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  1. Protein structure alignment is often modeled as the largest common point set (LCP) problem based on the Root Mean Square Deviation (RMSD), a measure commonly used to evaluate structural similarity. In the problem...

    Authors: Shuai Cheng Li

    Citation: Algorithms for Molecular Biology 2013 8:1

    Content type: Research

    Published on:

  2. Recently one step mutation matrices were introduced to model the impact of substitutions on arbitrary branches of a phylogenetic tree on an alignment site. This concept works nicely for the four-state nucleoti...

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

    Citation: Algorithms for Molecular Biology 2012 7:36

    Content type: Research

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  3. First proposed by Cavender and Felsenstein, and Lake, invariant based algorithms for phylogenetic reconstruction were widely dismissed by practicing biologists because invariants were perceived to have limited...

    Authors: Joseph P Rusinko and Brian Hipp

    Citation: Algorithms for Molecular Biology 2012 7:35

    Content type: Research

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  4. The selection of an evolutionary model to best fit given molecular data is usually a heuristic choice. In his seminal book, J. Felsenstein suggested that certain linear equations satisfied by the expected prob...

    Authors: Marta Casanellas, Jesús Fernández-Sánchez and Anna M Kedzierska

    Citation: Algorithms for Molecular Biology 2012 7:33

    Content type: Research

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  5. Recently, we have identified a randomized quartet phylogeny algorithm that has O(n logn) runtime with high probability, which is asymptotically optimal. Our algorithm has high probability of returning the correct...

    Authors: Jakub Truszkowski, Yanqi Hao and Daniel G Brown

    Citation: Algorithms for Molecular Biology 2012 7:32

    Content type: Research

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  6. Reconciliation is the commonly used method for inferring the evolutionary scenario for a gene family. It consists in “embedding” inferred gene trees into a known species tree, revealing the evolution of the ge...

    Authors: Krister M Swenson, Andrea Doroftei and Nadia El-Mabrouk

    Citation: Algorithms for Molecular Biology 2012 7:31

    Content type: Research

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  7. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, comput...

    Authors: Sebastian Wandelt and Ulf Leser

    Citation: Algorithms for Molecular Biology 2012 7:30

    Content type: Research

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  8. Because of the large volume of data and the intrinsic variation of data intensity observed in microarray experiments, different statistical methods have been used to systematically extract biological informati...

    Authors: Vadim Farztdinov and Fionnuala McDyer

    Citation: Algorithms for Molecular Biology 2012 7:29

    Content type: Research

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  9. We study the sparsification of dynamic programming based on folding algorithms of RNA structures. Sparsification is a method that improves significantly the computation of minimum free energy (mfe) RNA structu...

    Authors: Fenix WD Huang and Christian M Reidys

    Citation: Algorithms for Molecular Biology 2012 7:28

    Content type: Research

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  10. The metagenomics approach allows the simultaneous sequencing of all genomes in an environmental sample. This results in high complexity datasets, where in addition to repeats and sequencing errors, the number ...

    Authors: Olga Tanaseichuk, James Borneman and Tao Jiang

    Citation: Algorithms for Molecular Biology 2012 7:27

    Content type: Research

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  11. Understanding the evolution of biological networks can provide insight into how their modular structure arises and how they are affected by environmental changes. One approach to studying the evolution of thes...

    Authors: Rob Patro, Emre Sefer, Justin Malin, Guillaume Marçais, Saket Navlakha and Carl Kingsford

    Citation: Algorithms for Molecular Biology 2012 7:25

    Content type: Research

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  12. Cancer sequencing projects are now measuring somatic mutations in large numbers of cancer genomes. A key challenge in interpreting these data is to distinguish driver mutations, mutations important for cancer dev...

    Authors: Fabio Vandin, Eli Upfal and Benjamin J Raphael

    Citation: Algorithms for Molecular Biology 2012 7:23

    Content type: Research

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  13. Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary model...

    Authors: Yu Lin, Vaibhav Rajan and Bernard ME Moret

    Citation: Algorithms for Molecular Biology 2012 7:21

    Content type: Research

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  14. The notion of DNA motif is a mathematical abstraction used to model regions of the DNA (known as Transcription Factor Binding Sites, or TFBSs) that are bound by a given Transcription Factor to regulate gene expre...

    Authors: Maria Federico, Mauro Leoncini, Manuela Montangero and Paolo Valente

    Citation: Algorithms for Molecular Biology 2012 7:20

    Content type: Research

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  15. The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the stud...

    Authors: Maria Ortiz-Estevez, Ander Aramburu and Angel Rubio

    Citation: Algorithms for Molecular Biology 2012 7:19

    Content type: Software article

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  16. Analysis of elementary modes (EMs) is proven to be a powerful constraint-based method in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their la...

    Authors: Sayed-Amir Marashi, Laszlo David and Alexander Bockmayr

    Citation: Algorithms for Molecular Biology 2012 7:17

    Content type: Research

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  17. For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD...

