Publications

2022

1. Bouland, G.A., Mahfouz, A., Reinders, M.J.T. The rise of sparser single-cell RNAseq datasets; consequences and opportunities. Preprint at https://www.biorxiv.org/content/10.1101/2022.05.20.492823v1 (2022).

2. Bruinsma, B., Pattij, T., Mansvelder, H.D. Prefrontal cortical to mediodorsal thalamus projection neurons regulate post-error adaptive control of behavior. eNeuro 9, ENEURO.0254-22.2022; 1523/ENEURO.0254-22.2022 (2022).

3. Donega, V., van der Geest, A.T., Sluijs, J.A., van Dijk, R.E. et al. Single-cell profiling of human subventricular zone progenitors identifies SFRP1 as a target to re-activate progenitors. Nat. Commun. 13, 1036; 1038/s41467-022-28626-9 (2022).

4. van Elzelingen, W., Goedhoop, J., Warnaar, P.J., Arbab, T. et al. A unidirectional but not uniform striatal landscape of dopamine signaling for motivational stimuli. Proc. Natl. Acad. Sci. U.S.A. 119, e2117270119; 10.1073/pnas.2117270119 (2022).

5. van Elzelingen, W., Warnaar, P.J., Matos, J., Bastet, W. et al. Striatal dopamine dynamics during action-sequence habit formation are stable and region-specific. Curr. Biol. 32, 1163-1174.e6; 10.1016/j.cub.2021.12.027 (2022).

6. Galakhova, A.A., Hunt, S., Wilbers, R., Heyer, D.B. et al. Evolution of cortical neurons supporting human cognition. Trends Cogn. Sci. 26, 909-922; 1016/j.tics.2022.08.012 (2022).

7. Goedhoop, J., van den Boom, B.J.G., Robke, R., Veen, F. et al. Nucleus-accumbens dopamine tracks aversive stimulus duration and prediction but not value or prediction error. eLife 11:e82711; 7554/eLife.82711 (2022).

8. van de Haar, L.L., Riga, D, Boer, J.E., Garritsen, O. et al. Molecular signatures and cellular diversity during mouse habenula development. Cell Rep. 40, 111029; 1016/j.celrep.2022.111029 (2022).

9. Hunt, S., Leibner, Y., Mertens, E.J., Barros-Zulaica, N, et al. Strong and reliable synaptic communication between pyramidal neurons in adult human cerebral cortex. Cereb. Cortex. bhac246; 10.1093/cercor/bhac246 (2022).

10. Jorstad, N.L., Song, J.H.T., Exposito-Alonso, D., Suresh, H. et al. Comparative transcriptomics reveals human-specific cortical features. Preprint at https://www.biorxiv.org/content/10.1101/2022.09.19.508480v1 (2022).

11. Kakava-Georgiadou, N., Drkelic, V., Garner, K.M., Luijendijk et al. Molecular profile and response to energy deficit of leptin-receptor neurons in the lateral hypothalamus. Sci. Rep. 12, 13374; 10.1038/s41598-022-16492-w (2022).

12. Koutlas, I., Linders, L.E., van der Starre, S.E., Wolterink-Donselaar, I.G. et al. Characterizing and TRAPing a social stress-activated neuronal ensemble in the ventral tegmental area. Front. Behav. Neurosci. 16, 936087; 3389/fnbeh.2022.936087 (2022).

13. Linders, L.E., Patrikiou, L., Soiza-Reilly, M., Schut, E.H.S. et al. Stress-driven potentiation of lateral hypothalamic synapses onto ventral tegmental area dopamine neurons causes increased consumption of palatable food. Nat. Commun. 13, 6898; 10.1038/s41467-022-34625-7 (2022).

14. Michielsen, L., Lotfollahi, M., Strobl, D., Sikkema, L. et al. Single-cell reference mapping to construct and extend cell type hierarchies. Preprint at https://www.biorxiv.org/content/10.1101/2022.07.07.499109v1 (2022).

15. Michielsen, L., Reinders, M.J.T., Mahfouz, A. Predicting cell population-specific gene expression from genomic sequence. Preprint at https://www.biorxiv.org/content/10.1101/2022.09.06.506837v1 (2022).

16. Montalban, E., Giralt, A., Taing, L., Schut, E. et al. Translational profiling of mouse dopaminoceptive neurons reveals region-specific gene expression, exon usage, and striatal prostaglandin E2 modulatory effects. Mol. Psychiatry 27, 2068-2079 (2022).

17. Olislagers, M., Rademaker, K., Adan, R.A.H., Lin, B.D., Luykx, J.J. Comprehensive analyses of RNA-seq and genome-wide data point to enrichment of neuronal cell type subsets in neuropsychiatric disorders. Mol. Psychiatry 27, 947-955 (2022).

18. Romero, C., Werme, J., Jansen, P.R., Gelernter, J. et al. Exploring the genetic overlap between 12 psychiatric disorders. Nat. Genet., in press.

19. Schipper, M., Posthuma, D. Demystifying non-coding GWAS variants: an overview of computational tools and methods. Hum. Mol. Genet. 31, R73-R83 (2022).

20. Singh, A., Reinders, M.J.T., Mahfouz, A., Abdelaal T. TopoGAN: unsupervised manifold alignment of single-cell data. Preprint at https://www.biorxiv.org/content/10.1101/2022.04.27.489829v1 (2022).

