1,833,801 research outputs found
Additional file 1 of Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types
No full text<b>External Organisations</b><br/>Sharif University of Technology; University of Toronto; Macquarie University; University of New South Wales (UNSW); Rutgers University<b>Associated Persons</b><br/>Amin Ghareyazi (Creator); Amirreza Kazemi (Creator); Kimia Hamidieh (Creator); Hamed Dashti (Creator); Maedeh Sadat Tahaei (Creator); Hamid R. Rabiee (Creator); Iman Dehzangi (Creator)Additional file 1: Table S1. Complete list of candidate genes with their corresponding P-value for each cancer type separately. Table S2. Complete list of samples with their cancer type and identified subtypes. Table S3. Contribution of each cancer type in proposed cancer subtypes. Table S4. Top 100 significant genes with their corresponding P-value for each subtype separately. Table S5. Top 100 significant gene-motifs with their corresponding P-value for each subtype separately. Table S6: Full list of all enriched gene ontology associated with our identified subtypes. Sheet2: Full list of all enrich pathways associated with our identified subtypes. Table S7. Similarity of Cosmic Signatures and Pan-cancer subtypes
Additional file 1 of Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types
No full text<b>External Organisations</b><br/>Sharif University of Technology; Simon Fraser University; University of Toronto; Macquarie University; University of New South Wales (UNSW); Rutgers University<b>Associated Persons</b><br/>Amin Ghareyazi (Creator); Amirreza Kazemi (Creator); Kimia Hamidieh (Creator); Hamed Dashti (Creator); Maedeh Sadat Tahaei (Creator); Hamid R. Rabiee (Creator); Iman Dehzangi (Creator)Additional file 1: Table S1. Complete list of candidate genes with their corresponding P-value for each cancer type separately. Table S2. Complete list of samples with their cancer type and identified subtypes. Table S3. Contribution of each cancer type in proposed cancer subtypes. Table S4. Top 100 significant genes with their corresponding P-value for each subtype separately. Table S5. Top 100 significant gene-motifs with their corresponding P-value for each subtype separately. Table S6: Full list of all enriched gene ontology associated with our identified subtypes. Sheet2: Full list of all enrich pathways associated with our identified subtypes. Table S7. Similarity of Cosmic Signatures and Pan-cancer subtypes
DNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era
No full textBackground: Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples. Using reference genomes for each breed from the Bovine Pangenome Consortium, we investigated the influence of reference genome choice on the breed and parent-of-origin effects in methylome analyses. Results: Our findings revealed that ∼75% of CpG sites were shared between Angus and Brahman, ∼5% were breed specific, and ∼20% were unresolved. We demonstrated up to ∼2% quantification bias in global methylation when an incorrect reference genome was used. Furthermore, we found that SNPs impacted CpGs 13 times more than other autosomal sites (P < 5 × 10−324) and SVs contained 1.18 times (P < 5 × 10−324) more CpGs than non-SVs. We found a poor overlap between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) and suggest that DMRs may be impacting enhancers that target these DEGs. DMRs overlapped with imprinted genes, of which 1, DGAT1, which is important for fat metabolism and weight gain, was found in the breed-specific and sire-of-origin comparisons. Conclusions: This work demonstrates the need to consider reference genome effects to explore genetic and epigenetic differences accurately and identify DMRs involved in controlling certain genes.Callum MacPhillamy, Tong Chen, Stefan Hiendleder, John L. Williams, Hamid Alinejad-Rokny, and Wai Yee Lo
A Method to Avoid Gapped Sequential Patterns in Biological Sequences: Case Study: HIV and Cancer Sequences
No full textHamid Tibouchi, Portées (extraits)
No full textTibouchi Hamid. Hamid Tibouchi, Portées (extraits). In: Horizons Maghrébins - Le droit à la mémoire, N°49, 2003. Conte, conteurs et néo-conteurs. Usages et pratiques du conte et de l'oralité entre les deux rives de la Méditerranée. pp. 73-80
Artificial Intelligence, Bioinformatic and Systems Biology Approaches to Understanding Genome Evolution and Viral Control
No full textHuman immunodeficiency virus (HIV) continues to be a major global health problem. Decades of research have still not produced a successful vaccine and understanding many aspects of this virus and HIV infection continues to challenge researchers. In this thesis I have addressed several key questions about HIV biology and infection using a computational biology approach.
Macaque models of HIV infection play an important role in HIV research and yet the viral peptides presented by MHC Class-I and recognised by cytotoxic T-lymphocytes (CTL) in macaques are not well characterised. I developed an in-house bioinformatics pipeline to investigate novel CTL epitopes and their associated patterns of escape mutations in pigtailed macaques. I identified new potential CTL epitopes and numerous novel non-synonymous point mutations and regions of non-synonymous mutation associated with specific MHC-I haplotypes.
I also investigated the nature and distribution of APOBEC3-induced hypermutation signatures and whether this information provides clues about the HIV inhibition by different APOBEC3 enzymes such as APOBEC3G and APOPEC3F. I developed a new method for hypermutation detection. I also used a novel approach to identify preferential patterns of G-to-A mutation for both APOBEC3G and APOBEC3F.
The source of CpG depletion in the HIV genome is another aspect of HIV biology that is not well understood. My bioinformatics analyses suggest that the methylation mechanism may be responsible for depletion of CpG dinucleotides in the HIV genome. Importantly, the results showed that viral genome adaptation to the host CpG machinery is a highly specific pattern that is only observed in HIV and its simian counterpart, SIV.
