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Algorithms

Reaction Factoring and Bipartite Update Graphs Accelerate the Gillespie Algorithm for Large-Scale Biochemical Systems

Sagar Indurkhya, Jacob Beal

Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice

Melissa K. Friswell, Helen Gika, [ ... ], Andrew J. McBain

Parameter Identifiability and Redundancy in a General Class of Stochastic Carcinogenesis Models

Mark P. Little, Wolfgang F. Heidenreich, Guangquan Li

AutoEPG: Software for the Analysis of Electrical Activity in the Microcircuit Underpinning Feeding Behaviour of Caenorhabditis elegans

James Dillon, Ioannis Andrianakis, [ ... ], Christopher James

Pebble and Rock Band: Heuristic Resolution of Repeats and Scaffolding in the Velvet Short-Read de Novo Assembler

Daniel R. Zerbino, Gayle K. McEwen, Elliott H. Margulies, Ewan Birney

Vector Field Embryogeny

Till Steiner, Yaochu Jin, Bernhard Sendhoff

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

Patrick D. Schloss

Effective Identification of Conserved Pathways in Biological Networks Using Hidden Markov Models

Xiaoning Qian, Byung-Jun Yoon

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform

Dong Xu, Yang Zhang

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

Ferhat Ay, Fei Xu, Tamer Kahveci

Estimation of Immune Cell Densities in Immune Cell Conglomerates: An Approach for High-Throughput Quantification

Niels Halama, Inka Zoernig, [ ... ], Niels Grabe

BFAST: An Alignment Tool for Large Scale Genome Resequencing

Nils Homer, Barry Merriman, Stanley F. Nelson

A Unique, Consistent Identifier for Alternatively Spliced Transcript Variants

Alberto Riva, Graziano Pesole

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