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Ivan Erill

Ivan Erill

Associate Professor

Biological Sciences
Computer Science and Electrical Engineering

Biological Sciences Bldg BS-117

Education

Ph D Universitat Autònoma de Barcelona 2002

BS Universitat Autònoma de Barcelona 1996

About

Life is information. Information is processed both during an organism life-time and across generations by natural selection. In fact, life is probably the most complex information processing system ever created. As Robert Robbins fittingly put it, the DNA sequence of an organism is “the result of literally millions of maintenance revisions performed by the worst possible set of kludge–using, spaghetti–coding, opportunistic hackers (i.e. evolution) who delight in clever tricks like writing self–modifying code and relying upon undocumented system quirks”. As a result, deciphering molecular biology is the ultimate dream of a computer scientist.

Research Interests

My research interests lie primarily in the evolution of transcriptional regulatory networks in Bacteria, specifically on the co-evolution of transcription factors, their cognate binding sites and the regulatory networks they spawn to fulfill complex regulatory programs involved in key pathogenic processes, such as the transfer of antiobiotic resistance determinants or the creation of biofilms. My lab uses evolutionary simulations, biophysical and dynamic models, systems biology and comparative genomics approaches to probe into the evolution of transcriptional regulatory networks. My lab also works on the creation of community-oriented services for the annotation of scientific data, such as the CollecTF database (www.collectf.org) dedicated to compiling data on transcription factor-binding sites across the Bacteria domain. This work involves the design and development of biological databases, working in close collaboration with ontology development groups and core development teams at large biomedical data repositories, such as the NCBI and the EMBL-EBI.

Teaching Interests

Bioinformatics, computational biology, evolutionary biology, microbiology, biocuration, societal impacts of computers and biology

Selected Classes

  • Spring 2020 BIOL 615 – Systems Biology
  • BIOL 415 – Systems Biology
  • BIOL 316L – Phage Genome Analysis
  • BIOL 313 – Bioinformatics Intro

Intellectual Contributions

Koert, Matthew, Lopez-Perez, Julia, Mattson, Courtney, Steven, Caruso M., Erill, Ivan. (2021). . Peer Community in Genomics.

Adhikari, S, Erill, Ivan, Curtis, P D. (2021). . 3. 17 e1009433 PLoS genetics.

Kılıç, S, Sánchez-Osuna, M, Collado-Padilla, A, Barbé, J, Erill, Ivan. (2020). . Suppl 5. 21 466 BMC genomics.

Sánchez-Osuna, M, Cortés, P, Llagostera, M, Barbé, J, Erill, Ivan. (2020). . 11. 6 Microbial genomics.

Goulet, T L., Erill, Ivan, Ascunce, M S., Finley, S J., Javan, G T. (2020). . 11 566968 Frontiers in physiology.

Baron, S F., Crossman, A N., Malik, S, Sidhu, P, Nehra, K, Jamdagni, P, Erill, Ivan, Temple, L M. (2020). . 35. 9 Microbiology resource announcements.

Chen, Q, Britto, R, Erill, Ivan, Jeffery, C J., Liberzon, A, Magrane, M, Onami, J I., Robinson-Rechavi, M, Sponarova, J, Zobel, J, Verspoor, K. (2020). . 2. 18 91-103 Genomics, proteomics & bioinformatics.

Steven, Caruso M., deCarvalho, Tagide, Huynh, Anthony, Morcos, George, Kuo, Nansen, Parsa, Shabnam, Erill, Ivan. (2019). . 12. 11 1134 Basel: Viruses.

Sánchez-Osuna, M, Cortés, P, Barbé, J, Erill, Ivan. (2019). . 9 3332 Frontiers in microbiology.

Blocker, Devin, Koert, Matthew, Mattson, Courtney, Patel, Harsh, Patel, Priya, Patel, Rishit, Paudel, Hemanta, Erill, Ivan, Steven, Caruso M. (2018). . 12. 7 e00993-1018 Washington, DC: Microbiology Resource Announcements.

