Read by QxMD icon Read


Edison Ong, Zuoshuang Xiang, Bin Zhao, Yue Liu, Yu Lin, Jie Zheng, Chris Mungall, Mélanie Courtot, Alan Ruttenberg, Yongqun He
Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee ( is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry...
October 12, 2016: Nucleic Acids Research
Ariadne H A G Ooms, Samantha Gadd, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard A Moore, Marco A Marra, Vicki Huff, Jeffrey S Dome, Yueh-Yun Chi, Jing Tian, James I Geller, Charles G Mullighan, Jing Ma, David A Wheeler, Oliver A Hampton, Amy L Walz, Marry M van den Heuvel-Eibrink, Ronald R de Krijger, Nicole Ross, Julie M Gastier-Foster, Elizabeth J Perlman
PURPOSE: To investigate the role and significance of TP53 mutation in diffusely anaplastic Wilms tumors (DAWTs). EXPERIMENTAL DESIGN: All DAWTs registered on National Wilms Tumor Study-5 (n = 118) with available samples were analyzed for TP53 mutations and copy loss. Integrative genomic analysis was performed on 39 selected DAWTs. RESULTS: Following analysis of a single random sample, 57 DAWTs (48%) demonstrated TP53 mutations, 13 (11%) copy loss without mutation, and 48 (41%) lacked both [defined as TP53-wild-type (wt)]...
October 4, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Pier Luigi Buttigieg, Evangelos Pafilis, Suzanna E Lewis, Mark P Schildhauer, Ramona L Walls, Christopher J Mungall
BACKGROUND: The Environment Ontology (ENVO; ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description...
2016: Journal of Biomedical Semantics
Michel Dumontier, Alasdair J G Gray, M Scott Marshall, Vladimir Alexiev, Peter Ansell, Gary Bader, Joachim Baran, Jerven T Bolleman, Alison Callahan, José Cruz-Toledo, Pascale Gaudet, Erich A Gombocz, Alejandra N Gonzalez-Beltran, Paul Groth, Melissa Haendel, Maori Ito, Simon Jupp, Nick Juty, Toshiaki Katayama, Norio Kobayashi, Kalpana Krishnaswami, Camille Laibe, Nicolas Le Novère, Simon Lin, James Malone, Michael Miller, Christopher J Mungall, Laurens Rietveld, Sarala M Wimalaratne, Atsuko Yamaguchi
Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets...
2016: PeerJ
David P Hill, Peter D'Eustachio, Tanya Z Berardini, Christopher J Mungall, Nikolai Renedo, Judith A Blake
The concept of a biological pathway, an ordered sequence of molecular transformations, is used to collect and represent molecular knowledge for a broad span of organismal biology. Representations of biomedical pathways typically are rich but idiosyncratic presentations of organized knowledge about individual pathways. Meanwhile, biomedical ontologies and associated annotation files are powerful tools that organize molecular information in a logically rigorous form to support computational analysis. The Gene Ontology (GO), representing Molecular Functions, Biological Processes and Cellular Components, incorporates many aspects of biological pathways within its ontological representations...
2016: Database: the Journal of Biological Databases and Curation
Damian Smedley, Max Schubach, Julius O B Jacobsen, Sebastian Köhler, Tomasz Zemojtel, Malte Spielmann, Marten Jäger, Harry Hochheiser, Nicole L Washington, Julie A McMurry, Melissa A Haendel, Christopher J Mungall, Suzanna E Lewis, Tudor Groza, Giorgio Valentini, Peter N Robinson
The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially for single-nucleotide and other small non-coding variants. Here we present Genomiser, an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders...
September 1, 2016: American Journal of Human Genetics
Julie A McMurry, Sebastian Köhler, Nicole L Washington, James P Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine, Julius O B Jacobsen, Daniel Keith, Bryan Laraway, Jeremy Nguyen Xuan, Kent Shefchek, Nicole A Vasilevsky, Zhou Yuan, Suzanna E Lewis, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel
The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease traits. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer...
August 2016: Genetics
Lijoy Varghese, Bruce Mungall, Xu-Hao Zhang, Bernard Hoet
A recently published paper that assessed the comparative cost-effectiveness of the 2 pneumococcal conjugate vaccines (PCVs) in Malaysia and Hong Kong reported that the 13-valent PCV vaccine (PCV13) is a better choice compared to the 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PHiD-CV or PCV10) from both a payer and societal perspective as well as under various scenarios. However, the analysis relied on a large number of assumptions that were either erroneous or did not take into account the most recent body of evidence available...
