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  1. Content type: Research

    Pareto optimization combines independent objectives by computing the Pareto front of its search space, defined as the set of all solutions for which no other candidate solution scores better under all objectives....

    Authors: Cédric Saule and Robert Giegerich

    Citation: Algorithms for Molecular Biology 2015 10:22

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  2. Content type: Research

    The increase of protein–protein interaction (PPI) data of different species makes it possible to identify common subnetworks (conserved protein complexes) across species via local alignment of their PPI networ...

    Authors: Wei Peng, Jianxin Wang, Fangxiang Wu and Pan Yi

    Citation: Algorithms for Molecular Biology 2015 10:21

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  3. Content type: Research

    The problem of enumerating bubbles with length constraints in directed graphs arises in transcriptomics where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced ...

    Authors: Gustavo Sacomoto, Vincent Lacroix and Marie-France Sagot

    Citation: Algorithms for Molecular Biology 2015 10:20

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  4. Content type: Research

    Analogous to genomic sequence alignment, biological network alignment identifies conserved regions between networks of different species. Then, function can be transferred from well- to poorly-annotated specie...

    Authors: Joseph Crawford, Yihan Sun and Tijana Milenković

    Citation: Algorithms for Molecular Biology 2015 10:19

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  5. Content type: Research

    Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for produci...

    Authors: Vladimír Boža, Broňa Brejová and Tomáš Vinař

    Citation: Algorithms for Molecular Biology 2015 10:18

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  6. Content type: Research

    The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core...

    Authors: Sharon Bruckner, Falk Hüffner and Christian Komusiewicz

    Citation: Algorithms for Molecular Biology 2015 10:16

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  7. Content type: Research

    Autocatalytic sets are considered to be fundamental to the origin of life. Prior theoretical and computational work on the existence and properties of these sets has relied on a fast algorithm for detectingsel...

    Authors: Wim Hordijk, Joshua I Smith and Mike Steel

    Citation: Algorithms for Molecular Biology 2015 10:15

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  8. Content type: Research

    Structural variation in genomes can be revealed by many (dis)similarity measures. Rearrangement operations, such as the so called double-cut-and-join (DCJ), are large-scale mutations that can create complex ch...

    Authors: Fábio V Martinez, Pedro Feijão, Marília DV Braga and Jens Stoye

    Citation: Algorithms for Molecular Biology 2015 10:13

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  9. Content type: Research

    During evolution, global mutations may alter the order and the orientation of the genes in a genome. Such mutations are referred to as rearrangement events, or simply operations. In unichromosomal genomes, the...

    Authors: Gustavo Rodrigues Galvão, Orlando Lee and Zanoni Dias

    Citation: Algorithms for Molecular Biology 2015 10:12

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  10. Content type: Research

    The body-bar Pebble Game (PG) algorithm is commonly used to calculate network rigidity properties in proteins and polymeric materials. To account for fluctuating interactions such as hydrogen bonds, an ensembl...

    Authors: Luis C González, Hui Wang, Dennis R Livesay and Donald J Jacobs

    Citation: Algorithms for Molecular Biology 2015 10:11

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  11. Content type: Research

    Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing ...

    Authors: Steve Hoffmann, Peter F Stadler and Korbinian Strimmer

    Citation: Algorithms for Molecular Biology 2015 10:10

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  12. Content type: Research

    This paper presents a constraint-based method for improving protein docking results. Efficient constraint propagation cuts over 95% of the search time for finding the configurations with the largest contact su...

    Authors: Ludwig Krippahl and Pedro Barahona

    Citation: Algorithms for Molecular Biology 2015 10:9

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  13. Content type: Review article

    Interaction sites on protein surfaces mediate virtually all biological activities, and their identification holds promise for disease treatment and drug design. Novel algorithmic approaches for the prediction ...

    Authors: Tristan T Aumentado-Armstrong, Bogdan Istrate and Robert A Murgita

    Citation: Algorithms for Molecular Biology 2015 10:7

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  14. Content type: Research

    Alignment-free methods are increasingly used to calculate evolutionary distances between DNA and protein sequences as a basis of phylogeny reconstruction. Most of these methods, however, use heuristic distance...

