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The use of proton transfer reaction mass spectrometry for high throughput screening of terpene synthases

Journal of mass spectrometry., 2023-06, Vol.58 (6), p.e4951-n/a

2023

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PanTools v3: functional annotation, classification and phylogenomics

Bioinformatics, 2022-09, Vol.38 (18), p.4403-4405

2022

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Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases

PLoS computational biology, 2021-03, Vol.17 (3), p.e1008197-e1008197

2021

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Geometricus represents protein structures as shape-mers derived from moment invariants

Bioinformatics, 2020-12, Vol.36 (Supplement_2), p.i718-i725

2020

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Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

BMC bioinformatics, 2020-06, Vol.21 (1), p.253-253, Article 253

2020

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GeneNoteBook, a collaborative notebook for comparative genomics

Bioinformatics, 2019-11, Vol.35 (22), p.4779-4781

2019

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poreTally: run and publish de novo nanopore assembler benchmarks

Bioinformatics, 2019-08, Vol.35 (15), p.2663-2664

2019

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Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis

Bioinformatics (Oxford, England), 2019-06, Vol.35 (12), p.2036-2042

2019

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TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Bioinformatics, 2018-11, Vol.34 (22), p.3864-3872

2018

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Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse

BMC bioinformatics, 2018-10, Vol.19 (1), p.373-373, Article 373

2018

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Efficient inference of homologs in large eukaryotic pan-proteomes

BMC bioinformatics, 2018-09, Vol.19 (1), p.340-340, Article 340

2018

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Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

Briefings in bioinformatics, 2018-05, Vol.19 (3), p.387-403

2018

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Computational pan-genomics: status, promises and challenges

Briefings in bioinformatics, 2018-01, Vol.19 (1), p.118-135

2018

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Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

PLoS computational biology, 2017-09, Vol.13 (9), p.e1005734

2017

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Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

BMC bioinformatics, 2016-12, Vol.17 (Suppl 16), p.437-437, Article 437

2016

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PanTools: representation, storage and exploration of pan-genomic data

Bioinformatics (Oxford, England), 2016-09, Vol.32 (17), p.i487-i493

2016

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Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

BMC bioinformatics, 2015-11, Vol.16 (352), p.352-352, Article 352

2015

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ACE: accurate correction of errors using K-mer tries

Bioinformatics, 2015-10, Vol.31 (19), p.3216-3218

2015

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Making the difference: integrating structural variation detection tools

Briefings in bioinformatics, 2015-09, Vol.16 (5), p.852-864

2015

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Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

PLoS computational biology, 2015-08, Vol.11 (8), p.e1004336-e1004336

2015

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SPiCE: a web-based tool for sequence-based protein classification and exploration

BMC bioinformatics, 2014-03, Vol.15 (1), p.93-93, Article 93

2014

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Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

Bioinformatics, 2013-11, Vol.29 (22), p.2826-2834

2013

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Pattern recognition in bioinformatics

Briefings in bioinformatics, 2013-09, Vol.14 (5), p.633-647

2013

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De novo detection of copy number variation by co-assembly

Bioinformatics, 2012-12, Vol.28 (24), p.3195-3202

2012

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GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

Bioinformatics (Oxford, England), 2012-06, Vol.28 (11), p.1429-1437

2012

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The use of proton transfer reaction mass spectrometry for high throughput screening of terpene synthases

PanTools v3: functional annotation, classification and phylogenomics

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases

Geometricus represents protein structures as shape-mers derived from moment invariants

Hap10: reconstructing accurate and long polyploid haplotypes using linked reads

GeneNoteBook, a collaborative notebook for comparative genomics

poreTally: run and publish de novo nanopore assembler benchmarks

Improved inference of intermolecular contacts through protein-protein interaction prediction using coevolutionary analysis

TriPoly: haplotype estimation for polyploids using sequencing data of related individuals

Predicting variant deleteriousness in non-human species: applying the CADD approach in mouse

Efficient inference of homologs in large eukaryotic pan-proteomes

Exploiting next-generation sequencing to solve the haplotyping puzzle in polyploids: a simulation study

Computational pan-genomics: status, promises and challenges

Sequence features of viral and human Internal Ribosome Entry Sites predictive of their activity

Selected proceedings of Machine Learning in Systems Biology: MLSB 2016

PanTools: representation, storage and exploration of pan-genomic data

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data

ACE: accurate correction of errors using K-mer tries

Making the difference: integrating structural variation detection tools

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

SPiCE: a web-based tool for sequence-based protein classification and exploration

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold

Pattern recognition in bioinformatics

De novo detection of copy number variation by co-assembly

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies

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