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  1. Content type: Research

    Hidden Markov Models power many state‐of‐the‐art tools in the field of protein bioinformatics. While excelling in their tasks, these methods of protein analysis do not convey directly information on medium‐ an...

    Authors: Witold Dyrka, Jean‐Christophe Nebel and Malgorzata Kotulska

    Citation: Algorithms for Molecular Biology 2013 8:31

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  2. Content type: Research

    In this paper, we present a novel approximation algorithm to solve the protein folding problem in HP model. Our algorithm is polynomial in terms of the length of the given HP string. The expected approximation...

    Authors: Abu Sayed Md Sohidull Islam and Mohammad Sohel Rahman

    Citation: Algorithms for Molecular Biology 2013 8:30

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  3. Content type: Review Article

    Post-Sanger sequencing methods produce tons of data, and there is a generalagreement that the challenge to store and process them must be addressedwith data compression. In this review we first answer the ques...

    Authors: Sebastian Deorowicz and Szymon Grabowski

    Citation: Algorithms for Molecular Biology 2013 8:25

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  4. Content type: Research

    Constructing species trees from multi-copy gene trees remains a challenging problem in phylogenetics. One difficulty is that the underlying genes can be incongruent due to evolutionary processes such as gene d...

    Authors: Ruchi Chaudhary, John Gordon Burleigh and David Fernández-Baca

    Citation: Algorithms for Molecular Biology 2013 8:28

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  5. Content type: Research

    We propose three algorithms for string edit distance with duplications and contractions. These include an efficient general algorithm and two improvements which apply under certain constraints on the cost func...

    Authors: Tamar Pinhas, Shay Zakov, Dekel Tsur and Michal Ziv-Ukelson

    Citation: Algorithms for Molecular Biology 2013 8:27

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  6. Content type: Research

    In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior d...

    Authors: Alexandra Gavryushkina, David Welch and Alexei J Drummond

    Citation: Algorithms for Molecular Biology 2013 8:26

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  7. Content type: Software article

    Positional weight matrix (PWM) remains the most popular for quantification of transcription factor (TF) binding. PWM supplied with a score threshold defines a set of putative transcription factor binding sites...

    Authors: Ilya E Vorontsov, Ivan V Kulakovskiy and Vsevolod J Makeev

    Citation: Algorithms for Molecular Biology 2013 8:23

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  8. Content type: Research

    Classical approaches to compute the genomic distance are usually limited to genomes with the same content and take into consideration only rearrangements that change the organization of the genome (i.e. positi...

    Authors: Poly H da Silva, Raphael Machado, Simone Dantas and Marília DV Braga

    Citation: Algorithms for Molecular Biology 2013 8:21

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  9. Content type: Research

    Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein ...

    Authors: Natalie E Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A Pevzner, Adam Godzik and Kira Vyatkina

    Citation: Algorithms for Molecular Biology 2013 8:19

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  10. Content type: Research

    A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of ...

    Authors: Akshay Deepak, David Fernández-Baca and Michelle M McMahon

    Citation: Algorithms for Molecular Biology 2013 8:18

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  11. Content type: Research

    We propose a novel graph theoretic method to estimate haplotype population size from genotype data. The method considers only the potential sharing of haplotypes between individuals and is based on transformin...

    Authors: Bjarni V Halldórsson, Dima Blokh and Roded Sharan

    Citation: Algorithms for Molecular Biology 2013 8:17

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  12. Content type: Research

    Gene expression data could likely be a momentous help in the progress of proficient cancer diagnoses and classification platforms. Lately, many researchers analyze gene expression data using diverse computatio...

    Authors: Mohd Saberi Mohamad, Sigeru Omatu, Safaai Deris, Michifumi Yoshioka, Afnizanfaizal Abdullah and Zuwairie Ibrahim

    Citation: Algorithms for Molecular Biology 2013 8:15

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  13. Content type: Research

    The search for distant homologs has become an import issue in genome annotation. A particular difficulty is posed by divergent homologs that have lost recognizable sequence similarity. This same problem also a...

