A meta-analysis of the genomic and transcriptomic composition of complex life

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

Insights into hominid evolution from the gorilla genome sequence

(2012) Aylwyn Scally et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Identification of intergenic trans-regulatory RNAs containing a disease-linked SNP sequence and targeting cell cycle progression/differentiation pathways in multiple common human disorders

(2011) Anna B. Glinskii et al.   CELL CYCLE

Epigenetic regulation of transposable element derived human gene promoters

(2011) Ahsan Huda et al.   GENE

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch

(2011) A. C. Roman et al.   GENOME RESEARCH

The genome of Tetranychus urticae reveals herbivorous pest adaptations

(2011) Miodrag Grbić et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

(2011) Tim R Mercer et al.   NATURE BIOTECHNOLOGY

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2011

(2011) T. R. Dreszer et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

The relationship between proteome size, structural disorder and organism complexity

(2011) Eva Schad et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

(2010) Jennifer C. Chow et al.   CELL

Angiogenin-induced tRNA-derived Stress-induced RNAs Promote Stress-induced Stress Granule Assembly

(2010) Mohamed M. Emara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans

(2010) Ryan J Taft et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Human tRNA-derived small RNAs in the global regulation of RNA silencing

(2010) D. Haussecker et al.   RNA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates

(2010) Noa Sela et al.   GENOME BIOLOGY

Deconstructing the Dogma

(2009) John S. Mattick   Annals of the New York Academy of Sciences

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Generalised Entropy of Curves for the Analysis and Classification of Dynamical Systems

(2009) Aldo Balestrino et al.   Entropy

Angiogenin cleaves tRNA and promotes stress-induced translational repression

(2009) Satoshi Yamasaki et al.   JOURNAL OF CELL BIOLOGY

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Ensembl's 10th year

(2009) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs derived from snoRNAs

(2009) R. J. Taft et al.   RNA

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

Sponge Genes Provide New Insight into the Evolutionary Origin of the Neurogenic Circuit

(2008) Gemma S. Richards et al.   CURRENT BIOLOGY

Noncoding RNA in development

(2008) Paulo P. Amaral et al.   MAMMALIAN GENOME