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Insertions and deletions as phylogenetic signal in an alignment-free context

PLoS computational biology, 2022-08, Vol.18 (8), p.e1010303-e1010303

2022

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S-conLSH: alignment-free gapped mapping of noisy long reads

BMC bioinformatics, 2021-02, Vol.22 (1), p.64-64, Article 64

2021

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Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

BMC bioinformatics, 2006-02, Vol.7 (1), p.62-62, Article 62

2006

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Benchmarking of alignment-free sequence comparison methods

Genome Biology, 2019-07, Vol.20 (1), p.144-144, Article 144

2019

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The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances

PloS one, 2020-02, Vol.15 (2), p.e0228070-e0228070

2020

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rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

PLoS computational biology, 2016-10, Vol.12 (10), p.e1005107-e1005107

2016

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Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage

BMC bioinformatics, 2019-12, Vol.20 (Suppl 20), p.638-638, Article 638

2019

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Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

Nucleic acids research, 2014-07, Vol.42 (Web Server issue), p.W7

2014

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Sequence Comparison Without Alignment: The SpaM Approaches

Methods in molecular biology (Clifton, N.J.), 2021, Vol.2231, p.121

Morgenstern, Burkhard

2021

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Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42

Nature biotechnology, 2007-09, Vol.25 (9), p.1007-1014

2007

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Meta-analysis of pathway enrichment: combining independent and dependent omics data sets

PloS one, 2014-02, Vol.9 (2), p.e89297-e89297

2014

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Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

PLoS computational biology, 2016-06, Vol.12 (6), p.e1004985-e1004985

2016

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MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data

Metabolomics, 2015-06, Vol.11 (3), p.764-777

2015

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DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

Algorithms for molecular biology, 2008-05, Vol.3 (1), p.6-6, Article 6

2008

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The role of recombination in the emergence of a complex and dynamic HIV epidemic

Retrovirology, 2010-03, Vol.7 (1), p.25-25, Article 25

2010

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Algorithms in Bioinformatics: 14th International Workshop, WABI 2014, Wroclaw, Poland, September 8-10, 2014. Proceedings

2014, 2014

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Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments

Frontiers in microbiology, 2020-08, Vol.11, p.1876-1876

2020

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Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems

Applied and Environmental Microbiology, 2009-06, Vol.75 (12), p.4035-4045

2009

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Phylogeny reconstruction based on the length distribution of k -mismatch common substrings

Algorithms for molecular biology, 2017-12, Vol.12 (1), p.27-27, Article 27

2017

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DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment

BMC bioinformatics, 2005-03, Vol.6 (1), p.66-66

2005

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A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

BMC bioinformatics, 2006-05, Vol.7 (1), p.265-265, Article 265

2006

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Gene prediction in metagenomic fragments: a large scale machine learning approach

BMC bioinformatics, 2008-04, Vol.9 (1), p.217-217, Article 217

2008

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Fast and sensitive multiple alignment of large genomic sequences

BMC bioinformatics, 2003-12, Vol.4 (1), p.66-66

2003

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Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison

Bioinformatics (Oxford, England), 2014-07, Vol.30 (14), p.2000-2008

2014

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OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

BMC bioinformatics, 2009-07, Vol.10 (1), p.219-219, Article 219

2009

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Insertions and deletions as phylogenetic signal in an alignment-free context

S-conLSH: alignment-free gapped mapping of noisy long reads

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Benchmarking of alignment-free sequence comparison methods

The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances

rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison

Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

Sequence Comparison Without Alignment: The SpaM Approaches

Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42

Meta-analysis of pathway enrichment: combining independent and dependent omics data sets

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

The role of recombination in the emergence of a complex and dynamic HIV epidemic

Algorithms in Bioinformatics: 14th International Workshop, WABI 2014, Wroclaw, Poland, September 8-10, 2014. Proceedings

Verticillium longisporum Elicits Media-Dependent Secretome Responses With Capacity to Distinguish Between Plant-Related Environments

Rhizobium sp. Strain NGR234 Possesses a Remarkable Number of Secretion Systems

Phylogeny reconstruction based on the length distribution of k -mismatch common substrings

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

Gene prediction in metagenomic fragments: a large scale machine learning approach

Fast and sensitive multiple alignment of large genomic sequences

Kmacs: the k-mismatch average common substring approach to alignment-free sequence comparison

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

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