keyword
MENU ▼
Read by QxMD icon Read
search

bioinformatics

keyword
https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#1
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into 'best practices' for automated analysis of NGS datasets) still requires significant programming investment and expertise. Results: We present Kronos , a software platform for facilitating the development and execution of modular, auditable and distributable bioinformatics workflows...
June 26, 2017: GigaScience
https://www.readbyqxmd.com/read/28655158/coretracker-accurate-codon-reassignment-prediction-applied-to-mitochondrial-genomes
#2
Noutahi Emmanuel, Calderon Virginie, Blanchette Mathieu, Lang B Franz, El-Mabrouk Nadia
Motivation: Codon reassignments have been reported across all domains of life. With the increasing number of sequenced genomes, the development of systematic approaches for genetic code detection is essential for accurate downstream analyses. Three automated prediction tools exist so far: FACIL, GenDecoder and Bagheera; the last two respectively restricted to metazoan mitochondrial genomes and CUG reassignments in yeast nuclear genomes. These tools can only analyze a single genome at a time and are often not followed by a validation procedure, resulting in a high rate of false positives...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655153/the-ksea-app-a-web-based-tool-for-kinase-activity-inference-from-quantitative-phosphoproteomics
#3
Danica D Wiredja, Mehmet Koyutürk, Mark R Chance
Summary: Computational characterization of differential kinase activity from phosphoproteomics datasets is critical for correctly inferring cellular circuitry and how signaling cascades are altered in drug treatment and/or disease. Kinase-Substrate Enrichment Analysis (KSEA) offers a powerful approach to estimating changes in a kinase's activity based on the collective phosphorylation changes of its identified substrates. However, KSEA has been limited to programmers who are able to implement the algorithms...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28655145/partitioned-learning-of-deep-boltzmann-machines-for-snp-data
#4
Moritz Hess, Stefan Lenz, Tamara J Blätte, Lars Bullinger, Harald Binder
Motivation: Learning the joint distributions of measurements, and in particular identification of an appropriate low-dimensional manifold, has been found to be a powerful ingredient of deep leaning approaches. Yet, such approaches have hardly been applied to single nucleotide polymorphism (SNP) data, probably due to the high number of features typically exceeding the number of studied individuals. Results: After a brief overview of how deep Boltzmann machines (DBMs), a deep learning approach, can be adapted to SNP data in principle, we specifically present a way to alleviate the dimensionality problem by partitioned learning...
June 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28654912/identification-of-dysregulated-long-non-coding-rnas-micrornas-mrnas-in-tnm-i-stage-lung-adenocarcinoma
#5
Ziqiang Tian, Shiwang Wen, Yuefeng Zhang, Xinqiang Shi, Yonggang Zhu, Yanzhao Xu, Huilai Lv, Guiying Wang
Lung adenocarcinoma (LUAD) is the primary subtype in lung cancer, which is the leading cause of cancer-related death worldwide. This study aimed to investigate the aberrant expression profiling of long non-coding RNA (lncRNA) in TNM I stage (stage I) LUAD. The lncRNA/mRNA/miRNA expression profiling of stage I LUAD and adjacent non-tumor tissues from 4 patients were measured by RNA-sequencing. Total of 175 differentially expressed lncRNAs (DELs), 1321 differentially expressed mRNAs (DEMs) and 94 differentially expressed microRNAs (DEMIs) were identified in stage I LUAD...
June 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28654793/pure-total-flavonoids-from-citrus-improve-non-alcoholic-fatty-liver-disease-by-regulating-tlr-ccl-signaling-pathway-a-preliminary-high-throughput-omics-study
#6
Liyan Wu, Maoxiang Yan, Jianping Jiang, Beihui He, Wei Hong, Zhiyun Chen
OBJECTIVE: This study investigated the possible molecular mechanisms of pure total flavonoids from citrus (PTFC) for the treatment of non-alcoholic fatty liver disease (NAFLD) via toll-like receptor/C-C chemokine ligand (TLR/CCL) signaling pathways by monitoring the changes in gene expression profile in liver tissues induced by high-fat diet. METHODS: We performed systematical analyses on hepatic expression profiles of mRNAs in a high-fat diet (HFD)-induced steatotic animal model with or without PTFC treatment...
