@zhoujj2013
2017-12-20T04:11:05.000000Z
字数 8600
阅读 553
phdnote
The functions and unique featuresof long intergenic non-coding RNA
https://www.nature.com/articles/nrm.2017.104.pdf
Complexity and conservation of regulatory landscapes underlie evolutionary resilience of mammalian gene expression.
https://www.ncbi.nlm.nih.gov/pubmed/29180706
HEDD: Human Enhancer Disease Database.
https://www.ncbi.nlm.nih.gov/pubmed/29077884
The functions and unique features of long intergenic non-coding RNA
https://www.nature.com/articles/nrm.2017.104.pdf
YY1 Is a Structural Regulator of Enhancer-Promoter Loops
https://www.sciencedirect.com/science/article/pii/S009286741731317X
Programmable DNA looping using engineered bivalent dCas9 complexes
https://www.nature.com/articles/s41467-017-01873-x
Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene
http://www.sciencedirect.com/science/article/pii/S1097276517308390
Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro
https://skeletalmusclejournal.biomedcentral.com/articles/10.1186/s13395-017-0122-1
Functional assessment of human enhancer activities using whole-genome STARR-sequencing
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1345-5
BL-Hi-C is an efficient and sensitive approach for capturing structural and regulatory chromatin interactions
https://www.nature.com/articles/s41467-017-01754-3
A transcribed enhancer dictates mesendoderm specification in pluripotency
https://www.nature.com/articles/s41467-017-01804-w
7SK-BAF axis controls pervasive transcription at enhancers
https://www.nature.com/articles/nsmb.3176
Discovery and Characterization of Super-Enhancer-Associated Dependencies in Diffuse Large B Cell Lymphoma
http://www.sciencedirect.com/science/article/pii/S1535610813004911
Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
http://www.sciencedirect.com/science/article/pii/S0092867414011799
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0992-2
Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations
https://www.nature.com/articles/nature12716
How best to identify chromosomal interactions: a comparison of approaches
https://www.nature.com/articles/nmeth.4146
https://www.nature.com/articles/nature18606
In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells
http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31543-7 (by XQ)
A CREB-MPP7-AMOT Regulatory Axis Controls Muscle Stem Cell Expansion and Self-Renewal Competence
http://www.sciencedirect.com/science/article/pii/S2211124717314638?via%3Dihub (by Yuying)
Staufen1 inhibits MyoD translation to actively maintain muscle stem cell quiescence
http://www.pnas.org/content/114/43/E8996.abstract (by Xiaona)
Macrophage-released ADAMTS1 promotes muscle stem cell activation
https://www.nature.com/articles/s41467-017-00522-7 (by Xue Guang)
groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data
https://bioconductor.org/packages/release/bioc/html/groHMM.html
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0656-3
Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation(By Liangqiang)
https://www.nature.com/ng/journal/v49/n10/full/ng.3935.html
Two independent modes of chromatin organization revealed by cohesin removal(By Zac)
https://www.nature.com/nature/journal/v551/n7678/full/nature24281.html
Cohesin Loss Eliminates All Loop Domains(By Yingzhe)
http://www.cell.com/cell/abstract/S0092-8674(17)31120-0
Bivariate Genomic Footprinting Detects Changes in Transcription Factor Activity
http://www.sciencedirect.com/science/article/pii/S2211124717306095
Mocap: large-scale inference of transcription factor binding sites from chromatin accessibility
https://academic.oup.com/nar/article/3071708
LR-DNase: Predicting TF binding from DNase-seq data
https://www.biorxiv.org/content/early/2016/10/24/082594
Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome
http://www.sciencedirect.com/science/article/pii/S2211124714008729
The Elongation Factor Spt6 Maintains ESC Pluripotency by Controlling Super-Enhancers and Counteracting Polycomb Proteins
http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30667-6
HGFA Is an Injury-Regulated Systemic Factor that Induces the Transition of Stem Cells into G Alert
http://www.sciencedirect.com/science/article/pii/S2211124717304278?via%3Dihub
DNA damage signaling mediates the functional antagonism between replicative senescence and terminal muscle differentiation
http://genesdev.cshlp.org/content/31/7/648
Some papers are worth for review:
Cooperative Binding of Transcription Factors Orchestrates Reprogramming.
https://www.ncbi.nlm.nih.gov/pubmed/28111071
Transcription Factor Cooperativity in Early Adipogenic Hotspots and Super-Enhancers
http://www.cell.com/cell-reports/abstract/S2211-1247(14)00344-1
Molecular architecture of transcription factor hotspots in early adipogenesis.
https://www.ncbi.nlm.nih.gov/pubmed/24857666
Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling
https://www.ncbi.nlm.nih.gov/pubmed/28981893
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
http://www.cell.com/molecular-cell/abstract/S1097-2765(17)30546-4
PAF1 regulation of promoter-proximal pause release via enhancer activation
http://science.sciencemag.org/content/357/6357/1294.full
Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate.
https://www.ncbi.nlm.nih.gov/pubmed/28938112/
Recurrently deregulated lncRNAs in hepatocellular carcinoma
https://www.nature.com/articles/ncomms14421
Quantitative ChIP-Seq normalization reveals global modulation of the epigenome.
https://www.ncbi.nlm.nih.gov/pubmed/25437568
Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability
http://www.cell.com/molecular-cell/fulltext/S1097-2765(17)30496-3
Transposable elements are the primary source of novelty in primate gene regulation
http://genome.cshlp.org/content/27/10/1623.full
In Situ Capture of Chromatin Interactions by Biotinylated dCas9.
https://www.ncbi.nlm.nih.gov/pubmed/28841410
Chromatin accessibility dynamics of myogenesis at single cell resolution
https://www.biorxiv.org/content/early/2017/06/26/155473
Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements
http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3963.html?WT.feed_name=subjects_genetics
Complex multi-enhancer contacts captured by genome architecture mapping.
https://www.ncbi.nlm.nih.gov/pubmed/28273065
Transcriptional response to stress is pre-wired by promoter and enhancer architecture
https://www.nature.com/articles/s41467-017-00151-0
A pathology atlas of the human cancer transcriptome.
https://www.ncbi.nlm.nih.gov/pubmed/28818916
Synthetic spike-in standards for RNA-seq experiments.
https://www.ncbi.nlm.nih.gov/pubmed/21816910
Normalization of RNA-seq data using factor analysis of control genes or samples
http://www.nature.com/nbt/journal/v32/n9/full/nbt.2931.html
Super-Enhancer-Mediated RNA Processing Revealed by Integrative MicroRNA Network Analysis.
https://www.ncbi.nlm.nih.gov/pubmed/28283057
Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
https://www.ncbi.nlm.nih.gov/pubmed/19213877
Allelic reprogramming of 3D chromatin architecture during early mammalian development.
https://www.ncbi.nlm.nih.gov/pubmed/28703188
Heterogeneity of neuroblastoma cell identity defined by transcriptional circuitries.
https://www.ncbi.nlm.nih.gov/pubmed/28740262