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Bioinformatics, informatics

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https://www.readbyqxmd.com/read/29191560/msbis-a-multi-step-biomedical-informatics-screening-approach-for-identifying-medications-that-mitigate-the-risks-of-metoclopramide-induced-tardive-dyskinesia
#1
Dong Xu, Alexandrea G Ham, Rickey D Tivis, Matthew L Caylor, Aoxiang Tao, Steve T Flynn, Peter J Economen, Hung K Dang, Royal W Johnson, Vaughn L Culbertson
In 2009 the U.S. Food and Drug Administration (FDA) placed a black box warning on metoclopramide (MCP) due to the increased risks and prevalence of tardive dyskinesia (TD). In this study, we developed a multi-step biomedical informatics screening (MSBIS) approach leveraging publicly available bioactivity and drug safety data to identify concomitant drugs that mitigate the risks of MCP-induced TD. MSBIS includes (1) TargetSearch (http://dxulab.org/software) bioinformatics scoring for drug anticholinergic activity using CHEMBL bioactivity data; (2) unadjusted odds ratio (UOR) scoring for indications of TD-mitigating effects using the FDA Adverse Event Reporting System (FAERS); (3) adjusted odds ratio (AOR) re-scoring by removing the effect of cofounding factors (age, gender, reporting year); (4) logistic regression (LR) coefficient scoring for confirming the best TD-mitigating drug candidates...
November 22, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29177666/computational-analysis-of-the-chaperone-interaction-networks
#2
Ashwani Kumar, Kamran Rizzolo, Sandra Zilles, Mohan Babu, Walid A Houry
We provide computational protocols to identify chaperone interacting proteins using a combination of both physical (protein-protein) and genetic (gene-gene or epistatic) interaction data derived from the published large-scale proteomic and genomic studies for the budding yeast Saccharomyces cerevisiae. Using these datasets, we discuss bioinformatic analyses that can be employed to build comprehensive high-fidelity chaperone interaction networks. Given that many proteins typically function as complexes in the cell, we highlight various step-wise approaches for combining both the genetic and physical interaction datasets to decipher intra- and inter-connections for distinct chaperone- and non-chaperone-containing complexes in the network...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#3
REVIEW
Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S Kip, Eric W Klee, Stephen E Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L Temple-Smolkin, Karl V Voelkerding, Chen Wang, Alexis B Carter
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29136101/identification-of-topological-features-in-renal-tumor-microenvironment-associated-with-patient-survival
#4
Jun Cheng, Xiaokui Mo, Xusheng Wang, Anil Parwani, Qianjin Feng, Kun Huang
Motivation: As a highly heterogeneous disease, the progression of tumor is not only achieved by unlimited growth of the tumor cells, but also supported, stimulated, and nurtured by the microenvironment around it. However traditional qualitative and/or semi-quantitative parameters obtained by pathologist's visual examination have very limited capability to capture this interaction between tumor and its microenvironment. With the advent of digital pathology, computerized image analysis may provide a better tumor characterization and give new insights into this problem...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29092930/developing-cancer-informatics-applications-and-tools-using-the-nci-genomic-data-commons-api
#5
Shane Wilson, Michael Fitzsimons, Martin Ferguson, Allison Heath, Mark Jensen, Josh Miller, Mark W Murphy, James Porter, Himanso Sahni, Louis Staudt, Yajing Tang, Zhining Wang, Christine Yu, Junjun Zhang, Vincent Ferretti, Robert L Grossman
The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers...
November 1, 2017: Cancer Research
https://www.readbyqxmd.com/read/29063563/findings-from-the-section-on-bioinformatics-and-translational-informatics
#6
H Dauchel, T Lecroq
Objective: To summarize excellent current research and propose a selection of best papers published in 2016 in the field of Bioinformatics and Translational Informatics with applications in the health domain and clinical care. Methods: We provide a synopsis of the articles selected for the IMIA Yearbook 2017, from which we attempt to derive a synthetic overview of current and future activities in the field. As in 2016, a first step of selection was performed by querying MEDLINE with a list of MeSH descriptors completed by a list of terms adapted to the section coverage...
