Bayes Theorem
A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.
Sequence Analysis, DNA
Evolution, Molecular
Models, Genetic
Software
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Likelihood Functions
Base Sequence
Fossils
Algorithms
Markov Chains
RNA, Ribosomal, 18S
Biological Evolution
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
DNA, Mitochondrial
DNA, Ribosomal
Monte Carlo Method
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
Amino Acid Sequence
Computer Simulation
Molecular Sequence Annotation
High-Throughput Nucleotide Sequencing
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
Genome
Sequence Homology, Nucleic Acid
Species Specificity
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
DNA, Ribosomal Spacer
Databases, Nucleic Acid
Expressed Sequence Tags
RNA, Ribosomal, 16S
Cloning, Molecular
Classification
Sequence Analysis
Internet
RNA, Ribosomal, 28S
Phylogeography
Sequence Analysis, Protein
Genetics, Population
Polymerase Chain Reaction
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
Chromosome Mapping
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Genome, Human
Sequence Homology, Amino Acid
Databases, Factual
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
User-Computer Interface
Gene Library
Cluster Analysis
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Exome
INDEL Mutation
A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.
Genetic Speciation
Human Genome Project
Contig Mapping
Sequence Analysis, RNA
Haplotypes
RNA, Ribosomal, 5.8S
Genes
Information Storage and Retrieval
Database Management Systems
Open Reading Frames
Geography
Genes, rRNA
DNA Primers
Polymorphism, Single Nucleotide
DNA, Complementary
Genes, Mitochondrial
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Data Compression
Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.
Bacteria
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Ascomycota
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Genotype
Mutation
Sequence Homology
Selection, Genetic
Databases, Protein
Angiosperms
Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
DNA, Intergenic
RNA, Bacterial
Plastids
Genetic Markers
RNA, Ribosomal
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
Conserved Sequence
Gene Flow
Microsatellite Repeats
Restriction Mapping
Plants
Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.
Metagenome
Computer Graphics
Acari
Recombination, Genetic
Polymorphism, Genetic
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
DNA Restriction Enzymes
Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.
Genomic Library
Models, Statistical
Chromosomes, Artificial, Bacterial
DNA Barcoding, Taxonomic
Information Systems
Multilocus Sequence Typing
Biodiversity
CD-ROM
Nucleic Acid Hybridization
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Repetitive Sequences, Nucleic Acid
Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).
Lemur
Alleles
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Gene Expression Profiling
Sequence Tagged Sites
Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.
Physical Chromosome Mapping
Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)
Molecular Epidemiology
Basidiomycota
Phenotype
Fruiting Bodies, Fungal
Mutation Rate
Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation. (1/277092)
Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods. (+info)The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity. (2/277092)
The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription. (+info)The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping. (3/277092)
Left-right asymmetry in vertebrates is controlled by activities emanating from the left lateral plate. How these signals get transmitted to the forming organs is not known. A candidate mediator in mouse, frog and zebrafish embryos is the homeobox gene Pitx2. It is asymmetrically expressed in the left lateral plate mesoderm, tubular heart and early gut tube. Localized Pitx2 expression continues when these organs undergo asymmetric looping morphogenesis. Ectopic expression of Xnr1 in the right lateral plate induces Pitx2 transcription in Xenopus. Misexpression of Pitx2 affects situs and morphology of organs. These experiments suggest a role for Pitx2 in promoting looping of the linear heart and gut. (+info)Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development. (4/277092)
We have identified a novel gene in a gene trap screen that encodes a protein related to the DnaJ co-chaperone in E. coli. The gene, named Mrj (mammalian relative of DnaJ) was expressed throughout development in both the embryo and placenta. Within the placenta, expression was particularly high in trophoblast giant cells but moderate levels were also observed in trophoblast cells of the chorion at embryonic day 8.5, and later in the labyrinth which arises from the attachment of the chorion to the allantois (a process called chorioallantoic fusion). Insertion of the ROSAbetageo gene trap vector into the Mrj gene created a null allele. Homozygous Mrj mutants died at mid-gestation due to a failure of chorioallantoic fusion at embryonic day 8.5, which precluded formation of the mature placenta. At embryonic day 8.5, the chorion in mutants was morphologically normal and expressed the cell adhesion molecule beta4 integrin that is known to be required for chorioallantoic fusion. However, expression of the chorionic trophoblast-specific transcription factor genes Err2 and Gcm1 was significantly reduced. The mutants showed no abnormal phenotypes in other trophoblast cell types or in the embryo proper. This study indicates a previously unsuspected role for chaperone proteins in placental development and represents the first genetic analysis of DnaJ-related protein function in higher eukaryotes. Based on a survey of EST databases representing different mouse tissues and embryonic stages, there are 40 or more DnaJ-related genes in mammals. In addition to Mrj, at least two of these genes are also expressed in the developing mouse placenta. The specificity of the developmental defect in Mrj mutants suggests that each of these genes may have unique tissue and cellular activities. (+info)A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates. (5/277092)
The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates. (+info)Requirement of a novel gene, Xin, in cardiac morphogenesis. (6/277092)
A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping. (+info)Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region. (7/277092)
On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation. (+info)Mechanisms of GDF-5 action during skeletal development. (8/277092)
Mutations in GDF-5, a member of the TGF-beta superfamily, result in the autosomal recessive syndromes brachypod (bp) in mice and Hunter-Thompson and Grebe-type chondrodysplasias in humans. These syndromes are all characterised by the shortening of the appendicular skeleton and loss or abnormal development of some joints. To investigate how GDF-5 controls skeletogenesis, we overexpressed GDF-5 during chick limb development using the retrovirus, RCASBP. This resulted in up to a 37.5% increase in length of the skeletal elements, which was predominantly due to an increase in the number of chondrocytes. By injecting virus at different stages of development, we show that GDF-5 can increase both the size of the early cartilage condensation and the later developing skeletal element. Using in vitro micromass cultures as a model system to study the early steps of chondrogenesis, we show that GDF-5 increases chondrogenesis in a dose-dependent manner. We did not detect changes in proliferation. However, cell suspension cultures showed that GDF-5 might act at these stages by increasing cell adhesion, a critical determinant of early chondrogenesis. In contrast, pulse labelling experiments of GDF-5-infected limbs showed that at later stages of skeletal development GDF-5 can increase proliferation of chondrocytes. Thus, here we show two mechanisms of how GDF-5 may control different stages of skeletogenesis. Finally, our data show that levels of GDF-5 expression/activity are important in controlling the size of skeletal elements and provides a possible explanation for the variation in the severity of skeletal defects resulting from mutations in GDF-5. (+info)
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Columbea
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... integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003 ... Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. Accessed ... Biologists can then use this data to deduce which birds are at risk of lead poisoning. ... Molecular Biology and Evolution. 24 (1): 269-280. CiteSeerX 10.1.1.106.1680. doi:10.1093/molbev/msl158. PMID 17062634.. ...
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Integration of molecular sequence data and fossils" (PDF). Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC ... Molecular studies such as DNA-DNA hybridization (Sibley & Ahlquist, 1990)[full citation needed] and sequence analyses fail to ... 1990): Distribution and taxonomy of the birds of the world: A Study in Molecular Evolution. Yale University Press, New Haven, ... "Molecular Phylogenetics and Evolution. 30 (1): 140-151. doi:10.1016/S1055-7903(03)00159-3. PMID 15022765.. ...
Passerine
... based on nuclear and mitochondrial sequence data". Molecular Phylogenetics and Evolution. 29 (1): 126-138. doi:10.1016/S1055- ... a congruence analysis of heterogeneous mitochondrial and nuclear DNA sequence data". Molecular Phylogenetics and Evolution. 31 ... Advances in molecular biology and improved paleobiogeographical data gradually are revealing a clearer picture of passerine ... taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data" (PDF). Proceedings of the Royal Society B ...
Brown pelican
"The phylogenetic relationships of the extant pelicans inferred from DNA sequence data". Molecular Phylogenetics and Evolution. ... However, trees derived from genetic data disagree. In 1990, Charles Sibley and John E. Ahlquist's Unweighted Pair Group Method ... with Arithmetic Mean (UPGMA) tree based on DNA-DNA hybridization data found that the American white pelican, the pink-backed ...
Falconidae
e.g. Ericson et al., Diversification of Neoaves: integration of molecular sequence data and fossils, Biol Lett. 2007 Jun 22;3(3 ... "that is probably misplaced in the current phylogenetic listing but for which data indicating proper placement are not yet ...
Population history of indigenous peoples of the Americas
New insights from multilocus sequence data", 41(1) Genetics and Molecular Biology (2018). http://www.scielo.br/scielo.php? ... Scholars rely on archaeological data and written records from settlers from Europe. Most scholars writing at the end of the ... The University of Kansas, DNA sequences suggest 250 people made up original Native American founding population (2018/05/01) ... "Amateur website, but reports data from scholarly sources.. *Jeffrey Amherst and Smallpox Blankets "Lord Jeffrey Amherst's ...
Near passerine
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... However, molecular data does not support the traditional arrangement; it is now clear that "near passerines" and "higher ... "An unbiased molecular approach using 3′-UTRs resolves the avian family-level tree of life". Molecular Biology and Evolution ( ... Johansson, Ulf S. & Ericson, Per G. P. (2003): Molecular support for a sister group relationship between Pici and Galbulae ( ...
New World vulture
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-7. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... This was criticized, and an early DNA sequence study was based on erroneous data and subsequently retracted. There was then an ... They were especially common in the gut with Clostridia DNA sequence counts between 26% and 85% relative to total sequence ... ISBN 0-300-04969-2 Sibley, Charles G., and Jon E. Ahlquist (1991) Phylogeny and Classification of Birds: A Study in Molecular ...
Turkey vulture
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 1-5. doi:10.1098/rsbl.2006.0523. PMC 1834003. PMID ... 1991). Phylogeny and Classification of Birds: A Study in Molecular Evolution. Yale University Press. ISBN 0-300-04085-7. ... Molecular Phylogenetics and Evolution. 37 (2): 327-346. doi:10.1016/j.ympev.2005.04.010. ISSN 1055-7903. PMID 15925523. ... and classification of the Accipitridae based on DNA sequences of the RAG-1 exon". Journal of Avian Biology. 38 (5): 587-602. ...
Columbaves
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... "An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life". Molecular Biology and Evolution: 143 ... sequenced 3-prime untranslated region (3'UTR) from 429 species and 379 genera of birds found support of Columbaves in their ... A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature (2015). doi:10.1038/nature15697 ...
Jacamar
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... "Molecular support for a sister group relationship between Pici and Galbulae (Piciformes sensu Wetmore 1960" (PDF). Journal of ...
Aequorlitornithes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... 22 October 2015). "A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing". Nature. 526 (7574 ...
Eurypygimorphae
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... More recent molecular studies support their grouping together in Eurypygimorphae, which is usually recovered as the sister ... 2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569-573. Suh, ...
Columbimorphae
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... Molecular Phylogenetics and Evolution. 56 (2): 698-706. doi:10.1016/j.ympev.2010.04.016. PMID 20399870. v t e. ... using targeted next-generation DNA sequencing". Nature. 526 (7574): 569-573. Bibcode:2015Natur.526..569P. doi:10.1038/ ...
Galbuli
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... Johansson, Ulf S.; Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...
Puffbird
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... Molecular investigation of the Bucconidae in 2004 indicated that the nunlets (genus Nonnula) diverged from the common ancestor ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ... Witt, C.C. (2004), Rates of Molecular Evolution and their Application to Neotropical Avian Biogeography, Ph.D. dissertation, ...
Ardeae
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... An unbiased molecular approach using 3'UTRs resolves the avian family-level tree of life. Molecular Biology and Evolution. ...
Pici (taxon)
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... Johansson, Ulf S. & Ericson, Per G.P. (2003). "Molecular support for a sister group relationship between Pici and Galbulae ( ...
Vampyrella
Molecular sequence data exist for two families: Vampyrellidae and Leptophyridae. Frequently, Vampyrella is the only genus ...
Mirandornithes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... Molecular Phylogenetics and Evolution. 30 (1): 140-151. doi:10.1016/S1055-7903(03)00159-3. PMID 15022765. Mayr, G. (February ...
White-bellied go-away-bird
6 July 2006). "Diversification of Neoaves: integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547 ... "LC White-bellied Go-away-bird Criniferoides leucogaster". BirdLife International Data Zone. 2019. Dale A. Zimmerman, Birds of ...
Tadarida
Molecular sequence data indicate Tadarida is not a monophyletic taxon. The closest relative of Tadarida aegyptiaca of Africa ... "Toward a Molecular Phylogeny for the Molossidae (Chiroptera) of the Afro-Malagasy Region". Acta Chiropterologica. 13 (1): 1-16 ...
Pelecaniformes
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... but molecular and morphological studies indicate they are not such close relatives. They have been placed in their own orders, ...
Cretaceous-Paleogene extinction event
December 2006). "Diversification of Neoaves: integration of molecular sequence data and fossils". Biol. Lett. 2 (4): 543-7. doi ... Based on molecular sequencing and fossil dating, many species of birds (the Neoaves group in particular) appeared to radiate ... At present the most informative sequence of dinosaur-bearing rocks in the world from the K-Pg boundary is found in western ... In North America, the data suggests massive devastation and mass extinction of plants at the K-Pg boundary sections, although ...
Psittacopasserae
... integration of molecular sequence data and fossils". Biology Letters. 2 (4): 543-547. doi:10.1098/rsbl.2006.0523. PMC 1834003. ... The group was proposed following an alignment of nuclear intron sequences by Shannon Hackett et al. in 2008, it was formally ... However, the technique requires very extensive genomic data - in the 2011 paper, approximately 200,000 retroposon-containing ...
HOXD8
More reference expression data. Gene ontology. Molecular function. • transcription factor activity, sequence-specific DNA ... RNA polymerase II regulatory region sequence-specific DNA binding. • DNA binding. • sequence-specific DNA binding. • ... transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. • RNA ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Spottefuglar
Nuclear and mitochondrial sequence data reveal the major lineages of starlings, mynas and related taxa. Molecular Phylogenetics ... 1990): Distribution and taxonomy of the birds of the world: A Study in Molecular Evolution. Yale University Press, New Haven, ... Hunt, Jeffrey S.; Bermingham, Eldredge; & Ricklefs, Robert E. (2001): Molecular systematics and biogeography of Antillean ...
Hymenoscyphus fraxineus
The sequence has been published on the website OpenAshDieBack and offers clues to how the fungus infects trees. The study has ... Gross, A.; Grünig, C. R.; Queloz, V.; Holdenrieder, O. (2012). "A molecular toolkit for population genetic investigations of ... "National Biodiversity Data Centre. Retrieved 5 November 2012.. *^ http://www.agriculture.gov.ie/forestservice/ashdiebackchalara ... Teams from The Sainsbury Laboratory (TSL) and the John Innes Centre in Norwich sequenced the genome of the fungus in December ...
Quantitative trait locus
Once a region of DNA is identified as contributing to a phenotype, it can be sequenced. The DNA sequence of any genes in this ... INTERSNP - a software for genome-wide interaction analysis (GWIA) of case-control SNP data and analysis of quantitative traits ... Methods in Molecular Biology, Springer US, pp. 15-25, doi:10.1007/978-1-4939-9865-4_3, ISBN 9781493998654. , PMID 31541435. ... This can be done using BLAST, an online tool that allows users to enter a primary sequence and search for similar sequences ...
QIAGEN Silicon Valley
Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing data (NGS ... The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems ... IPA can be used with or without data. IPA helps researchers analyze data derived from expression and SNP microarrays, ... QIAGEN Silicon Valley's first product, IPA, was introduced in 2003, and is used to help researchers analyze omics data and ...
Eurasian magpie
... inferred from mtDNA data". Molecular Phylogenetics and Evolution. 29 (2): 250-257. doi:10.1016/S1055-7903(03)00096-4. PMID ... An analysis of mitochondrial DNA sequences published in 2003 confirmed that the black-billed magpie and the yellow-billed ... Molecular Phylogenetics and Evolution. 65 (2): 562-572. doi:10.1016/j.ympev.2012.07.011. PMID 22842292.. ...
Positron emission tomography
The statistics of data thereby obtained are much worse than those obtained through transmission tomography. A normal PET data ... 2003). "11C-metomidate PET imaging of adrenocortical cancer". European Journal of Nuclear Medicine and Molecular Imaging. 30 (3 ... Because the two scans can be performed in immediate sequence during the same session, with the patient not changing position ... Also, FBP treats the data deterministically-it does not account for the inherent randomness associated with PET data, thus ...
Leaf
There is a regularity in these angles and they follow the numbers in a Fibonacci sequence: 1/2, 2/3, 3/5, 5/8, 8/13, 13/21, 21/ ... Walls, R. L. (25 January 2011). "Angiosperm leaf vein patterns are linked to leaf functions in a global-scale data set". ... On the basis of molecular genetics, Eckardt and Baum (2010) concluded that "it is now generally accepted that compound leaves ...
