2023
Meyer-Nava, S., Shetty, A. V., and Rivera-Mulia, J. C. (2023). Repli-seq sample preparation using cell sorting with cell-permeant dyes. Current Protocols, 3, e945. https://doi.org/10.1002/cpz1.945
Shetty, A., Lim, S., Strell, P., Steer, C. J., Rivera-Mulia, J. C. and Low, W. C. (2023). In Silico Stage-Matching of Human, Marmoset, Mouse, and Pig Embryos to Enhance Organ Development Through Interspecies Chimerism. Cell Transplant. 32. https://doi.org/10.1177/09636897231158728
2022
SenNet Consortium: Lee, P., Benz, C., Blood, P., Börner, K., Campisi, J., Chen, F., Daldrup-Link, H., De Jager, P., Ding, L., Duncan, F. E., Eickelberg, O., Fan, R., Finkel, T., Furman, D., Garovic, V., Gehlenborg, N., Glass, C., Heckenbach, I., Bar-Joseph, Z., Katiyar, P., Kim, S.-J., Königshoff, M., Kuchel, G., Lee, H., Lee, J. H., Ma, J., Ma, Q., Melov, S., Metis, K., Mora, A. L., Musi, N., Neretti, N., Passos, J. F., Rahman, I., Rivera-Mulia, J. C., Robson, P., Rojas, M., Roy, A. L., Schilling, B., Shi, P., Silverstein, J., Suryadevera, V., Xie, J., Wang, J., Wong, A.-K. I. and Niedernhofer, L. (2022). NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health. Nat Aging (2022). https://doi.org/10.1038/s43587-022-00326-5
Meyer-Nava, S., Rivera-Mulia, J. C. (2022). You shall not pass! Unveiling the barriers for cohesin-mediated loop extrusion. Mol Cell. 82(14):2541-2543. https://doi.org/10.1016/j.molcel.2022.06.028.
Rivera-Mulia, J. C., Trevilla-Garcia, C. and Martinez-Cifuentes, S. (2022). Optimized Repli-Seq: Improved DNA replication timing Analysis by next-generation sequencing. Chromosome Res. https://doi.org/10.1007/s10577-022-09703-7.
Kodali, S., Meyer-Nava, S., Landry, S., Chakraborty, A., Rivera-Mulia, J. C. & Feng, W. Epigenomic signatures associated with spontaneous and replication stress-induced DNA double strand breaks. Front. Genet. 13, (2022). https://doi.org/10.3389/fgene.2022.907547
Gilbert, D. M., Rivera-Mulia, J. C. Methods of identifying cellular replication timing signatures and methods of use thereof. US Patent Number: 11238956. Patent Granted 01-02-2022. Expiration 05-07-2040.
2020
The ENCODE Project Consortium: Moore, J. E., Purcaro, M.J., Pratt, H.E., Epstein, C.B., Shoresh, N., Adrian, J., Kawli, T., Davis, C.A., Dobin, A., Kaul, R., Halow, J., Van Nostrand, E.L., Freese, P., Gorkin, D.U., Shen, Y., He, Y., Mackiewicz, M., Pauli-Behn, F., Williams, B.A., Mortazavi. A., Keller, C.A., Zhang, X., Elhajjajy, S.I., Huey, J., Dickel, D.E., Snetkova, V., Wei, X., Wang, X., Rivera-Mulia, J. C., et al. (2020). Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710. https://doi.org/10.1038/s41586-020-2493-4.
The ENCODE Project Consortium: Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, et al. (2020). Perspectives on ENCODE. Nature 583:693-698. https://doi.org/10.1038/s41586-020-2449-8.
Zhang, J., Lee, D., Dhiman, V., Jiang, P., Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., Gu, M., Li, S., Lou, S., Xu, J., Lochovsky, L., Ung, M., Ma, L., Yu, S., Cao, Q., Harmanci, A., Yan, K., Sethi, A., Gursoy, G., Rutenberg, M., Rozowsky, J., Warrell, J., Emani, P., Yang, Y., Galeev., T., Kong, X., Liu, S., Li, X., Krishnan, J., Feng, J., Rivera-Mulia, J. C., et al. (2020). An integrative ENCODE resource for cancer genomics. Nat Commun 11, 3696. https://doi.org/10.1038/s41467-020-14743-w.