August 2017: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/29054270/the-peptidome-comes-of-age-mass-spectrometry-based-characterization-of-the-circulating-cancer-peptidome
#7
David W Greening, Eugene A Kapp, Richard J Simpson
Peptides play a seminal role in most physiological processes acting as neurotransmitters, hormones, antibiotics, and immune regulation. In the context of tumor biology, it is hypothesized that endogenous peptides, hormones, cytokines, growth factors, and aberrant degradation of select protein networks (e.g., enzymatic activities, protein shedding, and extracellular matrix remodeling) are fundamental in mediating cancer progression. Analysis of peptides in biological fluids by mass spectrometry holds promise of providing sensitive and specific diagnostic and prognostic information for cancer and other diseases...
2017: Enzymes
https://www.readbyqxmd.com/read/28984207/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-summary-and-innovation-in-genomics
#8
EDITORIAL
Zhongming Zhao, Zhandong Liu, Ken Chen, Yan Guo, Genevera I Allen, Jiajie Zhang, W Jim Zheng, Jianhua Ruan
In this editorial, we first summarize the 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) that was held on December 8-10, 2016 in Houston, Texas, USA, and then briefly introduce the ten research articles included in this supplement issue. ICIBM 2016 included four workshops or tutorials, four keynote lectures, four conference invited talks, eight concurrent scientific sessions and a poster session for 53 accepted abstracts, covering current topics in bioinformatics, systems biology, intelligent computing, and biomedical informatics...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28984189/the-international-conference-on-intelligent-biology-and-medicine-icibm-2016-from-big-data-to-big-analytical-tools
#9
EDITORIAL
Zhandong Liu, W Jim Zheng, Genevera I Allen, Yin Liu, Jianhua Ruan, Zhongming Zhao
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28978020/mitochondrial-biomarkers-predict-tumor-progression-and-poor-overall-survival-in-gastric-cancers-companion-diagnostics-for-personalized-medicine
#10
Federica Sotgia, Michael P Lisanti
Here, we employed a bioinformatics approach to identify novel molecular determinants to predict tumor progression and overall survival in gastric cancer patients. In particular, we directly assessed whether nuclear-derived mRNA species encoding proteins involved in mitochondrial protein translation and OXPHOS are able to successfully predict clinical outcome in gastric cancer. As such, using in silico validation, we have now established the prognostic value of these mitochondrial biomarkers, in a defined population of gastric cancer patients...
September 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28968749/omics-analysis-system-for-precision-oncology-oasispro-a-web-based-omics-analysis-tool-for-clinical-phenotype-prediction
#11
Kun-Hsing Yu, Michael R Fitzpatrick, Luke Pappas, Warren Chan, Jessica Kung, Michael Snyder
Summary: Precision oncology is an approach that accounts for individual differences to guide cancer management. Omics signatures have been shown to predict clinical traits for cancer patients. However, the vast amount of omics information poses an informatics challenge in systematically identifying patterns associated with health outcomes, and no general-purpose data-mining tool exists for physicians, medical researchers, and citizen scientists without significant training in programming and bioinformatics...
