Localizing the proteome.

abstract：BACKGROUND:Hemispheric asymmetry in neuronal processes is a fundamental feature of the human brain and drives symptom lateralization in Parkinson's disease (PD), but its molecular determinants are unknown. Here, we identify divergent epigenetic patterns involved in hemispheric asymmetry by profiling DNA methylation in ...

journal_title：Genome biology

authors： Li P,Ensink E,Lang S,Marshall L,Schilthuis M,Lamp J,Vega I,Labrie V

更新日期：2020-03-09 00:00:00

abstract：BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...

journal_title：Genome biology

authors： Tripoli G,D'Elia D,Barsanti P,Caggese C

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:Type II DNA topoisomerases (TOP2) regulate DNA topology by generating transient double stranded breaks during replication and transcription. Topoisomerase II beta (TOP2B) facilitates rapid gene expression and functions at the later stages of development and differentiation. To gain new insight into the genom...

journal_title：Genome biology

authors： Uusküla-Reimand L,Hou H,Samavarchi-Tehrani P,Rudan MV,Liang M,Medina-Rivera A,Mohammed H,Schmidt D,Schwalie P,Young EJ,Reimand J,Hadjur S,Gingras AC,Wilson MD

更新日期：2016-08-31 00:00:00

abstract：BACKGROUND:Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental stud...

journal_title：Genome biology

authors： Coyne RS,Hannick L,Shanmugam D,Hostetler JB,Brami D,Joardar VS,Johnson J,Radune D,Singh I,Badger JH,Kumar U,Saier M,Wang Y,Cai H,Gu J,Mather MW,Vaidya AB,Wilkes DE,Rajagopalan V,Asai DJ,Pearson CG,Findly RC,Di

更新日期：2011-10-17 00:00:00

abstract：:According to a recent article published in Genome Biology, Duggan and coworkers sequenced and partially assembled five genomes of smallpox vaccines from the nineteenth century. No information regarding the ends of genomes was presented, and they are important to understand the evolutionary relationship of the differen...

journal_title：Genome biology

authors： Brinkmann A,Souza ARV,Esparza J,Nitsche A,Damaso CR

更新日期：2020-12-04 00:00:00

abstract：BACKGROUND:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...

journal_title：Genome biology

authors： Narsai R,Gouil Q,Secco D,Srivastava A,Karpievitch YV,Liew LC,Lister R,Lewsey MG,Whelan J

更新日期：2017-09-15 00:00:00

abstract：BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...

journal_title：Genome biology

authors： Marth GT,Yu F,Indap AR,Garimella K,Gravel S,Leong WF,Tyler-Smith C,Bainbridge M,Blackwell T,Zheng-Bradley X,Chen Y,Challis D,Clarke L,Ball EV,Cibulskis K,Cooper DN,Fulton B,Hartl C,Koboldt D,Muzny D,Smith R,Soug

更新日期：2011-09-14 00:00:00

abstract：:Injection of recombinant Cas9 protein and synthetic guide RNAs into mouse zygotes has been shown to facilitate gene disruption and knock-ins using the CRISPR system. These technologies may soon displace genetic modification using embryonic stem cells. ...

journal_title：Genome biology

authors： Skarnes WC

更新日期：2015-05-27 00:00:00

abstract：BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundr...

journal_title：Genome biology

authors： Crysnanto D,Pausch H

更新日期：2020-07-27 00:00:00

abstract：BACKGROUND:Long noncoding enhancer RNAs (lnc-eRNAs) are a subset of stable eRNAs identified from annotated lncRNAs. They might act as enhancer activity-related therapeutic targets in cancer. However, the underlying mechanism of epigenetic activation and their function in cancer initiation and progression remain largely...

journal_title：Genome biology

authors： Fang K,Huang W,Sun YM,Chen TQ,Zeng ZC,Yang QQ,Pan Q,Han C,Sun LY,Luo XQ,Wang WT,Chen YQ

更新日期：2020-11-03 00:00:00

abstract：BACKGROUND:Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). RESULTS:We used experimentally quantif...

journal_title：Genome biology

authors： Ballinger TJ,Bouwman BAM,Mirzazadeh R,Garnerone S,Crosetto N,Semple CA

更新日期：2019-02-08 00:00:00

abstract：BACKGROUND:One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved. RESULTS:We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separate...

journal_title：Genome biology

authors： Carter D,Durbin R

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...

journal_title：Genome biology

authors： McGovern A,Schoenfelder S,Martin P,Massey J,Duffus K,Plant D,Yarwood A,Pratt AG,Anderson AE,Isaacs JD,Diboll J,Thalayasingam N,Ospelt C,Barton A,Worthington J,Fraser P,Eyre S,Orozco G

