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Kalen Robeson, Silvana Duran-Ortiz, Deb Walter, Katie Troike, Nate Sulecki
Bioinformatics Journal Club
Top Papers in Regulatory and Systems Genomics
Gene Expression/Regulation:
1. Transcriptomics
a. Analysis of genomic variation in non-coding elements using population-scale
sequencing data from the 1000 Genomes Project
b. Guilt by association is the exception rather than the rule in gene networks
c. Systematic dissection of regulatory motifs in 2000 predicted human enhancers
using a massively parallel reporter assay
d. Promoter Sequence Determines the Relationship between Expression Level and
e. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep
f. Inferring interaction type in gene regulatory networks using co-expression data
2. Protein/DNA or Protein/Protein
a. Accurate inference of transcription factor binding from DNA sequence and
chromatin accessibility data
b. Comprehensive genome-wide protein-DNA interactions detected at singlenucleotide resolution
c. Discriminative prediction of mammalian enhancers from DNA sequence
d. Dynamic exchange at regulatory elements during chromatin remodeling
underlies assisted loading mechanism
e. Mapping and analysis of chromatin state dynamics in nine human cell types
f. DNaseI sensitivity QTLs are a major determinant of human expression variation
g. An expansive human regulatory lexicon encoded in transcription factor
h. Linking the signaling cascades and dynamic regulatory networks controlling
stress responses
i. Genomic regions flanking E-box binding sites influence DNA binding specificity of
bHLH transcription factors through DNA shape
j. Probing DNA shape and methylation state on a genomic scale with DNase I
k. Single-molecule dynamics of enhanceosome assembly in embryonic stem cells
l. Determination and inference of eukaryotic transcription factor sequence
m. Coregulation of transcription factor binding and nucleosome occupancy through
DNA features of mammalian enhancers
n. TFBSshape: a motif database for DNA shape features of transcription factor
binding sites
o. Quantitative modeling of transcription factor binding specificities using DNA
Expression in Cancer and Other Diseases:
1. An extensive microRNA-mediated network of RNA-RNA interactions regulates
established oncogenic pathways in glioblastoma
2. Prioritizing candidate disease genes by network-based boosting of genome-wide
association data
3. The human splicing code reveals new insights into the genetic determinants of disease
4. Integration of genomic data enables selective discovery of breast cancer drivers
1. A statistical framework for joint eQTL analysis in multiple tissues
2. Computational identification of diverse mechanisms underlying transcription factor-DNA
3. A community effort to assess and improve drug sensitivity prediction algorithms
4. Deconvolving the recognition of DNA shape from sequence
5. Elucidating Compound Mechanism of Action by Network Perturbation Analysis
6. A method to predict the impact of regulatory variants from DNA sequence
1. Transposition of native chromatin for fast and sensitive epigenomic profiling of open
chromatin, DNA-binding proteins and nucleosome
2. Large-scale imputation of epigenomic datasets for systematic annotation of diverse
human tissues
Expression During Development:
1. Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells
by modENCODE RNA-seq data
2. Enhancer loops appear stable during development and are associated with paused
3. Genotype-environment interactions reveal causal pathways that mediate genetic effects
on phenotype
4. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data
reveals hidden subpopulations of cells
5. Joint annotation of chromatin state and chromatin conformation reveals relationships
among domain types and identifies domains of cell type-specific expression
1. A high-resolution map of human evolutionary constraint using 29 mammals
2. Cofactor binding evokes latent differences in DNA binding specificity between Hox
3. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of
922 individuals