Algorithms for Molecular Biology

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Algorithms for Molecular Biology

ISSN Print: 1748-7188

ISSN Online:

Website: http://www.almob.org

Analysis of Metabolic Subnetworks by Flux Cone Projection

Sayed-Amir Marashi, Laszlo David, Alexander Bockmayr

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

Tanja Stadler, James H. Degnan

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

Stefan Enroth, Claes R Andersson, Robin Andersson, Claes Wadelius, Mats G Gustafsson, Jan Komorowski

TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison

Jafar Razmara, Safaai Deris, Sepideh Parvizpour

A normalization strategy for comparing tag count data

Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu

Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations

Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio

Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis

Susana Vinga, Alexandra M Carvalho, Alexandre P Francisco, Luís MS Russo, Jonas S Almeida

QTL/microarray approach using pathway information

Hirokazu Matsuda, Yukio Taniguchi, Hiroaki Iwaisaki

Fractal MapReduce decomposition of sequence alignment

Jonas S Almeida, Alexander Grüneberg, Wolfgang Maass, Susana Vinga

Tree-average distances on certain phylogenetic networks have their weights uniquely determined

Stephen J Willson

MRL and SuperFine+MRL: new supertree methods

Nam Nguyen, Siavash Mirarab, Tandy Warnow

Maximum Parsimony on Phylogenetic networks

Lavanya Kannan, Ward C Wheeler

Sampling solution traces for the problem of sorting permutations by signed reversals

Christian Baudet, Zanoni Dias, Marie-France Sagot

Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem

Sylvain Soliman

Fast structure similarity searches among protein models: efficient clustering of protein fragments

Federico Fogolari, Alessandra Corazza, Paolo Viglino, Gennaro Esposito

Computing evolutionary distinctiveness indices in large scale analysis

Iain Martyn, Tyler S Kuhn, Arne O Mooers, Vincent Moulton, Andreas Spillner

Ubiquity of synonymity: almost all large binary trees are not uniquely identified by their spectra or their immanantal polynomials

Frederick A Matsen, Steven N Evans

Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots

Frederick A Matsen, Aaron Gallagher

On the combinatorics of sparsification

Huang Fenix WD,Reidys Christian M

Invariant based quartet puzzling

Rusinko Joseph P,Hipp Brian

On the group theoretical background of assigning stepwise mutations onto phylogenies

Fischer Mareike,Klaere Steffen,Thi Nguyen Minh Anh,Haeseler Arndt von

Direct vs 2-stage approaches to structured motif finding

Federico Maria,Leoncini Mauro,Montangero Manuela,Valente Paolo

Bootstrapping phylogenies inferred from rearrangement data

Lin Yu,Rajan Vaibhav,Moret Bernard ME

Adaptive efficient compression of genomes

Wandelt Sebastian,Leser Ulf

Parsimonious reconstruction of network evolution

Patro Rob,Sefer Emre,Malin Justin,Mar？ais Guillaume

Stochastic errors vs. modeling errors in distance based phylogenetic reconstructions

Doerr Daniel,Gronau Ilan,Moran Shlomo,Yavneh Irad

Towards a practical O(nlogn) phylogeny algorithm

Truszkowski Jakub,Hao Yanqi,Brown Daniel G

Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments

Farztdinov Vadim,McDyer Fionnuala

Gene tree correction for reconciliation and species tree inference

Swenson Krister M,Doroftei Andrea,El-Mabrouk Nadia

Constructing perfect phylogenies and proper triangulations for three-state characters

Gysel Rob,Lam Fumei,Gusfield Dan

Finding driver pathways in cancer: models and algorithms

Vandin Fabio,Upfal Eli,Raphael Benjamin J

Efficient procedures for the numerical simulation of mid-size RNA kinetics

Aviram Iddo,Veltman Ilia,Churkin Alexander,Barash Danny

Getting DNA copy numbers without control samples

Ortiz-Estevez Maria,Aramburu Ander,Rubio Angel

Alignment-free phylogeny of whole genomes using underlying subwords

Comin Matteo,Verzotto Davide

Multi-membership gene regulation in pathway based microarray analysis

Stelios P Pavlidis, Annette M Payne, Stephen M Swift

Reducing the worst case running times of a family of RNA and CFG problems, using Valiant's approach

Shay Zakov, Dekel Tsur, Michal Ziv-Ukelson

Estimation of alternative splicing isoform frequencies from RNA-Seq data

Marius Nicolae, Serghei Mangul, Ion I M？ndoiu, Alex Zelikovsky

Listing all sorting reversals in quadratic time

Krister M Swenson, Ghada Badr, David Sankoff

Haplotypes versus genotypes on pedigrees

Bonnie B Kirkpatrick

A robust approach based on Weibull distribution for clustering gene expression data

Huakun Wang, Zhenzhen Wang, Xia Li, Binsheng Gong, Lixin Feng, Ying Zhou

Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences

Valery O Polyanovsky, Mikhail A Roytberg, Vladimir G Tumanyan

A Partial Least Squares based algorithm for parsimonious variable selection

Tahir Mehmood, Harald Martens, Solve S？b？, Jonas Warringer, Lars Snipen

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

Alexandra M Carvalho, Arlindo L Oliveira

DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach

Akdes Serin, Martin Vingron

A new, fast algorithm for detecting protein coevolution using maximum compatible cliques

Alex Rodionov, Alexandr Bezginov, Jonathan Rose, Elisabeth RM Tillier

Fast local fragment chaining using sum-of-pair gap costs

Christian Otto, Steve Hoffmann, Jan Gorodkin, Peter F Stadler

Sparse estimation for structural variability

Raghavendra Hosur, Rohit Singh, Bonnie Berger

An experimental study of Quartets MaxCut and other supertree methods

M Shel Swenson, Rahul Suri, C Randal Linder, Tandy Warnow

RNA Accessibility in cubic time

Stephan H Bernhart, Ullrike Mückstein, Ivo L Hofacker

ReCoil - an algorithm for compression of extremely large datasets of dna data

Vladimir Yanovsky