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Genome Biology

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https://www.readbyqxmd.com/read/28424087/heroes-of-peer-review-robert-lowe
#1
Robert Lowe
In the second of our series of articles celebrating peer reviewers, we talk to Robert Lowe, who is a Lecturer in computational biology at Queen Mary University of London, UK, and a valued reviewer for Genome Biology.
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28424085/the-within-host-population-dynamics-of-mycobacterium-tuberculosis-vary-with-treatment-efficacy
#2
Andrej Trauner, Qingyun Liu, Laura E Via, Xin Liu, Xianglin Ruan, Lili Liang, Huimin Shi, Ying Chen, Ziling Wang, Ruixia Liang, Wei Zhang, Wang Wei, Jingcai Gao, Gang Sun, Daniela Brites, Kathleen England, Guolong Zhang, Sebastien Gagneux, Clifton E Barry, Qian Gao
BACKGROUND: Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics...
April 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28407784/relationships-between-gut-microbiota-plasma-metabolites-and-metabolic-syndrome-traits-in-the-metsim-cohort
#3
Elin Org, Yuna Blum, Silva Kasela, Margarete Mehrabian, Johanna Kuusisto, Antti J Kangas, Pasi Soininen, Zeneng Wang, Mika Ala-Korpela, Stanley L Hazen, Markku Laakso, Aldons J Lusis
BACKGROUND: The gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finnish men from the Metabolic Syndrome In Men (METSIM) study. RESULTS: We investigate gut microbiota relationships with a variety of factors that have an impact on the development of metabolic and cardiovascular traits. We identify novel associations between gut microbiota and fasting serum levels of a number of metabolites, including fatty acids, amino acids, lipids, and glucose...
April 13, 2017: Genome Biology
https://www.readbyqxmd.com/read/28403905/h2a-monoubiquitination-in-arabidopsis-thaliana-is-generally-independent-of-lhp1-and-prc2-activity
#4
Yue Zhou, Francisco J Romero-Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets...
April 12, 2017: Genome Biology
https://www.readbyqxmd.com/read/28399939/multi-tissue-dna-methylation-age-predictor-in-mouse
#5
Thomas M Stubbs, Marc Jan Bonder, Anne-Katrien Stark, Felix Krueger, Ferdinand von Meyenn, Oliver Stegle, Wolf Reik
BACKGROUND: DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this epigenetic clock is unique to humans or conserved in the more experimentally tractable mouse. RESULTS: We have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages...
April 11, 2017: Genome Biology
https://www.readbyqxmd.com/read/28395661/deepcpg-accurate-prediction-of-single-cell-dna-methylation-states-using-deep-learning
#6
Christof Angermueller, Heather J Lee, Wolf Reik, Oliver Stegle
Recent technological advances have enabled DNA methylation to be assayed at single-cell resolution. However, current protocols are limited by incomplete CpG coverage and hence methods to predict missing methylation states are critical to enable genome-wide analyses. We report DeepCpG, a computational approach based on deep neural networks to predict methylation states in single cells. We evaluate DeepCpG on single-cell methylation data from five cell types generated using alternative sequencing protocols. DeepCpG yields substantially more accurate predictions than previous methods...
April 11, 2017: Genome Biology
https://www.readbyqxmd.com/read/28390427/synthex-a-synthetic-normal-based-dna-sequencing-tool-for-copy-number-alteration-detection-and-tumor-heterogeneity-profiling
#7
Grace O Silva, Marni B Siegel, Lisle E Mose, Joel S Parker, Wei Sun, Charles M Perou, Mengjie Chen
Changes in the quantity of genetic material, known as somatic copy number alterations (CNAs), can drive tumorigenesis. Many methods exist for assessing CNAs using microarrays, but considerable technical issues limit current CNA calling based upon DNA sequencing. We present SynthEx, a novel tool for detecting CNAs from whole exome and genome sequencing. SynthEx utilizes a "synthetic-normal" strategy to overcome technical and financial issues. In terms of accuracy and precision, SynthEx is highly comparable to array-based methods and outperforms sequencing-based CNA detection tools...
