Economos, Nicholas G Quijano, Elias Carufe, Kelly E W Perera, J Dinithi R Glazer, Peter M
Published in
Nucleic acids research
Despite the rapid and broad implementation of CRISPR-Cas9-based technologies, convenient tools to modulate dose, timing, and precision remain limited. Building on methods using synthetic peptide nucleic acids (PNAs) to bind RNA with unusually high affinity, we describe guide RNA (gRNA) spacer-targeted, or 'antispacer', PNAs as a tool to modulate Ca...
Ne, Enrico Crespo, Raquel Izquierdo-Lara, Ray Rao, Shringar Koçer, Selin Górska, Alicja van Staveren, Thomas Kan, Tsung Wai van de Vijver, David Dekkers, Dick
...
Published in
Nucleic acids research
A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and la...
Chappleboim, Alon Joseph-Strauss, Daphna Gershon, Omer Friedman, Nir
Published in
Nucleic acids research
In the last decade, multiple studies demonstrated that cells maintain a balance of mRNA production and degradation, but the mechanisms by which cells implement this balance remain unknown. Here, we monitored cells' total and recently-transcribed mRNA profiles immediately following an acute depletion of Xrn1-the main 5'-3' mRNA exonuclease-which was...
de Jong, Anne Kuipers, Oscar P Kok, Jan
Published in
Nucleic acids research
Recent advances in the field of high throughput (meta-)transcriptomics and proteomics call for easy and rapid methods enabling to explore not only single genes or proteins but also extended biological systems. Gene set enrichment analysis is commonly used to find relations in a set of genes and helps to uncover the biological meaning in results der...
Nguyen, Minh N Krutz, Nora L Limviphuvadh, Vachiranee Lopata, Andreas L Gerberick, G Frank Maurer-Stroh, Sebastian
Published in
Nucleic acids research
Proteins in food and personal care products can pose a risk for an immediate immunoglobulin E (IgE)-mediated allergic response. Bioinformatic tools can assist to predict and investigate the allergenic potential of proteins. Here we present AllerCatPro 2.0, a web server that can be used to predict protein allergenicity potential with better accuracy...
Liu, Zhu Mushayahama, Tremayne Queme, Bryan Ebert, Dustin Muruganujan, Anushya Mills, Caitlin Thomas, Paul D Mi, Huaiyu
Published in
Nucleic acids research
The Annotation Query (AnnoQ) (http://annoq.org/) is designed to provide comprehensive and up-to-date functional annotations for human genetic variants. The system is supported by an annotation database with ∼39 million human variants from the Haplotype Reference Consortium (HRC) pre-annotated with sequence feature annotations by WGSA and functional...
Nguyen, Thach Ramachandran, Haribaskar Martins, Soraia Krutmann, Jean Rossi, Andrea
Published in
Nucleic acids research
Genome engineering-induced cleavage sites can be resolved by non-homologous end joining (NHEJ) or homology-directed repair (HDR). Identifying genetically modified clones at the target locus remains an intensive and laborious task. Different workflows and software that rely on deep sequencing data have been developed to detect and quantify targeted ...
Emelianova, Mariia Gainullina, Anastasiia Poperechnyi, Nikolay Loboda, Alexander Artyomov, Maxim Sergushichev, Alexey
Published in
Nucleic acids research
Multiple high-throughput omics techniques provide different angles on systematically quantifying and studying metabolic regulation of cellular processes. However, an unbiased analysis of such data and, in particular, integration of multiple types of data remains a challenge. Previously, for this purpose we developed GAM web-service for integrative ...
Zhou, Guangyan Pang, Zhiqiang Lu, Yao Ewald, Jessica Xia, Jianguo
Published in
Nucleic acids research
Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of 'omics features of i...
Kampfrath, Michelle Staritzbichler, René Hernández, Guillermo Pérez Rose, Alexander S Tiemann, Johanna K S Scheuermann, Gerik Wiegreffe, Daniel Hildebrand, Peter W
Published in
Nucleic acids research
Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis....