keyword
MENU ▼
Read by QxMD icon Read
search

Bioinformatics, informatics

keyword
https://www.readbyqxmd.com/read/29922448/global-transcriptome-analysis-to-identify-critical-genes-involved-in-the-pathology-of-osteoarthritis
#1
X Zhang, Y Bu, B Zhu, Q Zhao, Z Lv, B Li, J Liu
Objectives: The aim of this study was to identify key pathological genes in osteoarthritis (OA). Methods: We searched and downloaded mRNA expression data from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) of joint synovial tissues from OA and normal individuals. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses were used to assess the function of identified DEGs. The protein-protein interaction (PPI) network and transcriptional factors (TFs) regulatory network were used to further explore the function of identified DEGs...
April 2018: Bone & Joint Research
https://www.readbyqxmd.com/read/29907252/opisthorchis-viverrini-draft-genome-biomedical-implications-and-future-avenues
#2
Neil D Young, Robin B Gasser
Opisthorchiasis is a neglected tropical disease of major proportion, caused by the carcinogenic, Asian liver fluke, Opisthorchis viverrini. This hepatobiliary disease is known to be associated with malignant cancer (cholangiocarcinoma, CCA) and affects millions of people in Southeast Asia. No vaccine is available, and only one drug (praziquantel) is routinely employed against the parasite. Despite technological advances, little is known about the molecular biology of the fluke itself and the disease complex that it causes in humans...
2018: Advances in Parasitology
https://www.readbyqxmd.com/read/29896534/gene-datasets-associated-with-mouse-cleft-palate
#3
Akiko Suzuki, Goo Jun, Nada Abdallah, Mona Gajera, Junichi Iwata
This article presents data on genes associated with cleft palate (CP), retrieved through both a full-text systematic review and a mouse genome informatics (MGI) database search. In order to group CP-associated genes according to function, pathway, biological process, and cellular component, the genes were analyzed using category enrichment bioinformatics tools, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). This approach provides invaluable opportunities for the identification of candidate pathways and genes in CP research...
June 2018: Data in Brief
https://www.readbyqxmd.com/read/29864527/bioinformatics-based-tools-in-drug-discovery-the-cartography-from-single-gene-to-integrative-biological-networks
#4
REVIEW
Pritika Ramharack, Mahmoud E S Soliman
Originally developed for the analysis of biological sequences, bioinformatics has advanced into one of the most widely recognized domains in the scientific community. Despite this technological evolution, there is still an urgent need for nontoxic and efficient drugs. The onus now falls on the 'omics domain to meet this need by implementing bioinformatics techniques that will allow for the introduction of pioneering approaches in the rational drug design process. Here, we categorize an updated list of informatics tools and explore the capabilities of integrative bioinformatics in disease control...
June 1, 2018: Drug Discovery Today
https://www.readbyqxmd.com/read/29858800/the-ipd-databases-cataloguing-and-understanding-allele-variants
#5
Jashan P Abraham, Dominic J Barker, James Robinson, Giuseppe Maccari, Steven G E Marsh
The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29780242/immune-informatic-analysis-and-design-of-peptide-vaccine-from-multi-epitopes-against-corynebacterium-pseudotuberculosis
#6
Daniela Droppa-Almeida, Elton Franceschi, Francine Ferreira Padilha
Caseous lymphadenitis (CLA) is a disease caused by Corynebacterium pseudotuberculosis bacteria that affects sheep and goats. The absence of a serologic diagnose is a factor that contributes for the disease dissemination, and due to the formation of granuloma, the treatment is very expensive. Therefore, prophylaxis is the approach with best cost-benefit relation; however, it still lacks an effective vaccine. In this sense, this work seeks to apply bioinformatic tools to design an effective vaccine against CLA, using CP40 protein as standard for the design of immunodominant epitopes, from which a total of 6 sequences were obtained, varying from 10 to 16 amino acid residues...
2018: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/29737976/uniform-resolution-of-compact-identifiers-for-biomedical-data
#7
Sarala M Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A McMurry, Niall Beard, Rafael Jimenez, Jeffrey S Grethe, Henning Hermjakob, Maryann E Martone, Tim Clark
Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such "compact identifiers" have been widely used in biomedical informatics to support global resource identification with local identifier assignment...
