keyword
MENU ▼
Read by QxMD icon Read
search

integrated omics

keyword
https://www.readbyqxmd.com/read/28231582/radiomics-in-head-and-neck-cancer-extracting-valuable-information-from-data-beyond-recognition
#1
Kathrin Scheckenbach, Lena Colter, Martin Wagenmann
In oncology, biomarkers that describe the characteristics of a malignancy on different levels (clinical, histological, molecular) and the patient's outcome and treatment response are increasingly integrated into the clinical routine. Extensive screening tools, "omics," offer incredible opportunities and vast amounts of data. During the last years, the field of "omics" gained a new promising partner, the "radiomics." Based on radiological imaging, multiple features can be extracted and linked to clinical, genomic, and histopathological data from other sources...
February 24, 2017: ORL; Journal for Oto-rhino-laryngology and its related Specialties
https://www.readbyqxmd.com/read/28228844/erratum-to-meta-analytic-support-vector-machine-for-integrating-multiple-omics-data
#2
SungHwan Kim, Jae-Hwan Jhong, JungJun Lee, Ja-Yong Koo
[This corrects the article DOI: 10.1186/s13040-017-0126-8.].
2017: BioData Mining
https://www.readbyqxmd.com/read/28219972/venomics-integrative-venom-proteomics-and-beyond
#3
REVIEW
Juan J Calvete
Venoms are integrated phenotypes that evolved independently in, and are used for predatory and defensive purposes by, a wide phylogenetic range of organisms. The same principles that contribute to the evolutionary success of venoms, contribute to making the study of venoms of great interest in such diverse fields as evolutionary ecology and biotechnology. Evolution is profoundly contingent, and nature also reinvents itself continuosly. Changes in a complex phenotypic trait, such as venom, reflect the influences of prior evolutionary history, chance events, and selection...
February 20, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28217003/reverse-genetics-and-high-throughput-sequencing-methodologies-for-plant-functional-genomics
#4
Anis Ben-Amar, Samia Daldoul, Götz M Reustle, Gabriele Krczal, Ahmed Mliki
In the post-genomic era, increasingly sophisticated genetic tools are being developed with the long-term goal of understanding how the coordinated activity of genes gives rise to a complex organism. With the advent of the next generation sequencing associated with effective computational approaches, wide variety of plant species have been fully sequenced giving a wealth of data sequence information on structure and organization of plant genomes. Since thousands of gene sequences are already known, recently developed functional genomics approaches provide powerful tools to analyze plant gene functions through various gene manipulation technologies...
December 2016: Current Genomics
https://www.readbyqxmd.com/read/28211524/epigenetic-and-genetic-dissections-of-uv-induced-global-gene-dysregulation-in-skin-cells-through-multi-omics-analyses
#5
Yao Shen, Milda Stanislauskas, Gen Li, Deyou Zheng, Liang Liu
To elucidate the complex molecular mechanisms underlying the adverse effects UV radiation (UVR) on skin homeostasis, we performed multi-omics studies to characterize UV-induced genetic and epigenetic changes. Human keratinocytes from a single donor treated with or without UVR were analyzed by RNA-seq, exome-seq, and H3K27ac ChIP-seq at 4 h and 72 h following UVR. Compared to the relatively moderate mutagenic effects of UVR, acute UV exposure induced substantial epigenomic and transcriptomic alterations, illuminating a previously underappreciated role of epigenomic and transcriptomic instability in skin pathogenesis...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28199197/childhood-cancers-and-systems-medicine
#6
William L Stone, Kathryn J Klopfenstein, M J Hajianpour, Marcela I Popescu, Cathleen M Cook, Koymangalath Krishnan
Despite major advances in treatment, pediatric cancers in the 5-16 age group remain the most common cause of disease death, and one out of eight children with cancer will not survive. Among children that do survive, some 60% suffer from late effects such as cancer recurrence and increased risk of obesity. This paper will provide a broad overview of pediatric oncology in the context of systems medicine. Systems medicine utilizes an integrative approach that relies on patient information gained from omics technology...
March 1, 2017: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28198675/predicting-disease-related-genes-using-integrated-biomedical-networks
#7
Jiajie Peng, Kun Bai, Xuequn Shang, Guohua Wang, Hansheng Xue, Shuilin Jin, Liang Cheng, Yadong Wang, Jin Chen
BACKGROUND: Identifying the genes associated to human diseases is crucial for disease diagnosis and drug design. Computational approaches, esp. the network-based approaches, have been recently developed to identify disease-related genes effectively from the existing biomedical networks. Meanwhile, the advance in biotechnology enables researchers to produce multi-omics data, enriching our understanding on human diseases, and revealing the complex relationships between genes and diseases...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28193460/multi-omics-a-critical-technical-perspective-on-integrative-lipidomics-approaches
#8
Dominik Kopczynski, Cristina Coman, Rene P Zahedi, Kristina Lorenz, Albert Sickmann, Robert Ahrends
During the past decades, high-throughput approaches for analyzing different molecular classes such as nucleic acids, proteins, metabolites, and lipids have grown rapidly. These approaches became powerful tools for getting a fundamental understanding of biological systems. Considering each approach and its results separately, relations and causal connections between these classes have no chance to be revealed, since only separate molecular snapshots are provided. Only a combined approach, not fully established yet, with the integration of the corresponding data, might yield a comprehensive and complete understanding of biological processes, such as crosstalk and interactions in signaling pathways...
