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https://www.readbyqxmd.com/read/29027401/identification-of-dna-methylation-associated-gene-signatures-in-endometrial-cancer-via-integrated-analysis-of-dna-methylation-and-gene-expression-systematically
#1
Chuandi Men, Hongjuan Chai, Xumin Song, Yue Li, Huawen Du, Qing Ren
OBJECTIVE: Endometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC. METHODS: The data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed...
November 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/29026940/advanced-bioanalytics-for-precision-medicine
#2
Aldo Roda, Elisa Michelini, Cristiana Caliceti, Massimo Guardigli, Mara Mirasoli, Patrizia Simoni
Precision medicine is a new paradigm that combines diagnostic, imaging, and analytical tools to produce accurate diagnoses and therapeutic interventions tailored to the individual patient. This approach stands in contrast to the traditional "one size fits all" concept, according to which researchers develop disease treatments and preventions for an "average" patient without considering individual differences. The "one size fits all" concept has led to many ineffective or inappropriate treatments, especially for pathologies such as Alzheimer's disease and cancer...
October 12, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29024724/paxgene-fixation-enables-comprehensive-metabolomic-and-proteomic-analyses-of-tissue-specimens-by-maldi-msi
#3
Christian Urban, Achim Buck, Jens T Siveke, Florian Lordick, Birgit Luber, Axel Walch, Michaela Aichler
An alcohol-based non-crosslinking tissue fixative, PAXgene Tissue System, has been proposed as alternative fixation method to formalin, providing superior and morphological preservation. To date, metabolites have not been assessed in PAXgene-fixed tissues. The study focuses on a comparison between PAXgene and standard formalin fixation for metabolomic analysis by MALDI mass spectrometry imaging. Therefore, fifty-six samples from seven mice organs were fixed with PAXgene (PFPE) or formalin (FFPE), embedded in paraffin, and processed to a tissue microarray...
October 9, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29021832/pharmacogenomics-in-the-treatment-of-mood-disorders-strategies-and-opportunities-for-personalized-psychiatry
#4
REVIEW
Azmeraw T Amare, Klaus Oliver Schubert, Bernhard T Baune
Personalized medicine (personalized psychiatry in a specific setting) is a new model towards individualized care, in which knowledge from genomics and other omic pillars (microbiome, epigenomes, proteome, and metabolome) will be combined with clinical data to guide efforts to new drug development and targeted prescription of the existing treatment options. In this review, we summarize pharmacogenomic studies in mood disorders that may lay the foundation towards personalized psychiatry. In addition, we have discussed the possible strategies to integrate data from omic pillars as a future path to personalized psychiatry...
September 2017: EPMA Journal
https://www.readbyqxmd.com/read/29020009/genome-sequences-of-lower-great-lakes-microcystis-sp-reveal-strain-specific-genes-that-are-present-and-expressed-in-western-lake-erie-blooms
#5
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
https://www.readbyqxmd.com/read/29019032/nanotechnology-as-a-delivery-tool-for-precision-cancer-therapies
#6
Bhawna Sharma, Rachael M Crist, Pavan P Adiseshaiah
Genomic analyses from patients with cancer have improved the understanding of the genetic elements that drive the disease, provided new targets for treating this relentless disease, and offered criteria for stratifying patient populations that will benefit most from treatments. In the last decade, several new targeted therapies have been approved by the FDA based on these omics findings, leading to significantly improved survival and quality of life for select patient populations. However, many of these precision medicines, e...
October 10, 2017: AAPS Journal
https://www.readbyqxmd.com/read/29018224/integrative-analysis-of-genomic-and-epigenomic-regulation-of-the-transcriptome-in-liver-cancer
#7
Hyun Goo Woo, Ji-Hye Choi, Sarah Yoon, Byul A Jee, Eun Ju Cho, Jeong-Hoon Lee, Su Jong Yu, Jung-Hwan Yoon, Nam-Joon Yi, Kwang-Woong Lee, Kyung-Suk Suh, Yoon Jun Kim
Hepatocellular carcinoma harbors numerous genomic and epigenomic aberrations of DNA copy numbers and DNA methylation. Transcriptomic deregulation by these aberrations plays key driver roles in heterogeneous progression of cancers. Here, we profile DNA copy numbers, DNA methylation, and messenger RNA expression levels from 64 cases of hepatocellular carcinoma specimens. We find that the frequencies of the aberrancies of the DNA copy-number-correlated (CNVcor) expression genes and the methylation-correlated expression (METcor) genes are co-regulated significantly...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28994524/-clinical-value-evaluation-of-chinese-herbal-formula-in-context-of-multi-omics-network
#8
Bing Li, Fei Han, Zhong Wang, Yong-Yan Wang
Clinical value evaluation is the key issue to solve the problems such as high repetition rate, fuzzy clinical positioning, broad indications and unclear clinical values in Chinese herbal formula(Chinese patent medicine). By analyzing the challenges and opportunities of Chinese herbal formula in clinical value evaluation, this paper introduced a strategy of multi-omic network analysis. Through comparative analysis of three stroke treatment formulas, we suggested their different characteristic advantages for variant symptoms or phenotypes of stroke, which may provide reference for rational clinical choice...
