Article

Bone marrow breakout lesions act as key sites for tumor-immune cell diversification in multiple myeloma.
Lutz, R. ORCID: https://orcid.org/0009-0004-6214-308X, Poos, A.M. ORCID: https://orcid.org/0009-0009-4325-3933, Solé-Boldo, L. ORCID: https://orcid.org/0000-0002-6974-9066, John, L. ORCID: https://orcid.org/0000-0001-8178-6890, Wagner, J. ORCID: https://orcid.org/0000-0002-5087-3657, Prokoph, N. ORCID: https://orcid.org/0000-0002-6429-9895, Baertsch, M.A. ORCID: https://orcid.org/0000-0002-4000-6904, Vonficht, D., Palit, S., Brobeil, A., Mechtersheimer, G. ORCID: https://orcid.org/0000-0002-9442-3930, Hildenbrand, N. ORCID: https://orcid.org/0000-0002-3988-2018, Hemmer, S. ORCID: https://orcid.org/0009-0000-8696-2099, Steiger, S. ORCID: https://orcid.org/0000-0002-4845-5042, Horn, S., Pepke, W. ORCID: https://orcid.org/0000-0001-9690-4511, Spranz, D.M., Rehnitz, C., Sant, P. ORCID: https://orcid.org/0000-0001-9301-3211, Mallm, J.P. ORCID: https://orcid.org/0000-0002-7059-4030, Friedrich, M.J. ORCID: https://orcid.org/0000-0002-6401-3623, Reichert, P., Huhn, S., Trumpp, A. ORCID: https://orcid.org/0000-0002-6212-3466, Rippe, K. ORCID: https://orcid.org/0000-0001-9951-9395, Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, Fröhling, S. ORCID: https://orcid.org/0000-0001-7907-4595, Müller-Tidow, C. ORCID: https://orcid.org/0000-0002-7166-5232, Hübschmann, D. ORCID: https://orcid.org/0000-0002-6041-7049, Goldschmidt, H. ORCID: https://orcid.org/0000-0003-0961-0035, Willimsky, G. ORCID: https://orcid.org/0000-0002-9693-948X, Sauer, S., Raab, M.S., Haas, S. ORCID: https://orcid.org/0000-0001-9227-2051 and Weinhold, N. ORCID: https://orcid.org/0000-0002-5464-3234
Science Immunology 10 (104): eadp6667. February 2025

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V. ORCID: https://orcid.org/0000-0002-8362-9634, Beneyto-Calabuig, S., Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Velten, L., Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632 and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
Bioinformatics 40 (9): btae512. September 2024

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. ORCID: https://orcid.org/0000-0002-1398-2846 and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
Bioinformatics 40 (7): btae471. July 2024

Single-cell multi-omics analysis identifies context-specific gene regulatory gates and mechanisms.
Malekpour, S.A. ORCID: https://orcid.org/0000-0002-3525-3548, Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170 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. ORCID: https://orcid.org/0000-0003-1259-5040, Demerdash, Y., Sood, S., Grünschläger, F., Pilz, F., Itani, A.R. ORCID: https://orcid.org/0000-0001-7608-822X, Kuck, A., Marot-Lassauzaie, V. ORCID: https://orcid.org/0000-0002-8362-9634, Haas, S. ORCID: https://orcid.org/0000-0001-9227-2051, Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170 and Essers, M.A. ORCID: https://orcid.org/0000-0003-3117-1809
Life Science Alliance 7 (3): e202302309. March 2024

Adjustments to the reference dataset design improve cell type label transfer.
Mölbert, C. ORCID: https://orcid.org/0000-0003-3580-4968 and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
Frontiers in Bioinformatics 3 : 1150099. 5 April 2023

