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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