On the Immortality of Television Sets: "Function" in the Human Genome According to the Evolution-Free Gospel of ENCODE

Can ENCODE tell us how much junk DNA we carry in our genome?

(2012) Deng-Ke Niu et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Handling False Positives in the Genomic Era

(2012) A. M. Moyer   CLINICAL CHEMISTRY

The C-value paradox, junk DNA and ENCODE

(2012) Sean R. Eddy   CURRENT BIOLOGY

Why Transcription Factor Binding Sites Are Ten Nucleotides Long

(2012) A. J. Stewart et al.   GENETICS

What does our genome encode?

(2012) J. A. Stamatoyannopoulos   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

ENCODE explained

(2012) Joseph R. Ecker et al.   NATURE

Error prone

(2012)   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

Genomics' Big Talker

(2012) E. Pennisi   SCIENCE

Limiting Your Options

(2012)   SCIENCE

Areas to Watch

(2012)   SCIENCE

The End of "Small Science"?

(2012) B. Alberts   SCIENCE

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

(2012) L. D. Ward et al.   SCIENCE

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

De novo DNA methyltransferases: oncogenes, tumor suppressors, or both?

(2012) Agustin F. Fernandez et al.   TRENDS IN GENETICS

Functional analysis of transcription factor binding sites in human promoters

(2012) Troy W Whitfield et al.   GENOME BIOLOGY

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

Alu expression in human cell lines and their retrotranspositional potential

(2012) Andrew J Oler et al.   Mobile DNA

Putatively Noncoding Transcripts Show Extensive Association with Ribosomes

(2011) Benjamin A. Wilson et al.   Genome Biology and Evolution

What fraction of the human genome is functional?

(2011) C. P. Ponting et al.   GENOME RESEARCH

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

(2011) A. P. Jason de Koning et al.   PLoS Genetics

Inactivation of miR-34a by aberrant CpG methylation in multiple types of cancer

(2010) Dmitri Lodygin et al.   CELL CYCLE

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

Between a chicken and a grape: estimating the number of human genes

(2010) Mihaela Pertea et al.   GENOME BIOLOGY

THE SEVENTH DATA RELEASE OF THE SLOAN DIGITAL SKY SURVEY

(2009) Kevork N. Abazajian et al.   ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES

Accurate and fast methods to estimate the population mutation rate from error prone sequences

(2009) Bjarne Knudsen et al.   BMC BIOINFORMATICS

The regulated retrotransposon transcriptome of mammalian cells

(2009) Geoffrey J Faulkner et al.   NATURE GENETICS

Genome-wide discovery of functional transcription factor binding sites by comparative genomics: The case of Stat3

(2009) F. Vallania et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In What Sense Does ‘Nothing Make Sense Except in the Light of Evolution’?

(2008) Paul Edmund Griffiths   ACTA BIOTHEORETICA

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Apophenia, theory of mind and schizotypy: Perceiving meaning and intentionality in randomness

(2008) S FYFE et al.   CORTEX

Testing for Neutrality in Samples With Sequencing Errors

(2008) G. Achaz   GENETICS

Genome-wide nucleotide-level mammalian ancestor reconstruction

(2008) B. Paten et al.   GENOME RESEARCH

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

(2008) B. Paten et al.   GENOME RESEARCH

Deletion of Many Yeast Introns Reveals a Minority of Genes that Require Splicing for Function

(2008) Julie Parenteau et al.   MOLECULAR BIOLOGY OF THE CELL

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

The effects of deleterious mutations on evolution in non-recombining genomes

(2008) Vera B. Kaiser et al.   TRENDS IN GENETICS