Using orthologous and paralogous proteins to identify specificity determining residues.

abstract：:A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...

journal_title：Genome biology

authors： Berletch JB,Yang F,Disteche CM

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:MicroRNAs (miRNAs) are oligoribonucleotides with an important role in regulation of gene expression at the level of translation. Despite imperfect target complementarity, they can also significantly reduce mRNA levels. The validity of miRNA target gene predictions is difficult to assess at the protein level....

journal_title：Genome biology

authors： Arora A,Simpson DA

更新日期：2008-01-01 00:00:00

abstract：:Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...

journal_title：Genome biology

authors： Cheng Y,Tsai SQ

更新日期：2018-12-22 00:00:00

abstract：BACKGROUND:Mutation rates vary across the genome. Many trans factors that influence mutation rates have been identified, as have specific sequence motifs at the 1-7-bp scale, but cis elements remain poorly characterized. The lack of understanding regarding why different sequences have different mutation rates hampers o...

journal_title：Genome biology

authors： Duan C,Huan Q,Chen X,Wu S,Carey LB,He X,Qian W

更新日期：2018-09-14 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：:A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...

journal_title：Genome biology

authors： Worden AZ,Dupont C,Allen AE

更新日期：2011-06-27 00:00:00

abstract：BACKGROUND:While large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characteriz...

journal_title：Genome biology

authors： Angelova M,Charoentong P,Hackl H,Fischer ML,Snajder R,Krogsdam AM,Waldner MJ,Bindea G,Mlecnik B,Galon J,Trajanoski Z

更新日期：2015-03-31 00:00:00

abstract：:We propose a novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio. We present a Bayesian analysis of this ratio, which leads us to suggest two rules for choosing a cut-off on the ranked list of p ...

journal_title：Genome biology

authors： Blangiardo M,Richardson S

更新日期：2007-01-01 00:00:00

abstract：:The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...

journal_title：Genome biology

authors： Westhof E

更新日期：2010-01-01 00:00:00

abstract：BACKGROUND:Maps depicting binary interactions between proteins can be powerful starting points for understanding biological systems. A proven technology for generating such maps is high-throughput yeast two-hybrid screening. In the most extensive screen to date, a Gal4-based two-hybrid system was used recently to detec...

journal_title：Genome biology

authors： Stanyon CA,Liu G,Mangiola BA,Patel N,Giot L,Kuang B,Zhang H,Zhong J,Finley RL Jr

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBSs) in regulatory regions through footprinting. Recent studies have demonstrated the sequence b...

journal_title：Genome biology

authors： Karabacak Calviello A,Hirsekorn A,Wurmus R,Yusuf D,Ohler U

更新日期：2019-02-21 00:00:00

abstract：BACKGROUND:DNA methylation plays an essential role in regulating gene expression under a variety of conditions and it has therefore been hypothesized to underlie the transitions between life cycle stages in parasitic nematodes. So far, however, 5'-cytosine methylation has not been detected during any developmental stag...

journal_title：Genome biology

authors： Gao F,Liu X,Wu XP,Wang XL,Gong D,Lu H,Xia Y,Song Y,Wang J,Du J,Liu S,Han X,Tang Y,Yang H,Jin Q,Zhang X,Liu M

更新日期：2012-10-17 00:00:00

abstract：:Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...

journal_title：Genome biology

authors： Jiang Y,Zhang NR,Li M

更新日期：2017-04-26 00:00:00

abstract：:mtcPTM is an online repository of human and mouse phosphosites in which data are hierarchically organized to preserve biologically relevant experimental information, thus allowing straightforward comparisons of phosphorylation patterns found under different conditions. The database also contains the largest available ...

journal_title：Genome biology

authors： Jiménez JL,Hegemann B,Hutchins JR,Peters JM,Durbin R

更新日期：2007-01-01 00:00:00

abstract：:DNA sequence data are being produced at an ever-increasing rate. The Bowtie sequence-alignment algorithm uses advanced data structures to help data analysis keep pace with data generation. ...

journal_title：Genome biology

authors： Flicek P

更新日期：2009-01-01 00:00:00

abstract：:The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...

journal_title：Genome biology

authors： Liang S,Tippens ND,Zhou Y,Mort M,Stenson PD,Cooper DN,Yu H

更新日期：2017-01-18 00:00:00

abstract：BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...

