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A flexible statistical framework is developed for the analysis of read counts from RNA-Seq gene expression studies. It provides the ability to analyse complex experiments involving multiple treatment conditions and block...

Computational properties of use of biological organisms or to the construction of computers can emerge as collective properties of systems having a large number of simple equivalent components (or neurons). The physical ...

The University of Wisconsin Genetics Computer Group (UWGCG) has been organized to develop computational tools for the analysis and publication of biological sequence data. A group of programs that will interact with each...

Protein quantification without isotopic labels has been a long-standing interest in the proteomics field. However, accurate and robust proteome-wide quantification with label-free approaches remains a challenge. We devel...

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological inte...

BACKGROUND: In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reporte...

Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information ...

A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating know...

Artificial neural net models have been studied for many years in the hope of achieving human-like performance in the fields of speech and image recognition. These models are composed of many nonlinear computational eleme...

UNLABELLED: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software...

Abstract Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1–4 , the structures of around 100,000 un...

Abstract The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a ...

The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comp...

Subjects / keywords: molecular biology, biological structure analysis, genome analysis, sequence analysis, phylogeny, biological computation; Science: Biology (General): Genetics

Subjects / keywords: synthetic biology, biosensors, biological computation, engineering biology; Science: Biology (General)

Microarrays can measure the expression of thousands of genes to identify changes in expression between different biological states. Methods are needed to determine the significance of these changes while accounting for t...

BACKGROUND: Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns a...

Use of the real-time polymerase chain reaction (PCR) to amplify cDNA products reverse transcribed from mRNA is on the way to becoming a routine tool in molecular biology to study low abundance gene expression. Real-time ...

Subjects / keywords: Biology; Simple (philosophy); DNA; Salting out; Computational biology; Genetics; Biological system; Molecular biology; Philosophy; Aqueous solution; Epistemology; Chemistry

Subjects / keywords: Real-time polymerase chain reaction; Quantitative analysis (chemistry); Delta; Computational biology; Sample (material); Biology; Biological system; Computer science; Molecular biology; Gene; Chromatography; Chemistry

Subjects / keywords: psychiatric function, psychiatry dysfunction, cognition, mental dysfunction, computational modelling; Medicine: Medicine (General): Computer applications to medicine. Medical informatics; Medicine: Internal medicine: Neu...

Subjects / keywords: neural networks, computational neuroscience, decision making, neurons, brain modelling; Medicine: Internal medicine: Neurosciences. Biological psychiatry. Neuropsychiatry

Subjects / keywords: computational biology, biological systems, biological modelling; Science: Biology (General)