Google Scholar

A complete list of publications is also available on Google Scholar.


Preprints

  • Righell D.*, Weber L.M.*, Crowell H.L.*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.+, and Risso D.+ (2021), SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor, bioRxiv, 2021.01.27.428431v1. Links to: Paper, R/Bioconductor package.

  • Hippen A.A., Falco M.M., Weber L.M., Erkan E.P., Zhang K., Doherty J.A., Vähärautio A., Greene C.S., and Hicks S.C. (2021), miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data, bioRxiv, 2021.03.03.433798v1. Links to: Paper, R/Bioconductor package.

  • Pardo B., Spangler A., Weber L.M., Hicks S.C., Jaffe A.E., Martinowich K., Maynard K.R., and Collado-Torres L. (2021), spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data, bioRxiv, 2021.04.29.440149v1. Links to: Paper, R/Bioconductor package.

  • Weber L.M., Hippen A.A., Hickey P.F., Berrett K.C., Gertz J., Doherty J.A., Greene C.S., and Hicks S.C. (2020), Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design, bioRxiv, v1, 371963. Links to: Paper, Code, Data, Data (controlled access).

  • Tiberi S., Crowell H.L., Weber L.M., Samartsidis P., and Robinson M.D. (2020), distinct: a novel approach to differential distribution analyses, bioRxiv, v1, 394213. Links to: Paper.


Published papers

  • 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.+ (2021), Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex, Nature Neuroscience, 24, 425-436. Links to: Paper, Web application, R/Bioconductor package, Code for paper, Code for web application.

  • 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, 34, 3, 4204–4218. Links to: Paper.

  • 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. Links to: Paper.

  • 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., 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.

  • 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. Links to: Paper.

  • 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.

  • 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. Links 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. Links 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. Links to: Paper.