Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.

abstract：:High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...

journal_title：Genome biology

authors： Levine M

更新日期：2008-01-01 00:00:00

abstract：:PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...

journal_title：Genome biology

authors： Wang C,Lin H

更新日期：2021-01-08 00:00:00

abstract：BACKGROUND:The development of mass spectrometric (MS) techniques now allows the investigation of very complex protein mixtures ranging from subcellular structures to tissues. Body fluids are also popular targets of proteomic analysis because of their potential for biomarker discovery. Seminal plasma has not yet receive...

journal_title：Genome biology

authors： Pilch B,Mann M

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:The influence of genetic variation on complex diseases is potentially mediated through a range of highly dynamic epigenetic processes exhibiting temporal variation during development and later life. Here we present a catalogue of the genetic influences on DNA methylation (methylation quantitative trait loci ...

journal_title：Genome biology

authors： Gaunt TR,Shihab HA,Hemani G,Min JL,Woodward G,Lyttleton O,Zheng J,Duggirala A,McArdle WL,Ho K,Ring SM,Evans DM,Davey Smith G,Relton CL

更新日期：2016-03-31 00:00:00

abstract：:Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells fro...

journal_title：Genome biology

authors： Lun ATL,Riesenfeld S,Andrews T,Dao TP,Gomes T,participants in the 1st Human Cell Atlas Jamboree.,Marioni JC

更新日期：2019-03-22 00:00:00

abstract：:Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. We have developed the uncorrelated shrunken centroid (USC) and error-weighted, uncorrelated shrunken centroid (EWUSC) algorithms...

journal_title：Genome biology

authors： Yeung KY,Bumgarner RE

更新日期：2003-01-01 00:00:00

abstract：:From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...

journal_title：Genome biology

authors： Amrein H

更新日期：2000-01-01 00:00:00

abstract：:Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...

journal_title：Genome biology

authors： Gerdes P,Richardson SR,Mager DL,Faulkner GJ

更新日期：2016-05-09 00:00:00

abstract：:Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...

journal_title：Genome biology

authors： Moses AM,Hériché JK,Durbin R

更新日期：2007-01-01 00:00:00

abstract：BACKGROUND:To understand the heterogeneous behaviors of individual cancer cells, it is essential to investigate gene expression levels as well as their divergence between different individual cells. Recent advances in next-generation sequencing-related technologies have enabled us to conduct a single-cell RNA-Seq analy...

journal_title：Genome biology

authors： Suzuki A,Matsushima K,Makinoshima H,Sugano S,Kohno T,Tsuchihara K,Suzuki Y

更新日期：2015-04-03 00:00:00

abstract：BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...

journal_title：Genome biology

authors： Hershberg R,Tang H,Petrov DA

更新日期：2007-01-01 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：:Cytoscape is one of the most successful network biology analysis and visualization tools, but because of its interactive nature, its role in creating reproducible, scalable, and novel workflows has been limited. We describe Cytoscape Automation (CA), which marries Cytoscape to highly productive workflow systems, for e...

journal_title：Genome biology

authors： Otasek D,Morris JH,Bouças J,Pico AR,Demchak B

更新日期：2019-09-02 00:00:00

abstract：BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...

journal_title：Genome biology

authors： Wu J,Xie X

更新日期：2006-01-01 00:00:00

abstract：BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...

journal_title：Genome biology

authors： Zuccolo A,Bowers JE,Estill JC,Xiong Z,Luo M,Sebastian A,Goicoechea JL,Collura K,Yu Y,Jiao Y,Duarte J,Tang H,Ayyampalayam S,Rounsley S,Kudrna D,Paterson AH,Pires JC,Chanderbali A,Soltis DE,Chamala S,Barbazuk B,So

更新日期：2011-01-01 00:00:00

abstract：:Although chromosomal deletions and inversions are important in cancer, conventional methods for detecting DNA rearrangements require laborious indirect assays. Here we develop fluorescent reporters to rapidly quantify CRISPR/Cas9-mediated deletions and inversions. We find that inversion depends on the non-homologous e...

journal_title：Genome biology

authors： Li Y,Park AI,Mou H,Colpan C,Bizhanova A,Akama-Garren E,Joshi N,Hendrickson EA,Feldser D,Yin H,Anderson DG,Jacks T,Weng Z,Xue W

