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Genome

About: Genome is a research topic. Over the lifetime, 74231 publications have been published within this topic receiving 3819713 citations.


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Journal ArticleDOI
14 Oct 2005-Science
TL;DR: A high-resolution genetic map of the human genome is presented, based on statistical analyses of genetic variation data, and more than 25,000 recombination hotspots are identified, together with motifs and sequence contexts that play a role in hotspot activity.
Abstract: Genetic maps, which document the way in which recombination rates vary over a genome, are an essential tool for many genetic analyses. We present a high-resolution genetic map of the human genome, based on statistical analyses of genetic variation data, and identify more than 25,000 recombination hotspots, together with motifs and sequence contexts that play a role in hotspot activity. Differences between the behavior of recombination rates over large (megabase) and small (kilobase) scales lead us to suggest a two-stage model for recombination in which hotspots are stochastic features, within a framework in which large-scale rates are constrained.

1,134 citations

01 Mar 2011
TL;DR: In this paper, a massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs was reported, and several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set.
Abstract: Multiple myeloma is an incurable malignancy of plasma cells, and its pathogenesis is poorly understood. Here we report the massively parallel sequencing of 38 tumour genomes and their comparison to matched normal DNAs. Several new and unexpected oncogenic mechanisms were suggested by the pattern of somatic mutation across the data set. These include the mutation of genes involved in protein translation (seen in nearly half of the patients), genes involved in histone methylation, and genes involved in blood coagulation. In addition, a broader than anticipated role of NF-κB signalling was indicated by mutations in 11 members of the NF-κB pathway. Of potential immediate clinical relevance, activating mutations of the kinase BRAF were observed in 4% of patients, suggesting the evaluation of BRAF inhibitors in multiple myeloma clinical trials. These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge.

1,134 citations

Journal ArticleDOI
TL;DR: A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloropleft proteins strongly affects plastid genome phylogeny.
Abstract: Chloroplasts were once free-living cyanobacteria that became endosymbionts, but the genomes of contemporary plastids encode only ≈5–10% as many genes as those of their free-living cousins, indicating that many genes were either lost from plastids or transferred to the nucleus during the course of plant evolution. Previous estimates have suggested that between 800 and perhaps as many as 2,000 genes in the Arabidopsis genome might come from cyanobacteria, but genome-wide phylogenetic surveys that could provide direct estimates of this number are lacking. We compared 24,990 proteins encoded in the Arabidopsis genome to the proteins from three cyanobacterial genomes, 16 other prokaryotic reference genomes, and yeast. Of 9,368 Arabidopsis proteins sufficiently conserved for primary sequence comparison, 866 detected homologues only among cyanobacteria and 834 other branched with cyanobacterial homologues in phylogenetic trees. Extrapolating from these conserved proteins to the whole genome, the data suggest that ≈4,500 of Arabidopsis protein-coding genes (≈18% of the total) were acquired from the cyanobacterial ancestor of plastids. These proteins encompass all functional classes, and the majority of them are targeted to cell compartments other than the chloroplast. Analysis of 15 sequenced chloroplast genomes revealed 117 nuclear-encoded proteins that are also still present in at least one chloroplast genome. A phylogeny of chloroplast genomes inferred from 41 proteins and 8,303 amino acids sites indicates that at least two independent secondary endosymbiotic events have occurred involving red algae and that amino acid composition bias in chloroplast proteins strongly affects plastid genome phylogeny.

