| Integrating single-cell transcriptomic data across different conditions, technologies, and species |
927 |
| SignalP 5.0 improves signal peptide predictions using deep neural networks |
440 |
| A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life |
368 |
| Dimensionality reduction for visualizing single-cell data using UMAP |
326 |
| Wearable biosensors for healthcare monitoring |
278 |
| Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype |
267 |
| Repair of double-strand breaks induced by CRISPR-Cas9 leads to large deletions and complex rearrangements |
202 |
| Nanopore sequencing and assembly of a human genome with ultra-long reads |
191 |
| A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo |
173 |
| Assembly of long, error-prone reads using repeat graphs |
163 |
| Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors |
149 |
| A comparison of single-cell trajectory inference methods |
136 |
| Biopharmaceutical benchmarks 2018 |
134 |
| Determining cell type abundance and expression from bulk tissues with digital cytometry |
116 |
| An in vivo model of functional and vascularized human brain organoids |
106 |
| Targeted delivery of a PD-1-blocking scFv by CAR-T cells enhances anti-tumor efficacy in vivo |
105 |
| A CRISPR-Cas9 gene drive targeting doublesex causes complete population suppression in caged Anopheles gambiae mosquitoes |
100 |
| Human embryonic stem cell-derived cardiomyocytes restore function in infarcted hearts of non-human primates |
97 |
| Efficient proximity labeling in living cells and organisms with TurboID |
96 |
| Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain |
91 |
| Improving cytidine and adenine base editors by expression optimization and ancestral reconstruction |
90 |
| Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients |
82 |
| Deep learning enables rapid identification of potent DDR1 kinase inhibitors |
78 |
| Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome |
77 |
| NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice |
75 |
| De novo domestication of wild tomato using genome editing |
75 |
| Enhancing T cell therapy through TCR-signaling-responsive nanoparticle drug delivery |
74 |
| Multiplexed droplet single-cell RNA-sequencing using natural genetic variation |
74 |
| Phase 1 clinical study of an embryonic stem cell-derived retinal pigment epithelium patch in age-related macular degeneration |
74 |
| Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain |
73 |
| Predicting the mutations generated by repair of Cas9-induced double-strand breaks |
70 |
| Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing |
70 |
| IL-7 and CCL19 expression in CAR-T cells improves immune cell infiltration and CAR-T cell survival in the tumor |
70 |
| Recon3D enables a three-dimensional view of gene variation in human metabolism |
61 |
| Adenine base editing in mouse embryos and an adult mouse model of Duchenne muscular dystrophy |
61 |
| Fast, long-term, super-resolution imaging with Hessian structured illumination microscopy |
60 |
| An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities |
60 |
| Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars |
59 |
| CAR-T cells secreting BiTEs circumvent antigen escape without detectable toxicity |
58 |
| Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria |
58 |
| A universal SNP and small-indel variant caller using deep neural networks |
58 |
| Deep learning massively accelerates super-resolution localization microscopy |
57 |
| Domestication of wild tomato is accelerated by genome editing |
56 |
| Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion |
56 |
| Base editing with a Cpf1-cytidine deaminase fusion |
56 |
| A highly specific SpCas9 variant is identified by in vivo screening in yeast |
56 |
| Toward a new generation of smart skins |
55 |
| Deep learning in biomedicine |
54 |
| Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection |
52 |
| Accessing analytes in biofluids for peripheral biochemical monitoring |
51 |
| Breeding crops to feed 10 billion |
51 |
| In vivo molecular imaging for immunotherapy using ultra-bright near-infrared-IIb rare-earth nanoparticles |
51 |
| Rhizoshere microbiome structure alters to enable wilt resistance in tomato |
51 |
| Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection |
51 |
| CRISPR DNA base editors with reduced RNA off-target and self-editing activities |
50 |
| 520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses |
50 |
| Efficient C-to-T base editing in plants using a fusion of nCas9 and human APOBEC3A |
50 |
| Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells |
49 |
| Tubuloids derived from human adult kidney and urine for personalized disease modeling |
49 |
| Increasing the specificity of CRISPR systems with engineered RNA secondary structures |
49 |
| Delivery of mRNA vaccines with heterocyclic lipids increases anti-tumor efficacy by STING-mediated immune cell activation |
48 |
| Broad-spectrum resistance to bacterial blight in rice using genome editing |
48 |
| A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells |
47 |
| Random access in large-scale DNA data storage |
46 |
| A human gut bacterial genome and culture collection for improved metagenomic analyses |
45 |
| Optimized base editors enable efficient editing in cells, organoids and mice |
44 |
| A genetically encoded fluorescent acetylcholine indicator for in vitro and in vivo studies |
44 |
| Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS) |
44 |
