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Genome Biology

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https://www.readbyqxmd.com/read/30016986/making-genome-browsers-portable-and-personal
#1
Aziz Khan, Xuegong Zhang
GIVE is a framework and library for creating portable and personalized genome browsers. It makes visualizing genomic data as easy as building a laboratory homepage.
July 18, 2018: Genome Biology
https://www.readbyqxmd.com/read/30016975/give-portable-genome-browsers-for-personal-websites
#2
Xiaoyi Cao, Zhangming Yan, Qiuyang Wu, Alvin Zheng, Sheng Zhong
Growing popularity and diversity of genomic data demand portable and versatile genome browsers. Here, we present an open source programming library called GIVE that facilitates the creation of personalized genome browsers without requiring a system administrator. By inserting HTML tags, one can add to a personal webpage interactive visualization of multiple types of genomics data, including genome annotation, "linear" quantitative data, and genome interaction data. GIVE includes a graphical interface called HUG (HTML Universal Generator) that automatically generates HTML code for displaying user chosen data, which can be copy-pasted into user's personal website or saved and shared with collaborators...
July 18, 2018: Genome Biology
https://www.readbyqxmd.com/read/30012220/exome-chip-meta-analysis-identifies-novel-loci-associated-with-cardiac-conduction-including-adamts6
#3
Bram P Prins, Timothy J Mead, Jennifer A Brody, Gardar Sveinbjornsson, Ioanna Ntalla, Nathan A Bihlmeyer, Marten van den Berg, Jette Bork-Jensen, Stefania Cappellani, Stefan Van Duijvenboden, Nikolai T Klena, George C Gabriel, Xiaoqin Liu, Cagri Gulec, Niels Grarup, Jeffrey Haessler, Leanne M Hall, Annamaria Iorio, Aaron Isaacs, Ruifang Li-Gao, Honghuang Lin, Ching-Ti Liu, Leo-Pekka Lyytikäinen, Jonathan Marten, Hao Mei, Martina Müller-Nurasyid, Michele Orini, Sandosh Padmanabhan, Farid Radmanesh, Julia Ramirez, Antonietta Robino, Molly Schwartz, Jessica van Setten, Albert V Smith, Niek Verweij, Helen R Warren, Stefan Weiss, Alvaro Alonso, David O Arnar, Michiel L Bots, Rudolf A de Boer, Anna F Dominiczak, Mark Eijgelsheim, Patrick T Ellinor, Xiuqing Guo, Stephan B Felix, Tamara B Harris, Caroline Hayward, Susan R Heckbert, Paul L Huang, J W Jukema, Mika Kähönen, Jan A Kors, Pier D Lambiase, Lenore J Launer, Man Li, Allan Linneberg, Christopher P Nelson, Oluf Pedersen, Marco Perez, Annette Peters, Ozren Polasek, Bruce M Psaty, Olli T Raitakari, Kenneth M Rice, Jerome I Rotter, Moritz F Sinner, Elsayed Z Soliman, Tim D Spector, Konstantin Strauch, Unnur Thorsteinsdottir, Andrew Tinker, Stella Trompet, André Uitterlinden, Ilonca Vaartjes, Peter van der Meer, Uwe Völker, Henry Völzke, Melanie Waldenberger, James G Wilson, Zhijun Xie, Folkert W Asselbergs, Marcus Dörr, Cornelia M van Duijn, Paolo Gasparini, Daniel F Gudbjartsson, Vilmundur Gudnason, Torben Hansen, Stefan Kääb, Jørgen K Kanters, Charles Kooperberg, Terho Lehtimäki, Henry J Lin, Steven A Lubitz, Dennis O Mook-Kanamori, Francesco J Conti, Christopher H Newton-Cheh, Jonathan Rosand, Igor Rudan, Nilesh J Samani, Gianfranco Sinagra, Blair H Smith, Hilma Holm, Bruno H Stricker, Sheila Ulivi, Nona Sotoodehnia, Suneel S Apte, Pim van der Harst, Kari Stefansson, Patricia B Munroe, Dan E Arking, Cecilia W Lo, Yalda Jamshidi
BACKGROUND: Genome-wide association studies conducted on QRS duration, an electrocardiographic measurement associated with heart failure and sudden cardiac death, have led to novel biological insights into cardiac function. However, the variants identified fall predominantly in non-coding regions and their underlying mechanisms remain unclear. RESULTS: Here, we identify putative functional coding variation associated with changes in the QRS interval duration by combining Illumina HumanExome BeadChip genotype data from 77,898 participants of European ancestry and 7695 of African descent in our discovery cohort, followed by replication in 111,874 individuals of European ancestry from the UK Biobank and deCODE cohorts...
