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https://www.readbyqxmd.com/read/29036542/database-resources-of-the-big-data-center-in-2018
#1
(no author information available yet)
The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations)...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035928/what-did-we-learn-from-omics-studies-in-osteoarthritis
#2
Cristina Ruiz-Romero, Ignacio Rego-Perez, Francisco J Blanco
PURPOSE OF REVIEW: 'Omics' technologies developed for the massive analysis of the major biologically relevant molecules (genes, proteins, metabolites) have been applied to the study of osteoarthritis (OA) for more than a decade. RECENT FINDINGS: 'Omics' studies have undoubtedly contributed to increase the knowledge on pathogenic processes related with OA and have provided hundreds to thousands of molecules that might have a putative biomarker utility for this disease...
October 13, 2017: Current Opinion in Rheumatology
https://www.readbyqxmd.com/read/29033902/analyzing-the-complex-regulatory-landscape-of-hfq-an-integrative-multi-omics-approach
#3
Lucia Grenga, Govind Chandra, Gerhard Saalbach, Carla V Galmozzi, G√ľnter Kramer, Jacob G Malone
The ability of bacteria to respond to environmental change is based on the ability to coordinate, redirect and fine-tune their genetic repertoire as and when required. While we can learn a great deal from reductive analysis of individual pathways and global approaches to gene regulation, a deeper understanding of these complex signaling networks requires the simultaneous consideration of several regulatory layers at the genome scale. To highlight the power of this approach we analyzed the Hfq transcriptional/translational regulatory network in the model bacterium Pseudomonas fluorescens...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29032385/exercise-training-response-heterogeneity-physiological-and-molecular-insights
#4
REVIEW
Lauren M Sparks
The overall beneficial effects of exercise are well studied, but why some people do not respond favourably to exercise is less understood. The National Institutes of Health Common Fund has recently launched the large-scale discovery project 'Molecular Transducers of Physical Activity in Humans' to examine the physiological and molecular (i.e. genetic, epigenetic, lipidomic, metabolomic, proteomic, etc.) responses to exercise training. A nationwide, multicentre clinical trial such as this one also provides a unique opportunity to robustly investigate the non-response to exercise in thousands of individuals that have undergone supervised aerobic- and resistance-based exercise training interventions...
October 14, 2017: Diabetologia
https://www.readbyqxmd.com/read/29029599/liverwiki-a-wiki-based-database-for-human-liver
#5
Tao Chen, Mansheng Li, Qiang He, Lei Zou, Youhuan Li, Cheng Chang, Dongyan Zhao, Yunping Zhu
BACKGROUND: Recent advances in omics technology have produced a large amount of liver-related data. A comprehensive and up-to-date source of liver-related data is needed to allow biologists to access the latest data. However, current liver-related data sources each cover only a specific part of the liver. It is difficult for them to keep pace with the rapid increase of liver-related data available at those data resources. Integrating diverse liver-related data is a critical yet formidable challenge, as it requires sustained human effort...
October 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29027766/kinetic-modeling-of-mammalian-cell-culture-bioprocessing-the-quest-to-advance-biomanufacturing
#6
REVIEW
Sarantos Kyriakopoulos, Kok Siong Ang, Meiyappan Lakshmanan, Zhuangrong Huang, Seongkyu Yoon, Rudiyanto Gunawan, Dong-Yup Lee
Kinetic modeling is the most suitable framework to describe the dynamic behavior of mammalian cell culture although its industrial application is still in its infancy. Herein, we review mammalian bioprocess relevant kinetic models and found that the simple unstructured-unsegregated approach utilizing empirical Monod type kinetics based on limiting substrates and inhibitory metabolites is commonly used due to the traceability and simple formalism. Notably, the available kinetic models are typically small to moderate in size and the development of large-scale models is severely hampered by the scarcity of kinetic data and limitations in current parameter estimation methods...
October 13, 2017: Biotechnology Journal
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
#7
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/29025326/onco-proteogenomics-multi-omics-level-data-integration-for-accurate-phenotype-prediction
#8
Lampros Dimitrakopoulos, Ioannis Prassas, Eleftherios P Diamandis, George S Charames
The overall goal of translational oncology is to identify molecular alterations indicative of cancer or of responsiveness to specific therapeutic regimens. While next-generation sequencing has played a pioneering role in this quest, the latest advances in proteomic technologies promise to provide a holistic approach to the further elucidation of tumor biology. Genetic information may be written in DNA and flow from DNA to RNA to protein, according to the central dogma of molecular biology, but the observed phenotype is dictated predominantly by the DNA protein coding region-derived proteotype...
