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1
Protein sequence design with a learned potential
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Protein sequence design with a learned potential

Nature communications, 2022-02, Vol.13 (1), p.746-746, Article 746 [Peer Reviewed Journal]

2022. The Author(s). ;The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2022 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-022-28313-9 ;PMID: 35136054

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2
Fast and sensitive taxonomic classification for metagenomics with Kaiju
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Fast and sensitive taxonomic classification for metagenomics with Kaiju

Nature communications, 2016-04, Vol.7 (1), p.11257-11257, Article 11257 [Peer Reviewed Journal]

Copyright Nature Publishing Group Apr 2016 ;Copyright © 2016, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/ncomms11257 ;PMID: 27071849

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3
A crowdsourcing open platform for literature curation in UniProt
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A crowdsourcing open platform for literature curation in UniProt

PLoS biology, 2021-12, Vol.19 (12), p.e3001464-e3001464 [Peer Reviewed Journal]

2021 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2021 Wang et al 2021 Wang et al ;ISSN: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.3001464 ;PMID: 34871295

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4
ECNet is an evolutionary context-integrated deep learning framework for protein engineering
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ECNet is an evolutionary context-integrated deep learning framework for protein engineering

Nature communications, 2021-09, Vol.12 (1), p.5743-14, Article 5743 [Peer Reviewed Journal]

2021. The Author(s). ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2021 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-021-25976-8 ;PMID: 34593817

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5
Accurately clustering biological sequences in linear time by relatedness sorting
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Accurately clustering biological sequences in linear time by relatedness sorting

Nature communications, 2024-04, Vol.15 (1), p.3047-3047 [Peer Reviewed Journal]

2024. The Author(s). ;The Author(s) 2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2024 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-024-47371-9 ;PMID: 38589369

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6
ProtGPT2 is a deep unsupervised language model for protein design
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ProtGPT2 is a deep unsupervised language model for protein design

Nature communications, 2022-07, Vol.13 (1), p.4348-4348, Article 4348 [Peer Reviewed Journal]

The Author(s) 2022. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2022 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-022-32007-7 ;PMID: 35896542

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7
Publisher Correction: Thymosin α1 represents a potential potent single-molecule-based therapy for cystic fibrosis
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Publisher Correction: Thymosin α1 represents a potential potent single-molecule-based therapy for cystic fibrosis

Nature medicine, 2018-09, Vol.24 (9), p.1482-1482 [Peer Reviewed Journal]

Copyright Nature Publishing Group Sep 2018 ;ISSN: 1078-8956 ;EISSN: 1546-170X ;DOI: 10.1038/s41591-018-0099-2 ;PMID: 29934535

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8
AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence
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AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

Scientific reports, 2021-06, Vol.11 (1), p.12728-12728, Article 12728 [Peer Reviewed Journal]

This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021 ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/s41598-021-91456-0 ;PMID: 34135355

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9
Dimers of DNA-PK create a stage for DNA double-strand break repair
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Dimers of DNA-PK create a stage for DNA double-strand break repair

Nature structural & molecular biology, 2021-01, Vol.28 (1), p.13-19 [Peer Reviewed Journal]

The Author(s), under exclusive licence to Springer Nature America, Inc. 2020. ;ISSN: 1545-9993 ;EISSN: 1545-9985 ;DOI: 10.1038/s41594-020-00517-x ;PMID: 33077952

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10
Sensitive protein alignments at tree-of-life scale using DIAMOND
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Sensitive protein alignments at tree-of-life scale using DIAMOND

Nature methods, 2021-04, Vol.18 (4), p.366-368 [Peer Reviewed Journal]

COPYRIGHT 2021 Nature Publishing Group ;The Author(s) 2021. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2021 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-021-01101-x ;PMID: 33828273

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11
Improved protein structure prediction using potentials from deep learning
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Improved protein structure prediction using potentials from deep learning

Nature (London), 2020-01, Vol.577 (7792), p.706-710 [Peer Reviewed Journal]

