Simon Anders
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Computer Science
Simon Anders's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science University of California, Berkeley
- Bachelors Computer Science University of California, Berkeley
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(Suggest an Edit or Addition)Simon Anders's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (2014) (43922)
- HTSeq—a Python framework to work with high-throughput sequencing data (2014) (14763)
- Differential expression analysis for sequence count data (2010) (13372)
- Orchestrating high-throughput genomic analysis with Bioconductor (2015) (2623)
- Detecting differential usage of exons from RNA-seq data (2012) (1300)
- Count-based differential expression analysis of RNA sequencing data using R and Bioconductor (2013) (1009)
- Accounting for technical noise in single-cell RNA-seq experiments (2013) (861)
- Love MI, Huber W, Anders S.. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol 15: 550 (2014) (514)
- Differential expression of RNA-Seq data at the gene level – the DESeq package (2012) (508)
- ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data (2009) (459)
- A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples (2020) (426)
- Di↵erential analysis of count data - the DESeq2 package (2014) (382)
- Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements (2013) (362)
- Gene expression across mammalian organ development (2019) (344)
- RNA-Seq workflow: gene-level exploratory analysis and differential expression (2015) (294)
- Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain (2019) (210)
- Analysing RNA-Seq data with the DESeq package (2011) (160)
- Genome-wide analysis of mRNA decay patterns during early Drosophila development (2010) (116)
- An efficient method for genome-wide polyadenylation site mapping and RNA quantification (2013) (110)
- Drug-perturbation-based stratification of blood cancer (2017) (109)
- Analysing high-throughput sequencing data in Python with HTSeq 2.0 (2021) (108)
- Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. (2011) (107)
- Drift and conservation of differential exon usage across tissues in primate species (2013) (107)
- FourCSeq: analysis of 4C sequencing data (2015) (85)
- Transcriptome and translatome co-evolution in mammals (2020) (74)
- An Evaluation of High-Throughput Approaches to QTL Mapping in Saccharomyces cerevisiae (2013) (74)
- Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling (2017) (69)
- Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels (2020) (67)
- Visualization of genomic data with the Hilbert curve (2009) (66)
- SARS-CoV-2 RNA Extraction Using Magnetic Beads for Rapid Large-Scale Testing by RT-qPCR and RT-LAMP (2020) (64)
- DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis* (2020) (60)
- Alanine Tails Signal Proteolysis in Bacterial Ribosome-Associated Quality Control (2019) (57)
- Single-cell polyadenylation site mapping reveals 3′ isoform choice variability (2015) (55)
- Endothelial GATA4 controls liver fibrosis and regeneration by preventing a pathogenic switch in angiocrine signaling. (2020) (52)
- EpiSmokEr: a robust classifier to determine smoking status from DNA methylation data. (2019) (50)
- Nonparametric Analysis of Thermal Proteome Profiles Reveals Novel Drug-binding Proteins (2019) (46)
- JNJ872 inhibits influenza A virus replication without altering cellular antiviral responses. (2016) (38)
- EpiSmokEr: A robust classifier to determine smoking status from DNA methylation data (2018) (38)
- Publisher Correction: Building an international consortium for tracking coronavirus health status (2020) (37)
- Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma (2017) (32)
- Improved binding site assignment by high-resolution mapping of RNA–protein interactions using iCLIP (2015) (29)
- analysis of count data { the DESeq2 package (2015) (28)
- A Framework for Multi-Omic Prediction of Treatment Response to Biologic Therapy for Psoriasis. (2019) (24)
