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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...
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 ...
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...
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...
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...
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 ...
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...
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...
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...
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...
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...
A growing spectrum of applications for natural and synthetic polymers, whether in industry or for biomedical research, demands for fast and universally applicable tools to determine the mechanical properties o...
The NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual sear...
Information management systems are essential to capture data be it for public health and human disease, sustainable agriculture, or plant and animal biosecurity. In public health, the term patient registry is ...
Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of ...
The fundamental challenge in optimally aligning homologous sequences is to define a scoring scheme that best reflects the underlying biological processes. Maximising the overall number of matches in the alignm...
Methylation plotter is a Web tool that allows the visualization of methylation data in a user-friendly manner and with publication-ready quality. The user is asked to introduce a file containing the methylatio...
A multi-million dollar research initiative involving the National Institutes of Health (NIH), Wellcome Trust and African scientists has been launched. The initiative, referred to as H3Africa, is an acronym tha...
Myotis species of bats such as the Indiana Bat and Little Brown Bat are facing population declines because of White-nose syndrome (WNS). These species also face threats from anthropogenic activities such as wind ...
The Erratum to this article has been published in Source Code for Biology and Medicine 2014 9:122
When compared to Sanger sequencing technology, next-generation sequencing (NGS) technologies are hindered by shorter sequence read length, higher base-call error rate, non-uniform coverage, and platform-specif...
The development of Next Generation Sequencing (NGS) during the last decade has created an unprecedented amount of sequencing data, as well as the ability to rapidly sequence specimens of interest. Read-based B...
Genetic Analyses in large sample populations are important for a better understanding of the variation between populations, for designing conservation programs, for detecting rare mutations which may be risk f...
A well-known problem in cluster analysis is finding an optimal number of clusters reflecting the inherent structure of the data. PFClust is a partitioning-based clustering algorithm capable, unlike many widely...
The original article was published in Source Code for Biology and Medicine 2013 8:21
We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end...
Multiobjective sequence alignment brings the advantage of providing a set of alignments that represent the trade-off between performing insertion/deletions and matching symbols from both sequences. Each of the...
Cellular events play a central role in the understanding of biological processes and functions, providing insight on both physiological and pathogenesis mechanisms. Automatic extraction of mentions of such eve...
Genome sequencing has become routine, however genome assembly still remains a challenge despite the computational advances in the last decade. In particular, the abundance of repeat elements in genomes makes i...
Molecular descriptors have been extensively used in the field of structure-oriented drug design and structural chemistry. They have been applied in QSPR and QSAR models to predict ADME-Tox properties, which sp...
Rare disease registries (RDRs) are an essential tool to improve knowledge and monitor interventions for rare diseases. If designed appropriately, patient and disease related information captured within them ca...
The Erratum to this article has been published in Source Code for Biology and Medicine 2014 9:4
Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisitio...
When acquiring simple three-dimensional (3d) trajectory data it is common to accumulate large coordinate data sets. In order to examine integrity and consistency of object tracking, it is often necessary to ra...
Protein-protein interaction (PPI) plays a core role in cellular functions. Massively parallel supercomputing systems have been actively developed over the past few years, which enable large-scale biological pr...
The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoper...
The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, ...
Electron Paramagnetic Resonance (EPR) is a non-destructive, non-invasive technique useful for the characterization of organic moieties in primitive carbonaceous matter related to the origin of life. The classi...
Traditional flow cytometry data analysis is largely based on interactive and time consuming analysis of series two dimensional representations of up to 20 dimensional data. Recent technological advances have i...
The suffix -ome conveys “comprehensiveness” in some way. The idea of the Corpasome started half-jokingly, acknowledging the efforts to sequence five members of my family. After the unexpected response from man...
Identifying and quantifying pathological changes in brain electrical activity is important for investigations of brain injury and neurological disease. An example is the development of epilepsy, a secondary co...
Processing and pattern recognition of myoelectric signals have been at the core of prosthetic control research in the last decade. Although most studies agree on reporting the accuracy of predicting predefined...
Non-negative matrix factorization (NMF) has been introduced as an important method for mining biological data. Though there currently exists packages implemented in R and other programming languages, they eith...
The annotation of surface exposed bacterial membrane proteins is an important step in interpretation and validation of proteomic experiments. In particular, proteins detected by cell surface protease shaving e...
Surrogate variable analysis (SVA) is a powerful method to identify, estimate, and utilize the components of gene expression heterogeneity due to unknown and/or unmeasured technical, genetic, environmental, or ...
Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but al...
The whole-genome sequences of many non-model organisms have recently been determined. Using these genome sequences, next-generation sequencing based experiments such as RNA-seq and ChIP-seq have been performed...
In population association studies, standard methods of statistical inference assume that study subjects are independent samples. In genetic association studies, it is therefore of interest to diagnose undocume...
Large-scale sequence studies requiring BLAST-based analysis produce huge amounts of data to be parsed. BLAST parsers are available, but they are often missing some important features, such as keeping all infor...
Data processing in the bioinformatics field often involves the handling of diverse software programs in one workflow. The field is lacking a set of standards for file formats so that files have to be processed...
High–throughput (HT) technologies provide huge amount of gene expression data that can be used to identify biomarkers useful in the clinical practice. The most frequently used approaches first select a set of ...
MicroRNAs (miRNAs) constitute the largest family of noncoding RNAs involved in gene silencing and represent critical regulators of cell and tissue differentiation. Microarray expression profiling of miRNAs is ...
Source Code for Biology and Medicine