All Stories

  1. Disease category-specific annotation of variants using an ensemble learning framework
  2. 20th International Workshop on Data Mining in Bioinformatics (BIOKDD 2021)
  3. Plasma Metabolic Phenotypes of HPV-Associated versus Smoking-Associated Head and Neck Cancer and Patient Survival
  4. LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data
  5. EWASplus: a computational tool to expand EWAS coverage from the array to the whole epigenome.
  6. Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis
  7. Glucocorticoid receptor wields chromatin interactions to tune transcription for cytoskeleton stabilization in podocytes
  8. Author Correction: Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form
  9. Truncation of mutant huntingtin in knock-in mice demonstrates exon1 huntingtin is a key pathogenic form
  10. Lack of RAN-mediated toxicity in Huntington’s disease knock-in mice
  11. Application of topic models to a compendium of ChIP-Seq datasets uncovers recurrent transcriptional regulatory modules
  12. An Integrated System Biology Approach Yields Drug Repositioning Candidates for the Treatment of Heart Failure
  13. Regulatory annotation of genomic intervals based on tissue-specific expression QTLs
  14. Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure
  15. Inferring Spatial Organization of Individual Topologically Associated Domains via Piecewise Helical Model
  16. RT States: systematic annotation of the human genome using cell type-specific replication timing programs
  17. A comprehensive review of computational prediction of genome-wide features
  18. Use replication timing data from multiple cell types to annotate human genome
  19. EWS/ETS-Driven Ewing Sarcoma Requires BET Bromodomain Proteins
  20. Use cloud-based distributed systems to speed up merging of large collection of VCF files.
  21. Special collection of bioinformatics in the era of precision medicine
  22. Using DIVAN to assess disease/trait-associated single nucleotide variants in genome-wide scale
  23. CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington’s disease
  24. Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome
  25. Omicseq: searching omics data without using metadata
  26. 10.1038/srep46398
  27. An approach of identifying differential nucleosome regions in multiple samples
  28. Computationally Tractable Multivariate HMM in Genome-Wide Mapping Studies
  29. Disease-specific non-coding variant annotation
  30. Genome-Wide STAT3 Binding Analysis after Histone Deacetylase Inhibition Reveals Novel Target Genes in Dendritic Cells
  31. The single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data
  32. A continuum of admixture in the Western Hemisphere revealed by the African Diaspora genome
  33. Use historical data to improve detection of differential expressed genes.
  34. MLL1 and MLL1 fusion proteins have distinct functions in regulating leukemic transcription program
  35. Heat Shock Protein Beta-1 Modifies Anterior to Posterior Purkinje Cell Vulnerability in a Mouse Model of Niemann-Pick Type C Disease
  36. R package to test GWAS SNP enrichment in any genomic interval(s)
  37. Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes
  38. One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies
  39. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates
  40. Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing
  41. Base-resolution methylation patterns accurately predict transcription factor bindings in vivo
  42. A novel statistical method for quantitative comparison of multiple ChIP-seq datasets
  43. Systems biology and metagenomics: a showcase of Chinese bioinformatics researchers and their work
  44. Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma
  45. Reciprocal occupancy of BCL6 and STAT5 on Growth Hormone target genes: contrasting transcriptional outcomes and promoter-specific roles of p300 and HDAC3
  46. Direct Amplification, Sequencing and Profiling of Chlamydia trachomatis Strains in Single and Mixed Infection Clinical Samples
  47. H2B Ubiquitylation Promotes RNA Pol II Processivity via PAF1 and pTEFb
  48. Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer
  49. The central role of EED in the orchestration of polycomb group complexes
  50. Targeting MLL1 H3K4 Methyltransferase Activity in Mixed-Lineage Leukemia
  51. EgoNet: identification of human disease ego-network modules
  52. Insulator function and topological domain border strength scale with architectural protein occupancy
  53. Allogeneic T cell responses are regulated by a specific miRNA-mRNA network
  54. Impaired replication elongation in Tetrahymena mutants deficient in histone H3 Lys 27 monomethylation
  55. Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data
  56. Bayesian Inference of Spatial Organizations of Chromosomes
  57. Sparsely correlated hidden Markov models with application to genome-wide location studies
  58. A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks
  59. Characterization of the EZH2-MMSET Histone Methyltransferase Regulatory Axis in Cancer
  60. Exploring the Cooccurrence Patterns of Multiple Sets of Genomic Intervals