Ebola
Genome-sequencing showed that this outbreak was not related to the 2014-15 West Africa Ebola virus outbreak, but was the same ... Klenk, Hans-Dieter; Feldmann, Heinz (2004). Ebola and Marburg viruses: molecular and cellular biology (Limited preview). ... "Ebolavirus - Pathogen Safety Data Sheets". Public Health Agency of Canada. 17 September 2001. Archived from the original on 20 ... Genome sequencing suggests that this outbreak, the 11th outbreak since the virus was first discovered in the country in 1976, ...
Mallard
Mitochondrial DNA data for the D-loop sequence suggests that mallards may have evolved in the general area of Siberia. Mallard ... "Molecular Phylogenetics and Evolution. 70: 402-411. doi:10.1016/j.ympev.2013.08.008. ISSN 1095-9513. PMID 23994490.. ... McCracken, Kevin G.; Johnson, William P.; Sheldon, Frederick H. (2001). "Molecular population genetics, phylogeography, and ... Molecular Ecology (published January 2013). 22 (1): 41-55. doi:10.1111/mec.12098. PMID 23110616.. ...
GABRA4
More reference expression data. Gene ontology. Molecular function. • ion channel activity. • benzodiazepine receptor activity. ... 2004). "Complete sequencing and characterization of 21,243 full-length human cDNAs". Nat. Genet. 36 (1): 40-45. doi:10.1038/ ... "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci. U.S.A ...
Substance P
"Molecular Biology of the Cell. 6 (5): 509-24. doi:10.1091/mbc.6.5.509. PMC 301212 . PMID 7545030.. ... Preclinical data support the notion that Substance P is an important element in pain perception. The sensory function of ... Huston JP, Hasenöhrl RU, Boix F, Gerhardt P, Schwarting RK (1993). "Sequence-specific effects of neurokinin substance P on ... Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). ...
Octopus
The California two-spot octopus has had its genome sequenced, allowing exploration of its molecular adaptations.[151] Having ... Relevant data at Google Ngram Viewer.. *^ "Octopus". Oxforddictionaries.com. 2014. Retrieved 4 February 2014.. ... Octopuses and other coleoid cephalopods are capable of greater RNA editing (which involves changes to the nucleic acid sequence ... Strugnell, J.; Nishiguchi, M. K. (2007). "Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) inferred from ...
Caulobacter crescentus
"Journal of Molecular Biology. 409 (1): 28-35. doi:10.1016/j.jmb.2011.02.041. PMC 3108490. PMID 21371478.. ... Yale University's data strongly suggest a model in which TipN regulates the orientation of the polarity axis by providing a ... In 2010, the Caulobacter NA1000 strain was sequenced and all differences with the CB15 "wild type" strain were identified.[6] ... Detailed study of the molecular development of these cells as they progress through the cell cycle has enabled researchers to ...
Passerine - Simple English Wikipedia, the free encyclopedia
... taxonomic and biogeographic implications of an analysis of nuclear DNA sequence data. Proceedings of the Royal Society B. 269: ... Evidence on their evolution comes from comparative anatomy, the fossil record and molecular biology. It is thought that the ...
PAX8
More reference expression data. Gene ontology. Molecular function. • DNA binding. • sequence-specific DNA binding. • ... RNA polymerase II core promoter sequence-specific DNA binding. • RNA polymerase II transcription factor activity, sequence- ... "Molecular and Cellular Biology. 21 (2): 524-33. doi:10.1128/MCB.21.2.524-533.2001. PMC 86614. PMID 11134340.. ... "Molecular and Cellular Biology. 13 (10): 6024-35. doi:10.1128/mcb.13.10.6024. PMC 364662. PMID 8413205.. ...
Pinophyta
A new classification and linear sequence based on molecular data can be found in an article by Christenhusz et al.[7] ... Phylogeny of the Pinophyta based on cladistic analysis of molecular data.[5] ... In discussing the data obtained from the one 11 m tall white spruce, Fraser et al. (1964)[16] speculated that if the ... but recent research into DNA sequences suggests that this interpretation leaves the Pinales without Taxales as paraphyletic, ...
Lyme disease
Molecular and Cellular Probes. 31: 22-27. doi:10.1016/j.mcp.2016.08.003. PMID 27523487. Archived (PDF) from the original on 20 ... "Lyme Disease Data and surveillance". Lyme Disease. Centers for Disease Control and Prevention. 5 February 2019. Archived from ... revealed the presence of the DNA sequence of Borrelia burgdorferi making him the earliest known human with Lyme disease.[242] ... "Molecular Medicine. 14 (3-4): 205-12. doi:10.2119/2007-00091.Rupprecht. PMC 2148032. PMID 18097481. Archived from the original ...
Agnatha - Simple English Wikipedia, the free encyclopedia
Recent molecular data from rRNA,[4] and from mtDNA,[5] show that these living agnathans are monophyletic. There are about 100 ... 28S and 18S ribosomal DNA sequences support the monophyly of lampreys and hagfishes. Molecular Biology and Evolution 15 (12): ... Molecular phylogenetics and evolution. 22, 2, 184-192. [4] *↑ Janvier, Philippe 2010. MicroRNAs revive old views about jawless ... Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly ...
Alkali metal
"National Nuclear Data Center: Brookhaven National Laboratory. Retrieved 4 October 2012.. *^ Patton, I. Jocelyn; Waldbauer, L. J ... 8).[66] Upon heating of KC8, the elimination of potassium atoms results in the conversion in sequence to KC24, KC36, KC48 and ... in a molecular dynamics (MD) simulation study". Biophys. Chem. 120 (1): 1-9. doi:10.1016/j.bpc.2005.10.002. PMID 16253415.. ... Allred, A. L. (1961). "Electronegativity values from thermochemical data". J. Inorg. Nucl. Chem. 17 (3-4): 215-221. doi:10.1016 ...
പാസിയാനിഡേ - വിക്കിപീഡിയ
"Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix". ... 2] [3] മോളിക്കുലർ ഫൈലൊ ജെനെറ്റിക്സ്(Molecular phylogenetics) ഇവ ഇരു കുടുബമാണെന്ന് ഉറപ്പിച്ചു [4][5] For example, some ... Kimball, R. T.; Braun, E. L.; Zwartjes, P. W.; Crowe, T. M.; Ligon, J. D. (1999). "A molecular phylogeny of the pheasants and ... partridges suggests that these lineages are not monophyletic". Molecular Phylogenetics and Evolution. 11 (1): 38-54. doi: ...
Žagatas - Vikipēdija
... based on nucleotide sequence data. Journal of Avian Biology 36: 222-234. ... inferred from mtDNA data. Molecular Phylogenetics and Evolution 29: 250-257. ...
GenBank
Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often ... "Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That ... The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, ... Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an accession number ...
Brassicaceae
Hall, J.C.; Sytsma, K.J.; Iltis, H.H. (2002). "Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data". ... based on molecular and pollen data, and the description of a new family of Brassicales, Borthwickiaceae" (PDF). Taxon. 61 (3): ... The small Eurasian weed Arabidopsis thaliana is widely used as model organism in the study of the molecular biology of ... Although a substantial effort was made through molecular phylogenetic studies, the relationships within the Brassicaceae have ...
Progesterone receptor
More reference expression data. Gene ontology. Molecular function. • DNA binding. • sequence-specific DNA binding. • ... "Molecular and Cellular Biology. 20 (9): 3102-15. doi:10.1128/MCB.20.9.3102-3115.2000. PMC 85605. PMID 10757795.. ... "Molecular and Cellular Biology. 19 (2): 1182-9. doi:10.1128/mcb.19.2.1182. PMC 116047. PMID 9891052.. ... "Molecular and Cellular Biology. 18 (8): 4471-87. doi:10.1128/mcb.18.8.4471. PMC 109033. PMID 9671457.. ...
Reptile
... molecular) and fossil (morphological) data to obtain its results.[25] ... As of 2013, three turtle genomes have been sequenced.[33] The results place turtles as a sister clade to the archosaurs, the ... Hideyuki Mannena & Steven S.-L. Li (1999). "Molecular evidence for a clade of turtles". Molecular Phylogenetics and Evolution. ... Classically, turtles were considered to be related to the primitive anapsid reptiles.[32] Molecular work has usually placed ...
Computed tomography laser mammography
It is optical molecular imaging for hemoglobin both oxygenated and deoxygenated. The technology uses laser in the same way ... A laser detector measures the intensity drop and the data is collected as the laser detector moves across the breast creating a ...
