Deconvoluting simulated metagenomes: the performance of hard- and soft- clustering algorithms applied to metagenomic chromosome conformation capture (3C)

Link-Prediction Enhanced Consensus Clustering for Complex Networks

(2016) Matthew Burgess et al.   PLoS One

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering

(2015) Chris Gaiteri et al.   Scientific Reports

FactoMineR: AnRPackage for Multivariate Analysis

(2015) Sébastien Lê et al.   Journal of Statistical Software

A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

(2014) David Coil et al.   BIOINFORMATICS

High-quality genome (re)assembly using chromosomal contact data

(2014) Hervé Marie-Nelly et al.   Nature Communications

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Overlapping community detection in networks

(2013) Jierui Xie et al.   ACM COMPUTING SURVEYS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing

(2013) Siddarth Selvaraj et al.   NATURE BIOTECHNOLOGY

OClustR: A new graph-based algorithm for overlapping clustering

(2013) Airel Pérez-Suárez et al.   NEUROCOMPUTING

Revealing Long-Range Interconnected Hubs in Human Chromatin Interaction Data Using Graph Theory

(2013) R. E. Boulos et al.   PHYSICAL REVIEW LETTERS

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

(2013) Todd J Treangen et al.   GENOME BIOLOGY

Identifying functional modules in interaction networks through overlapping Markov clustering

(2012) Y.-K. Shih et al.   BIOINFORMATICS

High-throughput microbial population genomics using the Cortex variation assembler

(2012) Zamin Iqbal et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Entropy and the Complexity of Graphs Revisited

(2012) Abbe Mowshowitz et al.   Entropy

A decade of 3C technologies: insights into nuclear organization

(2012) E. de Wit et al.   GENES & DEVELOPMENT

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

A game-theoretic framework to identify overlapping communities in social networks

(2010) Wei Chen et al.   DATA MINING AND KNOWLEDGE DISCOVERY

A history of graph entropy measures

(2010) Matthias Dehmer et al.   INFORMATION SCIENCES

Detecting the overlapping and hierarchical community structure in complex networks

(2009) Andrea Lancichinetti et al.   NEW JOURNAL OF PHYSICS

Benchmarks for testing community detection algorithms on directed and weighted graphs with overlapping communities

(2009) Andrea Lancichinetti et al.   PHYSICAL REVIEW E

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

A comparison of extrinsic clustering evaluation metrics based on formal constraints

(2008) Enrique Amigó et al.   Information Retrieval Journal

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Benchmark graphs for testing community detection algorithms

(2008) Andrea Lancichinetti et al.   PHYSICAL REVIEW E