- FourCSeq : analysis of 4 C sequencing data (2015) (24)
- Screening for SARS-CoV-2 infections with colorimetric RT-LAMP and LAMP sequencing (2020) (23)
- proDA: Probabilistic Dropout Analysis for Identifying Differentially Abundant Proteins in Label-Free Mass Spectrometry (2019) (22)
- Multi-Omics Studies towards Novel Modulators of Influenza A Virus–Host Interaction (2016) (20)
- Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): a structured summary of a study protocol for a cluster-randomised, two-factorial controlled trial (2021) (20)
- DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis. (2020) (18)
- High throughput screening of novel AAV capsids identifies variants for transduction of adult NSCs within the subventricular zone (2021) (17)
- Differential analysis of RNA-Seq data at the gene level using the DESeq 2 package (2013) (17)
- Analyzing RNA-seq data with DESeq 2 ( PDF ) (2017) (15)
- A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles (2020) (14)
- Spatial aspects of oncogenic signalling determine the response to combination therapy in slice explants from Kras‐driven lung tumours (2018) (13)
- Gene set enrichment analysis of the bronchial epithelium implicates contribution of cell cycle and tissue repair processes in equine asthma (2018) (11)
- Inferring differential exon usage in RNA-Seq data with the DEXSeq package (2015) (11)
- An efficient method for genome-wide polyadenylation site mapping and RNA quantification (2013) (10)
- Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction (2016) (9)
- BioC 2012: Analyzing RNA-seq data for dierential exon usage with the DEXSeq package (2012) (9)
- Neurofilament light and heterogeneity of disease progression in amyotrophic lateral sclerosis: development and validation of a prediction model to improve interventional trials (2021) (9)
- Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins (2018) (8)
- Single cell 3’UTR analysis identifies changes in alternative polyadenylation throughout neuronal differentiation and in autism (2020) (8)
- Focused multidimensional scaling: interactive visualization for exploration of high-dimensional data (2019) (8)
- Exploring dimension-reduced embeddings with Sleepwalk (2019) (7)
- Proteogenomics refines the molecular classification of chronic lymphocytic leukemia (2022) (7)
- Activation of Tryptophan and Phenylalanine Catabolism in the Remission Phase of Allergic Contact Dermatitis: A Pilot Study (2016) (6)
- Corrigendum: Accounting for technical noise in single-cell RNA-seq experiments (2014) (5)
- Colorimetric RT-LAMP and LAMP-sequencing forDetecting SARS-CoV-2 RNA in Clinical Samples. (2021) (5)
- Neural lineage induction reveals multi-scale dynamics of 3D chromatin organization (2014) (4)
- Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 (2014) (4)
- Cellular development and evolution of the mammalian cerebellum (2021) (4)
- Effectiveness and cost-effectiveness of four different strategies for SARS-CoV-2 surveillance in the general population (CoV-Surv Study): study protocol for a two-factorial randomized controlled multi-arm trial with cluster sampling (2021) (3)
- Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain (2022) (3)
- Beginner ’ s guide to using the DESeq 2 package (2014) (3)
- An evaluation of high-throughput approaches to QTL mapping in S. cerevisiae (2013) (2)
- Interferon regulates neural stem cell function at all ages by orchestrating mTOR and cell cycle (2023) (2)
- Computational analysis of ligand dose range thermal proteome profiles (2020) (2)
- Interferon adjusts stem cell output in the young and old brain to meet demand independently of its antiviral function (2022) (1)
- Dissecting intratumor heterogeneity of nodal B cell lymphomas on the transcriptional, genetic, and drug response level (2019) (1)
- Analysing high-throughput sequencing data in Python with HTSeq 2.0 (2022) (1)
- Interferon regulates stem cell function at all ages by orchestrating mTOR and cell cycle (2022) (1)
- Visualising very long data vectors with the Hilbert curve Description of the Bioconductor packages (2008) (1)
