keyword
MENU ▼
Read by QxMD icon Read
search

integrated omics

keyword
https://www.readbyqxmd.com/read/29679008/improving-wood-properties-for-wood-utilization-through-multi-omics-integration-in-lignin-biosynthesis
#1
Jack P Wang, Megan L Matthews, Cranos M Williams, Rui Shi, Chenmin Yang, Sermsawat Tunlaya-Anukit, Hsi-Chuan Chen, Quanzi Li, Jie Liu, Chien-Yuan Lin, Punith Naik, Ying-Hsuan Sun, Philip L Loziuk, Ting-Feng Yeh, Hoon Kim, Erica Gjersing, Todd Shollenberger, Christopher M Shuford, Jina Song, Zachary Miller, Yung-Yun Huang, Charles W Edmunds, Baoguang Liu, Yi Sun, Ying-Chung Jimmy Lin, Wei Li, Hao Chen, Ilona Peszlen, Joel J Ducoste, John Ralph, Hou-Min Chang, David C Muddiman, Mark F Davis, Chris Smith, Fikret Isik, Ronald Sederoff, Vincent L Chiang
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels. Lignin is polymerized from three monomers (monolignols) produced by a grid-like pathway. The pathway in wood formation of Populus trichocarpa has at least 21 genes, encoding enzymes that mediate 37 reactions on 24 metabolites, leading to lignin and affecting wood properties. We perturb these 21 pathway genes and integrate transcriptomic, proteomic, fluxomic and phenomic data from 221 lines selected from ~2000 transgenics (6-month-old)...
April 20, 2018: Nature Communications
https://www.readbyqxmd.com/read/29678131/secimtools-a-suite-of-metabolomics-data-analysis-tools
#2
Alexander S Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M Fear, Joseph Gerken, Xinlei Mi, Ali Ashrafi, Alison M Morse, Lauren M McIntyre
BACKGROUND: Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data...
April 20, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29678086/implementing-systems-medicine-a-medical-informatics-perspective
#3
Matthias Ganzinger, Matthias Gietzelt, Christian Karmen, Blanca Flores, Petra Knaup
Systems medicine is a paradigm for translating in silico methods developed for modelling biological systems into the field of medicine. Such approaches rely on the integration of as many data sources as possible, both in the dimension of disease knowledge and patient data. This is a challenging task that can only be implemented in clinical routine with the help of suitable information technology from the field of Medical Informatics. For the research project "Clinically-applicable, omics-based assessment of survival, side effects, and targets in multiple myeloma" (CLIOMMICS) we developed a prototypical systems medicine application system...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29677503/revolutionizing-precision-oncology-through-collaborative-proteogenomics-and-data-sharing
#4
Henry Rodriguez, Stephen R Pennington
The integration of proteomics into precision oncology presents opportunities that may transform the molecular analysis of cancer and accelerate basic and clinical cancer research. This Commentary discusses the importance of international collaboration and data sharing inspired by the Cancer Moonshot to accelerate the progress of multi-omic precision medicine-an approach that addresses the global diversity of people and of cancers.
April 19, 2018: Cell
https://www.readbyqxmd.com/read/29672823/developmental-disorders-with-intellectual-disability-driven-by-chromatin-dysregulation-clinical-overlaps-and-molecular-mechanisms
#5
REVIEW
L Larizza, P Finelli
Advances in genomic analyses based on next generation sequencing and integrated omics approaches, have accelerated in an unprecedented way the discovery of causative genes of developmental delay (DD) and intellectual disability (ID) disorders. Chromatin dysregulation has been recognized as common pathomechanism of mendelian DD/ID syndromes due to mutation in genes encoding chromatin regulators referred as transcriptomopathies or epigenetic disorders. Common to these syndromes are the wide phenotypic breadth and the recognition of groups of distinct syndromes with shared signs besides cognitive impairment, likely mirroring common molecular mechanisms...
April 19, 2018: Clinical Genetics
https://www.readbyqxmd.com/read/29668946/a-system-biology-perspective-on-environment-host-microbe-interactions
#6
Lianmin Chen, Sanzhima Garmaeva, Alexandra Zherankova, Jingyuan Fu, Cisca Wijmenga
A vast, complex and dynamic consortium of microorganisms known as the gut microbiome colonizes the human gut. Over the past few decades we have developed an increased awareness of its important role in human health. In this review we discuss the role of the gut microbiome in complex diseases and the possible causal scenarios behind its interactions with the host genome and environmental factors. We then propose a new analysis framework that combines a systems biology approach, cross-kingdom integration of multiple levels of omics data, and innovative in vitro models to yield an integrated picture of human host-microbe interactions...
