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Genome Biology

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https://www.readbyqxmd.com/read/28100256/transcriptomic-signatures-differentiate-survival-from-fatal-outcomes-in-humans-infected-with-ebola-virus
#1
Xuan Liu, Emily Speranza, César Muñoz-Fontela, Sam Haldenby, Natasha Y Rickett, Isabel Garcia-Dorival, Yongxiang Fang, Yper Hall, Elsa-Gayle Zekeng, Anja Lüdtke, Dong Xia, Romy Kerber, Ralf Krumkamp, Sophie Duraffour, Daouda Sissoko, John Kenny, Nichola Rockliffe, E Diane Williamson, Thomas R Laws, Magassouba N'Faly, David A Matthews, Stephan Günther, Andrew R Cossins, Armand Sprecher, John H Connor, Miles W Carroll, Julian A Hiscox
BACKGROUND: In 2014, Western Africa experienced an unanticipated explosion of Ebola virus infections. What distinguishes fatal from non-fatal outcomes remains largely unknown, yet is key to optimising personalised treatment strategies. We used transcriptome data for peripheral blood taken from infected and convalescent recovering patients to identify early stage host factors that are associated with acute illness and those that differentiate patient survival from fatality. RESULTS: The data demonstrate that individuals who succumbed to the disease show stronger upregulation of interferon signalling and acute phase responses compared to survivors during the acute phase of infection...
January 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28100280/erratum-to-the-whole-genome-sequence-of-the-mediterranean-fruit-fly-ceratitis-capitata-wiedemann-reveals-insights-into-the-biology-and-adaptive-evolution-of-a-highly-invasive-pest-species
#2
Alexie Papanicolaou, Marc F Schetelig, Peter Arensburger, Peter W Atkinson, Joshua B Benoit, Kostas Bourtzis, Pedro Castañera, John P Cavanaugh, Hsu Chao, Christopher Childers, Ingrid Curril, Huyen Dinh, HarshaVardhan Doddapaneni, Amanda Dolan, Shannon Dugan, Markus Friedrich, Giuliano Gasperi, Scott Geib, Georgios Georgakilas, Richard A Gibbs, Sarah D Giers, Ludvik M Gomulski, Miguel González-Guzmán, Ana Guillem-Amat, Yi Han, Artemis G Hatzigeorgiou, Pedro Hernández-Crespo, Daniel S T Hughes, Jeffery W Jones, Dimitra Karagkouni, Panagiota Koskinioti, Sandra L Lee, Anna R Malacrida, Mosè Manni, Kostas Mathiopoulos, Angela Meccariello, Monica Munoz-Torres, Shwetha C Murali, Terence D Murphy, Donna M Muzny, Georg Oberhofer, Félix Ortego, Maria D Paraskevopoulou, Monica Poelchau, Jiaxin Qu, Martin Reczko, Hugh M Robertson, Andrew J Rosendale, Andrew E Rosselot, Giuseppe Saccone, Marco Salvemini, Grazia Savini, Patrick Schreiner, Francesca Scolari, Paolo Siciliano, Sheina B Sim, George Tsiamis, Enric Ureña, Ioannis S Vlachos, John H Werren, Ernst A Wimmer, Kim C Worley, Antigone Zacharopoulou, Stephen Richards, Alfred M Handler
No abstract text is available yet for this article.
January 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28100273/erratum-to-quartz-seq-a-highly-reproducible-and-sensitive-single-cell-rna-sequencing-method-reveals-non-genetic-gene-expression-heterogeneity
#3
Yohei Sasagawa, Itoshi Nikaido, Tetsutaro Hayashi, Hiroki Danno, Kenichiro D Uno, Takeshi Imai, Hiroki R Ueda
No abstract text is available yet for this article.
January 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28100260/iregnet3d-three-dimensional-integrated-regulatory-network-for-the-genomic-analysis-of-coding-and-non-coding-disease-mutations
#4
Siqi Liang, Nathaniel D Tippens, Yaoda Zhou, Matthew Mort, Peter D Stenson, David N Cooper, Haiyuan Yu
The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-DNA and chromatin-chromatin interactions for the analysis of both coding and non-coding disease-associated mutations to obtain mechanistic insights into their functional impact. Using iRegNet3D, we find that disease-associated mutations may perturb the regulatory network through diverse mechanisms including chromatin looping...
January 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28093077/genome-informatics-2016
#5
Davide Chicco, Michael M Hoffman
A report on the Genome Informatics conference, held at the Wellcome Genome Campus Conference Centre, Hinxton, United Kingdom, 19-22 September 2016.
January 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28093075/gavin-gene-aware-variant-interpretation-for-medical-sequencing
#6
K Joeri van der Velde, Eddy N de Boer, Cleo C van Diemen, Birgit Sikkema-Raddatz, Kristin M Abbott, Alain Knopperts, Lude Franke, Rolf H Sijmons, Tom J de Koning, Cisca Wijmenga, Richard J Sinke, Morris A Swertz
We present Gene-Aware Variant INterpretation (GAVIN), a new method that accurately classifies variants for clinical diagnostic purposes. Classifications are based on gene-specific calibrations of allele frequencies from the ExAC database, likely variant impact using SnpEff, and estimated deleteriousness based on CADD scores for >3000 genes. In a benchmark on 18 clinical gene sets, we achieve a sensitivity of 91.4% and a specificity of 76.9%. This accuracy is unmatched by 12 other tools. We provide GAVIN as an online MOLGENIS service to annotate VCF files and as an open source executable for use in bioinformatic pipelines...
