Showcases

Publications by Data Intuitive people

Keywords

viash, workflow modules, reusable workflows, data workflows, single-cell omics, transcriptomics, transcription factors, senescence, sex-specific gene expression, human cell atlas, benchmarking, open problems, data analysis, spatial omics, scverse, multimodal data integration, DNA integration, RNA integration, protein integration, trajectory inference, dyngen, multi-modal simulation, gene regulatory networks, SCENIC workflow, data visualization, mixed data types, funkyheatmap, R packages, containerization, Rockerverse, bioinformatics, omics tools, computational biology, publications, CZI, Viash Hub, biological data, high-dimensional data, systems biology, cell types, omics benchmarking, predictive modeling, NeurIPS23, hackathon, single-cell analysis, container-based workflows, scientific software

Key Publications and Contributions

Publications

List of publications by Data Intuitive experts and publications in coorporation with clients and reearch institutions.

funkyheatmap - Visualising data frames with mixed data types (2025)

This paper introduces funkyheatmap, a tool to visualize data frames with mixed data types in a flexible and informative way.

publication

data visualization

R packages

Cannoodt, R., Deconinck, L., Couckuyt, A., Markov, N. S., Zappia, L., Luecken, M. D., Interlandi, M., Saeys, Y.†, & Saelens, W.† (2025).

Viash: A Meta-Framework for Building Reusable Workflow Modules (2024)

This article introduces Viash, a framework for creating reusable workflow modules for data workflows.

publication

viash

workflows

Cannoodt, R., Cannoodt, H., Schaumont, D., Waldrant, K., Van de Kerckhove, E., Boschmans, A., De Maeyer, D., & Verbeiren, T. (2024).

Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues. (2024)

This paper presents Tabula Sapiens 2.0, an expanded human cell atlas with new donors, tissues, and analyses of transcription factors, senescence, sex-specific gene expression, and a web tool for exploring donor health data.

publication

single-cell omics

viash

Stephen R Quake, The Tabula Sapiens Consortium, Data Analysis: Cannoodt, R.

Defining and Benchmarking Open Problems in Single-Cell Analysis (2024)

This paper defines and benchmarks key open problems in single-cell analysis, providing a comprehensive overview of challenges and solutions in the field.

publication

benchmarking

single-cell omics

Luecken, M., Gigante, S., Burkhardt, D., Cannoodt, R., Strobl, D., Markov, N., Zappia, L., Palla, G., Lewis, W., Dimitrov, D., Vinyard, M., Magruder, D., Andersson, A., Dann, E., Qin, Q., Otto, D., Klein, M., Botvinnik, O., Deconinck, L.,Waldrant, K., Rieck, B., Ahlmann-Eltze, C., Beltrame, E. da V., Benz, A., González-Blas, C. B., Chen, A., DeMeo, B., Ergen, C., Floc’hlay, S., Gayoso, A., Hicks, S., Ji, Y., Kleshchevnikov, V., Manno, G. L., Lombardo, M., Lopez, R., Righelli, D., Sarkar, H., Svensson, V., Tong, A., Xing, G., Xu, C., Bloom, J., Pisco, A., Saez-Rodriguez, J., Wulsin, D., Pinello, L., Saeys, Y., Theis, F., & Krishnaswamy, S. (2024).

A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types (2024)

NeurIPS23 Competition Analysis Paper

publication

benchmarking

single-cell omics

Artur Szałata, Andrew Benz, Robrecht Cannoodt,, Mauricio Cortes, Jason Fong, Sunil Kuppasani, Richard Lieberman, Tianyu Liu, Javier A. Mas-Rosario, Rico Meinl, Jalil Nourisa, Jared Tumiel, Tin M. Tunjic, Mengbo Wang, Noah Weber, Hongyu Zhao, Benedict Anchang, Fabian J Theis, Malte D Luecken, Daniel B Burkhardt

VIB Hackathon on Spatial Omics Tools and Methods (2024)

This publication presents the outcomes of the VIB Hackathon on spatial omics tools and methods, highlighting advancements in computational biology and data analysis.