July 17, 2018: Genome Biology
https://www.readbyqxmd.com/read/30005597/from-squiggle-to-basepair-computational-approaches-for-improving-nanopore-sequencing-read-accuracy
#4
REVIEW
Franka J Rang, Wigard P Kloosterman, Jeroen de Ridder
Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5% and 15%. Here, we review computational approaches determining the nanopore sequencing error rate...
July 13, 2018: Genome Biology
https://www.readbyqxmd.com/read/30001206/alternative-dna-secondary-structure-formation-affects-rna-polymerase-ii-promoter-proximal-pausing-in-human
#5
Karol Szlachta, Ryan G Thys, Naomi D Atkin, Levi C T Pierce, Stefan Bekiranov, Yuh-Hwa Wang
BACKGROUND: Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA. RESULTS: The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding...
July 12, 2018: Genome Biology
https://www.readbyqxmd.com/read/30001199/dnmt3a-and-tet1-cooperate-to-regulate-promoter-epigenetic-landscapes-in-mouse-embryonic-stem-cells
#6
Tianpeng Gu, Xueqiu Lin, Sean M Cullen, Min Luo, Mira Jeong, Marcos Estecio, Jianjun Shen, Swanand Hardikar, Deqiang Sun, Jianzhong Su, Danielle Rux, Anna Guzman, Minjung Lee, Lei Stanley Qi, Jia-Jia Chen, Michael Kyba, Yun Huang, Taiping Chen, Wei Li, Margaret A Goodell
BACKGROUND: DNA methylation is a heritable epigenetic mark, enabling stable but reversible gene repression. In mammalian cells, DNA methyltransferases (DNMTs) are responsible for modifying cytosine to 5-methylcytosine (5mC), which can be further oxidized by the TET dioxygenases to ultimately cause DNA demethylation. However, the genome-wide cooperation and functions of these two families of proteins, especially at large under-methylated regions, called canyons, remain largely unknown...
July 12, 2018: Genome Biology
https://www.readbyqxmd.com/read/29986741/splicing-heterogeneity-separating-signal-from-noise
#7
Yihan Wan, Daniel R Larson
Single-cell analyses have revealed a tremendous variety among cells in the abundance and chemical composition of RNA. Much of this heterogeneity is due to alternative splicing by the spliceosome. Little is known about how many of the resulting isoforms are biologically functional or just provide noise with little to no impact. The dynamic nature of the spliceosome provides numerous opportunities for regulation but is also the source of stochastic fluctuations. We discuss possible origins of splicing stochasticity, the experimental approaches for studying heterogeneity in isoforms, and the potential biological significance of noisy splicing in development and disease...
July 9, 2018: Genome Biology
https://www.readbyqxmd.com/read/29983116/horizontal-transfer-of-bovb-and-l1-retrotransposons-in-eukaryotes
#8
Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson
BACKGROUND: Transposable elements (TEs) are mobile DNA sequences, colloquially known as jumping genes because of their ability to replicate to new genomic locations. TEs can jump between organisms or species when given a vector of transfer, such as a tick or virus, in a process known as horizontal transfer. Here, we propose that LINE-1 (L1) and Bovine-B (BovB), the two most abundant TE families in mammals, were initially introduced as foreign DNA via ancient horizontal transfer events...
July 9, 2018: Genome Biology
https://www.readbyqxmd.com/read/29973285/a-large-scale-whole-genome-sequencing-analysis-reveals-highly-specific-genome-editing-by-both-cas9-and-cpf1-cas12a-nucleases-in-rice
#9
Xu Tang, Guanqing Liu, Jianping Zhou, Qiurong Ren, Qi You, Li Tian, Xuhui Xin, Zhaohui Zhong, Binglin Liu, Xuelian Zheng, Dengwei Zhang, Aimee Malzahn, Zhiyun Gong, Yiping Qi, Tao Zhang, Yong Zhang
BACKGROUND: Targeting specificity has been a barrier to applying genome editing systems in functional genomics, precise medicine and plant breeding. In plants, only limited studies have used whole-genome sequencing (WGS) to test off-target effects of Cas9. The cause of numerous discovered mutations is still controversial. Furthermore, WGS-based off-target analysis of Cpf1 (Cas12a) has not been reported in any higher organism to date. RESULTS: We conduct a WGS analysis of 34 plants edited by Cas9 and 15 plants edited by Cpf1 in T0 and T1 generations along with 20 diverse control plants in rice...
