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https://www.readbyqxmd.com/read/27912059/microbiota-diurnal-rhythmicity-programs-host-transcriptome-oscillations
#1
Christoph A Thaiss, Maayan Levy, Tal Korem, Lenka Dohnalová, Hagit Shapiro, Diego A Jaitin, Eyal David, Deborah R Winter, Meital Gury-BenAri, Evgeny Tatirovsky, Timur Tuganbaev, Sara Federici, Niv Zmora, David Zeevi, Mally Dori-Bachash, Meirav Pevsner-Fischer, Elena Kartvelishvily, Alexander Brandis, Alon Harmelin, Oren Shibolet, Zamir Halpern, Kenya Honda, Ido Amit, Eran Segal, Eran Elinav
The intestinal microbiota undergoes diurnal compositional and functional oscillations that affect metabolic homeostasis, but the mechanisms by which the rhythmic microbiota influences host circadian activity remain elusive. Using integrated multi-omics and imaging approaches, we demonstrate that the gut microbiota features oscillating biogeographical localization and metabolome patterns that determine the rhythmic exposure of the intestinal epithelium to different bacterial species and their metabolites over the course of a day...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#2
Eleanor Jameson, Martin Taubert, Sara Coyotzi, Yin Chen, Özge Eyice, Hendrik Schäfer, J Colin Murrell, Josh D Neufeld, Marc G Dumont
Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of (13)C, (18)O, or (15)N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labeled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labeled populations by targeted gene analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27899048/the-method-for-breast-cancer-grade-prediction-and-pathway-analysis-based-on-improved-multiple-kernel-learning
#3
Tianci Song, Yan Wang, Wei Du, Sha Cao, Yuan Tian, Yanchun Liang
Breast cancer histologic grade represents the morphological assessment of the tumor's malignancy and aggressiveness, which is vital in clinically planning treatment and estimating prognosis for patients. Therefore, the prediction of breast cancer grade can markedly elevate the detection of early breast cancer and efficiently guide its treatment. With the advent of high-throughput profiling technology, a large number of data of different types are rapidly generated, and each data provides its unique biological insight...
November 29, 2016: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/27897013/harnessing-big-data-for-precision-medicine-infrastructures-and-applications
#4
Kun-Hsing Yu, Steven N Hart, Rachel Goldfeder, Qiangfeng Cliff Zhang, Stephen C J Parker, Michael Snyder
Precision medicine is a health management approach that accounts for individual differences in genetic backgrounds and environmental exposures. With the recent advancements in high-throughput omics profiling technologies, collections of large study cohorts, and the developments of data mining algorithms, big data in biomedicine is expected to provide novel insights into health and disease states, which can be translated into personalized disease prevention and treatment plans. However, petabytes of biomedical data generated by multiple measurement modalities poses a significant challenge for data analysis, integration, storage, and result interpretation...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27897002/a-methylation-to-expression-feature-model-for-generating-accurate-prognostic-risk-scores-and-identifying-disease-targets-in-clear-cell-kidney-cancer
#5
Jeffrey A Thompson, Carmen J Marsit
Many researchers now have available multiple high-dimensional molecular and clinical datasets when studying a disease. As we enter this multi-omic era of data analysis, new approaches that combine different levels of data (e.g. at the genomic and epigenomic levels) are required to fully capitalize on this opportunity. In this work, we outline a new approach to multi-omic data integration, which combines molecular and clinical predictors as part of a single analysis to create a prognostic risk score for clear cell renal cell carcinoma...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896993/frequent-subgraph-mining-of-personalized-signaling-pathway-networks-groups-patients-with-frequently-dysregulated-disease-pathways-and-predicts-prognosis
#6
Arda Durmaz, Tim A D Henderson, Douglas Brubaker, Gurkan Bebek
MOTIVATION: Large scale genomics studies have generated comprehensive molecular characterization of numerous cancer types. Subtypes for many tumor types have been established; however, these classifications are based on molecular characteristics of a small gene sets with limited power to detect dysregulation at the patient level. We hypothesize that frequent graph mining of pathways to gather pathways functionally relevant to tumors can characterize tumor types and provide opportunities for personalized therapies...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896961/imaging-genomics
#7
L I Shen, Lee A D Cooper
