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Source Code for Biology and Medicine

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  1. Content type: Methodology

    Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical prac...

    Authors: Alice Mantoan, Claudio Pizzolato, Massimo Sartori, Zimi Sawacha, Claudio Cobelli and Monica Reggiani

    Citation: Source Code for Biology and Medicine 2015 10:12

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  2. Content type: Research

    Inference of gene networks from expression data is an important problem in computational biology. Many algorithms have been proposed for solving the problem efficiently. However, many of the available implemen...

    Authors: Maciej Fronczuk, Adrian E. Raftery and Ka Yee Yeung

    Citation: Source Code for Biology and Medicine 2015 10:11

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  3. Content type: Software

    It is now widely-accepted that DNA sequences defining DNA-protein interactions functionally depend upon local biophysical features of DNA backbone that are important in defining sites of binding interaction in...

    Authors: Connor H. Fortin, Katharina V. Schulze and Gregory A. Babbitt

    Citation: Source Code for Biology and Medicine 2015 10:10

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  4. Content type: Software

    High-throughput primer design is routinely performed in a wide number of molecular applications including genotyping specimens using traditional PCR techniques as well as assembly PCR, nested PCR, and primer w...

    Authors: Damien M. O’Halloran

    Citation: Source Code for Biology and Medicine 2015 10:8

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  5. Content type: Research

    Malaria has been a major life threatening mosquito borne disease from long since. Unavailability of any effective vaccine and recent emergence of multi drug resistant strains of malaria pathogen Plasmodium falcip...

    Authors: Md. Anayet Hasan, Md. Habibul Hasan Mazumder, Afrin Sultana Chowdhury, Amit Datta and Md. Arif Khan

    Citation: Source Code for Biology and Medicine 2015 10:7

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  6. Content type: Software

    MicroRNA expression can be quantified using sequencing techniques or commercial microRNA-expression arrays. Recently, the AgiMicroRna R-package was published that enabled systematic preprocessing and statistical ...

    Authors: Maarten LJ Coonen, Daniel HJ Theunissen, Jos CS Kleinjans and Danyel GJ Jennen

    Citation: Source Code for Biology and Medicine 2015 10:4

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  7. Content type: Software

    The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These inte...

    Authors: Matthew Carr and Cait E MacPhee

    Citation: Source Code for Biology and Medicine 2015 10:3

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  8. Content type: Methodology

    The graphical visualization of gene expression data using heatmaps has become an integral component of modern-day medical research. Heatmaps are used extensively to plot quantitative differences in gene expres...

    Authors: Bohdan B Khomtchouk, Derek J Van Booven and Claes Wahlestedt

    Citation: Source Code for Biology and Medicine 2014 9:30

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  9. Content type: Methodology

    Eelgrass is a cosmopolitan seagrass species that provides important ecological services in coastal and near-shore environments. Despite its relevance, loss of eelgrass habitats is noted worldwide. Restoration ...

    Authors: Héctor Echavarría-Heras, Cecilia Leal-Ramírez, Enrique Villa-Diharce and Oscar Castillo

    Citation: Source Code for Biology and Medicine 2014 9:29

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  10. Content type: Research

    Successfully automated sigmoidal curve fitting is highly challenging when applied to large data sets. In this paper, we describe a robust algorithm for fitting sigmoid dose-response curves by estimating four p...

    Authors: Thuy Tuong Nguyen, Kyungmin Song, Yury Tsoy, Jin Yeop Kim, Yong-Jun Kwon, Myungjoo Kang and Michael Adsetts Edberg Hansen

    Citation: Source Code for Biology and Medicine 2014 9:27

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  11. Content type: Software review

    In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of ...

    Authors: Robert V Baron, Charles Kollar, Nandita Mukhopadhyay and Daniel E Weeks

    Citation: Source Code for Biology and Medicine 2014 9:26

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  12. Content type: Methodology

    Whole genomes, whole exomes and transcriptomes of tumour samples are sequenced routinely to identify the drivers of cancer. The systematic sequencing and analysis of tumour samples, as well other oncogenomic e...

    Authors: Mike Gavrielides, Simon J Furney, Tim Yates, Crispin J Miller and Richard Marais

    Citation: Source Code for Biology and Medicine 2014 9:25

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  13. Content type: Software review

    Researchers usually employ bar graphs to show two groups of data, which can be easily manipulated to yield false impressions. To some extent, scatterplot can retain the real data values and the spread of the d...

    Authors: Yong Xu, Fuquan Zhang, Guoqiang Wang, Hongbao Cao, Zaohuo Cheng and Yin Yao Shugart

    Citation: Source Code for Biology and Medicine 2014 9:23

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  14. Content type: Methodology

    Commonly when designing studies, researchers propose to measure several independent variables in a regression model, a subset of which are identified as the main variables of interest while the rest are retain...

    Authors: David Keith Williams and Zoran Bursac

    Citation: Source Code for Biology and Medicine 2014 9:24

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  15. Content type: Software review

    The analysis of a series of experimental data is an essential procedure in virtually every field of research. The information contained in the data is extracted by fitting the experimental data to a mathematic...

    Authors: Christoph Wiedemann, Peter Bellstedt and Matthias Görlach

    Citation: Source Code for Biology and Medicine 2014 9:21

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  16. Content type: Brief reports

    For over 400 years, due to the reassortment of their segmented genomes, influenza viruses evolve extremely quickly and cause devastating epidemics. This reassortment arises because two flu viruses can infect t...

    Authors: Michel Petitjean and Anne Vanet

    Citation: Source Code for Biology and Medicine 2014 9:18

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