June 24, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28654728/finding-similar-nucleotide-sequences-using-network-blast-searches
#7
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654712/identifying-significantly-impacted-pathways-and-putative-mechanisms-with-ipathwayguide
#8
Sidra Ahsan, Sorin Drăghici
iPathwayGuide is a gene expression analysis tool that provides biological context and inferences from data generated by high-throughput sequencing. iPathwayGuide utilizes a systems biology approach to identify significantly impacted signaling pathways, Gene Ontology terms, disease processes, predicted microRNAs, and putative mechanisms based on the given differential expression signature. By using a novel analytical approach called Impact Analysis, iPathwayGuide considers the role, position, and relationships of each gene within a pathway, which results in a significant reduction in false positives, as well as a better ability to identify the truly impacted pathways and putative mechanisms that can explain all measured gene expression changes...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28654306/gene-expression-profile-of-peripheral-blood-mononuclear-cells-in-response-to-intracerebral-hemorrhage
#9
Ming Sang, Xuanbin Wang, Hanyao Zhang, Xiaodong Sun, Xudong Ding, Puqing Wang, Rong Jiao, Huaxian Cheng, Sijun Yang, Guibin Zhang
RNA-sequencing, a powerful tool, yields a comprehensive view of whole transcriptome. Intracerebral hemorrhage (ICH) is a devastating form of stroke. To date, RNA-sequencing analysis of ICH has not been reported. Peripheral blood mononuclear cells (PBMCs) were used as a source of mRNA for gene expression profile analysis in stroke. In this study, we performed transcriptome analyses for PBMCs from four ICH patients and four healthy volunteers on Illumina platform. We identified 4040 significantly differentially expressed genes (DEGs)...
June 27, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28654083/targeted-metagenomic-sequencing-data-of-human-gut-microbiota-associated-with-blastocystis-colonization
#10
Léa Siegwald, Christophe Audebert, Gaël Even, Eric Viscogliosi, Ségolène Caboche, Magali Chabé
In the past decade, metagenomics studies have become widespread due to the arrival of second-generation sequencing platforms characterized by low costs, high throughput and short read lengths. Today, although benchtop sequencers are considered to be accurate platforms to deliver data for targeted metagenomics studies, the limiting factor has become the analysis of these data. In a previous paper, we performed an Ion Torrent PGM 16S rDNA gene sequencing of faecal DNAs from 48 Blastocystis-colonized patients and 48 Blastocystis-negative subjects, in order to decipher the impact of this widespread protist on gut microbiota composition and diversity...
June 27, 2017: Scientific Data
https://www.readbyqxmd.com/read/28654059/comprehensive-dna-methylation-analysis-using-a-methyl-cpg-binding-domain-capture-based-method-in-chronic-lymphocytic-leukemia-patients
#11
Santhilal Subhash, Meena Kanduri
The role of long noncoding RNAs (lncRNAs) in cancer is coming to the forefront due to growing interest in understanding their mechanistic functions during cancer development and progression. Despite this, the global epigenetic regulation of lncRNAs and repetitive sequences in cancer has not been well investigated, particularly in chronic lymphocytic leukemia (CLL). This study focuses on a unique approach: the immunoprecipitation-based capture of double-stranded, methylated DNA fragments using methyl-binding domain (MBD) proteins, followed by next-generation sequencing (MBD-seq)...
June 16, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28654001/profiling-the-extended-cleavage-specificity-of-the-house-dust-mite-protease-allergens-der-p-1-der-p-3-and-der-p-6-for-the-prediction-of-new-cell-surface-protein-substrates
#12
Alain Jacquet, Vincenzo Campisi, Martyna Szpakowska, Marie-Eve Dumez, Moreno Galleni, Andy Chevigné
House dust mite (HDM) protease allergens, through cleavages of critical surface proteins, drastically influence the initiation of the Th2 type immune responses. However, few human protein substrates for HDM proteases have been identified so far, mainly by applying time-consuming target-specific individual studies. Therefore, the identification of substrate repertoires for HDM proteases would represent an unprecedented key step toward a better understanding of the mechanism of HDM allergic response. In this study, phage display screenings using totally or partially randomized nonameric peptide substrate libraries were performed to characterize the extended substrate specificities (P₅-P₄') of the HDM proteases Der p 1, Der p 3 and Der p 6...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28653987/the-emerging-role-of-zfp217-in-adipogenesis
#13
Hong Xiang, Zhu-Xia Zhong, Yong-Dong Peng, Si-Wen Jiang
Zinc finger protein 217 (Zfp217), a member of the krüppel-type zinc finger protein family, plays diverse roles in cell differentiation and development of mammals. Despite extensive research on the functions of Zfp217 in cancer, pluripotency and reprogramming, its physiological roles in adipogenesis remain unknown. Our previous RNA sequencing data suggest the involvement of Zfp217 in adipogenesis. In this study, the potential function of Zfp217 in adipogenesis was investigated through bioinformatics analysis and a series of experiments...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28653984/multiple-isoforms-of-anril-in-melanoma-cells-structural-complexity-suggests-variations-in-processing
#14
Debina Sarkar, Ali Oghabian, Pasani K Bodiyabadu, Wayne R Joseph, Euphemia Y Leung, Graeme J Finlay, Bruce C Baguley, Marjan E Askarian-Amiri
The long non-coding RNA ANRIL, antisense to the CDKN2B locus, is transcribed from a gene that encompasses multiple disease-associated polymorphisms. Despite the identification of multiple isoforms of ANRIL, expression of certain transcripts has been found to be tissue-specific and the characterisation of ANRIL transcripts remains incomplete. Several functions have been associated with ANRIL. In our judgement, studies on ANRIL functionality are premature pending a more complete appreciation of the profusion of isoforms...