February 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28188532/pathway-informed-discovery-and-targeted-proteomic-workflows-using-mass-spectrometry
#9
Caroline S Chu, Christine A Miller, Andy Gieschen, Steve M Fischer
Recent advancements in mass spectrometry (MS) and data analysis software have enabled new strategies for biological discovery using proteomics. Proteomics has evolved from routine discovery and identification of proteins to integrated multi-omics projects relating specific proteins to their genes and metabolites. Using additional information, such as that contained in biological pathways, has enabled the use of targeted protein quantitation for monitoring fold changes in expression as well as biomarker discovery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28187711/poppante-population-and-pedigree-association-testing-for-quantitative-data
#10
Alessia Visconti, Mashael Al-Shafai, Wadha A Al Muftah, Shaza B Zaghlool, Massimo Mangino, Karsten Suhre, Mario Falchi
BACKGROUND: Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28187412/omics-fusion-a-platform-for-integrative-analysis-of-omics-data
#11
Benedikt G Brink, Annica Seidel, Nils Kleinbölting, Tim W Nattkemper, Stefan P Albaum
We present Omics Fusion, a new web-based platform for integrative analysis of omics data. Omics Fusion provides a collection of new and established tools and visualization methods to support researchers in exploring omics data, validating results or understanding how to adjust experiments in order to make new discoveries. It is easily extendible and new visualization methods are added continuously. It is available for free under: https://fusion.cebitec.uni-bielefeld.de/.
December 18, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28187207/a-multi-objective-constraint-based-approach-for-modeling-genome-scale-microbial-ecosystems
#12
Marko Budinich, Jérémie Bourdon, Abdelhalim Larhlimi, Damien Eveillard
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients...
2017: PloS One
https://www.readbyqxmd.com/read/28185573/rgmatch-matching-genomic-regions-to-proximal-genes-in-omics-data-integration
#13
Pedro Furió-Tarí, Ana Conesa, Sonia Tarazona
BACKGROUND: The integrative analysis of multiple genomics data often requires that genome coordinates-based signals have to be associated with proximal genes. The relative location of a genomic region with respect to the gene (gene area) is important for functional data interpretation; hence algorithms that match regions to genes should be able to deliver insight into this information. RESULTS: In this work we review the tools that are publicly available for making region-to-gene associations...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28185567/from-comorbidities-of-chronic-obstructive-pulmonary-disease-to-identification-of-shared-molecular-mechanisms-by-data-integration
#14
David Gomez-Cabrero, Jörg Menche, Claudia Vargas, Isaac Cano, Dieter Maier, Albert-László Barabási, Jesper Tegnér, Josep Roca
BACKGROUND: Deep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations have generated high-resolution molecular maps of putative relevance for understanding disease initiation and progression. Yet, it is unclear how to advance an observation of comorbidity relations (one disease to others) to a molecular understanding of the driver processes and associated biomarkers. RESULTS: Since Chronic Obstructive Pulmonary disease (COPD) has emerged as a central hub in temporal comorbidity networks, we developed a systematic integrative data-driven framework to identify shared disease-associated genes and pathways, as a proxy for the underlying generative mechanisms inducing comorbidity...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28183433/mechanisms-of-the-development-of-allergy-medall-introducing-novel-concepts-in-allergy-phenotypes
#15
REVIEW
Josep M Anto, Jean Bousquet, Mubeccel Akdis, Charles Auffray, Thomas Keil, Isabelle Momas, Dirkje S Postma, Rudolf Valenta, Magnus Wickman, Anne Cambon-Thomsen, Tari Haahtela, Bart N Lambrecht, Karin C Lodrup Carlsen, Gerard H Koppelman, Jordi Sunyer, Torsten Zuberbier, Isabelle Annesi-Maesano, Albert Arno, Carsten Bindslev-Jensen, Giuseppe De Carlo, Francesco Forastiere, Joachim Heinrich, Marek L Kowalski, Dieter Maier, Erik Melén, Henriette A Smit, Marie Standl, John Wright, Anna Asarnoj, Marta Benet, Natalia Ballardini, Judith Garcia-Aymerich, Ulrike Gehring, Stefano Guerra, Cynthia Hohmann, Inger Kull, Christian Lupinek, Mariona Pinart, Ingebjorg Skrindo, Marit Westman, Delphine Smagghe, Cezmi Akdis, Niklas Andersson, Claus Bachert, Stephane Ballereau, Ferran Ballester, Xavier Basagana, Anna Bedbrook, Anna Bergstrom, Andrea von Berg, Bert Brunekreef, Emilie Burte, Kai-Hakon Carlsen, Leda Chatzi, Jonathan M Coquet, Mirela Curin, Pascal Demoly, Esben Eller, Maria Pia Fantini, Leena von Hertzen, Vergard Hovland, Benedicte Jacquemin, Jocelyne Just, Theresa Keller, Renata Kiss, Manolis Kogevinas, Sibylle Koletzko, Susanne Lau, Irina Lehmann, Nicolas Lemonnier, Mika Mäkelä, Jordi Mestres, Peter Mowinckel, Rachel Nadif, Martijn C Nawijn, Johan Pellet, Isabelle Pin, Daniela Porta, Fanny Rancière, Emmanuelle Rial-Sebbag, Yvan Saeys, Martijn J Schuijs, Valerie Siroux, Christina G Tischer, Mathies Torrent, Raphaelle Varraso, Kalus Wenzel, Cheng-Jian Xu
