keyword
MENU ▼
Read by QxMD icon Read
search

Multiomics

keyword
https://www.readbyqxmd.com/read/29199496/recent-trends-on-the-role-of-epigenomics-metabolomics-and-noncoding-rnas-in-rationalizing-mood-stabilizing-treatment
#1
Claudia Pisanu, Theodora Katsila, George P Patrinos, Alessio Squassina
Mood stabilizers are the cornerstone in treatment of mood disorders, but their use is characterized by high interindividual variability. This feature has stimulated intensive research to identify predictive biomarkers of response and disentangle the molecular bases of their clinical efficacy. Nevertheless, findings from studies conducted so far have only explained a small proportion of the observed variability, suggesting that factors other than DNA variants could be involved. A growing body of research has been focusing on the role of epigenetics and metabolomics in response to mood stabilizers, especially lithium salts...
December 4, 2017: Pharmacogenomics
https://www.readbyqxmd.com/read/29187204/experimental-design-and-quantitative-analysis-of-microbial-community-multiomics
#2
REVIEW
Himel Mallick, Siyuan Ma, Eric A Franzosa, Tommi Vatanen, Xochitl C Morgan, Curtis Huttenhower
Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data...
November 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/29186684/pancreatic-adenocarcinoma-therapeutic-targets-revealed-by-tumor-stroma-cross-talk-analyses-in-patient-derived-xenografts
#3
Rémy Nicolle, Yuna Blum, Laetitia Marisa, Celine Loncle, Odile Gayet, Vincent Moutardier, Olivier Turrini, Marc Giovannini, Benjamin Bian, Martin Bigonnet, Marion Rubis, Nabila Elarouci, Lucile Armenoult, Mira Ayadi, Pauline Duconseil, Mohamed Gasmi, Mehdi Ouaissi, Aurélie Maignan, Gwen Lomberk, Jean-Marie Boher, Jacques Ewald, Erwan Bories, Jonathan Garnier, Anthony Goncalves, Flora Poizat, Jean-Luc Raoul, Veronique Secq, Stephane Garcia, Philippe Grandval, Marine Barraud-Blanc, Emmanuelle Norguet, Marine Gilabert, Jean-Robert Delpero, Julie Roques, Ezequiel Calvo, Fabienne Guillaumond, Sophie Vasseur, Raul Urrutia, Aurélien de Reyniès, Nelson Dusetti, Juan Iovanna
Preclinical models based on patient-derived xenografts have remarkable specificity in distinguishing transformed human tumor cells from non-transformed murine stromal cells computationally. We obtained 29 pancreatic ductal adenocarcinoma (PDAC) xenografts from either resectable or non-resectable patients (surgery and endoscopic ultrasound-guided fine-needle aspirate, respectively). Extensive multiomic profiling revealed two subtypes with distinct clinical outcomes. These subtypes uncovered specific alterations in DNA methylation and transcription as well as in signaling pathways involved in tumor-stromal cross-talk...
November 28, 2017: Cell Reports
https://www.readbyqxmd.com/read/29174548/the-role-of-transforming-growth-factor-%C3%AE-in-human-hepatocarcinogenesis-mechanistic-and-therapeutic-implications-from-an-integrative-multiomics-approach
#4
EDITORIAL
Jens U Marquardt
No abstract text is available yet for this article.
November 21, 2017: Gastroenterology
https://www.readbyqxmd.com/read/29132754/the-engineering-potential-of-rhodosporidium-toruloides-as-a-workhorse-for-biotechnological-applications
#5
REVIEW
Young-Kyoung Park, Jean-Marc Nicaud, Rodrigo Ledesma-Amaro
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism...