Lee, Martin, Puglisi, Kayla M., Erill, Ivan, Steven, Caruso M. (2018). . 25. 6 e00493-18 Washington, DC: Genome Announcements.

Ammari, Mais, Aryamontri, Andrew Chatr., Attrill, Helen, Bairoch, Amos, Berardini, Tanya, Blake, Judith, Chen, Qingyu, Collado-Vides, Julio, Dauga, Delphine, Dudley, Joel, Engel, Stacia, Erill, Ivan, Fey, Petra, Gibson, Richard, Hermjakob, Henning, Holliday, Gemma, Howe, Doug, Hunter, Chris, Landsman, David, Lovering, Ruth, Manthravadi, Deepa, Marchler-Bauer, Aron, Matthews, Beverley, McDonagh, Ellen, Meldal, Birgit, Micklem, Gos, Mietchen, Daniel, Mungall, Christopher, Pruitt, Kim, Rajamanickam, Vidhya Sagar., Reecy, James, Rey, Alix, Shameer, Khader, Shipitsyna, Aleksandra, Toribio, Ana Luisa, Tuli, Mary Ann, Uetz, Peter, Wittig, Ulrike, Wood, Valerie. (2018). . 4. 16 e2002846 PLoS biology.

Erill, Ivan, Steven, Caruso M. (2018). . 3. 6 e01480-17 Washington, DC: Genome Announcements.

Erill, Ivan, Steven, Caruso M., Hu, Jim. (2018). . 6. 39 18 Tested Studies for Laboratory Teaching.

Hanauer, David I., Graham, Mark J., Betancur, Laura, Bobrownicki, Aiyana, Cresawn, Steven G., Garlena, Rebecca A., Jacobs-Sera, Deborah, Kaufmann, Nancy, Pope, Welkin H., Russell, Daniel A., Jacobs, William R., Sivanathan, Viknesh, Asai, David J., Hatfull, Graham F., Steven, Caruso M., Erill, Ivan. (2017). . 201718188 Washington, DC: Proceedings of the National Academy of Sciences.

Sánchez-Osuna, M, Barbé, J, Erill, Ivan. (2017). . 9. 19 3465-3474 Environmental microbiology.

Erill, Ivan, Steven, Caruso M. (2017). . 31. 5 e00700-17 Washington, DC: Genome Announcements.

Erill, Ivan, Steven, Caruso M. (2017). . 29. 5 e00701-17 Washington, DC: Genome Announcements.

Erill, Ivan, Puigvert, M, Legrand, L, Guarischi-Sousa, R, Vandecasteele, C, Setubal, J C., Genin, S, Guidot, A, Valls, M. (2017). . 8 504 Frontiers in plant science.

Erill, Ivan, Steven, Caruso M. (2016). . 5. 4 Washington, DC: Genome announcements.

O'Neill, P K., Erill, Ivan. (2016). . 1. 17 406 BMC bioinformatics.

Erill, Ivan, Steven, Caruso M. (2016). . 5. 4 e00953–16 Washington, DC: Genome Announcements.

Kılıç, Sefa, Erill, Ivan. (2016). . (Supp.8). 17 277 BMC Bioinformatics.

Erill, Ivan, Campoy, S, Kılıç, S, Barbé, J. (2016). . 3 33 Frontiers in molecular biosciences.

Hobbs, E T., Pereira, T, O'Neill, P K., Erill, Ivan. (2016). . 11 19 Algorithms for molecular biology : AMB.

Kılıç, Sefa, Sagitova, Dinara, Wolfish, Shoshannah, Bely, Benoit, Courtot, Melanie, Ciufo, Stacy, Tatusova, Tatiana, O’Donovan, Claire, Chibucos, Marcus C., Martin, Maria J., Erill, Ivan. (2016). . baw055. Database (Oxford).

