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  1. Chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are...

    Authors: Darya Filippova, Rob Patro, Geet Duggal and Carl Kingsford
    Citation: Algorithms for Molecular Biology 2014 9:14
  2. Progressive methods offer efficient and reasonably good solutions to the multiple sequence alignment problem. However, resulting alignments are biased by guide-trees, especially for relatively distant sequences.

    Authors: Michał Modzelewski and Norbert Dojer
    Citation: Algorithms for Molecular Biology 2014 9:12
  3. The number of genome-wide association studies (GWAS) has increased rapidly in the past couple of years, resulting in the identification of genes associated with different diseases. The next step in translating...

    Authors: Usha Kuppuswamy, Seshan Ananthasubramanian, Yanli Wang, Narayanaswamy Balakrishnan and Madhavi K Ganapathiraju
    Citation: Algorithms for Molecular Biology 2014 9:10
  4. Circular string matching is a problem which naturally arises in many biological contexts. It consists in finding all occurrences of the rotations of a pattern of length m in a text of length n. There exist optima...

    Authors: Carl Barton, Costas S Iliopoulos and Solon P Pissis
    Citation: Algorithms for Molecular Biology 2014 9:9
  5. Identifying ligand-binding sites is a key step to annotate the protein functions and to find applications in drug design. Now, many sequence-based methods adopted various predicted results from other classifie...

    Authors: Chun Fang, Tamotsu Noguchi and Hayato Yamana
    Citation: Algorithms for Molecular Biology 2014 9:7
  6. Change point problems arise in many genomic analyses such as the detection of copy number variations or the detection of transcribed regions. The expanding Next Generation Sequencing technologies now allow to ...

    Authors: Alice Cleynen, Michel Koskas, Emilie Lebarbier, Guillem Rigaill and Stéphane Robin
    Citation: Algorithms for Molecular Biology 2014 9:6
  7. The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n3) time using Nussinov’s dynamic programming algorithm....

    Authors: Balaji Venkatachalam, Dan Gusfield and Yelena Frid
    Citation: Algorithms for Molecular Biology 2014 9:5
  8. Multiple sequence alignment (MSA) is an extremely useful tool for molecular and evolutionary biology and there are several programs and algorithms available for this purpose. Although previous studies have com...

    Authors: Fabiano Sviatopolk-Mirsky Pais, Patrícia de Cássia Ruy, Guilherme Oliveira and Roney Santos Coimbra
    Citation: Algorithms for Molecular Biology 2014 9:4
  9. The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental ch...

    Authors: Arnon Mazza, Irit Gat-Viks, Hesso Farhan and Roded Sharan
    Citation: Algorithms for Molecular Biology 2014 9:1
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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