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
More biology from the sequence [PDF]
Genome Biology, 2001 A report on the Cold Spring Harbor meeting on Genome Sequencing and Biology, Cold Spring Harbor, NY, USA, 9-13 May ...
Taylor, M S
core +7 more sources
The EM Algorithm and the Rise of Computational Biology [PDF]
Statistical Science 2010, Vol. 25, No. 4, 476-491, 2011 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. Of interest to us is the key role played by the EM algorithm during this transformation. We survey the use of the EM algorithm
Citable Link +3 more
arxiv +6 more sources
Biology Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models [PDF]
arXivLarge language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored.
Haonan He +14 more
arxiv +3 more sources
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence [PDF]
Nature, 1998 Stewart T. Cole +41 more
openalex +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
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
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
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