    Authors: Federico Fogolari, Alessandra Corazza, Paolo Viglino and Gennaro Esposito

    Citation: Algorithms for Molecular Biology 2012 7:16

    Content type: Research

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  18. There are several common ways to encode a tree as a matrix, such as the adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of the natural random walk), and the matrix of pairwise dist...

    Authors: Frederick A Matsen and Steven N Evans

    Citation: Algorithms for Molecular Biology 2012 7:14

    Content type: Research

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  19. The dramatic fall in the cost of genomic sequencing, and the increasing convenience of distributed cloud computing resources, positions the MapReduce coding pattern as a cornerstone of scalable bioinformatics ...

    Authors: Jonas S Almeida, Alexander Grüneberg, Wolfgang Maass and Susana Vinga

    Citation: Algorithms for Molecular Biology 2012 7:12

    Content type: Research

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  20. Through the wealth of information contained within them, genome-wide association studies (GWAS) have the potential to provide researchers with a systematic means of associating genetic variants with a wide var...

    Authors: Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski and Tero Aittokallio

    Citation: Algorithms for Molecular Biology 2012 7:11

    Content type: Research

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  21. Chaos Game Representation (CGR) is an iterated function that bijectively maps discrete sequences into a continuous domain. As a result, discrete sequences can be object of statistical and topological analyses ...

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

    Citation: Algorithms for Molecular Biology 2012 7:10

    Content type: Research

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  22. Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing p...

    Authors: Lavanya Kannan and Ward C Wheeler

    Citation: Algorithms for Molecular Biology 2012 7:9

    Content type: Research

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  23. We present optimal linear time algorithms for computing the Shapley values and 'heightened evolutionary distinctiveness' (HED) scores for the set of taxa in a phylogenetic tree. We demonstrate the efficiency o...

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

    Citation: Algorithms for Molecular Biology 2012 7:6

    Content type: Research

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  24. High-throughput sequencing, such as ribonucleic acid sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) analyses, enables various features of organisms to be compared through tag coun...

    Authors: Koji Kadota, Tomoaki Nishiyama and Kentaro Shimizu

    Citation: Algorithms for Molecular Biology 2012 7:5

    Content type: Research

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  25. Supertree methods combine trees on subsets of the full taxon set together to produce a tree on the entire set of taxa. Of the many supertree methods, the most popular is MRP (Matrix Representation with Parsimo...

    Authors: Nam Nguyen, Siavash Mirarab and Tandy Warnow

    Citation: Algorithms for Molecular Biology 2012 7:3

    Content type: Research

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  26. High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive reg...

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

    Citation: Algorithms for Molecular Biology 2012 7:2

    Content type: Research

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  27. A combined quantitative trait loci (QTL) and microarray-based approach is commonly used to find differentially expressed genes which are then identified based on the known function of a gene in the biological ...

    Authors: Hirokazu Matsuda, Yukio Taniguchi and Hiroaki Iwaisaki

    Citation: Algorithms for Molecular Biology 2012 7:1

    Content type: Research

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  28. In genomics, a commonly encountered problem is to extract a subset of variables out of a large set of explanatory variables associated with one or several quantitative or qualitative response variables. An exa...

    Authors: Tahir Mehmood, Harald Martens, Solve Sæbø, Jonas Warringer and Lars Snipen

    Citation: Algorithms for Molecular Biology 2011 6:27

    Content type: Research

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  29. Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely use...

    Authors: Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler and Ivo L Hofacker

    Citation: Algorithms for Molecular Biology 2011 6:26

    Content type: Software article

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  30. Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the "quality" of the obtained alignments, i.e. how closely...

    Authors: Valery O Polyanovsky, Mikhail A Roytberg and Vladimir G Tumanyan

    Citation: Algorithms for Molecular Biology 2011 6:25

    Content type: Research

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  31. Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowled...

    Authors: Stelios P Pavlidis, Annette M Payne and Stephen M Swift

    Citation: Algorithms for Molecular Biology 2011 6:22

    Content type: Research

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  32. We consider the following problem: Given an undirected network and a set of sender–receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting ...

    Authors: Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier and Johannes Uhlmann

    Citation: Algorithms for Molecular Biology 2011 6:21

    Content type: Research

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  33. The MatrixMatchMaker algorithm was recently introduced to detect the similarity between phylogenetic trees and thus the coevolution between proteins. MMM finds the largest common submatrices between pairs of p...

    Authors: Alex Rodionov, Alexandr Bezginov, Jonathan Rose and Elisabeth RM Tillier

    Citation: Algorithms for Molecular Biology 2011 6:17

    Content type: Research

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  34. When inferring phylogenetic trees different algorithms may give different trees. To study such effects a measure for the distance between two trees is useful. Quartet distance is one such measure, and is the n...

    Authors: Jesper Nielsen, Anders K Kristensen, Thomas Mailund and Christian NS Pedersen

    Citation: Algorithms for Molecular Biology 2011 6:15

    Content type: Research

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