factor occupancy and gene expression Effects of
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
factor occupancy and gene expression Effects of sequence variation
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
factor occupancy and gene expression Effects of sequence variation
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
... most allelic differences in occupancy were subtle and associated with disruption of weak or noncanonical motifs. We also measured genome-wide differential allelic expression of genes with and without heterozygous exonic variants in the same cells. We found that genes with differential allelic expres ...
Practice Guidelines for the Molecular Diagnosis of Haemophilia B.
... In some circumstances, despite a family history of haemophilia, neither an index case nor a known obligate carrier may be available. In such cases mutation analysis may still be undertaken in a potential carrier but the report must stress that the failure to identify a causative mutation does not pr ...
... In some circumstances, despite a family history of haemophilia, neither an index case nor a known obligate carrier may be available. In such cases mutation analysis may still be undertaken in a potential carrier but the report must stress that the failure to identify a causative mutation does not pr ...
Proof-of-principle rapid noninvasive prenatal diagnosis
... carriers in addition to the mother in family 2 (Figure 1). For family 1, the N370S carrier father was completely homozygous for the entire consensus N370S sequence. This precluded the use of the N370S haplotype for NIPD of his allele. Nonetheless, the familial mutation-linked haplotype of the father ...
... carriers in addition to the mother in family 2 (Figure 1). For family 1, the N370S carrier father was completely homozygous for the entire consensus N370S sequence. This precluded the use of the N370S haplotype for NIPD of his allele. Nonetheless, the familial mutation-linked haplotype of the father ...
Guidelines for interpretation of 16S rRNA gene sequence
... sharp values were mainly made for practical purposes for interpretation of their large sequence dataset. On the other hand, Janda and Abbott suggested that a minimum of .99 %, and ideally .99.5 %, sequence similarity be used for species identification in their recommended guidelines (Janda & Abbott, ...
... sharp values were mainly made for practical purposes for interpretation of their large sequence dataset. On the other hand, Janda and Abbott suggested that a minimum of .99 %, and ideally .99.5 %, sequence similarity be used for species identification in their recommended guidelines (Janda & Abbott, ...
Package `biomartr`
... Description Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interf ...
... Description Perform metagenomic data retrieval and functional annotation retrieval. In detail, this package aims to provide users with a standardized way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interf ...
characterizing the genetic bases of autosomal recessive disorders
... and their families. Elucidating the genetic bases of such disorders is essential to improve their clinical outcome and for implementing effective prevention programs. In this dissertation, the genetic bases of seven autosomal recessive disorders in consanguineous families were investigated using hom ...
... and their families. Elucidating the genetic bases of such disorders is essential to improve their clinical outcome and for implementing effective prevention programs. In this dissertation, the genetic bases of seven autosomal recessive disorders in consanguineous families were investigated using hom ...
The Johns Hopkins University - American University of Beirut
... “reference sequences” for all ‘worked’ genome. • Historically, these used to be referred to as “GenBank-Gold”. • RefSeq are either genomic, mRNA or protein sequences. • Not all sequences are in RefSeq • All RefSeq sequences are assembled/taken from things in GenBank. Lecture 2.2 ...
... “reference sequences” for all ‘worked’ genome. • Historically, these used to be referred to as “GenBank-Gold”. • RefSeq are either genomic, mRNA or protein sequences. • Not all sequences are in RefSeq • All RefSeq sequences are assembled/taken from things in GenBank. Lecture 2.2 ...
Short Tandem Repeat Polymorphism and Cancer Risk: Influence of
... longer CAG repeats are found to be associated with lower risk of prostate cancer. However, not all epidemiologic studies have found evidence in support of this relationship. In a recent article by Giovannucci (2), 12 published studies on this subject were discussed. One third of the studies showed a ...
... longer CAG repeats are found to be associated with lower risk of prostate cancer. However, not all epidemiologic studies have found evidence in support of this relationship. In a recent article by Giovannucci (2), 12 published studies on this subject were discussed. One third of the studies showed a ...
