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Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing

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Temporal Dynamic Methods for Bulk RNA-Seq Time Series Data

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A systematic review of transcriptomic studies of the human endometrium reveals inconsistently reported differentially expressed genes

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Transcriptomic Profiling Using Next Generation Sequencing - Advances, Advantages, and Challenges

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Lnc-CC3 increases metastasis in cervical cancer by increasing Slug expression

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Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy

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Standardising RNA profiling based biomarker application in cancer—The need for robust control of technical variables

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An integrative transcriptome study reveals Ddit4/Redd1 as a key regulator of cancer cachexia in rodent models

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Thinking points for effective batch correction on biomedical data

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Heterogeneous Large Datasets Integration Using Bayesian Factor Regression

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A signature of circadian rhythm genes in driving anaplastic thyroid carcinoma malignant progression

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Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking

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Identification of copper-related biomarkers and potential molecule mechanism in diabetic nephropathy

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Genetic and Nongenetic Variation Revealed for the Principal Components of Human Gene Expression

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Gene expression: Biomarker of antidepressant therapy?

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Biological Processes Discovered by High-Throughput Sequencing

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Fingolimod downregulates brain sphingosine-1-phosphate receptor 1 levels but does not promote remyelination or neuroprotection in the cuprizone model

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Cell-free microRNAs in Parkinson’s disease: potential biomarkers that provide new insights into disease pathogenesis

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Integrative computational epigenomics to build data-driven gene regulation hypotheses

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Accommodating site variation in neuroimaging data using normative and hierarchical Bayesian modelsPreprint

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A clinical prognostic model related to T cells based on machine learning for predicting the prognosis and immune response of ovarian cancer

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On the Identification of Circulating Tumor Cells in Breast Cancer

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A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk

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Lessons learned in the analysis of high-dimensional data in vaccinomics

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Alcohol and the methylome: Design and analysis considerations for research using human samples

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Meta-Analysis in Gene Expression Studies

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Evaluating hepatocellular carcinoma cell lines for tumour samples using within‐sample relative expression orderings of genes

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Epigenome-wide association studies for systemic autoimmune diseases: The road behind and the road ahead

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Tightly integrated genomic and epigenomic data mining using tensor decomposition

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Mendelian Randomization and the Environmental Epigenetics of Health: a Systematic Review

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Quantify and control reproducibility in high-throughput experiments

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A Bayesian non-parametric mixed-effects model of microbial growth curves

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BatchServer: A Web Server for Batch Effect Evaluation, Visualization, and Correction

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Machine learning model for predicting Major Depressive Disorder using RNA-Seq data: optimization of classification approach

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Enhancing PCORnet Clinical Research Network data completeness by integrating multistate insurance claims with electronic health records in a cloud environment aligned with CMS security and privacy requirements

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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post- chemotherapy tissues

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Systems biology approach to understanding post-traumatic stress disorder

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The propagation of perturbations in rewired bacterial gene networks

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Comparative genomic evidence for the involvement of schizophrenia risk genes in antipsychotic effects

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Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys

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Comparative Transcriptomics across Nematode Life Cycles Reveal Gene Expression Conservation and Correlated Evolution in Adjacent Developmental Stages

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Statistical Analysis and Interpolation of Compositional Data in Materials Science

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When to use Quantile Normalization?Preprint

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A unified evolution-driven deep learning framework for virus variation driver prediction

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The Impact and Role of Artificial Intelligence (AI) in Healthcare: Systematic Review

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Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)

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Tamoxifen therapy benefit predictive signature coupled with prognostic signature of post-operative recurrent risk for early stage ER+ breast cancer

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Single-Cell RNA Sequencing of Human T Cells

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Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies

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Batch Effects Correction with Unknown Subtypes

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SNP genotype calling and quality control for multi-batch-based studies

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Single-center versus multi-center data sets for molecular prognostic modeling: a simulation study

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Estimating and Accounting for Unobserved Covariates in High-Dimensional Correlated Data

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Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth

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A simple, scalable approach to building a cross-platform transcriptome atlas

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Omixer: multivariate and reproducible sample randomization to proactively counter batch effects in omics studies

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Machine learning alternative to systems biology should not solely depend on data

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Principles of phosphoproteomics and applications in cancer research

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Artificial intelligence in liver imaging: methods and applications

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Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity

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Recent advances in endothelial colony-forming cells: from the transcriptomic perspective

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Designing, Performing, and Interpreting a Microarray-Based Gene Expression Study

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Bugs, Stool, and the Irritable Bowel Syndrome: Too Much Is as Bad as Too Little?

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Intra- and Inter-Individual Variance of Gene Expression in Clinical Studies

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Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

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Mass Spectrometry Analysis Using MALDIquant

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Detecting hidden batch factors through data-adaptive adjustment for biological effects

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Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives

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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues

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Eliminating accidental deviations to minimize generalization error and maximize replicability: applications in connectomics and genomicsPreprint

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Scalable Transcriptome Preparation for Massive Parallel Sequencing

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Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology

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Replication Study: Wnt activity defines colon cancer stem cells and is regulated by the microenvironment

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A General Approach to Sensitivity Analysis for Mendelian Randomization

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Identification of key genes and functions of circulating tumor cells in multiple cancers through bioinformatic analysis

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Using Machine Learning to Identify Biomarkers Affecting Fat Deposition in Pigs by Integrating Multisource Transcriptome Information

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Reproducibility and Concordance of Differential DNA Methylation and Gene Expression in Cancer

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Improved Normalization of Systematic Biases Affecting Ion Current Measurements in Label-free Proteomics Data

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Matrix Denoising for Weighted Loss Functions and Heterogeneous Signals

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Normalization and Statistical Analysis of Multiplexed Bead-based Immunoassay Data Using Mixed-effects Modeling

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