Results 1 to 10 of about 4,078,643 (261)

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, Christopher Quince, Aaron E. Darling, Rayan Chikhi   +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, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi   +5 more
doaj   +1 more source

Mapping-friendly sequence reductions: Going beyond homopolymer compression

iScience, 2022
Summary: Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present in ...
Luc Blassel, Paul Medvedev, Rayan Chikhi
doaj   +1 more source

SaPt-CNN-LSTM-AR-EA: a hybrid ensemble learning framework for time series-based multivariate DNA sequence prediction [PDF]

PeerJ, 2023
Biological sequence data mining is hot spot in bioinformatics. A biological sequence can be regarded as a set of characters. Time series is similar to biological sequences in terms of both representation and mechanism.
Wu Yan, Li Tan, Li Meng-Shan, Sheng Sheng, Wang Jun, Wu Fu-an   +5 more
doaj   +2 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, Kortine Annina Kleinheinz, Vanessa Isabell Jurtz, Henrike Zschach, Ole Lund, Morten Nielsen, Mette Voldby Larsen   +6 more
doaj   +1 more source

RBPSpot: Learning on appropriate contextual information for RBP binding sites discovery

iScience, 2021
Summary: Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using
Nitesh Kumar Sharma, Sagar Gupta, Ashwani Kumar, Prakash Kumar, Upendra Kumar Pradhan, Ravi Shankar   +5 more
doaj   +1 more source

TarO : a target optimisation system for structural biology [PDF]

, 2008
This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434).
Naismith, Jim, Barton, Geoffrey J, Naismith, James H, William N. Hunter, White, Malcolm F, McMahon, Stephen, Hunter, William N., vanNiekerk, C. A. Johannes, Overton, Ian M., Hunter, William, van Niekerk, C. A. Johannes, van Niekerk, C A, Barton, Geoffrey, Carter, Lester, Geoffrey J. Barton, Naismith, James, Hunter, W N, Carter, Lester G., Overton, Ian; id_orcid, Dawson, Alice, McMahon, S A, Dawson, A, David M. A. Martin, McMahon, Stephen A., White, Malcolm F., Martin, David, Scott Cameron, White, Malcolm, Barton, G J, Cameron, Scott, Naismith, James H., Ian M. Overton, James H. Naismith, Cameron, S, Malcolm F. White, Barton, Geoffrey J.; id_orcid, Lester G. Carter, Carter, L G, Alice Dawson, Martin, D M, Martin, David M. A.; id_orcid, C. A. Johannes Van Niekerk, Stephen A. Mcmahon, Overton, I M, Overton, Ian   +44 more
core   +1 more source

Localization of T cell clonotypes using the Visium spatial transcriptomics platform

STAR Protocols, 2022
Summary: We present a protocol to localize T cell receptor clones using the Visium spatial transcriptomics platform. This approach permits simultaneous localization of both gene expression and T cell clonotypes in situ within tissue sections.
William H. Hudson, Lisa J. Sudmeier
doaj   +1 more source

Intrinsic sequence specificity of the Cas1 integrase directs new spacer acquisition [PDF]

, 2015
This work was supported by a grant from the Biotechnology and Biological Sciences Research Council (REF: BB/M000400/1 to MFW).The adaptive prokaryotic immune system CRISPR-Cas provides RNA-mediated protection from invading genetic elements.
Bolt, Edward, White, Malcolm F., Rollie, C, White, Malcolm F, Anna Sophie Brinkmann, Malcolm F White, Clare Rollie, Edward L Bolt, Brinkmann, Anna Sophie, Rollie, Clare, Bolt, EL, Rollie, Clare Jane Catherine, Schneider, Stefanie, White, MF, Stefanie Schneider, Bolt, Edward L., Schneider, S, Brinkmann, AS   +17 more
core   +1 more source

Nutritional Systems Biology Modeling: From Molecular Mechanisms to Physiology [PDF]

, 2009
The use of computational modeling and simulation has increased in many biological fields, but despite their potential these techniques are only marginally applied in nutritional sciences.
Ommen, Ben van, De Roos Baukje, Ommen, Ben van,, van Ommen Ben, van Ommen, Ben, Graaf, A.A. de, Martin Adiels, Adiels, Martin,, Rullmann, Johan A.C., Roos, Baukje de, Kevin D. Hall, de Graaf Albert A., Freidig, Andreas P.,, Hall, Kevin D.,, Neema Jamshidi, Andreas P. Freidig, Adiels, M., Hall, Kevin D, Hall Kevin D., Baukje De Roos, Johan A C Rullmann, Rullmann, J.A.C., Ben van Ommen, Graaf, Albert A. de, Rullmann Johan A.C., Freidig, Andreas P, Andreas P Freidig, Jamshidi Neema, Jamsheedi, Neema, Heinemann, M., Heinemann Matthias, Roos, B. de, Johan A.C. Rullmann, Adiels Martin, De Roos, Baukje, Ommen, B. van, Albert A de Graaf, Jamshidi, Neema,, de Graaf, Albert A, Adiels, Martin, Hall, K.D., Freidig, Andreas P., Heinemann, Matthias,, Hall, Kevin D., Roos, Baukje de,, Rullmann, Johan A C, Heinemann, Matthias; id_orcid, Albert A. de Graaf, Freidig Andreas P., Rullmann, Johan AC, Graaf, Albert A. de,, Freidig, A.P., Heinemann, Matthias, Matthias Heinemann, Rullmann, Johan A.C.,, Jamshidi, Neema, Jamshidi, N., Kevin D Hall   +57 more
core   +3 more sources