2022
Preprint: Van Bavel, C., Thiels, W., Jelier, R., 2022 Cell shape characterization, alignment and comparison using FlowShape. bioRxiv. doi: 10.1101/2022.12.08.519700
Preprint: Cuvelier, M., Thiels, W., Jelier, R., Smeets, B. 2022. Stability of asymmetric cell division under confinement: A deformable cell model of cytokinesis applied to C. elegans development. bioRxiv. doi: 10.1101/2022.03.17.484706
2021
Caroti, F., Thiels, W., Vansalmbrouck, M., Jelier, R., 2021 Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell. Front. Cell Dev. Biol. 9:702741
Thiels, W., Smeets, B., Cuvelier, M., Caroti, F., Jelier, R., 2021 spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos. Bioinformatics btab557.
Jankele, R., Jelier, R., Gönczy P., 2021 Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis. eLife 10:e61714.
Helsen, J., Jelier R., 2021. Experimental evolution to understand the interplay between genetics and adaptation. In: Evolutionary Systems Biology 2.0, Advances in Experimental Medicine and Biology. Springer, New York, NY, 115-134; preprint
2020
Helsen, J., Voordeckers, K., Vanderwaeren, L., Santermans, T., Tsontaki, M., Verstrepen, K.J., Jelier R. 2020. Gene loss predictably drives evolutionary adaptation. Molecular Biology and Evolution 37 (10), 2989-3002
Watteyne, J., Peymen, K., Van der Auwera, P., Borghgraef, C., Vandewyer, E., Van Damme, S., Rutten, I., Lammertyn, J., Jelier, R., Schoofs, L., Beets, I. 2020 Neuromedin U signaling regulates retrieval of learned salt avoidance in a C. elegans gustatory circuit. Nature Communications 11 (1), 1-16
2019
Helsen, J., Frickel, J., Jelier, R., Verstrepen, K.J. 2019. Network hubs affect evolvability. PLOS Biology, 17 (1), Art.No. ARTN e3000111
2018
Molenaars, M., Janssens, G.E., Santermans, T., Lezzerini, M., Jelier, R., MacInnes, A.W., Houtkooper, R.H. 2018. Mitochondrial ubiquinone-mediated longevity is marked by reduced cytoplasmic mRNA translation. Life Science Alliance, 1 (5), Art.No. ARTN e201800082.
2017
Hastings, J., Mains, A., Artal-Sanz, M., Bergmann, S., Braeckman, B.P., Bundy, J., Cabreiro, F., Dobson, P., Ebert, P., Hattwell, J., Hefzi, H., Houtkooper, R.H., Jelier, R., Joshi, C., Kothamachu, V.B., Lewis, N., Lourenço, A.B., Nie, Y., Norvaisas, P., Pearce, J., Riccio, C., Rodriguez, N., Santermans, T., Scarcia, P., Schirra, H.J., Sheng, M., Smith, R., Suriyalaksh, M., Towbin, B., Tuli, M.A., Weeghel, M.V., Weinkove, D., Zečić, A., Zimmermann, J., Novère, N.L., Kaleta, C., Witting, M., Casanueva, O. (2017). WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series. Worm, 6, Art.No. 2, e1373939-e1373939.
2016
Jelier, R*., AV. Kruger, J. Swoger, T. Zimmermann and B: Lehner*, "Compensatory cell movements confer robustness to mechanical deformation during embryonic development", 2016. Cell Systems, 3 (2), 160-171 manuscript and figures.
2015
Jelier, R*., AV. Krueger*, O. Dzyubachyk, T. Zimmerman, EM. Meijering, and B. Lehner. 2015. Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis. Dev Biol 398 (2): 153–162. (* shared first author)
Voordeckers, K., J. Kominek, A. Das, A. Espinosa-Cantu, D. De Maeyer, A. Arslan, M. Van Pee, E. van der Zande, W. Meert, Y. Yang, B. Zhu, K. Marchal, A. DeLuna, V. van Noort, R. Jelier, and KJ. Verstrepen. 2015. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PLoS Genet 11 (11): 1005635.
2014
Essers, PB., J. Nonnekens, YJ. Goos, MC. Betist, MD. Viester, B. Mossink, N. Lansu, HC. Korswagen, R. Jelier, AB. Brenkman, and AW. MacInnes. 2014. A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension. Cell Rep pii: S2211-1247(14)01058-4.
2011
Jelier,R., Jennifer I Semple, Rosa Garcia-Verdugo, and B. Lehner. 2011. Predicting phenotypic variation in
yeast from individual genome sequences. Nat Genet 43 (12): 1270–1274.
Jelier, R., JJ. Goeman, KM. Hettne, MJ. Schuemie, JT den Dunnen, and PAC. ’t Hoen. 2011. Literature- aided interpretation of gene expression data with the weighted global test. Brief Bioinform 12 (5): 518–529.
Francesconi, M., R. Jelier, and B. Lehner. 2011. Integrated genome-scale prediction of detrimental mutations in transcription networks. PLoS Genet 7 (5): 1002077.
2009
Dzyubachyk, O, R. Jelier, B. Lehner, W. Niessen, and E. Meijering. 2009. Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data. Conf Proc IEEE Eng Med Biol Soc 2009: 5356–5359.
2008
Jelier, R., MJ. Schuemie, A. Veldhoven, LCJ. Dorssers, GW Jenster, and JA. Kors. 2008. Anni 2.0: a
multipurpose text-mining tool for the life sciences. Genome Biol 9 (6): 96.
Jelier, R., PAC. ’t Hoen, E. Sterrenburg, JT. den Dunnen, GJB van Ommen, JA. Kors, and B. Mons. 2008. Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics 9: 291.
Jelier, R., MJ. Schuemie, PJ. Roes, EM. van Mulligen, and JA. Kors. 2008. Literature-based concept profiles for gene annotation: the issue of weighting. Int J Med Inform 77 (5): 354–362.
Jelier, R. 2008. Text Mining applied to Molecular Biology. Doctoral Thesis, Erasmus University Rotterdam.
2007 and before
Jelier, R., GW Jenster, LCJ Dorssers, BJ. Wouters, PJM Hendriksen, B. Mons, R. Delwel, and JA. Kors. 2007. Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinformatics 8: 14.
Jelier R., GW. Jenster, LCJ. Dorssers, van der Eijk CC, van Mulligen EM, Mons B, et al. Co- occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics. 2005 May;21(9):2049–2058.
Alako, BTF., A. Veldhoven, S. van Baal, R. Jelier, S. Verhoeven, T. Rullmann, J. Polman, and GW. Jenster. 2005. CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics 6: 51.
Schuemie, MJ., M. Weeber, BJA. Schijvenaars, EM. van Mulligen, CC. van der Eijk, R. Jelier, B. Mons, and JA. Kors. 2004. Distribution of information in biomedical abstracts and full-text publications. Bioinformatics 20 (16): 2597–2604.
Miscellaneous
Schuemie, MJ., R. Jelier, and J. A. Kors. 2007. Peregrine: Lightweight gene name normal- ization by dictionary lookup. In Proceedings of the biocreative, Vol. 2, 23–25. (Peregrine is a software written by Dr. Schuemie and myself. It was commercialised and sold by the department)
Jelier, R., MJ. Schuemie, CC. van der Eijk, M. Weeber, E van Mulligen, B. Schijvenaars, B. Mons, and JA. Kors. 2003. Searching for GeneRIFs: concept-based query expansion and Bayes classification. In Proceedings of TREC, 167–174. (This paper scored best for one of the competition's tasks.)
