Abstract:
:The last 20 years have been a remarkable era for biology and medicine. One of the most significant achievements has been the sequencing of the first human genomes, which has laid the foundation for profound insights into human genetics, the intricacies of regulation and development, and the forces of evolution. Incredibly, as we look into the future over the next 20 years, we see the very real potential for sequencing more than 1 billion genomes, bringing even deeper insight into human genetics as well as the genetics of millions of other species on the planet. Realizing this great potential for medicine and biology, though, will only be achieved through the integration and development of highly scalable computational and quantitative approaches that can keep pace with the rapid improvements to biotechnology. In this perspective, I aim to chart out these future technologies, anticipate the major themes of research, and call out the challenges ahead. One of the largest shifts will be in the training used to prepare the class of 2035 for their highly interdisciplinary world.
journal_name
Genome Resjournal_title
Genome researchauthors
Schatz MCdoi
10.1101/gr.191684.115subject
Has Abstractpub_date
2015-10-01 00:00:00pages
1417-22issue
10eissn
1088-9051issn
1549-5469pii
gr.191684.115journal_volume
25pub_type
杂志文章相关文献
GENOME RESEARCH文献大全abstract::Comparative analysis of the protein sequences encoded in the four euryarchaeal species whose genomes have been sequenced completely (Methanococcus jannaschii, Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Pyrococcus horikoshii) revealed 1326 orthologous sets, of which 543 are represented in all fou...
journal_title:Genome research
pub_type: 杂志文章
doi:
更新日期:1999-07-01 00:00:00
abstract::Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.164996.113
更新日期:2014-03-01 00:00:00
abstract::The primate-specific multisequence family chAB4 is represented with approximately 40 copies within the haploid human genome. Former analyis revealed that unusually long repetition units ( > 35 kb) are distributed to at least eight different chromosomal loci. Remarkably varying copy-numbers within the genomes of closel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6.4.267
更新日期:1996-04-01 00:00:00
abstract::In mammals, genome-wide chromatin maps and immunofluorescence studies show that broad domains of repressive histone modifications are present on pericentromeric and telomeric repeats and on the inactive X chromosome. However, only a few autosomal loci such as silent Hox gene clusters have been shown to lie in broad do...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.080861.108
更新日期:2009-02-01 00:00:00
abstract::Here we describe software tools for the automated detection of DNA restriction fragments resolved on agarose fingerprinting gels. We present a mathematical model for the location and shape of the restriction fragments as a function of fragment size, with model parameters determined empirically from "marker" lanes cont...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.904303
更新日期:2003-05-01 00:00:00
abstract::Obesity is reaching epidemic proportions in developed countries and represents a significant risk factor for hypertension, heart disease, diabetes, and dyslipidemia. Splicing mutations constitute at least 14% of disease-causing mutations, thus implicating polymorphisms that affect splicing as likely candidates for dis...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.6661308
更新日期:2008-02-01 00:00:00
abstract::The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.134080.111
更新日期:2012-10-01 00:00:00
abstract::Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CAR...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.103473.109
更新日期:2010-07-01 00:00:00
abstract::Large-scale genetic studies are highly dependent on efficient and scalable multiplex SNP assays. In this study, we report the development of Molecular Inversion Probe technology with four-color, single array detection, applied to large-scale genotyping of up to 12,000 SNPs per reaction. While generating 38,429 SNP ass...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.3185605
更新日期:2005-02-01 00:00:00
abstract::The identification and interpretation of the regulatory signals within the human genome remain among the greatest goals and most difficult challenges in genome analysis. The ability to predict the temporal and spatial control of transcription is likely to require a combination of methods to address the contribution of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.180601
更新日期:2001-09-01 00:00:00
abstract::The Mouse Genome Sequencing Consortium and the RIKEN Genome Exploration Research grouphave generated large sets of sequence data representing the mouse genome and transcriptome, respectively. These data provide a valuable foundation for genomic research. The challenges for the informatics community are how to integrat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.991003
更新日期:2003-06-01 00:00:00
abstract::The vomeronasal system of mice is thought to be specialized in the detection of pheromones. Two multigene families have been identified that encode proteins with seven putative transmembrane domains and that are expressed selectively in subsets of neurons of the vomeronasal organ. The products of these vomeronasal rec...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.10.12.1958
更新日期:2000-12-01 00:00:00
abstract::Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.228429.117
更新日期:2018-04-01 00:00:00
abstract::Fetal liver intriguingly consists of hepatic parenchymal cells and hematopoietic stem/progenitor cells. Human fetal liver aged 22 wk of gestation (HFL22w) corresponds to the turning point between immigration and emigration of the hematopoietic system. To gain further molecular insight into its developmental and functi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.175501
