MouseCyc: a curated biochemical pathways database for the laboratory mouse.

Abstract:

:Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc http://mousecyc.jax.org. MouseCyc has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human.

journal_name

Genome Biol

journal_title

Genome biology

authors

Evsikov AV,Dolan ME,Genrich MP,Patek E,Bult CJ

doi

10.1186/gb-2009-10-8-r84

subject

Has Abstract

pub_date

2009-01-01 00:00:00

pages

R84

issue

8

eissn

1474-7596

issn

1474-760X

pii

gb-2009-10-8-r84

journal_volume

10

pub_type

杂志文章
  • Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray.

    abstract::The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-7-r61

    authors: Carter MG,Sharov AA,VanBuren V,Dudekula DB,Carmack CE,Nelson C,Ko MS

    更新日期:2005-01-01 00:00:00

  • Where is genomics going next?

    abstract::We polled the Editorial Board of Genome Biology to ask where they see genomics going in the next few years. Here are some of their responses. ...

    journal_title:Genome biology

    pub_type: 社论,面试

    doi:10.1186/s13059-019-1626-2

    authors: Cheifet B

    更新日期:2019-01-22 00:00:00

  • Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial.

    abstract:BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, a...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2006-7-10-r90

    authors: Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FM

    更新日期:2006-01-01 00:00:00

  • CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

    abstract::To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02043-x

    authors: Tian L,Li Y,Edmonson MN,Zhou X,Newman S,McLeod C,Thrasher A,Liu Y,Tang B,Rusch MC,Easton J,Ma J,Davis E,Trull A,Michael JR,Szlachta K,Mullighan C,Baker SJ,Downing JR,Ellison DW,Zhang J

    更新日期:2020-05-28 00:00:00

  • Transcriptional regulation of metastatic [Id]entity by KLF17.

    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

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2009-10-11-244

    authors: Iwanicki MP,Brugge JS

    更新日期:2009-01-01 00:00:00

  • Benchmarking of computational error-correction methods for next-generation sequencing data.

    abstract:BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-01988-3

    authors: Mitchell K,Brito JJ,Mandric I,Wu Q,Knyazev S,Chang S,Martin LS,Karlsberg A,Gerasimov E,Littman R,Hill BL,Wu NC,Yang HT,Hsieh K,Chen L,Littman E,Shabani T,Enik G,Yao D,Sun R,Schroeder J,Eskin E,Zelikovsky A,S

    更新日期:2020-03-17 00:00:00

  • mirMark: a site-level and UTR-level classifier for miRNA target prediction.

    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

    pub_type: 杂志文章

    doi:10.1186/s13059-014-0500-5

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

    更新日期:2014-01-01 00:00:00

  • A reappraisal of the phylogenetic placement of the Aquilegia whole-genome duplication.

    abstract::The accurate placement of an ancient whole-genome duplication (WGD) in relation to the lineage divergence is important. Here, we re-investigated the Aquilegia coerulea WGD and found it is more likely lineage-specific rather than shared by all eudicots. ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02212-y

    authors: Shi T,Chen J

    更新日期:2020-12-08 00:00:00

  • The relationship between proteome size, structural disorder and organism complexity.

    abstract:BACKGROUND:Sequencing the genomes of the first few eukaryotes created the impression that gene number shows no correlation with organism complexity, often referred to as the G-value paradox. Several attempts have previously been made to resolve this paradox, citing multifunctionality of proteins, alternative splicing, ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2011-12-12-r120

    authors: Schad E,Tompa P,Hegyi H

    更新日期:2011-12-19 00:00:00

  • Concept recognition for extracting protein interaction relations from biomedical text.

    abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-s2-s9

    authors: Baumgartner WA Jr,Lu Z,Johnson HL,Caporaso JG,Paquette J,Lindemann A,White EK,Medvedeva O,Cohen KB,Hunter L

    更新日期:2008-01-01 00:00:00

  • Design and computational analysis of single-cell RNA-sequencing experiments.

    abstract::Single-cell RNA-sequencing (scRNA-seq) has emerged as a revolutionary tool that allows us to address scientific questions that eluded examination just a few years ago. With the advantages of scRNA-seq come computational challenges that are just beginning to be addressed. In this article, we highlight the computational...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/s13059-016-0927-y

    authors: Bacher R,Kendziorski C

    更新日期:2016-04-07 00:00:00

  • PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.

