He has directed the Millennium Nucleus Center for Web Research, RIBIDI (an Ibero American project funded by CYTED), and a project funded by Yahoo! Research, apart from smaller projects. He has participated in various research projects, such as the Millennium Institute for Cell Dynamics and Biotechnology, an ECOS/CONICYT project (Chile-France cooperation), AMYRI (a CYTED project), and a Fondef project. He currently participates in the Center for Biotecnology and Bioengineering (CeBiB) and the Millennium Institute for Foundational Research on Data (IMFD).
He has been PC (co-)chair of several conferences: SPIRE 2001, SCCC 2004, SPIRE 2005, SIGIR 2005 Posters, IFIP TCS 2006, a track of ENC 2007, SISAP 2008, SISAP 2012, LATIN 2016, SPIRE 2018, and CPM 2018. He co-created SISAP on 2008, and was Steering Committee member of SPIRE, LATIN, and SISAP. He is the Editor in Chief of the ACM Journal of Experimental Algorithmics and a member of the Editorial Board of Information Retrieval and Information Systems. He has been guest editor of special issues in ACM SIGSPATIAL, Journal of Discrete Algorithmics, Information Systems, and Algorithmica. He has given around 50 invited talks in several universities and international conferences, including 12 plenary talks and 5 tutorials in international conferences. He created in 2005 the Workshop on Compression, Text, and Algorithms, which has become a permanent satellite of SPIRE. He is an ACM Distinguished Member.
He has coauthored two books published by Cambridge University Press, about 25 book chapters, 10 proceedings of international conferences (editor), more than 160 papers in international journals, and over 240 in international conferences. He is one of the most prolific and highly cited authors in Latin America.
He has advised 6 postdocs, 18 PhDs, 17 MScs, and 24 undergraduate theses.