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Nature Biotechnology
ISSN 0733-222X · Nature Portfolio · 158 artikel di indeks
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Artikel Jurnal Teks lengkap
Detection of mosaic and population-level structural variants with Sniffles2
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a repeat aware clustering coupled with a fast consensus sequence…
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Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition
Mass spectrometry (MS)-based proteomics aims to characterize comprehensive proteomes in a fast and reproducible manner. Here we present the narrow-window data-independent acquisition (nDIA) strategy consisting of high-resolution MS1 scans with parallel tandem MS (MS/MS) scans of ~200 Hz using 2-Th…
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A small-molecule TNIK inhibitor targets fibrosis in preclinical and clinical models
Idiopathic pulmonary fibrosis (IPF) is an aggressive interstitial lung disease with a high mortality rate. Putative drug targets in IPF have failed to translate into effective therapies at the clinical level. We identify TRAF2- and NCK-interacting kinase (TNIK) as an anti-fibrotic target using a…
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In vivo human T cell engineering with enveloped delivery vehicles
Viruses and virally derived particles have the intrinsic capacity to deliver molecules to cells, but the difficulty of readily altering cell-type selectivity has hindered their use for therapeutic delivery. Here, we show that cell surface marker recognition by antibody fragments displayed on…
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Engineered virus-like particles for transient delivery of prime editor ribonucleoprotein complexes in vivo
Prime editing enables precise installation of genomic substitutions, insertions and deletions in living systems. Efficient in vitro and in vivo delivery of prime editing components, however, remains a challenge. Here we report prime editor engineered virus-like particles (PE-eVLPs) that deliver…
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Efficient evolution of human antibodies from general protein language models
Natural evolution must explore a vast landscape of possible sequences for desirable yet rare mutations, suggesting that learning from natural evolutionary strategies could guide artificial evolution. Here we report that general protein language models can efficiently evolve human antibodies by…
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Pangenome graph construction from genome alignments with Minigraph-Cactus
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High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq
In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further…
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High-throughput microbial culturomics using automation and machine learning
Pure bacterial cultures remain essential for detailed experimental and mechanistic studies in microbiome research, and traditional methods to isolate individual bacteria from complex microbial ecosystems are labor-intensive, difficult-to-scale and lack phenotype-genotype integration. Here we…
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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine
The human microbiome influences the efficacy and safety of a wide variety of commonly prescribed drugs. Designing precision medicine approaches that incorporate microbial metabolism would require strain- and molecule-resolved, scalable computational modeling. Here, we extend our previous resource…
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Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing
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Accurate isoform discovery with IsoQuant using long reads
Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation…
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Predicting transcriptional outcomes of novel multigene perturbations with GEARS
Understanding cellular responses to genetic perturbation is central to numerous biomedical applications, from identifying genetic interactions involved in cancer to developing methods for regenerative medicine. However, the combinatorial explosion in the number of possible multigene perturbations…
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Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice
Antibiotic treatments have detrimental effects on the microbiome and lead to antibiotic resistance. To develop a phage therapy against a diverse range of clinically relevant Escherichia coli, we screened a library of 162 wild-type (WT) phages, identifying eight phages with broad coverage of E…
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Fast and accurate protein structure search with Foldseek
As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing tertiary amino acid interactions within proteins as sequences over…
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Large language models generate functional protein sequences across diverse families
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Integrative analysis of multimodal mass spectrometry data in MZmine 3