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1
BioGPT: generative pre-trained transformer for biomedical text generation and mining
BioGPT: generative pre-trained transformer for biomedical text generation and mining
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BioGPT: generative pre-trained transformer for biomedical text generation and mining

Briefings in bioinformatics, 2022-11, Vol.23 (6) [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbac409 ;PMID: 36156661

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2
Community challenges in biomedical text mining over 10 years: success, failure and the future
Community challenges in biomedical text mining over 10 years: success, failure and the future
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Community challenges in biomedical text mining over 10 years: success, failure and the future

Briefings in bioinformatics, 2016-01, Vol.17 (1), p.132-144 [Peer Reviewed Journal]

Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US. ;Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US. 2015 ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbv024 ;PMID: 25935162

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3
ProteinBERT: a universal deep-learning model of protein sequence and function
ProteinBERT: a universal deep-learning model of protein sequence and function
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ProteinBERT: a universal deep-learning model of protein sequence and function

Bioinformatics, 2022-04, Vol.38 (8), p.2102-2110 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. 2022 ;The Author(s) 2022. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btac020 ;PMID: 35020807

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4
Biomedical named entity recognition and linking datasets: survey and our recent development
Biomedical named entity recognition and linking datasets: survey and our recent development
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Biomedical named entity recognition and linking datasets: survey and our recent development

Briefings in bioinformatics, 2020-12, Vol.21 (6), p.2219-2238 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2020 ;The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbaa054 ;PMID: 32602538

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5
An extensive review of tools for manual annotation of documents
An extensive review of tools for manual annotation of documents
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An extensive review of tools for manual annotation of documents

Briefings in bioinformatics, 2021-01, Vol.22 (1), p.146-163 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. All rights reserved. 2019 ;The Author(s) 2019. Published by Oxford University Press. All rights reserved. ;ISSN: 1477-4054 ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbz130 ;PMID: 31838514

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6
Recent advances in biomedical literature mining
Recent advances in biomedical literature mining
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Recent advances in biomedical literature mining

Briefings in Bioinformatics, 2021-05, Vol.22 (3) [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;2020. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the associated terms available at https://academic.oup.com/journals/pages/coronavirus . ;The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2020 ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbaa057 ;PMID: 32422651

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7
Exploring prevalence of wound infections and related patient characteristics in homecare using natural language processing
Exploring prevalence of wound infections and related patient characteristics in homecare using natural language processing
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Exploring prevalence of wound infections and related patient characteristics in homecare using natural language processing

International wound journal, 2022-01, Vol.19 (1), p.211-221 [Peer Reviewed Journal]

2021 The Authors. published by Medicalhelplines.com Inc (3M) and John Wiley & Sons Ltd. ;2021 The Authors. International Wound Journal published by Medicalhelplines.com Inc (3M) and John Wiley & Sons Ltd. ;ISSN: 1742-4801 ;EISSN: 1742-481X ;DOI: 10.1111/iwj.13623 ;PMID: 34105873

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8
MHCRoBERTa: pan-specific peptide–MHC class I binding prediction through transfer learning with label-agnostic protein sequences
MHCRoBERTa: pan-specific peptide–MHC class I binding prediction through transfer learning with label-agnostic protein sequences
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MHCRoBERTa: pan-specific peptide–MHC class I binding prediction through transfer learning with label-agnostic protein sequences

Briefings in bioinformatics, 2022-05, Vol.23 (3) [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2022 ;The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbab595 ;PMID: 35443027

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9
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases
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Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

Briefings in bioinformatics, 2019-09, Vol.20 (5), p.1878-1912 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. 2018 ;The Author(s) 2018. Published by Oxford University Press. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bby061 ;PMID: 30084866

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10
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain
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BIOSSES: a semantic sentence similarity estimation system for the biomedical domain

Bioinformatics (Oxford, England), 2017-07, Vol.33 (14), p.i49-i58 [Peer Reviewed Journal]

The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com ;The Author 2017. Published by Oxford University Press. 2017 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btx238 ;PMID: 28881973

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11
BioRED: a rich biomedical relation extraction dataset
BioRED: a rich biomedical relation extraction dataset
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BioRED: a rich biomedical relation extraction dataset

Briefings in bioinformatics, 2022-09, Vol.23 (5) [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. 2022 ;The Author(s) 2022. Published by Oxford University Press. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbac282 ;PMID: 35849818

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12
Text mining approaches for dealing with the rapidly expanding literature on COVID-19
Text mining approaches for dealing with the rapidly expanding literature on COVID-19
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Text mining approaches for dealing with the rapidly expanding literature on COVID-19

Briefings in Bioinformatics, 2021-03, Vol.22 (2), p.781-799 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. 2020 ;The Author(s) 2020. Published by Oxford University Press. ;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: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbaa296 ;PMID: 33279995

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13
A novel antibacterial peptide recognition algorithm based on BERT
A novel antibacterial peptide recognition algorithm based on BERT
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A novel antibacterial peptide recognition algorithm based on BERT

Briefings in bioinformatics, 2021-11, Vol.22 (6) [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbab200 ;PMID: 34037687

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14
Corpus domain effects on distributional semantic modeling of medical terms
Corpus domain effects on distributional semantic modeling of medical terms
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Corpus domain effects on distributional semantic modeling of medical terms

Bioinformatics (Oxford, England), 2016-12, Vol.32 (23), p.3635-3644 [Peer Reviewed Journal]

The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. ;The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com 2016 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btw529 ;PMID: 27531100

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15
A survey on deep learning in DNA/RNA motif mining
A survey on deep learning in DNA/RNA motif mining
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A survey on deep learning in DNA/RNA motif mining

Briefings in bioinformatics, 2021-07, Vol.22 (4) [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. 2020 ;The Author(s) 2020. Published by Oxford University Press. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbaa229 ;PMID: 33005921

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16
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification
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AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification

Briefings in bioinformatics, 2022-07, Vol.23 (4) [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. 2022 ;The Author(s) 2022. Published by Oxford University Press. ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbac272 ;PMID: 35817396

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17
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models
BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models
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BERT-Kcr: prediction of lysine crotonylation sites by a transfer learning method with pre-trained BERT models

Bioinformatics (Oxford, England), 2022-01, Vol.38 (3), p.648-654 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021 ;The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btab712 ;PMID: 34643684

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18
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource
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Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource

Briefings in bioinformatics, 2024-05, Vol.25 (3) [Peer Reviewed Journal]

The Author(s) 2024. Published by Oxford University Press. 2024 ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbae132

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19
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
GOSemSim: an R package for measuring semantic similarity among GO terms and gene products
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GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

Bioinformatics, 2010-04, Vol.26 (7), p.976-978 [Peer Reviewed Journal]

2015 INIST-CNRS ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btq064 ;PMID: 20179076

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20
Neural representational similarity between L1 and L2 in spoken and written language processing
Neural representational similarity between L1 and L2 in spoken and written language processing
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Neural representational similarity between L1 and L2 in spoken and written language processing

Human brain mapping, 2020-12, Vol.41 (17), p.4935-4951 [Peer Reviewed Journal]

2020 The Authors. published by Wiley Periodicals LLC. ;2020 The Authors. Human Brain Mapping published by Wiley Periodicals LLC. ;2020. This article 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. ;ISSN: 1065-9471 ;EISSN: 1097-0193 ;DOI: 10.1002/hbm.25171 ;PMID: 32820847

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