Towards reliable quantification of cell state velocities.
Marot-Lassauzaie, V. ORCID: https://orcid.org/0000-0002-8362-9634, Bouman, B.J. ORCID: https://orcid.org/0000-0003-1259-5040, Donaghy, F.D. ORCID: https://orcid.org/0000-0001-6892-0186, Demerdash, Y., Essers, M.A.G. and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
PLoS Computational Biology 18 (9): e1010031. 28 September 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C. ORCID: https://orcid.org/0000-0003-2526-1621, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Leiz, J. ORCID: https://orcid.org/0000-0002-6531-7047, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Cao, S. ORCID: https://orcid.org/0000-0001-7195-8193, Skopnik, C.M. ORCID: https://orcid.org/0000-0002-6089-4769, Klocke, J. ORCID: https://orcid.org/0000-0002-7723-9234, Hardenberg, J.H. ORCID: https://orcid.org/0000-0001-9548-2118, Stockmann, H. ORCID: https://orcid.org/0000-0002-0934-7620, Gotthardt, I. ORCID: https://orcid.org/0000-0001-6033-0093, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Bachmann, S., Hocke, A.C. ORCID: https://orcid.org/0000-0002-6935-8612, Corman, V., Busch, J., Schneider, W., Himmerkus, N. ORCID: https://orcid.org/0000-0002-2910-6728, Bleich, M. ORCID: https://orcid.org/0000-0002-1745-2295, Eckardt, K.U. ORCID: https://orcid.org/0000-0003-3823-0920, Enghard, P. ORCID: https://orcid.org/0000-0002-7254-3931, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142
Genome Medicine 14 (1): 103. 9 September 2022

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, Lun, A.T.L. ORCID: https://orcid.org/0000-0002-3564-4813, Morgan, M.D. ORCID: https://orcid.org/0000-0003-0757-0711 and Marioni, J.C.
Nature Biotechnology 36 (5): 421-427. May 2018

Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, 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. ORCID: https://orcid.org/0000-0001-9280-9170, Büttner, M., Theis, F.J., Marr, C. and Buettner, F.
Bioinformatics 32 (8): 1241-1243. 15 April 2016

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, 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. ORCID: https://orcid.org/0000-0001-9280-9170, 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. ORCID: https://orcid.org/0000-0001-9280-9170, 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

Conference or Workshop Item

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. ORCID: https://orcid.org/0000-0001-9280-9170, 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

Sparse control of force field dynamics.
Bongini, M., Fornasier, M., Fröhlich, F. and Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170
In: 7th International Conference on NETwork Games, COntrol and OPtimization (NetGCoop), 29 - 31 Oct 2014, Trento, Italy. 8 June 2017

Review

Single-cell multi-omics and lineage tracing to dissect cell fate decision-making.
Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170 and Ludwig, L.S. ORCID: https://orcid.org/0000-0002-2916-2164
Stem Cell Reports 18 (1): 13-25. 10 January 2023

Letter

Resolving intra-tumor heterogeneity and clonal evolution of core-binding factor acute myeloid leukemia patients with single-cell resolution.
Hablesreiter, Raphael, Strzelecka, Paulina M. ORCID: https://orcid.org/0000-0003-0226-6788, Kopp, Klara, Estrada, Natalia, Dolnik, Anna, Tilgner, Marlon, Fustero-Torre, Coral, Thol, Felicitas, Heidel, Florian H., Heuser, Michael, Haghverdi, Laleh ORCID: https://orcid.org/0000-0001-9280-9170, Bullinger, Lars ORCID: https://orcid.org/0000-0002-5890-5510, Christen, Friederike and Damm, Frederik
Experimental Hematology & Oncology 14 (1): 127. 28 October 2025

Preprint

Exovelo: cell states velocity estimation without parameter fitting.
Kolb, Yiftach Josef ORCID: https://orcid.org/0009-0002-3752-3326 and Haghverdi, Laleh ORCID: https://orcid.org/0000-0001-9280-9170
bioRxiv : 2025.07.02.662720v2. 12 September 2025