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Genomics & Informatics

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https://read.qxmd.com/read/30602101/opinion-strategy-of-semi-automatically-annotating-full-text-corpus-of-genomics-amp-informatics
#1
Hyun-Seok Park
There is a community need for an annotated corpus consisting of the full texts of biomedical journal articles. In response to community needs, a prototype version of full text corpus of Genomics & Informatics, called GNI version 1.0 has been recently published, with 499 annotated full text articles available as a corpus resource. However, GNI needs to be updated, as the texts were shallow-parsed, and annotated with several existing parsers. I list issues associated with upgrading annotations, and give opinion on methodology to develop next version of GNI corpus based on a semi-automatic strategy for more linguistically rich corpus annotation...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602100/integration-of-a-large-scale-genetic-analysis-workbench-increases-the-accessibility-of-a-high-performance-pathway-based-analysis-method
#2
Sungyoung Lee, Taesung Park
The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset-namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602099/hiscom-ggi-software-for-hierarchical-structural-component-analysis-of-gene-gene-interactions
#3
Sungkyoung Choi, Sungyoung Lee, Taesung Park
Gene-gene interaction (GGI) analysis is known to play an important role in explain missing heritability issue. Many previous studies have already proposed software to analyze GGI, but most methods focus on a binary phenotype in case-control design. In this study, we developed 'Hierarchical structural CoMponent analysis of Gene-Gene Interactions' (HisCoM-GGI) software for gene-gene interaction analysis with a continuous phenotype. The HisCoM-GGI method considers hierarchical structural relationships between genes and SNPs, that enables both gene-level and SNP-level interaction analysis in a single model...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602098/efmdr-fast-an-application-of-empirical-fuzzy-multifactor-dimensionality-reduction-for-fast-execution
#4
Sangseob Leem, Taesung Park
Gene-gene interaction is a key factor to explain the missing heritability. Many methods have been proposed to identify gene-gene interactions. Multi-factor dimensionality reduction (MDR) is a well-known method for gene-gene interaction detection by reduction from genotypes of SNP combination to a binary variable with a value of high risk or low risk. This method is widely expanded to own a specific objective. Among those expansions, fuzzy-MDR used the fuzzy-set theory for the membership of high risk or low risk and increase the detection rates of gene-gene interactions...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602097/coex-seq-convert-a-variety-of-measurements-of-gene-expression-in-rna-seq
#5
Sang Cheol Kim, Donghyeon Yu, Seong Beom Cho
Next generation sequencing (NGS), a high-throughput DNA sequencing technology, is widely used for molecular biological studies. In NGS, RNA-sequencing (RNA-Seq), which is a short-read massively parallel sequencing, is a major quantitative transcriptome tool for different transcriptome studies. To utilize the RNA-Seq data, various quantification and analysis methods have been developed to solve specific research goals, including identification of differentially expressed genes and detection of novel transcripts...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602096/somatic-mutations-from-whole-exome-sequencing-analysis-of-the-patients-with-biliary-tract-cancer
#6
Kyong-Ah Yoon, Sang Myung Woo, Yun-Hee Kim, Sun-Young Kong, Sung-Sik Han, Sang-Jae Park, Woo Jin Lee
Biliary tract cancer (BTC) is one of the rare cancers and associated with poor prognosis. To understand genetic characteristics of BTC, we analyzed whole exome sequencing (WES) data and identified somatic mutations in the patients with BTC. Tumors and matched blood or normal samples were obtained from seven patients with cholangiocarcinoma who were underwent surgical resection. We discovered inactivating mutations of tumor suppressor genes including APC, TP53, and ARID1A genes in three patients. Activating mutations of KRAS and NRAS were also identified...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602095/rna-seq-de-novo-assembly-and-differential-transcriptome-analysis-of-korean-medicinal-herb-cirsium-japonicum-var-spinossimum
#7
Neha Samir Roy, Jung-A Kim, Ah-Young Choi, Yong-Wook Ban, Nam-Il Park, Kyong-Cheul Park, Hee-Sun Yang, Ik-Young Choi, Soonok Kim