May 8, 2018: Scientific Data
https://www.readbyqxmd.com/read/29731866/microrna-hsa-let-7e-5p-as-a-potential-prognosis-marker-for-rectal-carcinoma-with-liver-metastases
#8
Wenfeng Chen, Guosheng Lin, Yizhou Yao, Jishen Chen, Hanli Shui, Qinghai Yang, Xiaoya Wang, Xiaoyuan Weng, Ling Sun, Fei Chen, Sheng Yang, Yufeng Yang, Yongjian Zhou
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that target mRNAs for translational repression or cleavage. The present study was conducted to identify differentially expressed miRNAs in primary tumor tissues of rectal carcinoma (RC) that may be associated with heterochrony hepatic metastasis (HHM). Samples were collected exclusively from patients with RC but not colon cancer (CC); Next-generation high-throughput sequencing technology and bioinformatics tools were used to profile and analyze small RNAs and their corresponding targets in primary tumor tissues with HHM (n=2) or without metastases (non-metastatic, NM; n=2)...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29695735/integrative-annotation-and-knowledge-discovery-of-kinase-post-translational-modifications-and-cancer-associated-mutations-through-federated-protein-ontologies-and-resources
#9
Liang-Chin Huang, Karen E Ross, Timothy R Baffi, Harold Drabkin, Krzysztof J Kochut, Zheng Ruan, Peter D'Eustachio, Daniel McSkimming, Cecilia Arighi, Chuming Chen, Darren A Natale, Cynthia Smith, Pascale Gaudet, Alexandra C Newton, Cathy Wu, Natarajan Kannan
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workflows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontology, neXtProt, and the Mouse Genome Informatics to identify key knowledge gaps in the functional coverage of the human kinome and prioritize understudied kinases, cancer variants and post-translational modifications (PTMs) for functional studies...
April 25, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29677992/biomedical-informatics-how-to-choose-the-best-tool-for-each-task
#10
Fábio Maia, Luís Bastião Silva, José Luís Oliveira
The ever-increasing number of bioinformatics software tools that are publicly available, is leading to greater expectations about its regular use in clinical practice. However, from the end-users' perspective, they face many time the challenge of choosing the right tool for each task, from a panoply of solutions that have been developed over the years. In this paper, we propose a benchmarking methodology, based on a set of performance indicators, which can be used to identify the best methods and tools for each particular use case, both in research as in clinical practice...
2018: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/29653352/online-molecular-image-repository-and-analysis-system-a-multicenter-collaborative-open-source-infrastructure-for-molecular-imaging-research-and-application
#11
Mahabubur Rahman, Hiroshi Watabe
Molecular imaging serves as an important tool for researchers and clinicians to visualize and investigate complex biochemical phenomena using specialized instruments; these instruments are either used individually or in combination with targeted imaging agents to obtain images related to specific diseases with high sensitivity, specificity, and signal-to-noise ratios. However, molecular imaging, which is a multidisciplinary research field, faces several challenges, including the integration of imaging informatics with bioinformatics and medical informatics, requirement of reliable and robust image analysis algorithms, effective quality control of imaging facilities, and those related to individualized disease mapping, data sharing, software architecture, and knowledge management...
May 1, 2018: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29539190/mseqdr-mvtool-a-mitochondrial-dna-web-and-api-resource-for-comprehensive-variant-annotation-universal-nomenclature-collation-and-reference-genome-conversion
#12
Lishuang Shen, Marcella Attimonelli, Renkui Bai, Marie T Lott, Douglas C Wallace, Marni J Falk, Xiaowu Gai
Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service...
March 14, 2018: Human Mutation
https://www.readbyqxmd.com/read/29515813/cloud-based-adaptive-exon-prediction-for-dna-analysis
#13
Srinivasareddy Putluri, Md Zia Ur Rahman, Shaik Yasmeen Fathima
Cloud computing offers significant research and economic benefits to healthcare organisations. Cloud services provide a safe place for storing and managing large amounts of such sensitive data. Under conventional flow of gene information, gene sequence laboratories send out raw and inferred information via Internet to several sequence libraries. DNA sequencing storage costs will be minimised by use of cloud service. In this study, the authors put forward a novel genomic informatics system using Amazon Cloud Services, where genomic sequence information is stored and accessed for processing...
February 2018: Healthcare Technology Letters
https://www.readbyqxmd.com/read/29475039/genes-and-micrornas-associated-with-mouse-cleft-palate-a-systematic-review-and-bioinformatics-analysis
#14
Akiko Suzuki, Nada Abdallah, Mona Gajera, Goo Jun, Peilin Jia, Zhongming Zhao, Junichi Iwata
Cleft palate (CP) is the most prevalent craniofacial deformity, with ethnic and geographic variation in prevalence in humans. Mice have been used as an animal model to study the cause(s) of CP by several approaches, including genetic and chemical-induced approaches. Mouse genetic approaches revealed that significant amounts of genes are involved in the CP pathology. The aim of this study was to identify common features of CP-associated genes and to explore the roles of microRNAs (miRNAs) as important post-transcriptional regulators that may be involved in the regulation of CP genes...
