Integrating sequence and structural biology with DAS [PDF]
BMC Bioinformatics, 2007 Background The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.
Finn Robert D +5 more
doaj +13 more sources
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence [PDF]
Nature, 1998 S. Cole +41 more
semanticscholar +2 more sources
Strainberry: automated strain separation in low-complexity metagenomes using long reads
Nature Communications, 2021 Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and ...
Riccardo Vicedomini +3 more
doaj +1 more source
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Microbiome, 2023 Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources.
Camila Duitama González +5 more
doaj +1 more source
Predicting multiple conformations via sequence clustering and AlphaFold2
Nature, 2023 AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein’s biological function often depends on multiple conformational substates2, and disease-causing point mutations often ...
Hannah K. Wayment-Steele +8 more
semanticscholar +1 more source
Mega-scale experimental analysis of protein folding stability in biology and design
Nature, 2023 Large-scale assays using cDNA display proteolysis are used to measure the folding stabilities of protein domains, providing a method to quantify the effects of mutations on protein folding, with applications in protein design.
Kotaro Tsuboyama +8 more
semanticscholar +1 more source
100th Anniversary of Macromolecular Science Viewpoint: Opportunities in the Physics of Sequence-Defined Polymers [PDF]
, 2020 Polymer science has been driven by ever-increasing molecular complexity, as polymer synthesis expands an already-vast palette of chemical and architectural parameter space.
Perry, Sarah L., Sing, Charles E.
core +3 more sources
HostPhinder: A Phage Host Prediction Tool
Viruses, 2016 The current dramatic increase of antibiotic resistant bacteria has revitalised the interest in bacteriophages as alternative antibacterial treatment. Meanwhile, the development of bioinformatics methods for analysing genomic data places high-throughput ...
Julia Villarroel +6 more
doaj +1 more source
The EM Algorithm and the Rise of Computational Biology [PDF]
, 2010 In the past decade computational biology has grown from a cottage industry with a handful of researchers to an attractive interdisciplinary field, catching the attention and imagination of many quantitatively-minded scientists.
Citable Link +3 more
core +3 more sources
BERTology Meets Biology: Interpreting Attention in Protein Language Models [PDF]
bioRxiv, 2020 Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability.
Jesse Vig +5 more
semanticscholar +1 more source