Preprint: Van Bavel, C., Thiels, W., Jelier, R., 2022 Cell shape characterization, alignment and comparison using FlowShape. bioRxiv. doi: 10.1101/2022.12.08.519700
Preprint: Cuvelier, M., Thiels, W., Jelier, R., Smeets, B. 2022. Stability of asymmetric cell division under confinement: A deformable cell model of cytokinesis applied to C. elegans development. bioRxiv. doi: 10.1101/2022.03.17.484706
2021
Caroti, F., Thiels, W., Vansalmbrouck, M., Jelier, R., 2021 Wnt Signaling Induces Asymmetric Dynamics in the Actomyosin Cortex of the C. elegans Endomesodermal Precursor Cell. Front. Cell Dev. Biol. 9:702741
Thiels, W., Smeets, B., Cuvelier, M., Caroti, F., Jelier, R., 2021 spheresDT/Mpacts-PiCS: cell tracking and shape retrieval in membrane-labeled embryos. Bioinformatics btab557.
Jankele, R., Jelier, R., Gönczy P., 2021 Physically asymmetric division of the C. elegans zygote ensures invariably successful embryogenesis. eLife 10:e61714.
Helsen, J., Jelier R., 2021. Experimental evolution to understand the interplay between genetics and adaptation. In: Evolutionary Systems Biology 2.0, Advances in Experimental Medicine and Biology. Springer, New York, NY, 115-134; preprint
2020
Helsen, J., Voordeckers, K., Vanderwaeren, L., Santermans, T., Tsontaki, M., Verstrepen, K.J., Jelier R. 2020. Gene loss predictably drives evolutionary adaptation. Molecular Biology and Evolution 37 (10), 2989-3002
Watteyne, J., Peymen, K., Van der Auwera, P., Borghgraef, C., Vandewyer, E., Van Damme, S., Rutten, I., Lammertyn, J., Jelier, R., Schoofs, L., Beets, I. 2020 Neuromedin U signaling regulates retrieval of learned salt avoidance in a C. elegans gustatory circuit. Nature Communications 11 (1), 1-16
2019
Helsen, J., Frickel, J., Jelier, R., Verstrepen, K.J. 2019. Network hubs affect evolvability. PLOS Biology, 17 (1), Art.No. ARTN e3000111
2018
Molenaars, M., Janssens, G.E., Santermans, T., Lezzerini, M., Jelier, R., MacInnes, A.W., Houtkooper, R.H. 2018. Mitochondrial ubiquinone-mediated longevity is marked by reduced cytoplasmic mRNA translation. Life Science Alliance, 1 (5), Art.No. ARTN e201800082.
2017
Hastings, J., Mains, A., Artal-Sanz, M., Bergmann, S., Braeckman, B.P., Bundy, J., Cabreiro, F., Dobson, P., Ebert, P., Hattwell, J., Hefzi, H., Houtkooper, R.H., Jelier, R., Joshi, C., Kothamachu, V.B., Lewis, N., Lourenço, A.B., Nie, Y., Norvaisas, P., Pearce, J., Riccio, C., Rodriguez, N., Santermans, T., Scarcia, P., Schirra, H.J., Sheng, M., Smith, R., Suriyalaksh, M., Towbin, B., Tuli, M.A., Weeghel, M.V., Weinkove, D., Zečić, A., Zimmermann, J., Novère, N.L., Kaleta, C., Witting, M., Casanueva, O. (2017). WormJam: A consensus C. elegans Metabolic Reconstruction and Metabolomics Community and Workshop Series. Worm, 6, Art.No. 2, e1373939-e1373939.
2016
Jelier, R*., AV. Kruger, J. Swoger, T. Zimmermann and B: Lehner*, "Compensatory cell movements confer robustness to mechanical deformation during embryonic development", 2016. Cell Systems, 3 (2), 160-171 manuscript and figures.
2015
Jelier, R*., AV. Krueger*, O. Dzyubachyk, T. Zimmerman, EM. Meijering, and B. Lehner. 2015. Comprehensive single cell-resolution analysis of the role of chromatin regulators in early C. elegans embryogenesis. Dev Biol 398 (2): 153–162. (* shared first author)
Voordeckers, K., J. Kominek, A. Das, A. Espinosa-Cantu, D. De Maeyer, A. Arslan, M. Van Pee, E. van der Zande, W. Meert, Y. Yang, B. Zhu, K. Marchal, A. DeLuna, V. van Noort, R. Jelier, and KJ. Verstrepen. 2015. Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PLoS Genet 11 (11): 1005635.