January 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28093074/insights-into-the-design-and-interpretation-of-iclip-experiments
#7
Nejc Haberman, Ina Huppertz, Jan Attig, Julian König, Zhen Wang, Christian Hauer, Matthias W Hentze, Andreas E Kulozik, Hervé Le Hir, Tomaž Curk, Christopher R Sibley, Kathi Zarnack, Jernej Ule
BACKGROUND: Ultraviolet (UV) crosslinking and immunoprecipitation (CLIP) identifies the sites on RNAs that are in direct contact with RNA-binding proteins (RBPs). Several variants of CLIP exist, which require different computational approaches for analysis. This variety of approaches can create challenges for a novice user and can hamper insights from multi-study comparisons. Here, we produce data with multiple variants of CLIP and evaluate the data with various computational methods to better understand their suitability...
January 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28081708/identifying-aggressive-prostate-cancer-foci-using-a-dna-methylation-classifier
#8
Kamilla Mundbjerg, Sameer Chopra, Mehrdad Alemozaffar, Christopher Duymich, Ranjani Lakshminarasimhan, Peter W Nichols, Manju Aron, Kimberly D Siegmund, Osamu Ukimura, Monish Aron, Mariana Stern, Parkash Gill, John D Carpten, Torben F Ørntoft, Karina D Sørensen, Daniel J Weisenberger, Peter A Jones, Vinay Duddalwar, Inderbir Gill, Gangning Liang
BACKGROUND: Slow-growing prostate cancer (PC) can be aggressive in a subset of cases. Therefore, prognostic tools to guide clinical decision-making and avoid overtreatment of indolent PC and undertreatment of aggressive disease are urgently needed. PC has a propensity to be multifocal with several different cancerous foci per gland. RESULTS: Here, we have taken advantage of the multifocal propensity of PC and categorized aggressiveness of individual PC foci based on DNA methylation patterns in primary PC foci and matched lymph node metastases...
January 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28077169/distinct-5-methylcytosine-profiles-in-poly-a-rna-from-mouse-embryonic-stem-cells-and-brain
#9
Thomas Amort, Dietmar Rieder, Alexandra Wille, Daria Khokhlova-Cubberley, Christian Riml, Lukas Trixl, Xi-Yu Jia, Ronald Micura, Alexandra Lusser
BACKGROUND: Recent work has identified and mapped a range of posttranscriptional modifications in mRNA, including methylation of the N6 and N1 positions in adenine, pseudouridylation, and methylation of carbon 5 in cytosine (m5C). However, knowledge about the prevalence and transcriptome-wide distribution of m5C is still extremely limited; thus, studies in different cell types, tissues, and organisms are needed to gain insight into possible functions of this modification and implications for other regulatory processes...
January 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28038679/the-incredible-complexity-of-rna-splicing
#10
Christelle Robert, Mick Watson
Alternative splice isoforms are common and important and have been shown to impact many human diseases. A new study by Nellore et al. offers a comprehensive study of splice junctions in humans by re-analyzing over 21,500 public human RNA sequencing datasets.
December 30, 2016: Genome Biology
https://www.readbyqxmd.com/read/28038678/human-splicing-diversity-and-the-extent-of-unannotated-splice-junctions-across-human-rna-seq-samples-on-the-sequence-read-archive
#11
Abhinav Nellore, Andrew E Jaffe, Jean-Philippe Fortin, José Alquicira-Hernández, Leonardo Collado-Torres, Siruo Wang, Robert A Phillips Iii, Nishika Karbhari, Kasper D Hansen, Ben Langmead, Jeffrey T Leek
BACKGROUND: Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. RESULTS: We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations...
December 30, 2016: Genome Biology
https://www.readbyqxmd.com/read/27998290/methylome-evolution-in-plants
#12
REVIEW
Amaryllis Vidalis, Daniel Živković, René Wardenaar, David Roquis, Aurélien Tellier, Frank Johannes
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale...
December 20, 2016: Genome Biology
https://www.readbyqxmd.com/read/27993162/tet-enzymes-double-agents-in-the-transposable-element-host-genome-conflict
#13
Patricia Gerdes, Sandra R Richardson, Geoffrey J Faulkner
The mouse genome is replete with retrotransposon sequences, from evolutionarily young elements with mutagenic potential that must be controlled, to inactive molecular fossils whose sequences can be domesticated over evolutionary time to benefit the host genome. In an exciting new study, de la Rica and colleagues have uncovered a complex relationship between ten-eleven translocation (TET) proteins and retrotransposons in mouse embryonic stem cells (ESCs), implicating TETs as enhancers in the exaptation and function of retroelement sequences...
