Lukas Weber | Profiles RNS

Lukas M. Weber, PhD

Assistant Professor

Boston University School of Public Health

Biostatistics

PhD, University of Zurich
MSc, University of Zurich
MA, University of Western Australia
BSc, Australian National University
BSc, University of Western Australia

Websites

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ORCID : 0000-0002-3282-1730

Dr. Lukas M. Weber is an Assistant Professor in the Department of Biostatistics, School of Public Health, at Boston University.

His research is in statistical genomics and biomedical data science on the development of statistical and computational methods, open-source software, and collaborative analyses for data from high-throughput genomic technologies, primarily applied to biological questions in neuroscience and cancer biology. Currently, his research is focused on data from spatial transcriptomics and single-cell platforms.

He has implemented methods and other analysis tools in a number of R software packages, and supports principles of open and reproducible science, including the development of open-source software, reproducibility of analyses, benchmarking against existing and baseline methods, providing accessible code and data resources, and publication of preprints. He has instructed several workshops on R programming and computational skills.

His training includes a postdoctoral fellowship in the Department of Biostatistics at Johns Hopkins University, a PhD in Biostatistics at the University of Zurich, Switzerland, and a MSc in Statistics at ETH Zurich, Switzerland.

BU Research

Unsupervised Statistical Methods for Data-driven Analyses in Spatially Resolved Transcriptomics Data
01/01/2024 - 12/31/2026 (PI)
NIH/National Human Genome Research Institute
5R00HG012229-04

Title

Yr	Title	Project-Sub Proj	Pubs

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.

iCite Analysis Copy PMIDs To Clipboard

Mas-Peiro S, Muntané-Carol G, Ternacle J, Veiga-Fernandez G, Vilalta V, Campelo-Parada F, Nuche J, Nombela-Franco L, Asmarats L, Regueiro A, Del Trigo M, Indolfi C, Cheema A, Del Val D, Alperi A, Esposito G, Muñoz-García A, Serra V, Romaguera R, Weber L, Gautier P, Fernández-Herrero I, Nardi G, Anduaga Í, Sorrentino S, Mariani A, Mohammadi S, Avvedimento M, Rodés-Cabau J. Cardiac Structural Complications Following TAVR. Circ Cardiovasc Interv. 2026 Feb 05; e015991. PMID: 41641532

Zhang Y, Joehanes R, Huan T, Weber LM, Yang Q, Lunetta KL, Levy D, Liu C. Integration of latent factor analysis into multivariable Mendelian randomization. Eur J Epidemiol. 2026 Jan 12.View Related Profiles.

Liu, Chunyu
Levy, Daniel
Lunetta, Kathryn
Weber, Lukas
Yang, Qiong

PMID: 41524881; DOI: 10.1007/s10654-025-01324-8;

Crowell HL, Dong Y, Billato I, Cai P, Emons M, Gunz S, Guo B, Li M, Mahmoud A, Manukyan A, Pagès H, Panwar P, Rao S, Sargeant CJ, Kern LS, Ramos M, Sun J, Totty M, Carey VJ, Chen Y, Collado-Torres L, Ghazanfar S, Hansen KD, Martinowich K, Maynard KR, Patrick E, Righelli D, Risso D, Tiberi S, Waldron L, Gottardo R, Robinson MD, Hicks SC, Weber LM. Orchestrating Spatial Transcriptomics Analysis with Bioconductor. bioRxiv. 2025 Nov 21. PMID: 41332620; PMCID: PMC12667768; DOI: 10.1101/2025.11.20.688607;

Weber L, Dos Anjos Cunha L, Morales MA, Rubio A, Zhang S. Phaseless Auxiliary-Field Quantum Monte Carlo Method for Cavity-QED Matter Systems. J Chem Theory Comput. 2025 Mar 25; 21(6):2909-2917. PMID: 39823201

