OOIR: Observatory of International Research

Papers

(The TQCC of GigaScience is 13. 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 2020-05-01 to 2024-05-01.)

Article	Citations
Twelve years of SAMtools and BCFtools	4810
Significantly improving the quality of genome assemblies through curation	771
SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data	586
HTSlib: C library for reading/writing high-throughput sequencing data	190
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	185
An improved pig reference genome sequence to enable pig genetics and genomics research	182
IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring	169
Construction of a chromosome-scale long-read reference genome assembly for potato	158
TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads	152
BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters	99
A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas	93
GALLO: An R package for genomic annotation and integration of multiple data sources in livestock for positional candidate loci	88
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	85
Recommendations to enhance rigor and reproducibility in biomedical research	81
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome	74
Long-read assembly of the Brassica napus reference genome Darmor-bzh	68
Comparison of long-read methods for sequencing and assembly of a plant genome	59
Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples	59
Inferring microbiota functions from taxonomic genes: a review	56
Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K)	48
Parliament2: Accurate structural variant calling at scale	48
Chromosome-level genome assembly of the hard-shelled mussel Mytilus coruscus, a widely distributed species from the temperate areas of East Asia	47
SnpHub: an easy-to-set-up web server framework for exploring large-scale genomic variation data in the post-genomic era with applications in wheat	43
Preventing dataset shift from breaking machine-learning biomarkers	42
Genomic data imputation with variational auto-encoders	41

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology	40
CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing	40
Chromosome-level draft genome of a diploid plum (Prunus salicina)	40
Assessment of fecal DNA extraction protocols for metagenomic studies	37
Multimodal signal dataset for 11 intuitive movement tasks from single upper extremity during multiple recording sessions	36
long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data	35
A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment	35
Technical workflows for hyperspectral plant image assessment and processing on the greenhouse and laboratory scale	35
Accelerated deciphering of the genetic architecture of agricultural economic traits in pigs using a low-coverage whole-genome sequencing strategy	34
A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals	34
Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle	33
Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation	33
Galactic Circos: User-friendly Circos plots within the Galaxy platform	32
DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach	32
Understanding the impact of preprocessing pipelines on neuroimaging cortical surface analyses	32
BiSulfite Bolt: A bisulfite sequencing analysis platform	32
A map of tumor–host interactions in glioma at single-cell resolution	31
NuCLS: A scalable crowdsourcing approach and dataset for nucleus classification and segmentation in breast cancer	31
The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features	31
Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning–based neural network	30
Streamlining data-intensive biology with workflow systems	29
The Gene Expression Deconvolution Interactive Tool (GEDIT): accurate cell type quantification from gene expression data	28
The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity	28
CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems	28
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense	27
Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function	27
Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis	26
Fractional ridge regression: a fast, interpretable reparameterization of ridge regression	26
Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding	26
An improved ovine reference genome assembly to facilitate in-depth functional annotation of the sheep genome	26
Genome size evolution in the diverse insect order Trichoptera	25
The germline mutational process in rhesus macaque and its implications for phylogenetic dating	25
Multi-stage malaria parasite recognition by deep learning	25
How to remove or control confounds in predictive models, with applications to brain biomarkers	24
De novo genome assemblies of butterflies	24
Building the mega single-cell transcriptome ocular meta-atlas	23
Population modeling with machine learning can enhance measures of mental health	23
Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana	23
The chromosome-level draft genome of Dalbergia odorifera	23
Graph2GO: a multi-modal attributed network embedding method for inferring protein functions	23
A microbial gene catalog of anaerobic digestion from full-scale biogas plants	23
A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma	22
Genome sequence and genetic diversity analysis of an under-domesticated orphan crop, white fonio (Digitaria exilis)	22
Efficient DNA sequence compression with neural networks	22
Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences	22
Scientometric trends for coronaviruses and other emerging viral infections	22
Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing	21
Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat	21
NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy	21
Localized effect of treated wastewater effluent on the resistome of an urban watershed	21

U-Limb: A multi-modal, multi-center database on arm motion control in healthy and post-stroke conditions	21
EHRtemporalVariability: delineating temporal data-set shifts in electronic health records	21
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design	21
Label3DMaize: toolkit for 3D point cloud data annotation of maize shoots	21
A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae	20
Mantis: flexible and consensus-driven genome annotation	20
0s and 1s in marine molecular research: a regional HPC perspective	20
ISA API: An open platform for interoperable life science experimental metadata	19
A haplotype-resolved,de novogenome assembly for the wood tiger moth (Arctia plantaginis) through trio binning	19
Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome	19
Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data	19
Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation	19
Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data	18
iGenomics: Comprehensive DNA sequence analysis on your Smartphone	18
Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package	18
Interpreting k-mer–based signatures for antibiotic resistance prediction	18
Trajectories, bifurcations, and pseudo-time in large clinical datasets: applications to myocardial infarction and diabetes data	18
The rise of genomics in snake venom research: recent advances and future perspectives	18
MB-GAN: Microbiome Simulation via Generative Adversarial Network	17
Comparative analysis of common alignment tools for single-cell RNA sequencing	17
Loop detection using Hi-C data with HiCExplorer	17
Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis	17
TinderMIX: Time-dose integrated modelling of toxicogenomics data	17
Correcting for experiment-specific variability in expression compendia can remove underlying signals	17
Two high-qualityde novogenomes from single ethanol-preserved specimens of tiny metazoans (Collembola)	17
Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats	17
Association mapping across a multitude of traits collected in diverse environments in maize	17
A molecular map of lung neuroendocrine neoplasms	16
An in vitro whole-cell electrophysiology dataset of human cortical neurons	16
A new mass spectral library for high-coverage and reproducible analysis of the Plasmodium falciparum–infected red blood cell proteome	16
A hybrid pipeline for reconstruction and analysis of viral genomes at multi-organ level	16
Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes	16
Desiderata for the development of next-generation electronic health record phenotype libraries	16
TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data	15
Message in a Bottle—Metabarcoding enables biodiversity comparisons across ecoregions	15
Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal	15
M2aia—Interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data	15
Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss	15
An extensible big data software architecture managing a research resource of real-world clinical radiology data linked to other health data from the whole Scottish population	15
Multi-modal data collection for measuring health, behavior, and living environment of large-scale participant cohorts	14
Efficient real-time selective genome sequencing on resource-constrained devices	14
Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads	14
High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa	14
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods	14
Integrative computational epigenomics to build data-driven gene regulation hypotheses	13
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch	13
Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy	13
Centering inclusivity in the design of online conferences—An OHBM–Open Science perspective	13
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing	13
Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis	13
MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations	13
DENTIST—using long reads for closing assembly gaps at high accuracy	13
AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology	13
Spacemake: processing and analysis of large-scale spatial transcriptomics data	13
Smash++: an alignment-free and memory-efficient tool to find genomic rearrangements	13
A single-cell RNA-sequencing training and analysis suite using the Galaxy framework	13