April 2018: Mechanisms of Development
https://www.readbyqxmd.com/read/29435179/identifying-characteristic-mirnas-genes-and-risk-pathways-of-multiple-sclerosis-based-on-bioinformatics-analysis
#15
Deling Luo, Jin Fu
Multiple sclerosis is a chronic autoimmune disorder of the central nervous system. In MS, the genetic susceptibility is high and currently there is no effective treatment. MicroRNA, a small non-coding RNA, plays a vital role in immune responses. Aberrant or dysfunctional miRNAs may cause several diseases, including MS, thus miRNAs and miRNA related genes may be therapeutic weapons against MS. Here, we identified 21 miRNAs in peripheral blood mono-nuclear cells from over 600 persons, including healthy controls...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29419817/investigation-of-the-spatial-structure-and-interactions-of-the-genome-at-sub-kilobase-pair-resolution-using-t2c
#16
Petros Kolovos, Rutger W W Brouwer, Christel E M Kockx, Michael Lesnussa, Nick Kepper, Jessica Zuin, A M Ali Imam, Harmen J G van de Werken, Kerstin S Wendt, Tobias A Knoch, Wilfred F J van IJcken, Frank Grosveld
Chromosome conformation capture (3C) and its derivatives (e.g., 4C, 5C and Hi-C) are used to analyze the 3D organization of genomes. We recently developed targeted chromatin capture (T2C), an inexpensive method for studying the 3D organization of genomes, interactomes and structural changes associated with gene regulation, the cell cycle, and cell survival and development. Here, we present the protocol for T2C based on capture, describing all experimental steps and bio-informatic tools in full detail. T2C offers high resolution, a large dynamic interaction frequency range and a high signal-to-noise ratio...
March 2018: Nature Protocols
https://www.readbyqxmd.com/read/29385081/disseminating-metaproteomic-informatics-capabilities-and-knowledge-using-the-galaxy-p-framework
#17
Clemens Blank, Caleb Easterly, Bjoern Gruening, James Johnson, Carolin A Kolmeder, Praveen Kumar, Damon May, Subina Mehta, Bart Mesuere, Zachary Brown, Joshua E Elias, W Judson Hervey, Thomas McGowan, Thilo Muth, Brook Nunn, Joel Rudney, Alessandro Tanca, Timothy J Griffin, Pratik D Jagtap
The impact of microbial communities, also known as the microbiome, on human health and the environment is receiving increased attention. Studying translated gene products (proteins) and comparing metaproteomic profiles may elucidate how microbiomes respond to specific environmental stimuli, and interact with host organisms. Characterizing proteins expressed by a complex microbiome and interpreting their functional signature requires sophisticated informatics tools and workflows tailored to metaproteomics. Additionally, there is a need to disseminate these informatics resources to researchers undertaking metaproteomic studies, who could use them to make new and important discoveries in microbiome research...
January 31, 2018: Proteomes
https://www.readbyqxmd.com/read/29363432/a-bioinformatics-potpourri
#18
EDITORIAL
Christian Schönbach, Jinyan Li, Lan Ma, Paul Horton, Muhammad Farhan Sjaugi, Shoba Ranganathan
The 16th International Conference on Bioinformatics (InCoB) was held at Tsinghua University, Shenzhen from September 20 to 22, 2017. The annual conference of the Asia-Pacific Bioinformatics Network featured six keynotes, two invited talks, a panel discussion on big data driven bioinformatics and precision medicine, and 66 oral presentations of accepted research articles or posters. Fifty-seven articles comprising a topic assortment of algorithms, biomolecular networks, cancer and disease informatics, drug-target interactions and drug efficacy, gene regulation and expression, imaging, immunoinformatics, metagenomics, next generation sequencing for genomics and transcriptomics, ontologies, post-translational modification, and structural bioinformatics are the subject of this editorial for the InCoB2017 supplement issues in BMC Genomics, BMC Bioinformatics, BMC Systems Biology and BMC Medical Genomics...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29316298/improving-the-safety-assessment-of-chemicals-and-drug-candidates-by-the-integration-of-bioinformatics-and-chemoinformatics-data
#19
REVIEW
Thomas Steger-Hartmann, Francois Pognan
The application of read-across and in silico tools for regulatory decision-making has been limited for pharmaceutical compounds to the assessment of genotoxic impurity. In contrast, the broad availability of toxicity data for industrial chemicals has triggered regulatory frameworks for read-across (e.g. ECHA Read-Across Assessment Framework), software tools and public databases for an automated process of gap filling in the context of safety assessment. This MiniReview provides an overview of the currently existing in silico and read-across approaches for chemicals together with recent developments for pharmaceutical compounds in these areas...
January 7, 2018: Basic & Clinical Pharmacology & Toxicology
https://www.readbyqxmd.com/read/29234465/ten-quick-tips-for-machine-learning-in-computational-biology
#20
REVIEW
Davide Chicco
Machine learning has become a pivotal tool for many projects in computational biology, bioinformatics, and health informatics. Nevertheless, beginners and biomedical researchers often do not have enough experience to run a data mining project effectively, and therefore can follow incorrect practices, that may lead to common mistakes or over-optimistic results. With this review, we present ten quick tips to take advantage of machine learning in any computational biology context, by avoiding some common errors that we observed hundreds of times in multiple bioinformatics projects...
2017: BioData Mining
keyword
keyword
116037
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"