April 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28381262/structuring-supplemental-materials-in-support-of-reproducibility
#8
Dov Greenbaum, Joel Rozowsky, Victoria Stodden, Mark Gerstein
Supplements are increasingly important to the scientific record, particularly in genomics. However, they are often underutilized. Optimally, supplements should make results findable, accessible, interoperable, and reusable (i.e., "FAIR"). Moreover, properly off-loading to them the data and detail in a paper could make the main text more readable. We propose a hierarchical organization for supplements, with some parts paralleling and "shadowing" the main text and other elements branching off from it, and we suggest a specific formatting to make this structure explicit...
April 5, 2017: Genome Biology
https://www.readbyqxmd.com/read/28376841/erratum-to-rapid-transcriptional-plasticity-of-duplicated-gene-clusters-enables-a-clonally-reproducing-aphid-to-colonise-diverse-plant-species
#9
Thomas C Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldón, Anna Jordan, Irene Julca, Graeme J Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara Lopez-Gomollon, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel R G Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C C Wilson, Cock van Oosterhout, David Swarbreck, Saskia A Hogenhout
No abstract text is available yet for this article.
April 4, 2017: Genome Biology
https://www.readbyqxmd.com/read/28372568/coming-out-the-experience-of-lgbt-people-in-stem
#10
Ben Barres, Beth Montague-Hellen, Jeremy Yoder
Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three openly LGBT+ researchers on their experiences in biology.
April 4, 2017: Genome Biology
https://www.readbyqxmd.com/read/28366169/functional-implications-of-neandertal-introgression-in-modern-humans
#11
Michael Dannemann, Kay Prüfer, Janet Kelso
BACKGROUND: Admixture between early modern humans and Neandertals approximately 50,000-60,000 years ago has resulted in 1.5-4% Neandertal ancestry in the genomes of present-day non-Africans. Evidence is accumulating that some of these archaic alleles are advantageous for modern humans, while others are deleterious; however, the major mechanism by which these archaic alleles act has not been fully explored. RESULTS: Here we assess the contributions of introgressed non-synonymous and regulatory variants to modern human protein and gene expression variation...
April 3, 2017: Genome Biology
https://www.readbyqxmd.com/read/28356141/genomic-history-of-the-origin-and-domestication-of-common-bean-unveils-its-closest-sister-species
#12
Martha Rendón-Anaya, Josaphat M Montero-Vargas, Soledad Saburido-Álvarez, Anna Vlasova, Salvador Capella-Gutierrez, José Juan Ordaz-Ortiz, O Mario Aguilar, Rosana P Vianello-Brondani, Marta Santalla, Luis Delaye, Toni Gabaldón, Paul Gepts, Robert Winkler, Roderic Guigó, Alfonso Delgado-Salinas, Alfredo Herrera-Estrella
BACKGROUND: Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. RESULTS: We sequenced the genomes of 29 accessions representing 12 Phaseolus species...
March 29, 2017: Genome Biology
https://www.readbyqxmd.com/read/28351423/epigenetic-aging-signatures-in-mice-livers-are-slowed-by-dwarfism-calorie-restriction-and-rapamycin-treatment
#13
Tina Wang, Brian Tsui, Jason F Kreisberg, Neil A Robertson, Andrew M Gross, Michael Ku Yu, Hannah Carter, Holly M Brown-Borg, Peter D Adams, Trey Ideker
BACKGROUND: Global but predictable changes impact the DNA methylome as we age, acting as a type of molecular clock. This clock can be hastened by conditions that decrease lifespan, raising the question of whether it can also be slowed, for example, by conditions that increase lifespan. Mice are particularly appealing organisms for studies of mammalian aging; however, epigenetic clocks have thus far been formulated only in humans. RESULTS: We first examined whether mice and humans experience similar patterns of change in the methylome with age...
March 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28351406/cidr-ultrafast-and-accurate-clustering-through-imputation-for-single-cell-rna-seq-data
#14
Peijie Lin, Michael Troup, Joshua W K Ho
Most existing dimensionality reduction and clustering packages for single-cell RNA-seq (scRNA-seq) data deal with dropouts by heavy modeling and computational machinery. Here, we introduce CIDR (Clustering through Imputation and Dimensionality Reduction), an ultrafast algorithm that uses a novel yet very simple implicit imputation approach to alleviate the impact of dropouts in scRNA-seq data in a principled manner. Using a range of simulated and real data, we show that CIDR improves the standard principal component analysis and outperforms the state-of-the-art methods, namely t-SNE, ZIFA, and RaceID, in terms of clustering accuracy...