Imaging genomics is an emerging research field, where integrative analysis of imaging and omics data is performed to provide new insights into the phenotypic characteristics and genetic mechanisms of normal and/or disordered biological structures and functions, and to impact the development of new diagnostic, therapeutic and preventive approaches. The Imaging Genomics Session at PSB 2017 aims to encourage discussion on fundamental concepts, new methods and innovative applications in this young and rapidly evolving field...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896739/integrating-heterogeneous-datasets-for-cancer-module-identification
#8
A K M Azad
The availability of multiple heterogeneous high-throughput datasets provides an enabling resource for cancer systems biology. Types of data include: Gene expression (GE), copy number aberration (CNA), miRNA expression, methylation, and protein-protein Interactions (PPI). One important problem that can potentially be solved using such data is to determine which of the possible pair-wise interactions among genes contributes to a range of cancer-related events, from tumorigenesis to metastasis. It has been shown by various studies that applying integrated knowledge from multi-omics datasets elucidates such complex phenomena with higher statistical significance than using a single type of dataset individually...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#9
Fabio Tordini, Marco Aldinucci, Luciano Milanesi, Pietro Liò, Ivan Merelli
Publicly available multi-omic databases, in particular if associated with medical annotations, are rich resources with the potential to lead a rapid transition from high-throughput molecular biology experiments to better clinical outcomes for patients. In this work, we propose a model for multi-omic data integration (i.e., genetic variations, gene expression, genome conformation, and epigenetic patterns), which exploits a multi-layer network approach to analyse, visualize, and obtain insights from such biological information, in order to use achieved results at a macroscopic level...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895649/-omics-and-plant-responses-to-botrytis-cinerea
#10
REVIEW
Synan F AbuQamar, Khaled Moustafa, Lam-Son P Tran
Botrytis cinerea is a dangerous plant pathogenic fungus with wide host ranges. This aggressive pathogen uses multiple weapons to invade and cause serious damages on its host plants. The continuing efforts of how to solve the "puzzle" of the multigenic nature of B. cinerea's pathogenesis and plant defense mechanisms against the disease caused by this mold, the integration of omic approaches, including genomics, transcriptomics, proteomics and metabolomics, along with functional analysis could be a potential solution...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27891181/whole-genome-sequencing-and-comparative-genomic-analysis-of-escherichia-coli-o91-strains-isolated-from-symptomatic-and-asymptomatic-human-carriers
#11
Taesoo Kwon, Young-Seok Bak, Young-Hee Jung, Young-Bin Yu, Jong Tae Choi, Cheorl-Ho Kim, Jung-Beom Kim, Won Kim, Seung-Hak Cho
BACKGROUND: The Shiga toxin-producing Escherichia coli (STEC) O91:H21 strains NCCP15736 and NCCP15737 were isolated during a single outbreak in Korea, NCCP15736 from a symptomatic carrier and NCCP15737 from an asymptomatic carrier. To investigate genomic differences between the two strains, we performed whole-genome sequencing of both strains and conducted a comparative genomic analysis. RESULTS: Using the Illumina HiSeq 2000 platform and Rapid Annotation using the Subsystem Technology (RAST) server, whole-genome sequences of NCCP15736 and NCCP15737 were obtained and annotated...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27891171/a-rapid-approach-to-investigate-spatiotemporal-distribution-of-phytohormones-in-rice
#12
Wen-Jing Cai, Tian-Tian Ye, Qing Wang, Bao-Dong Cai, Yu-Qi Feng
BACKGROUND: Phytohormones play crucial roles in almost all stages of plant growth and development. Accurate and simultaneous determination of multiple phytohormones enabled us to better understand the physiological functions and the regulatory networks of phytohormones. However, simultaneous determination of multiple phytohormones in plant is still a challenge due to their low concentrations, structural and chemical diversity, and complex matrix of plant tissues. Therefore, development of a simple and selective method for the simultaneous determination of multiple phytohormones is highly needed...
2016: Plant Methods
https://www.readbyqxmd.com/read/27890772/integrative-analysis-of-dna-methylation-and-gene-expression-in-butyrate-treated-cho-cells
#13
Anna Wippermann, Oliver Rupp, Karina Brinkrolf, Raimund Hoffrogge, Thomas Noll
The cellular mechanisms responsible for the versatile properties of CHO cells as the major production cell line for biopharmaceutical molecules are not entirely understood yet, although several 'omics' data facilitate the understanding of CHO cells and their reactions to environmental conditions. However, genome-wide studies of epigenetic processes such as DNA methylation are still limited. To prove the applicability and usefulness of integrating DNA methylation and gene expression data in a biotechnological context, we exemplarily analyzed the time course of cellular reactions upon butyrate addition in antibody-producing CHO cells by whole-genome bisulfite sequencing and CHO-specific cDNA microarrays...
