| 1 | Challenges and Opportunities in the Clinical Translation of High-Resolution Spatial Transcriptomics | 30.5 | 30 | Citations (PDF) |
| 2 | Scalable image-based visualization and alignment of spatial transcriptomics datasets | 5.8 | 6 | Citations (PDF) |
| 3 | JoVE Video Dataset 2024, , | | 0 | Citations (PDF) |
| 4 | Generation and Downstream Analysis of Single-Cell and Single-Nuclei Transcriptomes in Brain Organoids | 0.3 | 0 | Citations (PDF) |
| 5 | miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner | 5.2 | 21 | Citations (PDF) |
| 6 | Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure | 13.7 | 31 | Citations (PDF) |
| 7 | Rapid nuclear deadenylation of mammalian messenger RNA | 3.5 | 18 | Citations (PDF) |
| 8 | Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease | 28.6 | 275 | Citations (PDF) |
| 9 | Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche | 13.7 | 49 | Citations (PDF) |
| 10 | Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids | 16.0 | 89 | Citations (PDF) |
| 11 | Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN | 13.7 | 19 | Citations (PDF) |
| 12 | SLAM‐Drop
‐seq reveals
mRNA
kinetic rates throughout the cell cycle | 6.7 | 25 | Citations (PDF) |
| 13 | Spatiotemporal, optogenetic control of gene expression in organoids | 24.6 | 78 | Citations (PDF) |
| 14 | Expression of Circ_Satb1 Is Decreased in Mesial Temporal Lobe Epilepsy and Regulates Dendritic Spine Morphology | 3.4 | 24 | Citations (PDF) |
| 15 | Optocoder: computational decoding of spatially indexed bead arrays | 2.2 | 1 | Citations (PDF) |
| 16 | Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury | 9.6 | 100 | Citations (PDF) |
| 17 | Spacemake: processing and analysis of large-scale spatial transcriptomics data | 3.2 | 30 | Citations (PDF) |
| 18 | Cell type diversity in a developing octopus brain | 13.7 | 77 | Citations (PDF) |
| 19 | MicroRNAs are deeply linked to the emergence of the complex octopus brain | 10.9 | 44 | Citations (PDF) |
| 20 | Long-term imaging reveals behavioral plasticity during C. elegans dauer exit | 3.9 | 6 | Citations (PDF) |
| 21 | Kidney Single-cell Transcriptomes Predict Spatial Corticomedullary Gene Expression and Tissue Osmolality Gradients | 0.4 | 39 | Citations (PDF) |
| 22 | Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome | 13.7 | 116 | Citations (PDF) |
| 23 | Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy | 3.5 | 263 | Citations (PDF) |
| 24 | Parallel genetics of regulatory sequences using scalable genome editing in vivo | 6.3 | 15 | Citations (PDF) |
| 25 | Generation of Human Brain Organoids for Mitochondrial Disease Modeling | 0.3 | 5 | Citations (PDF) |
| 26 | NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport | 14.4 | 128 | Citations (PDF) |
| 27 | Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy | 3.8 | 12 | Citations (PDF) |
| 28 | Generation of Human Brain Organoids for Mitochondrial Disease Modeling | 0.3 | 0 | Citations (PDF) |
| 29 | Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts | 15.5 | 99 | Citations (PDF) |
| 30 | A Highly Conserved Circular RNA Is Required to Keep Neural Cells in a Progenitor State in the Mammalian Brain | 6.3 | 81 | Citations (PDF) |
| 31 | Tracing tumorigenesis in a solid tumor model at single-cell resolution | 13.7 | 55 | Citations (PDF) |
| 32 | The transcriptome dynamics of single cells during the cell cycle | 6.7 | 82 | Citations (PDF) |
| 33 | Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data | 2.6 | 24 | Citations (PDF) |
