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  1. Research

    CyNetworkBMA: a Cytoscape app for inferring gene regulatory networks

    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...

    Maciej Fronczuk, Adrian E. Raftery and Ka Yee Yeung

    Source Code for Biology and Medicine 2015 10:11

    Published on: 11 November 2015

  2. Software

    TRX-LOGOS - a graphical tool to demonstrate DNA information content dependent upon backbone dynamics in addition to base sequence

    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...

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

    Source Code for Biology and Medicine 2015 10:10

    Published on: 25 September 2015

  3. Software

    PrimerView: high-throughput primer design and visualization

    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...

    Damien M. O’Halloran

    Source Code for Biology and Medicine 2015 10:8

    Published on: 4 June 2015

  4. Research

    Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment

    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...

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

    Source Code for Biology and Medicine 2015 10:7

    Published on: 22 May 2015

  5. Software

    MagiCMicroRna: a web implementation of AgiMicroRna using shiny

    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 ...

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

    Source Code for Biology and Medicine 2015 10:4

    Published on: 26 March 2015

  6. Software

    Membrainy: a ‘smart’, unified membrane analysis tool

    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...

    Matthew Carr and Cait E MacPhee

    Source Code for Biology and Medicine 2015 10:3

    Published on: 7 March 2015

  7. Software

    LocusTrack: Integrated visualization of GWAS results and genomic annotation

    Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechan...

    Gabriel Cuellar-Partida, Miguel E Renteria and Stuart MacGregor

    Source Code for Biology and Medicine 2015 10:1

    Published on: 3 February 2015

  8. Methodology

    HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline

    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...

    Bohdan B Khomtchouk, Derek J Van Booven and Claes Wahlestedt

    Source Code for Biology and Medicine 2014 9:30

    Published on: 24 December 2014

  9. Methodology

    Using the value of Lin’s concordance correlation coefficient as a criterion for efficient estimation of areas of leaves of eelgrass from noisy digital images

    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 ...

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

    Source Code for Biology and Medicine 2014 9:29

    Published on: 20 December 2014

  10. Research

    Robust dose-response curve estimation applied to high content screening data analysis

    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...

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

    Source Code for Biology and Medicine 2014 9:27

    Published on: 10 December 2014

  11. Software review

    Mega2: validated data-reformatting for linkage and association analyses

    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 ...

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

    Source Code for Biology and Medicine 2014 9:26

    Published on: 5 December 2014

  12. Methodology

    Onco-STS: a web-based laboratory information management system for sample and analysis tracking in oncogenomic experiments

    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...

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

    Source Code for Biology and Medicine 2014 9:25

    Published on: 5 December 2014

  13. Software review

    plot2groups: an R package to plot scatter points for two groups of values

    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...

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

    Source Code for Biology and Medicine 2014 9:23

    Published on: 3 December 2014

  14. Methodology

    Three algorithms and SAS macros for estimating power and sample size for logistic models with one or more independent variables of interest in the presence of covariates

    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...

    David Keith Williams and Zoran Bursac

    Source Code for Biology and Medicine 2014 9:24

    Published on: 15 November 2014

  15. Software review

    PREdator: a python based GUI for data analysis, evaluation and fitting

    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...

    Christoph Wiedemann, Peter Bellstedt and Matthias Görlach

    Source Code for Biology and Medicine 2014 9:21

    Published on: 24 September 2014

  16. Research

    EC2KEGG: a command line tool for comparison of metabolic pathways

    Next-generation sequencing and metagenome projects yield a large number of new genomes that need further annotations, such as identification of enzymes and metabolic pathways, or analysis of metabolic strategi...

    Aleksey Porollo

    Source Code for Biology and Medicine 2014 9:19

    Published on: 2 September 2014

  17. Brief reports

    VIRAPOPS2 supports the influenza virus reassortments

    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...

    Michel Petitjean and Anne Vanet

    Source Code for Biology and Medicine 2014 9:18

    Published on: 17 August 2014

  18. Research

    A dedicated database system for handling multi-level data in systems biology

    Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic...

    Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew and Jens Nielsen

    Source Code for Biology and Medicine 2014 9:17

    Published on: 10 July 2014

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