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1
3D Extracellular Matrix Mimics: Fundamental Concepts and Role of Materials Chemistry to Influence Stem Cell Fate
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3D Extracellular Matrix Mimics: Fundamental Concepts and Role of Materials Chemistry to Influence Stem Cell Fate

Biomacromolecules, 2020-06, Vol.21, p.1968-1994 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1525-7797 ;EISSN: 1526-4602 ;DOI: 10.1021/acs.biomac.0c00045

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2
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
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GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Bioinformatics, 2019-11, Vol.36 (6), p.1925-1927 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz848 ;PMID: 31730192

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3
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
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GTDB-Tk v2: memory friendly classification with the genome taxonomy database

Bioinformatics (Oxford, England), 2022-11, Vol.38 (23), p.5315-5316 [Peer Reviewed Journal]

The Author(s) 2022. Published by Oxford University Press. ;The Author(s) 2022. Published by Oxford University Press. 2022 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btac672 ;PMID: 36218463

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4
GraphDTA: predicting drug–target binding affinity with graph neural networks
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GraphDTA: predicting drug–target binding affinity with graph neural networks

Bioinformatics, 2021-05, Vol.37 (8), p.1140-1147 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2020 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btaa921

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5
Multiple Functions of MYB Transcription Factors in Abiotic Stress Responses
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Multiple Functions of MYB Transcription Factors in Abiotic Stress Responses

International journal of molecular sciences, 2021-06, Vol.22 (11), p.6125 [Peer Reviewed Journal]

2021 by the authors. 2021 ;ISSN: 1422-0067 ;ISSN: 1661-6596 ;EISSN: 1422-0067 ;DOI: 10.3390/ijms22116125 ;PMID: 34200125

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6
The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research
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The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research

PLoS biology, 2020-07, Vol.18 (7), p.e3000410-e3000410 [Peer Reviewed Journal]

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: 1545-7885 ;ISSN: 1544-9173 ;EISSN: 1545-7885 ;DOI: 10.1371/journal.pbio.3000410 ;PMID: 32663219

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7
BioBERT: a pre-trained biomedical language representation model for biomedical text mining
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BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Bioinformatics, 2020-02, Vol.36 (4), p.1234-1240 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz682 ;PMID: 31501885

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8
Complete H-1 and C-13 NMR spectral assignment of D-glucofuranose
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Complete H-1 and C-13 NMR spectral assignment of D-glucofuranose

Carbohydrate research, 2022, Vol.511 [Peer Reviewed Journal]

ISSN: 1873-426X ;ISSN: 0008-6215 ;EISSN: 1873-426X ;DOI: 10.1016/j.carres.2021.108477

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9
Graph embedding on biomedical networks: methods, applications and evaluations
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Graph embedding on biomedical networks: methods, applications and evaluations

Bioinformatics, 2020-02, Vol.36 (4), p.1241-1251 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz718 ;PMID: 31584634

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10
Noncoding RNA:RNA Regulatory Networks in Cancer
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Noncoding RNA:RNA Regulatory Networks in Cancer

International journal of molecular sciences, 2018-04, Vol.19 (5), p.1310 [Peer Reviewed Journal]

Copyright MDPI AG 2018 ;2018 by the authors. 2018 ;ISSN: 1422-0067 ;ISSN: 1661-6596 ;EISSN: 1422-0067 ;DOI: 10.3390/ijms19051310 ;PMID: 29702599

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11
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
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RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

Bioinformatics, 2019-11, Vol.35 (21), p.4453-4455 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz305 ;PMID: 31070718

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12
Scaling tree-based automated machine learning to biomedical big data with a feature set selector
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Scaling tree-based automated machine learning to biomedical big data with a feature set selector

Bioinformatics, 2020-01, Vol.36 (1), p.250-256 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz470 ;PMID: 31165141

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13
fastp: an ultra-fast all-in-one FASTQ preprocessor
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fastp: an ultra-fast all-in-one FASTQ preprocessor

Bioinformatics, 2018-09, Vol.34 (17), p.i884-i890 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty560 ;PMID: 30423086

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14
Minimap2: pairwise alignment for nucleotide sequences
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Minimap2: pairwise alignment for nucleotide sequences

Bioinformatics, 2018-09, Vol.34 (18), p.3094-3100 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty191 ;PMID: 29750242

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15
ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
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ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Bioinformatics, 2019-02, Vol.35 (3), p.526-528 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2018 ;Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty633 ;PMID: 30016406

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16
TISIDB: an integrated repository portal for tumor–immune system interactions
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TISIDB: an integrated repository portal for tumor–immune system interactions

Bioinformatics, 2019-10, Vol.35 (20), p.4200-4202 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2019 ;The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz210 ;PMID: 30903160

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17
Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences
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Compound-protein interaction prediction with end-to-end learning of neural networks for graphs and sequences

Bioinformatics, 2019-01, Vol.35 (2), p.309-318 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty535 ;PMID: 29982330

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18
ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes
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ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

Bioinformatics, 2018-07, Vol.34 (13), p.2263-2270 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty053 ;PMID: 29408954

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19
Nextstrain: real-time tracking of pathogen evolution
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Nextstrain: real-time tracking of pathogen evolution

Bioinformatics, 2018-12, Vol.34 (23), p.4121-4123 [Peer Reviewed Journal]

The Author(s) 2018. Published by Oxford University Press. 2018 ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/bty407 ;PMID: 29790939

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20
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
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KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

Bioinformatics, 2020-04, Vol.36 (7), p.2251-2252 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press. 2019 ;The Author(s) 2019. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz859 ;PMID: 31742321

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