July 26, 2016: Human Vaccines & Immunotherapeutics
Alexander D Diehl, Terrence F Meehan, Yvonne M Bradford, Matthew H Brush, Wasila M Dahdul, David S Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E Van Slyke, Nicole A Vasilevsky, Melissa A Haendel, Judith A Blake, Christopher J Mungall
BACKGROUND: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. CONSTRUCTION AND CONTENT: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologies in coordination with the CL...
2016: Journal of Biomedical Semantics
Jerven T Bolleman, Christopher J Mungall, Francesco Strozzi, Joachim Baran, Michel Dumontier, Raoul J P Bonnal, Robert Buels, Robert Hoehndorf, Takatomo Fujisawa, Toshiaki Katayama, Peter J A Cock
BACKGROUND: Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. DESCRIPTION: We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences...
2016: Journal of Biomedical Semantics
Lauren C Chong, David D W Twa, Anja Mottok, Susana Ben-Neriah, Bruce W Woolcock, Yongjun Zhao, Kerry J Savage, Marco A Marra, David W Scott, Randy D Gascoyne, Ryan D Morin, Andrew J Mungall, Christian Steidl
Programmed death ligands (PDLs) are immune-regulatory molecules that are frequently affected by chromosomal alterations in B-cell lymphomas. Although PDL copy-number variations are well characterized, a detailed and comprehensive analysis of structural rearrangements (SRs) and associated phenotypic consequences is largely lacking. Here, we used oligonucleotide capture sequencing of 67 formalin-fixed paraffin-embedded tissues derived from primary B-cell lymphomas and 1 cell line to detect and characterize, at base-pair resolution, SRs of the PDL locus (9p24...
September 1, 2016: Blood
Andrew McPherson, Andrew Roth, Emma Laks, Tehmina Masud, Ali Bashashati, Allen W Zhang, Gavin Ha, Justina Biele, Damian Yap, Adrian Wan, Leah M Prentice, Jaswinder Khattra, Maia A Smith, Cydney B Nielsen, Sarah C Mullaly, Steve Kalloger, Anthony Karnezis, Karey Shumansky, Celia Siu, Jamie Rosner, Hector Li Chan, Julie Ho, Nataliya Melnyk, Janine Senz, Winnie Yang, Richard Moore, Andrew J Mungall, Marco A Marra, Alexandre Bouchard-Côté, C Blake Gilks, David G Huntsman, Jessica N McAlpine, Samuel Aparicio, Sohrab P Shah
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples from seven patients), identifying constituent clones and quantifying their relative abundances at multiple intraperitoneal sites. Through whole-genome and single-nucleus sequencing, we identified evolutionary features including mutation loss, convergence of the structural genome and temporal activation of mutational processes that patterned clonal progression. We then determined the precise clonal mixtures comprising each tumor sample...
July 2016: Nature Genetics
Jiwen Xin, Adam Mark, Cyrus Afrasiabi, Ginger Tsueng, Moritz Juchler, Nikhil Gopal, Gregory S Stupp, Timothy E Putman, Benjamin J Ainscough, Obi L Griffith, Ali Torkamani, Patricia L Whetzel, Christopher J Mungall, Sean D Mooney, Andrew I Su, Chunlei Wu
Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe and, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information...
2016: Genome Biology
Katayoon Kasaian, Sam M Wiseman, Blair A Walker, Jacqueline E Schein, Martin Hirst, Richard A Moore, Andrew J Mungall, Marco A Marra, Steven J M Jones
Medullary thyroid cancer (MTC) is a malignancy of the calcitonin-producing parafollicular cells of the thyroid gland. Surgery is the only curative treatment for this cancer. External beam radiation therapy is reserved for adjuvant treatment of MTC with aggressive features. Targeted therapeutics vandetanib and cabozantinib are approved for the treatment of aggressive and metastatic tumors that are not amenable to surgery. The use of these multikinase inhibitors are supported by the observed overactivation of the RET oncoprotein in a large subpopulation of MTCs...
March 2016: Cold Spring Harbor Molecular Case Studies
Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch'ng, Rebecca Deyell, Peter Eirew, Alexandra Fok, Karen Gelmon, Cheryl Ho, David Huntsman, Martin Jones, Katayoon Kasaian, Aly Karsan, Sreeja Leelakumari, Yvonne Li, Howard Lim, Yussanne Ma, Colin Mar, Monty Martin, Richard Moore, Andrew Mungall, Karen Mungall, Erin Pleasance, S Rod Rassekh, Daniel Renouf, Yaoqing Shen, Jacqueline Schein, Kasmintan Schrader, Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, Marco A Marra
Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted "panel" sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care...
