Open AccessBook Chapter10.1007/978-3-642-21260-4_14

Algorithms to detect multiprotein modularity conserved during evolution

- 27 May 2011

- pp 111-122

TL;DR: This paper presents a biologically motivated graph theoretic set of algorithm goals complementary to previous evaluation measures, demonstrates that Produles attains these goals more comprehensively than previous algorithms, and exhibits certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures.

Abstract: Detecting essential multiprotein modules that change infrequently during evolution is a challenging algorithmic task that is important for understanding the structure, function, and evolution of the biological cell. In this paper, we present a linear-time algorithm, Produles, that improves on the running time of previous algorithms. We present a biologically motivated graph theoretic set of algorithm goals complementary to previous evaluation measures, demonstrate that Produles attains these goals more comprehensively than previous algorithms, and exhibit certain recurrent anomalies in the performance of previous algorithms that are not detected by previous measures.

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1. What contributions have the authors mentioned in the paper "Algorithms to detect multi-protein modularity conserved during evolution" ?

An algorithmic framework for evaluation is presented that facilitates evaluation of algorithms for detecting conserved modularity with respect to their algorithmic goals.

2. What have the authors stated for future works in "Algorithms to detect multi-protein modularity conserved during evolution" ?

Promising future directions are discussed in Appendix I.

Citations

•Proceedings Article•10.1145/2488608.2488724

A simple, combinatorial algorithm for solving SDD systems in nearly-linear time

Jonathan A. Kelner, +3 more

- 01 Jun 2013

TL;DR: In this paper, the authors present a simple combinatorial algorithm that solves symmetric diagonally dominant (SDD) linear systems in nearly linear time. But it does not use recursive preconditioning, spectral sparsification, or even the Chebyshev Method or Conjugate Gradient.

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193

•Journal Article•10.1109/TCBB.2011.125

Algorithms to Detect Multiprotein Modularity Conserved during Evolution

Luqman Mushila Hodgkinson, +1 more

- 01 Jul 2012

- IEEE/ACM Transactions on Computational B...

TL;DR: This paper defines a measure of modularity for interactomes and presents a linear-time algorithm, Produles, for detecting multiprotein modularity conserved during evolution that improves on the running time of previous algorithms for related problems and offers desirable theoretical guarantees.

...read moreread less

Modularity Conserved during Evolution: Algorithms and Analysis

Luqman Hodgkinson

- 01 Jan 2013

TL;DR: This dissertation presents the development of algorithms to detect modularity in protein interaction networks and techniques of analysis for interpreting the results, and presents statistical methods that may be useful for this purpose.

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•Book Chapter•10.1007/978-3-642-21260-4_14

Algorithms to detect multiprotein modularity conserved during evolution

Luqman Mushila Hodgkinson, +1 more

- 27 May 2011

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•Dissertation

Iterative methods, combinatorial optimization, and linear programming beyond the universal barrier

Aaron Daniel Sidford

- 01 Jan 2015

TL;DR: This thesis provides the first theoretical improvements in decades for multiple classic problems ranging from linear programming to linear system solving to maximum flow and a faster asymptotic running time than conjugate gradient for solving a broad class of symmetric positive definite systems of equations.

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References

Journal Article•10.1016/S0022-2836(05)80360-2

Basic Local Alignment Search Tool

Stephen F. Altschul, +4 more

- 01 Oct 1990

- Journal of Molecular Biology

TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.

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98.8K

•Journal Article•10.1093/BIOINFORMATICS/BTH456

GO: :TermFinder---open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Elizabeth I. Boyle, +6 more

- 12 Dec 2004

- Bioinformatics

TL;DR: GO::TermFinder comprises a set of object-oriented Perl modules for accessing Gene Ontology information and evaluating and visualizing the collective annotation of a list of genes to GO terms, which can be used to draw conclusions from microarray and other biological data.

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2.1K

Proceedings Article•10.1109/FOCS.2006.44

Local Graph Partitioning using PageRank Vectors

R. Andersen, +2 more

- 21 Oct 2006

TL;DR: An improved algorithm for computing approximate PageRank vectors, which allows us to find a cut with conductance at most oslash and approximately optimal balance in time O(m log4 m/oslash) in time proportional to its size.

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1.2K

•Journal Article•10.1073/PNAS.0409522102

Conserved patterns of protein interaction in multiple species

Roded Sharan, +8 more

- 08 Feb 2005

- Proceedings of the National Academy of S...

TL;DR: This comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae revealed 71 network regions that were conserved across all three species and many exclusive to the metazoans.

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887

•Journal Article•10.1186/1471-2105-9-405

iRefIndex: A consolidated protein interaction database with provenance

Sabry Razick, +2 more

- 30 Sep 2008

- BMC Bioinformatics

TL;DR: A unifying index that would facilitate searching for redundant interaction data and that would group together redundant interactionData while recording the methods used to perform this grouping is created.

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621

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Algorithms to detect multiprotein modularity conserved during evolution

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Most frequently asked questions

1. What contributions have the authors mentioned in the paper "Algorithms to detect multi-protein modularity conserved during evolution" ?

2. What have the authors stated for future works in "Algorithms to detect multi-protein modularity conserved during evolution" ?

Citations

A simple, combinatorial algorithm for solving SDD systems in nearly-linear time

Algorithms to Detect Multiprotein Modularity Conserved during Evolution

Modularity Conserved during Evolution: Algorithms and Analysis

Algorithms to detect multiprotein modularity conserved during evolution

Iterative methods, combinatorial optimization, and linear programming beyond the universal barrier

References

Basic Local Alignment Search Tool

GO: :TermFinder---open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes

Local Graph Partitioning using PageRank Vectors

Conserved patterns of protein interaction in multiple species

iRefIndex: A consolidated protein interaction database with provenance

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