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Computational Biology (3):
Recent article
Computational Biology
Nature Medicine (17)12 2011
Abstract
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Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
Nature Medicine (17)12 2011
Abstract
BMC Bioinformatics (12 Suppl 11) 2011
Abstract
Abstract
We present an application of in silico quantitative structure-activity relationship (QSAR) models to establish a new ligand-based computational approach for generating virtual libraries. The Free-Wilson methodology was applied to extract rules from two data sets containing compounds which were scree...
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PMID: 20981520
PDF is available here.
PDF is available here.
Abstract
We purified each individual NEAT domain of IsdX2 as a GST fusion and analyzed the specific function of each domain as it relates to heme acquisition and transport. NEAT domains 1, 3, 4, and 5 all bind heme, with domain 5 having the highest affinity. All NEATs associate with hemoglobin, but only NEAT...
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PMID: 21808055
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)9 2011
Abstract
We show that this protein has a general affinity for single-stranded DNA (ssDNA) as documented by Electrophoretic Mobility Shift Assay (EMSA). The apparent molecular weight of the monomer is about 12.7kDa as measured by HPLC-SEC. Moreover, isoelectrofocusing showed an isoelectric point for pV(VGJΦ)...
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PMID: 21586349
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)9 2011
Abstract
The survival motor neuron (SMN) protein plays an essential role in the assembly of uridine-rich small nuclear ribonuclear protein complexes. Phosphorylation of SMN can regulate its function, stability, and sub-cellular localization. This study shows that protein kinase A (PKA) phosph...
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PMID: 21609790
PDF is available here.
PDF is available here.
Abstract
Nature Reviews: Genetics (12)9 2011
Abstract
RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational pred...
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PMID: 21850044
PDF is available here.
PDF is available here.
Abstract
We reported one of these families previously in a paper on Wolcott-Rallison syndrome (WRS). WRS is characterized by increased apoptotic cell death as part of an uncontrolled unfolded protein response. Increased apoptosis has been shown to be a cause of microcephaly in animal models. An autopsy spec...
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PMID: 21835305
PDF is available here.
PDF is available here.
Abstract
We here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 u...
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PMID: 21619078
PDF is available here.
PDF is available here.
Abstract
We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the number of identifications, all data sets were searched against the target databases using two search engines, Mascot and Paragon. As a result,...
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PMID: 21615180
PDF is available here.
PDF is available here.
Abstract
We simulated mitochondrial deoxynucleotide metabolism and mitochondrial DNA replication. Our results indicate that the output from the mitochondrial salvage enzymes alone is inadequate to support a mitochondrial DNA replication duration of as long as 10 hours. We find that an external source of deox...
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PMID: 21829339
PDF is available here.
PDF is available here.
Abstract
Neurocritical care bioinformatics is a new field that focuses on the acquisition, storage and analysis of physiological and other data relevant to the bedside care of patients with acute neurological conditions such as traumatic brain injury or stroke. The main focus of neurocritical...
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PMID: 21750522
PDF is available here.
PDF is available here.
Abstract
We reassessed this question by performing a global investigation of a genome-scale human metabolic network, which had been reconstructed on the basis of experimental results. By elementary flux pattern analysis, we found numerous pathways on which gluconeogenesis from fatty acids is feasible in huma...
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PMID: 21814506
PDF is available here.
PDF is available here.
Abstract
We hypothesized that heterogeneity in urban environments would cause decelerating travelling waves in incipient epidemics. To test this hypothesis, we analysed data on the spread of West Nile virus (WNV) in New York City (NYC), the 1999 epicentre of the North American pandemic, during annual epizoot...
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PMID: 21829332
PDF is available here.
PDF is available here.
Abstract
We examine the game of indirect reciprocity when the reputations of players are not necessarily known to observers and to interacting players. We find that the trustful discriminator, which cooperates with good and unknown players and defects against bad players, realizes cooperative societies under...
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PMID: 21829335
PDF is available here.