    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

    pub_type: 杂志文章

    doi:10.1186/s13059-017-1364-2

    authors: Krakau S,Richard H,Marsico A

    更新日期:2017-12-28 00:00:00

  • Homologous recombination: from model organisms to human disease.

    abstract::Recent experiments show that properly controlled recombination between homologous DNA molecules is essential for the maintenance of genome stability and for the prevention of tumorigenesis. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2001-2-5-reviews1014

    authors: Modesti M,Kanaar R

    更新日期:2001-01-01 00:00:00

  • Histone variants: are they functionally heterogeneous?

    abstract::In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide rang...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/gb-2001-2-7-reviews0006

    authors: Brown DT

    更新日期:2001-01-01 00:00:00

  • Cytoscape Automation: empowering workflow-based network analysis.

    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

    pub_type: 杂志文章

    doi:10.1186/s13059-019-1758-4

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

    更新日期:2019-09-02 00:00:00

  • Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae.

    abstract:BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processe...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2008-9-5-r85

    authors: Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RA

    更新日期:2008-01-01 00:00:00

  • Having a BLAST with bioinformatics (and avoiding BLASTphemy).

    abstract::Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the princi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2001-2-10-reviews2002

    authors: Pertsemlidis A,Fondon JW 3rd

    更新日期:2001-01-01 00:00:00

  • Rapid gene isolation in barley and wheat by mutant chromosome sequencing.

    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

    pub_type: 杂志文章

    doi:10.1186/s13059-016-1082-1

    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

  • EMu: probabilistic inference of mutational processes and their localization in the cancer genome.

    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

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-4-r39

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

    更新日期:2013-04-29 00:00:00

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

    abstract:BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-5-r94

    authors: Tamames J,Moya A,Valencia A

    更新日期:2007-01-01 00:00:00

  • Quantitative reconstruction of leukocyte subsets using DNA methylation.

    abstract:BACKGROUND:Cell lineage-specific DNA methylation patterns distinguish normal human leukocyte subsets and can be used to detect and quantify these subsets in peripheral blood. We have developed an approach that uses DNA methylation to simultaneously quantify multiple leukocyte subsets, enabling investigation of immune m...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2014-15-3-r50

    authors: Accomando WP,Wiencke JK,Houseman EA,Nelson HH,Kelsey KT

    更新日期:2014-03-05 00:00:00

  • Inferring protein domain interactions from databases of interacting proteins.

    abstract::We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, Eij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In to...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-10-r89

    authors: Riley R,Lee C,Sabatti C,Eisenberg D

    更新日期:2005-01-01 00:00:00

  • A computational investigation of kinetoplastid trans-splicing.

    abstract::Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-11-r95

    authors: Gopal S,Awadalla S,Gaasterland T,Cross GA

    更新日期:2005-01-01 00:00:00

  • Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

    abstract:BACKGROUND:Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome se...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2013-14-6-r63

    authors: Jupe J,Stam R,Howden AJ,Morris JA,Zhang R,Hedley PE,Huitema E

    更新日期:2013-06-25 00:00:00

  • Emerging roles of chromatin in the maintenance of genome organization and function in plants.

    abstract::Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish bo...

    journal_title:Genome biology

    pub_type: 杂志文章,评审

    doi:10.1186/s13059-017-1236-9

    authors: Vergara Z,Gutierrez C

    更新日期:2017-05-23 00:00:00

  • Comparative genomics reveals a constant rate of origination and convergent acquisition of functional retrogenes in Drosophila.

    abstract:BACKGROUND:Processed copies of genes (retrogenes) are duplicate genes that originated through the reverse-transcription of a host transcript and insertion in the genome. This type of gene duplication, as any other, could be a source of new genes and functions. Using whole genome sequence data for 12 Drosophila species,...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2007-8-1-r11

    authors: Bai Y,Casola C,Feschotte C,Betrán E

    更新日期:2007-01-01 00:00:00

  • CircAtlas: an integrated resource of one million highly accurate circular RNAs from 1070 vertebrate transcriptomes.

    abstract::Existing circular RNA (circRNA) databases have become essential for transcriptomics. However, most are unsuitable for mining in-depth information for candidate circRNA prioritization. To address this, we integrate circular transcript collections to develop the circAtlas database based on 1070 RNA-seq samples collected...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/s13059-020-02018-y

    authors: Wu W,Ji P,Zhao F

    更新日期:2020-04-28 00:00:00

  • ProSplicer: a database of putative alternative splicing information derived from protein, mRNA and expressed sequence tag sequence data.

    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

    pub_type: 杂志文章

    doi:10.1186/gb-2003-4-4-r29

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

    更新日期:2003-01-01 00:00:00

  • Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

    abstract:BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2005-6-5-r42

    authors: Brochier C,Gribaldo S,Zivanovic Y,Confalonieri F,Forterre P

    更新日期:2005-01-01 00:00:00

  • EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

    abstract::The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

    journal_title:Genome biology

    pub_type: 杂志文章

    doi:10.1186/gb-2009-10-2-r14

    authors: Bock C,Halachev K,Büch J,Lengauer T

    更新日期:2009-02-10 00:00:00