The thesis finally reports a meta-analysis approach to investigate the effect of gene expression level on the clonal expansion process of latently-infected cells during HIV treatment. The results of this analysis show that among the HIV proviruses that integrated into genes, those integrated into poorly expressed genes are more likely to become clonally expanded.
In conclusion, my findings shed light on several important components of the host immune system and their roles in viral control and viral evolution. These findings have implications for the future design of immunotherapies and vaccines against HIV
Genetic and Epigenetic Regulation in Angus and Brahman Cattle
No full textAngus and Brahman cattle represent two economically important subspecies of cattle with contrasting phenotypes. The Angus cattle breed is representative of the taurine subspecies and has been bred for excellent meat production traits, and the Brahman cattle breed is representative of the indicine subspecies and has been bred for its ability to thrive in harsh conditions. Knowledge of genetic regulation is fundamental to our understanding of what causes these contrasting phenotypes in cattle breeds. Gene regulatory differences can arise because of genetic and epigenetic differences among the breeds, which can shed light on what contributes to the different phenotypes. Despite this knowledge being crucial to understanding how complex traits are controlled, relatively little is known about genetic and epigenetic regulatory differences between the cattle subspecies. This thesis investigated genetic and epigenetic differences between cattle subspecies by using Angus to represent taurine cattle and Brahman to represent indicine cattle in an effort to elucidate factors responsible for their distinct phenotypes. Enhancers are a key genetic regulatory element, but relatively little is known about this DNA element in the cattle genome. The performance of nine machine learning (ML) models and four DNA representations was evaluated to determine the best combination to predict enhancers across species to cattle using models trained on high-quality enhancers in human and mouse. To evaluate the usefulness of cross-species prediction in general, the ML models were also applied to find pig and dog enhancers. For identifying enhancers in cattle, pig and dog, the combination of convolutional neural networks and one-hot encoding to represent the DNA sequence performed the best. They predicted a similar proportion of enhancers in these genomes as what has been estimated to be the proportion of enhancers in the human genome. Whole genome bisulfite sequencing (WGBS) data was generated from Brahman, Angus and reciprocally crossed progeny using fetal liver samples to investigate differential methylation between the Brahman and Angus breeds. The reciprocal crosses were used to investigate the parent-of-origin effects on DNA methylation to determine what role dam and sire genetics had on the progeny's methylome. As breed-specific reference genomes are available for Brahman and Angus, the impact of reference genome choice was investigated to determine how this affects downstream analyses. The methylation analysis identified tens of thousands of differentially methylated regions (DMRs) that were breed-specific and parent-of-origin-specific. One of the DMRs may be controlling the expression of Dgat1 in a breed and sire-of-origin manner. Genome comparison revealed around 75% of CpGs were shared between Brahman and Angus, with around 5% (~one million CpGs) being breed-specific. Moreover, single nucleotide polymorphisms (SNPs) and structural variants (SVs) between Brahman and Angus were 8-fold (p-value < 0.05) and 1.13-fold (p-value < 0.05) higher in CpGs, respectively, and a quantification bias of 2% was observed when the incorrect reference genome was used for analysis. MicroRNA (miRNA) expression data was generated from the same samples that were used to generate WGBS data. This expression data was used to identify differentially expressed, breed-specific and parent-of-origin-specific miRNAs. Fourteen differentially expressed miRNAs (DEMs) were observed between the breeds, with the dam-of-origin and sire-of-origin comparisons identifying one and five DEMs, respectively. Genes that were predicted to be targets of the DEMs were significantly (p-value <0.05) more likely to be differentially expressed than genes not predicted to be targets of the DEMs. The expression of these miRNAs was then correlated with mRNA expression from the same samples and used to identify gene regulatory pathways that may be under microRNA control. MiRNAs that may be involved in regulating heat tolerance in Brahman and fat gain in Angus were identified, as well as a series of signalling pathways that, through differential gene regulation, may contribute to phenotypic differences between Brahman and Angus cattle. Overall, this thesis identified genetic and epigenetic regions of interest between Brahman and Angus that can help shed light on the causes of the contrasting phenotypes observed between Brahman and Angus cattle. This information will benefit future functional studies that look to pinpoint causative elements controlling these traits.Thesis (Ph.D.) -- University of Adelaide, School of Animal and Veterinary Sciences, 202
Cioccolato Jar / Imran Abdul Hamid @ Hamid
No full textCioccolato Jar is a business that are selling Choco jar of multiple types as their main product. The types of Choco jar that Cioccolato Jar sell are original Cioccolato jar which use melted milk chocolate as their base and Cioccolato White which use melted white chocholate. Both types come with 2 choice of cereal which is bubble rice and baby crunch. Cioccolato Jar Products are suitable for everyone regardless of their age and gender as it does not contain any harmful ingredients. For now, Our Target market are teenagers and kids as they tend to like sweet snacks.
Cioccolato Jar currently operates in Klang and through online only. This due to Cioccolato Jar is fully operates from the home of the founder. Cioccolato Jar is promoting their products on Facebook. Currently our Facebook page has reached 133 total likes. We are expecting the number to grow in the future.
Cioccolato Jar is owned and managed by Imran Bin Abdul Hamid @ Hamid, a student of UiTM Selangor. He is the sole founder of Cioccolato and he alone produce all the products by himself. Imran manages the business from home and provide delivery across all states in Malaysia including Sabah and Sarawak by using the courier service such as J&t Express and Dhl eCommerce. In the future, we expect this business to grow successfully as the demand of the chocojar are high and chocolate is the most favored snacks for all layer of generations
Indonesiaku: sepilihan sajak Hamid Jabbar
No full textBuku ini berisi puisi-puisi pilihan karya Hamid Jabba
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