Space, the current frontier, where “space” means geospatial as often assumed in spatial statistics. These are the voyages of the starship Voyager. Its ongoing mission, to explore strange new worlds, to seek out new views and new neighborhoods, to boldly go where Lambda has never gone before.
My name is Lambda, she/her. I live in Hahamongna, Tongva/Kizh/Gabrieleno territory, or in Anglo terms, Pasadena, Los Angeles (LA) County. One of my favorite aspects of LA is that there are many crazy people, crazy in cool ways. Hopefully I’m one of them. I’m a left-wing heterodox Muslim convert Aspie cultural rebel zero waster living in LA without a car for 10 years.
This blog is about Voyager. On the one hand, spatial -omics data analysis inspired by the geospatial tradition. On the other hand, the starship Voyager, which is my human powered ship that made me learn about the different cultures and landscapes of LA. Starship Voyager also made me think about spatial statistics and inspired many ideas in the R package Voyager project. This is the personal side of the “from geospatial to spatial -omics” on R package Voyager’s documentation website.
Education
California Institute of Technology | Pasadena, CA | postdoc | June 2023 - present
California Institute of Technology | Pasadena, CA | PhD in Biology | Sept 2017 - June 2023
University of California, Los Angeles | Los Angeles, CA | B.S. in Molecular, Cell, and Developmental Biology (highest departmental honor), and Computation and Systems Biology (valedictorian), summa cum laude, Phi Beta Kappa | Sept 2013 - June 2017
Bioconductor packages
Voyager | From geospatial to spatial -omics based on SFE
SpatialFeatureExperiment (SFE) | S4 class using Simple Features to represent geometries for spatial -omics data based on SpatialExperiment and SingleCellExperiment
SFEData | Example datasets for Voyager and SFE
spatialDE | R wrapper of SpatialDE
BUSpaRse | R utilities for kallisto bustools from their early days; kept for historical reasons, use the newest version of kallisto and bustools instead of this package.
Publications
Voyager: exploratory single-cell genomics data analysis with geospatial statistics Lambda Moses, Pétur Helgi Einarsson, Kayla C Jackson, Laura Luebbert, Ali Sina Booeshaghi, Sindri Emmanúel Antonsson, Páll Melsted, Lior Pachter bioRxiv. 2023 July. doi: 10.1101/2023.07.20.549945
Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX Kayla Jackson, A. Sina Booeshaghi, Ángel Gálvez-Merchán, Lambda Moses, Tara Chari, Lior Pachter bioRxiv. 2023 June. doi: 10.1101/2023.06.28.546949
The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice Brie K. Fuqua, Lambda Moses, Stela McLachlan, Calvin Pan, Richard C. Davis, Simon T. Hui, Nam Che, Zhiqiang Zhou, Carmen Ng, Sarada Charugundla, Montgomery Blencowe, Zara Saleem, Aika Miikeda, Beyza Ozdemir, Chester Hui, Thy Li, Clara L. Stolin, Marianne Kozuch, Jie Zhou, Kathryn Page, Hiro Irimagawa, Nam Ku, Kodi Taraszka, Nathan LaPierre, David W. Killilea, David M. Frazer, Xia Yang, Eleazar Eskin, Chris D. Vulpe, Aldons J. Lusis. bioRxiv. 2023 June. doi: 10.1101/2023.06.05.543764
Museum of spatial transcriptomics. Moses L, Pachter L. Nature Methods. 2022 May;19(5):534-546. doi: 10.1038/s41592-022-01409-2. Epub 2022 Mar 10. Erratum in: Nature Methods. 2022 Apr 19;: PMID: 35273392.
Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Melsted P, Booeshaghi AS, Liu L, Gao F, Moses L, Min KHJ, da Veiga Beltrame E, Hjörleifsson KE, Gehring J, Pachter L. Nature Biotechnology. 2021 Jul;39(7):813-818. doi: 10.1038/s41587-021-00870-2. Epub 2021 Apr 1. PMID: 33795888.
Presentations
2023 | Workshop: Voyager: Exploratory spatial data analysis from geospatial to spatial -omics, Bioconductor Conference, Dana-Farber Cancer Institute
2023 | Invited talk: Voyager: Exploratory spatial data analysis from geospatial to spatial -omics, Cedars-Sinai Medical Center
2023 | Invited talk: From geospatial to spatial -omics with SpatialFeatureExperiment and Voyager, Advanced Biomedical Computation series, Brigham & Women’s Hospital, Harvard Medical School
2022 | Package demo: SpatialFeatureExperiment: An S4 Class Bringing Geospatial Tools To Spatial Omics, Bioconductor Conference, Seattle Children’s Hospital (video)
2020 | Short talk: Museum of Spatial Transcriptomics, Bioconductor Conference (video)