| 34 | Resolving the Kidney’s Reaction to Acute Dehydration on the Single-Cell Level | 0.4 | 0 | Citations (PDF) |
| 35 | Roles of Long Noncoding RNAs and Circular RNAs in Translation | 7.2 | 44 | Citations (PDF) |
| 36 | FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control | 24.6 | 179 | Citations (PDF) |
| 37 | Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program | 13.7 | 145 | Citations (PDF) |
| 38 | Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat | 4.6 | 18 | Citations (PDF) |
| 39 | Identification of proteins and miRNAs that specifically bind an mRNA in vivo | 13.7 | 35 | Citations (PDF) |
| 40 | The Translational Landscape of the Human HeartCell, 2019, 178, 242-260.e29 | 33.6 | 599 | Citations (PDF) |
| 41 | PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells | 8.1 | 1,618 | Citations (PDF) |
| 42 | Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7 | 13.7 | 48 | Citations (PDF) |
| 43 | Gene expression cartography | 37.9 | 303 | Citations (PDF) |
| 44 | Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics | 36.3 | 481 | Citations (PDF) |
| 45 | Post-transcriptional Regulation by 3′ UTRs Can Be Masked by Regulatory Elements in 5′ UTRs | 6.3 | 29 | Citations (PDF) |
| 46 | Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo | 6.6 | 36 | Citations (PDF) |
| 47 | Spatiotemporal m(i)RNA Architecture and 3′ UTR Regulation in the C. elegans Germline | 7.7 | 54 | Citations (PDF) |
| 48 | Single-Cell Transcriptomics Characterizes Cell Types in the Subventricular Zone and Uncovers Molecular Defects Impairing Adult Neurogenesis | 6.3 | 205 | Citations (PDF) |
| 49 | A Single-Cell Transcriptome Atlas of the Mouse Glomerulus | 0.4 | 167 | Citations (PDF) |
| 50 | RCAS: an RNA centric annotation system for transcriptome-wide regions of interest | 15.5 | 30 | Citations (PDF) |
| 51 | RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation | 3.8 | 23 | Citations (PDF) |
| 52 | Circ-ZNF609 Is a Circular RNA that Can Be Translated and Functions in Myogenesis | 13.3 | 2,022 | Citations (PDF) |
| 53 | Translation of CircRNAs | 13.3 | 1,752 | Citations (PDF) |
| 54 | A map of human circular RNAs in clinically relevant tissues | 3.7 | 348 | Citations (PDF) |
| 55 | The
Drosophila
embryo at single-cell transcriptome resolution | 36.3 | 434 | Citations (PDF) |
| 56 | RNA localization is a key determinant of neurite-enriched proteome | 13.7 | 241 | Citations (PDF) |
| 57 | Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function | 36.3 | 1,198 | Citations (PDF) |
| 58 | Cell fixation and preservation for droplet-based single-cell transcriptomics | 3.9 | 227 | Citations (PDF) |
| 59 | Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection | 8.1 | 53 | Citations (PDF) |
| 60 | The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex | 8.1 | 218 | Citations (PDF) |
| 61 | Epigenetic dynamics of monocyte-to-macrophage differentiation | 3.2 | 90 | Citations (PDF) |
| 62 | Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development | 22.6 | 199 | Citations (PDF) |
| 63 | The Lupus Autoantigen La Prevents Mis-channeling of tRNA Fragments into the Human MicroRNA Pathway | 13.3 | 128 | Citations (PDF) |
| 64 | Identification and Characterization of Circular RNAs As a New Class of Putative Biomarkers in Human Blood | 2.3 | 617 | Citations (PDF) |
| 65 | DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation | 15.5 | 145 | Citations (PDF) |
| 66 | microRNAs Regulate Cell-to-Cell Variability of Endogenous Target Gene Expression in Developing Mouse Thymocytes | 3.2 | 25 | Citations (PDF) |
