Heuristic algorithms in computational molecular biology

Authors:
Richard M. Karp
Affiliations:
University of California at Berkeley, United States and International Computer Science Institute, Berkeley, CA, United States
Venue:
Journal of Computer and System Sciences
Year:
2011

Citing 11
Cited 4

Fast approximation algorithms for fractional packing and covering problems

Mathematics of Operations Research
A threshold of ln n for approximating set cover

Journal of the ACM (JACM)
On the hardness of approximating minimization problems

Journal of the ACM (JACM)
A polyhedral approach to sequence alignment problems

Discrete Applied Mathematics - Special volume on combinatorial molecular biology
The Maximum Weight Trace Problem in Multiple Sequence Alignment

CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
Fast Heuristics for the Maximum Feasible Subsystem Problem

INFORMS Journal on Computing
Beating Simplex for Fractional Packing and Covering Linear Programs

FOCS '07 Proceedings of the 48th Annual IEEE Symposium on Foundations of Computer Science
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks

WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Topology-Free Querying of Protein Interaction Networks

RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Pairwise global alignment of protein interaction networks by matching neighborhood topology

RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Detecting disease-specific dysregulated pathways via analysis of clinical expression profiles

RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology

A parameterized complexity tutorial

LATA'12 Proceedings of the 6th international conference on Language and Automata Theory and Applications
A basic parameterized complexity primer

The Multivariate Algorithmic Revolution and Beyond
A refined complexity analysis of degree anonymization in graphs

ICALP'13 Proceedings of the 40th international conference on Automata, Languages, and Programming - Volume Part II
Improved approximation algorithms for low-density instances of the Minimum Entropy Set Cover Problem

Information Processing Letters

Quantified Score

Hi-index	0.00

Visualization

Abstract

In this paper we develop a framework for designing and validating heuristic algorithms for NP-hard problems arising in computational biology and other application areas. We introduce two areas of current research in which we are applying the framework: implicit hitting set problems and analysis of protein-protein interaction networks, with emphasis on a specific problem in each area: multi-genome alignment and colorful connected graph detection.