OOIR: Observatory of International Research

Papers

(The H4-Index of Genome Research is 47. 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 2020-03-01 to 2024-03-01.)

Article	Citations
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads	407
Accurate and complete genomes from metagenomes	251
Accurate and efficient detection of gene fusions from RNA sequencing data	203
Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA	158
Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N	99
Functional annotation of human long noncoding RNAs via molecular phenotyping	96
Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle	95
Accessing NCBI data using the NCBI Sequence Viewer and Genome Data Viewer (GDV)	94
Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains	93
Advances in spatial transcriptomic data analysis	93
Single-cell analysis of human embryos reveals diverse patterns of aneuploidy and mosaicism	90
Mapping genome variation of SARS-CoV-2 worldwide highlights the impact of COVID-19 super-spreaders	85
A single-cell tumor immune atlas for precision oncology	81
Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities	73
Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii	72
Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing	72
Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing	68
Ultralow-input single-tube linked-read library method enables short-read second-generation sequencing systems to routinely generate highly accurate and economical long-range sequencing information	65
Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays	64
Analysis of Hi-C data using SIP effectively identifies loops in organisms from C. elegans to mammals	63
Cross-species analysis of enhancer logic using deep learning	63
Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution	61
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis	61
Data structures based on k-mers for querying large collections of sequencing data sets	58
Detection and characterization of jagged ends of double-stranded DNA in plasma	57

Semisupervised adversarial neural networks for single-cell classification	56
Sequencing identifies multiple early introductions of SARS-CoV-2 to the New York City region	56
Quantitative analysis of Y-Chromosome gene expression across 36 human tissues	55
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data	55
Accurate reconstruction of bacterial pan- and core genomes with PEPPAN	54
Evolution of genome structure in theDrosophila simulansspecies complex	54
Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types	54
Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules	54
Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment	53
Gene expression networks in the Drosophila Genetic Reference Panel	53
Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences	52
Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control	51
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease	51
Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control	51
Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants	50
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes	50
Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver	49
Parallel bimodal single-cell sequencing of transcriptome and chromatin accessibility	48
High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation	48
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states	48
Decoding the function of bivalent chromatin in development and cancer	47
Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics	47