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Bioinformatics, informatics

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https://www.readbyqxmd.com/read/28637687/inhibition-of-cdk4-6-by-palbociclib-significantly-extends-survival-in-medulloblastoma-patient-derived-xenograft-mouse-models
#1
Michelle L Cook Sangar, Laura A Genovesi, Madison W Nakamoto, Melissa J Davis, Sue E Knoblaugh, Pengxiang Ji, Amanda Millar, Brandon Wainwright, James M Olson
  <p>Bioinformatics analysis followed by in vivo studies in patient-derived xenograft models were used to identify and validate CDK 4/6 inhibition as an effective therapeutic strategy for medulloblastoma, particularly Group 3 MYC-amplified tumors which have the worst clinical prognosis.</p> <br />Experimental Design: <p>A protein interaction network derived from a Sleeping Beauty mutagenesis model of medulloblastoma was used to identify potential novel therapeutic targets.  The top hit from this analysis was validated in vivo using patient-derived xenograft models of medulloblastoma implanted subcutaneously in the flank and orthotopically in the cerebellum of mice...
June 21, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28625502/a-computable-phenotype-improves-cohort-ascertainment-in-a-pediatric-pulmonary-hypertension-registry
#2
Alon Geva, Jessica L Gronsbell, Tianxi Cai, Tianrun Cai, Shawn N Murphy, Jessica C Lyons, Michelle M Heinz, Marc D Natter, Nandan Patibandla, Jonathan Bickel, Mary P Mullen, Kenneth D Mandl
OBJECTIVES: To compare registry and electronic health record (EHR) data mining approaches for cohort ascertainment in patients with pediatric pulmonary hypertension (PH) in an effort to overcome some of the limitations of registry enrollment alone in identifying patients with particular disease phenotypes. STUDY DESIGN: This study was a single-center retrospective analysis of EHR and registry data at Boston Children's Hospital. The local Informatics for Integrating Biology and the Bedside (i2b2) data warehouse was queried for billing codes, prescriptions, and narrative data related to pediatric PH...
June 15, 2017: Journal of Pediatrics
https://www.readbyqxmd.com/read/28609000/the-role-of-informatics-in-patient-centered-care-and-personalized-medicine
#3
Matthew G Hanna, Liron Pantanowitz
The practice of cytopathology has dramatically changed due to advances in genomics and information technology. Cytology laboratories have accordingly become increasingly dependent on pathology informatics support to meet the emerging demands of precision medicine. Pathology informatics deals with information technology in the laboratory, and the impact of this technology on workflow processes and staff who interact with these tools. This article covers the critical role that laboratory information systems, electronic medical records, and digital imaging plays in patient-centered personalized medicine...
June 2017: Cancer
https://www.readbyqxmd.com/read/28586416/bridging-the-gap-between-reproducibility-and-translation-data-resources-and-approaches
#4
Caroline J Zeiss, Linda K Johnson
Animal research has constituted a fundamental means to achieve groundbreaking therapies for human disease. However, for complex diseases, promising preclinical results have failed to translate to the clinic. Reasons for this disparity are multifactorial. These include the challenges inherent in modeling complex disease in animals, as well issues of study design, reproducibility and operational norms within the biomedical research enterprise. In this issue, we explore the range of information resources available for the comparative study of disease, as well as challenges to the ultimate translation of preclinical findings...
June 6, 2017: ILAR Journal
https://www.readbyqxmd.com/read/28557600/integration-of-technical-bioinformatic-and-variant-assessment-approaches-in-the-validation-of-a-targeted-next-generation-sequencing-panel-for-myeloid-malignancies
#5
Mariam Thomas, Mahadeo A Sukhai, Tong Zhang, Roozbeh Dolatshahi, Djamel Harbi, Swati Garg, Maksym Misyura, Trevor Pugh, Tracy L Stockley, Suzanne Kamel-Reid
CONTEXT: - Detection of variants in hematologic malignancies is increasingly important because of a growing number of variants impacting diagnosis, prognosis, and treatment response, and as potential therapeutic targets. The use of next-generation sequencing technologies to detect variants in hematologic malignancies in a clinical diagnostic laboratory setting allows for efficient identification of routinely tested markers in multiple genes simultaneously, as well as the identification of novel and rare variants in other clinically relevant genes...
June 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28505286/pixie-an-algorithm-for-automated-ion-mobility-arrival-time-extraction-and-collision-cross-section-calculation-using-global-data-association
#6
Jian Ma, Cameron P Casey, Xueyun Zheng, Yehia M Ibrahim, Christopher S Wilkins, Ryan S Renslow, Dennis G Thomas, Samuel H Payne, Matthew E Monroe, Richard D Smith, Justin G Teeguarden, Erin S Baker, Thomas O Metz
Motivation: Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses...
May 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28504421/bioinformatics-analysis-on-molecular-mechanism-of-green-tea-compound-epigallocatechin-3-gallate-against-ovarian-cancer
#7
S Xinqiang, Z Mu, C Lei, L Y Mun
Epigallocatechin-3-gallate (EGCG) is the most abundant and biologically active catechin in green tea, and it exerts multiple effects in humans through mechanisms that remain to be clarified. The present study used bioinformatics to identify possible mechanisms by which EGCG reduces the risk of ovarian cancer. Possible human protein targets of EGCG were identified in the PubChem database, possible human gene targets were identified in the National Center for Biotechnology Information database, and then both sets of targets were analyzed using Ingenuity Pathway Analysis (IPA)...
May 15, 2017: Clinical and Translational Science
https://www.readbyqxmd.com/read/28453672/primerize-2d-automated-primer-design-for-rna-multidimensional-chemical-mapping
#8
Siqi Tian, Rhiju Das
Summary: Rapid RNA synthesis of comprehensive single mutant libraries and targeted multiple mutant libraries is enabling new multidimensional chemical approaches to solve RNA structures. PCR assembly of DNA templates and in vitro transcription allow synthesis and purification of hundreds of RNA mutants in a cost-effective manner, with sharing of primers across constructs allowing significant reductions in expense. However, these protocols require organization of primer locations across numerous 96 well plates and guidance for pipetting, non-trivial tasks for which informatics and visualization tools can prevent costly errors...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453668/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#9
Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Paša-Tolic, 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...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#10
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28187415/estimation-of-biomass-composition-from-genomic-and-transcriptomic-information
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
Adrian Bickerstaffe, Thilina Ranaweera, Travis Endersby, Christopher Ellis, Sanjaya Maddumarachchi, George E Gooden, Paul White, Eric K Moses, Alex W Hewitt, John L Hopper
Summary: 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...
February 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27995389/equipping-physiologists-with-an-informatics-tool-chest-toward-an-integerated-mitochondrial-phenome
#19
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
#20
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
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