Download Group 3

Bioinformatics Journal Club Top10 papers ranking
Yichao Li, Xiao Liu, Prateek Kulkarni, Shriwas Pratik, Thapa Eliza
1. Epigenetics
I.
II.
III.
Large-scale imputation of epigenomic datasets for systematic annotation of diverse
human tissues
Transposition of native chromatin for fast and sensitive epigenomic profiling of open
chromatin, DNA-binding proteins and nucleosome position
Joint annotation of chromatin state and chromatin conformation reveals relationships
among domain types and identifies domains of cell type-specific expression
2. Nucleic acid protein interaction
I.
II.
III.
IV.
V.
VI.
Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning
Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide
resolution.
Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH
transcription factors through DNA shape
Cofactor binding evokes latent differences in DNA binding specificity between Hox
proteins.
Computational identification of diverse mechanisms underlying transcription factor-DNA
occupancy
An extensive microRNA-mediated network of RNA-RNA interactions regulates
established oncogenic pathways in glioblastoma
3. Regulatory sequence
I.
II.
III.
IV.
V.
VI.
An expansive human regulatory lexicon encoded in transcription factor footprints
Promoter Sequence Determines the Relationship between Expression Level and Noise
A method to predict the impact of regulatory variants from DNA sequence
Accurate inference of transcription factor binding from DNA sequence and chromatin
accessibility data.
Dynamic exchange at regulatory elements during chromatin remodeling underlies
assisted loading mechanism.
Linking the signaling cascades and dynamic regulatory networks controlling stress
responses
VII.
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells
by modENCODE RNA-seq data
4. Predicting Enhancers
I.
II.
III.
IV.
Discriminative prediction of mammalian enhancers from DNA sequence.
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a
massively parallel reporter assay
Coregulation of transcription factor binding and nucleosome occupancy through DNA
features of mammalian enhancers
Enhancer loops appear stable during development and are associated with paused
polymerase
5. Single cell RNA sequencing
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals
hidden subpopulations of cells
6. Structural Bioinformatics
I.
II.
III.
IV.
V.
TFBSshape: a motif database for DNA shape features of transcription factor binding sites
Deconvolving the recognition of DNA shape from sequence
Probing DNA shape and methylation state on a genomic scale with DNase I
Quantitative modeling of transcription factor binding specificities using DNA shape
DNaseI sensitivity QTLs are a major determinant of human expression variation
7. Genome wide association study/ Genome analysis
I.
II.
III.
IV.
V.
VI.
Analysis of genomic variation in non-coding elements using population-scale sequencing
data from the 1000 Genomes Project.
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of
922 individuals
A high-resolution map of human evolutionary constraint using 29 mammals
Mapping and analysis of chromatin state dynamics in nine human cell types.
Prioritizing candidate disease genes by network-based boosting of genome-wide
association data.
Integration of genomic data enables selective discovery of breast cancer drivers
8. Data mining
I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
Guilt by association is the exception rather than the rule in gene networks
Genotype-environment interactions reveal causal pathways that mediate genetic effects
on phenotype
A statistical framework for joint eQTL analysis in multiple tissues
Single-molecule dynamics of enhanceosome assembly in embryonic stem cells
Determination and inference of eukaryotic transcription factor sequence specificity
A community effort to assess and improve drug sensitivity prediction algorithms
inferring interaction type in gene regulatory networks using co-expression data
Elucidating Compound Mechanism of Action by Network Perturbation Analysis
The human splicing code reveals new insights into the genetic determinants of disease