| U-Net: deep learning for cell counting, detection, and morphometry |
151 |
| Species-level functional profiling of metagenomes and metatranscriptomes |
139 |
| Accurate detection of complex structural variations using single-molecule sequencing |
126 |
| ilastik: interactive machine learning for (bio) image analysis |
114 |
| fMRIPrep: a robust preprocessing pipeline for functional MRI |
114 |
| Fast, sensitive and accurate integration of single-cell data with Harmony |
104 |
| Strelka2: fast and accurate calling of germline and somatic variants |
102 |
| Deep generative modeling for single-cell transcriptomics |
93 |
| Highly parallel direct RNA sequencing on an array of nanopores |
92 |
| Acoustic tweezers for the life sciences |
90 |
| High-performance calcium sensors for imaging activity in neuronal populations and microcompartments |
82 |
| Deep learning enables cross-modality super-resolution in fluorescence microscopy |
78 |
| Content-aware image restoration: pushing the limits of fluorescence microscopy |
76 |
| Deep learning for cellular image analysis |
75 |
| Bias, robustness and scalability in single-cell differential expression analysis |
72 |
| Real-time cryo-electron microscopy data preprocessing with Warp |
72 |
| A comparison of methods to assess cell mechanical properties |
72 |
| Engineering of human brain organoids with a functional vascular-like system |
70 |
| Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments |
70 |
| High-definition spatial transcriptomics for in situ tissue profiling |
67 |
| Flow-enhanced vascularization and maturation of kidney organoids in vitro |
66 |
| SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information |
65 |
| STED super-resolved microscopy |
61 |
| SAVER: gene expression recovery for single-cell RNA sequencing |
60 |
| Qiita: rapid, web-enabled microbiome meta-analysis |
58 |
| Reliability of human cortical organoid generation |
58 |
| Machine-learning-guided directed evolution for protein engineering |
56 |
| scmap: projection of single-cell RNA -seq data across data sets |
53 |
| BoxCar acquisition method enables single-shot proteomics at a depth of 000 proteins in 100 minutes |
53 |
| Genetically engineered cerebral organoids model brain tumor formation |
51 |
| Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning |
51 |
| Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics |
50 |
| Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study |
48 |
| Fast interpolation-based t-SNE for improved visualization of single-cell RNA-seq data |
47 |
| Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells |
47 |
| Systematic characterization of maturation time of fluorescent proteins in living cells |
47 |
| Induction of myelinating oligodendrocytes in human cortical spheroids |
46 |
| Software tools for automated transmission electron microscopy |
46 |
| Fast animal pose estimation using deep neural networks |
45 |
| Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy |
45 |
| FRET as a biomolecular research tool-understanding its potential while avoiding pitfalls |
43 |
| Stability, affinity, and chromatic variants of the glutamate sensor iGluSnFR |
43 |
| Burden-driven feedback control of gene expression |
42 |
| A genetically encoded fluorescent sensor for in vivo imaging of GABA |
41 |
| Inferring single-trial neural population dynamics using sequential auto-encoders |
41 |
| Nanopore native RNA sequencing of a human poly(A) transcriptome |
41 |
| Super-resolution fight club: assessment of 2D and 3D single-molecule localization microscopy software |
40 |
| Nanoparticles for super-resolution microscopy and single-molecule tracking |
40 |
| FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data |
40 |
| An enhanced CRISPR repressor for targeted mammalian gene regulation |
40 |
| Expansion microscopy: principles and uses in biological research |
40 |
| Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution |
40 |
| Imaging cellular ultrastructures using expansion microscopy (U-ExM) |
40 |
| Three-photon imaging of mouse brain structure and function through the intact skull |
39 |
| Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction |
39 |
| Quantitative mapping and minimization of super-resolution optical imaging artifacts |
39 |
| Spatial organization of the somatosensory cortex revealed by osmFISH |
38 |
| DART-seq: an antibody-free method for global m(6)A detection |
37 |
| Using deep learning to model the hierarchical structure and function of a cell |
36 |
| An improved MS2 system for accurate reporting of the mRNA life cycle |
36 |
| Best practices and benchmarks for intact protein analysis for top-down mass spectrometry |
36 |
| High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis |
35 |
| Light-sheet microscopy in the near-infrared II window |
35 |
| CRISPR off-target analysis in genetically engineered rats and mice |
34 |
| Faster, sharper, and deeper: structured illumination microscopy for biological imaging |
34 |
| Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts |
34 |
| MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices |
33 |
| Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9 |
33 |
| Capturing the interactome of newly transcribed RNA |
33 |
| Automated, parallel mass spectrometry imaging and structural identification of lipids |
32 |
| RNA-protein interaction detection in living cells |
32 |
| Biological plasticity rescues target activity in CRISPR knock outs |
32 |
| Methods to study RNA-protein interactions |
32 |
| Supervised classification enables rapid annotation of cell atlases |
31 |
| SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues |
31 |
| A test metric for assessing single-cell RNA-seq batch correction |
31 |
| cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data |
31 |
| Supermultiplexed optical imaging and barcoding with engineered polyynes |
31 |
| A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue |
30 |
| Evaluation of variability in human kidney organoids |
30 |
| Brillouin microscopy: an emerging tool for mechanobiology |
29 |
| Kilohertz frame-rate two-photon tomography |
29 |
| Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments |
29 |
| The cryo-EM method microcrystal electron diffraction (MicroED) |
29 |
| Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl |
29 |
| A genetically encoded near-infrared fluorescent calcium ion indicator |
28 |
| Real-time 3D single-molecule localization using experimental point spread functions |
28 |
| Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry |
27 |
| Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling |
27 |
| A cheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms |
27 |
| A permanent window for the murine lung enables high-resolution imaging of cancer metastasis |
26 |
| NAMD goes quantum: an integrative suite for hybrid simulations |
26 |
| TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding |
26 |
| Nuclear pores as versatile reference standards for quantitative superresolution microscopy |
26 |
| Exploring single-cell data with deep multitasking neural networks |
26 |
| Real-time volumetric microscopy of in vivo dynamics and large-scale samples with SCAPE 2.0 |
25 |
| Deep generative models of genetic variation capture the effects of mutations |
25 |
| A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps |
24 |
| High-speed volumetric imaging of neuronal activity in freely moving rodents |
24 |
| Real-time fluorescence and deformability cytometry |
24 |
| Joint analysis of heterogeneous single-cell RNA-seq dataset collections |
23 |
| idtracker.ai: tracking all individuals in small or large collectives of unmarked animals |
23 |
| A robust and versatile platform for image scanning microscopy enabling super-resolution FLIM |
23 |
| Rapid and efficient induction of functional astrocytes from human pluripotent stem cells |
23 |
| Widespread bacterial protein histidine phosphorylation revealed by mass spectrometry-based proteomics |
23 |
| Single-cell chromatin immunocleavage sequencing (scChIC-seq) to profile histone modification |
23 |
| Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging |
22 |
| Cellular barcoding: lineage tracing, screening and beyond |
22 |
| Resolving systematic errors in widely used enhancer activity assays in human cells |
22 |
| Improved Ribo-seq enables identification of cryptic translation events |
22 |
| Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs |
22 |
| Assessment of network module identification across complex diseases |
22 |
| Parameter-free image resolution estimation based on decorrelation analysis |
22 |
| Engineered signaling centers for the spatially controlled patterning of human pluripotent stem cells |
21 |
| LADL: light-activated dynamic looping for endogenous gene expression control |
21 |
| Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution |
21 |
| An online resource for GPCR structure determination and analysis |
21 |
| Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling |
21 |
| Mapping the physical network of cellular interactions |
21 |
| Generation and post-injury integration of human spinal cord neural stem cells |
21 |
| On the design of CRISPR-based single-cell molecular screens |
21 |
| Unified rational protein engineering with sequence-based deep representation learning |
21 |
| Reducing effects of particle adsorption to the air-water interface in cryo-EM |
20 |
| Artifact-free high-density localization microscopy analysis |
20 |
| CMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules |
20 |
| Detecting repeated cancer evolution from multiregion tumor sequencing data |
20 |
| Self-interference 3D super-resolution microscopy for deep tissue investigations |
20 |
| Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning |
20 |
| Biological imaging of chemical bonds by stimulated Raman scattering microscopy |
20 |
| Data denoising with transfer learning in single-cell transcriptomics |
20 |
| High-density multi-fiber photometry for studying large-scale brain circuit dynamics |
20 |
| A pH-correctable, DNA-based fluorescent reporter for organellar calcium |
20 |
| Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins |
