Key publications are described in more detail on the Research page. For a complete list of publications, see also Google Scholar.


Spatial transcriptomics
  • Maynard K.R.*, Collado-Torres L.*, Weber L.M., Uytingco C., Barry B.K., Williams S.R., Catallini J.L. II, Tran M.N., Besich Z., Tippani M., Chew J., Yin Y., Kleinman J.E., Hyde T.M., Rao N., Hicks S.C., Martinowich K.+, Jaffe A.E.+ (2020), Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex, bioRxiv, v1. Links to: Paper, Web application, R/Bioconductor package, Code for paper, Code for web application.

Key papers

Differential analysis in high-dimensional cytometry
  • Weber L.M., Nowicka N., Soneson C., and Robinson M.D. (2019), diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering, Communications Biology, 2, 183. Links to: Paper, R/Bioconductor package, Code, Data.

  • Nowicka N., Krieg C., Crowell H.L., Weber L.M., Hartmann F.J., Guglietta S., Becher B., Levesque M.P., and Robinson M.D. (2017; updated 2019), CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets, F1000Research, 6:748, v3. Links to: Paper, R/Bioconductor package.

  • Weber L.M. and Robinson M.D. (2016), Comparison of clustering methods for high‐dimensional single‐cell flow and mass cytometry data, Cytometry Part A, 89A, 12, 1084–1096. Links to: Paper, Code, Data.

  • Weber L.M. and Soneson C. (2019), HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats, F1000Research, 8:1459, v2. Links to: Paper, R/Bioconductor package.

  • Weber L.M., Saelens W., Cannoodt R., Soneson C., Hapfelmeier A., Gardner P.P., Boulesteix A.-L., Saeys Y., and Robinson M.D. (2019), Essential guidelines for computational method benchmarking, Genome Biology, 20, 125. Link to: Paper.

Collaboration papers

  • Shaul M.E., Eyal O., Guglietta S., Aloni P., Zlotnik A., Forkosh E., Levy L., Weber L.M., Levin Y., Pomerantz A., Nechushtan H., Eruslanov E., Singhal S., Robinson M.D., Krieg C., and Fridlender Z.G. (2020), Circulating neutrophil subsets in advanced lung cancer patients exhibit unique immune signature and relate to prognosis, FASEB Journal. Link to: Paper.

  • Krieg C., Nowicka M., Guglietta S., Schindler S., Hartmann F.J., Weber L.M., Dummer R., Robinson M.D., Levesque M.P.* and Becher B.* (2018), High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy, Nature Medicine, 24, 2, 144–153. Link to: Paper.

  • Hartmann F.J., Bernard-Valnet R., Quériault C., Mrdjen D., Weber L.M., Galli E., Krieg C., Robinson M.D., Nguyen X.-H., Dauvilliers Y., Liblau R.S., and Becher B. (2016), High-dimensional single-cell analysis reveals the immune signature of narcolepsy, Journal of Experimental Medicine, 213, 12, 2621–2633. Link to: Paper.

  • Burger A.*, Lindsay H.*, Felker A., Hess C., Anders C., Chiavacci E., Zaugg J., Weber L.M., Catena R., Jinek M., Robinson M.D., and Mosimann C. (2016), Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes, Development, 143, 2025–2037. Link to: Paper.

  • Robinson M.D., Kahraman A., Law C.W., Lindsay H., Nowicka M., Weber L.M., and Zhou X. (2014), Statistical methods for detecting differentially methylated loci and regions, Frontiers in Genetics, 5, 324. Link to: Paper.