Browse by Research Team

2024

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. and Haghverdi, L.
Bioinformatics 40 (7): btae471. July 2024

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
Malekpour, S.A., Haghverdi, L. and Sadeghi, M.
Briefings in Bioinformatics 25 (3): bbae180. May 2024

Single-cell time series analysis reveals the dynamics of HSPC response to inflammation.
Bouman, B.J., Demerdash, Y., Sood, S., Grünschläger, F., Pilz, F., Itani, A.R., Kuck, A., Marot-Lassauzaie, V., Haas, S., Haghverdi, L. and Essers, M.A.
Life Science Alliance 7 (3): e202302309. March 2024

2023

Adjustments to the reference dataset design improve cell type label transfer.
Mölbert, C. and Haghverdi, L.
Frontiers in Bioinformatics 3 : 1150099. 5 April 2023

Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
Haghverdi, L. and Ludwig, L.S.
Stem Cell Reports 18 (1): 13-25. 10 January 2023

2022

Towards reliable quantification of cell state velocities.
Marot-Lassauzaie, V., Bouman, B.J., Donaghy, F.D., Demerdash, Y., Essers, M.A.G. and Haghverdi, L.
PLoS Computational Biology 18 (9): e1010031. 28 September 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C., Kocks, C., Leiz, J., Karaiskos, N., Boltengagen, A., Cao, S., Skopnik, C.M., Klocke, J., Hardenberg, J.H., Stockmann, H., Gotthardt, I., Obermayer, B., Haghverdi, L., Wyler, E., Landthaler, M., Bachmann, S., Hocke, A.C., Corman, V., Busch, J., Schneider, W., Himmerkus, N., Bleich, M., Eckardt, K.U., Enghard, P., Rajewsky, N. and Schmidt-Ott, K.M.
Genome Medicine 14 (1): 103. 9 September 2022

2021

KDD Health Day/DSHealth 2021: Joint KDD 2021 Health Day and 2021 KDD Workshop on Applied Data Science for Healthcare: state of XAI and trustworthiness in health.
Wang, F., Chakraborty, P., Xu, T., Hsueh, P.Y.S., Sun, X., Stiglic, G., Crane, G., Bian, J., Haghverdi, L., Yao, L. and Buettner, F.
In: KDD '21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 14-18 Aug 2021, Virtual Event Singapore. 14 August 2021

2018

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi, L., Lun, A.T.L., Morgan, M.D. and Marioni, J.C.
Nature Biotechnology 36 (5): 421-427. May 2018

2017

Sparse control of force field dynamics.
Bongini, M., Fornasier, M., Fröhlich, F. and Haghverdi, L.
In: 7th International Conference on NETwork Games, COntrol and OPtimization (NetGCoop), 29 - 31 Oct 2014, Trento, Italy. 8 June 2017

2016

Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L., Büttner, M., Wolf, F.A., Buettner, F. and Theis, F.J.
Nature Methods 13 (10): 845-848. October 2016

destiny: diffusion maps for large-scale single-cell data in R.
Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C. and Buettner, F.
Bioinformatics 32 (8): 1241-1243. 15 April 2016

2015

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi, L., Buettner, F. and Theis, F.J.
Bioinformatics 31 (18): 2989-2998. 15 September 2015

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.
Ocone, A., Haghverdi, L., Mueller, N.S. and Theis, F.J.
Bioinformatics 31 (12): i89-i96. 15 June 2015

Decoding the regulatory network of early blood development from single-cell gene expression measurements.
Moignard, V., Woodhouse, S., Haghverdi, L., Lilly, A.J., Tanaka, Y., Wilkinson, A.C., Buettner, F., Macaulay, I.C., Jawaid, W., Diamanti, E., Nishikawa, S.I., Piterman, N., Kouskoff, V., Theis, F.J., Fisher, J. and Göttgens, B.
Nature Biotechnology 33 (3): 269-276. March 2015