Computational systems biology

A new approach to the maximum-flow problem

Journal of the ACM (JACM)

A fast parametric maximum flow algorithm and applications

SIAM Journal on Computing

Elements of information theory

Elements of information theory

Mining the gene expression matrix: inferring gene relationships from large scale gene expression data

IPCAT '97 Proceedings of the second international workshop on Information processing in cell and tissues

A clustering algorithm based on graph connectivity

Information Processing Letters

A Monte Carlo algorithm for fast projective clustering

Proceedings of the 2002 ACM SIGMOD international conference on Management of data

Discovering local structure in gene expression data: the order-preserving submatrix problem

Proceedings of the sixth annual international conference on Computational biology

Computers and Intractability: A Guide to the Theory of NP-Completeness

Computers and Intractability: A Guide to the Theory of NP-Completeness

Optimal algorithms for complete linkage clustering in d dimensions

Theoretical Computer Science

Greedy approximation algorithms for finding dense components in a graph

APPROX '00 Proceedings of the Third International Workshop on Approximation Algorithms for Combinatorial Optimization

The maximum edge biclique problem is NP-complete

Discrete Applied Mathematics

Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data

RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology

Clustering Large Graphs via the Singular Value Decomposition

Machine Learning

A New Conceptual Clustering Framework

Machine Learning

Subquadratic Approximation Algorithms for Clustering Problems in High Dimensional Spaces

Machine Learning

Sleeved coclustering

Proceedings of the tenth ACM SIGKDD international conference on Knowledge discovery and data mining

Biclustering Algorithms for Biological Data Analysis: A Survey

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

How Fast Is the k-Means Method?

Algorithmica

Performance guarantees for hierarchical clustering

Journal of Computer and System Sciences - Special issue on COLT 2002

Discovery of meaningful associations in genomic data using partial correlation coefficients

Bioinformatics

Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps

Bioinformatics

An empirical Bayes approach to inferring large-scale gene association networks

Bioinformatics

Handbook of Computational Molecular Biology (Chapman & All/Crc Computer and Information Science Series)

Handbook of Computational Molecular Biology (Chapman & All/Crc Computer and Information Science Series)

Graph mining: Laws, generators, and algorithms

ACM Computing Surveys (CSUR)

The complexity of detecting fixed-density clusters

Discrete Applied Mathematics

The Effectiveness of Lloyd-Type Methods for the k-Means Problem

FOCS '06 Proceedings of the 47th Annual IEEE Symposium on Foundations of Computer Science

Hierarchical multi-label prediction of gene function

Bioinformatics

Efficient Detection of Network Motifs

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

COPASI---a COmplex PAthway SImulator

Bioinformatics

Finding biclusters by random projections

Theoretical Computer Science

A PTAS for k-means clustering based on weak coresets

SCG '07 Proceedings of the twenty-third annual symposium on Computational geometry

Bi-criteria linear-time approximations for generalized k-mean/median/center

SCG '07 Proceedings of the twenty-third annual symposium on Computational geometry

Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis

Algorithmica

Ruling Out PTAS for Graph Min-Bisection, Dense k-Subgraph, and Bipartite Clique

SIAM Journal on Computing

Inapproximability Results for Sparsest Cut, Optimal Linear Arrangement, and Precedence Constrained Scheduling

FOCS '07 Proceedings of the 48th Annual IEEE Symposium on Foundations of Computer Science

Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks

Bioinformatics

Discerning static and causal interactions in genome-wide reverse engineering problems

Bioinformatics

A Sequential Algorithm for Generating Random Graphs

APPROX '07/RANDOM '07 Proceedings of the 10th International Workshop on Approximation and the 11th International Workshop on Randomization, and Combinatorial Optimization. Algorithms and Techniques

An optimal hierarchical clustering algorithm for gene expression data

Information Processing Letters

Reconstructing the topology of protein complexes

RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology

Network motif discovery using subgraph enumeration and symmetry-breaking

RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology

Inapproximability of maximum weighted edge biclique and its applications

TAMC'08 Proceedings of the 5th international conference on Theory and applications of models of computation

Parallel information theory based construction of gene regulatory networks

HiPC'08 Proceedings of the 15th international conference on High performance computing

Semi-Supervised Learning

Semi-Supervised Learning