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NYU - Nature Conference on Chemical Biology August 13-14, New York This conference will provide a forum for discussing innovative strategies for research in chemical biology. It will cover the breadth of chemical biology ranging from the construction DNA as material and sensors, regulation of gene expression, synthesis and derivatization of proteins, synthetic biology and the human microbiome. | | | |
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TABLE OF CONTENTS
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May 2018 Volume 50, Issue 5 |
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| Editorial Correspondence News & Views Letters Articles Analysis Technical Reports Amendments & Corrections | |
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Editorial | |
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Straws in a haystack p631 doi:10.1038/s41588-018-0125-9 |
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Correspondence | |
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No evidence for unknown archaic ancestry in South Asia pp632 - 633 Pontus Skoglund, Swapan Mallick, Nick Patterson & David Reich doi:10.1038/s41588-018-0097-9 |
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News & Views | |
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Letters | |
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Telobox motifs recruit CLF/SWN-PRC2 for H3K27me3 deposition via TRB factors in Arabidopsis pp638 - 644 Yue Zhou, Yuejun Wang, Kristin Krause, Tingting Yang, Joram A. Dongus et al. doi:10.1038/s41588-018-0109-9 This study provides genome-wide evidence of PRC2 recruitment by telomere-repeat-binding factors (TRBs) through telobox-related motifs in Arabidopsis. Telobox-related motifs recruit PRC2 through the interaction between TRBs and CLF/SWN. |
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The long tail of oncogenic drivers in prostate cancer pp645 - 651 Joshua Armenia, Stephanie A. M. Wankowicz, David Liu, Jianjiong Gao, Ritika Kundra et al. doi:10.1038/s41588-018-0078-z Meta-analysis of exome sequencing data identifies new recurrently mutated driver genes for prostate cancer. Comparison of primary and metastatic tumors further identifies genomic markers for advanced prostate cancer that may inform risk stratification. |
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Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability pp652 - 656 Pirro G. Hysi, Ana M. Valdes, Fan Liu, Nicholas A. Furlotte, David M. Evans et al. doi:10.1038/s41588-018-0100-5 Genome-wide meta-analysis identifies >100 loci associated with hair color variation in humans of European ancestry. These loci explain a large portion of the heritability of this trait & provide insights into pathways regulating hair pigmentation. |
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Deconvolution of seed and RNA-binding protein crosstalk in RNAi-based functional genomics pp657 - 661 doi:10.1038/s41588-018-0104-1 This study presents evidence that siRNAs or miRNAs with seed sequences that overlap RBP motifs have extended biological effects by perturbing RBP activity. Seed-to-RBP crosstalk contributes to off-target activity and growth phenotype modulation. |
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Polymer physics predicts the effects of structural variants on chromatin architecture pp662 - 667 Simona Bianco, Darío G. Lupiáñez, Andrea M. Chiariello, Carlo Annunziatella, Katerina Kraft et al. doi:10.1038/s41588-018-0098-8 The authors present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR correctly predicts ectopic contacts induced by pathogenic SVs at the mouse Epha4 locus. |
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Articles | |
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Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression pp668 - 681 Naomi R. Wray, Stephan Ripke, Manuel Mattheisen, Maciej Trzaskowski, Enda M. Byrne et al. doi:10.1038/s41588-018-0090-3 A genome-wide association meta-analysis of individuals with clinically assessed or self-reported depression identifies 44 independent risk loci. Comparisons with other psychiatric disorders and candidate gene analyses provide new insights into major depressive disorder. |
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Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets pp682 - 692 David C. Wedge, Gunes Gundem, Thomas Mitchell, Dan J. Woodcock, Inigo Martincorena et al. doi:10.1038/s41588-018-0086-z Joint analysis of new and previously published sequencing data for primary and metastatic prostate cancers identifies new candidate driver mutations and provides insights into disease progression and potential drug targets. |
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Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases pp693 - 698 Marie Verbanck, Chia-Yen Chen, Benjamin Neale & Ron Do doi:10.1038/s41588-018-0099-7 The MR-PRESSO test detects and corrects horizontal pleiotropy in multi-instrument Mendelian randomization (MR) analyses. Applying the MR-PRESSO test to 4,250 MR tests of complex traits and diseases finds horizontal pleiotropy in?>48% of causal relationships. |