Nacionalni centar za biotehnološke informacije
Datum osnivanja. 1988 .. Vrsta. Domaćin i uređivač niza baza podataka, relevantnih za biotehnologiju i biomedicinu i važan je ... "Sense from Sequences: Stephen F. Altschul on Bettering BLAST". 2000. Arhivirano s originala, 7. 10. 2007.. ... Journal of Molecular Biology. 215 (3): 403-410. doi:10.1016/s0022-2836(05)80360-2. PMID 2231712.. ... 8. 2007). GenBank: The Nucleotide Sequence Database. National Center for Biotechnology Information (US) - preko www.ncbi.nlm. ...
Free will
Science In Medicine: The JCI Textbook Of Molecular Medicine. Jones & Bartlett Learning. pp. 1061 ff. ISBN 0763750832.. ... On this doctrine events throughout eternity have been foreordained by some supernatural power in a causal sequence.. ... Others have argued that data such as the Bereitschaftspotential undermine epiphenomenalism for the same reason, that such ... Wagenaar, W. A. (1972). "Generation of random sequences by human subjects: A critical survey of literature". Psychological ...
Amaranthaceae
a b c d e Kai Müller, Thomas Borsch (2005): Phylogenetics of Amaranthaceae using matK/trnK sequence data - evidence from ... Molecular Phylogenetic Analysis Of Nuclear And Chloroplast Data Sets And A Revised Classification. - International Journal of ... Ivonne Sánchez del-Pino, Thomas Borsch, Timothy J. Motle (2009): trnL-F and rpl16 Sequence Data and Dense Taxon Sampling Reveal ... a b Gudrun Kadereit, Evgeny V. Mavrodiev, Elizabeth H. Zacharias, Alexander P. Sukhorukov (2010): Molecular phylogeny of ...
The detection of linkage disequilibrium in molecular sequence data. | Genetics
The detection of linkage disequilibrium in molecular sequence data. Message Subject (Your Name) has forwarded a page to you ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ... The detection of linkage disequilibrium in molecular sequence data.. R C Lewontin ...
Molecular systematics of Craterellus: cladistic analysis of
nuclear LSU rDNA sequence data | Mycological Research |...
Experts and Doctors on molecular sequence data in Switzerland
Locale about Experts and Doctors on molecular sequence data in Switzerland ... Experts and Doctors on molecular sequence data in Switzerland. Summary. Locale: Switzerland ... You are here: Locale , Experts and Doctors on molecular sequence data in Switzerland ... Based on these data we propose to assign species rank to six CSP of P. fortinii: P. turiciensis, P. letzii, P. europaea, P. ...
Experts and Doctors on molecular sequence data in Belgium
Research Topics about Experts and Doctors on molecular sequence data in Belgium ... Experts and Doctors on molecular sequence data in Belgium. Summary. Locale: Belgium ... You are here: Locale , Experts and Doctors on molecular sequence data in Belgium ... Our data indicate that TAXI-I belongs to a newly identified class of plant proteins for which a molecular function as glycoside ...
9781627035132: Deep Sequencing Data Analysis (Methods in Molecular Biology) - AbeBooks: 1627035133
Methods in Molecular Biology) (9781627035132) and a great selection of similar New, Used and Collectible Books available now at ... 1. Deep Sequencing Data Analysis (Methods in Molecular Biology) Published by Humana Press (2013) ... Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data ... Authoritative and practical, Deep Sequencing Data Analysis seeks to aid scientists in the further understanding of key data ...
Historical male-mediated introgression in horseshoe bats revealed by multilocus DNA sequence data - MAO - 2010 - Molecular...
UCI Machine Learning Repository: Molecular Biology (Promoter Gene Sequences) Data Set: Support
View ALL Data Sets Molecular Biology (Promoter Gene Sequences) Data Set Below are papers that cite this data set, with context ... Return to Molecular Biology (Promoter Gene Sequences) data set page. Ken Tang and Ponnuthurai N. Suganthan and Xi Yao and A. ... of real credit card transactions and two molecular biology sequence analysis data sets, were used in our experiments. The ... The six data sets are landsat, optdigits, vehicle, DNA thyroid disease and vowel data sets. Landsat. The Landsat data set is ...
Rheonix to Present Data on User-Defined Tests and Next-Generation Sequencing Library Preparation with its Automated Molecular...
Rheonix will present data from a user-defined assay for STIs and data that demonstrates new capabilities of its Encompass ... Rheonix to Present Data on User-Defined Tests and Next-Generation Sequencing Library Preparation with its Automated Molecular ... When sequenced on the Illumina platform, the resulting libraries yielded NGS sequence data indistinguishable from the labor- ... Rheonix will present data from a user-defined assay for STIs and data that demonstrates new capabilities of its Encompass ...
Identifying Molecular Drivers of Cancer via Comprehensive Sequencing of a Large Cohort with Matched Germline and Clinical Data ...
Eurosurveillance | S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and...
With the help of data generated from the World Health Organization Collaborating Centre for Reference and Research on Influenza ... S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and their relatedness ... S-OtrH3N2 viruses: use of sequence data for description of the molecular characteristics of the viruses and their relatedness ... 4 Institut Pasteur, Unit of Molecular Genetics of RNA Viruses, Department of Virology, Paris France 5 French National Centre ...
Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data | Cancer Research
Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data. Kevin J. Thompson, Xiaojia ... Molecular classification of triple negative breast cancer via RNA-sequencing data. [abstract]. In: Proceedings of the 105th ... Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data ... Abstract 5592: Molecular classification of triple negative breast cancer via RNA-sequencing data ...
Molecular Medicine Tri-Conference: Genomics & Sequencing Data Integration, Analysis and Visualization Symposium | globus
The Genomics & Sequencing Data Integration, Analysis and Visualization Symposium is a part of the Molecular Medicine Tri- ... Molecular Medicine Tri-Conference: Genomics & Sequencing Data Integration, Analysis and Visualization Symposium. ... As data shifts between research, sequencing labs, and the clinic, there is an ever-increasing volume of information generated ... Globus Genomics is a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing ...
Bioinformatics: Volume 1: Data, Sequence Analysis and Evolution. 2008. (Methods in Molecular Biology, Volume 452). illus. XII,...
Bioinformatics: Volume 1: Data, Sequence Analysis and Evolution. 2008. (Methods in Molecular Biology, Volume 452). illus. XII, ... Examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein ... structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes ...
EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth...
EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ... EARLY EVOLUTION OF EUKARYOTA AS INFERRED FROM THE COMBINED PHYLOGENY OF MULTIPLE MOLECULAR SEQUENCE DATA(Coevolution of Earth ...
Molecular systematics of the Western Cape genus Serruria Salisb. (Proteaceae L.) based on DNA sequence data
The plastid and nuclear data were therefore combined in order to analyse the data sets together. The molecular data does not ... Molecular systematics of the Western Cape genus Serruria Salisb. (Proteaceae L.) based on DNA sequence data. De Villiers, ... Based upon the strong monophyly of Serruria, DNA sequence data were collected for 53 of the 55 species from the plastid (rps16 ... Die plastied- en kern-data is derhalwe gekombineer om die datastelle saam te kan analiseer. Die molekulêre data ondersteun nie ...
Bayesian hypothesis testing of four-taxon topologies using molecular sequence data. - Semantic Scholar
... develop Bayesian inference to determine the posterior probability that a four-taxon topology is correct given the sequence data ... The reconstruction of phylogenetic trees from molecular sequences presents unusual problems for statistical inference. For ... Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.. *. Janet S. Sinsheimer, Jessica A Lake, ... article{Sinsheimer1996BayesianHT, title={Bayesian hypothesis testing of four-taxon topologies using molecular sequence data.}, ...
Molecular biology: Coordination of sequence data<...
Molecular biology : Coordination of sequence data. / Lesk, Arthur.. In: Nature, Vol. 314, No. 6009, 01.12.1985, p. 318-319.. ... Molecular biology : Coordination of sequence data. In: Nature. 1985 ; Vol. 314, No. 6009. pp. 318-319. ... Molecular biology: Coordination of sequence data. Nature. 1985 Dec 1;314(6009):318-319. https://doi.org/10.1038/314318b0 ... Lesk, A. (1985). Molecular biology: Coordination of sequence data. Nature, 314(6009), 318-319. https://doi.org/10.1038/314318b0 ...
Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data - MRC Weatherall...
To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here ... We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype. ... Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We ... The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere ...
