Top 10 Biorxiv Papers Today in Genomics


2.013 Mikeys
#1. Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing datasets
Perry Evans, Chao Wu, Amanda Lindy, Dianalee McKnight, Matthew Lebo, Mahdi Sarmady, Ahmad Abou Tayoun
Recent advances in DNA sequencing technologies have expanded our understanding of the molecular underpinnings for several genetic disorders, and increased the utilization of genomic tests by clinicians. Given the paucity of evidence to assess each variant, and the difficulty of experimentally evaluating a variants clinical significance, many of the thousand variants that can be generated by clinical tests are reported as variants of unknown clinical significance. However, the creation of population-scale variant databases can significantly improve clinical variant interpretation. Specifically, pathogenicity prediction for novel missense variants can now utilize features describing regional variant constraint. Constrained genomic regions are those that have an unusually low variant count in the general population. Several computational methods have been introduced to capture these regions and incorporate them into pathogenicity classifiers, but these methods have yet to be compared on an independent clinical variant dataset. Here...
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Predict pathogenic and benign missense variant status

Repository: pathopredictor
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Language: Jupyter Notebook
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Authors: 7
Total Words: 7367
Unqiue Words: 2019

2.006 Mikeys
#2. Resolving the 3D landscape of transcription-linked mammalian chromatin folding
Tsung-Han S Hsieh, Elena Slobodyanyuk, Anders S Hansen, Claudia Cattoglio, Oliver J Rando, Robert Tjian, Xavier Darzacq
Chromatin folding below the scale of topologically associating domains (TADs) remains largely unexplored in mammals. Here, we used a high-resolution 3C-based method, Micro-C, to probe links between 3D-genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregate TAD regions into "microTADs" with distinct regulatory features. Enhancer-promoter and promoter-promoter interactions extending from the edge of these domains predominantly link co-regulated loci, often independently of CTCF/Cohesin. Acute inhibition of transcription disrupts the gene-related folding features without altering higher-order chromatin structures. Intriguingly, we detect "two-start" zig-zag 30-nanometer chromatin fibers. Our work uncovers the finer-scale genome organization that establishes novel functional links between chromatin folding and gene regulation.
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Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
BioRxivCurator: Resolving the 3D landscape of transcription-linked mammalian chromatin folding https://t.co/9rYgkPvFXc
anamika13: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
CedricFeschotte: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
m_alexanian: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
i_jerko: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
CasCrispr: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
lekwen90: RT @Noncodarnia: The act of transcription in nuclear organization — again ! https://t.co/JCcq9eZhPb https://t.co/ZdzA9hDTWU
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Sample Sizes : [29548]
Authors: 7
Total Words: 9387
Unqiue Words: 2923

2.003 Mikeys
#3. Ultrastructural details of mammalian chromosome architecture
Nils Krietenstein, Sameer Abraham, Sergey Venev, Nezar Abdennur, Johan Gibcus, Tsung-Han Hsieh, Krishna Mohan Parsi, Liyan Yang, Rene Maehr, Leonid Mirny, Job Dekker, Oliver Rando
Over the past decade, 3C-related methods, complemented by increasingly detailed microscopic views of the nucleus, have provided unprecedented insights into chromosome folding in vivo. Here, to overcome the resolution limits inherent to the majority of genome-wide chromosome architecture mapping studies, we extend a recently-developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human embryonic stem cells and fibroblasts. Micro-C maps robustly capture well-described features of mammalian chromosome folding including A/B compartment organization, topologically associating domains (TADs), and cis interaction peaks anchored at CTCF binding sites, while also providing a detailed 1-dimensional map of nucleosome positioning and phasing genome-wide. Compared to high-resolution in situ Hi-C, Micro-C exhibits substantially improved signal-to-noise with an order of magnitude greater dynamic range, enabling not only localization of domain boundaries with single-nucleosome accuracy, but also resolving more...
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BiolaMJavierre: A little step beyond! Learning from Micro-C. https://t.co/Ynszt4cWFf
BioRxivCurator: Ultrastructural details of mammalian chromosome architecture https://t.co/gxQB0qOCyP
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Authors: 12
Total Words: 5322
Unqiue Words: 1878

