S. van Dongen

发表

Detecting microRNA binding and siRNA off-target effects from expression data

Anton J. Enright, A. Enright, S. van Dongen, 2008, Nature Methods.

An efficient algorithm for large-scale detection of protein families.

Anton J. Enright, C. Ouzounis, S. Dongen, 2002, Nucleic acids research.

Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs

Anton J. Enright, A. Schier, A. Enright, 2006, Science.

Requirement of bic/microRNA-155 for Normal Immune Function

Anton J. Enright, A. Enright, D. Vetrie, 2007, Science.

Long- and Short-Term Selective Forces on Malaria Parasite Genomes

Jon D. McAuliffe, A. Krogh, E. Dermitzakis, 2010, PLoS genetics.

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

Anton J. Enright, T. Spector, R. Mägi, 2012, PLoS genetics.

The two most common histological subtypes of malignant germ cell tumour are distinguished by global microRNA profiles, associated with differential transcription factor expression

Anton J. Enright, A. Enright, S. van Dongen, 2010, Molecular Cancer.

Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro

Lia S. Campos, Ben J. Woodhams, S. Teichmann, 2021, Nature Genetics.

Mirnovo: genome-free prediction of microRNAs from small RNA sequencing data and single-cells using decision forests

Anton J. Enright, Dimitrios M. Vitsios, Stijn van Dongen, 2017, Nucleic acids research.

Transposon‐driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution

Anton J. Enright, A. Enright, S. van Dongen, 2017, EMBO reports.

MiR-277/4989 regulate transcriptional landscape during juvenile to adult transition in the parasitic helminth Schistosoma mansoni

Anton J. Enright, Anna V. Protasio, J. Collins, 2017, PLoS neglected tropical diseases.

Lack of correlation between predicted and actual off-target effects of short-interfering RNAs targeting the human papillomavirus type 16 E7 oncogene

Anton J. Enright, S. Dongen, A. Enright, 2013, British Journal of Cancer.

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis.

A. Enright, S. van Dongen, M. Davis, 2016, Nucleic acids research.

Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells

R. Barker, T. Santarius, S. van Dongen, 2022, Neuron.

Multi-organ functions of yolk sac during human early development

Nicola K. Wilson, S. Ballereau, B. Göttgens, 2022, bioRxiv.

Myeloid cell interferon secretion restricts Zika flavivirus infection of developing and malignant human neural progenitor cells

R. Barker, T. Santarius, S. van Dongen, 2022, Neuron.

Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses

M. Bonder, E. Ballestar, S. van Dongen, 2022, Nature Communications.

Malignant germ cell tumors display common microRNA profiles resulting in global changes in expression of messenger RNA targets.

Anton J. Enright, A. Enright, S. van Dongen, 2010, Cancer research.

LIN28 Expression in malignant germ cell tumors downregulates let-7 and increases oncogene levels.

Anton J. Enright, A. Enright, S. van Dongen, 2013, Cancer research.

Using MCL to extract clusters from networks.

Stijn van Dongen, Cei Abreu-Goodger, S. van Dongen, 2012, Methods in molecular biology.

Large-scale analysis of microRNA expression, epi-transcriptomic features and biogenesis

Anton J. Enright, Dimitrios M. Vitsios, Stijn van Dongen, 2016, Nucleic acids research.

RNA editing of human microRNAs

Anton J. Enright, Richard Wooster, Michael R Stratton, 2006, Genome Biology.

Temporo-cerebellar connectivity underlies timing constraints in audition

D. Scholtens, S. van Dongen, M. Hafner, 2017, eLife.

Large-Scale Identification of MicroRNA Targets in Murine Dgcr8-Deficient Embryonic Stem Cell Lines

Anton J. Enright, A. Enright, I. Dunham, 2012, PloS one.

Cells of the human intestinal tract mapped across space and time

J. Marioni, R. Barker, S. van Dongen, 2021, Nature.

scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation

Ricardo J. Miragaia, K. Polanski, Michael J. T. Stubbington, 2019, Genome Biology.

Lung, spleen and oesophagus tissue remains stable for scRNAseq in cold preservation

Ricardo J. Miragaia, K. Polanski, K.B. Meyer, 2019, bioRxiv.

Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench

Vladimir Yu Kiselev, Martin Hemberg, Stijn van Dongen, 2020, bioRxiv.

Single-cell multi-omics analysis of the immune response in COVID-19

Frances E. Muldoon, Nicola K. Wilson, Kenneth G. C. Smith, 2021, Nature Medicine.

Single-cell roadmap of human gonadal development

M. Herbert, S. van Dongen, M. Haniffa, 2021, Nature.

Comparison of visualization tools for single-cell RNAseq data

Vladimir Yu Kiselev, Ni Huang, Batuhan Cakir, 2020, NAR genomics and bioinformatics.

Messenger RNA and microRNA profiling during early mouse EB formation.

Anton J. Enright, A. Enright, S. van Dongen, 2011, Gene expression patterns : GEP.

An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice

Anton J. Enright, H. Fuchs, K. Steel, 2009, Nature Genetics.

Targeted Deletion of MicroRNA-22 Promotes Stress-Induced Cardiac Dilation and Contractile Dysfunction

Anton J. Enright, A. Enright, A. Bradley, 2012, Circulation.

Comparison of visualisation tools for single-cell RNAseq data

Ni Huang, Pınar Pir, Martin Prete, 2020, bioRxiv.

Single-Cell Atlas of Common Variable Immunodeficiency reveals germinal center-associated epigenetic dysregulation in B cell responses

M. Bonder, E. Ballestar, S. van Dongen, 2021, bioRxiv.

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

Anton J. Enright, Stijn van Dongen, Cei Abreu-Goodger, 2013, Methods.

Transcriptional signals of dedifferentiation in human cancer

Matthew D. Young, S. van Dongen, S. Behjati, 2022, bioRxiv.

Depletion of HPV16 early genes induces autophagy and senescence in a cervical carcinogenesis model, regardless of viral physical state

Anton J. Enright, A. Enright, S. van Dongen, 2013, The Journal of pathology.

A screen for combination therapies in BRAF/NRAS wild type melanoma identifies nilotinib plus MEK inhibitor as a synergistic combination

Anton J. Enright, Anneliese O. Speak, A. Speak, 2017, bioRxiv.

Exploring regulatory networks of miR-96 in the developing inner ear

Anton J. Enright, K. Steel, A. Enright, 2016, Scientific Reports.

Many si/shRNAs can kill cancer cells by targeting multiple survival genes through an off-target mechanism

D. Scholtens, S. van Dongen, M. Hafner, 2017, bioRxiv.