PDF is available here.
Abstract
We combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry...
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PMID: 21829336
PDF is available here.
PDF is available here.
Abstract
We have built a mathematical model of T(H)17/iT(reg) differentiation that exhibits four different stable steady states, governed by pitchfork bifurcations with certain degrees of broken symmetry. According to the model, a group of precursor cells with some small cell-to-cell variability can differen...
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PMID: 21829337
PDF is available here.
PDF is available here.
Abstract
We automated a methodology first proposed elsewhere-that combines sequence similarity with assessing membership to the superfamily by conservation of structuraly key residues-to identify putative insulin-like peptides (ILPs) in completely sequenced genomes, and applied it as a pipeline to a group of...
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PMID: 21410328
PDF is available here.
PDF is available here.
Abstract
We built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without...
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PMID: 21760760
PDF is available here.
PDF is available here.
Abstract
We describe a human syndrome featuring craniosynostosis, maxillary hypoplasia, delayed tooth eruption, and supernumerary teeth. We performed homozygosity mapping in three unrelated consanguineous Pakistani families and localized the syndrome to a region in chromosome 9. Mutational analysis of candid...
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PMID: 21741611
PDF is available here.
PDF is available here.
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a s...
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PMID: 21793786
PDF is available here.
PDF is available here.
Abstract
We assess the impact of the F610A mutation on the functionality of AcrB by means of computational techniques, using doxorubicin as substrate. We found that the compound slides deeply inside the binding pocket after mutation, increasing the strength of the interaction. During subsequent conformationa...
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PMID: 21707050
PDF is available here.
PDF is available here.
Abstract
We propose this set of pathways warrants closer investigation to understand drivers of poor outcome in melanoma. Two gene expression microarray studies met REMARK-based criteria reflecting a genuine paucity of literature in the area. The 254 outcome-related genes were examined for correspondences wi...
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PMID: 21659462
PDF is available here.
PDF is available here.
Abstract
The present study describes the in silico prediction of the regulatory network of Leishmania infected human macrophages. The construction of the gene regulatory network requires the identification of Transcription Factor Binding Sites (TFBSs) in the regulatory regions (promoters, enhancers) of genes...
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PMID: 21093613
PDF is available here.
PDF is available here.
Abstract
We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an associ...
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PMID: 21738484
PDF is available here.
PDF is available here.
Abstract
362 nonredundant proteins were identified, 113 of which were expressed differentially between preeclampsia and normal pregnant group and 31 differential proteins among three groups. These differential proteins were associated with biological processes of blood coagulation, cell adhesion and differen...
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PMID: 21538910
PDF is available here.
PDF is available here.
Abstract
We present a subquadratic running time algorithm capable of computing an alignment that optimizes one of the most widely used measures of protein structure similarity, defined as the number of pairs of residues in two proteins that can be superimposed under a predefined distance cutoff. The algorith...
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PMID: 21714130
PDF is available here.
PDF is available here.
Abstract
Our results make the case that these two strategies greatly enhance the sampling of the conformational space near the native state. A detailed comparative analysis shows that our approach performs as well as state-of-the-art ab initio structure prediction protocols....
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PMID: 21714131
PDF is available here.
PDF is available here.
Abstract
We developed a directed weighted graph, the topology graph, to represent the secondary structure assignment problem. We prove that the problem of finding the valid topology with the minimum cost is NP hard. We developed an O(N(2)2(N)) dynamic programming algorithm to identify the topology with the m...
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PMID: 21714133
PDF is available here.
PDF is available here.
Abstract
Abstract
We are interested in creating a method that can detect the shared signature of a group of expression profiles, e.g. a group of samples from individuals with the same disease or a group of drugs that treat the same therapeutic indication. We have developed a novel Weighted Influence-Rank of Ranks (WI...
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PMID: 21714134
PDF is available here.
PDF is available here.
