26 Result(s)
within
Richard Bonneau
Bioinformatics
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Article
Open AccessProtein remote homology detection and structural alignment using deep learning
Exploiting sequence–structure–function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep lea...
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Article
OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
AlphaFold2 revolutionized structural biology with the ability to predict protein structures with exceptionally high accuracy. Its implementation, however, lacks the code and data required to train new models. ...
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Article
Open AccessPMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
Inferring gene regulatory networks (GRNs) from single-cell data is challenging due to heuristic limitations. Existing methods also lack estimates of uncertainty. Here we present Probabilistic Matrix Factorizat...
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Article
Open AccessStructure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
Modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity (TFA) making it difficult to separate covariance and regulatory interact...
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Article
Open AccessCRISPR arrays as high-resolution markers to track microbial transmission during influenza infection
Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether m...
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Protocol
Specificities of Modeling of Membrane Proteins Using Multi-Template Homology Modeling
Structures of membrane proteins are challenging to determine experimentally and currently represent only about 2% of the structures in the Protein Data Bank. Because of this disparity, methods for modeling mem...
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Article
Reply to: Examining microbe–metabolite correlations by linear methods
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Article
Macromolecular modeling and design in Rosetta: recent methods and frameworks
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions...
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Article
Open AccessCharacterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection
The abundance and diversity of antibiotic resistance genes (ARGs) in the human respiratory microbiome remain poorly characterized. In the context of influenza virus infection, interactions between the virus, t...
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Article
Learning representations of microbe–metabolite interactions
Integrating multiomics datasets is critical for microbiome research; however, inferring interactions across omics datasets has multiple statistical challenges. We solve this problem by using neural networks ( ...
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Article
Open AccessThe CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.
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Article
High-definition spatial transcriptomics for in situ tissue profiling
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures...
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Article
Open AccessAnalysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate
The organization of chromatin in the nucleus plays an essential role in gene regulation. About half of the mammalian genome comprises transposable elements. Given their repetitive nature, reads associated with...
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Article
Translating microbiome futures
A group of microbiome researchers discuss some of the challenges in develo** a new generation of microbiome therapies.
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Article
Open AccessFungi stabilize connectivity in the lung and skin microbial ecosystems
No microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes tha...
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Protocol
Generative Models for Quantification of DNA Modifications
There are multiple chemical modifications of cytosine that are important to the regulation and ultimately the functional expression of the genome. To date no single experiment can capture these separate modifi...
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Article
Open AccessComputing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP
Membrane proteins are underrepresented in structural databases, which has led to a lack of computational tools and the corresponding inappropriate use of tools designed for soluble proteins. For membrane prote...
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Article
Open AccessAn expanded evaluation of protein function prediction methods shows an improvement in accuracy
A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their rel...
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Article
FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
Screening of cells transduced with a lentivirus library harboring nucleosome-free regions of mammalian genomes identifies cis elements that regulate transcription.
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Article
Open AccessMulti-species integrative biclustering
We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, B...
