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ISSN: 2333-9721
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Algorithms for Molecular Biology

ISSN Print: 1748-7188

ISSN Online:

主页: http://www.almob.org

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Efficient unfolding pattern recognition in single molecule force spectroscopy data

Bill Andreopoulos, Dirk Labudde

A sub-cubic time algorithm for computing the quartet distance between two general trees

Jesper Nielsen, Anders K Kristensen, Thomas Mailund, Christian NS Pedersen

Random generation of RNA secondary structures according to native distributions

Markus E Nebel, Anika Scheid, Frank Weinberg

ViennaRNA Package 2.0

Ronny Lorenz, Stephan H Bernhart, Christian H？ner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker

Exploiting bounded signal flow for graph orientation based on cause–effect pairs

Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, Johannes Uhlmann

Prediction of plant promoters based on hexamers and random triplet pair analysis

A K M Azad, Saima Shahid, Nasimul Noman, Hyunju Lee

An FPT haplotyping algorithm on pedigrees with a small number of sites

Duong D Doan, Patricia A Evans

Efficient algorithms for the discovery of gapped factors

Alberto Apostolico, Cinzia Pizzi, Esko Ukkonen

WildSpan: mining structured motifs from protein sequences

Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu

Speeding up the Consensus Clustering methodology for microarray data analysis

Raffaele Giancarlo, Filippo Utro

WordCluster: detecting clusters of DNA words and genomic elements

Michael Hackenberg, Pedro Carpena, Pedro Bernaola-Galván, Guillermo Barturen, ángel M Alganza, José L Oliver

Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training

Tin Y Lam, Irmtraud M Meyer

Fast prediction of RNA-RNA interaction

Raheleh Salari, Rolf Backofen, S Cenk Sahinalp

Periodic pattern detection in sparse boolean sequences

Ivan Junier, Joan Hérisson, Fran？ois Képès

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Xiuwei Zhang, Bernard ME Moret

Robinson-Foulds Supertrees

Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca

Inverse folding of RNA pseudoknot structures

James ZM Gao, Linda YM Li, Christian M Reidys

Back-translation for discovering distant protein homologies in the presence of frameshift mutations

Marta G？rdea, Laurent Noé, Gregory Kucherov

Phylogenetic comparative assembly

Peter Husemann, Jens Stoye

Mimosa: Mixture model of co-expression to detect modulators of regulatory interaction

Matthew Hansen, Logan Everett, Larry Singh, Sridhar Hannenhalli

ANMM4CBR: a case-based reasoning method for gene expression data classification

Bangpeng Yao, Shao Li

A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup

Yelena Frid, Dan Gusfield

Jane: a new tool for the cophylogeny reconstruction problem

Chris Conow, Daniel Fielder, Yaniv Ovadia, Ran Libeskind-Hadas

A simulation study comparing supertree and combined analysis methods using SMIDGen

M Shel Swenson, Fran？ois Barban？on, Tandy Warnow, C Randal Linder

A markov classification model for metabolic pathways

Timothy Hancock, Hiroshi Mamitsuka

A tree-based method for the rapid screening of chemical fingerprints

Thomas G Kristensen, Jesper Nielsen, Christian NS Pedersen

Association of repeatedly measured intermediate risk factors for complex diseases with high dimensional SNP data

Sandra Waaijenborg, Aeilko H Zwinderman

Sequence embedding for fast construction of guide trees for multiple sequence alignment

Gordon Blackshields, Fabian Sievers, Weifeng Shi, Andreas Wilm, Desmond G Higgins

Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees

Christian Arnold, Peter F Stadler

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences

Darío Guerrero, Rocío Bautista, David P Villalobos, Francisco R Cantón, M Gonzalo Claros

Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms

Burton Chia, R Krishna Murthy Karuturi

Estimating the evidence of selection and the reliability of inference in unigenic evolution

Andrew D Fernandes, Benjamin P Kleinstiver, David R Edgell, Lindi M Wahl, Gregory B Gloor

Linear-time protein 3-D structure searching with insertions and deletions

Tetsuo Shibuya, Jesper Jansson, Kunihiko Sadakane

Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity

Binh Nguyen, Andreas Spillner, Brent C Emerson, Vincent Moulton

Challenges in experimental data integration within genome-scale metabolic models

Pierre-Yves Bourguignon, Areejit Samal, Fran？ois Képès, Jürgen Jost, Olivier C Martin

Predicting direct protein interactions from affinity purification mass spectrometry data

Ethan DH Kim, Ashish Sabharwal, Adrian R Vetta, Mathieu Blanchette

Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry

Hannes Planatscher, Jochen Supper, Oliver Poetz, Dieter Stoll, Thomas Joos, Markus F Templin, Andreas Zell

Constructing majority-rule supertrees

Jianrong Dong, David Fernández-Baca, FR McMorris

Module detection in complex networks using integer optimisation

Gang Xu, Laura Bennett, Lazaros G Papageorgiou, Sophia Tsoka

Survival associated pathway identification with group Lp penalized global AUC maximization

Zhenqiu Liu, Laurence S Magder, Terry Hyslop, Li Mao

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

Stefan E Seemann, Andreas S Richter, Jan Gorodkin, Rolf Backofen

Efficient algorithms for analyzing segmental duplications with deletions and inversions in genomes

Crystal L Kahn, Shay Mozes, Benjamin J Raphael

Sparsification of RNA structure prediction including pseudoknots

Mathias M？hl, Raheleh Salari, Sebastian Will, Rolf Backofen, S Cenk Sahinalp

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

Pavel V Mazin, Mikhail S Gelfand, Andrey A Mironov, Aleksandra B Rakhmaninova, Anatoly R Rubinov, Robert B Russell, Olga V Kalinina

On the use of cartographic projections in visualizing phylo-genetic tree space

Kenneth Sundberg, Mark Clement, Quinn Snell

FlexSnap: Flexible Non-sequential Protein Structure Alignment

Saeed Salem, Mohammed J Zaki, Chris Bystroff

Gravitation field algorithm and its application in gene cluster

Ming Zheng, Gui-xia Liu, Chun-guang Zhou, Yan-chun Liang, Yan Wang

Scoring function to predict solubility mutagenesis

Ye Tian, Christopher Deutsch, Bala Krishnamoorthy

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

Anne Kupczok, Heiko A Schmidt, Arndt von Haeseler

Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data

Gregory Nuel, Leslie Regad, Juliette Martin, Anne-Claude Camproux

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