November 10, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/29092936/software-for-the-integration-of-multiomics-experiments-in-bioconductor
#6
Marcel Ramos, Lucas Schiffer, Angela Re, Rimsha Azhar, Azfar Basunia, Carmen Rodriguez, Tiffany Chan, Phil Chapman, Sean R Davis, David Gomez-Cabrero, Aedin C Culhane, Benjamin Haibe-Kains, Kasper D Hansen, Hanish Kodali, Marie S Louis, Arvind S Mer, Markus Riester, Martin Morgan, Vince Carey, Levi Waldron
Multiomics experiments are increasingly commonplace in biomedical research and add layers of complexity to experimental design, data integration, and analysis. R and Bioconductor provide a generic framework for statistical analysis and visualization, as well as specialized data classes for a variety of high-throughput data types, but methods are lacking for integrative analysis of multiomics experiments. The MultiAssayExperiment software package, implemented in R and leveraging Bioconductor software and design principles, provides for the coordinated representation of, storage of, and operation on multiple diverse genomics data...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29080867/-multiomics-study-of-hepg2-cell-line-proteome
#7
E V Poverennaya, O I Kiseleva, E A Ponomarenko, S N Naryzhny, V G Zgoda, A V Lisitsa
Current proteomic studies are generally focused on the most abundant proteoforms encoded by canonical nucleic sequences. Transcriptomic and proteomic data, accumulated in a variety of postgenome sources and coupled with state-of-art analytical technologies, allow to start the identification of aberrant (non-canonical) proteoforms. The main sources of aberrant proteoforms are alternative splicing, single nucleotide polymorphism, and post-translational modifications. The aim of this work was to estimate the heterogeneity of HepG2 proteome...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29069414/the-biostudies-database-one-stop-shop-for-all-data-supporting-a-life-sciences-study
#8
Ugis Sarkans, Mikhail Gostev, Awais Athar, Ehsan Behrangi, Olga Melnichuk, Ahmed Ali, Jasmine Minguet, Juan Camillo Rada, Catherine Snow, Andrew Tikhonov, Alvis Brazma, Johanna McEntyre
BioStudies ( www.ebi.ac.uk/biostudies ) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication. BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces. The actual data can be stored either in BioStudies or remotely, or both. BioStudies imports supplementary data from Europe PMC, and is a resource for authors and publishers for packaging data during the manuscript preparation process...
October 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29049012/transcriptome-profiling-uncovers-potential-common-mechanisms-in-fetal-trisomies-18-and-21
#9
Marija Volk, Aleš Maver, Alenka Hodžić, Luca Lovrečić, Borut Peterlin
Human trisomies have recently been investigated using transcriptomics approaches to identify the gene expression (GE) signatures characteristic of each of these specific aneuploidy conditions. We hypothesized that the viability of cells with gross genomic imbalances might be associated with the activation of resilience mechanisms that are common to different trisomies and that are reflected by specific shared GE patterns. We report in this article our microarray GE analyses of amniocytes from fetuses with viable trisomy conditions, trisomy 21 or trisomy 18, to detect such common expression signatures...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29042495/impact-of-dietary-resistant-starch-on-the-human-gut-microbiome-metaproteome-and-metabolome
#10
Tanja V Maier, Marianna Lucio, Lang Ho Lee, Nathan C VerBerkmoes, Colin J Brislawn, Jörg Bernhardt, Regina Lamendella, Jason E McDermott, Nathalie Bergeron, Silke S Heinzmann, James T Morton, Antonio González, Gail Ackermann, Rob Knight, Katharina Riedel, Ronald M Krauss, Philippe Schmitt-Kopplin, Janet K Jansson
Diet can influence the composition of the human microbiome, and yet relatively few dietary ingredients have been systematically investigated with respect to their impact on the functional potential of the microbiome. Dietary resistant starch (RS) has been shown to have health benefits, but we lack a mechanistic understanding of the metabolic processes that occur in the gut during digestion of RS. Here, we collected samples during a dietary crossover study with diets containing large or small amounts of RS. We determined the impact of RS on the gut microbiome and metabolic pathways in the gut, using a combination of "omics" approaches, including 16S rRNA gene sequencing, metaproteomics, and metabolomics...
October 17, 2017: MBio
https://www.readbyqxmd.com/read/29023486/the-sea-cucumber-genome-provides-insights-into-morphological-evolution-and-visceral-regeneration
#11
Xiaojun Zhang, Lina Sun, Jianbo Yuan, Yamin Sun, Yi Gao, Libin Zhang, Shihao Li, Hui Dai, Jean-François Hamel, Chengzhang Liu, Yang Yu, Shilin Liu, Wenchao Lin, Kaimin Guo, Songjun Jin, Peng Xu, Kenneth B Storey, Pin Huan, Tao Zhang, Yi Zhou, Jiquan Zhang, Chenggang Lin, Xiaoni Li, Lili Xing, Da Huo, Mingzhe Sun, Lei Wang, Annie Mercier, Fuhua Li, Hongsheng Yang, Jianhai Xiang
Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers...