- Analyzing single-cell bisulfite sequencing data with scbs (2022) (1)
- DRUG PERTURBATION BASED STRATIFICATION OF LYMPHOPROLIFERATIVE DISORDERS (2017) (1)
- BADER: Bayesian analysis of differential expression in RNA sequencing data (2014) (1)
- Publisher Correction: Building an international consortium for tracking coronavirus health status (2020) (0)
- Abstract LB-305: A computational approach to identify recurrent somatic driver events in noncoding regions in human cancers (2015) (0)
- Abstract 3899: Discovery and clinical implementation of individualized therapies in acute myeloid leukemia based onex vivodrug sensitivity testing and multi-omics profiling (2018) (0)
- regions of the effect of variant size , type , and overlap with functional Relating CNVs to transcriptome data at fine resolution : Assessment Material (2011) (0)
- Interferon regulates stem cell output via post-transcriptional repression of Sox2 independent of its antiviral function in the brain (2022) (0)
- Supplementary Information : FourCSeq comparison with r 3 Cseq (2015) (0)
- Exchange Commands Between R and 'JavaScript' [R package jrc version 0.4.0] (2020) (0)
- Scalable RT‐LAMP‐based SARS‐CoV‐2 testing for infection surveillance with applications in pandemic preparedness (2023) (0)
- Contents Vol. 170, 2016 (2016) (0)
- Create Interactive Linked Charts with Minimal Code [R package rlc version 0.3.0] (2020) (0)
- genotype and phenotype data for conditions and segregants. Input format for R/qtl (2015) (0)
- The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes (2021) (0)
- TRANSCRIPTIONAL AND GENOMIC INTRA‐TUMOR HETEROGENEITY DRIVES SUBCLONE SPECIFIC DRUG RESPONSES IN DIFFUSE LARGE B CELL LYMPHOMA (2019) (0)
- Gene expression across mammalian organ development (2019) (0)
- In vivo high-throughput screening of novel adeno-associated viral capsids targeting adult neural stem cells in the subventricular zone (2021) (0)
- CSAMA 2014 : RNA-Seq differential expression workflow (2014) (0)
- BioC 2012 : Differential expression of RNA-Seq data at the gene level (2012) (0)
- Abstract 286: Transcriptomic features predicting drug sensitivity and resistance in acute myeloid leukemia (2018) (0)
- Package ‘ DESeq 2 ’ May 19 , 2022 Type Package (2018) (0)
- Processing and Visualisation of High-Throughput Sequencing Data with ShortRead and HilbertVis (2009) (0)
- Subgroups of T-Cell Prolymphocytic Leukemia (T-PLL) Discovered By High-Throughput Ex Vivo Drug Testing and Genetic Profiling (2015) (0)
- Transcriptome and translatome co-evolution in mammals (2020) (0)
- R/LinkedCharts: A novel approach for simple but powerful interactive data analysis (2022) (0)
- Abstract 458: Precision systems medicine in acute myeloid leukemia: real-time translation of tailored therapeutic opportunities arising from ex-vivo drug sensitivity testing and molecular profiling (2019) (0)
- Gene-Drug Interactions in AML Patients Identified By RNA Sequencing and Comprehensive Ex Vivo Drug Sensitivity and Resistance Testing (2017) (0)
- Interactively Explore Dimension-Reduced Embeddings [R package sleepwalk version 0.3.1] (2020) (0)
- Lung endothelium instructs dormancy of susceptible metastatic tumour cells (2022) (0)
- Proteogenomic Subtyping of Chronic Lymphocytic Leukemia Identifies a Novel Poor Outcome Subgroup with a Distinct Drug Response Profile (2020) (0)
- BioC 2014 : RNA-Seq workflow for differential gene expression (2014) (0)
- The bromodomain inhibitor JQ1 is a molecular glue targeting centromeres (2023) (0)
- Dissecting intratumour heterogeneity of nodal B-cell lymphomas at the transcriptional, genetic and drug-response levels (2020) (0)
- Author Correction: A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles (2021) (0)
- 827: Ex vivo combinatorial screen to identify drug sensitivity and rational treatment of chronic lymphocytic leukemia (2014) (0)
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What Schools Are Affiliated With Simon Anders?
Simon Anders is affiliated with the following schools:
