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Refined by: Journal Title: Plos Computational Biology remove
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1
Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate
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Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006392-e1006392 [Peer Reviewed Journal]

2018 Coggan et al 2018 Coggan et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1006392 ;PMID: 30161133

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2
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

PLoS computational biology, 2017-07, Vol.13 (7), p.e1005659-e1005659 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, et al. (2017) OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol 13(7): e1005659. https://doi.org/10.1371/journal.pcbi.1005659 ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, et al. (2017) OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol 13(7): e1005659. https://doi.org/10.1371/journal.pcbi.1005659 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005659 ;PMID: 28746339

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3
Multivariable association discovery in population-scale meta-omics studies
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Multivariable association discovery in population-scale meta-omics studies

PLoS computational biology, 2021-11, Vol.17 (11), p.e1009442 [Peer Reviewed Journal]

COPYRIGHT 2021 Public Library of Science ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1009442 ;PMID: 34784344

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4
BEAST 2: a software platform for Bayesian evolutionary analysis
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BEAST 2: a software platform for Bayesian evolutionary analysis

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003537 [Peer Reviewed Journal]

COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 Bouckaert et al 2014 Bouckaert et al ;2014 Bouckaert et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, et al. (2014) BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput Biol 10(4): e1003537. doi:10.1371/journal.pcbi.1003537 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003537 ;PMID: 24722319

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5
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads
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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

PLoS computational biology, 2017-06, Vol.13 (6), p.e1005595-e1005595 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595 ;2017 Wick et al 2017 Wick et al ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.1005595 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005595 ;PMID: 28594827

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6
Waste not, want not: why rarefying microbiome data is inadmissible
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Waste not, want not: why rarefying microbiome data is inadmissible

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003531-e1003531 [Peer Reviewed Journal]

COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 McMurdie, Holmes 2014 McMurdie, Holmes ;2014 McMurdie, Holmes. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: McMurdie PJ, Holmes S (2014) Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible. PLoS Comput Biol 10(4): e1003531. doi:10.1371/journal.pcbi.1003531 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003531 ;PMID: 24699258

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7
mixOmics: An R package for 'omics feature selection and multiple data integration
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mixOmics: An R package for 'omics feature selection and multiple data integration

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005752-e1005752 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Rohart F, Gautier B, Singh A, Lê Cao K-A (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 ;2017 Rohart et al 2017 Rohart et al ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Rohart F, Gautier B, Singh A, Lê Cao K-A (2017) mixOmics: An R package for ‘omics feature selection and multiple data integration. PLoS Comput Biol 13(11): e1005752. https://doi.org/10.1371/journal.pcbi.1005752 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005752 ;PMID: 29099853

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8
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches
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Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

PLoS computational biology, 2024-05, Vol.20 (5), p.e1012049-e1012049 [Peer Reviewed Journal]

Copyright: © 2024 Bloxham et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ;COPYRIGHT 2024 Public Library of Science ;2024 Bloxham et al 2024 Bloxham et al ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1012049 ;PMID: 38739654

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9
MUMmer4: A fast and versatile genome alignment system
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MUMmer4: A fast and versatile genome alignment system

PLoS computational biology, 2018-01, Vol.14 (1), p.e1005944-e1005944 [Peer Reviewed Journal]

COPYRIGHT 2018 Public Library of Science ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018) MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol 14(1): e1005944. https://doi.org/10.1371/journal.pcbi.1005944 ;2018 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A (2018) MUMmer4: A fast and versatile genome alignment system. PLoS Comput Biol 14(1): e1005944. https://doi.org/10.1371/journal.pcbi.1005944 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005944 ;PMID: 29373581

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10
Mixtures of strategies underlie rodent behavior during reversal learning
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Mixtures of strategies underlie rodent behavior during reversal learning

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011430-e1011430 [Peer Reviewed Journal]

Copyright: © 2023 Le et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ;2023 Le et al 2023 Le et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1011430 ;PMID: 37708113

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11
Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning
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Discovering molecular features of intrinsically disordered regions by using evolution for contrastive learning

PLoS computational biology, 2022-06, Vol.18 (6), p.e1010238-e1010238 [Peer Reviewed Journal]

2022 Lu et al 2022 Lu et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1010238 ;PMID: 35767567

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12
Deep supervised, but not unsupervised, models may explain IT cortical representation
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Deep supervised, but not unsupervised, models may explain IT cortical representation

PLoS computational biology, 2014-11, Vol.10 (11), p.e1003915-e1003915 [Peer Reviewed Journal]

COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 Khaligh-Razavi, Kriegeskorte 2014 Khaligh-Razavi, Kriegeskorte ;2014 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Khaligh-Razavi S-M, Kriegeskorte N (2014) Deep Supervised, but Not Unsupervised, Models May Explain IT Cortical Representation. PLoS Comput Biol 10(11): e1003915. doi:10.1371/journal.pcbi.1003915 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003915 ;PMID: 25375136

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13
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes
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Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes

PLoS computational biology, 2016-05, Vol.12 (5), p.e1004842-e1004842 [Peer Reviewed Journal]

COPYRIGHT 2016 Public Library of Science ;COPYRIGHT 2016 Public Library of Science ;2016 Kelleher et al 2016 Kelleher et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1004842 ;PMID: 27145223

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14
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
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Integrating Hi-C links with assembly graphs for chromosome-scale assembly

PLoS computational biology, 2019-08, Vol.15 (8), p.e1007273-e1007273 [Peer Reviewed Journal]

COPYRIGHT 2019 Public Library of Science ;COPYRIGHT 2019 Public Library of Science ;This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1007273 ;PMID: 31433799

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15
Deep neural networks rival the representation of primate IT cortex for core visual object recognition
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Deep neural networks rival the representation of primate IT cortex for core visual object recognition

PLoS computational biology, 2014-12, Vol.10 (12), p.e1003963-e1003963 [Peer Reviewed Journal]

COPYRIGHT 2014 Public Library of Science ;COPYRIGHT 2014 Public Library of Science ;2014 Cadieu et al 2014 Cadieu et al ;2014 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Cadieu CF, Hong H, Yamins DLK, Pinto N, Ardila D, Solomon EA, et al. (2014) Deep Neural Networks Rival the Representation of Primate IT Cortex for Core Visual Object Recognition. PLoS Comput Biol 10(12): e1003963. doi:10.1371/journal.pcbi.1003963 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1003963 ;PMID: 25521294

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16
Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants
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Modelling conformational state dynamics and its role on infection for SARS-CoV-2 Spike protein variants

PLoS computational biology, 2021-08, Vol.17 (8), p.e1009286-e1009286 [Peer Reviewed Journal]

COPYRIGHT 2021 Public Library of Science ;2021 Teruel et al 2021 Teruel et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1009286 ;PMID: 34351895

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17
Self-loops in evolutionary graph theory: Friends or foes?
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Self-loops in evolutionary graph theory: Friends or foes?

PLoS computational biology, 2023-09, Vol.19 (9), p.e1011387-e1011387 [Peer Reviewed Journal]

COPYRIGHT 2023 Public Library of Science ;2023 Sharma et al 2023 Sharma et al ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1011387 ;PMID: 37656739

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18
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data
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MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

PLoS computational biology, 2016-06, Vol.12 (6), p.e1004957-e1004957 [Peer Reviewed Journal]

COPYRIGHT 2016 Public Library of Science ;COPYRIGHT 2016 Public Library of Science ;2016 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. (2016) MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol 12(6): e1004957. doi:10.1371/journal.pcbi.1004957 ;2016 Huson et al 2016 Huson et al ;2016 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Huson DH, Beier S, Flade I, Górska A, El-Hadidi M, Mitra S, et al. (2016) MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol 12(6): e1004957. doi:10.1371/journal.pcbi.1004957 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1004957 ;PMID: 27327495

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19
An automated approach to the quantitation of vocalizations and vocal learning in the songbird
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An automated approach to the quantitation of vocalizations and vocal learning in the songbird

PLoS computational biology, 2018-08, Vol.14 (8), p.e1006437-e1006437 [Peer Reviewed Journal]

2018 Mets, Brainard 2018 Mets, Brainard ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/JOURNAL.PCBI.1006437 ;PMID: 30169523

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20
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
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Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

PLoS computational biology, 2017-01, Vol.13 (1), p.e1005324-e1005324 [Peer Reviewed Journal]

COPYRIGHT 2017 Public Library of Science ;COPYRIGHT 2017 Public Library of Science ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wang S, Sun S, Li Z, Zhang R, Xu J (2017) Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput Biol 13(1): e1005324. doi:10.1371/journal.pcbi.1005324 ;2017 Wang et al 2017 Wang et al ;2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Wang S, Sun S, Li Z, Zhang R, Xu J (2017) Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput Biol 13(1): e1005324. doi:10.1371/journal.pcbi.1005324 ;ISSN: 1553-7358 ;ISSN: 1553-734X ;EISSN: 1553-7358 ;DOI: 10.1371/journal.pcbi.1005324 ;PMID: 28056090

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