21. Tielbeek, J.J., Uffelmann, E., Williams, B.S., Colodro-Conde, L., Gagnon, É et al. Uncovering the genetic architecture of broad antisocial behavior through a genome-wide association study meta-analysis. Mol. Psychiatry; 10.1038/s41380-022-01793-3 (2022).

22. Zhang, M., Bouland, G.A., Holstege, H., Reinders, M.J.T. Identifying aging and Alzheimer’s disease associated somatic mutations in excitatory neurons from the human frontal cortex using whole genome sequencing and single cell RNA sequencing data. Preprint at https://www.medrxiv.org/content/10.1101/2022.05.25.22275538v1 (2022).

23. Zhang, Y., Miller, J.A., Park, J., Lelieveldt, B.P. et al. Reference-based cell type matching of spatial transcriptomics data. Preprint at https://www.biorxiv.org/content/10.1101/2022.03.28.486139v2 (2022).

2021

24. Abdelaal, T., Lelieveldt, B.P.F., Reinders, M.J.T., Mahfouz, A. SIRV: Spatial inference of RNA velocity at the single-cell resolution. Preprint at https://www.biorxiv.org/content/10.1101/2021.07.26.453774v1 (2021)

25. Aevermann, B.D., Zhang, Y., Novotny, M., Keshk, M. et al. A machine learning method for the discovery of minimum marker gene combinations for cell-type identification from single-cell RNA sequencing. Genome Res. 31, 1767-1780(2021).

26. Bakken, T.E., Jorstad, N.L., Hu, Q., Lake, B.B. et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598, 111-119 (2021)

27. Berg, J., Sorensen, S.A., Ting, J.T., Miller, J.A. et al. Human neocortical expansion involves glutamergic neuron diversification. Nature 598, 151-158 (2021).

28. Bouland, G.A., Mahfouz, A., Reinders, M.J.T. Differential analysis of binarized single-cell RNA sequencing data captures biological variation. NAR Genom. Bioinform. 3, lqab118; 10.1093/nargab/lqab118 (2021).

29. Keo, A., Dzyubachyk, O., van der Grond, J., Hafkemeijer, A. et al. Cingulate networks associated with gray matter loss in Parkinson’s disease show high expression of cholinergic genes in the healthy brain. Euro. J. Neurosci.53, 3727-3739 (2021)

30. de Kloet, S.F., Bruinsma, B., Terra, H., Heistek, T.S. et al. Bi-directional regulation of cognitive control by distinct prefrontal cortical output neurons to thalamus and striatum. Nat. Commun. 12, 1994; 10.1038/s41467-021-22260-7 (2021).

31. Meijer, M., Keo, A., van Leeuwen, J.M.C., Dzyubachyk, O., et al. Molecular characterization of the stress network in individuals at risk for schizophrenia. Neurobiol. Stress. 14, 100307; 10.1016/j.ynstr.2021.100307 (2021).

32. Michielsen, L., Reinders, J.T., Mahfouz, A. Hierarchical progressive learning of cell identities in single-cell data. Nat. Commun. 12, 2799; 10.1038/s41467-021-23196-8 (2021).

33. Moro, A., Van Nifterick, A., Toonen, R.F., Verhage, M. Dynamin controls neuropeptide secretion by organizing dense-core vesicle fusion sites. Sci. Adv. 7, eabf0659; 10.1126/sciadv.abf0659 (2021).

34. Robinson, R.A., Griffiths, S.C., van de Haar, L.L., Aricescu, A.R. et al. Simultaneous binding of guidance cues NET1 and RGM blocks extracellular NEO1 signaling. Cell 184, 2103-2120 (2021).

35. Uffelmann, E., Huang, Q.Q., Munung, N.S., de Vries, J. et al. Genome-wide association studies. Nat. Rev. Meth. Prim. 1, 59 (2021).

36. Wightman, D.P., Jansen, I.E., Savage, J.E., Shadrin, A.A. et al. A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer’s disease. Nat. Genet. 53, 1276-1282 (2021)

2020

37. Abdelaal, T., de Raadt, P., Lelieveldt, B.P.F., Reinders, M.J.T, Mahfouz A. SCHNEL: scalable clustering of high dimensional single-cell data. Bioinformatics 36, i849-i856; 10.1093/bioinformatics/btaa816 (2020).

38. Charrout, M., Reinders, M.J.T., Mahfouz, A. Untangling biological factors influencing trajectory inference from single cell data. NAR Genom. Bioinform. 2, lqaa053; 10.1093/nargab/lqaa053 (2020).

39. Terra, H., Bruinsma, B., de Kloet, S.F., van der Roest, M. et al. Prefrontal cortical projection neurons targeting dorsomedial striatum control behavioral inhibtion. Curr. Biol. 30, 4188-4200.e5; 10.1016/j.cub.2020.08.031 (2020).

40. Uffelmann, E., Posthuma, D. Emerging methods and resources for biological interrogation of neuropsychiatric polygenic signal. Biol. Psychiatry 89, 41-53; 10.1016/j.biopsych.2020.05.022 (2020).

41. Verhage, M., Sørensen, J.B. SNAREopathies: Diversity in mechanisms and symptoms. Neuron 107, 22-37 (2020).