Weber LM, Divecha HR, Tran MN, Kwon SH, Spangler A, Montgomery KD, Tippani M, Bharadwaj R, Kleinman JE, Page SC, Hyde TM, Collado-Torres L, Maynard KR, Martinowich K, Hicks SC. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. Elife. 2024 Jan 24; 12. PMID: 38266073; PMCID: PMC10945708; DOI: 10.7554/eLife.84628;

Tippani M, Divecha HR, Catallini JL, Kwon SH, Weber LM, Spangler A, Jaffe AE, Hyde TM, Kleinman JE, Hicks SC, Martinowich K, Collado-Torres L, Page SC, Maynard KR. VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biol Imaging. 2023; 3:e23. PMID: 38510173; PMCID: PMC10951916; DOI: 10.1017/S2633903X23000235;

Hippen AA, Omran DK, Weber LM, Jung E, Drapkin R, Doherty JA, Hicks SC, Greene CS. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors. Genome Biol. 2023 Oct 20; 24(1):239. PMID: 37864274; PMCID: PMC10588129; DOI: 10.1186/s13059-023-03077-7;

Weber LM, Saha A, Datta A, Hansen KD, Hicks SC. nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes. Nat Commun. 2023 Jul 10; 14(1):4059. PMID: 37429865; PMCID: PMC10333391; DOI: 10.1038/s41467-023-39748-z;

Ambrosini S, Montecucco F, Kolijn D, Pedicino D, Akhmedov A, Mohammed SA, Herwig M, Gorica E, Szabó PL, Weber L, Russo G, Vinci R, Matter CM, Liuzzo G, Brown PJ, Rossi FMV, Camici GG, Sciarretta S, Beltrami AP, Crea F, Podesser B, Lüscher TF, Kiss A, Ruschitzka F, Hamdani N, Costantino S, Paneni F. Methylation of the Hippo effector YAP by the methyltransferase SETD7 drives myocardial ischaemic injury: a translational study. Cardiovasc Res. 2023 Jan 18; 118(17):3374-3385. PMID: 35709329

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., Maynard K.R. VistoSeg: Processing utilities for high-resolution images for spatially resolved transcriptomics data. Biological Imaging. 2023; 3(e23).

Showing 10 of 28 results. Show More

Tiberi S., Crowell H.L., Samartsidis P., Weber L.M., Robinson M.D. distinct: a novel approach to differential distribution analyses. Annals of Applied Statistics. 2023; 17(2):1681-1700.
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., Hicks S.C. The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics. eLife (accepted / in press). 2023.
Hippen A.A., Davidson N.R., Barnard M.E., Weber L.M., Gertz J., Doherty J.A., Hicks S.C., Greene C.S. Deconvolution reveals compositional differences in high-grade serous ovarian cancer subtypes. bioRxiv (preprint). 2023.

Krieg C, Weber LM, Fosso B, Marzano M, Hardiman G, Olcina MM, Domingo E, El Aidy S, Mallah K, Robinson MD, Guglietta S. Complement downregulation promotes an inflammatory signature that renders colorectal cancer susceptible to immunotherapy. J Immunother Cancer. 2022 Sep; 10(9). PMID: 36137652

Kiss A, Wu P, Schlederer M, Pilz PM, Szabo PL, Li J, Weber L, Vraka C, Pichler V, Mitterhauser M, Zhang X, Zins K, Abraham D, Li S, Podesser BK, Hacker M, Li X. Sympathetic nerve innervation and metabolism in ischemic myocardium in response to remote ischemic perconditioning. Basic Res Cardiol. 2022 Aug 25; 117(1):42. PMID: 36008727

Pardo B, Spangler A, Weber LM, Page SC, Hicks SC, Jaffe AE, Martinowich K, Maynard KR, Collado-Torres L. spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data. BMC Genomics. 2022 Jun 10; 23(1):434. PMID: 35689177; PMCID: PMC9188087; DOI: 10.1186/s12864-022-08601-w;

