sgRNA Sequence Motifs Blocking Efficient CRISPR/Cas9-Mediated Gene Editing
Sign Up to like & getrecommendations! Published in 2019 at "Cell Reports"
DOI: 10.1016/j.celrep.2019.01.024
Abstract: Summary Cas9 nucleases can be programmed with single guide RNAs (sgRNAs) to mediate gene editing. High CRISPR/Cas9-mediated gene knockout efficiencies are essential for genetic screens and critically depend on the properties of the sgRNAs used.… read more here.
Keywords: gene editing; sequence motifs; crispr cas9; gene ... See more keywords
Modular arrangements of sequence motifs determine the functional diversity of KDM proteins
Sign Up to like & getrecommendations! Published in 2021 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbaa215
Abstract: Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions.… read more here.
Keywords: sequence motifs; arrangements sequence; modular arrangements; kdm proteins ... See more keywords
Read between the Lines: Diversity of Nontranslational Selection Pressures on Local Codon Usage
Sign Up to like & getrecommendations! Published in 2021 at "Genome Biology and Evolution"
DOI: 10.1093/gbe/evab097
Abstract: Abstract Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental… read more here.
Keywords: selection pressures; sequence motifs; codon usage; selection ... See more keywords
TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs.
Sign Up to like & getrecommendations! Published in 2023 at "Nucleic acids research"
DOI: 10.1093/nar/gkad355
Abstract: Eukaryotic genomes contain several types of recurrent sequence motifs, e.g. transcription factor motifs, miRNA binding sites, repetitive elements. CRISPR/Cas9 can facilitate identification and study of crucial motifs. We present transCRISPR, the first online tool dedicated… read more here.
Keywords: crispr cas9; tool; sequence motifs; sequence ... See more keywords
Functional 5′ UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks
Sign Up to like & getrecommendations! Published in 2017 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx751
Abstract: Abstract Biological networks are rich representations of the relationships between entities such as genes or proteins and have become increasingly complete thanks to various high-throughput network mapping experimental approaches. Here, we propose a method to… read more here.
Keywords: enrichment sequence; sequence motifs; local enrichment; motifs biological ... See more keywords
Sequence motifs recognized by the casposon integrase of Aciduliprofundum boonei
Sign Up to like & getrecommendations! Published in 2019 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkz447
Abstract: Abstract Casposons are a group of bacterial and archaeal DNA transposons encoding a specific integrase, termed casposase, which is homologous to the Cas1 enzyme responsible for the integration of new spacers into CRISPR loci. Here,… read more here.
Keywords: integrase; integration; sequence motifs; aciduliprofundum boonei ... See more keywords
Selection of sequence motifs and generative Hopfield-Potts models for protein families.
Sign Up to like & getrecommendations! Published in 2019 at "Physical review. E"
DOI: 10.1103/physreve.100.032128
Abstract: Statistical models for families of evolutionary related proteins have recently gained interest: In particular, pairwise Potts models as those inferred by the direct-coupling analysis have been able to extract information about the three-dimensional structure of… read more here.
Keywords: hopfield potts; potts; sequence motifs; potts models ... See more keywords
Motif-Aware PRALINE: Improving the alignment of motif regions
Sign Up to like & getrecommendations! Published in 2018 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1006547
Abstract: Protein or DNA motifs are sequence regions which possess biological importance. These regions are often highly conserved among homologous sequences. The generation of multiple sequence alignments (MSAs) with a correct alignment of the conserved sequence… read more here.
Keywords: aware praline; sequence motifs; motif regions; motif aware ... See more keywords
Representation learning of genomic sequence motifs with convolutional neural networks
Sign Up to like & getrecommendations! Published in 2019 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1007560
Abstract: Although convolutional neural networks (CNNs) have been applied to a variety of computational genomics problems, there remains a large gap in our understanding of how they build representations of regulatory genomic sequences. Here we perform… read more here.
Keywords: representation learning; sequence motifs; neural networks; convolutional neural ... See more keywords