journal_title：Genome biology

authors： Xia X,Kung AL

更新日期：2009-01-01 00:00:00

abstract：:A new study shows how a single cytokine, interleukin-4, regulates hematopoietic lineage choice by activating the JAK3-STAT6 pathway, which causes dendritic-cell-specific DNA demethylation. ...

journal_title：Genome biology

authors： Lennartsson A

更新日期：2016-02-01 00:00:00

abstract：BACKGROUND:Most studies of molecular evolution are focused on individual genes and proteins. However, understanding the design principles and evolutionary properties of molecular networks requires a system-wide perspective. In the present work we connect molecular evolution on the gene level with system properties of a...

journal_title：Genome biology

authors： Vitkup D,Kharchenko P,Wagner A

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to ...

journal_title：Genome biology

authors： Ghaffari S,Hanson C,Schmidt RE,Bouchonville KJ,Offer SM,Sinha S

更新日期：2021-01-07 00:00:00

abstract：BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...

journal_title：Genome biology

authors： Desjardins CA,Gundersen-Rindal DE,Hostetler JB,Tallon LJ,Fadrosh DW,Fuester RW,Pedroni MJ,Haas BJ,Schatz MC,Jones KM,Crabtree J,Forberger H,Nene V

更新日期：2008-01-01 00:00:00

abstract：:A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....

journal_title：Genome biology

authors： van Leeuwen F,van Steensel B

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:In multicellular organisms, alternative splicing is central to tissue differentiation and identity. Unicellular protists lack multicellular tissue but differentiate into variable cell types during their life cycles. The role of alternative splicing in transitions between cell types and establishing cellular ...

journal_title：Genome biology

authors： Yeoh LM,Goodman CD,Mollard V,McHugh E,Lee VV,Sturm A,Cozijnsen A,McFadden GI,Ralph SA

更新日期：2019-08-01 00:00:00

abstract：BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...

journal_title：Genome biology

authors： Conrad TM,Joyce AR,Applebee MK,Barrett CL,Xie B,Gao Y,Palsson BØ

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...

journal_title：Genome biology

authors： Pushker R,Mira A,Rodríguez-Valera F

更新日期：2004-01-01 00:00:00

abstract：BACKGROUND:DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational ...

journal_title：Genome biology

authors： Tomkova M,Tomek J,Kriaucionis S,Schuster-Böckler B

更新日期：2018-09-10 00:00:00

abstract：:An ancestral supersoldier phenotype of Pheidole ants can be recovered when selection for supersoldiers re-emerges, indicating that the developmental potential for caste pathways is retained. ...

journal_title：Genome biology

authors： Boomsma JJ,Nygaard S

更新日期：2012-02-22 00:00:00

abstract：BACKGROUND:Chromosome instability leads to aneuploidy, a state in which cells have abnormal numbers of chromosomes, and is found in two out of three cancers. In a chromosomal instable p53 deficient mouse model with accelerated lymphomagenesis, we previously observed whole chromosome copy number changes affecting all ly...

journal_title：Genome biology

authors： Bakker B,Taudt A,Belderbos ME,Porubsky D,Spierings DC,de Jong TV,Halsema N,Kazemier HG,Hoekstra-Wakker K,Bradley A,de Bont ES,van den Berg A,Guryev V,Lansdorp PM,Colomé-Tatché M,Foijer F

更新日期：2016-05-31 00:00:00

abstract：BACKGROUND:Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Altho...

journal_title：Genome biology

authors： Tewari AK,Yardimci GG,Shibata Y,Sheffield NC,Song L,Taylor BS,Georgiev SG,Coetzee GA,Ohler U,Furey TS,Crawford GE,Febbo PG

更新日期：2012-10-03 00:00:00

abstract：:Piwi-interacting RNAs (piRNAs) originate from genomic regions dubbed piRNA clusters. How cluster transcripts are selected for processing into piRNAs is not understood. We discuss evidence for the involvement of chromatin structure and maternally inherited piRNAs in determining their fate. ...

journal_title：Genome biology

authors： Le Thomas A,Tóth KF,Aravin AA

更新日期：2014-01-27 00:00:00