COPYRIGHT 2020 Nature Publishing Group ;COPYRIGHT 2020 Nature Publishing Group ;Copyright Nature Publishing Group Jan 30, 2020 ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/s41586-019-1923-7 ;PMID: 31942072

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12
Highly accurate protein structure prediction with AlphaFold
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Highly accurate protein structure prediction with AlphaFold

Nature (London), 2021-08, Vol.596 (7873), p.583-589 [Peer Reviewed Journal]

2021. The Author(s). ;COPYRIGHT 2021 Nature Publishing Group ;Copyright Nature Publishing Group Aug 26, 2021 ;The Author(s) 2021 ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/s41586-021-03819-2 ;PMID: 34265844

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13
Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase
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Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase

Biophysical journal, 2018-03, Vol.114 (6), p.1302-1312 [Peer Reviewed Journal]

2018 Biophysical Society ;Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved. ;2018 Biophysical Society. 2018 Biophysical Society ;ISSN: 0006-3495 ;EISSN: 1542-0086 ;DOI: 10.1016/j.bpj.2018.02.005 ;PMID: 29590588

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14
Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains
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Article
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Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains

Nature chemistry, 2022-02, Vol.14 (2), p.196-207 [Peer Reviewed Journal]

2021. The Author(s), under exclusive licence to Springer Nature Limited. ;The Author(s), under exclusive licence to Springer Nature Limited 2021. ;ISSN: 1755-4330 ;EISSN: 1755-4349 ;DOI: 10.1038/s41557-021-00840-w ;PMID: 34931046

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15
HydDB: A web tool for hydrogenase classification and analysis
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Article
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HydDB: A web tool for hydrogenase classification and analysis

Scientific reports, 2016-09, Vol.6 (1), p.34212-34212, Article 34212 [Peer Reviewed Journal]

Copyright Nature Publishing Group Sep 2016 ;Copyright © 2016, The Author(s) 2016 The Author(s) ;ISSN: 2045-2322 ;EISSN: 2045-2322 ;DOI: 10.1038/srep34212 ;PMID: 27670643

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16
Unified rational protein engineering with sequence-based deep representation learning
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Unified rational protein engineering with sequence-based deep representation learning

Nature methods, 2019-12, Vol.16 (12), p.1315-1322 [Peer Reviewed Journal]

COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group Dec 2019 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-019-0598-1 ;PMID: 31636460

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17
A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold
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Article
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A 3.8 Å resolution cryo-EM structure of a small protein bound to an imaging scaffold

Nature communications, 2019-04, Vol.10 (1), p.1864-1864, Article 1864 [Peer Reviewed Journal]

The Author(s) 2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2019 ;ISSN: 2041-1723 ;EISSN: 2041-1723 ;DOI: 10.1038/s41467-019-09836-0 ;PMID: 31015551

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18
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
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Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Nature methods, 2019-07, Vol.16 (7), p.603-606 [Peer Reviewed Journal]

COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group Jul 2019 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-019-0437-4 ;PMID: 31235882

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19
Machine-learning-guided directed evolution for protein engineering
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Machine-learning-guided directed evolution for protein engineering

Nature methods, 2019-08, Vol.16 (8), p.687-694 [Peer Reviewed Journal]

COPYRIGHT 2019 Nature Publishing Group ;Copyright Nature Publishing Group Aug 2019 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/s41592-019-0496-6 ;PMID: 31308553

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20
SignalP 5.0 improves signal peptide predictions using deep neural networks
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SignalP 5.0 improves signal peptide predictions using deep neural networks

Nature biotechnology, 2019-04, Vol.37 (4), p.420-423 [Peer Reviewed Journal]

2019© The Author(s), under exclusive licence to Springer Nature America, Inc. 2019 ;ISSN: 1087-0156 ;ISSN: 1546-1696 ;EISSN: 1546-1696 ;DOI: 10.1038/s41587-019-0036-z ;PMID: 30778233

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