    Authors: Sebastian Will, Michael F Siebauer, Steffen Heyne, Jan Engelhardt, Peter F Stadler, Kristin Reiche and Rolf Backofen

    Citation: Algorithms for Molecular Biology 2013 8:14

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  14. Content type: Research

    We generalize some current approaches for RNA tree alignment, which are traditionally confined to ordered rooted mappings, to also consider unordered unrooted mappings. We define the Homeomorphic Subtree Alignmen...

    Authors: Nimrod Milo, Shay Zakov, Erez Katzenelson, Eitan Bachmat, Yefim Dinitz and Michal Ziv-Ukelson

    Citation: Algorithms for Molecular Biology 2013 8:13

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  15. Content type: Research

    Reconciliation methods compare gene trees and species trees to recover evolutionary events such as duplications, transfers and losses explaining the history and composition of genomes. It is well-known that ge...

    Authors: Thi Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Jean-Philippe Doyon and Vincent Berry

    Citation: Algorithms for Molecular Biology 2013 8:12

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  16. Content type: Research

    We study a long standing conjecture on the necessary and sufficient conditions for the compatibility of multi-state characters: There exists a function f(r) such that, for any set C of r-state characters, C is co...

    Authors: Brad Shutters, Sudheer Vakati and David Fernández-Baca

    Citation: Algorithms for Molecular Biology 2013 8:11

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  17. Content type: Research

    Gene Ontology (GO) is a hierarchical vocabulary for the description of biological functions and locations, often employed by computational methods for protein function prediction. Due to the structure of GO, f...

    Authors: Yiannis AI Kourmpetis, Aalt DJ van Dijk and Cajo JF ter Braak

    Citation: Algorithms for Molecular Biology 2013 8:10

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  18. Content type: Research

    Estrogen is a chemical messenger that has an influence on many breast cancers as it helps cells to grow and divide. These cancers are often known as estrogen responsive cancers in which estrogen receptor occup...

    Authors: Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay and Edgar Wingender

    Citation: Algorithms for Molecular Biology 2013 8:9

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  19. Content type: Research

    Chromosome structure is closely related to its function and Chromosome Conformation Capture (3C) is a widely used technique for exploring spatial properties of chromosomes. 3C interaction frequencies are usual...

    Authors: Geet Duggal, Rob Patro, Emre Sefer, Hao Wang, Darya Filippova, Samir Khuller and Carl Kingsford

    Citation: Algorithms for Molecular Biology 2013 8:8

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  20. Content type: Research

    The large majority of optimization problems related to the inference of distance‐based trees used in phylogenetic analysis and classification is known to be intractable. One noted exception is found within the...

    Authors: Alberto Apostolico, Matteo Comin, Andres Dress and Laxmi Parida

    Citation: Algorithms for Molecular Biology 2013 8:7

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  21. Content type: Research

    The introduction of the double cut and join operation (DCJ) caused a flurry of research into the study of multichromosomal rearrangements. However, little of this work has incorporated indels (i.e., insertions...

    Authors: Phillip EC Compeau

    Citation: Algorithms for Molecular Biology 2013 8:6

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  22. Content type: Research

    Previous studies show that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian d...

    Authors: Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi and Ming Li

    Citation: Algorithms for Molecular Biology 2013 8:5

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  23. Content type: Research

    Phylogeny estimation from aligned haplotype sequences has attracted more and more attention in the recent years due to its importance in analysis of many fine-scale genetic data. Its application fields range f...

    Authors: Daniele Catanzaro, Ramamoorthi Ravi and Russell Schwartz

    Citation: Algorithms for Molecular Biology 2013 8:3

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  24. Content type: Research

    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

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  25. Content type: Research

    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

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  26. Content type: Research

    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

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  27. Content type: Research

    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

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  28. Content type: Research

    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

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  29. Content type: Research

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Research

    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

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  33. Content type: Research

    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

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  34. Content type: Research

    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

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  35. Content type: Research

    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

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  36. Content type: Research

    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

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  37. Content type: Research

    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

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  38. Content type: Software article

    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

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