1,134 citations

Journal ArticleDOI
Swapan Mallick1, Swapan Mallick2, Swapan Mallick3, Heng Li1, Mark Lipson2, Iain Mathieson2, Melissa Gymrek, Fernando Racimo4, Mengyao Zhao2, Mengyao Zhao1, Mengyao Zhao3, Niru Chennagiri3, Niru Chennagiri2, Niru Chennagiri1, Susanne Nordenfelt1, Susanne Nordenfelt2, Susanne Nordenfelt3, Arti Tandon1, Arti Tandon2, Pontus Skoglund1, Pontus Skoglund2, Iosif Lazaridis2, Iosif Lazaridis1, Sriram Sankararaman2, Sriram Sankararaman1, Sriram Sankararaman5, Qiaomei Fu2, Qiaomei Fu6, Qiaomei Fu1, Nadin Rohland2, Nadin Rohland1, Gabriel Renaud7, Yaniv Erlich8, Thomas Willems9, Carla Gallo10, Jeffrey P. Spence4, Yun S. Song11, Yun S. Song4, Giovanni Poletti10, Francois Balloux12, George van Driem13, Peter de Knijff14, Irene Gallego Romero15, Aashish R. Jha16, Doron M. Behar17, Claudio M. Bravi18, Cristian Capelli19, Tor Hervig20, Andrés Moreno-Estrada, Olga L. Posukh21, Elena Balanovska, Oleg Balanovsky22, Sena Karachanak-Yankova23, Hovhannes Sahakyan17, Hovhannes Sahakyan24, Draga Toncheva23, Levon Yepiskoposyan24, Chris Tyler-Smith25, Yali Xue25, M. Syafiq Abdullah26, Andres Ruiz-Linares12, Cynthia M. Beall27, Anna Di Rienzo16, Choongwon Jeong16, Elena B. Starikovskaya, Ene Metspalu28, Ene Metspalu17, Jüri Parik17, Richard Villems17, Richard Villems29, Richard Villems28, Brenna M. Henn30, Ugur Hodoglugil31, Robert W. Mahley32, Antti Sajantila33, George Stamatoyannopoulos34, Joseph Wee, Rita Khusainova35, Elza Khusnutdinova35, Sergey Litvinov35, Sergey Litvinov17, George Ayodo36, David Comas37, Michael F. Hammer38, Toomas Kivisild17, Toomas Kivisild39, William Klitz, Cheryl A. Winkler40, Damian Labuda41, Michael J. Bamshad34, Lynn B. Jorde42, Sarah A. Tishkoff11, W. Scott Watkins42, Mait Metspalu17, Stanislav Dryomov, Rem I. Sukernik43, Lalji Singh44, Lalji Singh5, Kumarasamy Thangaraj44, Svante Pääbo7, Janet Kelso7, Nick Patterson1, David Reich3, David Reich1, David Reich2 
13 Oct 2016-Nature
TL;DR: It is demonstrated that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.
Abstract: Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non-Africans.

1,133 citations

Journal ArticleDOI
TL;DR: MUMmer4 is described, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of Mummer to a 48- bit suffix array, and that offers improved speed through parallel processing of input query sequences.
Abstract: The MUMmer system and the genome sequence aligner nucmer included within it are among the most widely used alignment packages in genomics. Since the last major release of MUMmer version 3 in 2004, it has been applied to many types of problems including aligning whole genome sequences, aligning reads to a reference genome, and comparing different assemblies of the same genome. Despite its broad utility, MUMmer3 has limitations that can make it difficult to use for large genomes and for the very large sequence data sets that are common today. In this paper we describe MUMmer4, a substantially improved version of MUMmer that addresses genome size constraints by changing the 32-bit suffix tree data structure at the core of MUMmer to a 48-bit suffix array, and that offers improved speed through parallel processing of input query sequences. With a theoretical limit on the input size of 141Tbp, MUMmer4 can now work with input sequences of any biologically realistic length. We show that as a result of these enhancements, the nucmer program in MUMmer4 is easily able to handle alignments of large genomes; we illustrate this with an alignment of the human and chimpanzee genomes, which allows us to compute that the two species are 98% identical across 96% of their length. With the enhancements described here, MUMmer4 can also be used to efficiently align reads to reference genomes, although it is less sensitive and accurate than the dedicated read aligners. The nucmer aligner in MUMmer4 can now be called from scripting languages such as Perl, Python and Ruby. These improvements make MUMer4 one the most versatile genome alignment packages available.

1,131 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20242
20237,313
202214,209
20214,955
20205,080
20194,839