Carla M. Mann
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View article: BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration
BV-BRC: a unified bacterial and viral bioinformatics resource with expanded functionality and AI integration Open
The Bacterial and Viral Bioinformatics Resource Center (BV-BRC; https://www.bv-brc.org) is a comprehensive resource supporting research on bacterial and viral pathogens. It currently hosts over 14 million publicly available genomes and 33 …
View article: GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics Open
We seek to transform how new and emergent variants of pandemic-causing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSL…
View article: DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies
DeepSpeed4Science Initiative: Enabling Large-Scale Scientific Discovery through Sophisticated AI System Technologies Open
In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across …
View article: GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics Open
We seek to transform how new and emergent variants of pandemiccausing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLM…
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: Applications of machine learning to solve biological puzzles
Applications of machine learning to solve biological puzzles Open
The era of “big data” has led to the generation of more biological data than any human could hope to process. This flood of data has necessitated the development of computational methods to assist in analysis, and has made it possible to b…
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: 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…