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Algorithms for Molecular Biology, Volume 7
Volume 7, 2012
- Hirokazu Matsuda, Yukio Taniguchi, Hiroaki Iwaisaki:
QTL/microarray approach using pathway information. 1 - Stefan Enroth
, Claes R. Andersson, Robin Andersson
A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. 2 - Nam-phuong Nguyen
MRL and SuperFine+MRL: new supertree methods. 3 - Jafar Razmara
TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison. 4 - Koji Kadota
A normalization strategy for comparing tag count data. 5 - Iain Martyn
Computing evolutionary distinctiveness indices in large scale analysis. 6 - Tanja Stadler
A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree. 7 - Frederick A. Matsen IV, Aaron Gallagher:
Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots. 8 - Lavanya Kannan, Ward C. Wheeler:
Maximum Parsimony on Phylogenetic networks. 9 - Susana Vinga
Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis. 10 - Tapio Pahikkala
Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations. 11 - Jonas S. Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga
Fractal MapReduce decomposition of sequence alignment. 12 - Stephen J. Willson:
Tree-average distances on certain phylogenetic networks have their weights uniquely determined. 13 - Frederick A. Matsen IV, Steven N. Evans:
Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials. 14 - Sylvain Soliman
Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem. 15 - Federico Fogolari
Fast structure similarity searches among protein models: efficient clustering of protein fragments. 16 - Sayed-Amir Marashi
Analysis of Metabolic Subnetworks by Flux Cone Projection. 17 - Christian Baudet
Sampling solution traces for the problem of sorting permutations by signed reversals. 18 - Maria Ortiz-Estevez, Ander Aramburu
Getting DNA copy numbers without control samples. 19 - Maria Federico, Mauro Leoncini, Manuela Montangero
Direct vs 2-Stage Approaches to Structured Motif Finding. 20 - Yu Lin
Bootstrapping phylogenies inferred from rearrangement data. 21 - Daniel Doerr, Ilan Gronau, Shlomo Moran, Irad Yavneh:
Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions. 22 - Fabio Vandin, Eli Upfal
Finding Driver Pathways in Cancer: Models and Algorithms. 23 - Iddo Aviram, Ilia Veltman, Alexander Churkin, Danny Barash:
Efficient procedures for the numerical simulation of mid-size RNA kinetics. 24 - Rob Patro, Emre Sefer
Parsimonious reconstruction of network evolution. 25 - Rob Gysel, Fumei Lam, Dan Gusfield:
Constructing perfect phylogenies and proper triangulations for three-state characters. 26 - Olga Tanaseichuk, James Borneman, Tao Jiang
Separating metagenomic short reads into genomes via clustering. 27 - Fenix W. D. Huang, Christian M. Reidys:
On the combinatorics of sparsification. 28 - Vadim Farztdinov, Fionnuala McDyer:
Distributional fold change test - a statistical approach for detecting differential expression in microarray experiments. 29 - Sebastian Wandelt, Ulf Leser:
Adaptive efficient compression of genomes. 30 - Krister M. Swenson, Andrea Doroftei, Nadia El-Mabrouk:
Gene tree correction for reconciliation and species tree inference. 31 - Jakub Truszkowski
Towards a practical O(n log n) phylogeny algorithm. 32 - Marta Casanellas
The space of phylogenetic mixtures for equivariant models. 33 - Matteo Comin
Alignment-free phylogeny of whole genomes using underlying subwords. 34 - Joseph P. Rusinko, Brian Hipp:
Invariant based quartet puzzling. 35 - Mareike Fischer
On the group theoretical background of assigning stepwise mutations onto phylogenies. 36
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