November 24, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27888147/pathway-analysis-of-complex-diseases-for-gwas-extending-to-consider-rare-variants-multi-omics-and-interactions
#14
REVIEW
Patrick Y P Kao, Kim Hung Leung, Lawrence W C Chan, Shea Ping Yip, Maurice K H Yap
BACKGROUND: Genome-wide association studies (GWAS) is a major method for studying the genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of a disease is difficult because of their small effect sizes. To better explain disease mechanisms, pathway analysis is used to consolidate the effects of multiple variants, and hence increase the power of the study. While pathway analysis has previously been performed within GWAS only, it can now be extended to examining rare variants, other "-omics" and interaction data...
November 22, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27886581/a-multi-omic-approach-to-elucidate-low-dose-effects-of-xenobiotics-in-zebrafish-danio-rerio-larvae
#15
Susie S Y Huang, Jonathan P Benskin, Nik Veldhoen, Bharat Chandramouli, Heather Butler, Caren C Helbing, John R Cosgrove
Regulatory-approved toxicity assays such as the OECD Fish Embryo Toxicity Assay (TG236) allow correlation of chemical exposure to adverse morphological phenotypes. However, these assays are ineffective in assessing sub-lethal (i.e. low-dose) effects, or differentiating between similar phenotypes induced by different chemicals. Inclusion of multi-omic analyses in studies investigating xenobiotic action provides improved characterization of biological response, thereby enhancing prediction of toxicological outcomes in whole animals in the absence of morphological effects...
November 18, 2016: Aquatic Toxicology
https://www.readbyqxmd.com/read/27886242/exploring-the-molecular-basis-of-age-related-disease-comorbidities-using-a-multi-omics-graphical-model
#16
Jonas Zierer, Tess Pallister, Pei-Chien Tsai, Jan Krumsiek, Jordana T Bell, Gordan Lauc, Tim D Spector, Cristina Menni, Gabi Kastenmüller
Although association studies have unveiled numerous correlations of biochemical markers with age and age-related diseases, we still lack an understanding of their mutual dependencies. To find molecular pathways that underlie age-related diseases as well as their comorbidities, we integrated aging markers from four different high-throughput omics datasets, namely epigenomics, transcriptomics, glycomics and metabolomics, with a comprehensive set of disease phenotypes from 510 participants of the TwinsUK cohort...
November 25, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27884205/whole-genome-sequence-analysis-of-serum-amino-acid-levels
#17
Bing Yu, Paul S de Vries, Ginger A Metcalf, Zhe Wang, Elena V Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E Wagenknecht, Richard A Gibbs, Alanna C Morrison, Eric Boerwinkle
BACKGROUND: Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene-environment interactions. Whole genome sequence analysis of amino acid levels may establish a paradigm for analyzing quantitative risk factors. RESULTS: In a discovery cohort of 1872 African Americans and a replication cohort of 1552 European Americans we sequenced exons and whole genomes and measured serum levels of 70 amino acids...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27883025/mathiomica-an-integrative-platform-for-dynamic-omics
#18
George I Mias, Tahir Yusufaly, Raeuf Roushangar, Lavida R K Brooks, Vikas V Singh, Christina Christou
Multiple omics data are rapidly becoming available, necessitating the use of new methods to integrate different technologies and interpret the results arising from multimodal assaying. The MathIOmica package for Mathematica provides one of the first extensive introductions to the use of the Wolfram Language to tackle such problems in bioinformatics. The package particularly addresses the necessity to integrate multiple omics information arising from dynamic profiling in a personalized medicine approach. It provides multiple tools to facilitate bioinformatics analysis, including importing data, annotating datasets, tracking missing values, normalizing data, clustering and visualizing the classification of data, carrying out annotation and enumeration of ontology memberships and pathway analysis...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27881428/genome-transcriptome-and-proteome-the-rise-of-omics-data-and-their-integration-in-biomedical-sciences
#19
Claudia Manzoni, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, Raffaele Ferrari
Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine...
November 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27881245/the-transplantex-initiative
#20
EDITORIAL
Seiamak Bahram, Raphael Carapito, Pierre-Antoine Gourraud, Dominique Charron
TRANSPLANTEX, a French "investment for the future" initiated consortium of leading transplant units and research laboratories across France and a number of European countries aims to unravel, through mainly high-throughput genomics (and other omics) analyses of donor and recipients, novel (a) non-HLA, histocompatibility antigens, whether inside, or outside the MHC; (b) pre/post transplantation biomarkers. This shall lead to our better understanding of the pathophysiology of (and eventually designing better therapeutics for) the graft-versus-host disease in hematopoietic cell transplants and that of chronic graft rejection after kidney transplant...
November 2016: Human Immunology
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