C2H2 zinc finger proteins greatly expand the human regulatory lexicon

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

An improved predictive recognition model for Cys2-His2 zinc finger proteins

(2014) Ankit Gupta et al.   NUCLEIC ACIDS RESEARCH

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

(2013) N. C. Sheffield et al.   GENOME RESEARCH

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

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

(2012) J. Wang et al.   GENOME RESEARCH

Whole exome sequencing identified a novel zinc-finger geneZNF141associated with autosomal recessive postaxial polydactyly type A

(2012) Umm-e- Kalsoom et al.   JOURNAL OF MEDICAL GENETICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An optimized two-finger archive for ZFN-mediated gene targeting

(2012) Ankit Gupta et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Coevolution of retroelements and tandem zinc finger genes

(2011) J. H. Thomas et al.   GENOME RESEARCH

Sequence specificity is obtained from the majority of modular C2H2 zinc-finger arrays

(2011) Kathy N. Lam et al.   NUCLEIC ACIDS RESEARCH

Gain, Loss and Divergence in Primate Zinc-Finger Genes: A Rich Resource for Evolution of Gene Regulatory Differences between Species

(2011) Katja Nowick et al.   PLoS One

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

(2011) Dana V. Skarra et al.   PROTEOMICS

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

KRAB Zinc Finger Protein ZNF382 Is a Proapoptotic Tumor Suppressor That Represses Multiple Oncogenes and Is Commonly Silenced in Multiple Carcinomas

(2010) Y. Cheng et al.   CANCER RESEARCH

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

From the editors

(2010)   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

(2009) Dominic Schmidt et al.   METHODS

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

Adaptive Evolution in Zinc Finger Transcription Factors

(2009) Ryan O. Emerson et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

The Protein-Binding Potential of C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

PP4R4/KIAA1622 Forms a Novel Stable Cytosolic Complex with Phosphoprotein Phosphatase 4

(2008) Ginny I. Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Mouse segmental duplication and copy number variation

(2008) Xinwei She et al.   NATURE GENETICS

Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57

(2008) Deborah J G Mackay et al.   NATURE GENETICS

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY