Modular organization in the reductive evolution of protein-protein interaction networks.

abstract：BACKGROUND:The assessment and characterization of the gut microbiome has become a focus of research in the area of human autoimmune diseases. Ankylosing spondylitis is an inflammatory autoimmune disease and evidence showed that ankylosing spondylitis may be a microbiome-driven disease. RESULTS:To investigate the relat...

journal_title：Genome biology

authors： Wen C,Zheng Z,Shao T,Liu L,Xie Z,Le Chatelier E,He Z,Zhong W,Fan Y,Zhang L,Li H,Wu C,Hu C,Xu Q,Zhou J,Cai S,Wang D,Huang Y,Breban M,Qin N,Ehrlich SD

更新日期：2017-07-27 00:00:00

abstract：BACKGROUND:Many different methods exist to adjust for variability in cell-type mixture proportions when analyzing DNA methylation studies. Here we present the result of an extensive simulation study, built on cell-separated DNA methylation profiles from Illumina Infinium 450K methylation data, to compare the performanc...

journal_title：Genome biology

authors： McGregor K,Bernatsky S,Colmegna I,Hudson M,Pastinen T,Labbe A,Greenwood CM

更新日期：2016-05-03 00:00:00

abstract：:We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide m...

journal_title：Genome biology

authors： Beeravolu CR,Hickerson MJ,Frantz LAF,Lohse K

更新日期：2018-09-25 00:00:00

abstract：:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github....

journal_title：Genome biology

authors： Krakau S,Richard H,Marsico A

更新日期：2017-12-28 00:00:00

abstract：:A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...

journal_title：Genome biology

authors： Iwanicki MP,Brugge JS

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:The Asian tiger mosquito Aedes albopictus is globally expanding and has become the main vector for human arboviruses in Europe. With limited antiviral drugs and vaccines available, vector control is the primary approach to prevent mosquito-borne diseases. A reliable and accurate DNA sequence of the Ae. albop...

journal_title：Genome biology

authors： Palatini U,Masri RA,Cosme LV,Koren S,Thibaud-Nissen F,Biedler JK,Krsticevic F,Johnston JS,Halbach R,Crawford JE,Antoshechkin I,Failloux AB,Pischedda E,Marconcini M,Ghurye J,Rhie A,Sharma A,Karagodin DA,Jenrette J,Ga

更新日期：2020-08-26 00:00:00

abstract：BACKGROUND:We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and m...

journal_title：Genome biology

authors： Clark TG,Andrew T,Cooper GM,Margulies EH,Mullikin JC,Balding DJ

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...

journal_title：Genome biology

authors： Abdelaal T,Michielsen L,Cats D,Hoogduin D,Mei H,Reinders MJT,Mahfouz A

更新日期：2019-09-09 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:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...

journal_title：Genome biology

authors： Blanc V,Park E,Schaefer S,Miller M,Lin Y,Kennedy S,Billing AM,Ben Hamidane H,Graumann J,Mortazavi A,Nadeau JH,Davidson NO

更新日期：2014-06-19 00:00:00

abstract：BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...

journal_title：Genome biology

authors： Dal Santo S,Tornielli GB,Zenoni S,Fasoli M,Farina L,Anesi A,Guzzo F,Delledonne M,Pezzotti M

更新日期：2013-06-07 00:00:00

abstract：:Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...

journal_title：Genome biology

authors： Fan X,Zhang X,Wu X,Guo H,Hu Y,Tang F,Huang Y

更新日期：2015-07-23 00:00:00

abstract：:We describe a method for extracting Boolean implications (if-then relationships) in very large amounts of gene expression microarray data. A meta-analysis of data from thousands of microarrays for humans, mice, and fruit flies finds millions of implication relationships between genes that would be missed by other meth...

journal_title：Genome biology

authors： Sahoo D,Dill DL,Gentles AJ,Tibshirani R,Plevritis SK

更新日期：2008-10-30 00:00:00

abstract：:A report on the Epigenetic Engineering Meeting hosted by the Barts Institute of Cancer, held in London, UK, May 7, 2014. ...

journal_title：Genome biology

authors： Magnani L

更新日期：2014-01-01 00:00:00

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：:Your Gene structure Annotation Tool for Eukaryotes (yrGATE) provides an Annotation Tool and Community Utilities for worldwide web-based community genome and gene annotation. Annotators can evaluate gene structure evidence derived from multiple sources to create gene structure annotations. Administrators regulate the a...

journal_title：Genome biology

authors： Wilkerson MD,Schlueter SD,Brendel V

更新日期：2006-01-01 00:00:00

abstract：:A report on the 11th Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome Informatics, Cold Spring Harbor Laboratories, New York, USA, November 2-5, 2011. ...

journal_title：Genome biology

authors： Chambers EV,Kindt AS,Semple CA

更新日期：2011-12-28 00:00:00

abstract：BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...

journal_title：Genome biology

authors： Axmann IM,Kensche P,Vogel J,Kohl S,Herzel H,Hess WR

更新日期：2005-01-01 00:00:00

abstract：:ProSplicer is a database of putative alternative splicing information derived from the alignment of proteins, mRNA sequences and expressed sequence tags (ESTs) against human genomic DNA sequences. Proteins, mRNA and ESTs provide valuable evidence that can reveal splice variants of genes. The alternative splicing infor...

journal_title：Genome biology

authors： Huang HD,Horng JT,Lee CC,Liu BJ

更新日期：2003-01-01 00:00:00

abstract：:The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...

journal_title：Genome biology

authors： Schlueter SD,Wilkerson MD,Dong Q,Brendel V

更新日期：2006-01-01 00:00:00

abstract：:Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...

journal_title：Genome biology

authors： Ma Q,Chang HY

更新日期：2016-04-14 00:00:00

abstract：BACKGROUND:Catalytic RNAs, or ribozymes, are regarded as fossils of a prebiotic RNA world that have remained in the genomes of modern organisms. The simplest ribozymes are the small self-cleaving RNAs, like the hammerhead ribozyme, which have been historically considered biological oddities restricted to some RNA patho...

journal_title：Genome biology

authors： Cervera A,Urbina D,de la Peña M

更新日期：2016-06-23 00:00:00

abstract：:The majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins. This large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct TIR-domain-containing (TNL) and CC-domain-containing (CNL) subfamilies. The...

journal_title：Genome biology

authors： McHale L,Tan X,Koehl P,Michelmore RW

更新日期：2006-01-01 00:00:00

abstract：:The WOX genes form a plant-specific subclade of the eukaryotic homeobox transcription factor superfamily, which is characterized by the presence of a conserved DNA-binding homeodomain. The analysis of WOX gene expression and function shows that WOX family members fulfill specialized functions in key developmental proc...

journal_title：Genome biology

authors： van der Graaff E,Laux T,Rensing SA

更新日期：2009-01-01 00:00:00

abstract：BACKGROUND:Legume roots show a remarkable plasticity to adapt their architecture to biotic and abiotic constraints, including symbiotic interactions. However, global analysis of miRNA regulation in roots is limited, and a global view of the evolution of miRNA-mediated diversification in different ecotypes is lacking. ...

journal_title：Genome biology

authors： Formey D,Sallet E,Lelandais-Brière C,Ben C,Bustos-Sanmamed P,Niebel A,Frugier F,Combier JP,Debellé F,Hartmann C,Poulain J,Gavory F,Wincker P,Roux C,Gentzbittel L,Gouzy J,Crespi M

更新日期：2014-09-24 00:00:00

abstract：:Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensi...

journal_title：Genome biology

authors： Sharrock RA

更新日期：2008-01-01 00:00:00

abstract：BACKGROUND:The genetic provenance of domesticated plants and the routes along which they were disseminated in prehistory have been a long-standing source of debate. Much of this debate has focused on identifying centers of origins for individual crops. However, many important crops show clear genetic signatures of mult...

journal_title：Genome biology

authors： Poets AM,Fang Z,Clegg MT,Morrell PL

更新日期：2015-08-21 00:00:00

abstract：:How the mechanisms of dosage compensation distinguish the sex chromosomes from the autosomes has been something of a mystery. A recent study in Caenorhabditis elegans has identified clusters of two common DNA motifs as a cis-acting code for the recruitment of the DCC, the protein complex that mediates dosage compensat...

journal_title：Genome biology

authors： Deng X,Disteche CM

更新日期：2007-01-01 00:00:00

abstract：:MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...

journal_title：Genome biology

authors： Menor M,Ching T,Zhu X,Garmire D,Garmire LX

更新日期：2014-01-01 00:00:00

abstract：BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...

journal_title：Genome biology

authors： Thum KE,Shin MJ,Palenchar PM,Kouranov A,Coruzzi GM

更新日期：2004-01-01 00:00:00