Browse by Research Team

2024

Single-cell time series analysis reveals the dynamics of HSPC response to inflammation.
Bouman, B.J. and Demerdash, Y. and Sood, S. and Grünschläger, F. and Pilz, F. and Itani, A.R. and Kuck, A. and Marot-Lassauzaie, V. and Haas, S. and 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

Adjustments to the reference dataset design improves cell type label transfer.
Mölbert, C. and Haghverdi, L.
bioRxiv : 2023.01.25.525533. 26 January 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. and Bouman, B.J. and Donaghy, F.D. and Demerdash, Y. and 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. and Kocks, C. and Leiz, J. and Karaiskos, N. and Boltengagen, A. and Cao, S. and Skopnik, C.M. and Klocke, J. and Hardenberg, J.H. and Stockmann, H. and Gotthardt, I. and Obermayer, B. and Haghverdi, L. and Wyler, E. and Landthaler, M. and Bachmann, S. and Hocke, A.C. and Corman, V. and Busch, J. and Schneider, W. and Himmerkus, N. and Bleich, M. and Eckardt, K.U. and Enghard, P. and 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. and Chakraborty, P. and Xu, T. and Hsueh, P.Y.S. and Sun, X. and Stiglic, G. and Crane, G. and Bian, J. and Haghverdi, L. and 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. and Lun, A.T.L. and Morgan, M.D. and Marioni, J.C.
Nature Biotechnology 36 (5): 421-427. May 2018

2017

Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.
Haghverdi, L. and Lun, A.T.L. and Morgan, M.D. and Marioni, J.C.
bioRxiv : 165118. 18 July 2017

Sparse control of force field dynamics.
Bongini, M. and Fornasier, M. and 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. and Büttner, M. and Wolf, F.A. and 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. and Haghverdi, L. and Büttner, M. and Theis, F.J. and Marr, C. and Buettner, F.
Bioinformatics 32 (8): 1241-1243. 15 April 2016

Diffusion pseudotime robustly reconstructs lineage branching.
Haghverdi, L. and Büttner, M. and Wolf, F. A. and Buettner, F. and Theis, F.J.
bioRxiv : 041384. 2 March 2016

2015

destiny – diffusion maps for large-scale single-cell data in R.
Angerer, P. and Haghverdi, L. and Büttner, M. and Theis, F.J. and Marr, C. and Buettner, F.
bioRxiv : 023309. 9 October 2015

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi, L. and 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. and Haghverdi, L. and 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. and Woodhouse, S. and Haghverdi, L. and Lilly, A.J. and Tanaka, Y. and Wilkinson, A.C. and Buettner, F. and Macaulay, I.C. and Jawaid, W. and Diamanti, E. and Nishikawa, S.I. and Piterman, N. and Kouskoff, V. and Theis, F.J. and Fisher, J. and Göttgens, B.
Nature Biotechnology 33 (3): 269-276. March 2015