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https://www.readbyqxmd.com/read/27931036/clinical-exome-sequencing-reveals-mkrn3-pathogenic-variants-in-familial-and-nonfamilial-idiopathic-central-precocious-puberty
#1
Nelmar Valentina Ortiz-Cabrera, Rosa Riveiro-Álvarez, Miguel Ángel López-Martínez, Pilar Pérez-Segura, Isabel Aragón-Gómez, María José Trujillo-Tiebas, Leandro Soriano-Guillén
BACKGROUND/AIMS: Idiopathic central precocious puberty (ICPP) is the premature activation of the hypothalamic-pituitary-gonadal axis in the absence of organic disease. Up to now, just gain-of-function mutations of KISS1/KISS1R and loss-of-function mutations of the maternally imprinted gene MKRN3 are the known genetic causes of ICPP. Our intention is to evaluate variants present in genes related to the pubertal onset pathway that could act as disease-causing or predisposing variants. METHODS: We studied the clinical exome of 20 patients diagnosed with ICPP using the Illumina platform...
December 9, 2016: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/27930808/searching-the-mouse-genome-informatics-mgi-resources-for-information-on-mouse-biology-from-genotype-to-phenotype
#2
David R Shaw
The Mouse Genome Informatics (MGI) resource provides the research community with access to information on the genetics, genomics, and biology of the laboratory mouse. Core data in MGI include gene characterization and function, phenotype and disease model descriptions, DNA and protein sequence data, gene expression data, vertebrate homologies, SNPs, mapping data, and links to other bioinformatics databases. Semantic integration is supported through the use of standardized nomenclature, and through the use of controlled vocabularies such as the mouse Anatomical Dictionary, the Mammalian Phenotype Ontology, and the Gene Ontologies...
December 8, 2016: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/27881428/genome-transcriptome-and-proteome-the-rise-of-omics-data-and-their-integration-in-biomedical-sciences
#3
Claudia Manzoni, Demis A Kia, Jana Vandrovcova, John Hardy, Nicholas W Wood, Patrick A Lewis, Raffaele Ferrari
Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine...
November 22, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27854266/using-technology-bioinformatics-and-health-informatics-approaches-to-improve-learning-experiences-in-optometry-education-research-and-practice
#4
REVIEW
Vivek K Gupta, Veer B Gupta
Rapid advances in ocular diagnostic approaches and emerging links of pathological changes in the eye with systemic disorders have widened the scope of optometry as the front line of eye health care. Expanding professional requirements stipulate that optometry students get a meticulous training in relevant information and communication technologies (ICT) and various bioinformatics and health informatics software to meet current and future challenges. Greater incorporation of ICT approaches in optometry education can facilitate increased student engagement in shared learning experiences and improve collaborative learning...
November 15, 2016: Healthcare (Basel, Switzerland)
https://www.readbyqxmd.com/read/27830252/findings-from-the-section-on-bioinformatics-and-translational-informatics
#5
H Dauchel, T Lecroq
OBJECTIVES: To summarize excellent current research and propose a selection of best papers published in 2015 in the field of Bioinformatics and Translational Informatics with application in the health domain and clinical care. METHOD: We provide a synopsis of the articles selected for the IMIA Yearbook 2016, from which we attempt to derive a synthetic overview of current and future activities in the field. As last year, 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...
November 10, 2016: Yearbook of Medical Informatics
https://www.readbyqxmd.com/read/27807750/biobanks-and-their-clinical-application-and-informatics-challenges
#6
Lan Yang, Yalan Chen, Chunjiang Yu, Bairong Shen
Biobanks are one of the most important biomedical research resources and contribute to the development of biomarker detection, molecular diagnosis, translational medicine, and multidisciplinary disease research, as well as studies of interactions between genetic and environmental or lifestyle factors. Aiming for the wide clinical application of biobanks, biobanking efforts have recently switched from a focus on accumulating samples to both formalizing and sustaining collections in light of the rapid progress in the fields of personalized medicine and bioinformatics analysis...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27685099/separation-and-parallel-sequencing-of-the-genomes-and-transcriptomes-of-single-cells-using-g-t-seq
#7
Iain C Macaulay, Mabel J Teng, Wilfried Haerty, Parveen Kumar, Chris P Ponting, Thierry Voet
Parallel sequencing of a single cell's genome and transcriptome provides a powerful tool for dissecting genetic variation and its relationship with gene expression. Here we present a detailed protocol for G&T-seq, a method for separation and parallel sequencing of genomic DNA and full-length polyA(+) mRNA from single cells. We provide step-by-step instructions for the isolation and lysis of single cells; the physical separation of polyA(+) mRNA from genomic DNA using a modified oligo-dT bead capture and the respective whole-transcriptome and whole-genome amplifications; and library preparation and sequence analyses of these amplification products...
