M.J. (Marc Jan) Bonder

Assistant professorHe/Him

Faculty of Medical Sciences

E-mail:

m.j.bonder umcg.nl

Homepage ORCID Research Portal

Publications

A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines

Feng, C., Peets, E. M., Zhou, Y., Crepaldi, L., Usluer, S., Dunham, A., Braunger, J. M., Su, J., Strauss, M. E., Muraro, D., Xian Cheam, K. A., Bonder, M. J., Nogales, E. G., Cooper, S., Bassett, A., Leonard, S., Gu, Y., Fussing, B., Burke, D. & Parts, L., Stegle, O. & Velten, B., 11-Feb-2026, In: Cell Genomics. 6, 2, 23 p., 101076.

Research output: Contribution to journal › Article › Academic › peer-review

Federated single-cell QTL meta-analysis reveals novel disease mechanisms

eQTLgen Consortium, 23-Jan-2026, In: bioRxiv.

Research output: Contribution to journal › Article › Academic

Trans-eQTLs reveal the architecture of human gene regulatory networks.

IMI DIRECT Consortium, 5-Feb-2026, In: medRxiv : the preprint server for health sciences.

Research output: Contribution to journal › Article › Academic

Author Correction: Complex genetic variation in nearly complete human genomes (Nature, (2025), 644, 8076, (430-441), 10.1038/s41586-025-09140-6)

Logsdon, G. A., Ebert, P., Audano, P. A., Loftus, M., Porubsky, D., Ebler, J., Yilmaz, F., Hallast, P., Prodanov, T., Yoo, D. A., Paisie, C. A., Harvey, W. T., Zhao, X., Martino, G. V., Henglin, M., Munson, K. M., Rabbani, K., Chin, C. S., Gu, B. & Ashraf, H., Scholz, S., Austine-Orimoloye, O., Balachandran, P., Bonder, M. J., Cheng, H., Chong, Z., Crabtree, J., Gerstein, M., Guethlein, L. A., Hasenfeld, P., Hickey, G., Hoekzema, K., Hunt, S. E., Jensen, M., Jiang, Y., Koren, S., Kwon, Y., Li, C., Li, H., Li, J., Norman, P. J., Oshima, K. K., Paten, B., Phillippy, A. M., Pollock, N. R., Rausch, T., Rautiainen, M., Song, Y. & Söylev, A., 18-Sept-2025, In: Nature. 645, 8081, p. E6

Research output: Contribution to journal › Erratum

Complex genetic variation in nearly complete human genomes

Logsdon, G. A., Ebert, P., Audano, P. A., Loftus, M., Porubsky, D., Ebler, J., Yilmaz, F., Hallast, P., Prodanov, T., Yoo, D. A., Paisie, C. A., Harvey, W. T., Zhao, X., Martino, G. V., Henglin, M., Munson, K. M., Rabbani, K., Chin, C. S., Gu, B. & Ashraf, H., Scholz, S., Austine-Orimoloye, O., Balachandran, P., Bonder, M. J., Cheng, H., Chong, Z., Crabtree, J., Gerstein, M., Guethlein, L. A., Hasenfeld, P., Hickey, G., Hoekzema, K., Hunt, S. E., Jensen, M., Jiang, Y., Koren, S., Kwon, Y., Li, C., Li, H., Li, J., Norman, P. J., Oshima, K. K., Paten, B., Phillippy, A. M., Pollock, N. R., Rausch, T., Rautiainen, M., Song, Y., Söylev, A., Sulovari, A., Surapaneni, L., Tsapalou, V., Zhou, W., Zhou, Y., Zhu, Q., Zody, M. C., Mills, R. E., Devine, S. E., Shi, X., Talkowski, M. E., Chaisson, M. J. P., Dilthey, A. T., Konkel, M. K., Korbel, J. O., Lee, C., Beck, C. R., Eichler, E. E. & Marschall, T., 14-Aug-2025, In: Nature. 644, 8076, p. 430-441 12 p.

Research output: Contribution to journal › Article › Academic › peer-review

Genetic architecture and mechanisms of host-microbiome interactions from a multi-cohort analysis of outbred laboratory rats

Tonnelé, H., Chen, D., Morillo, F., Garcia-Calleja, J., Chitre, A. S., Johnson, B. B., Sanches, T. M., Cheng, R., Bonder, M. J., Gonzalez, A., Kosciolek, T., George, A. M., Han, W., Holl, K., Horvath, A., Ishiwari, K., King, C. P., Lamparelli, A. C., Martin, C. D. & Martinez, A. G., Netzley, A. H., Tripi, J. A., Wang, T., Bosch, E., Doris, P. A., Stegle, O., Chen, H., Flagel, S. B., Meyer, P. J., Richards, J. B., Robinson, T. E., Solberg Woods, L. C., Polesskaya, O., Knight, R., Palmer, A. A. & Baud, A., Dec-2025, In: Nature Communications. 16, 1, 17 p., 10126.

Research output: Contribution to journal › Article › Academic › peer-review

Optimized summary-statistic-based single-cell eQTL meta-analysis

sc-eQTLGen Consortium, Korshevniuk, M., Westra, H. J., Oelen, R., van der Wijst, M. G. P., Franke, L. & Bonder, M. J., 4-Aug-2025, In: Scientific Reports. 15, 1, 13 p., 28407.

Research output: Contribution to journal › Article › Academic › peer-review

Structural and transduction patterns of human-specific polymorphic SVA insertions

Human Genome Structural Variation Consortium, Kirby, A. E., Loftus, M., Golba, E. C. & Konkel, M. K., Dec-2025, In: Mobile dna. 16, 42, 16 p., 42.

Research output: Contribution to journal › Article › Academic › peer-review

Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions

Zhang, Z., Li, W., Zhan, Q., Aillaud, M., Botey-Bataller, J., Zoodsma, M., ter Horst, R., Joosten, L. A. B., Bock, C., Schulte, L. N., Xu, C. J., Netea, M. G., Bonder, M. J. & Li, Y., Dec-2025, In: Nature Communications. 16, 1, 16 p., 7134.

Research output: Contribution to journal › Article › Academic › peer-review

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Li, C., Bonder, M. J., Syed, S., Jensen, M., Gerstein, M. B., Zody, M. C., Chaisson, M. J. P., Talkowski, M. E., Marschall, T., Korbel, J. O., Eichler, E. E., Lee, C. & Shi, X., Dec-2024, In: Genome Research. 34, 12, p. 2304-2318 15 p.

Research output: Contribution to journal › Article › Academic › peer-review