Publications
Preprints
Published
Selected publications. For others, please click here.
| Trevor Long, Tapas Bhattacharyya, Andrea Repele, Madison Naylor, Sunil Nooti, Shawn Krueger, Manu (2023) The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation, G3 Genes|Genomes|Genetics, Volume 14, Issue 2, February 2024, jkad269. link |
| Nooti S, Naylor M, Long T, Groll B, Manu (2023) LucFlow: A method to measure Luciferase reporter expression in single cells. PLoS ONE 18(10): e0292317. link |
| Joanna-Elzbieta Handzlik and Manu (2022) Data-driven modeling predicts gene regulatory network dynamics during the differentiation of multipotential hematopoietic progenitors. PLoS Comput Biol 18(1): e1009779. link |
| Joanna-Elzbieta Handzlik, Yen Lee Loh, and Manu (2021) Dynamic Modeling of Transcriptional Gene Regulatory Networks. In: Methods in Molecular Biology 2328. link |
| David Fehr, Joanna-Elzbieta Handzlik, Manu, and Yen Lee Loh (2019) Classification-based inference of dynamical models of gene regulatory networks. G3 Genes|Genomes|Genetics 9(12): 4183–4195 link pdf |
| Andrea Repele and Manu (2019) Robust normalization of Luciferase reporter data. Methods and Protocols, 2(3): 62 link pdf |
| Andrea Repele, Shawn Krueger, Tapas Bhattacharyya, Michelle Y Tuineau, and Manu (2019) The regulatory control of Cebpa enhancers and silencers in the myeloid and red-blood cell lineages. PLoS One, 14(6): e0217580 link pdf |
| E. Bertolino, J. Reinitz, and Manu (2016) The analysis of novel distal Cebpa enhancers and silencers using a transcriptional model reveals the complex regulatory logic of hematopoietic lineage specification. Developmental Biology, 413: 128–141 link pdf |
| H. Wu, Manu , R. Jiao, and J. Ma (2015) Temporal and spatial dynamics of scaling-specific features of a gene regulatory network in Drosophila. Nature Communications, 6: 10031 link |
| Manu, M. Z. Ludwig, and M. Kreitman (2013) Sex-specific pattern formation during early Drosophila development. Genetics, 194(1): 163–73 link pdf |
| M. Z. Ludwig, Manu, R. Kittler, K. P. White, and M. Kreitman (2011) Consequences of eukaryotic enhancer architecture for gene expression dynamics, development, and fitness. PLoS Genetics, 7: e1002364 link pdf |
| Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, A. Kim, O. Radulescu, C. E. Vanario-Alonso, D. H. Sharp, M. Samsonova, and J. Reinitz (2009) Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biology, 7: e1000049 link pdf |
| Manu, S. Surkova, A. V. Spirov, V. Gursky, H. Janssens, A. Kim, O. Radulescu, C. E. Vanario-Alonso, D. H. Sharp, M. Samsonova, and J. Reinitz (2009) Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Computational Biology, 5: e1000303 link pdf |
| J. Jaeger, S. Surkova, M. Blagov, H. Janssens, D. Kosman, K. N. Kozlov, Manu, E. Myasnikova, C. E. Vanario- Alonso, M. Samsonova, D. H. Sharp, and J. Reinitz (2004) Dynamic control of positional information in the early Drosophila embryo. Nature, 430: 368–371 link |