November 2016: Nature Protocols
https://www.readbyqxmd.com/read/27663493/biospark-scalable-analysis-of-large-numerical-datasets-from-biological-simulations-and-experiments-using-hadoop-and-spark
#8
Max Klein, Rati Sharma, Chris H Bohrer, Cameron M Avelis, Elijah Roberts
: Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. AVAILABILITY AND IMPLEMENTATION: Source code is licensed under the Apache 2...
September 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27587087/advancing-systems-biology-in-the-international-conference-on-intelligent-biology-and-medicine-icibm-2015
#9
Zhongming Zhao, Yunlong Liu, Yufei Huang, Kun Huang, Jianhua Ruan
The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology...
August 26, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27577402/visualization-of-large-ontologies-in-university-education-from-a-tool-point-of-view
#10
Michael Schaaf, Franziska Jahn, Kais Tahar, Christian Kücherer, Alfred Winter, Barbara Paech
The realization of ontology visualization requirements in university education is a challenging task and should be supported by appropriate tools. This applies in particular, if the ontology to be visualized is based on a large text corpus that comprises a huge number of concepts, relations and annotations. In SNIK, we developed such an ontology of information management in hospitals in order to support the transfer of knowledge in the context of the university education. The challenge is to identify tools and methods, which are capable to support ontology visualization and usage as efficiently as possible...
2016: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/27573070/gfinder-a-web-based-bioinformatics-tool-for-the-analysis-of-n-glycopeptides
#11
Ju-Wan Kim, Heeyoun Hwang, Jong-Sun Lim, Hyoung-Joo Lee, Seul-Ki Jeong, Jong Shin Yoo, Young-Ki Paik
Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been made toward developing proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here, we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS...
August 30, 2016: Journal of Proteome Research
https://www.readbyqxmd.com/read/27535542/integration-of-bioinformatics-and-imaging-informatics-for-identifying-rare-psen1-variants-in-alzheimer-s-disease
#12
Kwangsik Nho, Emrin Horgusluoglu, Sungeun Kim, Shannon L Risacher, Dokyoon Kim, Tatiana Foroud, Paul S Aisen, Ronald C Petersen, Clifford R Jack, Leslie M Shaw, John Q Trojanowski, Michael W Weiner, Robert C Green, Arthur W Toga, Andrew J Saykin
BACKGROUND: Pathogenic mutations in PSEN1 are known to cause familial early-onset Alzheimer's disease (EOAD) but common variants in PSEN1 have not been found to strongly influence late-onset AD (LOAD). The association of rare variants in PSEN1 with LOAD-related endophenotypes has received little attention. In this study, we performed a rare variant association analysis of PSEN1 with quantitative biomarkers of LOAD using whole genome sequencing (WGS) by integrating bioinformatics and imaging informatics...
2016: BMC Medical Genomics
https://www.readbyqxmd.com/read/27453827/emerging-role-of-bioinformatics-tools-and-software-in-evolution-of-clinical-research
#13
REVIEW
Supreet Kaur Gill, Ajay Francis Christopher, Vikas Gupta, Parveen Bansal
Clinical research is making toiling efforts for promotion and wellbeing of the health status of the people. There is a rapid increase in number and severity of diseases like cancer, hepatitis, HIV etc, resulting in high morbidity and mortality. Clinical research involves drug discovery and development whereas clinical trials are performed to establish safety and efficacy of drugs. Drug discovery is a long process starting with the target identification, validation and lead optimization. This is followed by the preclinical trials, intensive clinical trials and eventually post marketing vigilance for drug safety...
July 2016: Perspectives in Clinical Research
https://www.readbyqxmd.com/read/27424424/-bioinformatics-a-key-role-in-oncology
#14
Timothée Olivier, Pierre Chappuis, Petros Tsantoulis
Bioinformatics is essential in clinical oncology and research. Combining biology, computer science and mathematics, bioinformatics aims to derive useful information from clinical and biological data, often poorly structured, at a large scale. Bioinformatics approaches have reclassified certain cancers based on their molecular and biological presentation, improving treatment selection. Many molecular signatures have been developed and, after validation, some are now usable in clinical practice. Other applications could facilitate daily practice, reduce the risk of error and increase the precision of medical decision-making...
