This special issue places its emphasis on the crossroadsbetween computational modeling and the biosciences. It isambitious but fruitful interdisciplinary research, and thisspecial issue aims to illustrate different presentations of it.It offers those advancing knowledge in some particular areathe view to related research activity and opportunities.
Many of the articles exemplify how mathematics andcomputer simulation inform experimentation to obtain newknowledge about nature. Some articles represent discoveriesand others review, introduce, test, or trial algorithms ortools that are potentially helpful to arrive at discoveries. Afew articles, however, are reversed in that they demonstratehow bioinspired algorithms or biological devices can solvehard computational challenges. Consider that manipulatingchemicals may compute an answer much faster than bymeans of the standard silicon-based computer and withinthis special issue there is an article by K. Li et al. describingthe principles by which such a DNA computer can compro-mise an encryption algorithm that is central to present daysecure communications.
One might classify the articles in this special issueinto three groupings: (1) those concerned with biologicalproblems from molecular cell biology to systems biology,(2) those which apply classification algorithms in cancerdiagnosis and methods of computer vision to anatomy, andfinally (3) those which offer new knowledge or possibilitiesin bioengineering and biomedicine.
The first grouping covers Systems Biology, an excitinginterdisciplinary field that marries experiments with com-puter simulations. Synthetic and systems biotechnology, forexample, is a technology at these frontiers that aims tosequester the services of micro-organisms for the benefit ofmankind. Its ability to produce foods in a vat that would
otherwise take up valuable land resources with conventionalagriculture will offer flexibility in food production. Intheir article, M.-J. Han et al. reveal how knowledge andunderstanding of cell physiology in the presence of oleic acidare obtained for E. coli. Interesting research about signalingnetworks in retina, as induced by light exposure in mice, ispresented by J. Krishnan et al. showing marked alterations ingene expression upon light exposure. Certain transcriptionfactors are discovered to be important for the responsesto light-induced retinal loss, revealing that many of theapoptosis-related genes are up- or downregulated in thisprocess. In their article, R. Moreno-Sanchez et al. offer a veryuseful review of metabolic control analysis (MCA), a toolthat represents a type of engineering control theory for cellbiology and when applicable MCA can help to grapple withan understanding of the complex control of the metabolicpathways.
Also in the first grouping, three articles by S. Huang andhis colleagues develop the emergent and interdisciplinaryfield of infectomics, which is the study of infectomes encodedby the genomes of microbes and their hosts. Infectomicshas potential to advance the rational strategies that willprevent and treat infectious diseases as these could requirea full appreciation of the infectomes that contribute tomicrobial infections. There is a need to figure out how todissect the dynamic duality relationship between symbiosisand pathogenesis in microbial infections, and advocatesof this new field oppose what they see as the misguided,though current and popular, reductionist and Manicheanviews of the microbe-human host relationship. Anotherarticle on the topic of infectious diseases by K.-Y. Hwaet al. investigates the emerging and life-threatening infectiousdisease known as SARS, where there is a compelling need
for the development of effective therapeutics. Their articlepresents interesting and potentially important findings, thatmolecular mimicry occurs between SARS-CoV and hostproteins. They investigate how to predict those peptidesthat are worthy of exploration for their biological activity.The article by L. Hamel et al. provides novel insight intothe field of phylogenetics with the idea of the spectra of atree, and reviewers identified its potential to compare withphylogenetic trees across different genes and for detectinglateral gene transfer.