Molecular approach in spider mites (Acari: Tetranychidae): Preliminary data on ribosomal DNA sequences - Semantic Scholar
The nucleotide sequence of a 300-bp fragment of the ITS2 was determined by direct sequencing and nucleotide divergence used for ... The resulting phylogenetic tree expressing interspecific relationships in genusTetranychus agrees with morphological data. The ... DNA sequence data were used to examine phylogenetic relationships between six species of economically important Tetranychidae ... Molecular approach in spider mites (Acari: Tetranychidae): Preliminary data on ribosomal DNA sequences. @article{ ...
Subjects: Molecular Sequence Data and Genes, Homeobox / Genre: Articles / Dates by Range: 1950-1999 - Digital Collections -...
Start Over You searched for: Subjects Molecular Sequence Data ✖Remove constraint Subjects: Molecular Sequence Data Subjects ... Amino Acid Sequence. Base Sequence. Genes, Homeobox. Molecular Sequence Data. Archival Collection:. The Marshall W. Nirenberg ... Amino Acid Sequence. Cloning, Molecular. Genes, Homeobox. RNA, Messenger. Molecular Sequence Data. Archival Collection:. The ... Molecular Sequence Data. Amino Acid Sequence. Archival Collection:. The Marshall W. Nirenberg Papers (Profiles in Science). ...
Molecular phylogeny of the genus Arum (Araceae) inferred from multi-locus sequence data and AFLPs :: MPG.PuRe
Molecular phylogeny of the genus Arum (Araceae) inferred from multi-locus sequence data and AFLPs ... Molecular phylogeny of the genus Arum (Araceae) inferred from multi-locus sequence data and AFLPs ... inferred from multi-locus sequence data and AFLPs. Taxon, 59(2), 405-415. doi:10.1002/tax.592006. ... Linz, J., Stökl, J., Urru, I., Krügel, T., Stensmyr, M. C., & Hansson, B. S. (2010). Molecular phylogeny of the genus Arum ( ...
Molecular Sequence Data Archives - Research on StationResearch on Station
Experts and Doctors on molecular sequence data in Denmark
Publications about Experts and Doctors on molecular sequence data in Denmark ... Experts and Doctors on molecular sequence data in Denmark. Summary. Locale: Denmark ... You are here: Locale , Experts and Doctors on molecular sequence data in Denmark ... The data suggest that the purified human GalNAc-transferase is a novel member of a family of polypeptide GalNAc-transferases, ...
Subjects: Amino Acid Sequence and Molecular Sequence Data / Genre: Articles - Digital Collections - National Library of...
Amino Acid Sequence Subjects Molecular Sequence Data ✖Remove constraint Subjects: Molecular Sequence Data Genre Articles ✖ ... Amino Acid Sequence. Base Sequence. Genes, Homeobox. Molecular Sequence Data. Archival Collection:. Profiles in Science. 3. The ... Amino Acid Sequence. Cloning, Molecular. Genes, Homeobox. RNA, Messenger. Molecular Sequence Data. Archival Collection:. ... Start Over You searched for: Subjects Amino Acid Sequence ✖Remove constraint Subjects: ...
Wikisource:WikiProject Open Access/Programmatic import from PubMed Central/DNA Barcoding for Community Ecology - How to Tackle...
Sequence data analysis, molecular species hypotheses[edit]. Sequences were aligned with ClustalW (reference), and maximum ... Cox1sequencing for community ecology[edit]. In Trigonopterus, it is possible to merely rely on cox1 sequence data to arrive at ... Maximum likelihood analyses of cox1 data included 1,002 Trigonopterus cox1 sequences and seven outgroups. The resulting cox1 ... Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should ...
DAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and Evolution
... data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically ... Posted by admin at 8:32 am Tagged with: Analysis, DAMBE, Evolution, Molecular Biology, Sequence Data 2,645 views. Sorry, the ... DAMBE 5.3.48 - Sequence Data Analysis in Molecular Biology and Evolution. DNA / Genome Analysis ... Molecular Biology and Evolution 30:1720-1728. Xia, X., and Xie. Z., 2001. DAMBE: Data analysis in molecular biology and ...
BIOINFTool: Bioinformatics and sequence data analysis in molecular biology using Matlab
... Mabrouk, Mai S.; Hamdy, Marwa; Mamdouh ... BIOINFTool: Bioinformatics and sequence data analysis in molecular biology using Matlab. Login ... genome sequences, and gene expression data. Techniques developed by computer scientists have enabled researchers at Celera ... resources that aid in the analysis of data. We can use these tools to analyze the data and interpret the results in a ...
Ridge regression estimated linear probability model predictions of O -glycosylation in proteins with structural and sequence...
... an appropriate set of non-O-glycosylatable sequences is hard to find. Three sequences from similar post-translational ... In particular, if a binary response is used to distinguish between O-glycosylated and non-O-glycosylated sequences, ... Thus, predicting the likelihood of O-glycosylation with sequence and structural information using classical regression analysis ... 4 , BMC Molecular and Cell Biology. Fig. 4. From: Ridge regression estimated linear probability model predictions of O- ...
Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data | Algorithms for Molecular Biology |...
The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from ... The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed ... model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. ... genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here ...
Evaluation of three read-depth based CNV detection tools using whole-exome sequencing data | Molecular Cytogenetics | Full Text
Paired CMA and WES data were acquired for 45 samples. A total of 219 CNVs (size ranged from 2.3 kb - 35 mb) identified on three ... Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and ... CNVs were called from WES data using XHMM, CoNIFER, and CNVnator with modified settings. All three software packages detected ... has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. ...
Base SequenceGeneticsGeneticPolymerase chain reGenesBioinformaticsPhylogeny2019GenomesPathologyEvolutionAlignmentAlgorithmsMultilocusProteinsEpidemiologyProteinNucleotideMitochondrialDatasetClassificationViralSystematicsRecombinationPhylogeneticsNext-generationPolymorphismSpecificityPhylogenetic treesNuclearAbstractMicroarrayAmino Acid2017MultiplexMorphologicalClinical and molecularGENBANKTaxaGenomicsExomeTumorMetricsAnalysesLaboratoryMeSHMethodsCohortLife Sciences
Base Sequence1
- Accurate genotyping of a human papilloma virus (HPV) isolated from clinical specimens depends on molecular identification of the unique and exclusive nucleotide base sequence in the hypervariable region of a highly conserved segment of the HPV L1 gene. (nih.gov)
Genetics2
- Molecular anthropology uses the tools and techniques of molecular genetics to answer anthropological questions, especially those concerning the origins and spread of humans across the globe. (jrank.org)
- This is an interdisciplinary course, and the goal is to involve students who have either a strong computer science background or a strong background in molecular biology (such as students in the genetics graduate program), but not necessarily both. (ubc.ca)
Genetic14
- Studies of genetic variation in natural populations at the sequence level usually show that most polymorphic sites are very asymmetrical in allele frequencies, with the rarer allele at a site near fixation. (genetics.org)
- Gfeller K, Roth M, Meile L, Teuber M. Sequence and genetic organization of the 19.3-kb erythromycin- and dalfopristin-resistance plasmid pLME300 from Lactobacillus fermentum ROT1. (labome.org)
- The new genetic revolution is fuelled by Deep Sequencing (or Next Generation Sequencing) apparatuses which, in essence, read billions of nucleotides per reaction. (abebooks.com)
- These genetic results, sharpened by ORIEN's clinical data and the significant size of the sample set, accurately elucidate known drivers of cancer, identify new genetic alterations, and reveal novel potential therapeutic targets. (genomeweb.com)
- Whole exome sequencing (WES) has been widely accepted as a robust and cost-effective approach for clinical genetic testing of small sequence variants. (biomedcentral.com)
- However, it was impossible to identify the population of blue whales the individuals belonged to, due to the lack of strong population genetic signals in the mitochondrial control region sequences. (sljol.info)
- This is a multi-institutional effort to aggregate detailed genetic (and molecular) data in connection with treatments and physician reported outcomes in patients with advanced cancer. (clinicaltrials.gov)
- Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. (cdc.gov)
- Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. (cdc.gov)
- Rasmus Nielsen is certainly one of these researchers, and his work so far has merged many population genetic and phylogenetic aspects of biological research under the umbrella of molecular evolution. (springer.com)
- In severe early-onset epilepsy, precise clinical and molecular genetic diagnosis is complex, as many metabolic and electro-physiological processes have been implicated in disease causation. (ox.ac.uk)
- It also uncovers unexpected genetic mechanisms and emphasizes the power of WGS as a clinical tool for making molecular diagnoses, particularly for highly heterogeneous disorders. (ox.ac.uk)
- To assess the genetic diversity and relationships between the isolates, we sequenced two housekeeping genes ( glmM and hspA ). (cdc.gov)
- This web-based application performed pairwise comparisons of HIV-1 protease and partial reverse transcriptase to measure sequence relatedness and identify sequences that were highly genetically similar at a genetic distance of ≤0.015 substitutions per site ( 6 , 7 ). (cdc.gov)