December 20, 2016: Genome Biology
https://www.readbyqxmd.com/read/27993155/the-genome-of-the-gulf-pipefish-enables-understanding-of-evolutionary-innovations
#14
C M Small, S Bassham, J Catchen, A Amores, A M Fuiten, R S Brown, A G Jones, W A Cresko
BACKGROUND: Evolutionary origins of derived morphologies ultimately stem from changes in protein structure, gene regulation, and gene content. A well-assembled, annotated reference genome is a central resource for pursuing these molecular phenomena underlying phenotypic evolution. We explored the genome of the Gulf pipefish (Syngnathus scovelli), which belongs to family Syngnathidae (pipefishes, seahorses, and seadragons). These fishes have dramatically derived bodies and a remarkable novelty among vertebrates, the male brood pouch...
December 20, 2016: Genome Biology
https://www.readbyqxmd.com/read/27993159/erratum-to-statistically-based-splicing-detection-reveals-neural-enrichment-and-tissue-specific-induction-of-circular-rna-during-human-fetal-development
#15
Linda Szabo, Robert Morey, Nathan J Palpant, Peter L Wang, Nastaran Afari, Chuan Jiang, Mana M Parast, Charles E Murry, Louise C Laurent, Julia Salzman
No abstract text is available yet for this article.
December 19, 2016: Genome Biology
https://www.readbyqxmd.com/read/27993146/erratum-to-rapid-scoring-of-genes-in-microbial-pan-genome-wide-association-studies-with-scoary
#16
Ola Brynildsrud, Jon Bohlin, Lonneke Scheffer, Vegard Eldholm
No abstract text is available yet for this article.
December 19, 2016: Genome Biology
https://www.readbyqxmd.com/read/27986087/a-novel-independence-test-for-somatic-alterations-in-cancer-shows-that-biology-drives-mutual-exclusivity-but-chance-explains-most-co-occurrence
#17
Sander Canisius, John W M Martens, Lodewyk F A Wessels
In cancer, mutually exclusive or co-occurring somatic alterations across genes can suggest functional interactions. Existing tests for such patterns make the unrealistic assumption of identical gene alteration probabilities across tumors. We present Discrete Independence Statistic Controlling for Observations with Varying Event Rates (DISCOVER), a novel test that is more sensitive than other methods and controls its false positive rate. A pan-cancer analysis using DISCOVER finds no evidence for widespread co-occurrence, and most co-occurrences previously detected do not exceed expectation by chance...
December 16, 2016: Genome Biology
https://www.readbyqxmd.com/read/27986083/imp-a-pipeline-for%C3%A2-reproducible-reference-independent-integrated-metagenomic-and-metatranscriptomic-analyses
#18
Shaman Narayanasamy, Yohan Jarosz, Emilie E L Muller, Anna Heintz-Buschart, Malte Herold, Anne Kaysen, Cédric C Laczny, Nicolás Pinel, Patrick May, Paul Wilmes
Existing workflows for the analysis of multi-omic microbiome datasets are lab-specific and often result in sub-optimal data usage. Here we present IMP, a reproducible and modular pipeline for the integrated and reference-independent analysis of coupled metagenomic and metatranscriptomic data. IMP incorporates robust read preprocessing, iterative co-assembly, analyses of microbial community structure and function, automated binning, as well as genomic signature-based visualizations. The IMP-based data integration strategy enhances data usage, output volume, and output quality as demonstrated using relevant use-cases...
December 16, 2016: Genome Biology
https://www.readbyqxmd.com/read/27978845/human-sex-development-targeted-technologies-to-improve-diagnosis
#19
Federica Buonocore, John C Achermann
A new study of disorders of sex development presents an improved targeted next-generation sequencing approach for their diagnosis.Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1105-y .
December 15, 2016: Genome Biology
https://www.readbyqxmd.com/read/27964752/extreme-genomic-erosion-after-recurrent-demographic-bottlenecks-in-the-highly-endangered-iberian-lynx
#20
Federico Abascal, André Corvelo, Fernando Cruz, José L Villanueva-Cañas, Anna Vlasova, Marina Marcet-Houben, Begoña Martínez-Cruz, Jade Yu Cheng, Pablo Prieto, Víctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frias, Paolo Ribeca, Salvador Capella-Gutiérrez, José M Rodríguez, Francisco Câmara, Ernesto Lowy, Luca Cozzuto, Ionas Erb, Michael L Tress, Jose L Rodriguez-Ales, Jorge Ruiz-Orera, Ferran Reverter, Mireia Casas-Marce, Laura Soriano, Javier R Arango, Sophia Derdak, Beatriz Galán, Julie Blanc, Marta Gut, Belen Lorente-Galdos, Marta Andrés-Nieto, Carlos López-Otín, Alfonso Valencia, Ivo Gut, José L García, Roderic Guigó, William J Murphy, Aurora Ruiz-Herrera, Tomas Marques-Bonet, Guglielmo Roma, Cedric Notredame, Thomas Mailund, M Mar Albà, Toni Gabaldón, Tyler Alioto, José A Godoy
BACKGROUND: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. RESULTS: We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics...
December 14, 2016: Genome Biology
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