OOIR: Observatory of International Research

Papers

(The TQCC of Nature Biotechnology is 74. The table below lists those papers that are above that threshold based on CrossRef citation counts. The publications cover those that have been published in the past four years, i.e., from 2019-03-01 to 2023-03-01.)

Article	Citations
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2	6843
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype	3782
SignalP 5.0 improves signal peptide predictions using deep neural networks	2429
Dimensionality reduction for visualizing single-cell data using UMAP	2246
Assembly of long, error-prone reads using repeat graphs	1612
Determining cell type abundance and expression from bulk tissues with digital cytometry	1405
Wearable biosensors for healthcare monitoring	1338
A comparison of single-cell trajectory inference methods	757
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome	593
CRISPResso2 provides accurate and rapid genome editing sequence analysis	549
Deep learning enables rapid identification of potent DDR1 kinase inhibitors	473
A laser-engraved wearable sensor for sensitive detection of uric acid and tyrosine in sweat	460
Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion	432
NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice	425
Breeding crops to feed 10 billion	403
High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell	378
Visualizing structure and transitions in high-dimensional biological data	378
Efficient integration of heterogeneous single-cell transcriptomes using Scanorama	376
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks	362
Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients	339
Broad-spectrum resistance to bacterial blight in rice using genome editing	331
Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing	321
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2	320
A human gut bacterial genome and culture collection for improved metagenomic analyses	320
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses	300
De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)	296
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection	279
In vivo molecular imaging for immunotherapy using ultra-bright near-infrared-IIb rare-earth nanoparticles	277
Minimum Information about an Uncultivated Virus Genome (MIUViG)	275
Accessing analytes in biofluids for peripheral biochemical monitoring	271
Predicting the mutations generated by repair of Cas9-induced double-strand breaks	270
CAR-T cells secreting BiTEs circumvent antigen escape without detectable toxicity	268
Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation	257
Characterization of cell fate probabilities in single-cell data with Palantir	251
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery	248
Plant gene editing through de novo induction of meristems	245
Toward a new generation of smart skins	237
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility	228
Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia	226
Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues	225
A large peptidome dataset improves HLA class I epitope prediction across most of the human population	225
Tubuloids derived from human adult kidney and urine for personalized disease modeling	222
Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore	219
An open resource for accurately benchmarking small variant and reference calls	212
The International Cancer Genome Consortium Data Portal	200
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2	199
Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution	196
Resistance gene cloning from a wild crop relative by sequence capture and association genetics	195
Increasing the specificity of CRISPR systems with engineered RNA secondary structures	194
Multi-omic measurements of heterogeneity in HeLa cells across laboratories	194
Evaluation of SARS-CoV-2 serology assays reveals a range of test performance	190
The functional landscape of the human phosphoproteome	189
Best practices for benchmarking germline small-variant calls in human genomes	187
CRISPR DNA base editors with reduced RNA off-target and self-editing activities	187
Specification of positional identity in forebrain organoids	182
Complete, closed bacterial genomes from microbiomes using nanopore sequencing	182
Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)	181
Protection of tissue physicochemical properties using polyfunctional crosslinkers	176
One-step genome editing of elite crop germplasm during haploid induction	174
Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages	168
Targeted isolation and cultivation of uncultivated bacteria by reverse genomics	168
Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes	166
FAIRsharing as a community approach to standards, repositories and policies	165
Predicting HLA class II antigen presentation through integrated deep learning	158
Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors	158
Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes	155
Continuous evolution of base editors with expanded target compatibility and improved activity	153
Blood metabolome predicts gut microbiome α-diversity in humans	152
Probing and engineering liquid-phase organelles	151
Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index	151
Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts	149
Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes	149
Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification	149
Errors in long-read assemblies can critically affect protein prediction	145
Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs	141
Design of stapled antimicrobial peptides that are stable, nontoxic and kill antibiotic-resistant bacteria in mice	136
Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides	132
Human 5′ UTR design and variant effect prediction from a massively parallel translation assay	130
Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes	129
Genome-wide target specificity of CRISPR RNA-guided adenine base editors	128
Deciphering eukaryotic gene-regulatory logic with 100 million random promoters	125
Polymer-stabilized Cas9 nanoparticles and modified repair templates increase genome editing efficiency	125
The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2	124
Antigen-specific therapeutic approaches for autoimmunity	120
Gene editing for immune cell therapies	117
Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs	115
Regenerating the field of cardiovascular cell therapy	113
Emerging technologies for improved deep brain stimulation	111
Single-cell metabolic profiling of human cytotoxic T cells	109
Next-generation interfaces for studying neural function	109
NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells	107
Phage combination therapies for bacterial wilt disease in tomato	107
Interleukin-23 engineering improves CAR T cell function in solid tumors	105
Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration	102
TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets	99
Ultrafast search of all deposited bacterial and viral genomic data	96
Precise gene replacement in rice by RNA transcript-templated homologous recombination	95
Overcoming genetic heterogeneity in industrial fermentations	94
Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing	94
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics	93
Real-time measurement of protein–protein interactions at single-molecule resolution using a biological nanopore	92
Self-organizing neuruloids model developmental aspects of Huntington’s disease in the ectodermal compartment	88
Rapid customization of Solanaceae fruit crops for urban agriculture	87
Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays	86
In vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma	85
Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces	85
Supercooling extends preservation time of human livers	82
Co-regulation map of the human proteome enables identification of protein functions	80
A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system	80
ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification	80
Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations	78
A DNA-of-things storage architecture to create materials with embedded memory	78
Spatial metagenomic characterization of microbial biogeography in the gut	77
Capturing sequence diversity in metagenomes with comprehensive and scalable probe design	77
Diagnostic kit for rice blight resistance	75
Engineered immune cells as highly sensitive cancer diagnostics	74