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Luis M. Rocha is Principal Investigator at the Instituto Gulbenkian da Ciencia, Oeiras, Portugal. He is also the George J. Klir Professor of Systems Science at the Thomas J. Watson College of Engineering and Applied Science, Binghamton University (State University of New York), where he leads the Complex Adaptive Systems and Computational Intelligence (CASCI) lab, and is director of the Consortium for Social and Biomedical Complexity, between Binghamton University and Indiana University. He has been the director of the NSF-NRT Interdisciplinary Training Program in Complex Networks and Systems (2017-2021), and Professor of Informatics in the Luddy School of Informatics, Computing, and Engineering at Indiana University (2004-2021), where he was also a member of the advisory council of the Indiana University Network Science Institute, and core faculty of the Cognitive Science Program . Dr. Rocha is a Fulbright Scholar and has been a Visiting Professor a the Center for Theoretical Physics at the Aix-Marseille University, France as well as the Neuroscience Program, at the Champalimaud Foundation and the NOVA School of Business and Economics in Portugal. His research is on complex networks & systems, computational & systems biology, and computational intelligence. He received his Ph.D in Systems Science in 1997 from the State University of New York at Binghamton. From 1998 to 2004 he was a permanent staff scientist at the Los Alamos National Laboratory, where he founded and led a Complex Systems Modeling Team during 1998-2002, and was part of the Santa Fe Institute research community. He has organized major conferences in the field such as the Tenth International Conference on the Simulation and Synthesis of Living Systems (Alife X), the Ninth European Conference on Artificial Life (ECAL 2007), and Complex Networks 2019. He has published many articles in scientific and technology journals, and has been the recipient of several scholarships and awards. At Indiana University, he has received the Indiana University, School of Informatics & Computing, Trustees Award for Teaching Excellence in 2006 and 2015 after developing the complex systems training program and syllabi for several courses.
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Identification

Personal identification

Full name
Luis Jorge Mateus Silva Rocha

Citation names

  • Luis M. Rocha
  • Rocha, L.
  • Rocha, L.M.

Author identifiers

Ciência ID
5A17-7176-424F
ORCID iD
0000-0001-9402-887X

Email addresses

  • rocha@igc.gulbenkian.pt (Professional)

Telephones

Mobile phone
  • 919492168 (Personal)

Addresses

  • Rua da Quinta Grande, 6, 2780, Oeiras, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Biophysics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Japanese Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
1992 - 1997
Concluded
 Systems Science and Computer Science (Doctor of Philosophy)
Binghamton University, United States
"Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Evolutionary Systems" (THESIS/DISSERTATION)
1988 - 1990
Concluded
 Systems Engineering (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
1985 - 1990
Concluded
 Mechanical and Systems Engineering (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
Affiliation

Science

Category
Host institution 		Employer
2004 - Current Principal Investigator (Research) Instituto Gulbenkian de Ciência, Portugal
Instituto Gulbenkian de Ciência, Portugal
1999 - 2004 Principal Investigator (Research) Los Alamos National Laboratory, United States
Los Alamos National Laboratory, United States
1997 - 1999 Postdoc (Research) Los Alamos National Laboratory, United States
Los Alamos National Laboratory, United States

Teaching in Higher Education

Category
Host institution 		Employer
2021/09/01 - Current Full Professor (University Teacher) Binghamton University Thomas J Watson School of Engineering and Applied Science, United States
2013 - 2022/05/31 Full Professor (University Teacher) Indiana University Bloomington, United States
Indiana University Bloomington, United States
2019/01/01 - 2021/06/30 Invited Full Professor (University Teacher) Universidade Nova de Lisboa Nova School of Business and Economics, Portugal
2004 - 2013 Associate Professor (University Teacher) Indiana University Bloomington, United States
Indiana University Bloomington, United States
Projects

Grant

Designation Funders
2017/09 - 2022/08 NRT: Interdisciplinary Training in Complex Networks and Systems
1735095
 National Science Foundation Directorate for Education and Human Resources
2018/09 - 2022/05 myAURA: Personalized Web Service for Epilepsy Management
R01LM012832
 National Library of Medicine
2018/03 - 2020/02 OPUS: Synthesizing Ecology with Ecological Networks
1754207
 National Science Foundation Directorate for Biological Sciences
2014/09 - 2018/07 Evidence-based Drug-Interaction Discovery: In-Vivo, In-Vitro and Clinical
1R01LM011945-01
R01LM011945
 National Library of Medicine
2010/02 - 2013/05 From Bio-Inspired to Institutional-Inspired Collective Robotics
104658
Provided by PTCRIS: 104658
 Governo da República Portuguesa Ministério da Ciência Tecnologia e Ensino Superior
2005/09 - 2009/08 DHB: Dynamics of Information Flow and Decisions in Social Networks
0527249
 National Science Foundation - Directorate for Social, Behavioral & Economic Sciences