Sauder, Amber Brooke., Quinn, McKenzie Rea., Brouillette, Alexis, Steven, Caruso M., Cresawn, Steven, Erill, Ivan, Lewis, Lynn, Loesser-Casey, Kathryn, Pate, Morgan, Crystal, Crystal, Stockwell, Stephanie, Temple, Louise. (2016). . February 2016. 489 243-251 Virology.

Erill, Ivan, Steven, Caruso M. (2015). . 5. 3 e01199–15 Washington, DC: Genome Announcements.

Erill, Ivan, Steven, Caruso M. (2015). . 5. 3 e01178–15 Washington, DC: Genome Announcements.

Hagemann, I S., O'Neill, P K., Erill, Ivan, Pfeifer, J D. (2015). . 9. 208 441-7 Cancer genetics.

Sanchez-Alberola, N, Campoy, S, Emerson, D, Barbé, J, Erill, Ivan. (2015). . 16. 197 2622-30 Journal of bacteriology.

Erill, Ivan. (2015). . 15. 197 2454-7 Journal of bacteriology.

Zamorano-Sánchez, David, Fong, Jiunn C., Kilic, Sefa, Erill, Ivan, Yildiz, Fitnat H. (2015). . 7. 197 1221-35 Journal of bacteriology.

Patrick, O'Neill K., Robert, Forder, Erill, Ivan. (2014). . 5. 21 373-384 Journal of Computational Biology.

Stringer, A M., Currenti, S, Bonocora, R P., Baranowski, C, Petrone, B L., Palumbo, M J., Reilly, A A., Zhang, Z, Erill, Ivan, Wade, J T. (2014). . 3. 196 660-71 Journal of bacteriology.

Cornish, J P., Sanchez-Alberola, N, O'Neill, P K., O'Keefe, R, Gheba, J, Erill, Ivan. (2014). . Bioinformatics (Oxford, England).

Kiliç, S, White, E R., Sagitova, D M., Cornish, J P., Erill, Ivan. (2014). . Database issue. 42 D156-60 Nucleic acids research.

O'Neill, P K., Or, M, Erill, Ivan. (2013). . 10. 8 e76177 PloS one.

Cornish, Joseph P., Matthews, Fialelei, Thomas, Julien R., Erill, Ivan. (2012). . 8 449-461 Evolutionary Bioinformatics.

Erill, Ivan. (2012). . Information Theory: New Research 1-28 Hauppauge, NY: Nova Science Publishers.

Anzaldi, Laura J., Muñoz-Fernandez, Daniel, Erill, Ivan. (2012). . 13 124 BMC Bioinformatics.

Sanchez-Alberola, Neus, Campoy, Susana, Barbe, Jordi, Erill, Ivan. (2012). . 58. 13 BMC Genomics.

Cambray, Guillaume, Sanchez-Alberola, Neus, Campoy, Susana, Guerin, Emilie, Da Re, Sandra, Gonzalez-Zorn, Bruno, Ploy, Marie-Cecile, Barbe, Jordi, Mazel, Didier, Erill, Ivan. (2011). . 1. 2 6 Mobile DNA.

Bhargava, Nidhi, Erill, Ivan. (2010). . 2. 5 49-51 Bioinformation.

Fox, Jesse M., Erill, Ivan. (2010). . 3. 17 185-196 DNA Research.

Guerin, Emilie, Cambray, Guillaume, Sanchez-Alberola, Neus, Campoy, Susana, Erill, Ivan, Da Re, Sandra, Gonzalez-Zorn, Bruno, Barbe, Jordi, Ploy, Marie-Cecile, Mazel, Didier. (2009). . 5930. 324 1034 Science.

Erill, Ivan, O'Neill, Michael C. (2009). . 57. 10 BMC Bioinformatics.

Hessheimer, A. J., Parramon, D., Guimera, A., Erill, Ivan, Rimola, A., Garcia-Valdecasas, J. C., Villa, R., Fondevila, C.. (2009). . 5. 88 716–22 Transplantation.

Erill, Ivan, Campoy, S, Barbé, J. (2007). . 6. 31 637-56 FEMS microbiology reviews.

