HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks

SWORD—a highly efficient protein database search

(2016) Robert Vaser et al.   BIOINFORMATICS

IMG/M: integrated genome and metagenome comparative data analysis system

(2016) I-Min A. Chen et al.   NUCLEIC ACIDS RESEARCH

Microbiome Data Science: Understanding Our Microbial Planet

(2016) Nikos C. Kyrpides et al.   TRENDS IN MICROBIOLOGY

SNAP

(2016) Jure Leskovec et al.   ACM Transactions on Intelligent Systems and Technology

Parallel Reproducible Summation

(2015) James Demmel et al.   IEEE TRANSACTIONS ON COMPUTERS

Comparing the performance of biomedical clustering methods

(2015) Christian Wiwie et al.   NATURE METHODS

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

(2015) Georgios A. Pavlopoulos et al.   GigaScience

Domain enhanced lookup time accelerated BLAST

(2012) Grzegorz M Boratyn et al.   Biology Direct

clusterMaker: a multi-algorithm clustering plugin for Cytoscape

(2012) John H Morris et al.   BMC BIOINFORMATICS

Fast Parallel Markov Clustering in Bioinformatics Using Massively Parallel Computing on GPU with CUDA and ELLPACK-R Sparse Format

(2012) A. Bustamam et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Parallel Sparse Matrix-Matrix Multiplication and Indexing: Implementation and Experiments

(2012) Aydin Buluç et al.   SIAM JOURNAL ON SCIENTIFIC COMPUTING

Adaptive seeds tame genomic sequence comparison

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

The Combinatorial BLAS: design, implementation, and applications

(2011) Aydın Buluç et al.   INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS

CALU: A Communication Optimal LU Factorization Algorithm

(2011) Laura Grigori et al.   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

SPICi: a fast clustering algorithm for large biological networks

(2010) Peng Jiang et al.   BIOINFORMATICS

jClust: a clustering and visualization toolbox

(2009) G. A. Pavlopoulos et al.   BIOINFORMATICS

Markov clustering versus affinity propagation for the partitioning of protein interaction graphs

(2009) James Vlasblom et al.   BMC BIOINFORMATICS

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

(2008) Y. Loewenstein et al.   BIOINFORMATICS

Fast unfolding of communities in large networks

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

Graph Clustering Via a Discrete Uncoupling Process

(2008) Stijn Van Dongen   SIAM JOURNAL ON MATRIX ANALYSIS AND APPLICATIONS

A survey of visualization tools for biological network analysis

(2008) Georgios A Pavlopoulos et al.   BioData Mining