Contract

Designation Funders
2018/09/26 - 2021/09/25 The sperm cell core genetic program - a combined clinical and basic research approach to the diagnosis of male infertility
PTDC/MEC-AND/30221/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2019 - 2021 Factors to promote healthy dialogue and behaviours in online school communities
DSAIPA/DS/0102/2019
Researcher
Fundação Calouste Gulbenkian, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade Lusófona de Humanidades e Tecnologias Centro de Investigação em Comunicação Aplicada Cultura e Novas Tecnologias, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018 - 2021 Identifying and predicting emergency admissions
DSAIPA/AI/0087/2018
Researcher
Fundação Calouste Gulbenkian, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

SPMS Serviços Partilhados do Ministério da Saúde EPE, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2011/03/01 - 2012 Collective Computation and Control in Complex Biochemical Systems
PTDC/EIA-CCO/114108/2009
Provided by PTCRIS: 114108
114108
Principal investigator
Fundação Calouste Gulbenkian, Portugal

Universidade do Minho, Portugal

Instituto Gulbenkian de Ciência, Portugal
Fundação para a Ciência e a Tecnologia

Governo da República Portuguesa Ministério da Ciência Tecnologia e Ensino Superior
Concluded
Outputs

Publications

Book
  1. Complex Networks & Their Applications X. Springer International Publishing. 2022.
    10.1007/978-3-030-93409-5
  2. Complex Networks & Their Applications X. Springer International Publishing. 2022.
    10.1007/978-3-030-93413-2
  3. Luis M. Rocha. Complex Networks and Their Applications VIII. 2020.
    10.1007/978-3-030-36683-4
  4. Luis M. Rocha. Complex Networks and Their Applications VIII. 2020.
    10.1007/978-3-030-36687-2
  5. Luis M. Rocha. Complex Networks and Their Applications VII. 2019.
    10.1007/978-3-030-05411-3
  6. Luis M. Rocha. Complex Networks and Their Applications VII. 2019.
    10.1007/978-3-030-05414-4
  7. Abi-Haidar, A.; Rocha, L.M.. Biomedical article classification using an agent-based model of T-cell cross-regulation. 2010.
    10.1007/978-3-642-14547-6_19
  8. Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Carreira, R.; Rocha, L.M.; Glez-Peña, D.; Méndez, J.R.; et al. Biomedical text mining applied to document retrieval and semantic indexing. 2009.
    10.1007/978-3-642-02481-8_146
  9. Luis M. Rocha. Progress in Artificial Intelligence. 2009.
    10.1007/978-3-642-04686-5
  10. Abi-Haidar, A.; Rocha, L.M.. Adaptive spam detection inspired by a cross-regulation model of immune dynamics: A study of concept drift. 2008.
    10.1007/978-3-540-85072-4_4
  11. Marques-Pita, M.; Mitchell, M.; Rocha, L.M.. The role of conceptual structure in designing cellular automata to perform collective computation. 2008.
    10.1007/978-3-540-85194-3_13
  12. Luis M. Rocha. Advances in Artificial Life. 2007.
    10.1007/978-3-540-74913-4
  13. Luis M. Rocha. Artificial Life X: Proceedings of the Tenth International Conference on the Simulation and Synthesis of Living Systems. MIT Press. 2006.
  14. Bollen, J.; Rocha, L.M.. An adaptive systems approach to the implementation and evaluation of digital library recommendation systems. 2000.
  15. Rocha, L.M.. Contextual genetic algorithms: Evolving developmental rules. 1995.
    10.1007/3-540-59496-5_312
Conference paper
  1. Luis M. Rocha. "Just In Time: Challenges and Opportunities of First Aid Care Information Sharing for Supporting Epileptic Seizure Response". 2021.
    10.1145/3449187
  2. Rocha, Luis. "Designing a minimalist socially aware robotic agent for the home". 2014.
  3. Kolchinsky, A.; Lourenço, A.; Li, L.; Rocha, L.M.. "Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions". 2013.
