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*  Genome cartography through domain annotation | Genome Biology | Full Text
Although the protein repertoires of distantly related species differ greatly, their domain repertoires do not. To account for ... and fusion and fission of genes. Although the protein repertoires of distantly related species differ greatly, their domain ... Homology assignments are guided by comparisons of HMMs or GPs with protein sequence databases, and by implementation of an ... which encodes a homolog of human fibroblast growth factor (FGF) [8]. On other occasions, protein homologs have subtle or ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2001-2-7-comment2006
*  TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis | PNAS
Genetic Analysis in Arabidopsis Defines a TIR-Containing, Truncated NLR Protein That Encodes RBA1.. To determine what genes are ... 2011) Structural and functional analysis of a plant resistance protein TIR domain reveals interfaces for self-association, ... RBA1 was not supported by Col-0 cDNA data and is not expressed in public Affymetrix databases, as is consistent with ... syringae, we identified HopBA1-related proteins in multiple species of the plant pathogen genus Erwinia. We found more ...
  http://www.pnas.org/content/114/10/E2053
*  cTFbase: a database for comparative genomics of transcription factors in cyanobacteria | BMC Genomics | Full Text
... domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase provides phylogenetic trees of ... 4) To search the database via protein ID, species or family;. (5) To perform a BLAST-based sequence similarity search. Users ... Therefore, the genome of fresh water or soil species encodes multiple capabilities in order to survive in this unstable ... The amino acid sequences of the protein-encoding genes of 21 cyanobacterial genomes were retrieved from the IMG database ( ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-8-104
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
Oleosin genes have been detected in numerous plant species. However, the presence of oleosin genes in the most basally ... osmotic stress genes and ion transport protein genes such as SOS1, AtP5CS1 and AtGSTU5. Overall, our results suggest that ... In the current study, the coding exons and flanking introns of the GATA6 gene, which encodes a zinc?finger transcription factor ... We searched eligible studies in Pubmed, Embase, and Web of Science databases. Six studies with a total of 556 patients were ...
  https://www.jove.com/visualize?author=Yuan+Fang
*  Synechocystis - Wikipedia
... as well as interaction networks in graphical web interfaces. CyanoBase: Cyanobacteria carry a complete set of genes for ... SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. SynechoNET is ... Additionally, RSF1010 encodes its own replication machinery, so that it does not depend on its host to possess the necessary ... In order to create plasmids-stable, replicating circular pieces of DNA-that will function successfully in multiple species, a ...
  https://en.wikipedia.org/wiki/Synechocystis
*  DeGNServer: Deciphering Genome-Scale Gene Networks through High Performance Reverse Engineering Analysis
ZMYND8 encodes a zinc finger protein with a complex role in maintaining pluripotency. Although only expressed at low levels, ... and it is more likely that we will need to evaluate genes in triples or quadrants. Even for those species with small genomes, ... The web interfaces are implemented in JAVA and JSP scripts. All backend integrated analysis algorithms are implemented with ... large amount of gene expression data sets from numerous labs has been published and deposited in public databases such as ...
  https://www.hindawi.com/journals/bmri/2013/856325/
*  Artificial intelligence in drug combination therapy, Briefings in Bioinformatics | 10.1093/bib/bby004 | DeepDyve
... such as hub-genes (i.e. genes which have connections to a significant number of other genes), cancer-essential genes and ... protein-protein interaction, chemical-chemical interaction and disease pathways. Three popular ML algorithms were used, and [44 ... For example, one rule in this system is [121, 122]: IF the value of RT codon number 151 is ATG (= it encodes methionine), THEN ... Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate ...
  https://www.deepdyve.com/lp/ou_press/artificial-intelligence-in-drug-combination-therapy-6030zVYUQM
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
The mitogenome is 16,790?bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 2 ... Reactive oxygen species (ROS)-mediated retinal pigment epithelium (RPE) cell apoptosis is an important contributor of AMD. In ... The ELF-EMF-induced G1 arrest was diminished when the CHK2 gene expression (which encodes checkpoint kinase 2; Chk2) was ... Candidate lncRNAs were searched in authorized databases. The significant lncRNAs were identified and confirmed through high- ...
  https://www.jove.com/visualize?author=Cheng-Zhi+Xu
*  Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization | BMC...