March 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28351387/dietary-restriction-protects-from-age-associated-dna-methylation-and-induces-epigenetic-reprogramming-of-lipid-metabolism
#15
Oliver Hahn, Sebastian Grönke, Thomas M Stubbs, Gabriella Ficz, Oliver Hendrich, Felix Krueger, Simon Andrews, Qifeng Zhang, Michael J Wakelam, Andreas Beyer, Wolf Reik, Linda Partridge
BACKGROUND: Dietary restriction (DR), a reduction in food intake without malnutrition, increases most aspects of health during aging and extends lifespan in diverse species, including rodents. However, the mechanisms by which DR interacts with the aging process to improve health in old age are poorly understood. DNA methylation could play an important role in mediating the effects of DR because it is sensitive to the effects of nutrition and can affect gene expression memory over time...
March 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28351383/diverse-interventions-that-extend-mouse-lifespan-suppress-shared-age-associated-epigenetic-changes-at-critical-gene-regulatory-regions
#16
John J Cole, Neil A Robertson, Mohammed Iqbal Rather, John P Thomson, Tony McBryan, Duncan Sproul, Tina Wang, Claire Brock, William Clark, Trey Ideker, Richard R Meehan, Richard A Miller, Holly M Brown-Borg, Peter D Adams
BACKGROUND: Age-associated epigenetic changes are implicated in aging. Notably, age-associated DNA methylation changes comprise a so-called aging "clock", a robust biomarker of aging. However, while genetic, dietary and drug interventions can extend lifespan, their impact on the epigenome is uncharacterised. To fill this knowledge gap, we defined age-associated DNA methylation changes at the whole-genome, single-nucleotide level in mouse liver and tested the impact of longevity-promoting interventions, specifically the Ames dwarf Prop1 (df/df) mutation, calorie restriction and rapamycin...
March 28, 2017: Genome Biology
https://www.readbyqxmd.com/read/28340624/medecom-discovery-and-quantification-of-latent-components-of-heterogeneous-methylomes
#17
Pavlo Lutsik, Martin Slawski, Gilles Gasparoni, Nikita Vedeneev, Matthias Hein, Jörn Walter
It is important for large-scale epigenomic studies to determine and explore the nature of hidden confounding variation, most importantly cell composition. We developed MeDeCom as a novel reference-free computational framework that allows the decomposition of complex DNA methylomes into latent methylation components and their proportions in each sample. MeDeCom is based on constrained non-negative matrix factorization with a new biologically motivated regularization function. It accurately recovers cell-type-specific latent methylation components and their proportions...
March 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28340618/are-cells-from-a-snowman-realistic-cryopreserved-tissues-as-a-source-for-single-cell-rna-sequencing-experiments
#18
Felipe A Vieira Braga, Sarah A Teichmann, Michael J T Stubbington
A recently published study in Genome Biology shows that cells isolated from cryopreserved tissues are a reliable source of genetic material for single-cell RNA-sequencing experiments.Please see related Method article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1171-9.
March 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28335812/cancerlocator-non-invasive-cancer-diagnosis-and-tissue-of-origin-prediction-using-methylation-profiles-of-cell-free-dna
#19
Shuli Kang, Qingjiao Li, Quan Chen, Yonggang Zhou, Stacy Park, Gina Lee, Brandon Grimes, Kostyantyn Krysan, Min Yu, Wei Wang, Frank Alber, Fengzhu Sun, Steven M Dubinett, Wenyuan Li, Xianghong Jasmine Zhou
We propose a probabilistic method, CancerLocator, which exploits the diagnostic potential of cell-free DNA by determining not only the presence but also the location of tumors. CancerLocator simultaneously infers the proportions and the tissue-of-origin of tumor-derived cell-free DNA in a blood sample using genome-wide DNA methylation data. CancerLocator outperforms two established multi-class classification methods on simulations and real data, even with the low proportion of tumor-derived DNA in the cell-free DNA scenarios...
March 24, 2017: Genome Biology
https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#20
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
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