Time for the zebrafish ENCODE

Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish

(2014) Kriti Kaushik et al.   PLoS One

Predictive modeling of anti-malarial molecules inhibiting apicoplast formation

(2013) Salma Jamal et al.   BMC BIOINFORMATICS

Zebrafish: A Multifaceted Tool for Chemical Biologists

(2013) Sandeep Basu et al.   CHEMICAL REVIEWS

Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos

(2013) Olivier Armant et al.   DEVELOPMENTAL BIOLOGY

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Systematic Pharmacogenomics Analysis of a Malay Whole Genome: Proof of Concept for Personalized Medicine

(2013) Mohd Zaki Salleh et al.   PLoS One

A Sequence-Based Variation Map of Zebrafish

(2013) Ashok Patowary et al.   Zebrafish

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Systematic analysis and functional annotation of variations in the genome of an Indian individual

(2012) Ashok Patowary et al.   HUMAN MUTATION

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

The rise of research networks

(2012) Jonathan Adams   NATURE

Lessons for big-data projects

(2012) Ewan Birney   NATURE

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

In vivo genome editing using a high-efficiency TALEN system

(2012) Victoria M. Bedell et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-wide analysis of small RNA expression in early zebrafish development

(2012) C. Wei et al.   RNA

Computational analysis and predictive modeling of small molecule modulators of microRNA

(2012) Salma Jamal et al.   Journal of Cheminformatics

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets

(2012) Vinita Periwal et al.   BMC Pharmacology & Toxicology

Human Genome Sequencing in Health and Disease

(2011) Claudia Gonzaga-Jauregui et al.   Annual Review of Medicine

The zebrafish transcriptome during early development

(2011) Liselotte Vesterlund et al.   BMC DEVELOPMENTAL BIOLOGY

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

In vivo protein trapping produces a functional expression codex of the vertebrate proteome

(2011) Karl J Clark et al.   NATURE METHODS

Analysis of genomic variation in non-coding elements using population-scale sequencing data from the 1000 Genomes Project

(2011) Xinmeng Jasmine Mu et al.   NUCLEIC ACIDS RESEARCH

zfishbook: connecting you to a world of zebrafish revertible mutants

(2011) K. J. Clark et al.   NUCLEIC ACIDS RESEARCH

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Zebrafish Enhancer TRAP Transgenic Line Database ZETRAP 2.0

(2011) Igor Kondrychyn et al.   Zebrafish

zTrap: zebrafish gene trap and enhancer trap database

(2010) Koichi Kawakami et al.   BMC DEVELOPMENTAL BIOLOGY

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

(2010) N. C. Riddle et al.   GENOME RESEARCH

Broad chromosomal domains of histone modification patterns in C. elegans

(2010) T. Liu et al.   GENOME RESEARCH

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Tiling Histone H3 Lysine 4 and 27 Methylation in Zebrafish Using High-Density Microarrays

(2010) Leif C. Lindeman et al.   PLoS One

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Non-STEM Undergraduates Become Enthusiastic Phage-Hunters

(2009) Steven M. Caruso et al.   CBE-Life Sciences Education

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

A crowdsourcing evaluation of the NIH chemical probes

(2009) Tudor I Oprea et al.   Nature Chemical Biology

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE

India Takes an Open Source Approach to Drug Discovery

(2008) Seema Singh   CELL

The complete genome of an individual by massively parallel DNA sequencing

(2008) David A. Wheeler et al.   NATURE

The diploid genome sequence of an Asian individual

(2008) Jun Wang et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

FishMap: A Community Resource for Zebrafish Genomics

(2008) Rajeshwari Meli et al.   Zebrafish

Metagenome Annotation Using a Distributed Grid of Undergraduate Students

(2008) Pascal Hingamp et al.   PLOS BIOLOGY