  4. Simas, T.; Rocha, L.M.. "Semi-metric networks for recommender systems". 2012.
    10.1109/WI-IAT.2012.245
  5. Karnik, S.; Subhadarshini, A.; Wang, Z.; Rocha, L.M.; Li, L.. "Extraction of drug-drug interactions using all paths graph kernel". 2011.
  6. Marques-Pita, M.; Rocha, L.M.. "Schema redescription in cellular automata: Revisiting emergence in complex systems". 2011.
    10.1109/ALIFE.2011.5954670
  7. Abi-Haidar, A.; Rocha, L.M.. "Collective classification of biomedical articles using T-cell cross-regulation". 2010.
  8. Marques-Pita, M.; Rocha, L.M.. "Conceptual structure in cellular automata: The density classification task". 2008.
  9. Abi-Haidar, A.; Rocha, L.M.. "Adaptive spam detection inspired by the immune system". 2008.
  10. Huang, C.-F.; Rocha, L.M.. "Tracking extreme in dynamic environments using a coevolutlonery agent-based model of genotype edition". 2005.
  11. Rocha, L.M.; Simas, T.; Rechtsteiner, A.; Di Giacomo, M.; Luce, R.. "MyLibrary@LANL: Proximity and semi-metric networks for a collaborative and recommender Web service". 2005.
    10.1109/WI.2005.106
  12. Huang, C.-F.; Rocha, L.M.. "Exploration of RNA editing and design of robust genetic algorithms". 2003.
    10.1109/CEC.2003.1299443
  13. Rocha, L.M.. "Combination of evidence in recommendation systems characterized by distance functions". 2002.
  14. Rocha, Luis Mateus. "Relative uncertainty: measuring uncertainty in discrete and nondiscrete domains". 1996.
  15. Rocha, Luis Mateus. "Interval based evidence sets". 1995.
  16. Rocha, Luis Mateus. "Cognitive categorization revisited: Extending interval valued fuzzy sets as simulation tools for concept combination". 1994.
Edited book
  1. Luis M. Rocha. Complex Networks & Their Applications IX. Springer International Publishing. 2021.
    10.1007/978-3-030-65347-7
  2. Luis M. Rocha. Complex Networks & Their Applications IX. Springer International Publishing. 2021.
    10.1007/978-3-030-65351-4
Journal article
  1. "Small cohort of patients with epilepsy showed increased activity on Facebook before sudden unexpected death". Epilepsy & Behavior 128 (2022): 108580-108580. http://dx.doi.org/10.1016/j.yebeh.2022.108580.
    10.1016/j.yebeh.2022.108580
  2. Santosh Manicka; Manuel Marques-Pita; Luis M. Rocha. "Effective connectivity determines the critical dynamics of biochemical networks". Journal of The Royal Society Interface (2022): https://doi.org/10.1098/rsif.2021.0659.
    10.1098/rsif.2021.0659
  3. "On the feasibility of dynamical analysis of network models of biochemical regulation". Bioinformatics (2022): https://arxiv.org/abs/2110.10821.
    10.48550/ARXIV.2110.10821
  4. Brattig Correia, Rion; Alain Barrat; Luis M. Rocha. "The metric backbone preserves community structure and is a primary transmission subgraph in contact networks". BioArxiv (2022): https://www.biorxiv.org/content/10.1101/2022.02.02.478784v1.
    Under revision • https://doi.org/10.1101/2022.02.02.478784
  5. Luis M. Rocha. "The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling". Proceedings of the National Academy of Sciences (2021):
    10.1073/pnas.2022598118
  6. Luis M. Rocha. "Translational Knowledge Discovery Between Drug Interactions and Pharmacogenetics.". Clinical pharmacology and therapeutics (2020): https://doi.org/10.1002/cpt.1745.
    10.1002/cpt.1745
  7. "Mining Social Media Data for Biomedical Signals and Health-Related Behavior". Annual Review of Biomedical Data Science 3 1 (2020): 433-458. https://doi.org/10.1146/annurev-biodatasci-030320-040844.
    Published • 10.1146/annurev-biodatasci-030320-040844
  8. Rion Brattig Correia; Luciana P. de Araújo Kohler; Mauro M. Mattos; Luis M. Rocha. "City-wide electronic health records reveal gender and age biases in administration of known drug–drug interactions". npj Digital Medicine (2019): https://doi.org/10.1038/s41746-019-0141-x.
