High-quality sequence clustering guided by network topology and multiple alignment likelihood

Ultra-fast sequence clustering from similarity networks with SiLiX

(2011) Vincent Miele et al.   BMC BIOINFORMATICS

Phylogeny Inference Based on Spectral Graph Clustering

(2011) Shu-Bo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Detecting Network Communities: An Application to Phylogenetic Analysis

(2011) Roberto F. S. Andrade et al.   PLoS Computational Biology

Improving the quality of protein similarity network clustering algorithms using the network edge weight distribution

(2010) Leonard Apeltsin et al.   BIOINFORMATICS

Enrichment of homologs in insignificant BLAST hits by co-complex network alignment

(2010) Like Fokkens et al.   BMC BIOINFORMATICS

Diversity of structure and function of response regulator output domains

(2010) Michael Y Galperin   CURRENT OPINION IN MICROBIOLOGY

Partitioning biological data with transitivity clustering

(2010) Tobias Wittkop et al.   NATURE METHODS

Homologous over-extension: a challenge for iterative similarity searches

(2010) Mileidy W. Gonzalez et al.   NUCLEIC ACIDS RESEARCH

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Deciphering the connectivity structure of biological networks using MixNet

(2009) Franck Picard et al.   BMC BIOINFORMATICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Strategies to Improve the Robustness of Agglomerative Hierarchical Clustering Under Data Source Variation for Speaker Diarization

(2008) K.J. Han et al.   IEEE Transactions on Audio Speech and Language Processing

Fast unfolding of communities in large networks

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

Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins

(2008) Nan Song et al.   PLoS Computational Biology