March 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28993761/pcr-and-omics-based-techniques-to-study-the-diversity-ecology-and-biology-of-anaerobic-fungi-insights-challenges-and-opportunities
#9
REVIEW
Joan E Edwards, Robert J Forster, Tony M Callaghan, Veronika Dollhofer, Sumit S Dagar, Yanfen Cheng, Jongsoo Chang, Sandra Kittelmann, Katerina Fliegerova, Anil K Puniya, John K Henske, Sean P Gilmore, Michelle A O'Malley, Gareth W Griffith, Hauke Smidt
Anaerobic fungi (phylum Neocallimastigomycota) are common inhabitants of the digestive tract of mammalian herbivores, and in the rumen, can account for up to 20% of the microbial biomass. Anaerobic fungi play a primary role in the degradation of lignocellulosic plant material. They also have a syntrophic interaction with methanogenic archaea, which increases their fiber degradation activity. To date, nine anaerobic fungal genera have been described, with further novel taxonomic groupings known to exist based on culture-independent molecular surveys...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28992596/deciphering-the-electric-code-of-geobacter-sulfurreducens-in-cocultures-with-pseudomonas-aeruginosa-via-swath-ms-proteomics
#10
Lucie Semenec, Andrew E Laloo, Benjamin L Schulz, Ismael A Vergara, Philip L Bond, Ashley E Franks
Interspecies electron transfer (IET) occurs in many microbial communities, enabling extracellular electron exchange for syntrophic utilization of mixed resources. Various mechanisms of IET have been characterized including direct IET (DIET) and hydrogen IET (HIT) but their evolution throughout syntrophic adaptation has not been investigated through an omics approach. A syntrophic coculture of Geobacter sulfurreducens and Pseudomonas aeruginosa was established and evolved in restricted medium. The medium required cooperative metabolism due to preferential utilization of formate and fumarate by P...
October 3, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/28992371/the-impact-of-the-omics-era-on-the-knowledge-and-use-of-lysobacter-spp-to-control-phytopathogenic-microorganisms
#11
REVIEW
Gerardo Puopolo, Selena Tomada, Ilaria Pertot
Omics technologies have had a tremendous impact on under-investigated genera of plant disease biocontrol agents such as Lysobacter. Strong evidence of the association between Lysobacter spp. and the rhizosphere has been obtained through culture independent methods, which has also contributed towards highlighting the relationship between Lysobacter abundance and soil suppressiveness. It is conceivable that the role played by Lysobacter spp. in soil suppressiveness is related to their ability to produce an impressive array of lytic enzymes and antibiotics...
October 9, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28992289/transcriptomics-in-kidney-biopsy-is-an-untapped-resource-for-precision-therapy-in-nephrology-a-systematic-review
#12
Francesco Paolo Schena, Ionut Nistor, Claudia Curci
Background: The diagnosis of glomerular diseases is based on the evaluation of histological lesions in renal tissue by means of light and electronic microscopy, and immunofluorescence technique. Frozen and archival formalin-fixed paraffin-embedded kidney biopsies represent a stored resource for high-throughput technologies. Transcriptomics makes it possible to study the whole gene-expression profile of cells and tissues in a specific period and/or condition. The results, whether considered alone or integrated with other omics data, could help to improve existing knowledge about the pathogenetic mechanisms of glomerulopathies...
