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Genome Biology

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https://www.readbyqxmd.com/read/29195502/omsv-enables-accurate-and-comprehensive-identification-of-large-structural-variations-from-nanochannel-based-single-molecule-optical-maps
#1
Le Li, Alden King-Yung Leung, Tsz-Piu Kwok, Yvonne Y Y Lai, Iris K Pang, Grace Tin-Yun Chung, Angel C Y Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J K Wu, Ernest T Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu, Ming Xiao, Kwok-Wai Lo, Pui-Yan Kwok, Ting-Fung Chan, Kevin Y Yip
We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers...
December 1, 2017: Genome Biology
https://www.readbyqxmd.com/read/29191225/landscape-and-evolution-of-tissue-specific-alternative-polyadenylation-across-drosophila-species
#2
Piero Sanfilippo, Jiayu Wen, Eric C Lai
BACKGROUND: Drosophila melanogaster has one of best-described transcriptomes of any multicellular organism. Nevertheless, the paucity of 3'-sequencing data in this species precludes comprehensive assessment of alternative polyadenylation (APA), which is subject to broad tissue-specific control. RESULTS: Here, we generate deep 3'-sequencing data from 23 developmental stages, tissues, and cell lines of D. melanogaster, yielding a comprehensive atlas of ~ 62,000 polyadenylated ends...
November 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/29187204/experimental-design-and-quantitative-analysis-of-microbial-community-multiomics
#3
REVIEW
Himel Mallick, Siyuan Ma, Eric A Franzosa, Tommi Vatanen, Xochitl C Morgan, Curtis Huttenhower
Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data...
November 30, 2017: Genome Biology
https://www.readbyqxmd.com/read/29187228/rnas-dynamic-and-mutable
#4
EDITORIAL
Mihaela Zavolan, Brenton R Graveley
No abstract text is available yet for this article.
November 29, 2017: Genome Biology
https://www.readbyqxmd.com/read/29187223/the-3-end-of-the-story-deciphering-combinatorial-interactions-that-control-mrna-fate
#5
Jeremy R Sanford, Luiz O F Penalva
A new study investigates how microRNAs affect the binding of proteins to RNA.
November 29, 2017: Genome Biology
https://www.readbyqxmd.com/read/29179779/evaluation-of-in-silico-algorithms-for-use-with-acmg-amp-clinical-variant-interpretation-guidelines
#6
Rajarshi Ghosh, Ninad Oak, Sharon E Plon
BACKGROUND: The American College of Medical Genetics and American College of Pathologists (ACMG/AMP) variant classification guidelines for clinical reporting are widely used in diagnostic laboratories for variant interpretation. The ACMG/AMP guidelines recommend complete concordance of predictions among all in silico algorithms used without specifying the number or types of algorithms. The subjective nature of this recommendation contributes to discordance of variant classification among clinical laboratories and prevents definitive classification of variants...
November 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/29178945/crispr-cas9-mediated-targeted-chromosome-elimination
#7
Erwei Zuo, Xiaona Huo, Xuan Yao, Xinde Hu, Yidi Sun, Jianhang Yin, Bingbing He, Xing Wang, Linyu Shi, Jie Ping, Yu Wei, Wenqin Ying, Wei Wei, Wenjia Liu, Cheng Tang, Yixue Li, Jiazhi Hu, Hui Yang
BACKGROUND: The CRISPR/Cas9 system has become an efficient gene editing method for generating cells carrying precise gene mutations, including the rearrangement and deletion of chromosomal segments. However, whether an entire chromosome could be eliminated by this technology is still unknown. RESULTS: Here we demonstrate the use of the CRISPR/Cas9 system to eliminate targeted chromosomes. Using either multiple cleavages induced by a single-guide RNA (sgRNA) that targets multiple chromosome-specific sites or a cocktail of multiple sgRNAs, each targeting one specific site, we found that a sex chromosome could be selectively eliminated in cultured cells, embryos, and tissues in vivo...
November 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/29169371/computational-biologists-moving-to-the-driver-s-seat
#8
Itai Yanai, Eva Chmielnicki
The recent shift of computational biologists from bioinformatics service providers to leaders of cutting-edge programs highlights the accompanying cultural and conceptual changes that should be implemented by funding bodies and academic institutions.
