Analysis and modelling of complex systems

ISSN: 1471-2105 (Online)

In this topical collection (557 articles)

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  1. Research article

    Improvement of the memory function of a mutual repression network in a stochastic environment by negative autoregulation

    A. B. M. Shamim Ul Hasan, Hiroyuki Kurata, Sebastian Pechmann Article:734
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  2. Research article

    Deriving a Boolean dynamics to reveal macrophage activation with in vitro temporal cytokine expression profiles

    Ricardo Ramirez, Allen Michael Herrera, Joshua Ramirez… Article:725
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  3. Software

    SIDEKICK: Genomic data driven analysis and decision-making framework

    Mark S Doderer, Kihoon Yoon, Kay A Robbins Article:611
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  4. Research article

    Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites

    Miriam R Kantorovitz, Zoi Rapti, Vladimir Gelev, Anny Usheva Article:604
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  5. Methodology article

    A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

    David J Russell, Samuel F Way, Andrew K Benson, Khalid Sayood Article:601
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  6. Methodology article

    A genome alignment algorithm based on compression

    Minh Duc Cao, Trevor I Dix, Lloyd Allison Article:599
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  7. Methodology Article

    Estimating network changes from lifespan measurements using a parsimonious gene network model of cellular aging

    Hong Qin Article:599
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  8. Research article

    Initial steps towards a production platform for DNA sequence analysis on the grid

    Angela CM Luyf, Barbera DC van Schaik, Michel de Vries, Frank Baas… Article:598
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  9. Software

    BIGSdb: Scalable analysis of bacterial genome variation at the population level

    Keith A Jolley, Martin CJ Maiden Article:595
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  10. Methodology article

    BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

    C Bannert, A Welfle, C aus dem Spring, D Schomburg Article:589
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  11. Methodology article

    IntelliGO: a new vector-based semantic similarity measure including annotation origin

    Sidahmed Benabderrahmane, Malika Smail-Tabbone, Olivier Poch… Article:588
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  12. Methodology article

    Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks

    Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima… Article:581
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  13. Software

    Pash 3.0: A versatile software package for read map** and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

    Cristian Coarfa, Fuli Yu, Christopher A Miller, Zuozhou Chen… Article:572
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  14. Methodology article

    Reticular alignment: A progressive corner-cutting method for multiple sequence alignment

    Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein Article:570
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  15. Software

    MetaGenyo: a web tool for meta-analysis of genetic association studies

    Jordi Martorell-Marugan, Daniel Toro-Dominguez… Article:563
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  16. Research article

    TESTLoc: protein subcellular localization prediction from EST data

    Yao-Qing Shen, Gertraud Burger Article:563
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  17. Research article

    Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

    Vamsi K Kundeti, Sanguthevar Rajasekaran, Hieu Dinh, Matthew Vaughn… Article:560
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  18. Research article

    Epigenetic domains found in mouse embryonic stem cells via a hidden Markov model

    Jessica L Larson, Guo-Cheng Yuan Article:557
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  19. Software

    Canary: an atomic pipeline for clinical amplicon assays

    Kenneth D. Doig, Jason Ellul, Andrew Fellowes, Ella R. Thompson… Article:555
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  20. Software

    pyAmpli: an amplicon-based variant filter pipeline for targeted resequencing data

    Matthias Beyens, Nele Boeckx, Guy Van Camp, Ken Op de Beeck… Article:554
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