| # | Title | Journal | Year | Citations |
|---|
|
| 1 | Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns | Cell | 2017 | 466 |
| 2 | Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study | Lancet Oncology, The | 2020 | 411 |
| 3 | The presence and impact of reference bias on population genomic studies of prehistoric human populations | PLoS Genetics | 2019 | 156 |
| 4 | Automated Training of Deep Convolutional Neural Networks for Cell Segmentation | Scientific Reports | 2017 | 106 |
| 5 | Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses | Physical Review Letters | 2017 | 96 |
| 6 | Improved breast cancer histological grading using deep learning | Annals of Oncology | 2022 | 95 |
| 7 | High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking | Philosophical Transactions of the Royal Society B: Biological Sciences | 2013 | 87 |
| 8 | Coherent diffraction of single Rice Dwarf virus particles using hard X-rays at the Linac Coherent Light Source | Scientific Data | 2016 | 66 |
| 9 | Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses | IUCrJ | 2017 | 66 |
| 10 | Femtosecond X-ray Fourier holography imaging of free-flying nanoparticles | Nature Photonics | 2018 | 59 |
| 11 | Coherent soft X-ray diffraction imaging of coliphage PR772 at the Linac coherent light source | Scientific Data | 2017 | 55 |
| 12 | Fourth Generation of Next‐Generation Sequencing Technologies: Promise and Consequences | Human Mutation | 2016 | 53 |
| 13 | Electrospray sample injection for single-particle imaging with x-ray lasers | Science Advances | 2019 | 53 |
| 14 | Considerations for three-dimensional image reconstruction from experimental data in coherent diffractive imaging | IUCrJ | 2018 | 43 |
| 15 | An end-to-end workflow for multiplexed image processing and analysis | Nature Protocols | 2023 | 42 |
| 16 | Container-based bioinformatics with Pachyderm | Bioinformatics | 2019 | 37 |
| 17 | TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data | Bioinformatics | 2020 | 35 |
| 18 | A hybrid method for the imputation of genomic data in livestock populations | Genetics Selection Evolution | 2017 | 34 |
| 19 | TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish | Scientific Reports | 2019 | 34 |
| 20 | Hummingbird: monitoring and analyzing flash X-ray imaging experiments in real time | Journal of Applied Crystallography | 2016 | 32 |
| 21 | SynQuant: an automatic tool to quantify synapses from microscopy images | Bioinformatics | 2020 | 30 |
| 22 | Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio | Scientific Reports | 2015 | 27 |
| 23 | Artificial Intelligence for Diagnosis and Gleason Grading of Prostate Cancer in Biopsies—Current Status and Next Steps | European Urology Focus | 2021 | 25 |
| 24 | ImageJ and CellProfiler: Complements in Open‐Source Bioimage Analysis | Current Protocols | 2021 | 23 |
| 25 | Automated identification of the mouse brain’s spatial compartments from in situ sequencing data | BMC Biology | 2020 | 22 |
| 26 | Genes in human obesity loci are causal obesity genes in C. elegans | PLoS Genetics | 2021 | 22 |
| 27 | Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa | Scientific Reports | 2019 | 20 |
| 28 | Deep Learning With Conformal Prediction for Hierarchical Analysis of Large-Scale Whole-Slide Tissue Images | IEEE Journal of Biomedical and Health Informatics | 2021 | 19 |
| 29 | Regular Use of Depot Medroxyprogesterone Acetate Causes Thinning of the Superficial Lining and Apical Distribution of Human Immunodeficiency Virus Target Cells in the Human Ectocervix | Journal of Infectious Diseases | 2022 | 18 |
| 30 | Next-Generation Pathology—Surveillance of Tumor Microecology | Journal of Molecular Biology | 2015 | 17 |
| 31 | Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103−CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium | Journal of Infectious Diseases | 2018 | 16 |
| 32 | Ptychographic wavefront characterization for single-particle imaging at x-ray lasers | Optica | 2021 | 15 |
| 33 | Morphological Features Extracted by AI Associated with Spatial Transcriptomics in Prostate Cancer | Cancers | 2021 | 15 |
| 34 | Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability | PLoS ONE | 2015 | 15 |
| 35 | A deep learning framework for characterization of genotype data | G3: Genes, Genomes, Genetics | 2022 | 15 |
| 36 | Image Analysis in Digital Pathology: Combining Automated Assessment of Ki67 Staining Quality with Calculation of Ki67 Cell Proliferation Index | Cytometry Part A: the Journal of the International Society for Analytical Cytology | 2019 | 13 |
| 37 | Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists | F1000Research | 2021 | 13 |
| 38 | Scaling Predictive Modeling in Drug Development with Cloud Computing | Journal of Chemical Information and Modeling | 2015 | 12 |
| 39 | Multi-Parametric Field Experiment Links Explosive Activity and Persistent Degassing at Stromboli | Frontiers in Earth Science | 2021 | 12 |
| 40 | The broad role of Nkx3.2 in the development of the zebrafish axial skeleton | PLoS ONE | 2021 | 12 |
| 41 | Convolutional Neural Networks as Summary Statistics for Approximate Bayesian Computation | IEEE/ACM Transactions on Computational Biology and Bioinformatics | 2021 | 10 |
| 42 | Spatial Statistics for Understanding Tissue Organization | Frontiers in Physiology | 2022 | 10 |
| 43 | Biolmg.org: A Catalog of Virtual Machine Images for the Life Sciences | Bioinformatics and Biology Insights | 2015 | 9 |
| 44 | Quantitative image analysis of protein expression and colocalisation in skin sections | Experimental Dermatology | 2018 | 9 |
| 45 | Increased apoptosis, reduced Wnt/β-catenin signaling, and altered tail development in zebrafish embryos exposed to a human-relevant chemical mixture | Chemosphere | 2021 | 9 |
| 46 | Machine learning for cell classification and neighborhood analysis in glioma tissue | Cytometry Part A: the Journal of the International Society for Analytical Cytology | 2021 | 9 |
| 47 | PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data | PLoS ONE | 2016 | 9 |
| 48 | A method for Boolean analysis of protein interactions at a molecular level | Nature Communications | 2022 | 9 |
| 49 | Quantitative high‐content/high‐throughput microscopy analysis of lipid droplets in subject‐specific adipogenesis models | Cytometry Part A: the Journal of the International Society for Analytical Cytology | 2017 | 8 |
| 50 | Evaluating the utility of brightfield image data for mechanism of action prediction | PLoS Computational Biology | 2023 | 8 |
