Resolving spatial inconsistencies in chromosome conformation data

Authors:
Geet Duggal;Rob Patro;Emre Sefer;Hao Wang;Darya Filippova;Samir Khuller;Carl Kingsford
Affiliations:
Department of Computer Science, University of Maryland, College Park, MD;Department of Computer Science, University of Maryland, College Park, MD;Department of Computer Science, University of Maryland, College Park, MD;Department of Electrical and Computer Engineering, University of Maryland, College Park, MD;Department of Computer Science, University of Maryland, College Park, MD;Department of Computer Science, University of Maryland, College Park, MD;Department of Computer Science, University of Maryland, College Park, MD
Venue:
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Year:
2012

Citing 3
Cited 0

Approximation algorithms for NP-hard problems

Approximation algorithms for NP-hard problems
An efficient fixed-parameter algorithm for 3-hitting set

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Bioinformatics

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Abstract

We introduce a new method for filtering noisy 3C interactions that selects subsets of interactions that obey metric constraints of various strictness. We demonstrate that, although the problem is computationally hard, near-optimal results are often attainable in practice using well-designed heuristics and approximation algorithms. Further, we show that, compared with a standard technique, this metric filtering approach leads to (a) subgraphs with higher total statistical significance, (b) lower embedding error, (c) lower sensitivity to initial conditions of the embedding algorithm, and (d) structures with better agreement with light microscopy measurements.