July 4, 2018: Genome Biology
https://www.readbyqxmd.com/read/29950183/post-translational-buffering-leads-to-convergent-protein-expression-levels-between-primates
#10
Sidney H Wang, Chiaowen Joyce Hsiao, Zia Khan, Jonathan K Pritchard
BACKGROUND: Differences in gene regulation between human and closely related species influence phenotypes that are distinctly human. While gene regulation is a multi-step process, the majority of research concerning divergence in gene regulation among primates has focused on transcription. RESULTS: To gain a comprehensive view of gene regulation, we surveyed genome-wide ribosome occupancy, which reflects levels of protein translation, in lymphoblastoid cell lines derived from human, chimpanzee, and rhesus macaque...
June 27, 2018: Genome Biology
https://www.readbyqxmd.com/read/29950165/hmmufotu-an-hmm-and-phylogenetic-placement-based-ultra-fast-taxonomic-assignment-and-otu-picking-tool-for-microbiome-amplicon-sequencing-studies
#11
Qi Zheng, Casey Bartow-McKenney, Jacquelyn S Meisel, Elizabeth A Grice
Culture-independent analysis of microbial communities frequently relies on amplification and sequencing of the prokaryotic 16S ribosomal RNA gene. Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships. Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs and taxonomy assignment. Compared to standard pipelines, HmmUFOtu more accurately and reliably recapitulates microbial community diversity and composition in simulated and real datasets without relying on heuristics or sacrificing speed or accuracy...
June 27, 2018: Genome Biology
https://www.readbyqxmd.com/read/29945659/cpg-island-composition-differences-are-a-source-of-gene-expression-noise-indicative-of-promoter-responsiveness
#12
Michael D Morgan, John C Marioni
BACKGROUND: Population phenotypic variation can arise from genetic differences between individuals, or from cellular heterogeneity in an isogenic group of cells or organisms. The emergence of gene expression differences between genetically identical cells is referred to as gene expression noise, the sources of which are not well understood. RESULTS: In this work, by studying gene expression noise between multiple cell lineages and mammalian species, we find consistent evidence of a role for CpG islands as sources of gene expression noise...
June 26, 2018: Genome Biology
https://www.readbyqxmd.com/read/29945655/deepcrispr-optimized-crispr-guide-rna-design-by-deep-learning
#13
Guohui Chuai, Hanhui Ma, Jifang Yan, Ming Chen, Nanfang Hong, Dongyu Xue, Chi Zhou, Chenyu Zhu, Ke Chen, Bin Duan, Feng Gu, Sheng Qu, Deshuang Huang, Jia Wei, Qi Liu
A major challenge for effective application of CRISPR systems is to accurately predict the single guide RNA (sgRNA) on-target knockout efficacy and off-target profile, which would facilitate the optimized design of sgRNAs with high sensitivity and specificity. Here we present DeepCRISPR, a comprehensive computational platform to unify sgRNA on-target and off-target site prediction into one framework with deep learning, surpassing available state-of-the-art in silico tools. In addition, DeepCRISPR fully automates the identification of sequence and epigenetic features that may affect sgRNA knockout efficacy in a data-driven manner...
June 26, 2018: Genome Biology
https://www.readbyqxmd.com/read/29925420/hepatic-steatosis-risk-is-partly-driven-by-increased-de-novo-lipogenesis-following-carbohydrate-consumption
#14
Francis W B Sanders, Animesh Acharjee, Celia Walker, Luke Marney, Lee D Roberts, Fumiaki Imamura, Benjamin Jenkins, Jack Case, Sumantra Ray, Samuel Virtue, Antonio Vidal-Puig, Diana Kuh, Rebecca Hardy, Michael Allison, Nita Forouhi, Andrew J Murray, Nick Wareham, Michele Vacca, Albert Koulman, Julian L Griffin
BACKGROUND: Diet is a major contributor to metabolic disease risk, but there is controversy as to whether increased incidences of diseases such as non-alcoholic fatty liver disease arise from consumption of saturated fats or free sugars. Here, we investigate whether a sub-set of triacylglycerols (TAGs) were associated with hepatic steatosis and whether they arise from de novo lipogenesis (DNL) from the consumption of carbohydrates. RESULTS: We conduct direct infusion mass spectrometry of lipids in plasma to study the association between specific TAGs and hepatic steatosis assessed by ultrasound and fatty liver index in volunteers from the UK-based Fenland Study and evaluate clustering of TAGs in the National Survey of Health and Development UK cohort...
June 20, 2018: Genome Biology
https://www.readbyqxmd.com/read/29921301/dropest-pipeline-for-accurate-estimation-of-molecular-counts-in-droplet-based-single-cell-rna-seq-experiments
#15
Viktor Petukhov, Jimin Guo, Ninib Baryawno, Nicolas Severe, David T Scadden, Maria G Samsonova, Peter V Kharchenko
Recent single-cell RNA-seq protocols based on droplet microfluidics use massively multiplexed barcoding to enable simultaneous measurements of transcriptomes for thousands of individual cells. The increasing complexity of such data creates challenges for subsequent computational processing and troubleshooting of these experiments, with few software options currently available. Here, we describe a flexible pipeline for processing droplet-based transcriptome data that implements barcode corrections, classification of cell quality, and diagnostic information about the droplet libraries...
