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Omics analysis

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https://www.readbyqxmd.com/read/27910903/prostate-cancer-patients-negative-biopsy-controls-discrimination-by-untargeted-metabolomics-analysis-of-urine-by-lc-qtof-upstream-information-on-other-omics
#1
M A Fernández-Peralbo, E Gómez-Gómez, M Calderón-Santiago, J Carrasco-Valiente, J Ruiz-García, M J Requena-Tapia, M D Luque de Castro, F Priego-Capote
The existing clinical biomarkers for prostate cancer (PCa) diagnosis are far from ideal (e.g., the prostate specific antigen (PSA) serum level suffers from lack of specificity, providing frequent false positives leading to over-diagnosis). A key step in the search for minimum invasive tests to complement or replace PSA should be supported on the changes experienced by the biochemical pathways in PCa patients as compared to negative biopsy control individuals. In this research a comprehensive global analysis by LC-QTOF was applied to urine from 62 patients with a clinically significant PCa and 42 healthy individuals, both groups confirmed by biopsy...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27909578/advances-in-analyzing-rna-diversity-in-eukaryotic-transcriptomes-peering-through-the-omics-lens
#2
REVIEW
Sushant Bangru, Auinash Kalsotra
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants...
2016: F1000Research
https://www.readbyqxmd.com/read/27908704/on-the-relationship-between-cell-cycle-analysis-with-ergodic-principles-and-age-structured-cell-population-models
#3
K Kuritz, D Stöhr, N Pollak, F Allgöwer
Cyclic processes, in particular the cell cycle, are of great importance in cell biology. Continued improvement in cell population analysis methods like fluorescence microscopy, flow cytometry, CyTOF or single-cell omics made mathematical methods based on ergodic principles a powerful tool in studying these processes. In this paper, we establish the relationship between cell cycle analysis with ergodic principles and age structured population models. To this end, we describe the progression of a single cell through the cell cycle by a stochastic differential equation on a one dimensional manifold in the high dimensional dataspace of cell cycle markers...
November 28, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27905518/pesticide-toxicogenomics-across-scales-in-vitro-transcriptome-predicts-mechanisms-and-outcomes-of-exposure-in-vivo
#4
Immacolata Porreca, Fulvio D'Angelo, Lucia De Franceschi, Alessandro Mattè, Michele Ceccarelli, Achille Iolascon, Alberto Zamò, Filomena Russo, Maria Ravo, Roberta Tarallo, Marzia Scarfò, Alessandro Weisz, Mario De Felice, Massimo Mallardo, Concetta Ambrosino
In vitro Omics analysis (i.e. transcriptome) is suggested to predict in vivo toxicity and adverse effects in humans, although the causal link between high-throughput data and effects in vivo is not easily established. Indeed, the chemical-organism interaction can involve processes, such as adaptation, not established in cell cultures. Starting from this consideration we investigate the transcriptomic response of immortalized thyrocytes to ethylenthiourea and chlorpyrifos. In vitro data revealed specific and common genes/mechanisms of toxicity, controlling the proliferation/survival of the thyrocytes and unrelated hematopoietic cell lineages...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27904969/metabolic-responses-and-omics-technologies-for-elucidating-the-effects-of-heat-stress-in-dairy-cows
#5
REVIEW
Li Min, Shengguo Zhao, He Tian, Xu Zhou, Yangdong Zhang, Songli Li, Hongjian Yang, Nan Zheng, Jiaqi Wang
Heat stress (HS) negatively affects various industries that rely on animal husbandry, particularly the dairy industry. A better understanding of metabolic responses in HS dairy cows is necessary to elucidate the physiological mechanisms of HS and offer a new perspective for future research. In this paper, we review the current knowledge of responses of body metabolism (lipid, carbohydrate, and protein), endocrine profiles, and bovine mammary epithelial cells during HS. Furthermore, we summarize the metabolomics and proteomics data that have revealed the metabolite profiles and differentially expressed proteins that are a feature of HS in dairy cows...