Cirsium japonicum belongs to the Asteraceae or Compositae family and is a medicinal plant in Asia that has a variety of effects, including tumour inhibition, improved immunity with flavones, and antidiabetic and hepatoprotective effects. Silymarin is synthesized by 4-coumaroyl-CoA via both the flavonoid and phenylpropanoid pathways to produce the immediate precursors taxifolin and coniferyl alcohol. Then, the oxidative radicalization of taxifolin and coniferyl alcohol produces silymarin. We identified the expression of genes related to the synthesis of silymarin in C...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602094/multi-block-analysis-of-genomic-data-using-generalized-canonical-correlation-analysis
#8
Inyoung Jun, Wooree Choi, Mira Park
Recently, there have been many studies in medicine related to genetic analysis. Many genetic studies have been studied to find genes associated with complex diseases. To find out how genes are related to disease, we need to understand not only the simple relationship of genotypes but also the way they are related to phenotype. Multi-block data, which is summation form of variable sets, is used for enhancing analysis of different block's relationship. By identifying relationships through multi-block data form, we can understand the association between the blocks is effective in understanding the correlation between them...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602093/ovarian-cancer-prognostic-prediction-model-using-rna-sequencing-data
#9
Seokho Jeong, Lydia Mok, Yong-Sang Song, TaeJin Ahn, Taesung Park
Ovarian cancer is one of the leading causes of cancer-related deaths in gynecologic malignancies. Over 70 % of ovarian cancer cases are high-grade serous ovarian cancers (HGSC) and have high death rates due to their resistance to chemotherapy. Despite advances in surgical and pharmaceutical therapies, overall survival rates are not good and accurate prediction of prognosis is not easy because of the highly heterogeneous nature of ovarian cancer. To improve patient's prognosis through proper treatment, we present a prognostic prediction model by integrating the high dimensional RNA sequencing data with their clinical data through the following steps: (1) gene filtration, (2) pre-screening, (3) gene marker selection (4) integrated study of selected gene markers and prediction model building...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602092/metabolic-syndrome-prediction-using-machine-learning-models-with-genetic-and-clinical-information-from-a-nonobese-healthy-population
#10
Eun Kyung Choe, Hwanseok Rhee, Seungjae Lee, Eunsoon Shin, Seung-Won Oh, Jong-Eun Lee, Seung Ho Choi
The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of nonobese Koreans through machine learning methods. A prediction model for MS was designed for a nonobese population using clinical and genetic polymorphism information with five machine learning algorithms, including naïve Bayes classification (NB). The analysis was performed in two stages (training and test sets)...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602091/storing-digital-information-in-the-long-read-dna
#11
TaeJin Ahn, Hamin Ban, Hyunsoo Park
There is urgent need in effective and cost-efficient data storage as worldwide requirement of data storage rapidly growing. DNA has introduced a new tool for storing digital information. Recent studies successfully store digital information such as text and gif animation. Previous studies tackle technical hurdles due to errors from DNA synthesis and sequencing. Studies also have focused on the strategy which makes use of 100-150 bps of read size in both synthesis and sequencing. In this paper, we suggest novel data encoding / decoding scheme which makes use of long read DNA (~1,000bp)...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602090/a-universal-analysis-pipeline-of-hybrid-capture-based-targeted-sequencing-data-with-unique-molecular-indexes-umis
#12
Min-Jung Kim, Si-Cho Kim, Young-Joon Kim
Hybrid capture-based targeted sequencing is increasingly used for genomic variants profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing PCR biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various studying groups for their own purpose...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602089/stadium-species-specific-trna-adaptive-index-compendium
#13
Jonghwan Yoon, Yeun-Jun Chung, Minho Lee
Due to the increasing interest in synonymous codons, several codon bias-related terms were introduced. As one measure of them, the tRNA adaptation index (tAI) was invented about a decade ago. The tAI is a measure of translational efficiency for a gene and is calculated based on the abundance of intracellular tRNA and the binding strength between a codon and a tRNA. The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602088/a-short-report-on-the-markov-property-of-dna-sequences-on-200-bp-genomic-units-of-roadmap-genomics-chromhmm-annotations-a-computational-perspective