2.002 Mikeys
#4. De novo phased assembly of the Vitis riparia grape genome
Nabil Girollet, Bernadette Rubio, Pierre-Francois Bert
Grapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.
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biorxivpreprint: De novo phased assembly of the Vitis riparia grape genome https://t.co/XmS0RVy5qe #bioRxiv
biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
gringene_bio: RT @biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
AW_NGS: RT @biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
the_mvierra: RT @biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
TJesse62: RT @biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
francois_sabot: RT @biorxiv_genomic: De novo phased assembly of the Vitis riparia grape genome https://t.co/fSbpSatjqU #biorxiv_genomic
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Authors: 3
Total Words: 6908
Unqiue Words: 2887

2.002 Mikeys
#5. Bayesian multivariate reanalysis of large genetic studies identifies many new associations
Michael C Turchin, Matthew Stephens
Genome-wide association studies (GWAS) have now been conducted for hundreds of phenotypes of relevance to human health. Many such GWAS involve multiple closely-related phenotypes collected on the same samples. However, the vast majority of these GWAS have been analyzed using simple univariate analyses, which consider one phenotype at a time. This is despite the fact that, at least in simulation experiments, multivariate analyses have been shown to be more powerful at detecting associations. Here, we conduct multivariate association analyses on 13 different publicly-available GWAS datasets that involve multiple closely-related phenotypes. These data include large studies of anthropometric traits (GIANT), plasma lipid traits (GlobalLipids), and red blood cell traits (HaemgenRBC). Our analyses identify many new associations (433 in total across the 13 studies), many of which replicate when follow-up samples are available. Overall, our results demonstrate that multivariate analyses can help make more effective use of data from both...
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biorxivpreprint: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/DYLOGnM23I #bioRxiv
biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #biorxiv_genomic
PromPreprint: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/aCBzqH7IjN
razoralign: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/a4bg2ETsbT
mikeweale: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
raffdoc: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
martielafreitas: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
CMehdi213: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
evogen_p: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
VasquezLouella: RT @biorxiv_genomic: Bayesian multivariate reanalysis of large genetic studies identifies many new associations https://t.co/bbYAtXSX7c #b…
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Authors: 2
Total Words: 12398
Unqiue Words: 3091

1.999 Mikeys
#6. Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing
Silke Peter, Mattia Bosio, Caspar Gross, Daniela Bezdan, Javier Gutierrez, Philipp Oberhettinger, Jan Liese, Wichard Vogel, Daniela Doerfel, Lennard Berger, Matthias Marschal, Matthias Willmann, Ivo Gut, Marta Gut, Ingo Autenrieth, Stephan Ossowski
Background: Infection of patients with multidrug-resistant (MDR) bacteria often leave very limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we evaluated the application of Nanopore sequencing technology in a hospital setting for monitoring the transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species. Results: In 2009 we experienced an outbreak with an extensively multidrug resistant P. aeruginosa harboring the carbapenemase enzyme blaIMP-8, and in 2012 the first Citrobacter freundii and Citrobacter werkmanii harboring the same enzyme were detected. Using Nanopore and Illumina sequencing we conducted a comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platforms pathoLogic and plasmIDent for Nanopore-based characterization of clinical isolates and...
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Repository: plasmIDent
User: imgag
Language: Nextflow
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Sample Sizes : [54, 34, 8, 5, 5, 3, 9, 5, 3, 45, 8, 40, 14]
Authors: 16
Total Words: 8790
Unqiue Words: 2586

1.999 Mikeys
#7. Deep evolutionary origin of nematode SL2 trans-splicing revealed by genome-wide analysis of the Trichinella spiralis transcriptome
Marius Alexander Wenzel, Christopher Johnston, Berndt Müller, Jonathan Pettitt, Bernadette Connolly
Spliced leader trans -splicing is intimately associated with the presence of eukaryotic operons, allowing the processing of polycistronic RNAs into individual mRNAs. Most of our understanding of spliced leader trans -splicing as it relates to operon gene expression comes from studies in C. elegans . In this organism, two distinct spliced leader trans -splicing events are recognised: SL1, which is used to replace the 5′ ends of pre-mRNAs that have a nascent monomethyl guanosine cap; and SL2, which provides the 5′ end to uncapped pre-mRNAs derived from polycistronic RNAs. Limited data on operons and spliced leader trans -splicing in other nematodes suggested that SL2-type trans -splicing is a relatively recent innovation, associated with increased efficiency of polycistronic processing, and confined to only one of the five major nematode clades, Clade V. We have conducted the first transcriptome-wide analysis of spliced leader trans -splicing in a nematode species, Trichinella spiralis , which belongs to a clade distantly related to...
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Authors: 5
Total Words: 12023
Unqiue Words: 3042