April 16, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29665821/plasma-proteomic-analysis-reveals-altered-protein-abundances-in-cardiovascular-disease
#7
Vasiliki Lygirou, Agnieszka Latosinska, Manousos Makridakis, William Mullen, Christian Delles, Joost P Schanstra, Jerome Zoidakis, Burkert Pieske, Harald Mischak, Antonia Vlahou
BACKGROUND: Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis...
April 17, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29660711/the-rhizosphere-microbiome-significance-in-rhizoremediation-of-polyaromatic-hydrocarbon-contaminated-soil
#8
REVIEW
Rhitu Kotoky, Jina Rajkumari, Piyush Pandey
Microbial communities are an essential part of plant rhizosphere and participate in the functioning of plants, including rhizoremediation of petroleum contaminants. Rhizoremediation is a promising technology for removal of polyaromatic hydrocarbons based on interactions between plants and microbiome in the rhizosphere. Root exudation in the rhizosphere provides better nutrient uptake for rhizosphere microbiome, and therefore it is considered to be one of the major factors of microbial community function in the rhizosphere that plays a key role in the enhanced PAH biodegradation...
April 13, 2018: Journal of Environmental Management
https://www.readbyqxmd.com/read/29657967/at-the-nexus-of-history-ecology-and-hydrobiogeochemistry-improved-predictions-across-scales-through-integration
#9
James C Stegen
To improve predictions of ecosystem function in future environments, we need to integrate the ecological and environmental histories experienced by microbial communities with hydrobiogeochemistry across scales. A key issue is whether we can derive generalizable scaling relationships that describe this multiscale integration. There is a strong foundation for addressing these challenges. We have the ability to infer ecological history with null models and reveal impacts of environmental history through laboratory and field experimentation...
March 2018: MSystems
https://www.readbyqxmd.com/read/29656435/a-multi-omic-study-reveals-btg2-as-a-reliable-prognostic-marker-for-early-stage-non-small-cell-lung-cancer
#10
Sipeng Shen, Ruyang Zhang, Yichen Guo, Elizabeth Loehrer, Yongyue Wei, Ying Zhu, Qianyu Yuan, Sebastian Moran, Thomas Fleischer, Maria Moksnes Bjaanaes, Anna Karlsson, Maria Planck, Johan Staaf, Åslaug Helland, Manel Esteller, Li Su, Feng Chen, David C Christiani
B-cell translocation gene 2 (BTG2) is a tumor suppressor protein and is known to be downregulated in several types of cancer. In this study, we investigated a potential role for BTG2 in early-stage non-small cell lung cancer (NSCLC) survival. We analysed BTG2 methylation data from 1,230 early-stage NSCLC patients from five international cohorts, as well as gene expression data from 3,038 lung cancer cases from multiple cohorts. Three CpG probes (cg01798157, cg06373167, cg23371584) that detected BTG2 hypermethylation in tumor tissues were associated with lower overall survival...
April 15, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29656009/omics-and-multi-omics-approaches-to-study-the-biosynthesis-of-secondary-metabolites-in-microorganisms
#11
REVIEW
Emilia Palazzotto, Tilmann Weber
Natural products produced by microorganisms represent the main source of bioactive molecules. The development of high-throughput (omics) techniques have importantly contributed to the renaissance of new antibiotic discovery increasing our understanding of complex mechanisms controlling the expression of biosynthetic gene clusters (BGCs) encoding secondary metabolites. In this context this review highlights recent progress in the use and integration of 'omics' approaches with focuses on genomics, transcriptomics, proteomics metabolomics meta-omics and combined omics as powerful strategy to discover new antibiotics...
April 12, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29650893/-towards-development-of-innovative-cancer-therapies-trans-omics-approach
#12
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29649979/ginseng-genome-database-an-open-access-platform-for-genomics-of-panax-ginseng
#13
Murukarthick Jayakodi, Beom-Soon Choi, Sang-Choon Lee, Nam-Hoon Kim, Jee Young Park, Woojong Jang, Meiyappan Lakshmanan, Shobhana V G Mohan, Dong-Yup Lee, Tae-Jin Yang
BACKGROUND: The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb...
April 12, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29649387/multi-omics-research-trends-in-sepsis-a-bibliometric-comparative-analysis-between-the-united-states-the-european-union-28-member-states-and-china
#14
Nikolaos Evangelatos, Kapaettu Satyamoorthy, Georgia Levidou, Pia Bauer, Helmut Brand, Christina Kouskouti, Hans Lehrach, Angela Brand
"-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China...
