C2H2 zinc finger proteins greatly expand the human regulatory lexicon (Q41410676)

30 September 2017

title

C2H2 zinc finger proteins greatly expand the human regulatory lexicon (English)

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30 September 2017

Ally Yang

6

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Kathy N Lam

object named as

Kathy N Lam

5

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Hamed S. Najafabadi

object named as

Hamed S Najafabadi

1

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Jack Greenblatt

11

object named as

Jack Greenblatt

1 reference

30 September 2017

12

Brendan J Frey

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30 September 2017

Sanie Mnaimneh

2

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30 September 2017

Frank W Schmitges

3

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30 September 2017

Michael Garton

4

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30 September 2017

Mihai Albu

7

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30 September 2017

Matthew T Weirauch

8

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30 September 2017

Ernest Radovani

9

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30 September 2017

Philip M Kim

10

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30 September 2017

Timothy R Hughes

13

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30 September 2017

language of work or name

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18 February 2015

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30 September 2017

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30 September 2017

volume

33

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30 September 2017

issue

5

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30 September 2017

page(s)

555-562

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DNA recognition by Cys2His2 zinc finger proteins

30 September 2017

cites work

1 reference

The discovery of zinc fingers and their applications in gene regulation and genome manipulation.

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Adaptive evolution in zinc finger transcription factors

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Evolutionary expansion and divergence in the ZNF91 subfamily of primate-specific zinc finger genes

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Initial sequencing and analysis of the human genome

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Function and Evolution of C2H2 Zinc Finger Arrays

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

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Zinc finger 81 (ZNF81) mutations associated with X-linked mental retardation

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Whole exome sequencing identified a novel zinc-finger gene ZNF141 associated with autosomal recessive postaxial polydactyly type A

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KAP1 controls endogenous retroviruses in embryonic stem cells

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Dynamic control of endogenous retroviruses during development.

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Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET.

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Coevolution of retroelements and tandem zinc finger genes

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Molecular characterization of a putative antiretroviral transcriptional factor, OTK18.

21 January 2018

1 reference

Embryonic stem cells use ZFP809 to silence retroviral DNAs

21 January 2018

1 reference

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

21 January 2018

1 reference

DNA-binding specificities of human transcription factors

21 January 2018

1 reference

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

21 January 2018

1 reference

An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins

21 January 2018

1 reference

Beyond the "recognition code": structures of two Cys2His2 zinc finger/TATA box complexes

21 January 2018

1 reference

Synergy between adjacent zinc fingers in sequence-specific DNA recognition

21 January 2018

1 reference

Keep your fingers off my DNA: protein-protein interactions mediated by C2H2 zinc finger domains

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The protein-binding potential of C2H2 zinc finger domains

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Three classes of C2H2 zinc finger proteins

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

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DNA-binding specificity of NGFI-A and related zinc finger transcription factors

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Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

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GREAT improves functional interpretation of cis-regulatory regions

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SVA elements: a hominid-specific retroposon family

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Regulated recruitment of HP1 to a euchromatic gene induces mitotically heritable, epigenetic gene silencing: a mammalian cell culture model of gene variegation

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KRAB zinc finger protein ZNF382 is a proapoptotic tumor suppressor that represses multiple oncogenes and is commonly silenced in multiple carcinomas.

21 January 2018

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Evolution of genes and genomes on the Drosophila phylogeny

21 January 2018

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Mouse segmental duplication and copy number variation

21 January 2018

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

21 January 2018

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

21 January 2018

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

21 January 2018

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Determination and inference of eukaryotic transcription factor sequence specificity

21 January 2018

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Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover

21 January 2018

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Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage

21 January 2018

1 reference

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

21 January 2018

1 reference

Different gene regulation strategies revealed by analysis of binding motifs

21 January 2018

1 reference

Identifying specificity profiles for peptide recognition modules from phage-displayed peptide libraries

21 January 2018

1 reference

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

21 January 2018

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Identifying DNA sequences recognized by a transcription factor using a bacterial one-hybrid system

21 January 2018

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

21 January 2018

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Clustering by passing messages between data points

21 January 2018

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Least angle regression

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Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival Forests

21 January 2018

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MEME SUITE: tools for motif discovery and searching

21 January 2018

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A compendium of RNA-binding motifs for decoding gene regulation.

21 January 2018

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3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

21 January 2018

1 reference

Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method

21 January 2018

1 reference

UCSF Chimera--a visualization system for exploratory research and analysis

21 January 2018

1 reference

WHAT IF: a molecular modeling and drug design program

21 January 2018

1 reference

The Amber biomolecular simulation programs

21 January 2018

1 reference

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

21 January 2018

1 reference

Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

1 reference

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

21 January 2018

1 reference

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

21 January 2018

1 reference

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

21 January 2018

1 reference

PP4R4/KIAA1622 forms a novel stable cytosolic complex with phosphoprotein phosphatase 4

21 January 2018

1 reference

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Fast gapped-read alignment with Bowtie 2

21 January 2018

1 reference

The Sequence Alignment/Map format and SAMtools

21 January 2018

1 reference

Estimating enrichment of repetitive elements from high-throughput sequence data

21 January 2018

1 reference

Model-based analysis of ChIP-Seq (MACS)

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

MEME-ChIP: motif analysis of large DNA datasets

21 January 2018

1 reference

Inferring direct DNA binding from ChIP-seq

21 January 2018

1 reference

The UCSC Table Browser data retrieval tool

21 January 2018

1 reference

FIMO: scanning for occurrences of a given motif

21 January 2018

1 reference

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

21 January 2018

1 reference

An integrated encyclopedia of DNA elements in the human genome

21 January 2018

1 reference

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

21 January 2018

1 reference

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Determining the specificity of protein–DNA interactions

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25690854

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A Catalogue of Eukaryotic Transcription Factor Types, Their Evolutionary Origin, and Species Distribution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25690854

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25690854

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NBT.3128

1 reference

30 September 2017

1 reference