Using ontologies to describe mouse phenotypes.

abstract：BACKGROUND:The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistanc...

journal_title：Genome biology

authors： Dharia NV,Sidhu AB,Cassera MB,Westenberger SJ,Bopp SE,Eastman RT,Plouffe D,Batalov S,Park DJ,Volkman SK,Wirth DF,Zhou Y,Fidock DA,Winzeler EA

更新日期：2009-02-13 00:00:00

abstract：BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...

journal_title：Genome biology

authors： Dudoit S,Fridlyand J

更新日期：2002-06-25 00:00:00

abstract：:Not so fast. The Iqbal et. al. study and the associated Whitelaw commentary highlight the appropriately high standards of study design and interpretation needed to obtain good evidence for or against epigenetic inheritance. Please see related article: www.dx.doi.org/10.1186/s13059-015-0714-1. ...

journal_title：Genome biology

authors： Nadeau JH

更新日期：2015-07-11 00:00:00

abstract：BACKGROUND:We have constructed Bayesian prior-based, amino-acid sequence profiles for the complete yeast mitochondrial proteome and used them to develop methods for identifying and characterizing the context of protein mutations that give rise to human mitochondrial diseases. (Bayesian priors are conditional probabilit...

journal_title：Genome biology

authors： Plasterer TN,Smith TF,Mohr SC

更新日期：2001-01-01 00:00:00

abstract：:The army of the men of death, in John Bunyan's memorable phrase, has a new recruit, and fear has a new face: a face wearing a surgical mask. ...

journal_title：Genome biology

authors： Petsko GA

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal ...

journal_title：Genome biology

authors： Yu J,Farjo R,MacNee SP,Baehr W,Stambolian DE,Swaroop A

更新日期：2003-01-01 00:00:00

abstract：BACKGROUND:Adenosine-to-inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive epitranscriptome feature. Tens of thousands of A-to-I editing events are defined in the mouse, yet the functional impact of most is unknown. Editing causing protein recoding is the essential function of ADAR2, but an essential rol...

journal_title：Genome biology

authors： Heraud-Farlow JE,Chalk AM,Linder SE,Li Q,Taylor S,White JM,Pang L,Liddicoat BJ,Gupte A,Li JB,Walkley CR

更新日期：2017-09-05 00:00:00

abstract：BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but th...

journal_title：Genome biology

authors： Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt H

更新日期：2014-06-30 00:00:00

abstract：BACKGROUND:Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS:By investigating the whole-genome resequencing data of 93 ...

journal_title：Genome biology

authors： Cheng H,Liu J,Wen J,Nie X,Xu L,Chen N,Li Z,Wang Q,Zheng Z,Li M,Cui L,Liu Z,Bian J,Wang Z,Xu S,Yang Q,Appels R,Han D,Song W,Sun Q,Jiang Y

更新日期：2019-07-12 00:00:00

abstract：BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...

journal_title：Genome biology

authors： Bergman CM,Quesneville H,Anxolabéhère D,Ashburner M

更新日期：2006-01-01 00:00:00

abstract：:We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different...

journal_title：Genome biology

authors： Hayamizu TF,Mangan M,Corradi JP,Kadin JA,Ringwald M

更新日期：2005-01-01 00:00:00

abstract：BACKGROUND:The discovery of cytosine hydroxymethylation (5hmC) as a mechanism that potentially controls DNA methylation changes typical of neoplasia prompted us to investigate its behaviour in colon cancer. 5hmC is globally reduced in proliferating cells such as colon tumours and the gut crypt progenitors, from which t...

journal_title：Genome biology

authors： Uribe-Lewis S,Stark R,Carroll T,Dunning MJ,Bachman M,Ito Y,Stojic L,Halim S,Vowler SL,Lynch AG,Delatte B,de Bony EJ,Colin L,Defrance M,Krueger F,Silva AL,Ten Hoopen R,Ibrahim AE,Fuks F,Murrell A

更新日期：2015-04-01 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：:Recent genomic studies showing abnormalities in the fibroblast growth factor system in the postmortem brains of people with major depressive disorder support previous indications of a role for growth factors in mood disorders. Similar molecular pathways, volumetric changes, and the effects of exercise on mood suggest ...

journal_title：Genome biology

authors： Niculescu AB

更新日期：2005-01-01 00:00:00

abstract：:As the cost of sequencing continues to decrease and the amount of sequence data generated grows, new paradigms for data storage and analysis are increasingly important. The relative scaling behavior of these evolving technologies will impact genomics research moving forward. ...

journal_title：Genome biology

authors： Muir P,Li S,Lou S,Wang D,Spakowicz DJ,Salichos L,Zhang J,Weinstock GM,Isaacs F,Rozowsky J,Gerstein M

更新日期：2016-03-23 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：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：: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：:The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

journal_title：Genome biology

authors： Gardiner K,Davisson M

更新日期：2000-01-01 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：:Identification of causal mutations in barley and wheat is hampered by their large genomes and suppressed recombination. To overcome these obstacles, we have developed MutChromSeq, a complexity reduction approach based on flow sorting and sequencing of mutant chromosomes, to identify induced mutations by comparison to ...

journal_title：Genome biology

authors： Sánchez-Martín J,Steuernagel B,Ghosh S,Herren G,Hurni S,Adamski N,Vrána J,Kubaláková M,Krattinger SG,Wicker T,Doležel J,Keller B,Wulff BB

更新日期：2016-10-31 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:In eukaryotic organisms, gene expression is regulated at multiple levels during the processes of transcription and translation. The absence of a tight regulatory network for transcription in the human malaria parasite suggests that gene expression may largely be controlled at post-transcriptional and transla...

journal_title：Genome biology

authors： Bunnik EM,Chung DW,Hamilton M,Ponts N,Saraf A,Prudhomme J,Florens L,Le Roch KG

更新日期：2013-11-22 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: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：BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...

journal_title：Genome biology

authors： Lemay DG,Lynn DJ,Martin WF,Neville MC,Casey TM,Rincon G,Kriventseva EV,Barris WC,Hinrichs AS,Molenaar AJ,Pollard KS,Maqbool NJ,Singh K,Murney R,Zdobnov EM,Tellam RL,Medrano JF,German JB,Rijnkels M

更新日期：2009-01-01 00:00:00

abstract：:Interpretation of the clinical significance of genomic alterations remains the most severe bottleneck preventing the realization of personalized medicine in cancer. We propose a knowledge commons to facilitate collaborative contributions and open discussion of clinical decision-making based on genomic events in cancer...

journal_title：Genome biology

authors： Good BM,Ainscough BJ,McMichael JF,Su AI,Griffith OL

更新日期：2014-08-27 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：:A report of the First Golden Helix Symposium 'Copy Number Variation (CNV) and Genomic Alterations in Health and Disease', Athens, Greece, 28-29 November 2008. ...

journal_title：Genome biology

authors： Le Caignec C,Redon R

更新日期：2009-01-01 00:00:00

abstract：:Many existing pipelines for scRNA-seq data apply pre-processing steps such as normalization or imputation to account for excessive zeros or "drop-outs." Here, we extensively analyze diverse UMI data sets to show that clustering should be the foremost step of the workflow. We observe that most drop-outs disappear once ...

journal_title：Genome biology

authors： Kim TH,Zhou X,Chen M

更新日期：2020-08-06 00:00:00