids research
Zebra2 is a highly automated web-tool to search for subfamily-specific and conserved positions (i.e. the determinants of functional diversity as well as the key catalytic and structural residues) in protein superfamilies. The bioinformatic analysis is facilitated by Mustguseal-a companion web-server to automatically collect and superimpose a large ...
Giroux, Pierre Bhajun, Ricky Segard, Stéphane Picquenot, Claire Charavay, Céline Desquilles, Lise Pinna, Guillaume Ginestier, Christophe Denis, Josiane Cherradi, Nadia
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Published in
Nucleic acids research
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in the regulation of major pathways in eukaryotic cells through their binding to and repression of multiple mRNAs. With high-throughput methodologies, various outcomes can be measured that produce long lists of miRNAs that are often difficult to interpret. A common question is: after di...