March 2018: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29643545/-necessity-and-feasibility-of-data-sharing-of-cohort-studies
#15
Y Yang, H Y Zhao, S Y Zhan
Cohort study is one of the important epidemiological methods which plays an irreplaceable status and role in etiological study. Using cohort study design, we can accurately and continuously collect genetic and environmental information, and identify and validate omics biomarkers to provide evidences for precision public health and medicine. However, results from a new cohort would not be available for at least ten years, as five years would be needed for funding, planning and enrolment, and another five for following up even the earliest analyses of the most common diseases; results for most cancers would take longer, with an unaffordable budget for many research investigators or institutions...
April 18, 2018: Beijing da Xue Xue Bao. Yi Xue Ban, Journal of Peking University. Health Sciences
https://www.readbyqxmd.com/read/29621222/metabolomics-activity-screening-for-identifying-metabolites-that-modulate-phenotype
#16
Carlos Guijas, J Rafael Montenegro-Burke, Benedikt Warth, Mary E Spilker, Gary Siuzdak
Metabolomics, in which small-molecule metabolites (the metabolome) are identified and quantified, is broadly acknowledged to be the omics discipline that is closest to the phenotype. Although appreciated for its role in biomarker discovery programs, metabolomics can also be used to identify metabolites that could alter a cell's or an organism's phenotype. Metabolomics activity screening (MAS) as described here integrates metabolomics data with metabolic pathways and systems biology information, including proteomics and transcriptomics data, to produce a set of endogenous metabolites that can be tested for functionality in altering phenotypes...
April 5, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29619235/imethyl-an-integrative-database-of-human-dna-methylation-gene-expression-and-genomic-variation
#17
Shohei Komaki, Yuh Shiwa, Ryohei Furukawa, Tsuyoshi Hachiya, Hideki Ohmomo, Ryo Otomo, Mamoru Satoh, Jiro Hitomi, Kenji Sobue, Makoto Sasaki, Atsushi Shimizu
We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database...
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29617720/a-decade-of-genome-wide-association-studies-for-coronary-artery-disease-the-challenges-ahead
#18
Jeanette Erdmann, Thorsten Kessler, Loreto Munoz Venegas, Heribert Schunkert
In this review, we summarise current knowledge on the genetics of coronary artery disease, based on 10 years of genome-wide association studies. The discoveries began with individual studies using 200K single nucleotide polymorphism arrays and progressed to large-scale collaborative efforts, involving more than a hundred thousand people and up to 40 Mio genetic variants. We discuss the challenges ahead, including those involved in identifying causal genes and deciphering the links between risk variants and disease pathology...
March 30, 2018: Cardiovascular Research
https://www.readbyqxmd.com/read/29617661/integrated-genomic-analysis-of-the-ubiquitin-pathway-across-cancer-types
#19
Zhongqi Ge, Jake S Leighton, Yumeng Wang, Xinxin Peng, Zhongyuan Chen, Hu Chen, Yutong Sun, Fan Yao, Jun Li, Huiwen Zhang, Jianfang Liu, Craig D Shriver, Hai Hu, Helen Piwnica-Worms, Li Ma, Han Liang
Protein ubiquitination is a dynamic and reversible process of adding single ubiquitin molecules or various ubiquitin chains to target proteins. Here, using multidimensional omic data of 9,125 tumor samples across 33 cancer types from The Cancer Genome Atlas, we perform comprehensive molecular characterization of 929 ubiquitin-related genes and 95 deubiquitinase genes. Among them, we systematically identify top somatic driver candidates, including mutated FBXW7 with cancer-type-specific patterns and amplified MDM2 showing a mutually exclusive pattern with BRAF mutations...
April 3, 2018: Cell Reports
https://www.readbyqxmd.com/read/29616063/morphdb-prioritizing-genes-for-specialized-metabolism-pathways-and-gene-ontology-categories-in-plants
#20
Arthur Zwaenepoel, Tim Diels, David Amar, Thomas Van Parys, Ron Shamir, Yves Van de Peer, Oren Tzfadia
Recent times have seen an enormous growth of "omics" data, of which high-throughput gene expression data are arguably the most important from a functional perspective. Despite huge improvements in computational techniques for the functional classification of gene sequences, common similarity-based methods often fall short of providing full and reliable functional information. Recently, the combination of comparative genomics with approaches in functional genomics has received considerable interest for gene function analysis, leveraging both gene expression based guilt-by-association methods and annotation efforts in closely related model organisms...
2018: Frontiers in Plant Science
keyword
keyword
31748
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"