Xenbase: a genomic, epigenomic and transcriptomic model organism database

Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals inXenopus laevis

(2017) Yi Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

(2016) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

Measuring Absolute RNA Copy Numbers at High Temporal Resolution Reveals Transcriptome Kinetics in Development

(2016) Nick D.L. Owens et al.   Cell Reports

Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase

(2015) Peter D. Vize et al.   CYTOGENETIC AND GENOME RESEARCH

A New Nomenclature of Xenopus laevis Chromosomes Based on the Phylogenetic Relationship to Silurana/Xenopus tropicalis

(2015) Yoichi Matsuda et al.   CYTOGENETIC AND GENOME RESEARCH

The Xenopus ORFeome: A resource that enables functional genomics

(2015) Ian M. Grant et al.   DEVELOPMENTAL BIOLOGY

Xenbase: Core features, data acquisition, and data processing

(2015) Christina James-Zorn et al.   GENESIS

WormBase 2016: expanding to enable helminth genomic research

(2015) Kevin L. Howe et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

A Database of microRNA Expression Patterns in Xenopus laevis

(2015) Ayisha Ahmed et al.   PLoS One

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Xenbase, the Xenopus model organism database; new virtualized system, data types and genomes

(2014) J. Brad Karpinka et al.   NUCLEIC ACIDS RESEARCH

InterMine: extensive web services for modern biology

(2014) Alex Kalderimis et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud

(2014) K. Karimi et al.   Database-The Journal of Biological Databases and Curation

GEISHA: an evolving gene expression resource for the chicken embryo

(2013) Parker B. Antin et al.   NUCLEIC ACIDS RESEARCH

The International Mouse Phenotyping Consortium: past and future perspectives on mouse phenotyping

(2012) Steve D. M. Brown et al.   MAMMALIAN GENOME

An anatomically comprehensive atlas of the adult human brain transcriptome

(2012) Michael J. Hawrylycz et al.   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

A High-Resolution Anatomical Atlas of the Transcriptome in the Mouse Embryo

(2011) Graciana Diez-Roux et al.   PLOS BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources

(2009) Helen V. Firth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

An ontology for Xenopus anatomy and development

(2008) Erik Segerdell et al.   BMC DEVELOPMENTAL BIOLOGY