Supporting Information Parfenov et al. 10.1073/pnas.1416074111
... mean-centered the RPKM values and divided by their SD for each exon. The lengths of the composite exons were transformed using the square root of the length. DNA Methylation and mRNA Expression Analysis. The Infinium HM450k array was used for TCGA Head and Neck samples (13). This platform includes p ...
... mean-centered the RPKM values and divided by their SD for each exon. The lengths of the composite exons were transformed using the square root of the length. DNA Methylation and mRNA Expression Analysis. The Infinium HM450k array was used for TCGA Head and Neck samples (13). This platform includes p ...
Relatedness in the post-genomic era: is it still
... lineage paths in pedigrees (BOX 1) provides a mathematically beautiful structure that has historically been useful, but its weaknesses are apparent. Pedigree founders are typically assumed to be unrelated, but this is only realistic in certain settings, such as some designed breeding programmes or a ...
... lineage paths in pedigrees (BOX 1) provides a mathematically beautiful structure that has historically been useful, but its weaknesses are apparent. Pedigree founders are typically assumed to be unrelated, but this is only realistic in certain settings, such as some designed breeding programmes or a ...
Short Tandem Repeat Polymorphism and Cancer Risk: Influence of
... longer CAG repeats are found to be associated with lower risk of prostate cancer. However, not all epidemiologic studies have found evidence in support of this relationship. In a recent article by Giovannucci (2), 12 published studies on this subject were discussed. One third of the studies showed a ...
... longer CAG repeats are found to be associated with lower risk of prostate cancer. However, not all epidemiologic studies have found evidence in support of this relationship. In a recent article by Giovannucci (2), 12 published studies on this subject were discussed. One third of the studies showed a ...
History and Philosophy of Science
... • find matches to those short words and extend them to refine the candidate solution. This strategy accounts for the computational gains that this system makes over others that seek exact comparisons. The continued success of BLAST is attributable to • the speed in which it can find sequence matches ...
... • find matches to those short words and extend them to refine the candidate solution. This strategy accounts for the computational gains that this system makes over others that seek exact comparisons. The continued success of BLAST is attributable to • the speed in which it can find sequence matches ...
Genetic Mosaics and the Germ Line Lineage
... Recent sequencing studies using next-generation sequencing technology have documented that each individual’s genome contains at least 50–100 new point mutations that were not present in the genomes of either parent [25–31]. These are referred to as de novo mutations. Here, point mutations include si ...
... Recent sequencing studies using next-generation sequencing technology have documented that each individual’s genome contains at least 50–100 new point mutations that were not present in the genomes of either parent [25–31]. These are referred to as de novo mutations. Here, point mutations include si ...
a version - SEA
... cluster DO Gordonia phages. There is little nucleotide similarity between Finch and these genomes, but it shares 29-41 phams with each. 22 phams are shared among all of these phages, suggesting they may have a common evolutionary history. Most of these phages appear to be lytic, but we were able to ...
... cluster DO Gordonia phages. There is little nucleotide similarity between Finch and these genomes, but it shares 29-41 phams with each. 22 phams are shared among all of these phages, suggesting they may have a common evolutionary history. Most of these phages appear to be lytic, but we were able to ...
Alu repeat analysis in the complete human genome: trends and
... units separated by a poly ‘A’ stretch. The monomers, homologous to 7SL RNA, are absolutely identical except for a 30 bp insertion in the right monomer (Jelinek et al., 1980; Ullu and Tschudi, 1984). The 3 end of the Alu element has a long stretch of adenine residues, and is flanked by 4–10 bp of di ...
... units separated by a poly ‘A’ stretch. The monomers, homologous to 7SL RNA, are absolutely identical except for a 30 bp insertion in the right monomer (Jelinek et al., 1980; Ullu and Tschudi, 1984). The 3 end of the Alu element has a long stretch of adenine residues, and is flanked by 4–10 bp of di ...
Ensembl variation resources Open Access Database
... which focus either on the whole genome or selected functional regions of the genome such as protein coding regions, regulatory regions or sites of known disease mutations. One of the larger resources includes a comprehensive haplotype map of the human genome created by the International HapMap Proje ...
