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1
Twin-width I: tractable FO model checking
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Article
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Twin-width I: tractable FO model checking

Journal of the ACM, 2022-02, Vol.69 (1), p.1-46 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0004-5411 ;EISSN: 1557-735X ;DOI: 10.1145/3486655

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2
Optimization with Sparsity-Inducing Penalties
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Optimization with Sparsity-Inducing Penalties

Foundations and trends in machine learning, 2012 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 1935-8237 ;EISSN: 1935-8245 ;DOI: 10.1561/2200000015

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3
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
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Cooler: scalable storage for Hi-C data and other genomically labeled arrays

Bioinformatics, 2020-01, Vol.36 (1), p.311-316 [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 e-mail: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btz540 ;PMID: 31290943

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4
BBKNN: fast batch alignment of single cell transcriptomes
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BBKNN: fast batch alignment of single cell transcriptomes

Bioinformatics, 2020-02, Vol.36 (3), p.964-965 [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/btz625 ;PMID: 31400197

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5
Computing the Homology of Basic Semialgebraic Sets in Weak Exponential Time
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Article
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Computing the Homology of Basic Semialgebraic Sets in Weak Exponential Time

Journal of the ACM, 2019-01, Vol.66 (1), p.1-30 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0004-5411 ;EISSN: 1557-735X ;DOI: 10.1145/3275242

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6
New strategies to improve minimap2 alignment accuracy
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New strategies to improve minimap2 alignment accuracy

Bioinformatics, 2021-12, Vol.37 (23), p.4572-4574 [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: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btab705 ;PMID: 34623391

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7
Scaling read aligners to hundreds of threads on general-purpose processors
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Scaling read aligners to hundreds of threads on general-purpose processors

Bioinformatics, 2019-02, Vol.35 (3), p.421-432 [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/bty648 ;PMID: 30020410

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8
Algorithms for Big Data: DFG Priority Program 1736
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Book
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Algorithms for Big Data: DFG Priority Program 1736

ISBN: 9783031215346 ;ISBN: 3031215346 ;DOI: 10.1007/978-3-031-21534-6

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9
Data Clustering: Algorithms and Applications
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Book
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Data Clustering: Algorithms and Applications

2014 by Taylor & Francis Group, LLC ;ISBN: 9781466558212 ;ISBN: 1466558210 ;EISBN: 1315373513 ;EISBN: 9781315373515 ;EISBN: 9781466558229 ;EISBN: 1466558229 ;EISBN: 9781315360416 ;EISBN: 1315360411 ;EISBN: 9781315362786 ;EISBN: 1315362783 ;EISBN: 9781498785778 ;EISBN: 1498785778 ;DOI: 10.1201/9781315373515 ;OCLC: 856870768

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10
MolTrans: Molecular Interaction Transformer for drug–target interaction prediction
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MolTrans: Molecular Interaction Transformer for drug–target interaction prediction

Bioinformatics, 2021-05, Vol.37 (6), p.830-836 [Peer Reviewed Journal]

The Author(s) 2020. Published by Oxford University Press. 2020 ;The Author(s) 2020. Published by Oxford University Press. ;ISSN: 1367-4803 ;EISSN: 1460-2059 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btaa880 ;PMID: 33070179

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11
DeepDTA: deep drug-target binding affinity prediction
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DeepDTA: deep drug-target binding affinity prediction

Bioinformatics, 2018-09, Vol.34 (17), p.i821-i829 [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/bty593 ;PMID: 30423097

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12
Parallelization of MAFFT for large-scale multiple sequence alignments
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Parallelization of MAFFT for large-scale multiple sequence alignments

Bioinformatics, 2018-07, Vol.34 (14), p.2490-2492 [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/bty121 ;PMID: 29506019

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13
Faster Modular Composition
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Article
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Faster Modular Composition

Journal of the ACM, 2024-04 [Peer Reviewed Journal]

Distributed under a Creative Commons Attribution 4.0 International License ;ISSN: 0004-5411 ;EISSN: 1557-735X ;DOI: 10.1145/3638349

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14
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Bioinformatics, 2015-05, Vol.31 (10), p.1674-1676 [Peer Reviewed Journal]

The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;EISSN: 1460-2059 ;DOI: 10.1093/bioinformatics/btv033 ;PMID: 25609793

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15
STREME: accurate and versatile sequence motif discovery
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Article
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STREME: accurate and versatile sequence motif discovery

Bioinformatics (Oxford, England), 2021-09, Vol.37 (18), p.2834-2840 [Peer Reviewed Journal]

The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com. ;The Author(s) 2021. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com 2021 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btab203 ;PMID: 33760053

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16
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
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A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

Bioinformatics (Oxford, England), 2015-02, Vol.31 (4), p.587-589 [Peer Reviewed Journal]

The Author 2014. 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/btu661 ;PMID: 25338718

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17
YASARA View - molecular graphics for all devices - from smartphones to workstations
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Article
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YASARA View - molecular graphics for all devices - from smartphones to workstations

Bioinformatics (Oxford, England), 2014-10, Vol.30 (20), p.2981-2982 [Peer Reviewed Journal]

The Author 2014. Published by Oxford University Press. ;The Author 2014. Published by Oxford University Press. 2014 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btu426 ;PMID: 24996895

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18
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers
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ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

Bioinformatics (Oxford, England), 2014-06, Vol.30 (12), p.1771-1773 [Peer Reviewed Journal]

The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. ;The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com 2014 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btu097 ;PMID: 24532726

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19
Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo
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Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo

Bioinformatics (Oxford, England), 2017-06, Vol.33 (11), p.1630-1638 [Peer Reviewed Journal]

The Author 2017. Published by Oxford University Press. ;The Author 2017. Published by Oxford University Press. 2017 ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btx025 ;PMID: 28108445

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20
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
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Article
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MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

Bioinformatics, 2016-02, Vol.32 (4), p.605-607 [Peer Reviewed Journal]

The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com. ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;EISSN: 1460-2059 ;DOI: 10.1093/bioinformatics/btv638 ;PMID: 26515820

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