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View article: GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish
GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish Open
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Multiple design strategies for zebrafish gene targeting have previously been reported with widely varying frequencies…
View article: Efficient targeted integration directed by short homology in zebrafish and mammalian cells
Efficient targeted integration directed by short homology in zebrafish and mammalian cells Open
Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Here, we describe a set of resources to streamline reporter gene knock-ins in zebrafish and demonstrate the broader u…
View article: Author response: Efficient targeted integration directed by short homology in zebrafish and mammalian cells
Author response: Efficient targeted integration directed by short homology in zebrafish and mammalian cells Open
Article Figures and data Abstract Introduction Results Discussion Materials and methods Data availability References Decision letter Author response Article and author information Metrics Abstract Efficient precision genome engineering req…
View article: Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells
Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells Open
CRISPR and CRISPR-Cas effector proteins enable the targeting of DNA double-strand breaks to defined loci based on a variable length RNA guide specific to each effector. The guide RNAs are generally similar in size and form, consisting of a…
View article: Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells
Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells Open
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated (Cas) effector proteins enable the targeting of DNA double-strand breaks (DSBs) to defined loci based on a variable length RNA guide specific to each …
View article: The Gene Sculpt Suite: a set of tools for genome editing
The Gene Sculpt Suite: a set of tools for genome editing Open
The discovery and development of DNA-editing nucleases (Zinc Finger Nucleases, TALENs, CRISPR/Cas systems) has given scientists the ability to precisely engineer or edit genomes as never before. Several different platforms, protocols and v…
View article: Partner‐specific prediction of RNA‐binding residues in proteins: A critical assessment
Partner‐specific prediction of RNA‐binding residues in proteins: A critical assessment Open
RNA‐protein interactions play essential roles in regulating gene expression. While some RNA‐protein interactions are “specific”, that is, the RNA‐binding proteins preferentially bind to particular RNA sequence or structural motifs, others …
View article: GeneWeld: a method for efficient targeted integration directed by short homology
GeneWeld: a method for efficient targeted integration directed by short homology Open
Choices for genome engineering and integration involve high efficiency with little or no target specificity or high specificity with low activity. Here, we describe a targeted integration strategy, called GeneWeld, and a vector series for …
View article: Robust activation of microhomology-mediated end joining for precision gene editing applications
Robust activation of microhomology-mediated end joining for precision gene editing applications Open
One key problem in precision genome editing is the unpredictable plurality of sequence outcomes at the site of targeted DNA double stranded breaks (DSBs). This is due to the typical activation of the versatile Non-homologous End Joining (N…
View article: Toward Precision Molecular Surgery: Robust, Selective Induction of Microhomology-mediated End Joining <i>in vivo</i>
Toward Precision Molecular Surgery: Robust, Selective Induction of Microhomology-mediated End Joining <i>in vivo</i> Open
One key problem in precision genome editing is the resultant unpredictable plurality of sequence outcomes at the site of targeted DNA double-strand breaks (DSBs). This is due to the typical activation of the versatile Non-homologous End Jo…
View article: Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins
Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins Open
Sequence-based computational analyses of Rev-like proteins, together with helical wheel projections of oligomerization domains, reveal a conserved homogeneous structural basis for oligomerization by retroviral Rev-like proteins.
View article: MOESM2 of Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins
MOESM2 of Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins Open
Additional file 2. Complete dataset for sequences used in this study. For each SIV, HIV-1, HIV-2, EIAV, FIV, SRLV, BIV, BLV, PTLV, HERVK, MMTV, Jaagsiekte, and endogenous lentivirus Rev-like sequence, accession code information for the gen…
View article: Sequence-Based Prediction of RNA-Binding Residues in Proteins
Sequence-Based Prediction of RNA-Binding Residues in Proteins Open
View article: In Silico Prediction of Linear B-Cell Epitopes on Proteins
In Silico Prediction of Linear B-Cell Epitopes on Proteins Open
View article: A <i>Plasmodium</i>‐like virulence effector of the soybean cyst nematode suppresses plant innate immunity
A <i>Plasmodium</i>‐like virulence effector of the soybean cyst nematode suppresses plant innate immunity Open
Summary Heterodera glycines , the soybean cyst nematode, delivers effector proteins into soybean roots to initiate and maintain an obligate parasitic relationship. HgGLAND18 encodes a candidate H. glycines effector and is expressed through…
View article: Template-based protein–protein docking exploiting pairwise interfacial residue restraints
Template-based protein–protein docking exploiting pairwise interfacial residue restraints Open
Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable tem…
View article: Regulatory RNA: Session Introduction
Regulatory RNA: Session Introduction Open
Advances in both experimental and computational approaches to genome-wide analysis of RNA transcripts have dramatically expanded our understanding of the ubiquitous and diverse roles of regulatory non-coding RNAs. This conference session i…
View article: The Linear Model for Interface Conservation.
The Linear Model for Interface Conservation. Open
View article: Performance of HomPRIP on RB198.
Performance of HomPRIP on RB198. Open
The performance is shown for the Safe, Twilight, and Dark Zones, separately. Prediction coverage is the fraction of queries that can be predicted by HomPRIP in a given zone.
View article: Principal Components Analysis (PCA) of interface conservation scores and sequence alignment statistics.
Principal Components Analysis (PCA) of interface conservation scores and sequence alignment statistics. Open
Data points in the plot correspond to the projection of a 6-dimensional vector representing the pairwise alignment of a query and homolog sequence onto a 2-dimensional space defined by the first and second principal components. Blue lines …
View article: Boundaries of Safe, Twilight, and Dark Zones used by HomPRIP.
Boundaries of Safe, Twilight, and Dark Zones used by HomPRIP. Open
View article: Evaluation of Methods on the RB111 dataset.
Evaluation of Methods on the RB111 dataset. Open
The first 6 methods are sequence-based methods. The last 2 methods (indicated by **) are structure-based methods. Methods in each category are sorted in descending order of MCC. The highest value in each column is shown in bold font.
View article: REGULATORY RNA
REGULATORY RNA Open
View article: A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES
A MOTIF-BASED METHOD FOR PREDICTING INTERFACIAL RESIDUES IN BOTH THE RNA AND PROTEIN COMPONENTS OF PROTEIN-RNA COMPLEXES Open
Efforts to predict interfacial residues in protein-RNA complexes have largely focused on predicting RNA-binding residues in proteins. Computational methods for predicting protein-binding residues in RNA sequences, however, are a problem th…
View article: Computational prediction of protein interfaces: A review of data driven methods
Computational prediction of protein interfaces: A review of data driven methods Open
Reliably pinpointing which specific amino acid residues form the interface(s) between a protein and its binding partner(s) is critical for understanding the structural and physicochemical determinants of protein recognition and binding aff…