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2016 in Genome BiologyIF: 13.21
Jonathan F. Wendel80
Estimated H-index: 80
(Iowa State University),
Scott A. Jackson51
Estimated H-index: 51
(University of Georgia)
+ 1 AuthorsRod A. Wing80
Estimated H-index: 80
(International Rice Research Institute)
We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific...
76 Citations Source Cite
2014 in Genome ResearchIF: 10.10
Nastaran Heidari3
Estimated H-index: 3
(Stanford University),
Douglas H. Phanstiel10
Estimated H-index: 10
(Stanford University)
+ 5 AuthorsMichael Snyder130
Estimated H-index: 130
(Stanford University)
Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Cor...
121 Citations Source Cite
2015 in Genome BiologyIF: 13.21
Jarrod Chapman31
Estimated H-index: 31
(Joint Genome Institute),
Martin Mascher23
Estimated H-index: 23
(Leibniz Association)
+ 15 AuthorsDaniel S. Rokhsar65
Estimated H-index: 65
(Joint Genome Institute)
Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds tha...
124 Citations Download PDF Cite
2014 in Genome ResearchIF: 10.10
Jakob Skou Pedersen29
Estimated H-index: 29
(Aarhus University Hospital),
Eivind Valen26
Estimated H-index: 26
(University of Copenhagen)
+ 18 AuthorsLudovic Orlando51
Estimated H-index: 51
(University of Copenhagen)
Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytos...
63 Citations Download PDF Cite
2017 in Genome ResearchIF: 10.10
Neil Weisenfeld5
Estimated H-index: 5
,
Vijay Kumar2
Estimated H-index: 2
+ 2 AuthorsDavid B. Jaffe58
Estimated H-index: 58
Determining the genome sequence of an organism is challenging, yet fundamental to understanding its biology. Over the past decade, thousands of human genomes have been sequenced, contributing deeply to biomedical research. In the vast majority of cases, these have been analyzed by aligning sequence reads to a single reference genome, biasing the resulting analyses and, in general, failing to capture sequences novel to a given genome. Some de novo assemblies have been ...
62 Citations Download PDF Cite
2011 in Nature GeneticsIF: 27.13
Tina T. Hu15
Estimated H-index: 15
(University of Southern California),
Pedro Pattyn2
Estimated H-index: 2
(Ghent University)
+ 27 AuthorsYa-Long Guo12
Estimated H-index: 12
(Max Planck Society)
Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata. In comparison with the much smaller genome of A. thaliana, from which A. lyrata diverged about 10 million years ago, they find that the reduction in genome size is attributed to a large number of deletions across the genome.
524 Citations Download PDF Cite
2016 in Genome BiologyIF: 13.21
Alexander Peltzer7
Estimated H-index: 7
(Max Planck Society),
Günter Jäger10
Estimated H-index: 10
(University of Tübingen)
+ 4 AuthorsKay Nieselt26
Estimated H-index: 26
(University of Tübingen)
Background The automated reconstruction of genome sequences in ancient genome analysis is a multifaceted process.
43 Citations Download PDF Cite
2017 in Genome BiologyIF: 13.21
Yang Wu8
Estimated H-index: 8
(University of Queensland),
Zhili Zheng6
Estimated H-index: 6
(Wenzhou Medical College)
+ 1 AuthorsJian Yang75
Estimated H-index: 75
(University of Queensland)
Background Understanding the mapping precision of genome-wide association studies (GWAS), that is the physical distances between the top associated single-nucleotide polymorphisms (SNPs) and the causal variants, is essential to design fine-mapping experiments for complex traits and diseases.
15 Citations Source Cite
2014 in Genome BiologyIF: 13.21
David B. Neale38
Estimated H-index: 38
(University of California),
Jill L. Wegrzyn26
Estimated H-index: 26
(University of California)
+ 34 AuthorsCharles H. Langley46
Estimated H-index: 46
(University of California)
Background: The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. Results: We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotg...
217 Citations Download PDF Cite
2017 in Genome BiologyIF: 13.21
Jonas Paulsen9
Estimated H-index: 9
(University of Oslo),
Monika Sekelja8
Estimated H-index: 8
(University of Oslo)
+ 8 AuthorsPhilippe Collas45
Estimated H-index: 45
(University of Oslo)
Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles tha...
28 Citations Source Cite