All Stories

  1. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    Article • eLife, January 2024, eLife

    Lukas Weber

  2. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    Article • eLife, January 2024, eLife

    Lukas Weber

  3. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    Article • December 2023, eLife

    Lukas Weber

  4. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors

    Article • Genome Biology, October 2023, Springer Science + Business Media

    Professor Casey Greene, Lukas Weber

  5. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes

    Article • Nature Communications, July 2023, Springer Science + Business Media

    Lukas Weber

  6. Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

  7. distinct: A novel approach to differential distribution analyses

    Article • The Annals of Applied Statistics, June 2023, Institute of Mathematical Statistics

    Lukas Weber

  8. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    Article • February 2023, eLife

    Lukas Weber

  9. Performance of computational algorithms to deconvolve heterogeneous bulk tumor tissue depends on experimental factors

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

  10. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    Article • October 2022, Cold Spring Harbor Laboratory Press

    Lukas Weber

  11. Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy

    Article • Journal for ImmunoTherapy of Cancer, September 2022, BMJ

    Lukas Weber

  12. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

    Article • BMC Genomics, June 2022, Springer Science + Business Media

    Lukas Weber

  13. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes

    Article • May 2022, Cold Spring Harbor Laboratory Press

    Lukas Weber

  14. SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

    Article • Bioinformatics, April 2022, Oxford University Press (OUP)

    Lukas Weber

  15. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

    Article • F1000Research, March 2022, Faculty of 1000, Ltd.

    Lukas Weber

  16. An updated guide for the perplexed: cytometry in the high-dimensional era

    Article • Nature Immunology, September 2021, Springer Science + Business Media

    Lukas Weber

  17. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

    Article • GigaScience, September 2021, Oxford University Press (OUP)

    Professor Casey Greene, Lukas Weber

  18. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

    Article • PLoS Computational Biology, August 2021, PLOS

    Professor Casey Greene, Lukas Weber

  19. VistoSeg: processing utilities for high-resolution Visium/Visium-IF images for spatial transcriptomics data

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Lukas Weber

  20. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Lukas Weber

  21. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

  22. Publisher Correction: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

    Article • Nature Neuroscience, February 2021, Springer Science + Business Media

    Lukas Weber

  23. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

    Article • Nature Neuroscience, February 2021, Springer Science + Business Media

    Lukas Weber

  24. SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Lukas Weber

  25. Loss of C3aR induces immune infiltration and inflammatory microbiota in a new spontaneous model of colon cancer

    Article • January 2021, Cold Spring Harbor Laboratory Press

    Lukas Weber

  26. distinct: a novel approach to differential distribution analyses

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Lukas Weber

  27. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Lukas Weber

  28. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Lukas Weber

  29. Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis

    Article • The FASEB Journal, January 2020, Wiley

    Lukas Weber

  30. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

    Article • F1000Research, December 2019, Faculty of 1000, Ltd.

    Lukas Weber, Felix Hartmann

  31. HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

    Article • F1000Research, December 2019, Faculty of 1000, Ltd.

    Lukas Weber

  32. HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats

    Article • F1000Research, August 2019, Faculty of 1000, Ltd.

    Lukas Weber

  33. Essential guidelines for computational method benchmarking

    Article • June 2019, Springer Science + Business Media

    Wouter Saelens, Lukas Weber

  34. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

    Article • F1000Research, May 2019, Faculty of 1000, Ltd.

    Felix Hartmann, Lukas Weber

  35. diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

    Article • Communications Biology, May 2019, Springer Science + Business Media

    Lukas Weber

  36. Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

    Article • Nature Reports Stem Cells, July 2018, Springer Science + Business Media

    Felix Hartmann, Lukas Weber

  37. diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Lukas Weber

  38. High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

    Article • Nature Reports Stem Cells, January 2018, Nature

    Felix Hartmann, Lukas Weber

  39. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

    Article • F1000Research, November 2017, Faculty of 1000, Ltd.

    Felix Hartmann, Lukas Weber

  40. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets

    Article • F1000Research, May 2017, Faculty of 1000, Ltd.

    Felix Hartmann, Lukas Weber

  41. Comparison of clustering methods for high-dimensional single-cell flow and mass cytometry data

    Article • Cytometry Part A, December 2016, Wiley

    Lukas Weber

  42. High-dimensional single-cell analysis reveals the immune signature of narcolepsy

    Article • Journal of Experimental Medicine, November 2016, Rockefeller University Press

    Felix Hartmann, Lukas Weber

  43. A Retrospective Study of the Effectiveness of Four Different Treatments of Periodontal Disease in Equine Cheek Teeth

    Article • Journal of Veterinary Dentistry, June 2016, SAGE Publications

    Lukas Weber

  44. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes

    Article • Development, April 2016, The Company of Biologists

    Lukas Weber

  45. Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data

    Article • April 2016, Cold Spring Harbor Laboratory Press

    Lukas Weber

  46. The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Dr A. Bulak Arpat, Altuna A, Gina Cannarozzi, Lukas Weber

  47. Statistical methods for detecting differentially methylated loci and regions

    Article • Frontiers in Genetics, September 2014, Frontiers

    Lukas Weber