  61. MotifOrganizer a scalable model-based motif clustering tool for mammalian genomes
  62. Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
  63. Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression
  64. HiCNorm: removing biases in Hi-C data via Poisson regression
  65. The Histone Acetyltransferase MOF Is a Key Regulator of the Embryonic Stem Cell Core Transcriptional Network
  66. PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification
  67. GPUmotif: An Ultra-Fast and Energy-Efficient Motif Analysis Program Using Graphics Processing Units
  68. Cooperation between Polycomb and androgen receptor during oncogenic transformation
  69. FOXP3 Orchestrates H4K16 Acetylation and H3K4 Trimethylation for Activation of Multiple Genes by Recruiting MOF and Causing Displacement of PLU-1
  70. Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq
  71. Coordinated Regulation of Polycomb Group Complexes through microRNAs in Cancer
  72. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
  73. C/EBPβ Mediates Growth Hormone-Regulated Expression of Multiple Target Genes
  74. SAINT: probabilistic scoring of affinity purification–mass spectrometry data
  75. Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data
  76. A Global Protein Kinase and Phosphatase Interaction Network in Yeast
  77. An Integrated Network of Androgen Receptor, Polycomb, and TMPRSS2-ERG Gene Fusions in Prostate Cancer Progression
  78. A Double-Layered Mixture Model for the Joint Analysis of DNA Copy Number and Gene Expression Data
  79. On the detection and refinement of transcription factor binding sites using ChIP-Seq data
  80. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data
  81. Global Gene Expression Analysis Reveals Evidence for Decreased Lipid Biosynthesis and Increased Innate Immunity in Uninvolved Psoriatic Skin
  82. Computational and Functional Analysis of Growth Hormone (GH)-Regulated Genes Identifies the Transcriptional Repressor B-Cell Lymphoma 6 (Bc16) as a Participant in GH-Regulated Transcription
  83. Drug–Drug Interaction Prediction Assessment
  84. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data
  85. Progress toward personalized medicine for glaucoma
  86. Query Large Scale Microarray Compendium Datasets Using a Model-Based Bayesian Approach with Variable Selection
  87. A new probabilistic rule for drug–dug interaction prediction
  88. Advances in Statistical Bioinformatics
  89. Comparison of laboratory-based and phylogenetic methods to distinguish between Haemophilus influenzae and H. haemolyticus
  90. Family‐based SNP association study on 8q24 in bipolar disorder
  91. Genome-wide detection and characterization of positive selection in human populations
  92. A second generation human haplotype map of over 3.1 million SNPs
  93. p53-Mediated Activation of miRNA34 Candidate Tumor-Suppressor Genes
  94. CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
  95. Different normalization strategies for microarray gene expression traits affect the heritability estimation
  96. Operon Prediction for Sequenced Bacterial Genomes without Experimental Information
  97. Clustering microarray gene expression data using weighted Chinese restaurant process
  98. A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
  99. Energy, quiescence and the cellular basis of animal life spans
  101. An efficient comprehensive search algorithm for tagSNP selection using linkage disequilibrium criteria
  102. Improved Classification of Mass Spectrometry Database Search Results Using Newer Machine Learning Approaches
  103. A haplotype map of the human genome
  104. High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate (FDR) and Minimum Acceptable Strength (MAS)
  105. Protein Tyrosine Phosphatase Gene PTPN22 Polymorphism in Psoriasis: Lack of Evidence for Association
  106. Fine Mapping of the Psoriasis Susceptibility Gene PSORS1: A Reassessment of Risk Associated with a Putative Risk Haplotype Lacking HLA-Cw6
  107. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
  108. Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies
  109. Incorporating Genotyping Uncertainty in Haplotype Inference for Single-Nucleotide Polymorphisms
  110. Statistical resynchronization and Bayesian detection of periodically expressed genes
  111. Dynamic Programming Algorithms for Haplotype Block Partitioning and Tag SNP Selection Using Haplotype Data or Genotype Data
  112. Haplotype Inference and Its Application in Linkage Disequilibrium Mapping
  113. Identification of co-regulated genes through Bayesian clustering of predicted regulatory binding sites
  114. Scale Mixture Models with Applications to Bayesian Inference
  115. Partition-Ligation–Expectation-Maximization Algorithm for Haplotype Inference with Single-Nucleotide Polymorphisms
  116. Bayesian Haplotype Inference for Multiple Linked Single-Nucleotide Polymorphisms
  117. Multipoint Metropolis Method with Application to Hybrid Monte Carlo
  118. Model-Based Methods for Transcript Expression-Level Quantification in RNA-Seq
  119. Plate section
  120. Preface
  121. Statistical resynchronization and detection of periodic transcripts