Asthma, rhinitis, and eczema are complex diseases with multiple genetic and environmental factors interlinked through IgE-associated and non-IgE-associated mechanisms. Mechanisms of the Development of ALLergy (MeDALL; EU FP7-CP-IP; project no: 261357; 2010-2015) studied the complex links of allergic diseases at the clinical and mechanistic levels by linking epidemiologic, clinical, and mechanistic research, including in vivo and in vitro models. MeDALL integrated 14 European birth cohorts, including 44,010 participants and 160 cohort follow-ups between pregnancy and age 20 years...
February 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28176637/personalized-medicine-applied-to-forensic-sciences-new-advances-and-perspectives-for-a-tailored-forensic-approach
#16
Alessandro Santurro, Anna Maria Vullo, Marina Borro, Giovanna Gentile, Raffaele La Russa, Maurizio Simmaco, Paola Frati, Vittorio Fineschi
Personalized medicine (PM), included in P5 medicine (Personalized, Predictive, Preventive, Participative and Precision medicine) is an innovative approach to the patient, emerging from the need to tailor and to fit the profile of each individual. PM promises to dramatically impact also on forensic sciences and justice system in ways we are only beginning to understand. The application of omics (genomic, transcriptomics, epigenetics/imprintomics, proteomic and metabolomics) is ever more fundamental in the so called "molecular autopsy"...
February 7, 2017: Current Pharmaceutical Biotechnology
https://www.readbyqxmd.com/read/28174585/the-understanding-of-the-plant-iron-deficiency-responses-in-strategy-i-plants-and-the-role-of-ethylene-in-this-process-by-omic-approaches
#17
REVIEW
Wenfeng Li, Ping Lan
Iron (Fe) is an essential plant micronutrient but is toxic in excess. Fe deficiency chlorosis is a major constraint for plant growth and causes severe losses of crop yields and quality. Under Fe deficiency conditions, plants have developed sophisticated mechanisms to keep cellular Fe homeostasis via various physiological, morphological, metabolic, and gene expression changes to facilitate the availability of Fe. Ethylene has been found to be involved in the Fe deficiency responses of plants through pharmacological studies or by the use of ethylene mutants...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28170342/linking-childhood-allergic-asthma-phenotypes-with-endotype-through-integrated-systems-biology-current-evidence-and-research-needs
#18
Hyunok Choi, Won-Min Song, Bin Zhang
Asthma and other complex diseases results from a complex web of interactions involving inflammation, immunity, cell cycle, apoptosis, and metabolic perturbations across multiple organ systems. The extent to which various degrees of the age at onset, symptom severity, and the natural progression of the disease reflect multiple disease subtypes, influenced by unique process of development remains unknown. One of the most critical challenges to our understanding stems from incomplete understanding of the mechanisms...
February 7, 2017: Reviews on Environmental Health
https://www.readbyqxmd.com/read/28163971/solving-the-puzzle-what-is-behind-our-forefathers-anti-inflammatory-remedies
#19
REVIEW
Javier Rodriguez Villanueva, Jorge Martín Esteban, Laura Rodríguez Villanueva
Inflammation is a ubiquitous host response in charge of restoring normal tissue structure and function but is a double-edged sword, as the uncontrolled or excessive process can lead to the injury of host cells, chronic inflammation, chronic diseases, and also neoplastic transformation. Throughout history, a wide range of species has been claimed to have anti-inflammatory effects worldwide. Among them, Angelica sinensis, Tropaeolum majus, Castilleja tenuiflora, Biophytum umbraculum, to name just a few, have attracted the scientific and general public attention in the last years...
January 2017: Journal of Intercultural Ethnopharmacology
https://www.readbyqxmd.com/read/28162022/proteomic-analysis-of-red-blood-cells-and-the-potential-for-the-clinic-what-have-we-learned-so-far
#20
Angelo D'Alessandro, Lello Zolla
Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating "bags of hemoglobin". The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology...
February 4, 2017: Expert Review of Proteomics
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"