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(2020) Roland Wittler   Algorithms for Molecular Biology

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(2020) Elizabeth A. Miller et al.   mSphere

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Ultrafast search of all deposited bacterial and viral genomic data

(2019) Phelim Bradley et al.   NATURE BIOTECHNOLOGY

Building large updatable colored de Bruijn graphs via merging

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Improved representation of sequence Bloom trees

(2019) Robert S Harris et al.   BIOINFORMATICS

A space and time-efficient index for the compacted colored de Bruijn graph

(2018) Fatemeh Almodaresi et al.   BIOINFORMATICS

Dynamic compression schemes for graph coloring

(2018) Harun Mustafa et al.   BIOINFORMATICS

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(2018) Clare Turnbull et al.   BMJ-British Medical Journal

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(2018) Clare Turnbull et al.   BMJ-British Medical Journal

Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

(2018) Prashant Pandey et al.   Cell Systems

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Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage

(2016) Guillaume Holley et al.   Algorithms for Molecular Biology

TwoPaCo: an efficient algorithm to build the compacted de Bruijn graph from many complete genomes

(2016) Ilia Minkin et al.   BIOINFORMATICS

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

(2016) Rayan Chikhi et al.   BIOINFORMATICS

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

(2016) Dirk D. Dolle et al.   GENOME RESEARCH

Fast search of thousands of short-read sequencing experiments

(2016) Brad Solomon et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

(2016) Sara A. Byron et al.   NATURE REVIEWS GENETICS

Consistently faster and smaller compressed bitmaps with Roaring

(2016) Daniel Lemire et al.   SOFTWARE-PRACTICE & EXPERIENCE

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

(2016)   Microbiome

Bloofi: Multidimensional Bloom filters

(2015) Adina Crainiceanu et al.   INFORMATION SYSTEMS

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

BEETL-fastq: a searchable compressed archive for DNA reads

(2014) L. Janin et al.   BIOINFORMATICS

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

(2012) A. J. Cox et al.   BIOINFORMATICS

De novo assembly and genotyping of variants using colored de Bruijn graphs

(2012) Zamin Iqbal et al.   NATURE GENETICS

The 1000 Genomes Project: data management and community access

(2012) Laura Clarke et al.   NATURE METHODS

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

(2012) B. C. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH