Analyzing `omics data using hierarchical models
... Figure 1 Hierarchical modeling. (a) Many analysis techniques, such as t-statistics, consider each gene separately. Owing to different sources of biological and experimental variation, if triplicate measurements of the expression of the same gene are collected twice (blue dots and orange dots), the m ...
... Figure 1 Hierarchical modeling. (a) Many analysis techniques, such as t-statistics, consider each gene separately. Owing to different sources of biological and experimental variation, if triplicate measurements of the expression of the same gene are collected twice (blue dots and orange dots), the m ...
Meta-analysis of Prefrontal Cortex from Acute Ethanol Studies
... Webgestalt, a gene analysis toolkit, was used to further organize the genes. One of the most useful tools on this website is the Boolean operation tool which allows the intersection of two data sets. The gene ontology enriched DAG (directed acyclic graph) was used to place the genes in the myelin ge ...
... Webgestalt, a gene analysis toolkit, was used to further organize the genes. One of the most useful tools on this website is the Boolean operation tool which allows the intersection of two data sets. The gene ontology enriched DAG (directed acyclic graph) was used to place the genes in the myelin ge ...
Life: The Science of Biology, 8e
... STRs are recognizable if they lie between two restriction sites. Several different STRs can be used to determine the unique pattern for an individual. ...
... STRs are recognizable if they lie between two restriction sites. Several different STRs can be used to determine the unique pattern for an individual. ...
Biol 178 Exam4 Study Guide – DNA and Molecular
... 45. Gel _________ is a process that separates DNA or protein fragments according to their size, by causing them to migrate within a gel in response to an electric field. 46. In addition to bacteria, _______ can also be used as vectors to insert foreign DNA into host cells and create recombinant geno ...
... 45. Gel _________ is a process that separates DNA or protein fragments according to their size, by causing them to migrate within a gel in response to an electric field. 46. In addition to bacteria, _______ can also be used as vectors to insert foreign DNA into host cells and create recombinant geno ...
European workshop on Phenotype MicroArrays
... welcome to everyone participating in the 3rd Florence Conference that will take place from Thursday afternoon until Saturday lunchtime (September 1012, 2015). The title of this year’s event “Florence Conference on Phenotype MicroArray Analysis of Cells” reflects our aspiration to provide an opportun ...
... welcome to everyone participating in the 3rd Florence Conference that will take place from Thursday afternoon until Saturday lunchtime (September 1012, 2015). The title of this year’s event “Florence Conference on Phenotype MicroArray Analysis of Cells” reflects our aspiration to provide an opportun ...
The effect of DNA phase structure on DNA walks
... obvious that these walks do not distinguish between coding and non-coding strands. Both strands have exactly the same composition and the results don’t depend on the direction of the walk. Nevertheless, it was observed in several genomes that coding regions have higher (G + C)/(A + T ) ratio than th ...
... obvious that these walks do not distinguish between coding and non-coding strands. Both strands have exactly the same composition and the results don’t depend on the direction of the walk. Nevertheless, it was observed in several genomes that coding regions have higher (G + C)/(A + T ) ratio than th ...
Identification and Characterization of a Novel Human Testis
... the same study, tssk2 was found to be the orthologue of the human DGS-G gene, whose deletion is suspected to be involved in the pathogenesis of Di George and velocardiofacial syndromes (8). In this report we describe analysis of an area spanning approximately 100 kb of contiguous DNA sequence on hum ...
... the same study, tssk2 was found to be the orthologue of the human DGS-G gene, whose deletion is suspected to be involved in the pathogenesis of Di George and velocardiofacial syndromes (8). In this report we describe analysis of an area spanning approximately 100 kb of contiguous DNA sequence on hum ...
Tutorial 7: Constructing new databases using ARB
... ARB is most frequently utilized for management and analysis of SSU rRNA gene data, but it can be a very useful tool to align, manage, and compare sequence data from other genes. The features used for analysis of SSU rRNA genes are very similar as to working with other genes, but one difference is th ...
... ARB is most frequently utilized for management and analysis of SSU rRNA gene data, but it can be a very useful tool to align, manage, and compare sequence data from other genes. The features used for analysis of SSU rRNA genes are very similar as to working with other genes, but one difference is th ...
Male Latex Condom: Specification, Prequalification and Guidelines
... are made from the samples. Then measured drops are placed on the agar surface. A minimum of five separated drops from each dilution is required. Plates are allowed to dry and are incubated, and counts are made. When large sample volumes are available, particularly as in the case of water testing, th ...
... are made from the samples. Then measured drops are placed on the agar surface. A minimum of five separated drops from each dilution is required. Plates are allowed to dry and are incubated, and counts are made. When large sample volumes are available, particularly as in the case of water testing, th ...
Evolution of Gene Expression
... genome simultaneously. Today, microarrays are largely being replaced by a method known as RNA-seq that uses massively parallel sequencing to obtain quantitative measures of gene expression (i.e., RNA abundance). Techniques for measuring protein abundance (which is not always highly correlated with R ...
... genome simultaneously. Today, microarrays are largely being replaced by a method known as RNA-seq that uses massively parallel sequencing to obtain quantitative measures of gene expression (i.e., RNA abundance). Techniques for measuring protein abundance (which is not always highly correlated with R ...
GIN Transposons: Genetic Elements Linking Retrotransposons and
... of species that contain GIN2, it was not possible to confirm this result due to lack of data. In any case, the combined evidence indicates that GIN2 is an ancient gene, perhaps even more ancient than GIN1 given its presence in fishes, and that GIN1 and GIN2 are paralogs. The fact that GIN2 was not d ...
... of species that contain GIN2, it was not possible to confirm this result due to lack of data. In any case, the combined evidence indicates that GIN2 is an ancient gene, perhaps even more ancient than GIN1 given its presence in fishes, and that GIN1 and GIN2 are paralogs. The fact that GIN2 was not d ...
Low Levels of Nucleotide Diversity at Homoeologous Adh Loci in
... Levels and patterns of genetic diversity vary greatly within and among populations and species. This variation reflects the interplay of myriad historical factors and evolutionary forces, involving external forces such as natural selection, population size and history, gene flow, and breeding system ...
... Levels and patterns of genetic diversity vary greatly within and among populations and species. This variation reflects the interplay of myriad historical factors and evolutionary forces, involving external forces such as natural selection, population size and history, gene flow, and breeding system ...
DNA shuffling by random fragmentation and reassembly: In
... 3 s per cycle. Gel analysis showed that most of the PCR product was >>20 kb. After digestion with a unique enzyme (EcoO109), most of the product consisted of a single band of the expected size, which was gel purified, ligated, transformed, and plated on LB/ampicillin/X-Gal plates as described above. ...
... 3 s per cycle. Gel analysis showed that most of the PCR product was >>20 kb. After digestion with a unique enzyme (EcoO109), most of the product consisted of a single band of the expected size, which was gel purified, ligated, transformed, and plated on LB/ampicillin/X-Gal plates as described above. ...
Exercises
... length between 10,000 and 20,000. Go to the protein database, select the "sequence length" field, and enter "010000:020000" (The leading zero is necessary because the sequence length terms are all six-digit integers. When in doubt, use "List terms" to see the terms in a list; the range operator will ...
... length between 10,000 and 20,000. Go to the protein database, select the "sequence length" field, and enter "010000:020000" (The leading zero is necessary because the sequence length terms are all six-digit integers. When in doubt, use "List terms" to see the terms in a list; the range operator will ...
Bacterial but not protist gut microbiota align with ecological
... not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. ...
... not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. ...
slides
... another organism in its genome is called a “transgenic organism” Thus, a bacterium with a piece of human DNA in it is a transgenic bacterium! A plant engineered to contain a piece of DNA from another organism is also transgenic: we ...
... another organism in its genome is called a “transgenic organism” Thus, a bacterium with a piece of human DNA in it is a transgenic bacterium! A plant engineered to contain a piece of DNA from another organism is also transgenic: we ...
