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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...
Source Code for Biology and Medicine 2015 10:11
Published on: 11 November 2015
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...
Source Code for Biology and Medicine 2015 10:10
Published on: 25 September 2015
Software
In order to better define regions of similarity among related protein structures, it is useful to identify the residue-residue correspondences among proteins. Few codes exist for constructing a one-to-many mul...
Source Code for Biology and Medicine 2015 10:9
Published on: 5 August 2015
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...
Source Code for Biology and Medicine 2015 10:8
Published on: 4 June 2015
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...
Source Code for Biology and Medicine 2015 10:7
Published on: 22 May 2015
Software
Sequencing and genotyping technology advancements have led to massive, growing repositories of spatially explicit genetic data and increasing quantities of temporal data (i.e., ancient DNA). These data will al...
Source Code for Biology and Medicine 2015 10:6
Published on: 11 April 2015
Software
High-throughput transcriptional profiling using Next-Generation Sequencing (RNA-Seq) or microarray technology have become standard tools in molecular biology. Successful investigations of gene regulatory mecha...
Source Code for Biology and Medicine 2015 10:5
Published on: 2 April 2015
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 ...
Source Code for Biology and Medicine 2015 10:4
Published on: 26 March 2015
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...
Source Code for Biology and Medicine 2015 10:3
Published on: 7 March 2015
BRIEF REPORTS
Correctly modeling population structure is important for understanding recent evolution and for association studies in humans. While pre-existing knowledge of population history can be used to specify expected...
Source Code for Biology and Medicine 2015 10:2
Published on: 3 February 2015
Software
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...
Source Code for Biology and Medicine 2015 10:1
Published on: 3 February 2015
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...
Source Code for Biology and Medicine 2014 9:30
Published on: 24 December 2014
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 ...
Source Code for Biology and Medicine 2014 9:29
Published on: 20 December 2014
Erratum
Source Code for Biology and Medicine 2014 9:122
Published on: 20 December 2014
The original article was published in Source Code for Biology and Medicine 2014 9:9
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...
Source Code for Biology and Medicine 2014 9:27
Published on: 10 December 2014
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 ...
Source Code for Biology and Medicine 2014 9:26
Published on: 5 December 2014
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...
Source Code for Biology and Medicine 2014 9:25
Published on: 5 December 2014
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...
Source Code for Biology and Medicine 2014 9:23
Published on: 3 December 2014
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...
Source Code for Biology and Medicine 2014 9:24
Published on: 15 November 2014
Software review
Creating visually pleasing graphs in data visualization programs such as Matlab is surprisingly challenging. One common problem is that the positions and sizes of non-data elements such as textual annotations ...
Source Code for Biology and Medicine 2014 9:22
Published on: 21 October 2014
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...
Source Code for Biology and Medicine 2014 9:21
Published on: 24 September 2014
Software review
Bioinformatics data analysis is usually done sequentially by chaining together multiple tools. These are created by writing scripts and tracking the inputs and outputs of all stages. Writing such scripts requi...
Source Code for Biology and Medicine 2014 9:20
Published on: 18 September 2014
Research
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...
Source Code for Biology and Medicine 2014 9:19
Published on: 2 September 2014
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...
Source Code for Biology and Medicine 2014 9:18
Published on: 17 August 2014
Research
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...
Source Code for Biology and Medicine 2014 9:17
Published on: 10 July 2014