| Multi-omic measurements of heterogeneity in HeLa cells across laboratories |
44 |
| Scaffolds that mimic antigen-presenting cells enable ex vivo expansion of primary T cells |
43 |
| Metabolomics activity screening for identifying metabolites that modulate phenotype |
43 |
| Continuous evolution of base editors with expanded target compatibility and improved activity |
42 |
| Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks |
42 |
| Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine |
41 |
| Compendium of 941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery |
41 |
| Minimum Information about an Uncultivated Virus Genome (MIUViG) |
40 |
| Resistance gene cloning from a wild crop relative by sequence capture and association genetics |
40 |
| Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility |
39 |
| Efficient integration of heterogeneous single-cell transcriptomes using Scanorama |
38 |
| Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors |
38 |
| De novo assembly of haplotype-resolved genomes with trio binning |
37 |
| Visualizing structure and transitions in high-dimensional biological data |
35 |
| Specification of positional identity in forebrain organoids |
35 |
| Efficient generation of targeted large insertions by microinjection into two-cell-stage mouse embryos |
35 |
| Deep learning improves prediction of CRISPR-Cpf1 guide RNA activity |
35 |
| Variation graph toolkit improves read mapping by representing genetic variation in the reference |
35 |
| Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues |
34 |
| Intron retention is a source o neoepitopes in cancer |
34 |
| Linear assembly of a human centromere on the Y chromosome |
34 |
| Evaluation of 000 synthetic sequences reveals design principles to optimize translation in Escherichia coli |
34 |
| Targeted isolation and cultivation of uncultivated bacteria by reverse genomics |
33 |
| One-step genome editing of elite crop germplasm during haploid induction |
33 |
| Efficient base editing in methylated regions with a human APOBEC3A-Cas9 fusion |
33 |
| Blood metabolome predicts gut microbiome alpha-diversity in humans |
33 |
| Design of stapled antimicrobial peptides that are stable, nontoxic and kill antibiotic-resistant bacteria in mice |
32 |
| Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification |
32 |
| Photosynthetic artificial organelles sustain and control ATP-dependent reactions in a protocellular system |
32 |
| Gene editing for immune cell therapies |
32 |
| Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia |
32 |
| Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution |
32 |
| Chemical modification of PS-ASO therapeutics reduces cellular protein-binding and improves the therapeutic index |
32 |
| Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes |
31 |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell |
31 |
| Genome-wide target specificity of CRISPR RNA-guided adenine base editors |
31 |
| Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens |
29 |
| Characterization of cell fate probabilities in single-cell data with Palantir |
29 |
| An open resource for accurately benchmarking small variant and reference calls |
29 |
| Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration |
29 |
| Reversal of indoleamine 3-dioxygenase-mediated cancer immune suppression by systemic kynurenine depletion with a therapeutic enzyme |
29 |
| Regenerating the field of cardiovascular cell therapy |
29 |
| High-throughput determination of the antigen specificities of T cell receptors in single cells |
29 |
| Antigen-specific therapeutic approaches for autoimmunity |
28 |
| Clonal seeds from hybrid rice by simultaneous genome engineering of meiosis and fertilization genes |
28 |
| Best practices for benchmarking germline small-variant calls in human genomes |
27 |
| Engineered promoters enable constant gene expression at any copy number in bacteria |
27 |
| Inhibition of 53BP1 favors homology-dependent DNA repair and increases CRISPR-Cas9 genome-editing efficiency |
26 |
| Precise RNA editing by recruiting endogenous ADARs with antisense oligonucleotides |
26 |
| Next-generation interfaces for studying neural function |
25 |
| Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures |
25 |
| Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes |
24 |
| Predicting HLA class II antigen presentation through integrated deep learning |
24 |
| Precision mouse models with expanded tropism for human pathogens |
24 |
| Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs |
24 |
| Highly scalable generation of DNA methylation profiles in single cells |
24 |
| Highly efficient expression of circular RNA aptamers in cells using autocatalytic transcripts |
24 |
| Sugar release and growth of biofuel crops are improved by downregulation of pectin biosynthesis |
24 |
| TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets |
23 |
| Protection of tissue physicochemical properties using polyfunctional crosslinkers |
23 |
| Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells |
23 |
| Engineered immune cells as highly sensitive cancer diagnostics |
22 |
| De novo DNA synthesis using polymerase-nucleotide conjugates |
22 |
| Engineered toxin-intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations |
21 |
| Overcoming genetic heterogeneity in industrial fermentations |
21 |
| Genome-scale engineering of Saccharomyces cerevisiae with single-nucleotide precision |
21 |
| NFIA is a gliogenic switch enabling rapid derivation of functional human astrocytes from pluripotent stem cells |