publication

data analysis

scverse

spatial omics

Rombaut, B., Pollaris, L., Sang-aram, C., Cruysse, M. V., Cannoodt, R., Vernaillen, F., Defauw, A., Mortier, J., Ali, M., Bestak, K., Blampey, Q., Bortolomeazzi, M., Cauhy, P. V. M., Cetin, M., Dimitrov, D., Drummer, F., Giordani, L., Hada, A., Harbers, L., Ibarra-Arellano, M. A., Kiessling, P., Lehner, L., Mandal, S., Manzato, B., Marconato, L., Novella-Rausell, C., Okhtienko, A., Palla, G., Pikulska, D., Pulido-Vicuna, C. A., Sacchetti, G., Sudy, A., Van de Vreken, L., Vierdag, W.-M., Vlasov, V., Yasa, S. N., Dong, E. Y., Seurinck, R., & Saeys, Y. (2024).

Multimodal Single Cell Data Integration Challenge (2022)

This paper reviews the results of the multimodal single-cell data integration challenge, highlighting key lessons learned.

publication

benchmarking

single-cell omics

Lance, C., Luecken, M. D., Burkhardt, D. B., Cannoodt, R., Rautenstrauch, P., Laddach, A., Ubingazhibov, A., Cao, Z.-J., Deng, K., Khan, S., Liu, Q., Russkikh, N., Ryazantsev, G., Ohler, U., Pisco, A. O., Bloom, J., Krishnaswamy, S., & Theis, F. J. (2022).

A sandbox for prediction and integration of DNA, RNA, and proteins in single cells (2021)

This paper presents a sandbox environment for predicting and integrating DNA, RNA, and proteins in single-cell analysis.(2021)

publication

data analysis

single-cell omics

Luecken, M. D., Burkhardt, D. B., Cannoodt, R., Lance, C., Agrawal, A., Aliee, H., Chen, A. T., Deconinck, L., Detweiler, A. M., Granados, A. A., Huynh, S., Isacco, L., Kim, Y. J., Klein, D., Kumar, B. D., Kuppasani, S., Lickert, H., McGeever, A., Mekonen, H., Melgarejo, J. C., Morri, M., Müller, M., Neff, N., Paul, S., Rieck, B., Schneider, K., Steelman, S., Sterr, M., Treacy, D. J., Tong, A., Villani, A.-C., Wang, G., Yan, J., Zhang, C., Pisco, A. O., Krishnaswamy, S., Theis, F. J., & Bloom, J. M. (2021).

Recent Advances in Trajectory Inference from Single-Cell Omics Data (2021)

Recent Advances in Trajectory Inference from Single-Cell Omics Data (2021)

publication

data analysis

single-cell omics

Deconinck, L., Cannoodt, R., Saelens, W., Deplancke, B., & Saeys, Y. (2021).

Spearheading Future Omics Analyses Using Dyngen, a Multi-Modal Simulator of Single Cells (2021)

This article introduces dyngen, a multi-modal simulator for future omics analyses of single cells.

publication

benchmarking

single-cell omics

Cannoodt, R., Saelens, W., Deconinck, L., & Saeys, Y. (2021).

A Scalable SCENIC Workflow for Single-Cell Gene Regulatory Network Analysis (2020)

This paper introduces a scalable SCENIC workflow for analyzing gene regulatory networks in single-cell data.

publication

data analysis

single-cell omics

Van de Sande, B., Flerin, C., Davie, K., De Waegeneer, M., Hulselmans, G., Aibar, S., Seurinck, R., Saelens, W., Cannoodt, R., Rouchon, Q., Verbeiren, T., De Maeyer, D., Reumers, J., Saeys, Y., & Aerts, S. (2020).

The Rockerverse: Packages and Applications for Containerization with R (2020)

This paper explores the Rockerverse, a collection of packages and applications for containerization in R.

publication

data analysis

r

Nüst, D., Eddelbuettel, D., Bennett, D., Cannoodt, R., Clark, D., Daroczi, G., Edmondson, M., Fay, C., Hughes, E., Kjeldgaard, L., Lopp, S., Marwick, B., Nolis, H., Nolis, J., Ooi, H., Ram, K., Ross, N., Shepherd, L., Sólymos, P., Swetnam, T. L., Turaga, N., Van Petegem, C., Williams, J., & Xiao, N. (2020).

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