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Adaptive seeds tame genomic sequence comparison

Genome research, 2011-03, Vol.21 (3), p.487-493

2011

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Significant non-existence of sequences in genomes and proteomes

Nucleic acids research, 2021-04, Vol.49 (6), p.3139-3155

2021

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Improved DNA-Versus-Protein Homology Search for Protein Fossils

IEEE/ACM transactions on computational biology and bioinformatics, 2023-05, Vol.20 (3), p.1691-1699

2023

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Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Genome Biology, 2019-03, Vol.20 (1), p.58-17, Article 58

2019

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Parameters for accurate genome alignment

BMC bioinformatics, 2010-02, Vol.11 (1), p.80-80, Article 80

2010

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A survey of localized sequence rearrangements in human DNA

Nucleic acids research, 2018-02, Vol.46 (4), p.1661-1673

2018

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A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Genome medicine, 2020-07, Vol.12 (1), p.67-67, Article 67

2020

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Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells

Human molecular genetics, 2021-05, Vol.30 (7), p.552-563

2021

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Inferring transcription factor complexes from ChIP-seq data

Nucleic acids research, 2011-08, Vol.39 (15), p.e98-e98

2011

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Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

BMC medical genomics, 2021-01, Vol.14 (1), p.17-12, Article 17

2021

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Long-read sequencing identifies the pathogenic nucleotide repeat expansion in RFC1 in a Japanese case of CANVAS

Journal of human genetics, 2020-05, Vol.65 (5), p.475-480

2020

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Gentle masking of low-complexity sequences improves homology search

PloS one, 2011-12, Vol.6 (12), p.e28819-e28819

2011

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A simple method for finding related sequences by adding probabilities of alternative alignments

Genome research, 2024-09

Frith, Martin C.

2024

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Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

Scientific reports, 2017-11, Vol.7 (1), p.14789-8, Article 14789

2017

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Discovering sequence motifs with arbitrary insertions and deletions

PLoS computational biology, 2008-05, Vol.4 (4), p.e1000071

2008

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A code for transcription initiation in mammalian genomes

Genome Research, 2008-01, Vol.18 (1), p.1-12

2008

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Improved search heuristics find 20,000 new alignments between human and mouse genomes

Nucleic acids research, 2014-04, Vol.42 (7), p.e59-e59

2014

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Evaluation and application of RNA-Seq by MinION

DNA research, 2019-02, Vol.26 (1), p.55-65

2019

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A mostly traditional approach improves alignment of bisulfite-converted DNA

Nucleic acids research, 2012-07, Vol.40 (13), p.e100-e100

2012

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Genomic Targets of Nuclear Estrogen Receptors

Molecular endocrinology (Baltimore, Md.), 2004-08, Vol.18 (8), p.1859-1875

2004

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Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer-Giedion syndrome and Cornelia de Lange syndrome-4

Journal of human genetics, 2020-08, Vol.65 (8), p.667-674

2020

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Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer

DNA research, 2017-12, Vol.24 (6), p.585-596

2017

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Adding unaligned sequences into an existing alignment using MAFFT and LAST

Bioinformatics, 2012-12, Vol.28 (23), p.3144-3146

2012

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Split-alignment of genomes finds orthologies more accurately

Genome Biology, 2015-05, Vol.16 (1), p.106-106, Article 106

2015

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Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Genome Research, 2006-01, Vol.16 (1), p.11-19

2006

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Adaptive seeds tame genomic sequence comparison

Significant non-existence of sequences in genomes and proteomes

Improved DNA-Versus-Protein Homology Search for Protein Fossils

Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads

Parameters for accurate genome alignment

A survey of localized sequence rearrangements in human DNA

A pipeline for complete characterization of complex germline rearrangements from long DNA reads

Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells

Inferring transcription factor complexes from ChIP-seq data

Genome-wide survey of tandem repeats by nanopore sequencing shows that disease-associated repeats are more polymorphic in the general population

Long-read sequencing identifies the pathogenic nucleotide repeat expansion in RFC1 in a Japanese case of CANVAS

Gentle masking of low-complexity sequences improves homology search

A simple method for finding related sequences by adding probabilities of alternative alignments

Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

Discovering sequence motifs with arbitrary insertions and deletions

A code for transcription initiation in mammalian genomes

Improved search heuristics find 20,000 new alignments between human and mouse genomes

Evaluation and application of RNA-Seq by MinION

A mostly traditional approach improves alignment of bisulfite-converted DNA

Genomic Targets of Nuclear Estrogen Receptors

Long-read DNA sequencing fully characterized chromothripsis in a patient with Langer-Giedion syndrome and Cornelia de Lange syndrome-4

Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer

Adding unaligned sequences into an existing alignment using MAFFT and LAST

Split-alignment of genomes finds orthologies more accurately

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

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