Structure and function of the human Poly(ADP-ribose) polymerase enzyme family द्वारा Rood, Jennifer E. (Jennifer Evelyn)

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Algorithms for genomics and genetics : compression-accelerated search and admixture analysis द्वारा Loh, Po-Ru

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Engineering logic gates using synthetic SIRNAs in escherichia coli for gene silencing द्वारा Lim, Carol Yi Ting

“…The output of the logic circuit would also be much cleaner and more informative without any unwanted noise as siRNA control the translation level. The use of bioinformatic tools help to calculate the binding energy of the siRNA which gives a theoretical basis to evaluate the output efficiency of logic gates before doing the actual experiment. …”
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Molecular modeling and statistical analysis on proteins and lipids द्वारा Ping, Zhi

“…The findings of this research show the application of SCA technique in bioinformatic research and imply the significance of correlated residues in proteins besides highly-conserved ones. …”
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ZNF185 is a p53 target gene following DNA damage द्वारा Smirnov, A, Cappello, A, Lena, A, Anemona, L, Mauriello, A, Di Daniele, N, Annicchiarico-Petruzzelli, M, Melino, G, Candi, E

“…Upon genotoxic stress, caused by DNA-damaging drug etoposide and UVB irradiation, ZNF185 expression is up-regulated and in etoposide-treated cells, ZNF185 depletion does not affect cell proliferation and apoptosis, but interferes with actin cytoskeleton remodelling and cell polarization. Bioinformatic analysis of different types of epithelial cancers from both TCGA and GTEx databases showed a significant decrease in ZNF185 mRNA level compared to normal tissues. …”

Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton द्वारा Wickstead, B, Gull, K, Richards, T

“…Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA). Results: We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. …”

Analysis of iron and iron-interacting protein dynamics during T-cell activation द्वारा Teh, MR, Frost, JN, Armitage, AE, Drakesmith, H

“…Using a combination of mathematical modelling, bioinformatic analysis and experimental work, we studied how iron influences T-cells. …”

Most brain disease-associated and eQTL haplotypes are not located within transcription factor DNase-seq footprints in brain द्वारा Handel, A, Gallone, G, Cader, M, Ponting, C

“…We aimed to assess what proportion of variants associated with phenotypic or transcriptomic traits in human brain are located within transcription factor binding sites. The bioinformatic tools, Wellington and HINT, were used to infer transcription factor footprints from existing DNase-seq data derived from central nervous system tissues with high spatial resolution. …”

Analysis of Lupinus albus storage proteins by two-dimensional electrophoresis and mass spectrometry. द्वारा Wait, R, Gianazza, E, Brambilla, D, Eberini, I, Morandi, S, Arnoldi, A, Sirtori, C

“…Out of 72 spots submitted to mass spectrometry and compared with available protein databases, 42 correspond to fragments of beta-conglutin, the 7S globulin of lupin, spanning between positions 37 and 495 of the protein sequence. Using the bioinformatic tool BlastP, these peptides were compared to the alpha'-subunit of beta-conglycinin, the 7S globulin of soybean, this being the most active hypocholesterolemic component of soybean protein, as shown by in vitro and in vivo experiments. …”

The eukaryotic flagellum in health and disease द्वारा Farr, H

“…One further gene was identified by searching a gene locus for polycystic kidney disease, a disease linked to malfunction of the primary cilium. I carried out a bioinformatic screen on the selected genes to determine their phylogenetic distribution. …”

Microreact: Visualizing and sharing data for genomic epidemiology and phylogeography द्वारा Argimón, S, Abudahab, K, Goater, RJE, Fedosejev, A, Bhai, J, Glasner, C, Feil, EJ, Holden, MTG, Yeats, CA, Grundmann, H, Spratt, BG, Aanensen, DM

“…Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.…”

OMGene: mutual improvement of gene models through optimisation of evolutionary conservation द्वारा Dunne, M, Kelly, S

