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1
Neural networks to learn protein sequence-function relationships from deep mutational scanning data
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Neural networks to learn protein sequence-function relationships from deep mutational scanning data

Proceedings of the National Academy of Sciences - PNAS, 2021-11, Vol.118 (48) [Peer Reviewed Journal]

Copyright © 2021 the Author(s). Published by PNAS. ;Copyright National Academy of Sciences Nov 30, 2021 ;Copyright © 2021 the Author(s). Published by PNAS. 2021 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2104878118 ;PMID: 34815338

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2
UniProt: the Universal Protein Knowledgebase in 2023
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UniProt: the Universal Protein Knowledgebase in 2023

Nucleic acids research, 2023-01, Vol.51 (D1), p.D523-D531 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkac1052 ;PMID: 36408920

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3
Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins
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Comparative roles of charge, π, and hydrophobic interactions in sequence-dependent phase separation of intrinsically disordered proteins

Proceedings of the National Academy of Sciences - PNAS, 2020-11, Vol.117 (46), p.28795-28805 [Peer Reviewed Journal]

Copyright National Academy of Sciences Nov 17, 2020 ;2020 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2008122117 ;PMID: 33139563

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4
CDD/SPARCLE: the conserved domain database in 2020
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CDD/SPARCLE: the conserved domain database in 2020

Nucleic acids research, 2020-01, Vol.48 (D1), p.D265-D268 [Peer Reviewed Journal]

Published by Oxford University Press on behalf of Nucleic Acids Research 2019. 2019 ;Published by Oxford University Press on behalf of Nucleic Acids Research 2019. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz991 ;PMID: 31777944

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5
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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6
The InterPro protein families and domains database: 20 years on
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The InterPro protein families and domains database: 20 years on

Nucleic Acids Research, 2021-01, Vol.49 (D1), p.D344-D354 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. 2021 ;The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. ;2020. This work is licensed 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. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkaa977 ;PMID: 33156333

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7
InterPro in 2022
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InterPro in 2022

Nucleic acids research, 2023-01, Vol.51 (D1), p.D418-D427 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. 2023 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkac993 ;PMID: 36350672

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8
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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9
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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10
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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11
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Nucleic acids research, 2022-01, Vol.50 (D1), p.D439-D444 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022 ;The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkab1061 ;PMID: 34791371

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12
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Nucleic acids research, 2022-01, Vol.50 (D1), p.D543-D552 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 2022 ;The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkab1038 ;PMID: 34723319

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13
COVID-19: Drug Targets and Potential Treatments
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Article
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COVID-19: Drug Targets and Potential Treatments

Journal of Medicinal Chemistry, 2020-11 [Peer Reviewed Journal]

2020. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the associated terms available at https://www.acs.org/content/acs/en/terms.html ;DOI: 10.1021/acs.jmedchem.0c00606

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14
What Are 3' UTRs Doing?
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What Are 3' UTRs Doing?

Cold Spring Harbor perspectives in biology, 2019-10, Vol.11 (10), p.a034728 [Peer Reviewed Journal]

Copyright © 2019 Cold Spring Harbor Laboratory Press; all rights reserved. ;Copyright Cold Spring Harbor Laboratory Press Oct 2019 ;2019 ;ISSN: 1943-0264 ;EISSN: 1943-0264 ;DOI: 10.1101/cshperspect.a034728 ;PMID: 30181377

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15
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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16
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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17
MAFFT-DASH: integrated protein sequence and structural alignment
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Article
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MAFFT-DASH: integrated protein sequence and structural alignment

Nucleic acids research, 2019-07, Vol.47 (W1), p.W5-W10 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz342 ;PMID: 31062021

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18
KEGG as a reference resource for gene and protein annotation
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Article
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KEGG as a reference resource for gene and protein annotation

Nucleic acids research, 2016-01, Vol.44 (D1), p.D457-D462 [Peer Reviewed Journal]

The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2016 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkv1070 ;PMID: 26476454

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19
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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20
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences

Proceedings of the National Academy of Sciences - PNAS, 2021-04, Vol.118 (15), p.1 [Peer Reviewed Journal]

Copyright © 2021 the Author(s). Published by PNAS. ;COPYRIGHT 2021 National Academy of Sciences ;Copyright National Academy of Sciences Apr 13, 2021 ;Copyright © 2021 the Author(s). Published by PNAS. 2021 ;ISSN: 0027-8424 ;EISSN: 1091-6490 ;DOI: 10.1073/pnas.2016239118 ;PMID: 33876751

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