October 2017: PLoS Biology
https://www.readbyqxmd.com/read/28973931/systems-level-identification-of-pka-dependent-signaling-in-epithelial-cells
#12
Kiyoshi Isobe, Hyun Jun Jung, Chin-Rang Yang, J'Neka Claxton, Pablo Sandoval, Maurice B Burg, Viswanathan Raghuram, Mark A Knepper
G protein stimulatory α-subunit (Gαs)-coupled heptahelical receptors regulate cell processes largely through activation of protein kinase A (PKA). To identify signaling processes downstream of PKA, we deleted both PKA catalytic subunits using CRISPR-Cas9, followed by a "multiomic" analysis in mouse kidney epithelial cells expressing the Gαs-coupled V2 vasopressin receptor. RNA-seq (sequencing)-based transcriptomics and SILAC (stable isotope labeling of amino acids in cell culture)-based quantitative proteomics revealed a complete loss of expression of the water-channel gene Aqp2 in PKA knockout cells...
October 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28960106/multiomics-approach-to-asthma-navigating-the-network
#13
Merry-Lynn McDonald
No abstract text is available yet for this article.
October 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#14
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28867603/molecular-signatures-for-tumor-classification-an-analysis-of-the-cancer-genome-atlas-data
#15
Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape
Cancer classification in the clinic is primarily based on histological analysis in the proper clinical context, often supplemented by immunohistochemical and molecular studies. Recent genomic studies have shown the potential of integrated multiomics platforms for molecular classification. We performed unsupervised analyses of molecular platforms in The Cancer Genome Atlas data (n = 6216 samples) in comparison with tumor type. Our data showed that mRNA signatures and DNA methylation signatures mapped to histological diagnosis with high accuracy (95% and 88%, respectively) as individual platforms...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28859259/mass-spectrometry-based-lipidomics
#16
Ting Hu, Jin-Lan Zhang
Lipids, which have core functions in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases...
August 31, 2017: Journal of Separation Science
https://www.readbyqxmd.com/read/28768687/hit-ndrive-patient-specific-multidriver-gene-prioritization-for-precision-oncology
#17
Raunak Shrestha, Ermin Hodzic, Thomas Sauerwald, Phuong Dao, Kendric Wang, Jake Yeung, Shawn Anderson, Fabio Vandin, Gholamreza Haffari, Colin C Collins, S Cenk Sahinalp
Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the "random walk facility location" (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: "multihitting time," the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene...
September 2017: Genome Research
https://www.readbyqxmd.com/read/28729681/multiomics-analysis-of-the-giant-triton-snail-salivary-gland-a-crown-of-thorns-starfish-predator
#18
U Bose, T Wang, M Zhao, C A Motti, M R Hall, S F Cummins
The giant triton snail (Charonia tritonis) is one of the few natural predators of the adult Crown-of-Thorns starfish (COTS), a corallivore that has been damaging to many reefs in the Indo-Pacific. Charonia species have large salivary glands (SGs) that are suspected to produce either a venom and/or sulphuric acid which can immobilize their prey and neutralize the intrinsic toxic properties of COTS. To date, there is little information on the types of toxins produced by tritons. In this paper, the predatory behaviour of the C...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28691013/identification-of-pharmacologically-tractable-protein-complexes-in-cancer-using-the-r-based-network-clustering-and-visualization-program-mcoder
#19
Sungjin Kwon, Hyosil Kim, Hyun Seok Kim
Current multiomics assay platforms facilitate systematic identification of functional entities that are mappable in a biological network, and computational methods that are better able to detect densely connected clusters of signals within a biological network are considered increasingly important. One of the most famous algorithms for detecting network subclusters is Molecular Complex Detection (MCODE). MCODE, however, is limited in simultaneous analyses of multiple, large-scale data sets, since it runs on the Cytoscape platform, which requires extensive computational resources and has limited coding flexibility...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28618237/effect-of-sweetened-dried-cranberry-consumption-on-urinary-proteome-and-fecal-microbiome-in-healthy-human-subjects
#20
Nell Bekiares, Christian G Krueger, Jennifer J Meudt, Dhanansayan Shanmuganayagam, Jess D Reed
The relationship among diet, human health, and disease is an area of growing interest in biomarker research. Previous studies suggest that the consumption of cranberries (Vaccinium macrocarpon) could beneficially influence urinary and digestive health. The present study sought to determine if daily consumption of sweetened dried cranberries (SDC) changes the urinary proteome and fecal microbiome, as determined in a prospective sample of 10 healthy individuals. Baseline urine and fecal samples were collected from the subjects in the fasted (8-12 h) state...
June 15, 2017: Omics: a Journal of Integrative Biology
keyword
keyword
66872
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"