October 12, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/29021832/pharmacogenomics-in-the-treatment-of-mood-disorders-strategies-and-opportunities-for-personalized-psychiatry
#9
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/29018224/integrative-analysis-of-genomic-and-epigenomic-regulation-of-the-transcriptome-in-liver-cancer
#10
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/28993504/precision-transplant-medicine-biomarkers-to-the-rescue
#11
Maarten Naesens, Dany Anglicheau
The concept that individuals with the same disease and a similar clinical presentation may have very different outcomes and need very different therapies is not novel. With the development of many innovative tools derived from the omics technologies, transplant medicine is slowly entering the era of precision medicine. Biomarkers are the cornerstone of precision medicine, which aims to integrate biomarkers with traditional clinical information and tailor medical care to achieve the best outcome for an individual patient...
October 9, 2017: Journal of the American Society of Nephrology: JASN
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/28992051/new-insights-into-the-regulation-of-leaf-senescence-in-arabidopsis
#13
Jeongsik Kim, Jin Hee Kim, Jae Il Lyu, Hye Ryun Woo, Pyung Ok Lim
Plants undergo developmental changes throughout their life history. Senescence, the final stage in the life history of a leaf, is an important and unique developmental process whereby plants relocate nutrients from leaves to other developing organs, such as seeds, stems, or roots. Recent attempts to answer fundamental questions about leaf senescence have employed a combination of new ideas and advanced technologies. As senescence is an integral part of a plant's life history that is linked to earlier developmental stages, age-associated leaf senescence may be analysed from a life history perspective...
August 24, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28987922/the-impact-of-systems-biology-on-bioprocessing
#14
REVIEW
Kate Campbell, Jianye Xia, Jens Nielsen
Bioprocessing offers a sustainable and green approach to the production of chemicals. However, a bottleneck in introducing bioprocesses is cell factory development, which is costly and time-consuming. A systems biology approach can expedite cell factory design by using genome-wide analyses alongside mathematical modeling to characterize and predict cellular physiology. This approach can drive cycles of design, build, test, and learn implemented by metabolic engineers to optimize the cell factory performance...
October 4, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28983045/single-cell-epigenomics-recording-the-past-and-predicting-the-future
#15
REVIEW
Gavin Kelsey, Oliver Stegle, Wolf Reik
Single-cell multi-omics has recently emerged as a powerful technology by which different layers of genomic output-and hence cell identity and function-can be recorded simultaneously. Integrating various components of the epigenome into multi-omics measurements allows for studying cellular heterogeneity at different time scales and for discovering new layers of molecular connectivity between the genome and its functional output. Measurements that are increasingly available range from those that identify transcription factor occupancy and initiation of transcription to long-lasting and heritable epigenetic marks such as DNA methylation...
October 6, 2017: Science
https://www.readbyqxmd.com/read/28982688/deep-learning-based-multi-omics-integration-robustly-predicts-survival-in-liver-cancer
#16
Kumardeep Chaudhary, Olivier B Poirion, Liangqun Lu, Lana X Garmire
Identifying robust survival subgroups of hepatocellular carcinoma (HCC) will significantly improve patient care. Currently, endeavor of integrating multi-omics data to explicitly predict HCC survival from multiple patient cohorts is lacking. To fill in this gap, we present a deep learning (DL) based model on HCC that robustly differentiates survival subpopulations of patients in six cohorts. We build the DL based, survival-sensitive model on 360 HCC patients' data using RNA-seq, miRNA-seq and methylation data from TCGA, which predicts prognosis as good as an alternative model where genomics and clinical data are both considered...
October 5, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28981707/the-encyclopedia-of-proteome-dynamics-a-big-data-ecosystem-for-prote-omics
#17
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/28981577/-multi-omic-data-analysis-using-o-miner
#18
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/28971457/integrating-omic-technologies-in-alzheimer-s-disease
#19
Antigoni Avramouli, Panayiotis M Vlamos
Scientific advances in biomedical disciplines have allowed us to identify the underlying causes of many diseases with increased comprehension-leading the way towards precision medicine. In this context, unique disease and medical traits pave the way for the development of adapted disease management, drugs and therapies tailored to each patient. Bearing in mind that reductionism, an approach that has dominated biomedical research for many years and has resulted in the identification of definite cellular phenotypes and human diseases which are linked with specific integral molecules, we strongly believe that Alzheimer's Disease, one of the most common neurodegenerative diseases, could not be applied to the model of one disease-one assay-one drug...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28971064/models-of-models-a-translational-route-for-cancer-treatment-and-drug-development
#20
Lesley A Ogilvie, Aleksandra Kovachev, Christoph Wierling, Bodo M H Lange, Hans Lehrach
Every patient and every disease is different. Each patient therefore requires a personalized treatment approach. For technical reasons, a personalized approach is feasible for treatment strategies such as surgery, but not for drug-based therapy or drug development. The development of individual mechanistic models of the disease process in every patient offers the possibility of attaining truly personalized drug-based therapy and prevention. The concept of virtual clinical trials and the integrated use of in silico, in vitro, and in vivo models in preclinical development could lead to significant gains in efficiency and order of magnitude increases in the cost effectiveness of drug development and approval...
2017: Frontiers in Oncology
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