更新日期:2001-08-01 00:00:00
abstract::MicroRNAs (miRNAs) are major post-transcriptional regulators of gene expression, yet their origins and functional evolution in mammals remain little understood due to the lack of appropriate comparative data. Using RNA sequencing, we have generated extensive and comparable miRNA data for five organs in six species tha...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140269.112
更新日期:2013-01-01 00:00:00
abstract::We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). T...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.204214.116
更新日期:2016-10-01 00:00:00
abstract::Many CpG islands have tissue-dependent and differentially methylated regions (T-DMRs) in normal cells and tissues. To elucidate how DNA methyltransferases (Dnmts) participate in methylation of the genomic components, we investigated the genome-wide DNA methylation pattern of the T-DMRs with Dnmt1-, Dnmt3a-, and/or Dnm...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2431504
更新日期:2004-09-01 00:00:00
abstract::Remnants of more than 3 million transposable elements, primarily retroelements, comprise nearly half of the human genome and have generated much speculation concerning their evolutionary significance. We have exploited the draft human genome sequence to examine the distributions of retroelements on a genome-wide scale...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.388902
更新日期:2002-10-01 00:00:00
abstract::Recent studies have analyzed large-scale data sets of gene expression to identify genes associated with interindividual variation in phenotypes ranging from cancer subtypes to drug sensitivity, promising new avenues of research in personalized medicine. However, gene expression data alone is limited in its ability to ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.227066.117
更新日期:2018-08-01 00:00:00
abstract::The need for expeditious and inexpensive methods for high-throughput DNA sequencing has been highlighted by the accelerated pace of genome DNA sequencing over the past year. At the Joint Genome Institute, the throughput in terms of high-quality bases per day has increased over 20-fold during the past 18 mo, reaching a...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.167801
更新日期:2001-07-01 00:00:00
abstract::The discovery of the genetic code was one of the most important advances of modern biology. But there is more to a DNA code than protein sequence; DNA carries signals for splicing, localization, folding, and regulation that are often embedded within the protein-coding sequence. In this issue, Itzkovitz and Alon show t...
journal_title:Genome research
pub_type: 评论,杂志文章,评审
doi:10.1101/gr.6144007
更新日期:2007-04-01 00:00:00
abstract::Annotation transfer is a principal process in genome annotation. It involves "transferring" structural and functional annotation to uncharacterized open reading frames (ORFs) in a newly completed genome from experimentally characterized proteins similar in sequence. To prevent errors in genome annotation, it is import...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.183801
更新日期:2001-10-01 00:00:00
abstract::To elucidate the role of exon shuffling in shaping the complexity of the human genome/proteome, we have systematically analyzed intron phase distributions in the coding sequence of human protein domains. We found that introns at the boundaries of domains show high excess of symmetrical phase combinations (i.e., 0-0, 1...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.520702
更新日期:2002-11-01 00:00:00
abstract::Chemical cues influence a range of behavioral responses in rodents. The involvement of protein odorants and odorant receptors in mediating reproductive behavior, foraging, and predator avoidance suggests that their genes may have been subject to adaptive evolution. We have estimated the consequences of selection on ro...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.1940604
更新日期:2004-04-01 00:00:00
abstract::Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships po...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.7265208
更新日期:2008-03-01 00:00:00
abstract::Intra-tumor heterogeneity poses substantial challenges for cancer treatment. A tumor's composition can be deduced by reconstructing its mutational history. Central to current approaches is the infinite sites assumption that every genomic position can only mutate once over the lifetime of a tumor. The validity of this ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.220707.117
更新日期:2017-11-01 00:00:00
abstract::We present the sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster. Within this sequence, we predict 277 protein coding genes, of which 94 had been sequenced already in the course of studying the biology of their gene products, and examples of 12 different tran...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.173801
更新日期:2001-05-01 00:00:00
abstract::Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health o...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.171439.113
更新日期:2014-07-01 00:00:00
abstract::Inbred strains of the laboratory rat are widely used for identifying genetic regions involved in the control of complex quantitative phenotypes of biomedical importance. The draft genomic sequence of the rat now provides essential information for annotating rat quantitative trait locus (QTL) maps. Following the survey...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.2001604
更新日期:2004-04-01 00:00:00
abstract::We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3'-to-5' exonuclease proofreading activity of many DNA polymerases. The assay uses one or more primers labeled on the 3' nucleotide base, and can be implemented in a variety of formats including a one-...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.939903
更新日期:2003-05-01 00:00:00