Unsuitability of Using Ribosomal RNA as Loading Control for
... hours. The X-ray films were digitized using a transmission scanner and densitometry of the scanned images was performed using the Gel Doc 2000 image analyzer system and the Quantity One software system (BioRad, Spain). The capture and densitometry of the ethidium bromide-stained gel image were also ...
... hours. The X-ray films were digitized using a transmission scanner and densitometry of the scanned images was performed using the Gel Doc 2000 image analyzer system and the Quantity One software system (BioRad, Spain). The capture and densitometry of the ethidium bromide-stained gel image were also ...
rpoB gene sequence-based characterization of emerging non
... Over the past 10 years, 16S rRNA gene sequencing has contributed to the establishment of more than 45 novel species of non-tuberculous mycobacteria and to the description of emerging mycobacterial infections. Cumulative experience has indicated that this molecular tool underestimates the diversity o ...
... Over the past 10 years, 16S rRNA gene sequencing has contributed to the establishment of more than 45 novel species of non-tuberculous mycobacteria and to the description of emerging mycobacterial infections. Cumulative experience has indicated that this molecular tool underestimates the diversity o ...
Document
... Utilise known structure/function information to infer facts related to the predicted protein sequence Provide users with results from a number of standard algorithms/searches Provide users with cross-references (dbxrefs) to other resources Assign a simple one line description for each gene product ...
... Utilise known structure/function information to infer facts related to the predicted protein sequence Provide users with results from a number of standard algorithms/searches Provide users with cross-references (dbxrefs) to other resources Assign a simple one line description for each gene product ...
bioinformatics review - e
... Summary: Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Cur ...
... Summary: Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Cur ...
Expanding Yeast Knowledge Online.
... FTP. An interesting example is the Mammalian Homology to Yeast table, which allows users to view the results of a BLAST search comparing each yeast protein to all unique human, mouse, rat, cow and sheep protein sequences from a recent version of GenBank. The results are summarized in tables that con ...
... FTP. An interesting example is the Mammalian Homology to Yeast table, which allows users to view the results of a BLAST search comparing each yeast protein to all unique human, mouse, rat, cow and sheep protein sequences from a recent version of GenBank. The results are summarized in tables that con ...
Haritsa - CSE, IIT Bombay
... Limitations: RDBMS approach of “the world is a flat collection of tables with simple attributes” suits financial applications, NOT scientific (biological) applications In particular, taxonomic / spatial / sequence / multimedia data modeling and processing are very cumbersome and coarse BODHI ...
... Limitations: RDBMS approach of “the world is a flat collection of tables with simple attributes” suits financial applications, NOT scientific (biological) applications In particular, taxonomic / spatial / sequence / multimedia data modeling and processing are very cumbersome and coarse BODHI ...
Genetic Engineering and Biotechnology
... studying the genes responsible for the specialized functions of a particular cell type, such as brain or liver cells. And because cDNAs lack introns, they are shorter than the full versions of the genes, and therefore easier to work with. ...
... studying the genes responsible for the specialized functions of a particular cell type, such as brain or liver cells. And because cDNAs lack introns, they are shorter than the full versions of the genes, and therefore easier to work with. ...
Diapositive 1 - Institut Pasteur
... ● Although deletion analyses of PE/PPE genes were accompanied with phenotypic characteristics, the detailed molecular mechanisms responsible for the observed effects remain to be demonstrated ...
... ● Although deletion analyses of PE/PPE genes were accompanied with phenotypic characteristics, the detailed molecular mechanisms responsible for the observed effects remain to be demonstrated ...
RNA Structure, Function, and Synthesis RNA - Rose
... Template strand: the DNA sequence that the polymerase actually uses to guide the synthesis of the growing RNA strand. The template strand is complementary to both the RNA strand and the DNA coding strand. Upstream: on the 5´side of any given position on the coding strand. Downstream: on the 3´side o ...
... Template strand: the DNA sequence that the polymerase actually uses to guide the synthesis of the growing RNA strand. The template strand is complementary to both the RNA strand and the DNA coding strand. Upstream: on the 5´side of any given position on the coding strand. Downstream: on the 3´side o ...
Metagenomics
Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either ""shotgun"" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.