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Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity pp699 - 707 John B. Harley, Xiaoting Chen, Mario Pujato, Daniel Miller, Avery Maddox et al. doi:10.1038/s41588-018-0102-3 Linking transcription factors with disease loci implicates EBNA2, encoded by Epstein-Barr virus, in autoimmune diseases. Applying the method more widely identifies associations for hundreds of transcription factors, illuminating disease mechanisms. |
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Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma pp708 - 717 Ana C. deCarvalho, Hoon Kim, Laila M. Poisson, Mary E. Winn, Claudius Mueller et al. doi:10.1038/s41588-018-0105-0 Analysis of glioblastoma samples and derived neurospheres and xenografts shows that chromosomal and extrachromosomal alterations often display divergent inheritance patterns during cell culture and xenografting. |
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Analysis | |
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Inferring parsimonious migration histories for metastatic cancers pp718 - 726 Mohammed El-Kebir, Gryte Satas & Benjamin J. Raphael doi:10.1038/s41588-018-0106-z MACHINA is an algorithm that analyzes metastatic cancer sequence data to simultaneously infer clone trees and migration histories. Analysis of different metastatic cancer datasets provides more evidence for simple, rather than complex, migration patterns. |
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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder pp727 - 736 Donna M. Werling, Harrison Brand, Joon-Yong An, Matthew R. Stone, Lingxue Zhu et al. doi:10.1038/s41588-018-0107-y This study presents a framework to evaluate rare and de novo variation from whole-genome sequencing (WGS). The work suggests that robust results from WGS studies will require large cohorts and strategies that consider the substantial multiple-testing burden. |
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Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits pp737 - 745 Luke M. Evans, Rasool Tahmasbi, Scott I. Vrieze, Gonçalo R. Abecasis, Sayantan Das et al. doi:10.1038/s41588-018-0108-x This analysis compares methods for estimating the heritability and genetic architecture of complex traits using whole-genome data. The results provide guidance for best practices and proper interpretation of published heritability estimates. |
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Signatures of negative selection in the genetic architecture of human complex traits pp746 - 753 Jian Zeng, Ronald de Vlaming, Yang Wu, Matthew R. Robinson, Luke R. Lloyd-Jones et al. doi:10.1038/s41588-018-0101-4 BayesS estimates SNP-based heritability, polygenicity, and the relationship between effect size and minor allele frequency using genome-wide SNP data. Applying BayesS to UK Biobank data identifies signatures of natural selection for 23 complex traits. |
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Technical Reports | |
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Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture pp754 - 763 Da Lin, Ping Hong, Siheng Zhang, Weize Xu, Muhammad Jamal et al. doi:10.1038/s41588-018-0111-2 DLO Hi-C is a new method to investigate the 3D genome. It requires only two rounds of digestion and ligation and removes non-ligated DNA in a cost-effective step by purifying specific linker-ligated DNA fragments. |
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Amendments & Corrections | |
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Author Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells p764 Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li et al. doi:10.1038/s41588-017-0025-4 |
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Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis p764 Francesc Coll, Jody Phelan, Grant A. Hill-Cawthorne, Mridul B. Nair, Kim Mallard et al. doi:10.1038/s41588-018-0074-3 |
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Publisher Correction: TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells p764 Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li et al. doi:10.1038/s41588-017-0024-5 |
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Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity pp765 - 766 Valérie Turcot, Yingchang Lu, Heather M. Highland, Claudia Schurmann, Anne E. Justice et al. doi:10.1038/s41588-018-0050-y |
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Publisher Correction: Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity pp766 - 767 Valérie Turcot, Yingchang Lu, Heather M. Highland, Claudia Schurmann, Anne E. Justice et al. doi:10.1038/s41588-018-0082-3 |
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Publisher Correction: BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange-like syndrome p767 Gabrielle Olley, Morad Ansari, Hemant Bengani, Graeme R. Grimes, James Rhodes et al. doi:10.1038/s41588-018-0069-0 |
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Publisher Correction: Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes p768 Longsen Han, Chao Ren, Ling Li, Xiaoyan Li, Juan Ge et al. doi:10.1038/s41588-018-0077-0 |
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Publisher Correction: The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution p768 Jeramiah J. Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C. Keinath et al. doi:10.1038/s41588-018-0075-2 |
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