Polymerase chain re1
- Among other options, a heminested (nested) polymerase chain reaction (PCR) technology using two consecutive PCR replications of the target DNA in tandem with three consensus general primers may be used to detect a minute quantity of HPV DNA in crude proteinase K digestate of cervicovaginal cells, and to prepare the template for genotyping by automated direct DNA sequencing. (nih.gov)
Genes14
- Sequence comparisons suggest that tap is most closely related to two bHLH genes identified in several vertebrate species, neurogenin and neuroD, which are involved respectively in neural determination and in neuronal differentiation. (labome.org)
- Examines a selection of methods involving the generation and organization of data, including sequence data, RNA and protein structures, microarray expression data and functional annotations, methods for discovering the functional components of genomes, whether they be genes, alternative splice sites, non-coding RNAs or regulatory motifs, and several of the most interesting methods in phylogenetics and evolution. (koeltz.com)
- Techniques developed by computer scientists have enabled researchers at Celera Genomics, the Human Genome Project consortium, and other laboratories around the world to sequence the nearly 3 billion base pairs of the roughly 40,000 genes of the human genome. (must.edu.eg)
- Here, we compared the evolution of MHC class I and class II genes in three sister clades of common passerine birds, finches (Fringillinae and Carduelinae) and buntings (Emberizidae) using a uniform methodological (genotyping and data processing) approach and uniform sample sizes. (nature.com)
- Balasubramaniam S, Bray RD, Mulder RA, Sunnucks P, Pavlova A, Melville J (2016) New data from basal Australian songbird lineages show that complex structure of MHC class II β genes has early evolutionary origins within passerines. (nature.com)
- Clinical whole-genome sequencing in severe early-onset epilepsy reveals new genes and improves molecular diagnosis. (ox.ac.uk)
- Molecular diagnosis has historically been confined to sequential testing of candidate genes known to be associated with specific sub-phenotypes, but the diagnostic yield of this approach can be low. (ox.ac.uk)
- a molecular analysis of ribosomal genes and histone H3 sequence data. (thefreedictionary.com)
- We compared the sequences of two housekeeping genes ( hspA and glmM ) from these clones with those of 131 unrelated strains from patients living in different geographic regions. (cdc.gov)
- Clonal descent has been demonstrated by comparing alleles of genes such as vacA , flaA , and flaB of isolates infecting members of the same family ( 10 - 12 ) and by sequencing three housekeeping genes ( ureI , atpA , and ahpC ) ( 13 ). (cdc.gov)
- Analysis of the sequences of housekeeping genes ( atpD , scoB , glnA and recA ) showed that strains cluster according to their geographic origins ( 15 , 20 ). (cdc.gov)
- Analysis of the sequences the sequences of two housekeeping genes ( hspA and of housekeeping genes ( atpD , scoB , glnA and recA ) glmM ) from these clones with those of 131 unrelated showed that strains cluster according to their geographic strains from patients living in different geographic regions. (cdc.gov)
- Several mechanisms, such as point mutations, intragenic recombination, and introduction of foreign (African) alleles, sequenced two housekeeping genes ( glmM and hspA ). (cdc.gov)
- The data output of such high-throughput experiments typically becomes overwhelmingly large, and some statistical analyses must be performed to focus on the genes that are related to the experiment being conducted. (biomedcentral.com)
Bioinformatics6
- As a partner in the ORIEN Avatar program, Discovery Life Sciences' sequencing and bioinformatics laboratory, HudsonAlpha Discovery, has conducted high-yield, high-quality dual RNA/DNA isolation from formalin-fixed, paraffin-embedded (FFPE) specimens as well as whole-exome sequencing and RNA sequencing services on more than 30,000 tumor and non-tumor samples. (genomeweb.com)
- This Symposium will cover real-world use cases across many areas, including drug discovery and design, R&D, molecular modeling, next-generation sequencing, and bioinformatics. (globus.org)
- Bioinformatics: Volume 1: Data, Sequence Analysis and Evolution. (koeltz.com)
- Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and gene expression data. (must.edu.eg)
- With the availability of genomic data from multiple related species, molecular evolution has become one of the most active and fastest growing fields of study in genomics and bioinformatics. (springer.com)
- Bioinformatics involves the application of computational methods in order to address problems in molecular biology. (ubc.ca)
Phylogeny4
- Molecular phylogeny of Entomobrya (Collembola: Entomobryidae) from China: Color pattern groups and multiple origins. (semanticscholar.org)
- Marsupials (metatherians), with their position in vertebrate phylogeny and their unique biological features, have been studied for many years by a dedicated group of researchers, but it has only been since the sequencing of the first marsupial genome that their value has been more widely recognised. (hindawi.com)
- Traditionally, the practice has been to use one or more fossils as 'node calibrations' by associating their geologically derived age to a particular divergence in a molecular phylogeny. (royalsocietypublishing.org)
- The difficulty lies in determining the appropriate ancestral divergence in the molecular phylogeny to associate the fossil with and the details of how this should be achieved within a full statistical inference framework [ 6 - 8 ]. (royalsocietypublishing.org)
20193
- Computomics to provide analysis for the winners of the PacBio sequencing raffle at PAG 2019. (computomics.com)
- In WHO-convened Global Study of Origins of SARS-CoV-2: China Part released by the World Health Organization (WHO), SARS-CoV-2 surveillance data and virus cases reported in China are analyzed as far back as late 2019. (hsdl.org)
- 2019) based on molecular sequence data. (wikipedia.org)
Genomes12
- It is shown that more power can be achieved by increasing the length of sequence determined than by increasing the number of genomes sampled for the same total work. (genetics.org)
- Based upon the strong monophyly of Serruria, DNA sequence data were collected for 53 of the 55 species from the plastid (rps16 intron, atpB-rbcL intergenic spacer, trnL-F region and psbA-trnH intergenic spacer) and nuclear (internal transcribed spacer region or ITS) genomes in order to investigate evolutionary relationships within the genus. (sun.ac.za)
- Apart from this case, there was widespread agreement between the trees reconstructed using data from the two genomes. (sun.ac.za)
- Interpreting relationships of human immunodeficiency virus type 1 (HIV-1) sequences can be challenging because of their rapidly evolving genomes, but it may also lead to a better understanding of the underlying biology. (washington.edu)
- However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes. (biomedcentral.com)
- We present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. (biomedcentral.com)
- For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. (biomedcentral.com)
- Gen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. (biomedcentral.com)
- In order to manage and analyze the large amount of data generated from sequencing techniques, initiatives to develop appropriate tools and software have been undertaken by the N. gonorrhoeae scientific community worldwide [ 3 ] with a number of methods developed to assemble genomes, predict antimicrobial resistance (AMR), and investigate strain transmission through analysis of genomic molecular determinants. (biomedcentral.com)
- We utilize DNA sequence data from the nuclear, chloroplast, and mitochondrial genomes to infer historical processes of biodiversification. (duke.edu)
- We now have genome sequences for three distantly related marsupial species (the grey short-tailed opossum, the tammar wallaby, and Tasmanian devil), with the promise of many more genomes to be sequenced in the near future, making this a particularly exciting time in marsupial genomics. (hindawi.com)
- However, rapid progress has been made since the sequencing of the first and subsequent marsupial genomes. (hindawi.com)
Pathology2
- Human pathology due to a deficient alpha-oxidation is mostly linked to mutations in the gene coding for the second enzyme of the sequence, phytanoyl-CoA hydroxylase. (labome.org)
- ITHACA, N.Y.--( BUSINESS WIRE )-- Rheonix Inc. , a developer of fully automated molecular testing solutions, will highlight its Encompass Optimum ™ workstation at the Association for Molecular Pathology (AMP) Annual Meeting Nov. 10-12 in Charlotte, North Carolina. (businesswire.com)
Evolution15
- DAMBE (data analysis in molecular biology and evolution) is an integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. (mybiosoftware.com)
- DAMBE5: A comprehensive software package for data analysis in molecular biology and evolution. (mybiosoftware.com)
- Several studies have focused on the evolution of HIV-1, but there is little information to link sequence similarities and evolutionary histories of HIV-1 to the epidemiological information of the infected individual. (washington.edu)
- In the field of molecular evolution, inferences about past evolutionary events are made using molecular data from currently living species. (springer.com)
- Most studies in molecular evolution rely heavily on statistical procedures based on stochastic process modelling and advanced computational methods including high-dimensional numerical optimization and Markov Chain Monte Carlo. (springer.com)