November 30, 2016: International Journal of Biometeorology
https://www.readbyqxmd.com/read/27902843/ridge-estimation-of-the-var-1-model-and-its-time-series-chain-graph-from-multivariate-time-course-omics-data
#6
Viktorian Miok, Saskia M Wilting, Wessel N van Wieringen
Omics experiments endowed with a time-course design may enable us to uncover the dynamic interplay among genes of cellular processes. Multivariate techniques (like VAR(1) models describing the temporal and contemporaneous relations among variates) that may facilitate this goal are hampered by the high-dimensionality of the resulting data. This is resolved by the presented ridge regularized maximum likelihood estimation procedure for the VAR(1) model. Information on the absence of temporal and contemporaneous relations may be incorporated in this procedure...
November 7, 2016: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/27900688/degradation-network-reconstruction-guided-by-metagenomic-data
#7
Rafael Bargiela, Manuel Ferrer
Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900684/dna-rna-and-protein-based-stable-isotope-probing-for-high-throughput-biomarker-analysis-of-active-microorganisms
#8
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/27899567/expansion-of-the-gene-ontology-knowledgebase-and-resources
#9
(no author information available yet)
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899048/the-method-for-breast-cancer-grade-prediction-and-pathway-analysis-based-on-improved-multiple-kernel-learning
#10
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/27898765/transcriptome-assembly-and-comparison-of-an-allotetraploid-weed-species-annual-bluegrass-with-its-two-diploid-progenitor-species-schrad-and-kunth
#11
Shu Chen, J Scott McElroy, Fenny Dane, Leslie R Goertzen
Annual bluegrass ( L.) is one of the most widespread weed species in this world. As a young allotetraploid, has occupied diverse environments from Antarctic area to subtropical regions. To unveil the evolutionary mystery behind 's wide distribution, extensive adaptability and phenotypic plasticity needs collaboration from multiple research scopes from ecology and plant physiology to population genetics and molecular biology. However, the lack of omic data and reference has greatly hampered the study. This is the first comprehensive transcriptome study on species...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27898265/prospects-for-biological-soil-borne-disease-control-application-of-indigenous-versus-synthetic-microbiomes
#12
Mark Mazzola, Shiri Freilich
Biological disease control of soil-borne plant diseases has traditionally employed the biopesticide approach whereby single strains or strain mixtures are introduced into production systems through inundative/inoculative release. The approach has significant barriers that have long been recognized, including a generally limited spectrum of target pathogens for any given biocontrol agent andinadequate colonization of the host rhizosphere, which can plague progress in the utilization of this resource in commercial field-based crop production systems...
November 29, 2016: Phytopathology
https://www.readbyqxmd.com/read/27897013/harnessing-big-data-for-precision-medicine-infrastructures-and-applications
#13
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
#14
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
#15
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
#16
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/27895661/the-genome-conformation-as-an-integrator-of-multi-omic-data-the-example-of-damage-spreading-in-cancer
#17
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
#18
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/27894972/transcriptome-inference-and-systems-approaches-to-polypharmacology-and-drug-discovery-in-herbal-medicine
#19
Peng Li, Jianxin Chen, Wuxia Zhang, Bangze Fu, Wei Wang
ETHNOPHARMACOLOGICAL RELEVANCE: Herbal medicine is a concoction of numerous chemical ingredients, and it exhibits polypharmacological effects to act on multiple pharmacological targets, regulating different biological mechanisms and treating a variety of diseases. Thus, this complexity is impossible to deconvolute by the reductionist method of extracting one active ingredient acting on one biological target. AIM OF THE STUDY: To dissect the polypharmacological effects of herbal medicines and their underling pharmacological targets as well as their corresponding active ingredients...
November 25, 2016: Journal of Ethnopharmacology
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
#20
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
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