September 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28930581/biophysical-mechanisms-complementing-classical-cell-biology
#12
Richard H W Funk
This overview addresses phenomena in cell- and molecular biology which are puzzling by their fast and highly coordinated way of organization. Generally, it appears that informative processes probably involved are more on the biophysical than on the classical biochemical side. The coordination problem is explained within the first part of the review by the topic of endogenous electrical phenomena. These are found e.g. in fast tissue organization and reorganization processes like development, wound healing and regeneration...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28916932/informatics-for-nutritional-genetics-and-genomics
#13
Yuan Gao, Jiajia Chen
While traditional nutrition science is focusing on nourishing population, modern nutrition is aiming at benefiting individual people. The goal of modern nutritional research is to promote health, prevent diseases, and improve performance. With the development of modern technologies like bioinformatics, metabolomics, and molecular genetics, this goal is becoming more attainable. In this chapter, we will discuss the new concepts and technologies especially in informatics and molecular genetics and genomics, and how they have been implemented to change the nutrition science and lead to the emergence of new branches like nutrigenomics, nutrigenetics, and nutritional metabolomics...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28902453/implementing-a-web-based-introductory-bioinformatics-course-for-non-bioinformaticians-that-incorporates-practical-exercises
#14
Antony T Vincent, Yves Bourbonnais, Jean-Simon Brouard, Hélène Deveau, Arnaud Droit, Stéphane M Gagné, Michel Guertin, Claude Lemieux, Louis Rathier, Steve J Charette, Patrick Lagüe
A recent scientific discipline, bioinformatics, defined as using informatics for the study of biological problems, is now a requirement for the study of biological sciences. Bioinformatics has become such a powerful and popular discipline that several academic institutions have created programs in this field, allowing students to become specialized. However, biology students who are not involved in a bioinformatics program also need a solid toolbox of bioinformatics software and skills. Therefore, we have developed a completely online bioinformatics course for non-bioinformaticians, entitled "BIF-1901 Introduction à la bio-informatique et à ses outils (Introduction to bioinformatics and bioinformatics tools)," given by the Department of Biochemistry, Microbiology, and Bioinformatics of Université Laval (Quebec City, Canada)...
September 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28859346/data-science-priorities-for-a-university-hospital-based-institute-of-infectious-diseases-a-viewpoint
#15
Alain-Jacques Valleron
Automation of laboratory tests, bioinformatic analysis of biological sequences, and professional data management are used routinely in a modern university hospital-based infectious diseases institute. This dates back to at least the 1980s. However, the scientific methods of this 21st century are changing with the increased power and speed of computers, with the "big data" revolution having already happened in genomics and environment, and eventually arriving in medical informatics. The research will be increasingly "data driven," and the powerful machine learning methods whose efficiency is demonstrated in daily life will also revolutionize medical research...
August 15, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28851658/benzodiazepines-use-and-breast-cancer-risk-a-population-based-study-and-gene-expression-profiling-evidence
#16
Usman Iqbal, Tzu-Hao Chang, Phung-Anh Nguyen, Shabbir Syed-Abdul, Hsuan-Chia Yang, Chih-Wei Huang, Suleman Atique, Wei-Chung Yang, Max Moldovan, Wen-Shan Jian, Min-Huei Hsu, Yun Yen, Yu-Chuan Jack Li
The aim of this study was to investigate whether long-term use of Benzodiazepines (BZDs) is associated with breast cancer risk through the combination of population-based observational and gene expression profiling evidence. We conducted a population-based case-control study by using 1998 to 2009year Taiwan National Health Insurance Research Database and investigated the association between BZDs use and breast cancer risk. We selected subjects age of >20years old and six eligible controls matched for age, sex and the index date (i...
October 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/28822794/lipidomics-informatics-for-life-science
#17
D Schwudke, A Shevchenko, N Hoffmann, R Ahrends
Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines...
November 10, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28802167/induction-of-senescence-in-cancer-cells-by-5-aza-2-deoxycytidine-bioinformatics-and-experimental-insights-to-its-targets
#18
Jayarani F Putri, Nashi Widodo, Kazuichi Sakamoto, Sunil C Kaul, Renu Wadhwa
5'-Aza-2'-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy...
August 2, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28688561/uncovering-the-pathogenesis-of-microtia-using-bioinformatics-approach
#19
Liu Lei, Liu Zhenzhong, Lin Lin, Pan Bo
OBJECTIVE: Bioinformatics is widely used in the field of cancer research, but in the research of pathogenesis of congenital malformations the situation is different. The aim of this study was to explore the underlying mechanism using bioinformatics approach. METHODS: The data were available from Mouse Genome Informatics and Pubmed. Protein-protein interaction (PPI) network of pathogenic genes was conducted using STRING. Gene ontology and pathway enrichment analyses were also performed to pathogenic genes...
August 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28655203/kronos-a-workflow-assembler-for-genome-analytics-and-informatics
#20
M Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M Grande, Radhouane Aniba, Jasleen Grewal, Paul C Boutros, Ryan D Morin, Ali Bashashati, Sohrab P Shah
Background: The field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into "best practices" for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise. Results: We present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows...
July 1, 2017: GigaScience
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