OOIR: Observatory of International Research

Papers

(The TQCC of GigaScience is 12. 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
Twelve years of SAMtools and BCFtools	6415
Significantly improving the quality of genome assemblies through curation	967
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data	735
HTSlib: C library for reading/writing high-throughput sequencing data	233
A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event	206
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters	114
GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci	109
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas	104
Comparison of the two up-to-date sequencing technologies for genome assembly: HiFi reads of Pacific Biosciences Sequel II system and ultralong reads of Oxford Nanopore	102
Long-read assembly of the Brassica napus reference genome Darmor-bzh	76
Comparison of long-read methods for sequencing and assembly of a plant genome	67
Inferring microbiota functions from taxonomic genes: a review	64
Parliament2: Accurate structural variant calling at scale	57
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	52
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia	49
Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology	48
Preventing dataset shift from breaking machine-learning biomarkers	48
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	44
Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy	44
Chromosome-level draft genome of a diploid plum (Prunus salicina)	43
BiSulfite Bolt: A bisulfite sequencing analysis platform	42
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	41
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	41
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data	39
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	38

A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals	37
Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses	36
Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation	34
How to remove or control confounds in predictive models, with applications to brain biomarkers	33
Genome size evolution in the diverse insect order Trichoptera	33
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	33
The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity	33
Multi-stage malaria parasite recognition by deep learning	31
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data	31
Streamlining data-intensive biology with workflow systems	31
Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis	30
Fractional ridge regression: a fast, interpretable reparameterization of ridge regression	30
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense	30
Efficient DNA sequence compression with neural networks	29
Population modeling with machine learning can enhance measures of mental health	29
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	29
A microbial gene catalog of anaerobic digestion from full-scale biogas plants	28
U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	28
Loop detection using Hi-C data with HiCExplorer	27
De novo genome assemblies of butterflies	26
Building the mega single-cell transcriptome ocular meta-atlas	25
Association mapping across a multitude of traits collected in diverse environments in maize	25
Localized effect of treated wastewater effluent on the resistome of an urban watershed	25
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design	24
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	24
The rise of genomics in snake venom research: recent advances and future perspectives	24
Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing	24
Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data	24
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)	23
SYNPRED: prediction of drug combination effects in cancer using different synergy metrics and ensemble learning	23
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	23
Two high-qualityde novogenomes from single ethanol-preserved specimens of tiny metazoans (Collembola)	23
Mantis: flexible and consensus-driven genome annotation	22
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package	22
A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum–infected red blood cell proteome	22
Chromosomal genome ofTriplophysa bleekeriprovides insights into its evolution and environmental adaptation	22
ISA API: An open platform for interoperable life science experimental metadata	21
High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa	21
Desiderata for the development of next-generation electronic health record phenotype libraries	21
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing	20
0s and 1s in marine molecular research: a regional HPC perspective	20
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes	20
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	20
MB-GAN: Microbiome Simulation via Generative Adversarial Network	19
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data	19
An in vitro whole-cell electrophysiology dataset of human cortical neurons	18
Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads	18
Comparative analysis of common alignment tools for single-cell RNA sequencing	18
iGenomics: Comprehensive DNA sequence analysis on your Smartphone	18
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	18

Correcting for experiment-specific variability in expression compendia can remove underlying signals	17
Antibiotic resistance genes are differentially mobilized according to resistance mechanism	17
Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss	17
Efficient real-time selective genome sequencing on resource-constrained devices	17
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	16
DENTIST—using long reads for closing assembly gaps at high accuracy	16
Spacemake: processing and analysis of large-scale spatial transcriptomics data	16
Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective	16
Agricultural plant cataloging and establishment of a data framework from UAV-based crop images by computer vision	16
What the Phage: a scalable workflow for the identification and analysis of phage sequences	16
Myth-busting the provider-user relationship for digital sequence information	15
AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology	15
Multi-modal data collection for measuring health, behavior, and living environment of large-scale participant cohorts	15
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle	15
Evolution of complex genome architecture in gymnosperms	15
SSNOMBACTER: A collection of scattering-type scanning near-field optical microscopy and atomic force microscopy images of bacterial cells	15
A curated human cellular microRNAome based on 196 primary cell types	15
Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis	15
Benchmarking missing-values approaches for predictive models on health databases	14
Vulcan: Improved long-read mapping and structural variant calling via dual-mode alignment	14
Triku: a feature selection method based on nearest neighbors for single-cell data	14
Linking big biomedical datasets to modular analysis with Portable Encapsulated Projects	14
Genome diversity in Ukraine	14
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch	14
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations	14
The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis	14
Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population	13
Identification of a differentiation stall in epithelial mesenchymal transition in histone H3–mutant diffuse midline glioma	13
Clonality, inbreeding, and hybridization in two extremotolerant black yeasts	13
BIGwas: Single-command quality control and association testing for multi-cohort and biobank-scale GWAS/PheWAS data	13
Quantifying research interests in 7,521 mammalian species with h-index: a case study	13
Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework	13
Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers	13
RNAProt: an efficient and feature-rich RNA binding protein binding site predictor	13
Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts	13
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl	12
An analysis of security vulnerabilities in container images for scientific data analysis	12
Internet of Samples (iSamples): Toward an interdisciplinary cyberinfrastructure for material samples	12
Maternal plasma lipids are involved in the pathogenesis of preterm birth	12
Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater	12
Fluorescence microscopy datasets for training deep neural networks	12
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building coralsPorites luteaandIsopora palifera	12
A chromosome-level genome assembly and annotation of the desert horned lizard, Phrynosoma platyrhinos, provides insight into chromosomal rearrangements among reptiles	12
A high-throughput multiplexing and selection strategy to complete bacterial genomes	12
Chromosome-level genome assembly of the black widow spiderLatrodectus elegansilluminates composition and evolution of venom and silk proteins	12
Lilikoi V2.0: a deep learning–enabled, personalized pathway-based R package for diagnosis and prognosis predictions using metabolomics data	12
High-quality chromosome-level genome assembly and full-length transcriptome analysis of the pharaoh ant Monomorium pharaonis	12