August 1, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/28986783/protein-function-prediction
#13
Leonardo Magalhães Cruz, Sheyla Trefflich, Vinícius Almir Weiss, Mauro Antônio Alves Castro
Protein function is a concept that can have different interpretations in different biological contexts, and the number and diversity of novel proteins identified by large-scale "omics" technologies poses increasingly new challenges. In this review we explore current strategies used to predict protein function focused on high-throughput sequence analysis, as for example, inference based on sequence similarity, sequence composition, structure, and protein-protein interaction. Various prediction strategies are discussed together with illustrative workflows highlighting the use of some benchmark tools and knowledge bases in the field...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28983483/a-comprehensive-infrastructure-for-big-data-in-cancer-research-accelerating-cancer-research-and-precision-medicine
#14
Izumi V Hinkson, Tanja M Davidsen, Juli D Klemm, Anthony R Kerlavage, Warren A Kibbe
Advancements in next-generation sequencing and other -omics technologies are accelerating the detailed molecular characterization of individual patient tumors, and driving the evolution of precision medicine. Cancer is no longer considered a single disease, but rather, a diverse array of diseases wherein each patient has a unique collection of germline variants and somatic mutations. Molecular profiling of patient-derived samples has led to a data explosion that could help us understand the contributions of environment and germline to risk, therapeutic response, and outcome...
2017: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/28981707/the-encyclopedia-of-proteome-dynamics-a-big-data-ecosystem-for-prote-omics
#15
Alejandro Brenes, Vackar Afzal, Robert Kent, Angus I Lamond
Driven by improvements in speed and resolution of mass spectrometers (MS), the field of proteomics, which involves the large-scale detection and analysis of proteins in cells, tissues and organisms, continues to expand in scale and complexity. There is a resulting growth in datasets of both raw MS files and processed peptide and protein identifications. MS-based proteomics technology is also used increasingly to measure additional protein properties affecting cellular function and disease mechanisms, including post-translational modifications, protein-protein interactions, subcellular and tissue distributions...
September 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28981699/individual-specific-edge-network-analysis-for-disease-prediction
#16
Xiangtian Yu, Jingsong Zhang, Shaoyan Sun, Xin Zhou, Tao Zeng, Luonan Chen
Predicting pre-disease state or tipping point just before irreversible deterioration of health is a difficult task. Edge-network analysis (ENA) with dynamic network biomarker (DNB) theory opens a new way to study this problem by exploring rich dynamical and high-dimensional information of omics data. Although theoretically ENA has the ability to identify the pre-disease state during the disease progression, it requires multiple samples for such prediction on each individual, which are generally not available in clinical practice, thus limiting its applications in personalized medicine...
September 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28981577/-multi-omic-data-analysis-using-o-miner
#17
Ajanthah Sangaralingam, Abu Z Dayem Ullah, Jacek Marzec, Emanuela Gadaleta, Ai Nagano, Helen Ross-Adams, Jun Wang, Nicholas R Lemoine, Claude Chelala
Innovations in -omics technologies have driven advances in biomedical research. However, integrating and analysing the large volumes of data generated from different high-throughput -omics technologies remain a significant challenge to basic and clinical scientists without bioinformatics skills or access to bioinformatics support. To address this demand, we have significantly updated our previous O-miner analytical suite, to incorporate several new features and data types to provide an efficient and easy-to-use Web tool for the automated analysis of data from '-omics' technologies...
August 4, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28979258/tools-for-genomic-and-transcriptomic-analysis-of-microbes-at-single-cell-level
#18
REVIEW
Zixi Chen, Lei Chen, Weiwen Zhang
Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28977416/imota-an-interactive-multi-omics-tissue-atlas-for-the-analysis-of-human-mirna-target-interactions
#19
Valeria Palmieri, Christina Backes, Nicole Ludwig, Tobias Fehlmann, Fabian Kern, Eckart Meese, Andreas Keller
Web repositories for almost all 'omics' types have been generated-detailing the repertoire of representatives across different tissues or cell types. A logical next step is the combination of these valuable sources. With IMOTA (interactive multi omics tissue atlas), we developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between mRNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens. IMOTA also contains data on tissue-specific interactions, e...
August 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28974620/time-resolved-transposon-insertion-sequencing-reveals-genome-wide-fitness-dynamics-during-infection
#20
Guanhua Yang, Gabriel Billings, Troy P Hubbard, Joseph S Park, Ka Yin Leung, Qin Liu, Brigid M Davis, Yuanxing Zhang, Qiyao Wang, Matthew K Waldor
Transposon insertion sequencing (TIS) is a powerful high-throughput genetic technique that is transforming functional genomics in prokaryotes, because it enables genome-wide mapping of the determinants of fitness. However, current approaches for analyzing TIS data assume that selective pressures are constant over time and thus do not yield information regarding changes in the genetic requirements for growth in dynamic environments (e.g., during infection). Here, we describe structured analysis of TIS data collected as a time series, termed pattern analysis of conditional essentiality (PACE)...
October 3, 2017: MBio
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