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Bioinformatics, informatics

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
Max Klein, Rati Sharma, Chris Bohrer, Cameron Avelis, Elijah Roberts
: Data-parallel programming techniques can dramatically decrease the time needed to analyze large data sets. 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 data sets. 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
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...
2016: BMC Systems Biology
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
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
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
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
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
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...
July 16, 2016: Bioinformatics
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
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
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
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
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
Chunxue Bai
Respiratory diseases will become one of the top 3 leading causes of estimated mortality in 2020 and become about one third of total causes of estimated mortality. The journal of Translational Respiratory Medicine is a truly international, peer-reviewed journal devoted to the publication of articles on outstanding work with translational potentials between basic research and clinical application to understanding respiratory disease. Translational respiratory medicine will more focus on biomarker identification and validation in pulmonary diseases in combination with clinical informatics, targeted proteomics, bioinformatics, systems medicine, or mathematical science; on different translational strategies of cell-based therapy to clinical application to treat lung diseases; on targeted therapies in combination with personalized medicine; and on distant electronic medicine to monitor a large population of people's health...
December 2013: Translational Respiratory Medicine
T Fischer, K B Brothers, P Erdmann, M Langanke
BACKGROUND: Systems medicine is the name for an assemblage of scientific strategies and practices that include bioinformatics approaches to human biology (especially systems biology); "big data" statistical analysis; and medical informatics tools. Whereas personalized and precision medicine involve similar analytical methods applied to genomic and medical record data, systems medicine draws on these as well as other sources of data. Given this distinction, the clinical translation of systems medicine poses a number of important ethical and epistemological challenges for researchers working to generate systems medicine knowledge and clinicians working to apply it...
2016: BMC Medical Ethics
R B Altman
In 2004, medical informatics as a scientific community recognized an emerging field of "clinical bioinformatics" that included work bringing bioinformatics data and knowledge into the clinic. In the intervening decade, "translational biomedical informatics" has emerged as the umbrella term for the work that brings together biological entities and clinical entities. The major challenges continue: understanding the clinical significance of basic 'omics' (and other) measurements, and communicating this to increasingly empowered patients/consumers who often have access to this information outside usual medical channels...
2016: Yearbook of Medical Informatics
Nancy Pearl Solomon, Angela M Dietsch, Katie E Dietrich-Burns, Edda L Styrmisdottir, Christopher S Armao
PURPOSE: This report describes the development and preliminary analysis of a database for traumatically injured military service members with dysphagia. METHODS: A multidimensional database was developed to capture clinical variables related to swallowing. Data were derived from clinical records and instrumental swallow studies, and ranged from demographics, injury characteristics, swallowing biomechanics, medications, and standardized tools (e.g., Glasgow Coma Scale, Penetration-Aspiration Scale)...
May 2016: Military Medicine
Sumanta Mukherjee, Chiranjib Bhattacharyya, Nagasuma Chandra
MOTIVATION: T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics and are critically dependent on experimentally obtained training data. Analysis of a training set from Immune Epitope Database (IEDB) for several alleles indicates that the sampling of the peptide space is extremely sparse covering a tiny fraction of the possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction...
August 1, 2016: Bioinformatics
Brandy Verhalen, Gabriel J Starrett, Reuben S Harris, Mengxi Jiang
UNLABELLED: The APOBEC3 family of DNA cytosine deaminases has important roles in innate immunity and cancer. It is unclear how DNA tumor viruses regulate these enzymes and how these interactions, in turn, impact the integrity of both the viral and cellular genomes. Polyomavirus (PyVs) are small DNA pathogens that contain oncogenic potentials. In this study, we examined the effects of PyV infection on APOBEC3 expression and activity. We demonstrate that APOBEC3B is specifically upregulated by BK polyomavirus (BKPyV) infection in primary kidney cells and that the upregulated enzyme is active...
July 15, 2016: Journal of Virology
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