... which focus either on the whole genome or selected functional regions of the genome such as protein coding regions, regulatory regions or sites of known disease mutations. One of the larger resources includes a comprehensive haplotype map of the human genome created by the International HapMap Proje ...
Characteristics, causes and evolutionary consequences of male
... had evolved a reduced mutation rate, am estimates using Z–A, Z–W or A–W comparisons of chicken–turkey divergence do not differ significantly (Axelsson et al. 2004); had Z rate been reduced for other reasons than male-biased mutation, am estimated from Z–A and Z–W data would be lower than when estima ...
... had evolved a reduced mutation rate, am estimates using Z–A, Z–W or A–W comparisons of chicken–turkey divergence do not differ significantly (Axelsson et al. 2004); had Z rate been reduced for other reasons than male-biased mutation, am estimated from Z–A and Z–W data would be lower than when estima ...
Differential Gene Expression in the Siphonophore
... be full length, some to be missing one or both ends, and others to be fragmentary (i.e., different reference sequences may come from different parts of the same gene). To get multiple independent perspectives on the ability to assess differential expression when ...
... be full length, some to be missing one or both ends, and others to be fragmentary (i.e., different reference sequences may come from different parts of the same gene). To get multiple independent perspectives on the ability to assess differential expression when ...
PDF
... where TP, TN, FP and FN denote number of true positives, true negatives, false positives and false negatives, respecexons with 17% false positives. tively. We find that the accuracy of FirstEF is significantly higher for CpG-related than non-CpG-related genes. To study the performance of FirstEF on ...
... where TP, TN, FP and FN denote number of true positives, true negatives, false positives and false negatives, respecexons with 17% false positives. tively. We find that the accuracy of FirstEF is significantly higher for CpG-related than non-CpG-related genes. To study the performance of FirstEF on ...
Mechanisms and impact of genetic recombination in the evolution of
... [7]. In addition to geography, additional factors including, age, smoking and co-infection with other diseases such as HIV predispose individuals to pneumococcal infections [8]. At least 93 pneumococcal serotypes are known, based on the structure and antigenicity of the pneumococcal polysaccharide c ...
... [7]. In addition to geography, additional factors including, age, smoking and co-infection with other diseases such as HIV predispose individuals to pneumococcal infections [8]. At least 93 pneumococcal serotypes are known, based on the structure and antigenicity of the pneumococcal polysaccharide c ...
Phytic Acid and Inorganic Phosphate Composition in Soybean Lines
... followed by 45 cycles of 95°C for 20 seconds, 56°C for 20 seconds, and 72°C for 20 seconds. A melt curve was performed by reading every 0.2°C for 1 second from 52°C to 77° The wild-type (FN38) peak was present at 65°C, while the alternate (Gm-lpa-ZC2) peak was at 60°C; thus, the heterozygous peaks w ...
... followed by 45 cycles of 95°C for 20 seconds, 56°C for 20 seconds, and 72°C for 20 seconds. A melt curve was performed by reading every 0.2°C for 1 second from 52°C to 77° The wild-type (FN38) peak was present at 65°C, while the alternate (Gm-lpa-ZC2) peak was at 60°C; thus, the heterozygous peaks w ...
Isolation, Characterization, and Annotation: The Search for Novel
... and releasing mature phages from their previous host3. There are an estimated 1031 different bacteriophages on earth, making them one of the most numerous DNA-containing entities in existence4. Our research focuses on the isolation and characterization of mycobacteriophages, dsDNA tailed phages that ...
... and releasing mature phages from their previous host3. There are an estimated 1031 different bacteriophages on earth, making them one of the most numerous DNA-containing entities in existence4. Our research focuses on the isolation and characterization of mycobacteriophages, dsDNA tailed phages that ...
Whole genome sequencing
Whole genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group, and does not contain additional information on genetic relationships, origin or susceptibility to specific diseases. Also unlike full genome sequencing, SNP genotyping covers less than 0.1% of the genome. Almost all truly complete genomes are of microbes; the term ""full genome"" is thus sometimes used loosely to mean ""greater than 95%"". The remainder of this article focuses on nearly complete human genomes.High-throughput genome sequencing technologies have largely been used as a research tool and are currently being introduced in the clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.