All Stories

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