21 |
| Multiplexed precision genome editing with trackable genomic barcodes in yeast |
20 |
| ClampFISH detects indivicual nucleic acid molecules using click chemistry-based amplification |
20 |
| Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays |
20 |
| Probing and engineering liquid-phase organelles |
20 |
| Dual gene activation and knockout screen reveals directional dependencies in genetic networks |
20 |
| Co-regulation map of the human proteome enables identification of protein functions |
19 |
| Phage combination therapies for bacterial wilt disease in tomato |
19 |
| Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs |
19 |
| Capturing sequence diversity in metagenomes with comprehensive and scalable probe design |
19 |
| RNAi modulation of placental sFLT1 for the treatment of preeclampsia |
18 |
| T cell receptor fingerprinting enables in-death characterization of the interactions governing recognition of peptide-MHC complexes |
18 |
| Deep learning is combined with massive-scale citizen science to improve large-scale image classification |
18 |
| In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma |
18 |
| Functional interrogation and mining of natively paired human V-H: V-L antibody repertoires |
17 |
| Precise, automated control of conditions for high-throughput growth of yeast and bacteria with eVOLVER |
17 |
| Emerging technologies for improved deep brain stimulation |
17 |
| Genome-wide screening for functional long noncocing RNAs in human cells by Cas9 targeting of splice sites |
17 |
| An injectable bone marrow-like scaffold enhances T cell immunity after hematopoietic stem cell transplantation |
17 |
| Adenine base editors catalyze cytosine conversions in human cells |
17 |
| Supercooling extends preservation time of human livers |
17 |
| Global landscape of cell envelope protein complexes in Escherichia coli |
17 |
| High-throughput creation and functional profiling of DNA sequence variant libraries using CRISPR-Cas9 in yeast |
17 |
| Secure genome-wide association analysis using multiparty computation |
16 |
| A divalent siRNA chemical scaffold for potent and sustained modulation of gene expression throughout the central nervous system |
16 |
| Comprehensive multi-center assessment of small RNA-seq methods for quantitative miRNA profiling |
16 |
| A highly soluble Sleeping Beauty transposase improves control of gene insertion |
16 |
| Precise gene replacement in rice by RNA transcript-templated homologous recombination |
16 |
| Simultaneous quantification of protein-DNA contacts and transcriptomes in single cells |
16 |
| Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage |
15 |
| Synthetic evolution |
15 |
| Real-time measurement of protein-protein interactions at single-molecule resolution using a biological nanopore |
15 |
| High-quality genome sequences of uncultured microbes by assembly of read clouds |
15 |
| De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans |
15 |
| Self-organizing neuruloids model developmental aspects of Huntington's disease in the ectodermal compartment |
15 |
| Precision electronic medicine in the brain |
14 |
| Spatial metagenomic characterization of microbial biogeography in the gut |
14 |
| Multiplexed identification, quantification and genotyping of infectious agents using a semiconductor biochip |
14 |
| Biofortification of field-grown cassava by engineering expression of an iron transporter and ferritin |
14 |
| Meganuclease targeting of PCSK9 in macaque liver leads to stable reduction in serum cholesterol |
14 |
| Mood variations decoded from multi-site intracranial human brain activity |
14 |
| Harnessing type I CRISPR-Cas systems for genome engineering in human cells |
14 |
| Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias |
14 |
| Diagnostic kit for rice blight resistance |
13 |
| Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells |
13 |
| Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells |
13 |
| Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase |
13 |
| Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation |
13 |
| Data storage in DNA with fewer synthesis cycles using composite DNA letters |
12 |
| A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity |
12 |
| Ultrafast search of all deposited bacterial and viral genomic data |
12 |
| Inferring population dynamics from single-cell RNA-sequencing time series data |
12 |
| Human 5 ' UTR design and variant effect prediction from a massively parallel translation assay |
11 |
| Enhancing gene editing specificity by attenuating DNA cleavage kinetics |
11 |
| Reversal of siRNA - mediated gene silencing in vivo |
11 |
| Precision oncology in the age of integrative genomics |
11 |
| Virus stamping for targeted single-cell infection in vitro and in vivo |
11 |
| Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data |
10 |
| Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice |
10 |
| Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells |
10 |
| Integrated genomic profiling expands clinical options for patients with cancer |
10 |
| On-demand manufacturing of clinical-quality biopharmaceuticals |
10 |
| Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing |
10 |
| Labeling and identifying celltype-specific proteomes in the mouse brain |
10 |
| An oncolytic herpesvirus expressing E-cacherin improves survival in mouse models of glioblastoma |
9 |
| Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass |
9 |
