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Showcases

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Keywords

Data Intuitive Project Highlights, Biotech R&D Case Studies, Innovative Bioinformatics Applications, Advanced Data Analysis Showcase, Collaborative Research Successes

Key Publications and Contributions

Publications

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

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).

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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.

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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).

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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

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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).

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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).

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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).

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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).

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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).

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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).

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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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