Abella, Marc, Campoy, Susana, Erill, Ivan, Rojo, Fernando, Barbe, Jordi. (2007). . 24. 189 8855–62 J Bacteriol.

Erill, Ivan, Campoy, S., Mazon, G., Barbe, J.. (2006). . 1. 34 66–77 Nucleic Acids Res.

Mazon, G., Campoy, S., Erill, Ivan, Barbe, J.. (2006). . Pt 4. 152 1109–18 Microbiology.

Villa, R., Fondevila, C., Erill, Ivan, Guimera, A., Bombuy, E., Gomez-Suarez, C., Sacristan, J. C., Garcia-Valdecasas, J. C. (2006). . 3. 81 483–6 Transplantation.

Gomez, R., Ivorra, A., Villa, R., Godignon, P., Millan, J., Erill, Ivan, Sola, A., Hotter, G., Palacios, L.. (2006). . 1. 8 43–9 Biomed Microdevices.

Campoy, S., Salvador, N., Cortes, P., Erill, Ivan, Barbe, J.. (2005). . 15. 187 5367–75 J Bacteriol.

Erill, Ivan, Campoy, S., Rus, J., Fonseca, L., Ivorra, A., Navarro, Z., Plaza, J. A., Aguilo, J., Barbe, J.. (2004). . 11. 14 1558–1568 Journal of Micromechanics and Microengineering.

Erill, Ivan, Jara, M., Salvador, N., Escribano, M., Campoy, S., Barbe, J.. (2004). . 22. 32 6617–26 Nucleic Acids Res.

Mazon, G., Erill, Ivan, Campoy, S., Cortes, P., Forano, E., Barbe, J.. (2004). . Pt 11. 150 3783–95 Microbiology.

Abella, M., Erill, Ivan, Jara, M., Mazon, G., Campoy, S., Barbe, J.. (2004). . 1. 54 212–22 Mol Microbiol.

Erill, Ivan, Campoy, S., Erill, N., Barbe, J., Aguilo, J.. (2003). . 3. 96 685–692 Sensors and Actuators B-Chemical.

Erill, Ivan, Escribano, M., Campoy, S., Barbe, J.. (2003). . 17. 19 2225–36 Bioinformatics.

Cune, J., Erill, Ivan, Magnuson, J. K., Barbe, J.. (2002). . 21. 184 6073–80 J Bacteriol.

Erill, Ivan, Villa, Rosa, Goudignon, Philippe, Fonseca, Luis, Plaza, Jose A. (2000). . 4-5. 40 787–789 Microelectronics Reliability.

Research In Progress

Cusick, Kathleen, Erill, Ivan. “Intracellular Signaling in Alteromonas,” Scholarly (On-Going). Nov 1, 2017

Presentations

Hobbs, Elizabeth T. (Author), Goralski, Stephen M. (Author), Mitchell, Ashley (Author), Simpson, Andrew (Author), Dorjan, Leka (Author), Kotey, Emmanuel (Author), Sekira, Matthew (Author), Munro, James B. (Author), Nadendla, Suvarna (Author), Jackson, Rebecca (Author), Gonzalez-Agirre, Aitor (Author), Krallinger, Martin (Author), Giglio, Michelle (Author), Erill, Ivan (Author & Presenter). 11th International Conference on Biomedical Ontologies (ICBO). Oral Presentation. "Corpora as evolving entities: embedding corpora in biomedical ontologies," Bozen-Bolzano, Italy. (Sep 16, 2020).

Erill, Ivan (Author & Presenter). 23rd Evolutionary Biology Meeting at Marseilles. Oral Presentation. "Convergent evolution of a bacterial stress response," Association pour l'Etude de l'Evolution Biologique (AEEB). Marseilles, France. (Sep 24, 2019).

Sanchez-Osuna, Miquel, Cortés, Pilar, Barbé, Jordi, Erill, Ivan. Molecular Genetics of Bacteria and Phages Meeting. Oral Presentation. "Origin of the mobile di-hydro-pteroate synthase genes conferring sulfonamide resistance," University of Wisconsin. Madison, WI. (Aug 7, 2018).