| 67 | Circular RNAs in the Mammalian Brain Are Highly Abundant, Conserved, and Dynamically Expressed | 13.3 | 2,339 | Citations (PDF) |
| 68 | Extensive identification and analysis of conserved small ORFs in animals | 8.1 | 223 | Citations (PDF) |
| 69 | miR‐148a is upregulated by Twist1 and T‐bet and promotes Th1‐cell survival by regulating the proapoptotic gene Bim | 3.1 | 65 | Citations (PDF) |
| 70 | Paternal Diet Defines Offspring Chromatin State and Intergenerational ObesityCell, 2014, 159, 1352-1364 | 33.6 | 403 | Citations (PDF) |
| 71 | Binding site discovery from nucleic acid sequences by discriminative learning of hidden Markov models | 15.5 | 25 | Citations (PDF) |
| 72 | Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation | 7.3 | 680 | Citations (PDF) |
| 73 | Unambiguous Identification of miRNA:Target Site Interactions by Different Types of Ligation Reactions | 13.3 | 295 | Citations (PDF) |
| 74 | A Variety of Dicer Substrates in Human and C. elegansCell, 2014, 159, 1153-1167 | 33.6 | 116 | Citations (PDF) |
| 75 | circBase: a database for circular RNAs | 3.8 | 1,727 | Citations (PDF) |
| 76 | circRNA Biogenesis Competes with Pre-mRNA Splicing | 13.3 | 2,960 | Citations (PDF) |
| 77 | Paternal
RNA
contributions in the
Caenorhabditis elegans
zygote | 7.3 | 74 | Citations (PDF) |
| 78 | Conservation of mRNA and Protein Expression during Development of C. elegans | 6.3 | 118 | Citations (PDF) |
| 79 | Competition between target sites of regulators shapes post-transcriptional gene regulation | 46.9 | 255 | Citations (PDF) |
| 80 | RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing | 10.6 | 224 | Citations (PDF) |
| 81 | Circular RNAs are a large class of animal RNAs with regulatory potency | 37.9 | 7,572 | Citations (PDF) |
| 82 | Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation | 3.3 | 85 | Citations (PDF) |
| 83 | The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation | 3.2 | 31 | Citations (PDF) |
| 84 | doRiNA: a database of RNA interactions in post-transcriptional regulation | 15.5 | 195 | Citations (PDF) |
| 85 | miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades | 15.5 | 3,255 | Citations (PDF) |
| 86 | The SNF2‐like helicase HELLS mediates E2F3‐dependent transcription and cellular transformation | 7.3 | 78 | Citations (PDF) |
| 87 | Gene expression of pluripotency determinants is conserved between mammalian and planarian stem cells | 7.3 | 152 | Citations (PDF) |
| 88 | Select microRNAs are essential for early development in the sea urchin | 1.9 | 63 | Citations (PDF) |
| 89 | Transcriptome-wide Analysis of Regulatory Interactions of the RNA-Binding Protein HuR | 13.3 | 716 | Citations (PDF) |
| 90 | microRNAs and the Operon Paper | 4.1 | 15 | Citations (PDF) |
| 91 | In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target Sites | 13.3 | 153 | Citations (PDF) |
| 92 | De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics | 4.6 | 102 | Citations (PDF) |
| 93 | The Impact of miRNA Target Sites in Coding Sequences and in 3′UTRs | 2.3 | 273 | Citations (PDF) |
| 94 | Correlating Gene Expression Variation with cis-Regulatory Polymorphism in Saccharomyces cerevisiae | 2.4 | 31 | Citations (PDF) |
| 95 | Deciphering the porcine intestinal microRNA transcriptome | 3.3 | 73 | Citations (PDF) |
| 96 | The microRNA miR-182 is induced by IL-2 and promotes clonal expansion of activated helper T lymphocytes | 23.5 | 315 | Citations (PDF) |
