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Software
Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times the...
Source Code for Biology and Medicine 2017 12:6
Published on: 13 April 2017
Software
In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their s...
Source Code for Biology and Medicine 2017 12:5
Published on: 21 March 2017
Software
The analysis of complex networks both in general and in particular as pertaining to real biological systems has been the focus of intense scientific attention in the past and present. In this paper we introduc...
Source Code for Biology and Medicine 2017 12:4
Published on: 8 February 2017
Methodology
Local field potentials (LFPs) evoked by sensory stimulation are particularly useful in electrophysiological research. For instance, spike timing and current transmembrane current flow estimated from LFPs recor...
Source Code for Biology and Medicine 2017 12:3
Published on: 7 February 2017
Software
A growing trend in the biomedical community is the use of Next Generation Sequencing (NGS) technologies in genomics research. The complexity of downstream differential expression (DE) analysis is however still...
Source Code for Biology and Medicine 2017 12:2
Published on: 3 February 2017
Erratum
Source Code for Biology and Medicine 2017 12:1
Published on: 9 January 2017
The original article was published in Source Code for Biology and Medicine 2016 11:14
Software
Matched sequencing of both tumor and normal tissue is routinely used to classify variants of uncertain significance (VUS) into somatic vs. germline. However, assays used in molecular diagnostics focus on known...
Source Code for Biology and Medicine 2016 11:13
Published on: 15 December 2016
Software
Next-generation sequencing is making it critical to robustly and rapidly handle genomic ranges within standard pipelines. Standard use-cases include annotating sequence ranges with gene or other genomic annota...
Source Code for Biology and Medicine 2016 11:14
Published on: 15 December 2016
The Erratum to this article has been published in Source Code for Biology and Medicine 2017 12:1
Software
Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it....
Source Code for Biology and Medicine 2016 11:12
Published on: 17 August 2016
Software
In genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), read depth is important for assessing the quality of genotype calls and estimating allele dosage in polyploids. Howev...
Source Code for Biology and Medicine 2016 11:11
Published on: 11 July 2016
Software
Whole exome sequencing (WES) has provided a means for researchers to gain access to a highly enriched subset of the human genome in which to search for variants that are likely to be pathogenic and possibly pr...
Source Code for Biology and Medicine 2016 11:10
Published on: 1 July 2016
Software
To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are ...
Source Code for Biology and Medicine 2016 11:9
Published on: 24 June 2016
Software
Genomic deletions, inversions, and other rearrangements known collectively as structural variations (SVs) are implicated in many human disorders. Technologies for sequencing DNA provide a potentially rich sour...
Source Code for Biology and Medicine 2016 11:8
Published on: 18 June 2016
Methodology
The aim of this paper is to provide a general discussion, algorithm, and actual working programs of the deformation method for fast simulation of biological tissue formed by fibers and fluid. In order to demon...
Source Code for Biology and Medicine 2016 11:7
Published on: 15 April 2016
Software
Medulloblastoma (MB) is a highly malignant and heterogeneous brain tumour that is the most common cause of cancer-related deaths in children. Increasing availability of genomic data over the last decade had re...
Source Code for Biology and Medicine 2016 11:6
Published on: 11 April 2016
Software
Most genetic association studies use single-nucleotide polymorphisms (SNPs) as the research targets. However, resources to visualize the genomic map of candidate SNPs in a programming manner are limited. We ha...
Source Code for Biology and Medicine 2016 11:5
Published on: 2 April 2016
Research
Standardized schemas, databases, and public data repositories are needed for the studies of malaria vectors that encompass a remarkably diverse array of designs and rapidly generate large data volumes, often i...
Source Code for Biology and Medicine 2016 11:4
Published on: 28 March 2016
Research
MERS-CoV is a newly emerged human coronavirus reported closely related with HKU4 and HKU5 Bat coronaviruses. Bat and MERS corona-viruses are structurally related. Therefore, it is of interest to estimate the d...
Source Code for Biology and Medicine 2016 11:3
Published on: 9 March 2016
Brief reports
Quantitative co-localization studies strengthen the analysis of fluorescence microscopy-based assays and are essential for illustrating and understanding many cellular processes and interactions. In our earlie...
Source Code for Biology and Medicine 2016 11:2
Published on: 16 February 2016
Research
We previously presented a group theoretical model that describes psychiatric patient states or clinical data in a graded vector-like format based on modulo groups. Meanwhile, the Diagnostic and Statistical Manual...
Source Code for Biology and Medicine 2016 11:1
Published on: 19 January 2016
Methodology
Optimal ranking of literature importance is vital in overcoming article overload. Existing ranking methods are typically based on raw citation counts, giving a sum of ‘inbound’ links with no consideration of c...
Source Code for Biology and Medicine 2015 10:16
Published on: 9 December 2015
Software
One of the recent challenges of computational biology is development of new algorithms, tools and software to facilitate predictive modeling of big data generated by high-throughput technologies in biomedical ...
Source Code for Biology and Medicine 2015 10:15
Published on: 3 December 2015
Software
Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of ...
Source Code for Biology and Medicine 2015 10:14
Published on: 19 November 2015
Software
With the continued exponential growth in data volume, large-scale data mining and machine learning experiments have become a necessity for many researchers without programming or statistics backgrounds. WEKA (...
Source Code for Biology and Medicine 2015 10:13
Published on: 17 November 2015
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...
Source Code for Biology and Medicine 2015 10:12
Published on: 16 November 2015