Users can also check the changes of expression profiles of a set of either the treatments over control or genes via Slide View ... software tools can be easily applied to the large-scale expression data generated by other platforms and in other species. ... In addition, the relationships between genes and treatments over control are computed according to gene expression ratio and ... Users can view all treatments over control that affect the expression of a selected gene via Gene View, and view all genes that ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-433
*  Frontiers | Adaptation to high salt concentrations in halotolerant/halophilic fungi: a molecular perspective | Microbiology
In contrast, the genome of W. ichthyophaga is very compact, as only 4,884 protein-coding genes are predicted, which cover ... The most striking characteristics associated with H. werneckii are the large genetic redundancy, the expansion of genes ... no homologs of the HMG-domain-containing Mat1-1-2 protein were found in H. werneckii, which indicates that this species is ... 2004). The LETM1/YOL027 gene family encodes a factor of the mitochondrial K+ homeostasis with a potential role in the Wolf- ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2014.00199/full
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
The NF1 gene encodes for neurofibromin, a RAS GTPase-activating protein, and thus negatively regulates the RAS signaling ... Overexpression of MBD4 gene can cause the demethylation of numerous genes, and the remethylation of MBD4-associated genes can ... Electronic databases were systematically searched for studies published before May 2013. Pooled odds ratios (OR) and 95 % ... The most common consequence of Se-induced toxicity in plants is oxidative injury, but how Se induces reactive oxygen species ( ...
  https://www.jove.com/visualize?author=Jian+Chen
*  Protocols and Video Articles Authored by Jennifer Smith
May, 2010 , Pubmed ID: 20181716 The papillomavirus E2 open reading frame encodes the full-length E2 protein as well as an ... the same bacterial species on the same coral species). Here we extend these microbial studies to four of the major ecological ... regulating telomere-proximal genes in Y' elements. The factors implicated here are known to control adjacent genes at ... The user interfaces have been adapted to the work routines of the curators, creating a suite of tools that is intuitive and ...
  https://www.jove.com/author/Jennifer_Smith
*  Protocols and Video Articles Authored by Makoto Furutani-Seiki (Translated to Turkish)
Even when mutations of the two fish species cause a similar phenotype such as one-eyed-pinhead or parachute, more genes were ... The order and orientation of 633 protein-coding genes were deduced from 18,803,338 bp of DNA sequence, providing the ... We show here that the fss gene encodes a T-box transcription factor that is expressed in intermediate to anterior presomitic ... ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated ...
  https://www.jove.com/author/Makoto_Furutani-Seiki?language=Turkish
*  ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses | BMC Bioinformatics | Full...
Usability of existing repository interfaces. Designing easy-to-use and clean interfaces to assist data providers and data ... Giles J: Key biology databases go wiki. Nature 2007,445(7129):691-691.View ArticlePubMedGoogle Scholar. ... Our method, called BioPNG, encodes Affymetrix probe data as indicated in Figure 5(A). This method provides 12.4 times ... All of the methods discussed in this section are readily transferable from cDNA microarrays to tissue, protein, and ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S6-S18
*  Protocols and Video Articles Authored by John Love
The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers ... As a key species for global biogeochemical cycling, a variety of strains have been amassed in various culture collections. ... Fifteen databases were searched, resulting in eight papers that met the search criteria. Comparison of results and meta- ... This combination of genes enabled rational alterations to hydrocarbon chain length (Cn) and the production of branched alkanes ...
  https://www.jove.com/author/John_Love
*  Cis and trans interactions between genes encoding PAF1 complex and ESCRT machinery components in yeast | SpringerLink
However, the close proximity between yeast genes can complicate the interpretation of yeast... ... VPS36 is widely conserved among eukaryotes and encodes a protein that is part of the ESCRT (Endosomal Sorting Complexes R ... 2002; Jaehning 2010; Tomson and Arndt 2013). In budding yeast, Cdc73 and Rtf1 are the main interfaces for the physical ... it might not be preserved in other species (like mammals) (Rog et al. 2005; Dieckmann et al. 2016). However, it is possible ...
  https://link.springer.com/article/10.1007%2Fs00294-018-0828-6
*  Protocols and Video Articles Authored by Leila Green (Translated to Dutch)
6 genes), and endocytosis (10 genes) pathways. The changes in long term potentiation included mitogen-activated protein kinase ... A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were ... DSG1 encodes desmoglein 1, a major constituent of desmosomes, which connect the cell surface to the keratin cytoskeleton and ... Rheology and Morphology of Pristine Graphene/Polyacrylamide Gels ACS Applied Materials & Interfaces. Aug, 2013 , Pubmed ID: ...
  https://www.jove.com/author/Leila_Green?language=Dutch
*  JoVE | Peer Reviewed Scientific Video Journal - Methods and Protocols
... interactions can occur between genes in the same pathway or protein complex2 as the deletion of either gene alone is often ... The gene that encodes flavonoid 3-galacosyltransferase was also identified and isolated from the pear genome. ... Given the ever expanding number of model plant species for which complete genome sequences are available and the abundance of ... A series of programs and graphical interfaces were therefore developed to compare calculated KIs among samples in a semi- ...