| 97 | Integrative Analysis of the
Caenorhabditis elegans
Genome by the modENCODE Project | 36.3 | 1,014 | Citations (PDF) |
| 98 | High-resolution profiling and discovery of planarian small RNAs | 7.5 | 131 | Citations (PDF) |
| 99 | Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression | 24.6 | 101 | Citations (PDF) |
| 100 | Reexamining microRNA Site Accessibility in Drosophila: A Population Genomics Study | 2.3 | 14 | Citations (PDF) |
| 101 | A Human snoRNA with MicroRNA-Like Functions | 13.3 | 806 | Citations (PDF) |
| 102 | Widespread changes in protein synthesis induced by microRNAs | 37.9 | 3,269 | Citations (PDF) |
| 103 | Discovering microRNAs from deep sequencing data using miRDeep | 29.8 | 1,180 | Citations (PDF) |
| 104 | Dicer Ablation Affects Antibody Diversity and Cell Survival in the B Lymphocyte Lineage | 33.6 | 567 | Citations (PDF) |
| 105 | MiR-150 Controls B Cell Differentiation by Targeting the Transcription Factor c-Myb | 33.6 | 1,016 | Citations (PDF) |
| 106 | The evolution of gene regulation by transcription factors and microRNAs | 46.9 | 1,457 | Citations (PDF) |
| 107 | Natural selection on human microRNA binding sites inferred from SNP data | 25.2 | 444 | Citations (PDF) |
| 108 | A Genome-Wide Map of Conserved MicroRNA Targets in C. elegans | 3.6 | 401 | Citations (PDF) |
| 109 | Cell-type-specific signatures of microRNAs on target mRNA expression | 7.5 | 626 | Citations (PDF) |
| 110 | Combinatorial microRNA target predictions | 25.2 | 4,403 | Citations (PDF) |
| 111 | Silencing of microRNAs in vivo with ‘antagomirs’ | 37.9 | 3,879 | Citations (PDF) |
| 112 | microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets | 3.1 | 404 | Citations (PDF) |
| 113 | Title is missing! | 12.2 | 408 | Citations (PDF) |
| 114 | A cis element in the recombination activating gene locus regulates gene expression by counteracting a distant silencer | 23.5 | 77 | Citations (PDF) |
| 115 | A pancreatic islet-specific microRNA regulates insulin secretion | 37.9 | 2,038 | Citations (PDF) |
| 116 | Transcriptional Control in the Segmentation Gene Network of Drosophila | 5.0 | 225 | Citations (PDF) |
| 117 | Survival of Resting Mature B Lymphocytes Depends on BCR Signaling via the Igα/β Heterodimer | 33.6 | 555 | Citations (PDF) |
| 118 | Computational identification of microRNA targets | 1.9 | 284 | Citations (PDF) |
| 119 | Title is missing! | 12.2 | 14 | Citations (PDF) |
| 120 | Title is missing! | 3.0 | 84 | Citations (PDF) |
| 121 | Decay Rates of Human mRNAs: Correlation With Functional Characteristics and Sequence Attributes | 4.6 | 543 | Citations (PDF) |
| 122 | Probabilistic clustering of sequences: Inferring new bacterial regulons by comparative genomics | 7.5 | 59 | Citations (PDF) |
| 123 | Title is missing! | 3.0 | 194 | Citations (PDF) |
| 124 | The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons | 4.6 | 88 | Citations (PDF) |
| 125 | Circadian Regulation of Gene Expression Systems in the Drosophila Head | 11.0 | 461 | Citations (PDF) |
| 126 | A Probabilistic Cellular Automaton for Evolution | 1.0 | 2 | Citations (PDF) |
| 127 | Timing, Genetic Requirements and Functional Consequences of Somatic Hypermutation during B-Cell Development | 6.4 | 237 | Citations (PDF) |
| 128 | Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians | 0.7 | 62 | Citations (PDF) |
| 129 | miRNA regulation in brain tissue space: the 3′UTR perspective | 3.8 | 1 | Citations (PDF) |
| 130 | The history and function of a circular RNA | 13.7 | 0 | Citations (PDF) |
