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Ivan Erill

Ivan Erill

Full Professor

Biological Sciences
Computer Science and Electrical Engineering

Biological Sciences Bldg BS-117


Ph D Universitat Autònoma de Barcelona 2002

BS Universitat Autònoma de Barcelona 1996


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 2021 BIOL 316L – Phage Genome Analysis
  • BIOL 313 – Bioinformatics Intro
  • Spring 2020 BIOL 615 – Systems Biology
  • BIOL 415 – Systems Biology
  • BIOL 316L – Phage Genome Analysis
  • BIOL 313 – Bioinformatics Intro

Intellectual Contributions

Kumar, Soven Verma., Schaffer, Nicholas, Bharmal, Zainab, Mood, Quinn, Erill, Ivan, Steven, Caruso M. (2024). . e0006824 Washington, DC: Microbiology resource announcements.

Ismail, Ahmed, Saini, Tanuj, Al Qaffas, Ahmed, Erill, Ivan, Steven, Caruso M., Temple, Louise, Johnson, Allison A. (2023). . 2. 15 276 Basel: Viruses.

Sanchez-Osuna, Miquel, Barbe, Jordi, Erill, Ivan. (2023). . 2. 12 ANTIBIOTICS-BASEL.

Davis, F, Kakacek, B, Doorandish, D, Goldwasser, T, Agboha, N, Steven, Caruso M., Erill, Ivan. (2022). . 12. 11 e0099822 Washington, DC: Microbiology resource announcements.

Park, Y G., McCarthy, G F., Mustafa, H, Feild, G M., Puram, S, Younes, H A., Imam, D, Erill, Ivan, Steven, Caruso M. (2022). . 11. 11 e0092222 Washington, DC: Microbiology resource announcements.

Mascolo, E, Adhikari, S, Steven, Caruso M., deCarvalho, Tagide, Folch Salvador, A, Serra-Sagristà, J, Young, R, Erill, Ivan, Curtis, P D. (2022). . 13 918015 Frontiers in microbiology.

Nadendla, S, Jackson, R, Munro, J, Quaglia, F, Mészáros, B, Olley, D, Hobbs, Elizabeth T., Goralski, S M., Chibucos, M, Mungall, C J., Erill, Ivan, Giglio, M G. (2022). . D1. 50 D1515-D1521 Nucleic acids research.

Koert, Matthew, Lopez-Perez, Julia, Mattson, Courtney, Steven, Caruso M., Erill, Ivan. (2021). . 1 e16 Peer Community Journal.

Sánchez-Osuna, M, Cortés, P, Lee, M, Smith, Aaron, Barbé, J, Erill, Ivan. (2021). . 19. 49 11050-11066 Nucleic Acids Research.

Alvarez-Gonzalez, Sara, Erill, Ivan. (2021). . The 4th XoveTIC Conference 59. 7 3 Engineering Proceedings - MDPI.

Ramsey, J, McIntosh, B, Renfro, D, Aleksander, S A., LaBonte, S, Ross, C, Zweifel, A E., Liles, N, Farrar, S, Gill, J J., Erill, Ivan, Ades, S, Berardini, T Z., Bennett, J A., Brady, S, Britton, R, Carbon, S, Steven, Caruso M., Clements, D, Dalia, R, Defelice, M, Doyle, E L., Friedberg, I, Hughes, L, Johnson, A, Kowalski, J M., Li, D, Lovering, R C., Mans, T L., McCarthy, F, Moore, S D., Murphy, R, Paustian, T D., Perdue, S, Peterson, C N., Prüß, B M., Saha, M S., Sheehy, R R., Tansey, J T., Temple, L, Thorman, A W., Trevino, S, Vollmer, A C., Walbot, V, Willey, J, Siegele, D A., Hu, J C. (2021). . 10. 17 e1009463 PLoS computational biology.

Cusick, Kathleen, Iturbide, A, Gautam, P, Price, A, Polson, S, MacDonald, M, Erill, Ivan. (2021). . 9. 16 e0257800 PloS one.

Hobbs, Elizabeth T., Goralski, S M., Mitchell, A, Simpson, A, Leka, D, Kotey, E, Sekira, M, Munro, J B., Nadendla, S, Jackson, R, Gonzalez-Aguirre, A, Krallinger, M, Giglio, M, Erill, Ivan. (2021). . Frontiers in Research Metrics and Analytics.

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.

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

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

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 e01178–15 Washington, DC: Genome Announcements.

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

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

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

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

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.

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

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

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.

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

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

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

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

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

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.

Gautam, Pratima, Erill, Ivan, Cusick, Kathleen. . 1012. 11 Microorganisms.

Research In Progress

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


Lopez-Perez, Julia, Otero, Jenifer, Sanchez-Osuna, Miquel, Aranda, Jesus, Barbé, Jordi, Campoy, Susana, Erill, Ivan, Cortés, Pîlar, Llagostera, Montse. XIX Congress of the Spanish Microbiology Society. Poster. "Mutagenesis and lateral gene transfer as the molecular basis of reduced phage susceptibility mechanisms," (Jun 26, 2023).

Sanchez-Osuna, Miquel, Bierge, Paula, Pedrosa, Marc, Espasa, Mateu, Gasch, Oriol, Erill, Ivan, Pich, Oriol Quijada. ECCMID 2023. Poster. "Association between Staphylococcus aureus lineages causing bloodstream infections and clinically relevant genetic features," (Apr 17, 2023).

Otero, Jenifer, Lopez-Perez, Julia, Sanchez-Osuna, Miquel, Cabrera, Josep Maria, Campoy, Susana, Erill, Ivan, Barbé, Jordi, Cortés, Pîlar, Llagostera, Montse. Viruses of Microbes. Poster. "Mutagenesis and lateral gene transfer are involved in bacterial resistance and interference to bacteriophages," (Jul 22, 2022).

Sanchez-Osuna, Miquel, Bierge, Paula, Pedrosa, Marc, Espasa, Mateu, Gasch, Oriol, Erill, Ivan, Pich, Oriol Quijada. ECCMID 2022. Poster. "Genome-wide identification of Staphylococcus aureus genetic factors associated with increased risk of persistent bacteremia," (Apr 24, 2022).

Alvarez-Gonzalez, S (Author & Presenter), Erill, Ivan (Author). XoveTIC. Oral Presentation. "Design of Machine Learning Models for the Prediction of Transcription Factor Binding Regions in Bacterial DNA," Xunta de Galicia. (Oct 8, 2021).

Sanchez-Osuna, M (Author), Lee, M (Author), Cortes, P (Author), Smith, Aaron (Author), Barbé, J (Author), Erill, Ivan (Author & Presenter). New Approaches and Concepts in Microbiology. Oral Presentation. "Phage-like repressors orchestrate the SOS response in the Bacteroidetes," EMBO/EMBL. (Jul 7, 2021).

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," (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). (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. (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. (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," (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. (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. (Mar 17, 2016).

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. (Jun 14, 2015).

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. (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," (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). (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. (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. (May 15, 2013).