November 23, 2017: Genome Biology
https://www.readbyqxmd.com/read/29151363/functional-assessment-of-human-enhancer-activities-using-whole-genome-starr-sequencing
#9
Yuwen Liu, Shan Yu, Vineet K Dhiman, Tonya Brunetti, Heather Eckart, Kevin P White
BACKGROUND: Genome-wide quantification of enhancer activity in the human genome has proven to be a challenging problem. Recent efforts have led to the development of powerful tools for enhancer quantification. However, because of genome size and complexity, these tools have yet to be applied to the whole human genome. RESULTS:  In the current study, we use a human prostate cancer cell line, LNCaP as a model to perform whole human genome STARR-seq (WHG-STARR-seq) to reliably obtain an assessment of enhancer activity...
November 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/29149906/forebrain-specific-conditional-silencing-of-staufen2-alters-synaptic-plasticity-learning-and-memory-in-rats
#10
Stefan M Berger, Iván Fernández-Lamo, Kai Schönig, Sandra M Fernández Moya, Janina Ehses, Rico Schieweck, Stefano Clementi, Thomas Enkel, Sascha Grothe, Oliver von Bohlen Und Halbach, Inmaculada Segura, José María Delgado-García, Agnès Gruart, Michael A Kiebler, Dusan Bartsch
BACKGROUND: Dendritic messenger RNA (mRNA) localization and subsequent local translation in dendrites critically contributes to synaptic plasticity and learning and memory. Little is known, however, about the contribution of RNA-binding proteins (RBPs) to these processes in vivo. RESULTS: To delineate the role of the double-stranded RBP Staufen2 (Stau2), we generate a transgenic rat model, in which Stau2 expression is conditionally silenced by Cre-inducible expression of a microRNA (miRNA) targeting Stau2 mRNA in adult forebrain neurons...
November 17, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141666/intron-retention-enhances-gene-regulatory-complexity-in-vertebrates
#11
Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, Shaniko Shini, Graham J Lieschke, Justin J-L Wong, John E J Rasko
BACKGROUND: While intron retention (IR) is now widely accepted as an important mechanism of mammalian gene expression control, it remains the least studied form of alternative splicing. To delineate conserved features of IR, we performed an exhaustive phylogenetic analysis in a highly purified and functionally defined cell type comprising neutrophilic granulocytes from five vertebrate species spanning 430 million years of evolution. RESULTS: Our RNA-sequencing-based analysis suggests that IR increases gene regulatory complexity, which is indicated by a strong anti-correlation between the number of genes affected by IR and the number of protein-coding genes in the genome of individual species...
November 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141660/xcell-digitally-portraying-the-tissue-cellular-heterogeneity-landscape
#12
Dvir Aran, Zicheng Hu, Atul J Butte
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141659/rescue-of-high-specificity-cas9-variants-using-sgrnas-with-matched-5-nucleotides
#13
Sojung Kim, Taegeun Bae, Jaewoong Hwang, Jin-Soo Kim
We report that engineered Cas9 variants with improved specificity-eCas9-1.1 and Cas9-HF1-are often poorly active in human cells, when complexed with single guide RNAs (sgRNAs) with a mismatch at the 5' terminus, relative to target DNA sequences. Because the nucleotide at the 5' end of sgRNAs, expressed under the control of the commonly-used U6 promoter, is fixed to a guanine, these attenuated Cas9 variants are not useful at many target sites. By using sgRNAs with matched 5' nucleotides, produced by linking them to a self-cleaving ribozyme, the editing activity of Cas9 variants can be rescued without sacrificing high specificity...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141655/long-term-balancing-selection-contributes-to-adaptation-in-arabidopsis-and-its-relatives
#14
Qiong Wu, Ting-Shen Han, Xi Chen, Jia-Fu Chen, Yu-Pan Zou, Zi-Wen Li, Yong-Chao Xu, Ya-Long Guo
BACKGROUND: In contrast to positive selection, which reduces genetic variation by fixing beneficial alleles, balancing selection maintains genetic variation within a population or species and plays crucial roles in adaptation in diverse organisms. However, which genes, genome-wide, are under balancing selection and the extent to which these genes are involved in adaptation are largely unknown. RESULTS: We performed a genome-wide scan for genes under balancing selection across two plant species, Arabidopsis thaliana and its relative Capsella rubella, which diverged about 8 million generations ago...