“… <h4>Background</h4> <p>The accurate determination of the genomic coordinates for a given gene – its gene model – is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently available methods of computational gene prediction, while on the whole successful, frequently disagree on the model for a given predicted gene, with some or all of the variant gene models often failing to match the biologically observed structure. …”

An expanded family of proteins with BPI/LBP/PLUNC-like domains in trypanosome parasites: an association with pathogenicity? द्वारा Gluenz, E, Barker, A, Gull, K

“…In addition, ESs contain ESAGs (expression-site-associated genes), whose functions, with few exceptions, have remained elusive. A bioinformatic analysis of the ESAG5 gene of T. brucei showed that it encodes a protein with two BPI (bactericidal/permeability-increasing protein)/LBP (lipopolysaccharide-binding protein)/PLUNC (palate, lung and nasal epithelium clone)-like domains and that it belongs to a multigene family termed (GR)ESAG5 (gene related to ESAG5). …”

Mutational analysis of Rift Valley fever phlebovirus nucleocapsid protein indicates novel conserved, functional amino acids द्वारा Mottram, T, Li, P, Dietrich, I, Shi, X, Brennan, B, Varjak, M, Kohl, A

“…There is currently limited knowledge surrounding the roles of the RVFV nucleocapsid protein in viral infection other than its key functions: N protein multimerisation, encapsidation of the RNA genome and interactions with the RNA-dependent RNA polymerase, L. By bioinformatic comparison of the N sequences of fourteen phleboviruses, mutational analysis, minigenome assays and packaging assays, we have further characterised the RVFV N protein. …”

Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton. द्वारा Wickstead, B, Gull, K, Richards, T

“…Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA). RESULTS: We bioinformatically identified 1624 putative kinesin proteins, determined their protein domain architectures and calculated a comprehensive Bayesian phylogeny for the kinesin superfamily with statistical support. …”

Dicer-dependent transfer RNA-derived small RNAs and their role in gene regulation द्वारा Pong, SK

“…By using a combination of unbiased bioinformatic prediction and classic molecular biology methodologies, I have studied the role of tsRNAs in the regulation of gene expression. …”

OMIC technologies and vaccine development: From the identification of vulnerable individuals to the formulation of invulnerable vaccines द्वारा Cotugno, N, Ruggiero, A, Santilli, V, Manno, E, Rocca, S, Zicari, S, Amodio, D, Colucci, M, Rossi, P, Levy, O, Martinon-Torres, F, Pollard, A, Palma, P

“…Finally, we will discuss how system biology "OMICs" data can be used to design bioinformatic tools to predict the vaccination outcome providing genetic and molecular "signatures" of protective immune response. …”

Functional characterisation of naturally occurring mutations in human melanopsin द्वारा Rodgers, J, Peirson, SN, Hughes, S, Hankins, MW

“…Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants. …”

Neutralizing antibodies against West Nile virus identified directly from human B cells by single-cell analysis and next generation sequencing द्वारा Tsioris, Konstantinos, Gupta, Namita T., Ogunniyi, Adebola Oluwakayode, Qian, Feng, Yao, Yi, Wang, Xiaomei, Stern, Joel N. H., Chari, Raj, Briggs, Adrian W., Clouser, Christopher R., Vigneault, Francois, Church, George M., Garcia, Melissa N., Murray, Kristy O., Montgomery, Ruth R., Kleinstein, Steven H., Love, J. Christopher, Zimnisky, Ross Martin, Love, J. Christopher

“…Using the nucleotide coding sequences for WNV-specific antibodies derived from single cells, we revealed the ontogeny of expanded WNV-specific clones in the repertoires of recently infected subjects through NGS and bioinformatic analysis. This analysis also indicated that the humoral response to WNV did not depend on an anamnestic response, due to an unlikely previous exposure to the virus. …”
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Identification of a Gene Signature That Predicts Dependence upon YAP/TAZ-TEAD द्वारा Kanai, Ryan, Norton, Emily, Stern, Patrick, Hynes, Richard O., Lamar, John M.

“…Here, we used a combination of RNA-seq and bioinformatic analysis of metastatic melanoma cells to develop a YAP/TAZ gene signature. …”
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