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OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

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  1. Article

    Open Access

    Protein 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...

    Tymor Hamamsy, James T. Morton, Robert Blackwell, Daniel Berenberg in Nature Biotechnology (2024)

  2. Article

    Open Access

    PMF-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...

    Claudia Skok Gibbs, Omar Mahmood, Richard Bonneau, Kyunghyun Cho in Genome Biology (2024)

  3. Article

    Open Access

    Structure-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...

    Andreas Tjärnberg, Maggie Beheler-Amass, Christopher A. Jackson in Genome Biology (2024)

  4. Article

    Open Access

    CRISPR 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...

    Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon in Microbiome (2023)

  5. Article

    Open Access

    Characterization 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...

    Lingdi Zhang, Christian V. Forst, Aubree Gordon, Gabrielle Gussin in Microbiome (2020)

  6. Article

    Open Access

    The 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.

    Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee in Genome Biology (2019)

  7. Article

    Open Access

    Analysis 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...

    Ramya Raviram, Pedro P. Rocha, Vincent M. Luo, Emily Swanzey in Genome Biology (2018)

  8. Article

    Open Access

    Fungi 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...

    Laura Tipton, Christian L. Müller, Zachary D. Kurtz, Laurence Huang in Microbiome (2018)

  9. Article

    Open Access

    Computing 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...

    Julia Koehler Leman, Sergey Lyskov, Richard Bonneau in BMC Bioinformatics (2017)

  10. Article

    Open Access

    An 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...

    Yuxiang Jiang, Tal Ronnen Oron, Wyatt T. Clark, Asma R. Bankapur in Genome Biology (2016)

  11. Article

    Open Access

    Multi-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...

    Peter Waltman, Thadeous Kacmarczyk, Ashley R Bate, Daniel B Kearns in Genome Biology (2010)

  12. Article

    Open Access

    UniPep - a database for human N-linked glycosites: a resource for biomarker discovery

    There has been considerable recent interest in proteomic analyses of plasma for the purpose of discovering biomarkers. Profiling N-linked glycopeptides is a particularly promising method because the population of...

    Hui Zhang, Paul Loriaux, Jimmy Eng, David Campbell, Andrew Keller in Genome Biology (2006)

  13. Article

    Open Access

    Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks

    The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes int...

    David J Reiss, Nitin S Baliga, Richard Bonneau in BMC Bioinformatics (2006)

  14. Article

    Open Access

    The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo

    We present a method (the Inferelator) for deriving genome-wide transcriptional regulatory interactions, and apply the method to predict a large portion of the regulatory network of the archaeon Halobacterium NRC-...

    Richard Bonneau, David J Reiss, Paul Shannon, Marc Facciotti, Leroy Hood in Genome Biology (2006)

  15. Article

    Open Access

    The Gaggle: An open-source software system for integrating bioinformatics software and data sources

    Systems biologists work with many kinds of data, from many different sources, using a variety of software tools. Each of these tools typically excels at one type of analysis, such as of microarrays, of metabol...

    Paul T Shannon, David J Reiss, Richard Bonneau, Nitin S Baliga in BMC Bioinformatics (2006)

  16. Article

    Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

    Large fractions of all fully sequenced genomes code for proteins of unknown function. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understan...

    Richard Bonneau, Nitin S Baliga, Eric W Deutsch, Paul Shannon, Leroy Hood in Genome Biology (2004)