May 18, 2016: Revue Médicale Suisse
https://www.readbyqxmd.com/read/27423895/toppic-a-software-tool-for-top-down-mass-spectrometry-based-proteoform-identification-and-characterization
#15
Qiang Kou, Likun Xun, Xiaowen Liu
: Top-down mass spectrometry enables the observation of whole complex proteoforms in biological samples and provides crucial information complementary to bottom-up mass spectrometry. Because of the complexity of top-down mass spectra and proteoforms, it is a challenging problem to efficiently interpret top-down tandem mass spectra in high-throughput proteome-level proteomics studies. We present TopPIC, a tool that efficiently identifies and characterizes complex proteoforms with unknown primary structure alterations, such as amino acid mutations and post-translational modifications, by searching top-down tandem mass spectra against a protein database...
November 15, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27383682/metagenomics-and-bioinformatics-in-microbial-ecology-current-status-and-beyond
#16
Satoshi Hiraoka, Ching-Chia Yang, Wataru Iwasaki
Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases...
September 29, 2016: Microbes and Environments
https://www.readbyqxmd.com/read/27349566/nqo1-rs1800566-polymorph-is-more-prone-to-nox-induced-lung-injury-endorsing-deleterious-functionality-through-informatics-approach
#17
Zarrin Basharat, Abdelmonaem Messaoudi, Sehrish Ruba, Azra Yasmin
Gene-environment interaction studies have led to the identification of genetic mutations in individuals with increased susceptibility to pollution related diseases. rs1800566 polymorphism of NQO1, leading to P187S missense mutation in the transcribed antioxidant protein, causes individuals carrying this mutation more prone to NO2 induced lung inflammatory injury. Here, we report significant structural and functional changes incurred by NQO1 antioxidant protein as a result of alteration in its nucleotide (C609T) and hence, protein sequence...
October 10, 2016: Gene
https://www.readbyqxmd.com/read/27330567/biotriangle-a-web-accessible-platform-for-generating-various-molecular-representations-for-chemicals-proteins-dnas-rnas-and-their-interactions
#18
Jie Dong, Zhi-Jiang Yao, Ming Wen, Min-Feng Zhu, Ning-Ning Wang, Hong-Yu Miao, Ai-Ping Lu, Wen-Bin Zeng, Dong-Sheng Cao
BACKGROUND: More and more evidences from network biology indicate that most cellular components exert their functions through interactions with other cellular components, such as proteins, DNAs, RNAs and small molecules. The rapidly increasing amount of publicly available data in biology and chemistry enables researchers to revisit interaction problems by systematic integration and analysis of heterogeneous data. Currently, some tools have been developed to represent these components...
2016: Journal of Cheminformatics
https://www.readbyqxmd.com/read/27323540/-teaching-bio-medical-informatics-to-medical-students-in-the-faculty-of-medicine-in-the-galilee-goals-lessons-and-a-future-perspective
#19
Amir Kuperman, Itay Onn
Bioinformatics is a scientific discipline that deals with the processing of biological data by computers. In recent years, bioinformatic tools were applied to the analysis of medical databases in order to develop new pathways for diagnosis and to improve medical treatment. The best example is personalized medicine, which depends on bioinformatic analysis. Despite early assessments, bioinformatics didn't change the clinical landscape dramatically, and personalized medicine is still not a main approach in healthcare...
April 2016: Harefuah
https://www.readbyqxmd.com/read/27235801/from-frames-to-owl2-converting-the-foundational-model-of-anatomy
#20
Landon T Detwiler, Jose L V Mejino, James F Brinkley
OBJECTIVE: The Foundational Model of Anatomy (FMA) [Rosse C, Mejino JLV. A reference ontology for bioinformatics: the Foundational Model of Anatomy. J. Biomed. Inform. 2003;36:478-500] is an ontology that represents canonical anatomy at levels ranging from the entire body to biological macromolecules, and has rapidly become the primary reference ontology for human anatomy, and a template for model organisms. Prior to this work, the FMA was developed in a knowledge modeling language known as Protégé Frames...
May 2016: Artificial Intelligence in Medicine
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