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Ten Simple Rules for writing algorithmic bioinformatics conference papers

PLoS computational biology, 2020-04, Vol.16 (4), p.e1007742-e1007742

2020

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Informed and automated k-mer size selection for genome assembly

Bioinformatics, 2014-01, Vol.30 (1), p.31-37

2014

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Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

Nature communications, 2020-12, Vol.11 (1), p.6327-6327, Article 6327

2020

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De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm

Journal of computational biology, 2020-04, Vol.27 (4), p.472-484

2020

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Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Nature communications, 2021-01, Vol.12 (1), p.2-13, Article 2

2021

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What do Eulerian and Hamiltonian cycles have to do with genome assembly?

PLoS computational biology, 2021-05, Vol.17 (5), p.e1008928-e1008928

2021

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Author Correction: Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Nature communications, 2021-02, Vol.12 (1), p.992-992, Article 992

2021

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Y and W Chromosome Assemblies: Approaches and Discoveries

Trends in genetics, 2017-04, Vol.33 (4), p.266-282

2017

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ESKEMAP: exact sketch-based read mapping

Algorithms for molecular biology, 2024-05, Vol.19 (1), p.19-19

2024

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Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Nature communications, 2018-11, Vol.9 (1), p.4601-12, Article 4601

2018

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Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes

PLoS genetics, 2019-09, Vol.15 (9), p.e1008369-e1008369

2019

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Disk compression of k-mer sets

Algorithms for molecular biology, 2021-06, Vol.16 (1), p.10-10, Article 10

2021

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Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ

iScience, 2020-06, Vol.23 (6), p.101224-101224, Article 101224

2020

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A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Genome research, 2016-04, Vol.26 (4), p.530

2016

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Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Genome research, 2015-05, Vol.25 (5), p.736

2015

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Mapping-friendly sequence reductions: Going beyond homopolymer compression

iScience, 2022-11, Vol.25 (11), p.105305-105305, Article 105305

2022

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DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies

BMC genomics, 2019-08, Vol.20 (1), p.641-641, Article 641

2019

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Computability of Models for Sequence Assembly

Algorithms in Bioinformatics, p.289-301

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Modeling biological problems in computer science: a case study in genome assembly

Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1376-1383

Medvedev, Paul

2019

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Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics

Bioinformatics, 2019-02, Vol.35 (3), p.415-420

2019

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Correcting palindromes in long reads after whole-genome amplification

BMC genomics, 2018-11, Vol.19 (1), p.798-798, Article 798

2018

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Giraffe genome sequence reveals clues to its unique morphology and physiology

Nature communications, 2016-05, Vol.7 (1), p.11519-11519, Article 11519

2016

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Compacting de Bruijn graphs from sequencing data quickly and in low memory

Bioinformatics, 2016-06, Vol.32 (12), p.i201-i208

2016

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VarMatch: robust matching of small variant datasets using flexible scoring schemes

Bioinformatics (Oxford, England), 2017-05, Vol.33 (9), p.1301-1308

2017

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Improving the Power of Structural Variation Detection by Augmenting the Reference

PloS one, 2015-08, Vol.10 (8), p.e0136771-e0136771

2015

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Ten Simple Rules for writing algorithmic bioinformatics conference papers

Informed and automated k-mer size selection for genome assembly

Scalable multiple whole-genome alignment and locally collinear block construction with SibeliaZ

De Novo Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm

Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

What do Eulerian and Hamiltonian cycles have to do with genome assembly?

Author Correction: Error correction enables use of Oxford Nanopore technology for reference-free transcriptome analysis

Y and W Chromosome Assemblies: Approaches and Discoveries

ESKEMAP: exact sketch-based read mapping

Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon

Dosage regulation, and variation in gene expression and copy number of human Y chromosome ampliconic genes

Disk compression of k-mer sets

Scalable Pairwise Whole-Genome Homology Mapping of Long Genomes with BubbZ

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Accurate typing of short tandem repeats from genome-wide sequencing data and its applications

Mapping-friendly sequence reductions: Going beyond homopolymer compression

DiscoverY: a classifier for identifying Y chromosome sequences in male assemblies

Computability of Models for Sequence Assembly

Modeling biological problems in computer science: a case study in genome assembly

Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics

Correcting palindromes in long reads after whole-genome amplification

Giraffe genome sequence reveals clues to its unique morphology and physiology

Compacting de Bruijn graphs from sequencing data quickly and in low memory

VarMatch: robust matching of small variant datasets using flexible scoring schemes

Improving the Power of Structural Variation Detection by Augmenting the Reference

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