更新日期：2016-11-01 00:00:00

abstract：BACKGROUND:Rates of recombination can vary among genomic regions in eukaryotes, and this is believed to have major effects on their genome organization in terms of base composition, DNA repeat density, intron size, evolutionary rates and gene order. In highly self-fertilizing species such as Arabidopsis thaliana, howev...

journal_title：Genome biology

authors： Marais G,Charlesworth B,Wright SI

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets. We analyzed archaeal phylogeny using two concatenated datasets consistin...

journal_title：Genome biology

authors： Brochier C,Forterre P,Gribaldo S

更新日期：2004-01-01 00:00:00

abstract：:Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...

journal_title：Genome biology

authors： Hickey G,Heller D,Monlong J,Sibbesen JA,Sirén J,Eizenga J,Dawson ET,Garrison E,Novak AM,Paten B

更新日期：2020-02-12 00:00:00

abstract：:Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host genotype. ...

journal_title：Genome biology

authors： Derevnina L,Michelmore RW

更新日期：2015-03-02 00:00:00

abstract：:The genome-wide investigation of DNA methylation levels has been limited to reference transposable element positions. The methylation analysis of non-reference and mobile transposable elements has only recently been performed, but required both genome resequencing and MethylC-seq datasets. We have created epiTEome, a ...

journal_title：Genome biology

authors： Daron J,Slotkin RK

更新日期：2017-05-12 00:00:00

abstract：:Gene-expression profiling has yielded important information about simple systems, but complex tissues have not yet been widely profiled. Four recent studies of mammalian skeletal muscles have added to the catalogs of their gene expression differences, but have yet to lead to better understanding of the molecular proce...

journal_title：Genome biology

authors： Hampson R,Hughes SM

更新日期：2001-01-01 00:00:00

abstract：:Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalizat...

journal_title：Genome biology

authors： Oshlack A,Emslie D,Corcoran LM,Smyth GK

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of interming...

journal_title：Genome biology

authors： Bonhomme F,Rivals E,Orth A,Grant GR,Jeffreys AJ,Bois PR

更新日期：2007-01-01 00:00:00

abstract：:We describe a tool, THoR, that automatically creates and curates multiple sequence alignments representing protein domains. This exploits both PSI-BLAST and HMMER algorithms and provides an accurate and comprehensive alignment for any domain family. The entire process is designed for use via a web-browser, with simple...

journal_title：Genome biology

authors： Dickens NJ,Ponting CP

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Is it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes? RESULTS:A sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped ...

journal_title：Genome biology

authors： Dalrymple BP,Kirkness EF,Nefedov M,McWilliam S,Ratnakumar A,Barris W,Zhao S,Shetty J,Maddox JF,O'Grady M,Nicholas F,Crawford AM,Smith T,de Jong PJ,McEwan J,Oddy VH,Cockett NE,International Sheep Genomics Consortium.

更新日期：2007-01-01 00:00:00

abstract：:A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...

journal_title：Genome biology

authors： Weng Z,Guigó R

更新日期：2008-01-01 00:00:00

abstract：:Nuclear pore complexes, the conduits for information exchange between the nucleus and cytoplasm, appear broadly similar in eukaryotes from yeast to human. Precisely how nuclear pore complexes regulate macromolecular and ionic traffic remains unknown, but recent advances in the identification and characterization of co...

journal_title：Genome biology

authors： Adam SA

更新日期：2001-01-01 00:00:00

abstract：:Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...

journal_title：Genome biology

authors： Sandoval GJ,Hahn WC

更新日期：2017-05-22 00:00:00

abstract：:Identifying the biochemical basis of microbial phenotypes is a main objective of comparative genomics. Here we present a novel method using multivariate machine learning techniques for comparing automatically derived metabolic reconstructions of sequenced genomes on a large scale. Applying our method to 266 genomes di...

journal_title：Genome biology

authors： Kastenmüller G,Schenk ME,Gasteiger J,Mewes HW

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Obesity is a particularly complex disease that at least partially involves genetic and environmental perturbations to gene-networks connecting the hypothalamus and several metabolic tissues, resulting in an energy imbalance at the systems level. RESULTS:To provide an inter-tissue view of obesity with respec...

journal_title：Genome biology

authors： Dobrin R,Zhu J,Molony C,Argman C,Parrish ML,Carlson S,Allan MF,Pomp D,Schadt EE

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Alcoholism presents widespread social and human health problems. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Genetic factors that predispose to alcoholism remain largely unknown due to extensive genetic and environmental variation in hu...

journal_title：Genome biology

authors： Morozova TV,Anholt RR,Mackay TF

更新日期：2006-01-01 00:00:00

abstract：:Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...

journal_title：Genome biology

authors： Johnson CH

更新日期：2004-01-01 00:00:00