Citation Impact
Citing Papers
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
2016
HTSeq—a Python framework to work with high-throughput sequencing data
2014 Standout
Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility
2021 StandoutNobel
A sex-biased imbalance between Tfr, Tph, and atypical B cells determines antibody responses in COVID-19 patients
2023 StandoutNobel
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
2014 Standout
Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model
2019
Single-cell immunology of SARS-CoV-2 infection
2021
A survey of best practices for RNA-seq data analysis
2016 Standout
Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data
2018
Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions
2021 StandoutNobel
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
2019 Standout
Inference and analysis of cell-cell communication using CellChat
2021 Standout
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
2013
Computationally designed sensors detect endogenous Ras activity and signaling effectors at subcellular resolution
2024 StandoutNobel
The promise and challenge of therapeutic genome editing
2020 StandoutNatureNobel
Cobolt: integrative analysis of multimodal single-cell sequencing data
2021
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
2016
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
2019
Polyester : simulating RNA-seq datasets with differential transcript expression
2015
Determining cell type abundance and expression from bulk tissues with digital cytometry
2019 Standout
Merkel Cells Activate Sensory Neural Pathways through Adrenergic Synapses
2018 StandoutNobel
SC3: consensus clustering of single-cell RNA-seq data
2017
Catalytically Active Cas9 Mediates Transcriptional Interference to Facilitate Bacterial Virulence
2019 StandoutNobel
Single-cell RNA-seq denoising using a deep count autoencoder
2019
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes
2017 StandoutNobel
Genome-guided transcript assembly by integrative analysis of RNA sequence data
2014
INMEX—a web-based tool for integrative meta-analysis of expression data
2013
Multi-omics approaches to disease
2017
RNA-based recognition and targeting: sowing the seeds of specificity
2017 StandoutNobel
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
2019 Standout
Hallmarks of aging: An expanding universe
2023 Standout
Injury Induces Endogenous Reprogramming and Dedifferentiation of Neuronal Progenitors to Multipotency
2017
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors
2018
Revealing the vectors of cellular identity with single-cell genomics
2016
SCnorm: robust normalization of single-cell RNA-seq data
2017
Integrating single-cell transcriptomic data across different conditions, technologies, and species
2018 Standout
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
2019
Dictionary learning allows model-free pseudotime estimation of transcriptomic data
2022
Genome editing reveals a role for OCT4 in human embryogenesis
2017 Nature
Salmon provides fast and bias-aware quantification of transcript expression
2017 Standout
The single-cell transcriptional landscape of mammalian organogenesis
2019 StandoutNature
Optimizing exosomal RNA isolation for RNA-Seq analyses of archival sera specimens
2018
Computational and analytical challenges in single-cell transcriptomics
2015
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
2012
Dynamical features of thePlasmodium falciparumribosome during translation
2015 StandoutNobel
The use of miRNA microarrays for the analysis of cancer samples with global miRNA decrease
2013
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
2019 Standout
Comprehensive literature review and statistical considerations for microarray meta-analysis
2012
Deep generative modeling for single-cell transcriptomics
2018
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues
2021
Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells
2014
Lipid-droplet-accumulating microglia represent a dysfunctional and proinflammatory state in the aging brain
2020 StandoutNobel
Robust enumeration of cell subsets from tissue expression profiles
2015 Standout
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
2015 Standout
A comparison of single-cell trajectory inference methods
2019
A benchmark for RNA-seq quantification pipelines
2016
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories
2013
Broadening horizons: the role of ferroptosis in cancer
2021 Standout
Heterogeneous Effects of Direct Hypoxia Pathway Activation in Kidney Cancer
2015 StandoutNobel
svaseq: removing batch effects and other unwanted noise from sequencing data
2014
Power analysis of single-cell RNA-sequencing experiments
2017
Dictionary learning for integrative, multimodal and scalable single-cell analysis
2023 Standout
limma powers differential expression analyses for RNA-sequencing and microarray studies
2015 Standout
Long-Term Expansion of Functional Mouse and Human Hepatocytes as 3D Organoids
2018 StandoutNobel
HTR7 Mediates Serotonergic Acute and Chronic Itch
2015
Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer
2017 Standout
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
2012
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation
2016
Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy
2017 Standout
Field-resolved infrared spectroscopy of biological systems
2020 StandoutNatureNobel
Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
2019
Comprehensive Integration of Single-Cell Data
2019 Standout
STAR NET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data
2009
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
2016 Nature
Predictive models of subcellular localization of long RNAs
2019
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
2013
Stem cell-derived polarized hepatocytes
2020 StandoutNobel
Gene regulation by long non-coding RNAs and its biological functions
2020 Standout
Small RNAs are modified with N-glycans and displayed on the surface of living cells
2021 StandoutNobel
N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions
2015 StandoutNature
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
2015
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19
2020 Standout
Missing data and technical variability in single-cell RNA-sequencing experiments
2017
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
2015 Standout
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system
2016 StandoutNobel
Cell lineage and communication network inference via optimization for single-cell transcriptomics
2019
The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads
2019 Standout
MMAD: microarray microdissection with analysis of differences is a computational tool for deconvoluting cell type-specific contributions from tissue samples
2013
Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models
2021
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series
2014
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest
2022 Standout
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis
2018 Standout
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
2018 Standout
A systematic dissection of determinants and consequences of snoRNA-guided pseudouridylation of human mRNA
2022 StandoutNobel
Polysome profiling reveals translational control of gene expression in the human malaria parasite Plasmodium falciparum
2013
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
2012
Multi-omics enrichment analysis using the GeneTrail2 web service
2016
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
2013 Standout
TraV: A Genome Context Sensitive Transcriptome Browser
2014
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights
2021 Standout
Extracellular microRNAs in human circulation are associated with miRISC complexes that are accessible to anti-AGO2 antibody and can bind target mimic oligonucleotides
2020 StandoutNobel
Works of Davide Risso being referenced
Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
2018
A general and flexible method for signal extraction from single-cell RNA-seq data
2018
A-MADMAN: Annotation-based microarray data meta-analysis tool
2009
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
2015
Normalization of RNA-seq data using factor analysis of control genes or samples
2014
Silencing of Odorant Receptor Genes by G Protein βγ Signaling Ensures the Expression of One Odorant Receptor per Olfactory Sensory Neuron
2014
Orchestrating single-cell analysis with Bioconductor
2019
GC-Content Normalization for RNA-Seq Data
2011
mbkmeans: Fast clustering for single cell data using mini-batch k-means
2021
Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq
2019
Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications
2018
Normalizing single-cell RNA sequencing data: challenges and opportunities
2017
Deconstructing Olfactory Stem Cell Trajectories at Single-Cell Resolution
2017
Rapid non-uniform adaptation to conformation-specific KRAS(G12C) inhibition
2020 Nature
A comparison on effects of normalisations in the detection of differentially expressed genes
2009
A modified LOESS normalization applied to microRNA arrays: a comparative evaluation
2009