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A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Bioinformatics, 2011-03, Vol.27 (6), p.764-770

2011

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Accurate assembly of transcripts through phase-preserving graph decomposition

Nature biotechnology, 2017-12, Vol.35 (12), p.1167-1169

2017

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Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Genome Biology, 2018-02, Vol.19 (1), p.16-16, Article 16

2018

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Alignment and mapping methodology influence transcript abundance estimation

Genome Biology, 2020-09, Vol.21 (1), p.239-239, Article 239

2020

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Locality-sensitive hashing for the edit distance

Bioinformatics, 2019-07, Vol.35 (14), p.i127-i135

2019

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SQUID: transcriptomic structural variation detection from RNA-seq

Genome Biology, 2018-04, Vol.19 (1), p.52-52, Article 52

2018

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Identification of alternative topological domains in chromatin

Algorithms for molecular biology, 2014-05, Vol.9 (1), p.14-14, Article 14

2014

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VariantStore: an index for large-scale genomic variant search

Genome Biology, 2021-08, Vol.22 (1), p.231-231, Article 231

2021

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Network archaeology: uncovering ancient networks from present-day interactions

PLoS computational biology, 2011-04, Vol.7 (4), p.e1001119

2011

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Assembly complexity of prokaryotic genomes using short reads

BMC bioinformatics, 2010-01, Vol.11 (1), p.21-21, Article 21

2010

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Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Genome Biology, 2019-12, Vol.20 (1), p.287-287, Article 287

2019

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Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

Nucleic acids research, 2017-04, Vol.45 (7), p.3663

2017

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Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005777-e1005777

2017

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Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

BMC bioinformatics, 2011-04, Vol.12 (1), p.95-95, Article 95

2011

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Semi-nonparametric modeling of topological domain formation from epigenetic data

Algorithms for molecular biology, 2019-03, Vol.14 (1), p.4-4, Article 4

2019

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Fast search of thousands of short-read sequencing experiments

Nature biotechnology, 2016-03, Vol.34 (3), p.300-302

2016

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Exact transcript quantification over splice graphs

Algorithms for molecular biology, 2021-05, Vol.16 (1), p.5-5, Article 5

2021

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Global network alignment using multiscale spectral signatures

Bioinformatics, 2012-12, Vol.28 (23), p.3105-3114

2012

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The power of protein interaction networks for associating genes with diseases

Bioinformatics, 2010-04, Vol.26 (8), p.1057-1063

2010

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Context-aware seeds for read mapping

Algorithms for molecular biology, 2020-05, Vol.15 (1), p.10-10, Article 10

2020

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The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks

PloS one, 2013-03, Vol.8 (3), p.e58134

2013

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Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem

Algorithms for molecular biology, 2020-05, Vol.15 (1), p.9-9, Article 9

2020

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HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data

BMC bioinformatics, 2021-04, Vol.22 (1), p.174-174, Article 174

2021

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The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance

Bioinformatics, 2022-06, Vol.38 (Supplement_1), p.i404-i412

2022

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Quantifying the similarity of topological domains across normal and cancer human cell types

Bioinformatics, 2018-07, Vol.34 (13), p.i475-i483

2018

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A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Accurate assembly of transcripts through phase-preserving graph decomposition

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Alignment and mapping methodology influence transcript abundance estimation

Locality-sensitive hashing for the edit distance

SQUID: transcriptomic structural variation detection from RNA-seq

Identification of alternative topological domains in chromatin

VariantStore: an index for large-scale genomic variant search

Network archaeology: uncovering ancient networks from present-day interactions

Assembly complexity of prokaryotic genomes using short reads

Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads

Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings

Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies

Semi-nonparametric modeling of topological domain formation from epigenetic data

Fast search of thousands of short-read sequencing experiments

Exact transcript quantification over splice graphs

Global network alignment using multiscale spectral signatures

The power of protein interaction networks for associating genes with diseases

Context-aware seeds for read mapping

The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks

Detecting transcriptomic structural variants in heterogeneous contexts via the Multiple Compatible Arrangements Problem

HARVESTMAN: a framework for hierarchical feature learning and selection from whole genome sequencing data

The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance

Quantifying the similarity of topological domains across normal and cancer human cell types

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