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29141654/early-career-researchers-want-open-science
#15
Andrea Farnham, Christoph Kurz, Mehmet Ali Öztürk, Monica Solbiati, Oona Myllyntaus, Jordy Meekes, Tra My Pham, Clara Paz, Magda Langiewicz, Sophie Andrews, Liisa Kanninen, Chantal Agbemabiese, Arzu Tugce Guler, Jeffrey Durieux, Sarah Jasim, Olivia Viessmann, Stefano Frattini, Danagul Yembergenova, Carla Marin Benito, Marion Porte, Anaïs Grangeray-Vilmint, Rafael Prieto Curiel, Carin Rehncrona, Tareq Malas, Flavia Esposito, Kristina Hettne
Open Science is encouraged by the European Union and many other political and scientific institutions. However, scientific practice is proving slow to change. We propose, as early career researchers, that it is our task to change scientific research into open scientific research and commit to Open Science principles.
November 15, 2017: Genome Biology
https://www.readbyqxmd.com/read/29132403/the-interplay-of-demography-and-selection-during-maize-domestication-and-expansion
#16
Li Wang, Timothy M Beissinger, Anne Lorant, Claudia Ross-Ibarra, Jeffrey Ross-Ibarra, Matthew B Hufford
BACKGROUND: The history of maize has been characterized by major demographic events, including population size changes associated with domestication and range expansion, and gene flow with wild relatives. The interplay between demographic history and selection has shaped diversity across maize populations and genomes. RESULTS: We investigate these processes using high-depth resequencing data from 31 maize landraces spanning the pre-Columbian distribution of maize, and four wild teosinte individuals (Zea mays ssp...
November 13, 2017: Genome Biology
https://www.readbyqxmd.com/read/29117868/correction-to-quantitative-metagenomics-reveals-unique-gut-microbiome-biomarkers-in-ankylosing-spondylitis
#17
Chengping Wen, Zhijun Zheng, Tiejuan Shao, Lin Liu, Zhijun Xie, Emmanuelle Le Chatelier, Zhixing He, Wendi Zhong, Yongsheng Fan, Linshuang Zhang, Haichang Li, Chunyan Wu, Changfeng Hu, Qian Xu, Jia Zhou, Shunfeng Cai, Dawei Wang, Yun Huang, Maxime Breban, Nan Qin, Stanislav Dusko Ehrlich
Upon publication of the original article [1], it was noted that references 11 and 22 were miscited in the reference list.
November 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/29115978/depletion-of-somatic-mutations-in-splicing-associated-sequences-in-cancer-genomes
#18
Laurence D Hurst, Nizar N Batada
BACKGROUND: An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this methodology leads to identification of false-positive mutations. Here, using synonymous somatic mutations (SSMs) identified in over 4000 tumours across 15 different cancer types, we sought to test this assumption by focusing on coding regions required for splicing...
November 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/29115968/f-sclvm-scalable-and-versatile-factor-analysis-for-single-cell-rna-seq
#19
Florian Buettner, Naruemon Pratanwanich, Davis J McCarthy, John C Marioni, Oliver Stegle
Single-cell RNA-sequencing (scRNA-seq) allows studying heterogeneity in gene expression in large cell populations. Such heterogeneity can arise due to technical or biological factors, making decomposing sources of variation difficult. We here describe f-scLVM (factorial single-cell latent variable model), a method based on factor analysis that uses pathway annotations to guide the inference of interpretable factors underpinning the heterogeneity. Our model jointly estimates the relevance of individual factors, refines gene set annotations, and infers factors without annotation...
November 7, 2017: Genome Biology
https://www.readbyqxmd.com/read/29089032/new-reference-genome-sequences-of-hot-pepper-reveal-the-massive-evolution-of-plant-disease-resistance-genes-by-retroduplication
#20
Seungill Kim, Jieun Park, Seon-In Yeom, Yong-Min Kim, Eunyoung Seo, Ki-Tae Kim, Myung-Shin Kim, Je Min Lee, Kyeongchae Cheong, Ho-Sub Shin, Saet-Byul Kim, Koeun Han, Jundae Lee, Minkyu Park, Hyun-Ah Lee, Hye-Young Lee, Youngsill Lee, Soohyun Oh, Joo Hyun Lee, Eunhye Choi, Eunbi Choi, So Eui Lee, Jongbum Jeon, Hyunbin Kim, Gobong Choi, Hyeunjeong Song, JunKi Lee, Sang-Choon Lee, Jin-Kyung Kwon, Hea-Young Lee, Namjin Koo, Yunji Hong, Ryan W Kim, Won-Hee Kang, Jin Hoe Huh, Byoung-Cheorl Kang, Tae-Jin Yang, Yong-Hwan Lee, Jeffrey L Bennetzen, Doil Choi
BACKGROUND: Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS: We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C...
November 1, 2017: Genome Biology
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