    Authors: Burkhard Morgenstern, Bingyao Zhu, Sebastian Horwege and Chris André Leimeister

    Citation: Algorithms for Molecular Biology 2015 10:5

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  15. Content type: Research

    The data volume generated by Next-Generation Sequencing (NGS) technologies is growing at a pace that is now challenging the storage and data processing capacities of modern computer systems. In this context an...

    Authors: Matteo Comin, Andrea Leoni and Michele Schimd

    Citation: Algorithms for Molecular Biology 2015 10:4

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  16. Content type: SOFTWARE ARTICLE

    Phylogenetic tree reconciliation is the approach of choice for investigating the coevolution of sets of organisms such as hosts and parasites. It consists in a mapping between the parasite tree and the host tr...

    Authors: Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi and Marie-France Sagot

    Citation: Algorithms for Molecular Biology 2015 10:3

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  17. Content type: Research

    Metagenomics is the study of genetic materials derived directly from complex microbial samples, instead of from culture. One of the crucial steps in metagenomic analysis, referred to as “binning”, is to separa...

    Authors: Le Van Vinh, Tran Van Lang, Le Thanh Binh and Tran Van Hoai

    Citation: Algorithms for Molecular Biology 2015 10:2

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  18. Content type: Research

    The universal pacemaker (UPM) model extends the classical molecular clock (MC) model, by allowing each gene, in addition to its individual intrinsic rate as in the MC, to accelerate or decelerate according to ...

    Authors: Sagi Snir

    Citation: Algorithms for Molecular Biology 2014 9:26

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  19. Content type: Research

    Biclustering, the discovery of sets of objects with a coherent pattern across a subset of conditions, is a critical task to study a wide-set of biomedical problems, where molecular units or patients are meanin...

    Authors: Rui Henriques and Sara C Madeira

    Citation: Algorithms for Molecular Biology 2014 9:27

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  20. Content type: Research

    Finding new functional fragments in biological sequences is a challenging problem. Methods addressing this problem commonly search for clusters of pattern occurrences that are statistically significant. A meas...

    Authors: Mireille Régnier, Evgenia Furletova, Victor Yakovlev and Mikhail Roytberg

    Citation: Algorithms for Molecular Biology 2014 9:25

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  21. Content type: Research

    Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms...

    Authors: Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler and Christoph Flamm

    Citation: Algorithms for Molecular Biology 2014 9:23

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  22. Content type: Review article

    Sets of sequence data used in phylogenetic analysis are often plagued by both random noise and systematic biases. Since the commonly used methods of phylogenetic reconstruction are designed to produce trees it...

    Authors: Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska and Peter F Stadler

    Citation: Algorithms for Molecular Biology 2014 9:22

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  23. Content type: Research

    Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splic...

    Authors: Jing Qin, Markus Fricke, Manja Marz, Peter F Stadler and Rolf Backofen

    Citation: Algorithms for Molecular Biology 2014 9:19

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  24. Content type: Research

    Tandem duplication, in the context of molecular biology, occurs as a result of mutational events in which an original segment of DNA is converted into a sequence of individual copies. More formally, a repetition ...

    Authors: Carl Barton, Costas S Iliopoulos and Solon P Pissis

    Citation: Algorithms for Molecular Biology 2014 9:21

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  25. Content type: Research

    An important problem in systems biology is to model gene regulatory networks which can then be utilized to develop novel therapeutic methods for cancer treatment. Knowledge about which proteins/genes are dysre...

    Authors: Anwoy Kumar Mohanty, Aniruddha Datta and Vijayanagaram Venkatraj

    Citation: Algorithms for Molecular Biology 2014 9:20

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  26. Content type: Research

    RNA-RNA interaction plays an important role in the regulation of gene expression and cell development. In this process, an RNA molecule prohibits the translation of another RNA molecule by establishing stable ...

    Authors: Soheila Montaseri, Fatemeh Zare-Mirakabad and Nasrollah Moghadam-Charkari

    Citation: Algorithms for Molecular Biology 2014 9:17

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  27. Content type: Research

    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

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  28. Content type: Research

    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

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  29. Content type: Research

    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

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  30. Content type: Research

    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

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  31. Content type: Research

    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

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  32. Content type: Software article

    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

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  33. Content type: Research

    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

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  34. Content type: Research

    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

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  35. Content type: Research

    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

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  36. 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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