Publications

(2020). dyngen: a multi-modal simulator for spearheading new single-cell omics analyses. bioRxiv.

DOI

(2020). The Rockerverse: Packages and Applications for Containerization with R. arXiv.

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(2019). The RNA Atlas, a single nucleotide resolution map of the human transcriptome. bioRxiv.

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(2019). Essential guidelines for computational method benchmarking. Genome Biology.

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(2019). Trajectory-based differential expression analysis for single-cell sequencing data. bioRxiv.

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(2019). A comparison of single-cell trajectory inference methods. Nature Biotechnology.

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(2018). Network Inference from Single-Cell Transcriptomic Data. Methods in Molecular Biology.

DOI

(2018). The Transcription Factor ZEB2 Is Required to Maintain the Tissue-Specific Identities of Macrophages. Immunity.

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(2018). IncGraph: Incremental graphlet counting for topology optimisation. PLOS ONE.

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(2018). A comprehensive evaluation of module detection methods for gene expression data. Nature Communications.

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(2018). A comparison of single-cell trajectory inference methods: towards more accurate and robust tools. bioRxiv.

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(2018). Genomic Amplifications and Distal 6q Loss: Novel Markers for Poor Survival in High-risk Neuroblastoma Patients. JNCI: Journal of the National Cancer Institute.

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(2017). Early and late effects of pharmacological ALK inhibition on the neuroblastoma transcriptome. Oncotarget.

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(2016). SCORPIUS improves trajectory inference and identifies novel modules in dendritic cell development. bioRxiv.

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(2016). Computational methods for trajectory inference from single-cell transcriptomics. European Journal of Immunology.

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(2016). arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genetics in Medicine.

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(2015). Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma. Oncotarget.

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