Sarni, D., Sasaki, T., Tur-Sinai, M. I., Miron, K., Rivera-Mulia, J. C., Magnuson, B., et al. (2020). 3D genome organization contributes to genome instability at fragile sites. Nat Commun. 11, 3613. https://doi.org/10.1038/s41467-020-17448-2
Sati, S., Bonev B., Szabo, Q., Jost, D., Bensadoun, P., Serra, F., Loubiere, V., Papadopoulos, G. L., Rivera-Mulia, J. C., Fritsch, L., Bouret, P., Castillo, D., Gelpi, J. L., Orozco, M., Vaillant, C., Pellestor, F., Bantignies, F., Marti-Renom, M. A., Gilbert, D. M., Lemaitre, J. M., Cavalli, G. (2020). 4D Genome Rewiring during Oncogene-Induced and Replicative Senescence. Mol Cell. pii: S1097-2765(20)30155-6. https://doi.org/10.1016/j.molcel.2020.03.007.
2019
Rivera-Mulia, J. C., Sasaki, T., Trevilla-Garcia, C., Nakamichi, N., Knapp, D., Hammond, C., et al. (2019). Replication timing alterations in leukemia affect clinically-relevant chromosome domains. Blood Advances. 3(21):3201-3213. https://doi.org/10.1182/bloodadvances.2019000641.
Rivera-Mulia, J. C., Kim, S., Gabr, H., Chakraborty, A., Ay, F., Kahveci, T., Gilbert, D. M. (2019). Replication timing networks reveal a link between transcription regulatory circuits and replication timing control. Genome Research. 29(9):1415-1428. http://doi.org/10.1101/gr.247049.118.
Dileep, V., Wilson, K., Marchal, C., Lyu, X., Zhao, P., Li, B., Poulet, A., Bartlett, D., Rivera-Mulia, J. C., et al. (2019). Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment. Stem Cell Reports. http://doi.org/10.1016/j.stemcr.2019.05.021.
Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner J., Rivera-Mulia, J. C., Trevilla-Garcia, C., et al. (2019) Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell. Feb 7;176(4):816–8. https://doi.org/10.1016/j.cell.2018.11.036.
Poulet, A., Li, B., Rivera-Mulia, J. C., Dubos, T., Gilbert, D. M., Quin, Z. S. (2019). RT States: systematic annotation of the human genome using cell type-specific replication timing programs. Bioinformatics. 35(13), 2019, 2167–2176. https://doi.org/10.1093/bioinformatics/bty957.
2018
Rivera-Mulia, J. C., Dimond, A., Vera, D., Trevilla-Garcia, C., Sasaki, T., Zimmerman, J., Dupont, C., Gribnau, J., Fraser, P., Gilbert D. M. (2018). Allele-specific control of replication timing and genome organization during development. Genome Research, June; 28(6), 800–811. http://doi.org/10.1101/gr.232561.117.
Rivera-Mulia, J. C., Schwerer, H., Besnard, E., Desprat, R., Trevilla-García, C., Sima, J., Bensadoun, P., Zouaoui, A,. Gilbert, D. M. Lemaitre, J. M. (2018). Cellular senescence induces replication stress with almost no affect on DNA replication timing. Cell Cycle, August 21; 17(13), 1667–1681. http://doi.org/10.1080/15384101.2018.1491235.
Dixon, J., Xu, J., Dileep, V., Zhan, Y., Song, F., Le, V.T., Yardimci, G., Chakraborty, A., Bann, D., Wang Y., Clark, R., Zhang, L., Yang, H., Liu, T., Lyyanki, S., An, L., Pool, C., Sasaki, T., Rivera-Mulia, J. C., Ozadam, H., et al. (2018). Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics, September 10; 4(10), 1–1398. http://doi.org/10.1038/s41588-018-0195-8.
Marchal, C., Sasaki, T., Vera, D., Wilson, K., Sima, J., Rivera-Mulia, J. C., Trevilla-Garcia, C., et al. (2018). Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nature Protocols, March 29; 13(5), 819–839. http://doi.org/10.1038/nprot.2017.148.