June 19, 2018: Genome Biology
https://www.readbyqxmd.com/read/29890997/diversification-and-independent-domestication-of-asian-and-european-pears
#16
Jun Wu, Yingtao Wang, Jiabao Xu, Schuyler S Korban, Zhangjun Fei, Shutian Tao, Ray Ming, Shuaishuai Tai, Awais M Khan, Joseph D Postman, Chao Gu, Hao Yin, Danman Zheng, Kaijie Qi, Yong Li, Runze Wang, Cecilia H Deng, Satish Kumar, David Chagné, Xiaolong Li, Juyou Wu, Xiaosan Huang, Huping Zhang, Zhihua Xie, Xiao Li, Mingyue Zhang, Yanhong Li, Zhen Yue, Xiaodong Fang, Jiaming Li, Leiting Li, Cong Jin, Mengfan Qin, Jiaying Zhang, Xiao Wu, Yaqi Ke, Jian Wang, Huanmimg Yang, Shaoling Zhang
BACKGROUND: Pear (Pyrus) is a globally grown fruit, with thousands of cultivars in five domesticated species and dozens of wild species. However, little is known about the evolutionary history of these pear species and what has contributed to the distinct phenotypic traits between Asian pears and European pears. RESULTS: We report the genome resequencing of 113 pear accessions from worldwide collections, representing both cultivated and wild pear species. Based on 18,302,883 identified SNPs, we conduct phylogenetics, population structure, gene flow, and selective sweep analyses...
June 11, 2018: Genome Biology
https://www.readbyqxmd.com/read/29884221/tensorial-blind-source-separation-for-improved-analysis-of-multi-omic-data
#17
Andrew E Teschendorff, Han Jing, Dirk S Paul, Joni Virta, Klaus Nordhausen
There is an increased need for integrative analyses of multi-omic data. We present and benchmark a novel tensorial independent component analysis (tICA) algorithm against current state-of-the-art methods. We find that tICA outperforms competing methods in identifying biological sources of data variation at a reduced computational cost. On epigenetic data, tICA can identify methylation quantitative trait loci at high sensitivity. In the cancer context, tICA identifies gene modules whose expression variation across tumours is driven by copy-number or DNA methylation changes, but whose deregulation relative to normal tissue is independent of such alterations, a result we validate by direct analysis of individual data types...
June 8, 2018: Genome Biology
https://www.readbyqxmd.com/read/29880058/dissecting-an-adiposity-locus-with-an-arsenal-of-genomics
#18
Kim Lorenz, Benjamin F Voight
We discuss a recent study that has identified and validated the link between a type-2 diabetes (T2D) association and human adipose biology by means of KLF14 gene expression. In addition to being maternally imprinted, the contributed risk at this locus is greater in female carriers.
June 7, 2018: Genome Biology
https://www.readbyqxmd.com/read/29880023/hundreds-of-novel-composite-genes-and-chimeric-genes-with-bacterial-origins-contributed-to-haloarchaeal-evolution
#19
Raphaël Méheust, Andrew K Watson, François-Joseph Lapointe, R Thane Papke, Philippe Lopez, Eric Bapteste
BACKGROUND: Haloarchaea, a major group of archaea, are able to metabolize sugars and to live in oxygenated salty environments. Their physiology and lifestyle strongly contrast with that of their archaeal ancestors. Amino acid optimizations, which lowered the isoelectric point of haloarchaeal proteins, and abundant lateral gene transfers from bacteria have been invoked to explain this deep evolutionary transition. We use network analyses to show that the evolution of novel genes exclusive to Haloarchaea also contributed to the evolution of this group...
June 7, 2018: Genome Biology
https://www.readbyqxmd.com/read/29871653/sinc-seq-correlation-of-transient-gene-expressions-between-nucleus-and-cytoplasm-reflects-single-cell-physiology
#20
Mahmoud N Abdelmoez, Kei Iida, Yusuke Oguchi, Hidekazu Nishikii, Ryuji Yokokawa, Hidetoshi Kotera, Sotaro Uemura, Juan G Santiago, Hirofumi Shintaku
We report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA and cytRNA-sequencing (SINC-seq). SINC-seq constructs two individual RNA-seq libraries, nucRNA and cytRNA, per cell, quantifies gene expression in the subcellular compartments, and combines them to create novel single-cell RNA-seq data. Leveraging SINC-seq, we discover distinct natures of correlation among cytRNA and nucRNA that reflect the transient physiological state of single cells...
June 6, 2018: Genome Biology
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