Computational Biology Support: RECOMB Conference Series (Conference Support)

This funding was support for student and postdoctoral attendance at the Annual Recomb Conference from 2001 to 2005. The RECOMB Conference series was founded in 1997 to provide a scientific forum for theoretical advances in computational biology and their applications in molecular biology and medicine. The conference series aims at attracting research contributions in all areas of computational molecular biology. Typical, but not exclusive, the topics of interest are: Genomics, Molecular sequence analysis, Recognition of genes and regulatory elements, Molecular evolution, Protein structure, Structural genomics, Gene Expression, Gene Networks, Drug Design, Combinatorial libraries, Computational proteomics, and Structural and functional genomics. The origins of the conference came from the mathematical and computational side of the field, and there remains to be a certain focus on computational advances. However, the effective use of computational techniques to biological innovation is also an important aspect of the conference. The conference had a growing number of attendees, topping 300 in recent years and often exceeding 500. The conference program includes between 30 and 40 contributed papers, that are selected by a international program committee with around 30 experts during a rigorous review process rivaling the editorial procedure for top-rate scientific journals. In previous years papers selection has been made from up to 130--200 submissions from well over a dozen countries. 10-page extended abstracts of the contributed papers are collected in a volume published by ACM Press and Springer, and are available at the conference. Full versions of a selection of the papers are published annually in a special issue of the Journal of Computational Biology devoted to the RECOMB Conference. A further point in the program is a lively poster session. From 120-300 posters have been presented each year at RECOMB 2000. One of the highlights of each RECOMB conference is a collection of nine keynotes awarded to researchers of highest international esteem who are asked to inform the community about landmark advances in computational and experimental research and inject new directions into the field of computational molecular biology. This includes the following conference events: Next we present a list of the names of the students and postdocs supported. Those supported either presented a paper (10 in 2001, 6 in 2002, 7 in 2003, 14 in 2004, and 20 in 2006) or were they presenter of a poster. This support was vital to the quality and success of the Conference. At the conclusion we give the publication details of the relevant Recomb proceedings

Time-delayed models of gene regulatory networks

We discuss different mathematical models of gene regulatory networks as relevant to the onset and development of cancer. After discussion of alternativemodelling approaches, we use a paradigmatic two-gene network to focus on the role played by time delays in the dynamics of gene regulatory networks. We contrast the dynamics of the reduced model arising in the limit of fast mRNA dynamics with that of the full model. The review concludes with the discussion of some open problems

Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function

Bulletin of Mathematical Biology - facts, figures and comparisons

The Society for Mathematical Biology (SMB) owns the Bulletin of Mathematical Biology (BMB). This is an international journal devoted to the interface of mathematics and biology. At the 2003 SMB annual meeting in Dundee the Society asked the editor of the BMB to produce an analysis of impact factor, subject matter of papers, submission rates etc. Other members of the society were interested in the handling times of articles and wanted comparisons with other (appropriate) journals. In this article we present a brief history of the journal and report on how the journal impact factor has grown substantially in the last few years. We also present an analysis of subject areas of published papers over the past two years. We finally present data on times from receipt of paper to acceptance, acceptance to print (and to online publication) and compare these data with some other journals

Antismoking campaigns’ perception and gender differences: a comparison among EEG Indices

Human factors’ aim is to understand and evaluate the interactions between people and tasks, technologies, and environment. Among human factors, it is possible then to include the subjective reaction to external stimuli, due to individual’s characteristics and states of mind. These processes are also involved in the perception of antismoking public service announcements (PSAs), the main tool for governments to contrast the first cause of preventable deaths in the world: tobacco addiction. In the light of that, in the present article, it has been investigated through the comparison of different electroencephalographic (EEG) indices a typical item known to be able of influencing PSA perception, that is gender. In order to investigate the neurophysiological underpinnings of such different perception, we tested two PSAs: one with a female character and one with a male character. Furthermore, the experimental sample was divided into men and women, as well as smokers and nonsmokers. The employed EEG indices were the mental engagement (ME: the ratio between beta activity and the sum of alpha and theta activity); the approach/withdrawal (AW: the frontal alpha asymmetry in the alpha band); and the frontal theta activity and the spectral asymmetry index (SASI: the ratio between beta minus theta and beta plus theta). Results suggested that the ME and the AW presented an opposite trend, with smokers showing higher ME and lower AW than nonsmokers. The ME and the frontal theta also evidenced a statistically significant interaction between the kind of the PSA and the gender of the observers; specifically, women showed higher ME and frontal theta activity for the male character PSA. This study then supports the usefulness of the ME and frontal theta for purposes of PSAs targeting on the basis of gender issues and of the ME and the AW and for purposes of PSAs targeting on the basis of smoking habits

A computational model for real-time calculation of electric field due to transcranial magnetic stimulation in clinics

The aim of this paper is to propose an approach for an accurate and fast (real-time) computation of the electric field induced inside the whole brain volume during a transcranial magnetic stimulation (TMS) procedure. The numerical solution implements the admittance method for a discretized realistic brain model derived from Magnetic Resonance Imaging (MRI). Results are in a good agreement with those obtained using commercial codes and require much less computational time. An integration of the developed codewith neuronavigation toolswill permit real-time evaluation of the stimulated brain regions during the TMSdelivery, thus improving the efficacy of clinical applications

Metallochaperones regulate intracellular copper levels.

Copper (Cu) is an important enzyme co-factor that is also extremely toxic at high intracellular concentrations, making active efflux mechanisms essential for preventing Cu accumulation. Here, we have investigated the mechanistic role of metallochaperones in regulating Cu efflux. We have constructed a computational model of Cu trafficking and efflux based on systems analysis of the Cu stress response of Halobacterium salinarum. We have validated several model predictions via assays of transcriptional dynamics and intracellular Cu levels, discovering a completely novel function for metallochaperones. We demonstrate that in addition to trafficking Cu ions, metallochaperones also function as buffers to modulate the transcriptional responsiveness and efficacy of Cu efflux. This buffering function of metallochaperones ultimately sets the upper limit for intracellular Cu levels and provides a mechanistic explanation for previously observed Cu metallochaperone mutation phenotypes