2017
Rivera-Mulia, J. C., Desprat, R., Trevilla-Garcia, C., Cornacchia, D., Schwerer, H., Sasaki, T., Sima, J., Fells, T., Studer, L., Lemaitre, J. M., Gilbert, D. M. (2017). DNA replication timing alterations as a novel marker of progeroid diseases. Proc Natl Acad Sci USA. 114(51): E10972-E10980. https://doi.org/10.1073/pnas.1711613114.
Zhao, P. A., Rivera-Mulia, J. C., Gilbert, D. M. (2017). Replication Domains: Genome Compartmentalization into Functional Replication Units. Adv Exp Med Biol. https://doi.org/10.1007/978-981-10-6955-0_11.
Sasaki, T., Rivera-Mulia, J. C., Vera, D., Zimmerman, J., Das, S., Padget, M., Nakamichi, N., Chang, B., Tyner, J., Druker, B., Weng, A., Civin, C., Eaves, C., Gilbert D. M. (2017). Stability of patient-specific features of altered DNA replication timing in xenografts of primary human acute lymphoblastic leukemia. Experimental Hematology 51:71-82. e3. https://doi.org/10.1016/j.exphem.2017.04.004.
Silva-Santiago, E., Rivera‐Mulia, J. C., Aranda-Anzaldo, A. (2017). The Set of Structural DNA‐Nuclear Matrix Interactions in Neurons Is Cell‐Type Specific and Rather Independent of Functional Constraints. Journal of Cellular Biochemistry. 118:2151–2160. https://doi.org/10.1002/jcb.25852.
2016
Rivera-Mulia, J. C., Gilbert, D. M. (2016). Replicating large genomes: divide and conquer. Molecular Cell 62 (5), 756-765. https://doi.org/10.1016/j.molcel.2016.05.007.
Rivera-Mulia, J. C., Gilbert, D. M. (2016). Replication timing and transcriptional control: beyond cause and effect—part III. Current Opinion in Cell Biology 40, 168-178. https://doi.org/10.1016/j.ceb.2016.03.022.
2015
Rivera-Mulia, J. C., Buckley, Q., Sasaki, T., Zimmerman, J., Didier, R., Nazor, K., Loring, J. F., Lian, Z., Weissman, S., Robins, A. J., Schulz, T. C., Menendez, L., Kulik, M. J., Dalton, S., Gabr, H., Kahveci, T., Gilbert, D. M. (2015). Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells. Genome Research 25 (8), 1091-1103. http://www.genome.org/cgi/doi/10.1101/gr.187989.114.
Gabr, H., Rivera-Mulia, J. C., Gilbert, D. M., Kahveci, T. (2015). Computing interaction probabilities in signaling networks. EURASIP Journal on Bioinformatics and Systems Biology 2015 (1), 1. https://doi.org/10.1186/s13637-015-0031-8.
Dileep, V., Rivera-Mulia, J. C., Sima, J., Gilbert, D. M. (2016). Large-scale chromatin structure–function relationships during the cell cycle and development: insights from replication timing. Cold Spring Harbor symposia on quantitative biology, 027284. https://doi.org/10.1101/sqb.2015.80.027284.
2014
Hannibal, R. L., Chuong, E. B., Rivera-Mulia, J. C., Gilbert, D. M., Valouev, A., Baker, J. C. (2014). Copy Number Variation Is a Fundamental Aspect of the Placental Genome. PLoS Genetics 10, no. 5: e1004290. https://doi.org/10.1371/journal.pgen.1004290.
2011
Rivera-Mulia, J. C., Hernandez-Munoz, R., Martinez, F., Aranda-Anzaldo, A. (2011). DNA moves sequentially towards the nuclear matrix during DNA replication in vivo. BMC Cell Biol. 12 (1): 3. https://doi.org/10.1186/1471-2121-12-3.
2010
Rivera-Mulia, J. C. and Aranda-Anzaldo, A. (2010). Determination of the in vivo structural DNA loop organization in the genomic region of the rat albumin locus by means of a topological approach. DNA Res 17(1): 23-35. https://doi.org/10.1093/dnares/dsp027.
2008
Rivera-Mulia, J. C. and Aranda-Anzaldo, A. (2008). Structure and function of the fundamental unit of DNA replication (the replicon) in eukaryotes. Ciencia Ergo Sum (15): 269-286. (Spanish).