Showcases

A dynamic display of the NoWorkflow concept in action

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.

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).

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).

VIB Hackathon on Spatial Omics Tools and Methods

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

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

publication

benchmarking

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).

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).

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).

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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