Steven, Caruso M. (Author & Presenter), Erill, Ivan (Author). Tenth Annual NGRI SEA-Phages Symposium. Poster. "GOing forward: developing critical reading skills through an inter-campus GO annotation competition," Howard Hughes Medical Institute. Janelia Farms, Ashburn, VA. (Jun 9, 2018).

Erill, Ivan (Author & Presenter), Marc, Valls (Author), Marina, Puigvert (Author), Luke, Legrand (Author), Alice, Guidot (Author), Stephanne, Genin (Author). 6th International Bacterial Wilt Symposium. Oral Presentation. "Comparative analysis of Ralstonia solanacearum methylomes," Toulouse, France. (Jul 4, 2016).

Kılıç, Sefa (Author), Sagitova, Dinara (Author), Wolfish, Soshannah (Author), Bely, Benoit (Author), Courtot, Melanie (Author), Ciufo, Stacy (Author), Tatusova, Tatiana (Author), O'Donovan, Claire (Author), Chibucos, Marcus C. (Author), Martin, Maria J. (Author), Erill, Ivan (Author & Presenter). BioCuration 2016. Oral Presentation. "From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF," International Society for BioCuration. Geneva, Switzerland. (Apr 11, 2016).

Hobbs, Elizabeth T. (Author), Erill, Ivan (Author & Presenter). Applied Bioinformatics in the Life Sciences 2016. Poster. "Comparative analysis of stress response systems in the human gut microbiome," Vlaams Instituut voor Biotechnologie. Leuven, Belgium. (Mar 17, 2016).

Steven, Caruso M. (Author & Presenter), Erill, Ivan (Author & Presenter). Seventh Annual NGRI SEA-Phages Symposium. Poster. "Giving it a GO - enhancing bacteriophage genome annotation and student learning with the Gene Ontology Seventh Annual SEA-Phages Symposium," Howard Hughes Medical Institute. Janelia Farms, Ashburn, VA. (Jun 14, 2015).

Johnson, Allison (Author & Presenter), Lewis, Lynn (Author), Steven, Caruso M. (Author), Erill, Ivan (Author), Temple, Louise (Author). Seventh Annual NGRI SEA-Phages Symposium. Poster. "Host range of Bacillus phages. Seventh Annual SEA-Phages Symposium," Howard Hughes Medical Institute. Janelia Farms, Ashburn, VA. (Jun 14, 2015).

Sanchez-Alberola, Neus (Author), Campoy, Susana (Author), Emerson, David (Author), Barbé, Jordi (Author), Erill, Ivan (Author & Presenter). Molecular Genetics of Bacteria and Phages Meeting. Poster. "A SOS regulon under control of a non-canonical LexA-binding motif in the Betaproteobacteria," Madison, WI. (Aug 5, 2014).

Simmons, Caleb (Author & Presenter), Stachowiak, Alexandaer (Author), Rathinam, Muruhan (Author), Erill, Ivan (Author). South Eastern Population Ecology & Evolutionary Genetics (SEPEEG) meeting. Oral Presentation. "Computational Model of the Environmental Selection of the Feed Forward Loop Network Motif," American Society of Naturalists (ASN). Mountain Lake Biological Station, Pembroke, VA (USA). (Sep 28, 2013).

O'Neill, Patrick K. (Author & Presenter), Erill, Ivan (Author). Seventh q-bio Conference. Oral Presentation. "Exact Chemical Potentials for Prokaryotic Transcription Factors," National Institute of General Medical Sciences of the National Institutes of Health. St. John's College, Santa Fe, NM (USA). (Aug 8, 2013).

Kiliç, Sefa (Author & Presenter), Erill, Ivan (Author). Great Lakes Bioinformatics Conference. Poster. "A graph-based optimization system for comparative genomics of bacterial regulatory networks," International Society for Computational Biology. Pittsburgh, PA (USA). (May 15, 2013).