1.998 Mikeys
#8. Testing the omnigenic model for a behavioral trait in Drosophila melanogaster
Wenyu Zhang, Richard Guy Reeves, Diethard Tautz
The omnigenic model suggests the existence of core networks of genes for quantitative traits, which are influenced by modifiers that may encompass most, if not all expressed genes in the genome. We have studied pupation site choice behaviour in Drosophila to test this model. Based on a GWA analysis of the Drosophila Genetic Reference Panel (DGRP) stocks, we identify candidate genes and show for disrupted versions of the genes that most are indeed involved in the phenotype. These candidate genes also allowed us to identify a core network and we experimentally confirm the involvement of other members of this core network in the trait. Intriguingly, when randomly choosing 20 non-network genes we also find an involvement in the trait for most of them. Comparison of phenotypic effect sizes suggest that the core network genes have on average stronger effects. Our data thus confirm the predictions of an omnigenic genetic architecture.
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razibkhan: Testing the omnigenic model for a behavioral trait in Drosophila melanogaster https://t.co/2gCd4xte3z #genetics
big_data_kane: RT @biorxivpreprint: Testing the omnigenic model for a behavioral trait in Drosophila melanogaster https://t.co/zUora8XwHP #bioRxiv
HammedBadmos: RT @razibkhan: Testing the omnigenic model for a behavioral trait in Drosophila melanogaster https://t.co/2gCd4xte3z #genetics
jamilla_az: RT @razibkhan: Testing the omnigenic model for a behavioral trait in Drosophila melanogaster https://t.co/2gCd4xte3z #genetics
GiordanoBotta: RT @biorxiv_genomic: Testing the omnigenic model for a behavioral trait in Drosophila melanogaster https://t.co/xMYSavPGcD #biorxiv_genomic
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Total Words: 16873
Unqiue Words: 5273

1.998 Mikeys
#9. DNA accessibility is not the primary determinant of chromatin-mediated gene regulation
Razvan V Chereji, Peter R Eriksson, Josefina Ocampo, David J. Clark
DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.
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rchereji: RT @biorxivpreprint: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation https://t.co/PFeZIM7tJU #bioRx…
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Total Words: 10006
Unqiue Words: 2731

1.998 Mikeys
#10. OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine
Andres Lopez-Cortes, Cesar Paz-y-Mino, Santiago Guerrero, Alejandro Cabrera-Andrade, Stephen J. Barigye, Cristian R. Munteanu, Humberto Gonzalez-Diaz, Alejandro Pazos, Yunierkis Perez-Castillo, Eduardo Tejera
Breast cancer (BC) is a heterogeneous disease where each OncoOmics approach needs to be fully understood as a part of a complex network. Therefore, the main objective of this study was to analyze genetic alterations, signaling pathways, protein-protein interaction networks, protein expression, dependency maps and enrichment maps in 230 previously prioritized genes by the Consensus Strategy, the Pan-Cancer Atlas, the Pharmacogenomics Knowledgebase and the Cancer Genome Interpreter, in order to reveal essential genes to accelerate the development of precision medicine in BC. The OncoOmics essential genes were rationally filtered to 144, 48 (33%) of which were hallmarks of cancer and 20 (14%) were significant in at least three OncoOmics approaches: RAC1, AKT1 CCND1, PIK3CA, ERBB2, CDH1, MAPK14, TP53, MAPK1, SRC, RAC3, PLCG1, GRB2, MED1, TOP2A, GATA3, BCL2, CTNNB1, EGFR and CDK2. According to the Open Targets Platform, there are 111 drugs that are currently being analyzed in 3151 clinical trials in 39 genes. Lastly, there are more...
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biorxivpreprint: OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine https://t.co/Loq9DaSMkJ #bioRxiv
biorxiv_genomic: OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine https://t.co/E1NooOwlSb #biorxiv_genomic
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Authors: 10
Total Words: 16717
Unqiue Words: 4948

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