更新日期：2015-05-28 00:00:00

abstract：BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...

journal_title：Genome biology

authors： Zhou L,Tian S,Qin G

更新日期：2019-08-06 00:00:00

abstract：:Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process, specifically if the phenotype is subtle and scoring labour intensive. Here, we have re-sequenced the 120-Mb genome of a novel Arabidopsis clock mutant early bird (ebi-1) in Wassilewskija (Ws-2). We demonstrate the utility of seque...

journal_title：Genome biology

authors： Ashelford K,Eriksson ME,Allen CM,D'Amore R,Johansson M,Gould P,Kay S,Millar AJ,Hall N,Hall A

更新日期：2011-01-01 00:00:00

abstract：:Open chromatin profiling integrates information across diverse regulatory elements to reveal the transcriptionally active genome. Tn5 transposase and DNase I sequencing-based methods prefer native or high cell numbers. Here, we describe NicE-seq (nicking enzyme assisted sequencing) for high-resolution open chromatin p...

journal_title：Genome biology

authors： Ponnaluri VKC,Zhang G,Estève PO,Spracklin G,Sian S,Xu SY,Benoukraf T,Pradhan S

更新日期：2017-06-28 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：:Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...

journal_title：Genome biology

authors： Staiger D,Shin J,Johansson M,Davis SJ

更新日期：2013-06-24 00:00:00

abstract：:We describe here our experience in annotating the Drosophila melanogaster genome sequence, in the course of which we developed several new open-source software tools and a database schema to support large-scale genome annotation. We have developed these into an integrated and reusable software system for whole-genome ...

journal_title：Genome biology

authors： Mungall CJ,Misra S,Berman BP,Carlson J,Frise E,Harris N,Marshall B,Shu S,Kaminker JS,Prochnik SE,Smith CD,Smith E,Tupy JL,Wiel C,Rubin GM,Lewis SE

更新日期：2002-01-01 00:00:00

abstract：BACKGROUND:X chromosome inactivation is a spectacular example of epigenetic silencing. In order to deduce how this complex system evolved, we examined X inactivation in a model marsupial, the tammar wallaby (Macropus eugenii). In marsupials, X inactivation is known to be paternal, incomplete and tissue-specific, and oc...

journal_title：Genome biology

authors： Al Nadaf S,Waters PD,Koina E,Deakin JE,Jordan KS,Graves JA

更新日期：2010-01-01 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:The control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour ...

journal_title：Genome biology

authors： Malecki M,Bitton DA,Rodríguez-López M,Rallis C,Calavia NG,Smith GC,Bähler J

更新日期：2016-11-25 00:00:00

abstract：:The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...

journal_title：Genome biology

authors： Fischer A,Illingworth CJ,Campbell PJ,Mustonen V

更新日期：2013-04-29 00:00:00

abstract：BACKGROUND:Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Completed genome sequenc...

journal_title：Genome biology

authors： Mendum TA,Newcombe J,Mannan AA,Kierzek AM,McFadden J

更新日期：2011-12-30 00:00:00

abstract：BACKGROUND:The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. RESULTS:Here ...

journal_title：Genome biology

authors： St Laurent G,Shtokalo D,Dong B,Tackett MR,Fan X,Lazorthes S,Nicolas E,Sang N,Triche TJ,McCaffrey TA,Xiao W,Kapranov P

更新日期：2013-07-22 00:00:00

abstract：:How do naturally occurring polymorphisms in DNA sequence relate to variation in gene expression? Recent work to map genetic sources of expression variation has shown a surprising balance between cis and trans effects. Other work suggests some chromosomal clustering of genes by expression pattern. A synthesis of approa...

journal_title：Genome biology

authors： Hamilton BA

更新日期：2002-09-19 00:00:00

abstract：BACKGROUND:Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functio...

journal_title：Genome biology

authors： Cloonan N,Wani S,Xu Q,Gu J,Lea K,Heater S,Barbacioru C,Steptoe AL,Martin HC,Nourbakhsh E,Krishnan K,Gardiner B,Wang X,Nones K,Steen JA,Matigian NA,Wood DL,Kassahn KS,Waddell N,Shepherd J,Lee C,Ichikawa J,McKer

更新日期：2011-12-30 00:00:00