Abstract
We have found evidences that genome-wide changes in nucleosome occupancy play a critical role in controlling the rigorous parasite replication in infected red blood cells. However, the role of nucleosome positioning at remarkable locations such as transcriptional start sites (TSS) was not investigat...
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PMID: 20708104
PDF is available here.
PDF is available here.
Abstract
We present a model of plasticity induction for reinforcement learning in a population of leaky integrate and fire neurons which is based on a cascade of synaptic memory traces. Each synaptic cascade correlates presynaptic input first with postsynaptic events, next with the behavioral decisions and f...
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PMID: 21738460
PDF is available here.
PDF is available here.
Abstract
We developed a computational model of glutamatergic signaling at a prototypical dendritic spine to examine the patterns of NMDAR subtype activation at temporal and spatial resolutions that are difficult to obtain experimentally. We demonstrate that NMDAR subtypes have different dynamic ranges of act...
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PMID: 21738464
PDF is available here.
PDF is available here.
Abstract
We show that continuous depletion of the neural stem cell pool, as a consequence of their division, may contribute to the age-related decrease in hippocampal neurogenesis. Our results indicate that adult hippocampal stem cells, upon exiting their quiescent state, rapidly undergo a series of asymmetr...
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PMID: 21549330
PDF is available here.
PDF is available here.
Abstract
We used bioinformatics to generate a list of all efflux pumps from sequenced bacterial genomes and prioritized a subset of targets for cloning. The resulting library of 43 pumps was heterologously expressed in Escherichia coli, where we tested it against seven representative biofuels. By using a com...
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PMID: 21556065
PDF is available here.
PDF is available here.
Abstract
We developed a simple, safe, and rapid method to prepare highly purified outer membrane (OM) fragments from these pathogens. Shotgun proteomic analyses of OMs by trypsin shaving and mass spectrometry identified >155 proteins, the majority of which are clearly outer membrane proteins (OMPs). These in...
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PMID: 21391724
PDF is available here.
PDF is available here.
Abstract
We have used laser capture microdissection (LCM) to isolate microvessels from clinical samples of invasive ductal carcinoma (IDC), the most common form of malignant breast cancer, and from patient-matched adjacent nonmalignant tissue. This approach eliminates many of the problems associated with the...
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PMID: 21401208
PDF is available here.
PDF is available here.
Abstract
Childhood pilocytic astrocytoma is the most frequent brain tumor affecting children. Proteomics analysis is currently considered a powerful tool for global evaluation of protein expression and has been widely applied in the field of cancer research. In the present study, a series of...
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PMID: 21466243
PDF is available here.
PDF is available here.
Abstract
We have developed MassWiz, a novel empirical scoring function that gives appropriate weights to major ions, continuity of b-y ions, intensities, and the supporting neutral losses based on the instrument type. We tested MassWiz accuracy on 486,882 spectra from a standard mixture of 18 proteins genera...
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PMID: 21417338
PDF is available here.
PDF is available here.
Abstract
We observed decreased levels of mitochondrial proteins involved in oxidative phosphorylation and tricarboxylic acid cycle. Furthermore, deregulation of proteins of carbohydrate metabolism, the actin cytoskeleton, and extracellular matrix remodeling was observed. Proteomic observations were confirmed...
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PMID: 21417265
PDF is available here.
PDF is available here.
Abstract
We used an iTRAQ reference data on hepatocellular carcinoma (HCC) to design a two-stage functional analysis pipeline to widen and improve the proteome coverage and, subsequently, to unveil the molecular changes that occur during HCC progression in human tumorous tissue. The first involved functional...
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PMID: 21410269
PDF is available here.
PDF is available here.
Abstract
We used DIGE to compare protein expression in amastigote and promastigote forms of Leishmania chagasi. Nine hundred amastigote and promastigote spots were visualized. Five amastigote-specific, 25 promastigote-specific, and 10 proteins shared by the two parasite stages were identified. Furthermore, 4...
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PMID: 21355625
PDF is available here.
PDF is available here.