October 2015: Cold Spring Harbor Molecular Case Studies
Peter N Robinson, Christopher J Mungall, Melissa Haendel
Deep phenotyping followed by integrated computational analysis of genotype and phenotype is becoming ever more important for many areas of genomic diagnostics and translational research. The overwhelming majority of clinical descriptions in the medical literature are available only as natural language text, meaning that searching, analysis, and integration of medically relevant information in databases such as PubMed is challenging. The new journal Cold Spring Harbor Molecular Case Studies will require authors to select Human Phenotype Ontology terms for research papers that will be displayed alongside the manuscript, thereby providing a foundation for ontology-based indexing and searching of articles that contain descriptions of phenotypic abnormalities-an important step toward improving the ability of researchers and clinicians to get biomedical information that is critical for clinical care or translational research...
October 2015: Cold Spring Harbor Molecular Case Studies
Julia E Maxson, Rhonda E Ries, Yi-Cheng Wang, Robert B Gerbing, E Anders Kolb, Sarah L Thompson, Jaime M Guidry Auvil, Marco A Marra, Yussanne Ma, Zusheng Zong, Andrew J Mungall, Richard Moore, William Long, Patee Gesuwan, Tanja M Davidsen, Leandro C Hermida, Seamus B Hughes, Jason E Farrar, Jerald P Radich, Malcolm A Smith, Daniela S Gerhard, Alan S Gamis, Todd A Alonzo, Soheil Meshinchi
No abstract text is available yet for this article.
June 16, 2016: Blood
David W Craig, Sara Nasser, Richard Corbett, Simon K Chan, Lisa Murray, Christophe Legendre, Waibhav Tembe, Jonathan Adkins, Nancy Kim, Shukmei Wong, Angela Baker, Daniel Enriquez, Stephanie Pond, Erin Pleasance, Andrew J Mungall, Richard A Moore, Timothy McDaniel, Yussanne Ma, Steven J M Jones, Marco A Marra, John D Carpten, Winnie S Liang
Large-scale multiplexed identification of somatic alterations in cancer has become feasible with next generation sequencing (NGS). However, calibration of NGS somatic analysis tools has been hampered by a lack of tumor/normal reference standards. We thus performed paired PCR-free whole genome sequencing of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. We generated mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions...
2016: Scientific Reports
Batool F Kirmani, Diana Mungall Robinson, Ekokobe Fonkem, Kevin Graf, Jason H Huang
Posttraumatic seizures (PTS) have been recognized as a major complication of traumatic brain injury (TBI). The annual incidence of TBI in the United States is 1.7 million. The role of anticonvulsants in the treatment of posttraumatic epilepsy (PTE) remains uncertain. Based on current studies, however, anticonvulsants have been shown to reduce early PTS occurring within the first 7 days, but little to no benefits have been shown in late PTS occurring after 7 days. In this paper, we provide a mini review of the role of anticonvulsants and current advances in the management of PTE...
2016: Frontiers in Neurology
Yinghong Pan, Gordon Robertson, Lykke Pedersen, Emilia Lim, Anadulce Hernandez-Herrera, Amy C Rowat, Sagar L Patil, Clara K Chan, Yunfei Wen, Xinna Zhang, Upal Basu-Roy, Alka Mansukhani, Andy Chu, Payal Sipahimalani, Reanne Bowlby, Denise Brooks, Nina Thiessen, Cristian Coarfa, Yussanne Ma, Richard A Moore, Jacquie E Schein, Andrew J Mungall, Jinsong Liu, Chad V Pecot, Anil K Sood, Steven J M Jones, Marco A Marra, Preethi H Gunaratne
Ovarian cancer presents as an aggressive, advanced stage cancer with widespread metastases that depend primarily on multicellular spheroids in the peritoneal fluid. To identify new druggable pathways related to metastatic progression and spheroid formation, we integrated microRNA and mRNA sequencing data from 293 tumors from The Cancer Genome Atlas (TCGA) ovarian cancer cohort. We identified miR-509-3p as a clinically significant microRNA that is more abundant in patients with favorable survival in both the TCGA cohort (P = 2...
May 3, 2016: Oncotarget
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"