- This book provides an overview of the statistical theory and methods used in studies of molecular evolution. (springer.com)
- This book is suitable for statisticians seeking to learn more about applications in molecular evolution and molecular evolutionary biologists with an interest in learning more about the theory behind the statistical methods applied in the field. (springer.com)
- Most relevant statistical concepts are introduced in the book in the context of their application in molecular evolution, and the book should be accessible for most biology graduate students with an interest in quantitative methods and theory. (springer.com)
- His is an associate editor of the Journal of Molecular Evolution and has published more than fifty original papers in peer-reviewed journals on the topic of this book. (springer.com)
- I find Statistical Methods in Molecular Evolution very interesting and useful. (springer.com)
- This book gives an overview of his interests and current achievements in molecular evolution. (springer.com)
- In addition, these genome sequences have facilitated studies aimed at answering questions regarding gene and genome evolution and provided insight into the evolution of epigenetic mechanisms. (hindawi.com)
- Here I highlight the major advances in our understanding of evolution and disease, facilitated by marsupial genome projects, and speculate on the future contributions to be made by such sequences. (hindawi.com)
- The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. (royalsocietypublishing.org)
- It may be less widely appreciated by molecular evolutionary biologists that the statistical phylogenetic revolution in molecular evolution has also been mirrored in the increasing application of statistical phylogenetic reasoning in macroevolutionary and systematic studies of the fossil record [ 14 - 17 ]. (royalsocietypublishing.org)
Alignment4
- Multiple sequence alignment with hierarchical clustering. (semanticscholar.org)
- Exome targets were captured using the Agilent SureSelect Human All Exon V4 or V5 kit (Agilent Technologies, Santa Clara, CA). Raw sequencing data (FASTQ format) were generated via the Illumina HiSeq 2000 platform (Illumina, Inc., San Diego, CA). The Burrows Wheeler Alignment tool (BWA) v0.2.10 [ 17 ] was employed for sequencing data alignment to the Human Reference Genome (NCBI build 37, hg 19). (biomedcentral.com)
- Sequencing of RNA-Seq libraries, processing and alignment to reference genome RNA was sequenced on the Illumina HiSeq 2000 sequencer (Illumina, USA) with a single-ended, 51-bp run producing raw fastq files. (forgetmenotinitiative.org)
- Topics in molecular biology that will motivate the algorithmic content of the course include: sequence alignment, phylogenetic tree reconstruction, prediction of RNA and protein structure, gene finding and sequence annotation, gene expression, and biomolecular computing. (ubc.ca)
Algorithms2
- Detection of copy number variants (CNV) within WES data have become possible through the development of various algorithms and software programs that utilize read-depth as the main information. (biomedcentral.com)
- Class assignments will familiarize students with biological data and tools for understanding this data and will help students gain a solid understanding of principles for design and analysis of algorithms. (ubc.ca)
Multilocus4
- Jolly and Maiden initially developed BIGSdb (Bacterial Isolate Genome Sequence Database) [ 4 ] to store and investigate Multilocus Sequence Typing (MLST) profiles of sequences generated from multiple sources, such as multiple single amplicons or assembled contigs from sequencing technologies. (biomedcentral.com)
- Strain relationships within the family were determined by analyzing allelic variation at both loci and building phylogenetic trees and by using multilocus sequence typing. (cdc.gov)
- America, and Europe differ from those that are predomi- netic trees and by using multilocus sequence typing. (cdc.gov)
- Although standard variable typing regions (emm subtype, tee type, sof type, and multilocus sequence typing [MLST]) remained unchanged, uniquely the emergent clade had undergone six distinct regions of homologous recombination across the genome compared to the rest of the sequenced emm89 population. (whiterose.ac.uk)
Proteins1
- Analysis of sub-type specific mutation data from the BC cohort demonstrates an increased mutational load in ECM-related proteins, particularly the myosins, along with increased TP53 clonality in the non-LAR subtypes. (aacrjournals.org)
Epidemiology5
- Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals. (washington.edu)
- The Promise of Whole Genome Pathogen Sequencing for the Molecular Epidemiology of Emerging Aquaculture Pathogens. (ox.ac.uk)
- We outline, by way of comparison, how sequencing technology is transforming the molecular epidemiology of pathogens of public health importance, emphasizing the importance of community-oriented databases and analysis tools. (ox.ac.uk)
- Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae . (biomedcentral.com)
- The Homeland Security Digital Library (HSDL) maintains a collection of the Centers for Disease Control's (CDC) Morbidity and Mortality Weekly Report (MMWR), which collects and analyzes data from the United States Department of Health and Human Services (HHS) on epidemiology and public health. (hsdl.org)
Protein6
- The NH-alpha CH coupling constants of turkey lysozyme are compared to torsion-angle data from three crystal structures of the protein and the results are interpreted in terms of crystal-structure resolution and refinement. (labome.org)
- Vanderhaeghen R, De Clercq R, Karimi M, Van Montagu M, Hilson P, Van Lijsebettens M. Leader sequence of a plant ribosomal protein gene with complementarity to the 18S rRNA triggers in vitro cap-independent translation. (labome.org)
- SEView is a Java applet that represents known or predicted elements of a protein or nucleotide sequence. (epfl.ch)
- We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized α/β-barrel protein. (caltech.edu)
- A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. (caltech.edu)
- These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm. (caltech.edu)
Nucleotide1
- Our data base presently includes nucleotide sequences from multiple loci representing some 500-600 accessions of peatmosses. (duke.edu)
Mitochondrial3
- Analysis of sequences of the mitochondrial control region from baleen whales confirmed that the samples belonged to blue whales ( Balaenoptera musculus ). (sljol.info)
- We apply the method to mitochondrial data from several different species. (sussex.ac.uk)
- In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. (nih.gov)
Dataset1
- Figure 1 illustrates an example of sequence classification on a dataset of DNA sequences. (uci.edu)
Classification1
- The resultant phylogenetic reconstruction thus supports palynological data of this subsection, and indicates the urgent need for a revision of the current morphological classification of Salter (1944). (nrf.ac.za)
Viral6
- Data generated by this effort demonstrates that, in addition to detecting the presence of viral RNA, the system can distinguish early immunoglobulin M (IgM) antibodies from late immunoglobulin G (IgG) antibodies, thus providing more information on a patient's stage of infection. (businesswire.com)
- Using standard phylogenetic and phenetic techniques on 100 HIV-1 subtype B sequences, we were able to show some correlation between the viral sequences and the geographic area of infection and the risk of men who engage in sex with men. (washington.edu)
- To help identify more subtle relationships between the viral sequences, the method of multidimensional scaling (MDS) was performed. (washington.edu)
- That method identified statistically significant correlations between the viral sequences and the risk factors of men who engage in sex with men and individuals who engage in sex with injection drug users or use injection drugs themselves. (washington.edu)
- Here, we discuss the opportunities afforded by whole genome sequencing of bacterial and viral pathogens of aquaculture to mitigate disease emergence and spread. (ox.ac.uk)
- Prevention recommendations generated from national data (e.g., targeting preexposure prophylaxis for HIV-negative persons at high risk and implementing measures to maintain viral suppression among persons with HIV infection) also are relevant in a lower HIV-morbidity state. (cdc.gov)
Systematics1
- Molecular systematics of the Western Cape genus Serruria Salisb. (sun.ac.za)
Recombination1
- Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. (nih.gov)
Phylogenetics1
- The continual improvement of models and methods for statistical phylogenetic inference from molecular sequence data is well documented [ 4 , 5 ], and in recent years, it is arguably the case that molecular phylogenetics has taken primacy over the fossil record in providing a timescale for evolutionary history [ 1 ]. (royalsocietypublishing.org)
Next-generation3
- Rheonix will present data from a user-defined assay for sexually transmitted infections (STIs), as well as data that demonstrates new capabilities of its system in next-generation sequencing (NGS) library preparation. (businesswire.com)
- An overview of the changes of our diagnostic approach before and after the transition to next-generation sequencing is also reported. (elsevier.com)
- Due to the rapid development of "-omics" technology, such as DNA microarrays [ 1 ] and next-generation sequencing (NGS) [ 2 , 3 ], scientists are now able to quantify large numbers of transcripts from organisms simultaneously. (biomedcentral.com)