The first grouping of articles also covers specialistnumerical algorithms for gene sequencing, genomics, andproteomics. With genomic sequencing, an error in contigassembly causes serious error proliferation, and ConPath (P.-G. Kim et al.) is a tool that can address this problem. It con-structs scaffolds, ordering and orienting separate sequencecontigs by exploiting the mate-pair information betweencontig pairs. C.-K. Chan et al. develop the growing self-organized map (GSOM) for binning (the clustering of theseunassembled DNA sequences). They report improvementsover the binning that combines oligonucleotide frequencyand self-organizing maps (SOMs), and identify suitabletraining features and quantitative measures for assessingresults in this area. In their article, K. Han et al. develop analgorithm to search for the highly connected subgraphs inprotein interaction networks because this might be helpfulto predict protein function. The article by Mi-Young Kimexpounds a new approach to the very important problemof text mining of biomolecular text, and is specificallyconcerned with detecting gene interactions. There follow twoarticles in biological chemistry with computational chem-istry. C.-J. Kuo et al. solve the crystal structure of H. pyloriundecaprenyl pyrophosphate synthase and perform virtualscreening of inhibitors from a chemical library of thousandsof compounds. M. Muddassar et al. explore receptor-guided3D-QSAR to design IGF-1R inhibitors by pursuing carefulstatistical analysis to interpret the models that are obtainedwith the help of contour maps. The article by J.-C. Lueand W.-C. Fang proposes a compact integrated microsystemsolution for robust, real-time, and onsite genetic analysis.It uses a preceding VLSI differential logarithm microchipthat is designed to compute the logarithm of the normalizedinput fluorescence signals and a succeeding VLSI artificialneural network (ANN) processor chip to analyze the pro-cessed signals from the differential logarithm stage. It issubmitted that the version of ANN chosen is particularlyadept at recognizing the low-fluorescence patterns.
The second grouping includes cancer diagnosis, biomed-ical imaging and also computational anatomy (the study ofanatomical variability in health and disease via deformabletemplates as inspired by D’Arcy Wentworth Thompson).These fields sit in the frontiers of biosciences, image analysis,mathematics, and numerical methods. In this grouping, anumber of articles implement (D. Howard et al.), evaluate(N. A. Lee et al.), or introduce (J. Kolibal et al.) techniquesof image analysis to cluster, segment, or analyze images,or extract information or enrich biomedical images. Forexample, J. Woo et al. discuss multimodal data integration
for computer-aided ablation of atrial fibrillation. Y. Park et al.analyze the interpoint dissimilarity comparisons in the hip-pocampus shape space to distinguish between hippocampi ofsubjects with three conditions (clinically depressed, high risk,and control subject), and discover the high-risk populationcloser in shape space to the control population than to theclinically depressed population. Additionally, they find thatthe left hippocampi carry more information than do theright. In their article, N. A. Lee et al. examine performancein the segmentation of high-resolution MRI subvolumescontaining hippocampus, prefrontal cortex, and occipitallobe, as acquired on different scanners. They offer evidencethat the alternating kernel mixture algorithm outperformsalternatives on the ten datasets considered. The availabilityof powerful imaging and other sensors, the availability ofinformation technology, and the nature of modern threatspoint to population biometrics as a topic of enormouscurrent and future importance. Implementing biometricswell is hard and is not yet properly understood. Themethodological paper by Y. N. Shin et al. proposes a formalperformance evaluation model for a biometric recognitionsystem. They also implement face recognition systems basedon the proposed model. The model seems to be useful interms of database availability, compliance with standards,and evaluation costs. The proposed formalism may gaintraction for other biometrics, and it has the potential toinform strategies for population-based biomedical imagingperformance evaluation and standardization. The last articleof this second grouping by J. Wichard et al. evaluateshow bioinspired and computational intelligence algorithmscompare in providing reliable early cancer diagnosis.
The third grouping comprises articles which coveradvances in biomechanics, biophysics, and biomedicine. Itincludes a detailed biomechanics study by J. S. Merritt et al.on the equine distal forelimb, which is a common locationof injuries related to mechanical overload. These authorscombine analysis with experiment in a fairly thorough butconcise way to calculate the forces in the major tendons andjoint reaction from kinematic and kinetic data of walkingand trotting horses. Their findings point to the importanceof muscle tendon wrapping when evaluating joint loadingin the distal forelimb. The article by C. Handapangodaand M. Premaratne describes a novel numerical techniquefor modeling optical pulse propagation in inhomogeneousscattering and absorption cross-sections through weaklyscattering biological tissues. The design of implantableelectronic devices to interact with the nervous system is anactive field, the development of an efficient system for long-term stimulation of the optic nerve is rather timely (e.g., it isrequired to evaluate the long-term safety of retinal implants),and the methodological report by J. A. Zhou et al. describesthe design of a suprachoroidal electrical retinal stimulatorfor long-term application. Finally, two articles in the thirdcategory advance novel robots (H. Sawada et al.) and hapticsolutions (K.-U. Kyung et al.) that interact with the humansenses and which might prove helpful to the sensoriallyimpaired.
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