  https://www.jove.com/visualize/abstract/24637788/different-biosynthesis-patterns-among-flavonoid-3-glycosides-with
*  Parvoviridae - Wikipedia
... gene that encodes the replication initiator protein (called NS1 or Rep), and the VP (or cap) gene, which encodes a nested set ... Subfamily Densovirinae: Genus Ambidensovirus; type species: Lepidopteran ambidensovirus 1. Genus includes 6 recognized species ... The cell RNA polymerase II transcribes the virus genes and cell transcription factors play key roles. The primary transcript(s ... Since databases contain vast numbers of sequences that might be considered parvoviral in origin but are not real viruses, the ...
  https://en.wikipedia.org/wiki/Parvoviridae
*  Frontiers | SPRYSEC Effectors: A Versatile Protein-Binding Platform to Disrupt Plant Innate Immunity | Plant Science
The SPRY domain is wide-spread among eukaryotes and thought to be involved in mediating protein-protein interactions. Thus far ... which provide support for a model featuring these effectors as a versatile protein-binding platform for the nematodes to target ... which provide support for a model featuring these effectors as a versatile protein-binding platform for the nematodes to target ... The SPRY domain is wide-spread among eukaryotes and thought to be involved in mediating protein-protein interactions. Thus far ...
  https://www.frontiersin.org/articles/10.3389/fpls.2016.01575/full
*  delayed flowering1 Encodes a Basic Leucine Zipper Protein That Mediates Floral Inductive Signals at the Shoot Apex in Maize |...
Boisvert FM, Chenard CA, Richard S (2005) Protein interfaces in signaling regulated by arginine methylation. Sci STKE 2005: re2 ... dlf-like genes were found in rice and wheat. The rice dlf-like gene is predicted from genomic sequence (GenBank accession ... Homology comparisons with other plant databases identified two predicted proteins in monocots-one rice and one wheat-with ... furthering our understanding of the molecular basis of flowering in diverse plant species. ...
  http://www.plantphysiol.org/content/142/4/1523
*  The Light-Response BTB1 and BTB2 Proteins Assemble Nuclear Ubiquitin Ligases That Modify Phytochrome B and D Signaling in...
In addition to LRB1 and LRB2, Arabidopsis encodes a third related BTB protein (LRB3) with an identical NLS-BTB-BACK domain ... Species abbreviations are as follows: Arabidopsis (At), A. lyrata (Al), Vitis vinifera (Vv), G. max (Gm), P. trichocarpa (Pt), ... Sequence data for LRB1, LRB2, and LRB3 described in this article can be found in the GenBank/EMBL databases under accession ... Sequence identifiers and accession numbers for the other LRB genes in this study can be found in Supplemental Data Set S1. The ...
  http://www.plantphysiol.org/content/160/1/118.full
*  Linking genes to literature: text mining, information extraction, and retrieval applications for biology | Genome Biology |...
For example, in the sentence 'The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast ... of scholarly and scientific literature databases can be accessed online through search engines with simple query interfaces ... for example genes, proteins, or species. These systems make use of the word and sentence context to detect kinds of entities; ... and the PubGene system generates a graphical protein interaction network based on protein-protein literature co-occurrences [66 ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-s2-s8
*  Download Migration For Employment: Bilateral Agreements At A Crossroads 2004
Baldwin custom genes in Canada: download words and protein segments in Canadian Government Institute of Public Administration ... Will ' be me up, Scotty ' find accumulation? Quantum lines encodes it may. Since sort" -- a association read by a assembly ... species on the lexical circuits, clusters, and social authors understood for challenging psycholinguistic download Migration ... At General Convention 2006, The Episcopal Church reported not to the databases of the Windsor Report. , by Loretta Chosa ( ...
  http://jerodtate.com/library/download-Migration-For-Employment%3A-Bilateral-Agreements-At-A-Crossroads-2004.php
*  Review. Bioinformatics - a definition 1. As submitted to the Oxford English Dictionary - PDF
... databases contain DNA sequences for individual genes that encode protein and RNA products. Much like the composite protein ... The aim is to take a single protein and follow through an analysis that maximises our understanding of the protein it encodes. ... it is important to remember that different regions of the protein surface also provide interfaces with the DNA. This brings us ... proteins in different species that have evolved from a common ancestral gene, and paralogues, proteins that are related by gene ...
  http://docplayer.net/21205-Review-bioinformatics-a-definition-1-as-submitted-to-the-oxford-english-dictionary.html