Righelli D, Weber LM, Crowell HL, Pardo B, Collado-Torres L, Ghazanfar S, Lun ATL, Hicks SC, Risso D. SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor. Bioinformatics. 2022 May 26; 38(11):3128-3131. PMID: 35482478; PMCID: PMC9154247; DOI: 10.1093/bioinformatics/btac299;

Liechti T, Weber LM, Ashhurst TM, Stanley N, Prlic M, Van Gassen S, Mair F. An updated guide for the perplexed: cytometry in the high-dimensional era. Nat Immunol. 2021 Oct; 22(10):1190-1197. PMID: 34489590

Weber LM, Hippen AA, Hickey PF, Berrett KC, Gertz J, Doherty JA, Greene CS, Hicks SC. Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design. Gigascience. 2021 Sep 22; 10(9). PMID: 34553212; PMCID: PMC8458035; DOI: 10.1093/gigascience/giab062;

Hippen AA, Falco MM, Weber LM, Erkan EP, Zhang K, Doherty JA, Vähärautio A, Greene CS, Hicks SC. miQC: An adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. PLoS Comput Biol. 2021 Aug; 17(8):e1009290. PMID: 34428202; PMCID: PMC8415599; DOI: 10.1371/journal.pcbi.1009290;

Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, Hicks SC, Martinowich K, Jaffe AE. Publisher Correction: Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci. 2021 Apr; 24(4):612. PMID: 33603232

Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, Hicks SC, Martinowich K, Jaffe AE. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nat Neurosci. 2021 Mar; 24(3):425-436. PMID: 33558695; PMCID: PMC8095368; DOI: 10.1038/s41593-020-00787-0;

Petrillo M, Fabbri M, Kagkli DM, Querci M, Van den Eede G, Alm E, Aytan-Aktug D, Capella-Gutierrez S, Carrillo C, Cestaro A, Chan KG, Coque T, Endrullat C, Gut I, Hammer P, Kay GL, Madec JY, Mather AE, McHardy AC, Naas T, Paracchini V, Peter S, Pightling A, Raffael B, Rossen J, Ruppé E, Schlaberg R, Vanneste K, Weber LM, Westh H, Angers-Loustau A. A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing. F1000Res. 2021; 10:80. PMID: 35847383

Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD. Essential guidelines for computational method benchmarking. Genome Biol. 2019 Jun 20; 20(1):125. PMID: 31221194; PMCID: PMC6584985; DOI: 10.1186/s13059-019-1738-8;

Krieg C, Nowicka M, Guglietta S, Schindler S, Hartmann FJ, Weber LM, Dummer R, Robinson MD, Levesque MP, Becher B. Author Correction: High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy. Nat Med. 2018 Nov; 24(11):1773-1775. PMID: 29967347

Jerosch K, Pehlke H, Monien P, Scharf F, Weber L, Kuhn G, Braun MH, Abele D. Benthic meltwater fjord habitats formed by rapid glacier recession on King George Island, Antarctica. Philos Trans A Math Phys Eng Sci. 2018 Jun 28; 376(2122). PMID: 29760120

Nowicka M, Krieg C, Crowell HL, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP, Robinson MD. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Res. 2017; 6:748. PMID: 28663787

Robinson MD, Kahraman A, Law CW, Lindsay H, Nowicka M, Weber LM, Zhou X. Statistical methods for detecting differentially methylated loci and regions. Front Genet. 2014; 5:324. PMID: 25278959

This graph shows the total number of publications by year, by first, middle/unknown, or last author.

Bar chart showing 28 publications over 10 distinct years, with a maximum of 8 publications in 2023

Bar chart showing 28 publications over 10 distinct years, with a maximum of 8 publications in 2023

Year	Publications
2014	1
2017	1
2018	2
2019	1
2021	6
2022	4
2023	8
2024	1
2025	2
2026	2

2022 NIH NHGRI: K99/R00 Pathway to Independence Award

2021 Early Career Research Symbiont Award

Contact for Mentoring:

801 Massachusetts Ave
Boston MA 02118
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617.358.2222

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