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2009 |
| Mayoral, R. J., Pipkin, M. E., Pachkov, M., van Nimwegen, E., Rao, A. and Monticelli, S. (2009). MicroRNA-221-222 regulate the cell cycle in mast cells. J Immunol, 182(1), 433–445. |
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| Molina, N. and van Nimwegen, E. (2009). Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends Genet, 25(6), 243–247. |
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| Severin, J., Waterhouse, A. M., Kawaji, H., Lassmann, T., van Nimwegen, E., Balwierz, P. J., de Hoon, M. J., Hume, D. A., Carninci, P., Hayashizaki, Y., Suzuki, H., Daub, C. O., et al. (2009). FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol, 10(4), R39. |
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| Suzuki, H., Forrest, A. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J., Katayama, S., Schroder, K., et al. (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet, . |
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| Taddei, A., Van Houwe, G., Nagai, S., Erb, I., van Nimwegen, E. and Gasser, S. M. (2009). The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome Res, 19(4), 611–625. |
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| Balwierz, P. J., Carninci, P., Daub, C. O., Kawai, J., Hayashizaki, Y., Van Belle, W., Beisel, C. and van Nimwegen, E. J. (2009). Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol, 10(7), R79. |
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2008 |
| Molina, N. and van Nimwegen, E. (2008). The evolution of domain-content in bacterial genomes. Biol Direct, 3, 51. |
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| Schlecht, U., Erb, I., Demougin, P., Robine, N., Borde, V., van Nimwegen, E., Nicolas, A. and Primig, M. (2008). Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast. Mol Biol Cell, 19(5), 2193–2207. |
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| Berninger, P., Gaidatzis, D., van Nimwegen, E. and Zavolan, M. (2008). Computational analysis of small RNA cloning data. Methods, 44(1), 13–21. |
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| Chern, T. - M., Paul, N., van Nimwegen, E. and Zavolan, M. (2008). Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA Res, 15(2), 63–72. |
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| Burger, L. and van Nimwegen, E. (2008). Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method. Mol Syst Biol, 4, 165. |
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| Molina, N. and van Nimwegen, E. (2008). Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res, 18(1), 148–160. |
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2007 |
| Gaidatzis, D., van Nimwegen, E., Hausser, J. and Zavolan, M. (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC Bioinformatics, 8, 69. |
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| van Nimwegen, E. (2007). Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics, 8 Suppl 6, S4. |
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| Pachkov, M., Erb, I., Molina, N. and van Nimwegen, E. (2007). SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res, 35(Database issue), D127–31. |
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2006 |
| Chern, T. - M., van Nimwegen, E., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. and Zavolan, M. (2006). A simple physical model predicts small exon length variations. PLoS Genet, 2(4), e45. |
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| van Nimwegen, E., Paul, N., Sheridan, R. and Zavolan, M. (2006). SPA: a probabilistic algorithm for spliced alignment. PLoS Genet, 2(4), e24. |
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| Zavolan, M. and van Nimwegen, E. (2006). The types and prevalence of alternative splice forms. Curr Opin Struct Biol, 16(3), 362–367. |
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| van Nimwegen, E. (2006). Epidemiology. Influenza escapes immunity along neutral networks. Science, 314(5807), 1884–1886. |
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2005 |
| Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., et al. (2005). The transcriptional landscape of the mammalian genome. Science, 309(5740), 1559–1563. |
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| Speirs, C., van Nimwegen, E., Bolton, D., Zavolan, M., Duvall, M., Angleman, S., Siegel, R., Perelson, A. S. and Lenardo, M. J. (2005). Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. J Virol, 79(7), 4025–4032. |
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| Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E. and Zavolan, M. (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics, 6, 267. |
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2003 |
| Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., Magnasco, M. and Darnell, J. E. J. (2003). Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome Res, 13(8), 1863–1872. |
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2002 |
| van Nimwegen, E., Zavolan, M., Rajewsky, N. and Siggia, E. D. (2002). Probabilistic clustering of sequences: inferring new bacterial regulons by comparative genomics. Proc Natl Acad Sci U S A, 99(11), 7323–7328. |
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| Zavolan, M., van Nimwegen, E. and Gaasterland, T. (2002). Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res, 12(9), 1377–1385. |
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