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https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#1
Sophia Santos, Isabel Rocha
Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genome-scale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing lab experiments...
November 27, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28150231/protein-bioinformatics-databases-and-resources
#2
Chuming Chen, Hongzhan Huang, Cathy H Wu
Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28133812/antibodyomics-bioinformatics-technologies-for-understanding-b-cell-immunity-to-hiv-1
#3
REVIEW
Peter D Kwong, Gwo-Yu Chuang, Brandon J DeKosky, Tatyana Gindin, Ivelin S Georgiev, Thomas Lemmin, Chaim A Schramm, Zizhang Sheng, Cinque Soto, An-Suei Yang, John R Mascola, Lawrence Shapiro
Numerous antibodies have been identified from HIV-1-infected donors that neutralize diverse strains of HIV-1. These antibodies may provide the basis for a B cell-mediated HIV-1 vaccine. However, it has been unclear how to elicit similar antibodies by vaccination. To address this issue, we have undertaken an informatics-based approach to understand the genetic and immunologic processes controlling the development of HIV-1-neutralizing antibodies. As DNA sequencing comprises the fastest growing database of biological information, we focused on incorporating next-generation sequencing of B-cell transcripts to determine the origin, maturation pathway, and prevalence of broadly neutralizing antibody lineages (Antibodyomics1, 2, 4, and 6)...
January 2017: Immunological Reviews
https://www.readbyqxmd.com/read/28111446/functional-analysis-of-sh3-domain-containing-ring-finger-2-sh3rf2-during-the-myogenic-differentiation-of-qm7-cells
#4
Si Won Kim, Jeong Hyo Lee, Tae Sub Park
Objective: Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods: Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2) gene...
December 27, 2016: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28101273/who-scared-the-cat-a-molecular-crime-scene-investigation-laboratory-exercise
#5
Laura E Ott, Susan D Carson
This introductory laboratory exercise gives first-year life science majors or nonmajors an opportunity to gain knowledge and experience in basic bioinformatics and molecular biology laboratory techniques and analysis in the context of a mock crime scene investigation. In this laboratory, students determine if a human (Lady) or dog (Kona) committed the fictional crime of scaring a cat. Students begin by performing in silico PCR using provided dog- and human-specific PCR primers to determine the sequences to be amplified and predict PCR amplicon sizes...
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28055930/deep-learning-for-health-informatics
#6
Daniele Ravi, Charence Wong, Fani Deligianni, Melissa Berthelot, Javier Andreu-Perez, Benny Lo, Guang-Zhong Yang
With a massive influx of multimodality data, the role of data analytics in health informatics has grown rapidly in the last decade. This has also prompted increasing interests in the generation of analytical, data driven models based on machine learning in health informatics. Deep learning, a technique with its foundation in artificial neural networks, is emerging in recent years as a powerful tool for machine learning, promising to reshape the future of artificial intelligence. Rapid improvements in computational power, fast data storage, and parallelization have also contributed to the rapid uptake of the technology in addition to its predictive power and ability to generate automatically optimized high-level features and semantic interpretation from the input data...
January 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28003265/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#7
Qiang Kou, Si Wu, Nikola Tolić, Ljiljana Paša-Tolić, Yunlong Liu, Xiaowen Liu
MOTIVATION: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28003258/the-ark-a-customizable-web-based-data-management-tool-for-health-and-medical-research
#8
Adrian Bickerstaffe, Thilina Ranaweera, Travis Endersby, Christopher Ellis, Sanjaya Maddumarachchi, George E Gooden, Paul White, Eric K Moses, Alex W Hewitt, John L Hopper
The Ark is an open-source web-based tool that allows researchers to manage health and medical research data for humans and animals without specialized database skills or programming expertise. The system provides data management for core research information including demographic, phenotype, biospecimen and pedigree data, in addition to supporting typical investigator requirements such as tracking participant consent and correspondence, whilst also being able to generate custom data exports and reports. The Ark is 'study generic' by design and highly configurable via its web interface, allowing researchers to tailor the system to the specific data management requirements of their study...
December 21, 2016: Bioinformatics
https://www.readbyqxmd.com/read/27995389/equipping-physiologists-with-an-informatics-tool-chest-toward-an-integerated-mitochondrial-phenome
#9
Anders Olav Garlid, Jennifer S Polson, Keith D Garlid, Henning Hermjakob, Peipei Ping
Understanding the complex involvement of mitochondrial biology in disease development often requires the acquisition, analysis, and integration of large-scale molecular and phenotypic data. An increasing number of bioinformatics tools are currently employed to aid in mitochondrial investigations, most notably in predicting or corroborating the spatial and temporal dynamics of mitochondrial molecules, in retrieving structural data of mitochondrial components, and in aggregating as well as transforming mitochondrial centric biomedical knowledge...
December 20, 2016: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/27975279/an-introduction-to-proteome-bioinformatics
#10
Shivakumar Keerthikumar
High-throughput techniques are indispensable for aiding basic and translational research. Among them, recent advances in proteomics techniques have allowed biomedical researchers to characterize the proteome of multiple organisms. This remarkable advancement have been well complemented by proteome bioinformatics methods and tools. Proteome bioinformatics refers to the study and application of informatics in the field of proteomics. This chapter provides an overview of computational strategies, methods, and techniques reported in this book for bioinformatics analysis of protein data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27931036/clinical-exome-sequencing-reveals-mkrn3-pathogenic-variants-in-familial-and-nonfamilial-idiopathic-central-precocious-puberty
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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