Polymorphism3
- A recent study on sequence polymorphism of four FLC paralogs in B. oleracea indicated that they are not candidate in flowering time variation [ 22 ]. (biomedcentral.com)
- H. pylori is one of the most genetically diverse bacterial species, displaying from 2.7% to 8.0% of DNA sequence polymorphism ( 14 - 16 ). (cdc.gov)
- To look for evidence of intrafamilial infection, we isolat- sequence polymorphism (14-16). (cdc.gov)
Specificity1
- However, microarray technology is dependent on probe-target specificity and the 7 subtypes have yet to be validated using RNA sequencing data, and the presences of recurrent genomic alterations in the 7 subtypes are unknown. (aacrjournals.org)
Phylogenetic trees1
- The reconstruction of phylogenetic trees from molecular sequences presents unusual problems for statistical inference. (semanticscholar.org)
Nuclear2
- The plastid and nuclear data were therefore combined in order to analyse the data sets together. (sun.ac.za)
- and related genera (Orchidaceae: Oncidiinae) were evaluated using parsimony analyses of data from the internal transcribed spacers of nuclear ribosomal (nrITS DNA) and three plastid regions (matK, trnL-F, and the atpB-rbcL intergenic spacer region). (ucr.ac.cr)
Abstract1
- If a collaborating data producer has created an abstract, it will appear in the Other Abstract (OAB) field. (nih.gov)
Microarray3
- of MLP, as well as ensemble methods based on resampling techniques, such as bagging and boosting, have been applied to the analysis of DNA microarray data [192, 158, 54, 178, 185]. (uci.edu)
- We used DNA microarray data available on-line. (uci.edu)
- Based on microarray data from Stanford Microarray Database, two hNAT pairs were found to display significant inverse expression patterns before and after insulin injection. (mendeley.com)
Amino Acid2
- No amino acid sequence difference was found between the two strains. (labome.org)
- An automated sequence selection algorithm, based on the dead-end elimination theorem, was used to find the optimal amino acid sequence fitting the target structure. (caltech.edu)
20172
- Graph generated 15 March 2017 using data from PubMed using criteria . (cancerindex.org)
- HIV-1 sequence data reported in Wisconsin during 2014-2017 for persons with HIV infection diagnosed through August 15, 2017, were analyzed using Secure HIV-TRACE (Secure HIV TRAnsmission Cluster Engine). (cdc.gov)
Multiplex1
- Multiplex DNA sequencing. (harvard.edu)
Morphological8
- Previous molecular and morphological analyses performed on the South African subfamily Proteoideae have shown Serruria, a CFR endemic, to form a well-supported monophyletic group. (sun.ac.za)
- The molecular data does not support most of the groupings proposed by previous authors based on morphological data. (sun.ac.za)
- Pollen data "sensu" Dreyer (1996) supports the clades retrieved in this study, whereas very few morphological characters could be plotted as potential synapomorphies for these clades. (nrf.ac.za)
- Current projects in the lab include molecular phylogenetic analyses of familial and ordinal level relationships in the arthrodontous mosses, studies of hybridization using molecular and morphological markers, and investigations of cryptic speciation within geographically widespread species. (duke.edu)
- Morphological and molecular information is being used to explore geographic patterns in phylogenetic diversity within the peatmosses. (duke.edu)
- As you'll know if you've been keeping up with the results of the various big molecular and morphological analyses - and who hasn't - the avian cladogram is gradually coming together, though areas of debate and disagreement remain. (scienceblogs.com)
- Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. (royalsocietypublishing.org)
- We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. (royalsocietypublishing.org)
Clinical and molecular2
- The breadth and scope of the ORIEN Avatar clinical and molecular data enables the discovery of a wide array of DNA and RNA biomarkers, including those biomarkers associated with response to immuno-oncology agents. (genomeweb.com)
- In a previous study, we presented the clinical and molecular findings in 140 FCCM individuals. (cdc.gov)
GENBANK3
- A short target sequence of 40-60 bases excised from the computer-generated electropherogram is sufficient for BLAST determination of all clinically relevant HPV genotypes, based on the database stored in the GenBank. (nih.gov)
- All sequences generated and used in this study have been deposited in GenBank (Nos: MW740435-MW741429). (nature.com)
- Phylogenetic analyses were conducted using the combined ITS-1 and ITS-2 data sets from the present study and using reference sequences from the GenBank database. (springer.com)
Taxa2
- Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species. (wikisource.org)
- Our results provide an estimate of the distribution of fitness effects of weakly selected mutations and provide a possible explanation for why the molecular clock is fairly constant across taxa and time. (sussex.ac.uk)
Genomics3
- The Genomics & Sequencing Data Integration, Analysis and Visualization Symposium is a part of the Molecular Medicine Tri-Conference. (globus.org)
- Please join us for a talk by Ravi Madduri on the subject "Integrated Research Data Management and Analysis in NGS Using Globus Genomics. (globus.org)
- Globus Genomics is a robust, scale on-demand solution that provides end-to-end research data management for Next-Gen Sequencing Analysis using Galaxy, Globus Online and Amazon Web Services. (globus.org)
Exome1
- Here, we evaluated three representative and popular read-depth based CNV detection programs: the eXome-Hidden Markov Model (XHMM), the Copy Number Inference From Exome Reads (CoNIFER), and CNVnator using clinical grade WES data. (biomedcentral.com)
Tumor1
- 1 Laboratory for Molecular Development and Tumor Biology, Centre for Molecular Medicine (CMM), Stockholm, S-171 76, Sweden. (nih.gov)
Metrics1
- Third, the molecular laboratory is challenged to monitor its sequencing processes for nonrandom process variation and other quality metrics. (cdc.gov)
Analyses2
- Both parsimony and Bayesian analyses were carried out on each of these data sets. (sun.ac.za)
- Although molecular data in higher HIV-morbidity states have been analyzed ( 1 - 3 ), few analyses exist for lower morbidity states ( 4 ), such as Wisconsin, which reported 4.6 HIV diagnoses per 100,000 persons aged ≥13 years in 2016 ( 5 ). (cdc.gov)
Laboratory3
- This chapter discusses the principle and the essential technical elements in performing nested PCR DNA amplification for the detection of HPV from clinical specimens and short target sequence genotyping for HPV, using standard molecular biology laboratory equipment and commercially available reagents. (nih.gov)
- The authors use standard Health Level 7 laboratory result message formats in conjunction with international standards, Systematized Nomenclature of Medicine Clinical Terms and Human Genome Variant Society nomenclature, to represent, communicate, and store discrete gene sequence data within the EHR in a scalable fashion. (elsevier.com)
- The Operating Innovative Networks (OIN) workshop series is designed to equip university and laboratory network engineers with the knowledge and training needed to build next-gen campus networks that are optimized for data-intensive science. (globus.org)
MeSH1
- Important Note: As of October 2016, the publisher of the original article has the capability to edit the citation data in the PubMed record using the PubMed Data Management system, with the exception of MeSH data . (nih.gov)
Methods9
- Items related to Deep Sequencing Data Analysis (Methods in Molecular. (abebooks.com)
- Effectively, when carefully planned, any experimental question which can be translated into reading nucleic acids can be applied.In Deep Sequencing Data Analysis , expert researchers in the field detail methods which are now commonly used to study the multi-facet deep sequencing data field. (abebooks.com)
- Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible protocols, and key tips on troubleshooting and avoiding known pitfalls. (abebooks.com)
- When sequenced on the Illumina platform, the resulting libraries yielded NGS sequence data indistinguishable from the labor-intensive methods previously employed by the facility. (businesswire.com)
- 2008. (Methods in Molecular Biology, Volume 452). (koeltz.com)
- Using tree construction, MDS, and newly developed likelihood assignment methods on the original 100 samples we sequenced, and also on a set of blinded samples, we were able to predict demographic/risk group membership at a rate statistically better than by chance alone. (washington.edu)
- It includes an introductory section suitable for readers that are new to the field, a section discussing practical methods for data analysis, and more specialized sections discussing specific models and addressing statistical issues relating to estimation and model choice. (springer.com)
- It is my hope that it will also help the 'wet lab' molecular evolutionist to better understand mathematical and statistical methods. (springer.com)
- These membranes are then probed as many times as there are types of tags in the original pools, producing, in each cycle of probing, autoradiographs similar to those from standard DNA sequencing methods. (harvard.edu)
Cohort1
- Because of the ongoing advancements of molecular based oncology, this trial allows a detailed focus on molecular testing as part of any cohort. (clinicaltrials.gov)
Life Sciences1
- Thought leaders will discuss the convergence of cloud computing and big data to support life sciences research. (globus.org)