2014
Essers, PB., J. Nonnekens, YJ. Goos, MC. Betist, MD. Viester, B. Mossink, N. Lansu, HC. Korswagen, R. Jelier, AB. Brenkman, and AW. MacInnes. 2014. A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension. Cell Rep pii: S2211-1247(14)01058-4.
2011
Jelier,R., Jennifer I Semple, Rosa Garcia-Verdugo, and B. Lehner. 2011. Predicting phenotypic variation in
yeast from individual genome sequences. Nat Genet 43 (12): 1270–1274.
Jelier, R., JJ. Goeman, KM. Hettne, MJ. Schuemie, JT den Dunnen, and PAC. ’t Hoen. 2011. Literature- aided interpretation of gene expression data with the weighted global test. Brief Bioinform 12 (5): 518–529.
Francesconi, M., R. Jelier, and B. Lehner. 2011. Integrated genome-scale prediction of detrimental mutations in transcription networks. PLoS Genet 7 (5): 1002077.
2009
Dzyubachyk, O, R. Jelier, B. Lehner, W. Niessen, and E. Meijering. 2009. Model-based approach for tracking embryogenesis in Caenorhabditis elegans fluorescence microscopy data. Conf Proc IEEE Eng Med Biol Soc 2009: 5356–5359.
2008
Jelier, R., MJ. Schuemie, A. Veldhoven, LCJ. Dorssers, GW Jenster, and JA. Kors. 2008. Anni 2.0: a
multipurpose text-mining tool for the life sciences. Genome Biol 9 (6): 96.
Jelier, R., PAC. ’t Hoen, E. Sterrenburg, JT. den Dunnen, GJB van Ommen, JA. Kors, and B. Mons. 2008. Literature-aided meta-analysis of microarray data: a compendium study on muscle development and disease. BMC Bioinformatics 9: 291.
Jelier, R., MJ. Schuemie, PJ. Roes, EM. van Mulligen, and JA. Kors. 2008. Literature-based concept profiles for gene annotation: the issue of weighting. Int J Med Inform 77 (5): 354–362.
Jelier, R. 2008. Text Mining applied to Molecular Biology. Doctoral Thesis, Erasmus University Rotterdam.
2007 and before
Jelier, R., GW Jenster, LCJ Dorssers, BJ. Wouters, PJM Hendriksen, B. Mons, R. Delwel, and JA. Kors. 2007. Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. BMC Bioinformatics 8: 14.
Jelier R., GW. Jenster, LCJ. Dorssers, van der Eijk CC, van Mulligen EM, Mons B, et al. Co- occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Bioinformatics. 2005 May;21(9):2049–2058.
Alako, BTF., A. Veldhoven, S. van Baal, R. Jelier, S. Verhoeven, T. Rullmann, J. Polman, and GW. Jenster. 2005. CoPub Mapper: mining MEDLINE based on search term co-publication. BMC Bioinformatics 6: 51.
Schuemie, MJ., M. Weeber, BJA. Schijvenaars, EM. van Mulligen, CC. van der Eijk, R. Jelier, B. Mons, and JA. Kors. 2004. Distribution of information in biomedical abstracts and full-text publications. Bioinformatics 20 (16): 2597–2604.
Miscellaneous
Schuemie, MJ., R. Jelier, and J. A. Kors. 2007. Peregrine: Lightweight gene name normal- ization by dictionary lookup. In Proceedings of the biocreative, Vol. 2, 23–25. (Peregrine is a software written by Dr. Schuemie and myself. It was commercialised and sold by the department)
Jelier, R., MJ. Schuemie, CC. van der Eijk, M. Weeber, E van Mulligen, B. Schijvenaars, B. Mons, and JA. Kors. 2003. Searching for GeneRIFs: concept-based query expansion and Bayes classification. In Proceedings of TREC, 167–174. (This paper scored best for one of the competition's tasks.)