The second part of this survey examines biocomputing in intact multicellular organisms. The parallelism between creative problem solving and evolution is emphasized: both processes invoke heuristic searching and feature modularity prominently. Simonton’s chance-configuration theory of creative problem solving is recast in terms of pattern recognition and analyzed in terms of parallel and sequen...

This report summarizes the proceedings of the "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group (SIG) meeting held at the Intelligent Systems for Molecular Biology 2009 conference. The Genomic Standards Consortium (GSC) hosted this meeting to explore the bottlenecks and emerging solutions for obtaining biological insights through large-scale comparative analysis of metageno...

An energy transfer relationship between core-shell CdSe/ZnS quantum dots (QDs) and the optical protein bacteriorhodopsin (bR) is shown, demonstrating a distance-dependent energy transfer with 88.2% and 51.1% of the QD energy being transferred to the bR monomer at separation distances of 3.5 nm and 8.5 nm, respectively. Fluorescence lifetime measurements isolate nonradiative energy transfer, oth...

The paper examines the concept of hairpin-free words motivated from the biocomputing and bioinformatics fields. Hairpin (-free) DNA structures have numerous applications to DNA computing and molecular genetics in general. A word is called hairpin-free if it cannot be written in the form xvyθ(v)z, with certain additional conditions, for an involution θ (a function θ with the property that θ equa...

High-throughput sequencing technology has opened the door to the study of the human microbiome and its relationship with health and disease. This is both an opportunity and a significant biocomputing challenge. We present here a 3D visualization methodology and freely-available software package for facilitating the exploration and analysis of high-dimensional human microbiome data. Our visualiz...

Maintenance of the cellular redox balance has vital importance for correcting organism functioning. Methionine sulfoxide reductases (Msrs) are among the key members of the cellular antioxidant defence system. To work properly, methionine sulfoxide reductases need to be reduced by their biological partner, thioredoxin (Trx). This process, according to the available kinetic data, represents the s...

It has already been a year since Jack Leunissen, a former member of the editorial board of Briefings in Bioinformatics, passed away on 14 May 2012. Professor Dr Jack A.M. Leunissen was one of the pioneers of bioinformatics in the Netherlands, in Europe and around the world. Together with senior members of the European Molecular Biology Network (EMBnet), Jack worked with Henry Stewart Publicatio...