June 27, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28653889/bioinformatics-methods-for-identifying-differentially-expressed-genes-and-signaling-pathways-in-nano-silica-stimulated-macrophages
#15
Lin Zhang, Changfu Hao, Juan Li, Yaqian Qu, Lei Bao, Yiping Li, Zhongzheng Yue, Miao Zhang, Xinghao Yu, Huiting Chen, Jianhui Zhang, Di Wang, Wu Yao
The incidence of disease relating to nanoparticle exposure has been rising rapidly in recent years, for which there is no effective treatment. Macrophage is suggested to play a crucial role in the development of pulmonary disease. To investigate the changes in macrophage after being stimulated by nanometer silica dust and to explore potential biomarkers and signaling pathways, the gene chip GSE13005 was downloaded from Gene Expression Omnibus database, which contained 21 samples: 3 samples per group and 7 groups in total...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28653781/differential-expression-profile-of-long-non-coding-rna-in-cardiomyocytes-autophagy-induced-by-angiotensin-ii
#16
Ying Gu, Fan Yang, Ru-Ming Xu, Yun-Yan Zhang, Yang Li, Su-Xuan Liu, Guan-Xin Zhang, Guo-Kun Wang, Li-Ping Ma
Autophagy is a ubiquitous intracellular process for cellular homeostasis maintainance by recycling damaged protein and organelles. Dysregulation of cardiomyocytes autophagic activity is implicated in various heart diseases. Recent studies had demonstrated long non-coding RNAs (lncRNAs) played crucial roles on modulation of autophagic activity. In this study, we first established an angiotensin II-induced autophagy model on neonatal rat cardiomyocytes. Western blot assay confirmed that the expression of Beclin 1 and the conversion of soluble LC3-I to lipid bound LC3-II were significantly increased at 12h after angiotensin II stimulation, but the cardiomyocytes surface area and hypertrophic markers expression had no significant change...
June 27, 2017: Cell Biology International
https://www.readbyqxmd.com/read/28653608/microrna-138-inhibits-cell-growth-invasion-and-emt-of-non-small-cell-lung-cancer-via-sox4-p53-feedback-loop
#17
Dandan Li, Changjun He, Junfeng Wang, Yanbo Wang, Jianlong Bu, Xianglong Kong, Dawei Sun
Many studied have shown that down-regulated level of miR-138 is in a variety of cancers including non-small cell lung cancer (NSCLC). However, the precise mechanisms of miR-138 in NSCLC have not been well clarified. In this study, we investigated the biological functions and molecular mechanisms of miR-138 in NSCLC cell lines, discussing whether it could be a therapeutic biomarker of NSCLC in the future. In our study, we found that miR-138 is down-regulated in NSCLC tissues and cell lines. Moreover, the low level of miR-138 was associated with increased expression of SOX4 in NSCLC tissues and cell lines...
June 13, 2017: Oncology Research
https://www.readbyqxmd.com/read/28653605/knockdown-of-lncrna-hoxa11-antisense-promotes-glioma-cell-apoptosis-via-sponging-mir-140-5p
#18
Yan Cui, Lei Yi, Ming-Ming Zhang, Yu Zhou, Zhi-Gang Tan, Tao Huang, Yu-Gang Jiang
Long non-coding RNAs (lncRNAs) are proved as important regulators in many diseases, including multiple cancers. HOXA11antisense RNA (HOXA11-AS) is a novel identified lncRNA associated with cancer progression. However, the role of HOXA11-AS in glioma remains poorly understood and needs to be elucidated. The purpose of this study is to investigate the role and regulating mechanism of HOXA11-AS on gliomagenesis. Expression of HOXA11-AS was significantly up-regulated in glioma tissue and cell lines compared to the adjacent normal tissue and cells...
June 12, 2017: Oncology Research
https://www.readbyqxmd.com/read/28653102/identification-of-set11-from-staphylococcus-aureus-mu50-strain-as-a-ortholog-of-ssl7-via-bioinformatic-analysis-and-determination-of-its-possible-targets-from-human-serum-using-cnbr-pull-down-assays
#19
Ying Li, Xiaobao Chen, Nan Jia, Xuan Zhang, Jianye Zang
OBJECTIVES: To identify and characterize staphylococcus exotoxin-like (SET) protein Set11 from Staphylococcus aureus Mu50 strain and its possible targets proteins from human blood/serum. RESULTS: Set11 is a member of the staphylococcal superantigen-like (SSL) proteins (also called Staphylococcus exotoxin-like (SET) proteins) family that is found in staphylococcal strain Mu50. Its structure and function, however, remain unknown. We performed bioinformatics analysis of Set11: it had 90% sequence identity to SSL7 in NCTC 8325 strain, indicating Set11 is a SSL7 ortholog...
June 26, 2017: Biotechnology Letters
https://www.readbyqxmd.com/read/28652936/divide-and-conquer-dc-blast-fast-and-easy-blast-execution-within-hpc-environments
#20
Won Cheol Yim, John C Cushman
Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated...
2017: PeerJ
keyword
keyword
6050
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"