19 |
| In vivo RNA editing of point mutations via RNA-guided adenosine deaminases |
19 |
| BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples |
19 |
| Long-read sequence and assembly of segmental duplications |
19 |
| Metagenomic engineering of the mammalian gut microbiome in situ |
19 |
| CDeep3M-Plug-and-Play cloud-based deep learning for image segmentation |
19 |
| Laser phase plate for transmission electron microscopy |
19 |
| CRISPR-Sirius: RNA scaffolds for signal amplification in genome imaging |
19 |
| SpatialDE: identification of spatially variable genes |
19 |
| Learning representations of microbe-metabolite interactions |
19 |
| Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging |
18 |
| Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning |
18 |
| A proximity-tagging system to identify membrane protein-protein interactions |
18 |
| Efficient and precise editing of endogenous transcripts with SNAP-tagged ADARs |
18 |
| emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging |
18 |
| Identification of differentially methylated cell types in epigenome-wide association studies |
18 |
| BRCA-deficient mouse mammary tumor organoids to study cancer-drug resistance |
18 |
| The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue |
18 |
| High-precision automated reconstruction of neurons with flood-filling networks |
18 |
| FEAST: fast expectation-maximization for microbial source tracking |
17 |
| A synthetic-diploid benchmark for accurate variant-calling evaluation |
17 |
| An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions |
17 |
| Genome-wide SWAp-Tag yeast libraries for proteome exploration |
17 |
| Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution |
17 |
| Cell-type-specific and projection-specific brain-wide reconstruction of single neurons |
17 |
| Identification of spatial expression trends in single-cell gene expression data |
17 |
| Fast, in vivo voltage imaging using a red fluorescent indicator |
17 |
| C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2 |
17 |
| COMRADES determines in vivo RNA structures and interactions |
16 |
| T cell antigen discovery via trogocytosis |
16 |
| T cell antigen discovery via signaling and antigen-presenting bifunctional receptors |
16 |
| The GAGOme: a cell-based library of displayed glycosaminoglycans |
16 |
| Multicolor quantitative confocal imaging cytometry |
16 |
| Closed-loop all-optical interrogation of neural circuits in vivo |
16 |
| Mapping the 3D orientation of piconewton integrin traction forces |
16 |
| 4D functional ultrasound imaging of whole-brain activity in rodents |
15 |
| Liquid application method for time-resolved analyses by serial synchrotron crystallography |
15 |
| EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification |
15 |
| A human immune system mouse model with robust lymph node development |
15 |
| Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics |
15 |
| One-step generation of modular CAR-T cells with AAV-Cpf1 |
15 |
| An efficient auxin-inducible degron system with low basal degradation in human cells |
15 |
| Evaluating measures of association for single-cell transcriptomics |
15 |
| Reduced MEK inhibition preserves genomic stability in naive human embryonic stem cells |
15 |
| Trac-looping measures genome structure and chromatin accessibility |
15 |
| Analyzing complex single-molecule emission patterns with deep learning |
15 |
| NetSig: network-based discovery from cancer genomes |
15 |
| Aromatic F-19-C-13 TROSY: a background-free approach to probe biomolecular structure, function, and dynamics |
15 |
| A reassessment of DNA-immunoprecipitation-based genomic profiling |
14 |
| The hit-and-return system enables efficient time-resolved serial synchrotron crystallography |
14 |
| Detecting hierarchical genome folding with network modularity |
14 |
| Joint profiling of DNA methylation and chromatin architecture in single cells |
14 |
| Universal light-sheet generation with field synthesis |
14 |
| Multiplexed and single cell tracing of lipid metabolism |
14 |
| FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control |
14 |
| Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity |
13 |
| Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy |
13 |
| Instantaneous isotropic volumetric imaging of fast biological processes |
13 |
| Live imaging of mRNA using RNA-stabilized fluorogenic proteins |
13 |
| High throughput discovery of functional protein modifications by Hotspot Thermal Profiling |
13 |
| Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads |
13 |
| A hybridization-chain-reaction-based method for amplifying immunosignals |
13 |
| Imaging organoids: a bright future ahead |
13 |
| Biotinylation by antibody recognition-a method for proximity labeling |
13 |
| Organoids required! A new path to understanding human brain development and disease |
12 |
| Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure |
12 |
| Cell composition analysis of bulk genomics using single-cell data |
12 |
| GIGGLE: a search engine for large-scale integrated genome analysis |
12 |
