OOIR: Observatory of International Research

Papers

(The H4-Index of Genome Research is 44. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-11-01 to 2024-11-01.)

Article	Citations
Accurate and efficient detection of gene fusions from RNA sequencing data	277
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA	253
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N	155
Advances in spatial transcriptomic data analysis	134
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)	130
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities	105
A single-cell tumor immune atlas for precision oncology	100
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	86
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays	75
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes	73
Data structures based on k-mers for querying large collections of sequencing data sets	72
Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution	69
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment	68
Evolution of genome structure in theDrosophila simulansspecies complex	68
Semisupervised adversarial neural networks for single-cell classification	67
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules	67
Ligand-induced native G-quadruplex stabilization impairs transcription initiation	64
Decoding the function of bivalent chromatin in development and cancer	64
Mitochondrial DNA variation across 56,434 individuals in gnomAD	63
Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver	61
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states	59
Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states	59
A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing	58
Contamination detection in sequencing studies using the mitochondrial phylogeny	56
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control	55

Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease	55
Chromatin architecture transitions from zebrafish sperm through early embryogenesis	54
Structural variants are a major source of gene expression differences in humans and often affect multiple nearby genes	54
The Enterprise, a massive transposon carrying Spok meiotic drive genes	51
The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence	51
Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA	51
Multimodal single-cell/nucleus RNA sequencing data analysis uncovers molecular networks between disease-associated microglia and astrocytes with implications for drug repurposing in Alzheimer's diseas	50
Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data	48
Bayesian estimation of cell type–specific gene expression with prior derived from single-cell data	48
Acute depletion of METTL3 implicates N⁶-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome	48
Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression	47
Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs	46
The human ribosomal DNA array is composed of highly homogenized tandem clusters	46
A single-cell atlas reveals unanticipated cell type complexity in Drosophila ovaries	46
Thermal stress accelerates Arabidopsis thaliana mutation rate	46
Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences	45
A minimally destructive protocol for DNA extraction from ancient teeth	45
Targeted regulation of transcription in primary cells using CRISPRa and CRISPRi	44
Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis	44
Effective sequence similarity detection with strobemers	44