#14
Hyun-Seok Park
The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602087/functional-prediction-of-hypothetical-proteins-from-shigella-flexneri-and-validation-of-the-predicted-models-by-using-roc-curve-analysis
#15
Md Amran Gazi, Sultan Mahmud, Shah Mohammad Fahim, Mohammad Golam Kibria, Parag Palit, Md Rezaul Islam, Humaira Rashid, Subhasish Das, Mustafa Mahfuz, Tahmeed Ahmeed
Shigella spp. constitutes some of the key pathogens responsible for the global burden of diarrhoeal disease. With over 164 million reported cases per annum, shigellosis accounts for 1.1 million deaths each year. Majority of these cases occur among the children of the developing nations and the emergence of multi-drug resistance Shigella strains in clinical isolates demands the development of better/new drugs against this pathogen. The genome of Shigella flexneri was extensively analyzed and found 4,362 proteins among which the functions of 674 proteins, termed as hypothetical proteins (HPs) had not been previously elucidated...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602086/circulating-hotair-rna-is-potentially-up-regulated-in-coronary-artery-disease
#16
Niloofar Avazpour, Mohammadreza Hajjari, Saeed Yazdankhah, Azita Sahni, Ali Mohammad Foroughmand
Coronary artery disease (CAD) is one of the leading causes of death and disability all around the world. Recent studies have revealed that aberrantly regulated long non-coding RNA (lncRNA) as one of the main classes of cellular transcript play a key regulatory role in transcriptional and epigenetic pathways. Recent reports have demonstrated circulating long noncoding RNAs in blood can be potential biomarkers for CAD. HOTAIR is one of the most cited lncRNAs with a critical role in initiation and progression of the gene expression regulation...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602085/evaluation-of-16s-rrna-databases-for-taxonomic-assignments-using-mock-community
#17
Sang-Cheol Park, Sungho Won
Taxonomy identification is fundamental to all microbiology studies. Particularly in metagenomics, which identify the composition of microorganisms using thousands of sequences, its importance is even greater. Identification is inevitably affected by the choice of database. This study was conducted to evaluate the accuracy of three widely used 16S databases, Greengenes, Silva, and EzBioCloud, and to suggest basic guidelines for selecting reference databases. Using public mock community data, each database was used to assign taxonomy and to test its accuracy...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602084/identification-of-viral-taxon-specific-genes-vtsg-application-to-caliciviridae
#18
Shinduck Kang, Young-Chang Kim
Virus taxonomy was initially determined by clinical experiments based on phenotype. However, with the development of sequence analysis methods, genotype-based classification was also applied. With the development of genome sequence analysis technology, there is an increasing demand for virus taxonomy to be extended from in vivo and in vitro to in silico. In this study, we verified the consistency of the current ICTV taxonomy using an in silico approach, aiming to identify the specific sequence for each virus...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602083/the-genome-based-virus-taxonomy-with-ictv-database-extension
#19
Shinduck Kang, Young-Chang Kim
In 1966, the International Classification of Viruses (ICNV) was established to standardize the naming of viruses. In 1975, the organization was renamed 'ICTV', by which it is still known today. The primary virus classification provided by ICTV in 1971 was for viruses infecting vertebrates, which includes 19 genera, 2 families, and a further 24 unclassified groups. Presently, the 10th virus taxonomy has been published. However, early classification of viruses was based on the clinical results of "in vivo" and "in vitro", as well as on the shape of PhynoType virus...
December 2018: Genomics & Informatics
https://read.qxmd.com/read/30602082/an-advanced-understanding-of-uterine-microbial-ecology-associated-with-metritis-in-dairy-cows
#20
Soo Jin Jeon, Klibs N Galvão
Metritis, the inflammation of the uterus caused by polymicrobial infections, is a prevalent and costly disease to the dairy industry as it decreases milk yield, survival, and the welfare of dairy cows. Although the antibiotic ceftiofur is widely used for the treatment of metritis, endometrium and ovary function is compromised, resulting in subfertility and infertility. According to culture-dependent studies, uterine pathogens include Escherichia coli, Trueperella pyogenes, Fusobacterium necrophorum, and Prevotella melaninogenica...
December 2018: Genomics & Informatics
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