Google Scholar

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

Preprint articles

  • Hippen A.A., Davidson N.R., Barnard M.E., Weber L.M., Gertz J., Doherty J.A., Hicks S.C., and Greene C.S. (2023). Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes. bioRxiv (preprint). Paper.

Journal articles (accepted or in press)

  • Weber L.M.*, Divecha H.R.*, Tran M.N., Kwon S.H., Spangler A., Montgomery K.D., Tippani M., Bharadwaj R., Kleinman J.E., Page S.C., Hyde T.M., Collado-Torres L., Maynard K.R., Martinowich K.*, and Hicks S.C.* (2023). The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife Reviewed Preprint (accepted). Paper, R/Bioconductor data package, Code.

Journal articles (peer-reviewed and published)

  • Tippani M., Divecha H.R., Catallini II J.L., Kwon S.H., Weber L.M., Spangler A., Jaffe A.E., Hyde T.M., Kleinman J.E., Hicks S.C., Martinowich K., Collado-Torres L., Page S.C., and Maynard K.R. (2023). VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological Imaging, 3, e23. Paper, Software.

  • Hippen A.A., Omran D.K., Weber L.M., Jung E., Drapkin R., Doherty J.A., Hicks S.C., and Greene C.S. (2023). Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors. Genome Biology, 24, 239. Paper.

  • Weber L.M., Saha A., Datta A., Hansen K.D., and Hicks S.C. (2023). nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes. Nature Communications, 14, 4059. Paper, R/Bioconductor package, Code.

  • Tiberi S., Crowell H.L., Samartsidis P., Weber L.M., and Robinson M.D. (2023). distinct: a novel approach to differential distribution analyses. Annals of Applied Statistics, 17, 2, 1681–1700. Paper, R/Bioconductor package.

  • Krieg C., Weber L.M., Fosso B., Hardiman G., Mileti E., El Aidy S., Marzano M., Robinson M.D., and Guglietta S. (2022). Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy. Journal for ImmunoTherapy of Cancer, 10, e004717. Paper.

  • Pardo B., Spangler A., Weber L.M., Hicks S.C., Jaffe A.E., Martinowich K., Maynard K.R., and Collado-Torres L. (2022). spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics, 23, 434. Paper, R/Bioconductor package.

  • 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.* (2022). SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor. Bioinformatics, btac299. Paper, R/Bioconductor package.

  • Petrillo M., Fabbri M., Kagkli D.M. et al. (2022). A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Research, v2, 10, 80. Paper.

  • Weber L.M., Hippen A.A., Hickey P.F., Berrett K.C., Gertz J., Doherty J.A., Greene C.S., and Hicks S.C. (2021). Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. GigaScience, 10, 9, giab062. Paper, Code, Data, Data (controlled access).

  • Liechti T., Weber L.M., Ashhurst T.M., Stanley N., Prlic M., Van Gassen S., and Mair F. (2021). An updated guide for the perplexed: cytometry in the high-dimensional era. Nature Immunology, 22, 1190–1197. Paper.

  • 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. PLOS Computational Biology, 17, 8, e1009290. Paper, R/Bioconductor package.

  • 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. 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. 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. Paper.

  • Weber L.M. and Soneson C. (2019). HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats. F1000Research, 8, 1459, v2. 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. 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. 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. (2019). CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research, 6, 748, v4. 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, 1084–1096. (Note: Selected as an ‘Editor’s Choice’ article.) 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. 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. Paper.

  • Jackson K., Weber L.M., and Tennant M. (2016). A retrospective study of the effectiveness of four different treatments of periodontal disease in equine cheek teeth. Journal of Veterinary Dentistry, 33, 2, 83–89. 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, 1–7. Paper.