    10.1038/s41746-019-0141-x
  9. Ian B. Wood; Pedro L. Varela; Johan Bollen; Luis M. Rocha; Joana Gonçalves-Sá. "Author Correction: Human Sexual Cycles are Driven by Culture and Match Collective Moods". Scientific Reports 8 1 (2018): https://doi.org/10.1038/s41598-018-22522-3.
    10.1038/s41598-018-22522-3
  10. Luis M. Rocha. "CANA: A Python Package for Quantifying Control and Canalization in Boolean Networks.". Frontiers in physiology (2018): https://europepmc.org/articles/PMC6102667.
    10.3389/fphys.2018.01046
  11. Ian B. Wood; Pedro L. Varela; Johan Bollen; Luis M. Rocha; Joana Gonçalves-Sá. "Human Sexual Cycles are Driven by Culture and Match Collective Moods". Scientific Reports 7 1 (2017): https://doi.org/10.1038/s41598-017-18262-5.
    10.1038/s41598-017-18262-5
  12. Correia RB; Li L; Rocha LM. "MONITORING POTENTIAL DRUG INTERACTIONS AND REACTIONS VIA NETWORK ANALYSIS OF INSTAGRAM USER TIMELINES.". (2016): http://europepmc.org/abstract/med/26776212.
  13. Gates AJ; Rocha LM. "Control of complex networks requires both structure and dynamics.". (2016): http://europepmc.org/abstract/med/27087469.
    10.1038/srep24456
  14. Kolchinsky A; Lourenço A; Wu HY; Li L; Rocha LM. "Extraction of pharmacokinetic evidence of drug-drug interactions from the literature.". (2015): http://europepmc.org/abstract/med/25961290.
    10.1371/journal.pone.0122199
  15. Kolchinsky, A.; Gates, A.J.; Rocha, L.M.. "Modularity and the spread of perturbations in complex dynamical systems". Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 92 6 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84954286636&partnerID=MN8TOARS.
    10.1103/PhysRevE.92.060801
  16. Ciampaglia, G.L.; Shiralkar, P.; Rocha, L.M.; Bollen, J.; Menczer, F.; Flammini, A.. "Erratum : Correction: Computational fact checking from knowledge networks (PLoS ONE 10(6): e0128193. DOI:10.1371/journal.pone.0128193)". PLoS ONE 10 10 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84949591188&partnerID=MN8TOARS.
    10.1371/journal.pone.0141938
  17. Rocha, Luis. "Computational fact checking from knowledge networks". PLOS ONE. (2015):
    10.1371/journal.pone.0128193
  18. Rocha, Luis. "Distance Closures on Complex Networks". Network Science (2015):
    doi:10.1017/nws.2015.11
  19. Rocha, Luis. "Multi-scale integration and predictability in resting state brain activity". Frontiers in neuroinformatics (2014):
    10.3389/fninf.2014.00066
  20. Marques-Pita, M.; Rocha, L.M.. "Canalization and Control in Automata Networks: Body Segmentation in Drosophila melanogaster". PLoS ONE 8 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84874767199&partnerID=MN8TOARS.
    10.1371/journal.pone.0055946
  21. Wu, H.-Y.; Karnik, S.; Subhadarshini, A.; Wang, Z.; Philips, S.; Han, X.; Chiang, C.; et al. "An integrated pharmacokinetics ontology and corpus for text mining". BMC Bioinformatics 14 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84873033718&partnerID=MN8TOARS.
    10.1186/1471-2105-14-35
  22. Lourenço, A.; Conover, M.; Wong, A.; Nematzadeh, A.; Pan, F.; Shatkay, H.; Rocha, L.M.. "Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature". BMC Bioinformatics 13 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84864242556&partnerID=MN8TOARS.
    10.1186/1471-2105-13-180
  23. Krallinger, M.; Vazquez, M.; Leitner, F.; Salgado, D.; Chatr-aryamontri, A.; Winter, A.; Perfetto, L.; et al. "The Protein-Protein Interaction tasks of BioCreative III: Classification/ranking of articles and linking bio-ontology concepts to full text". BMC Bioinformatics 12 SUPPL. 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80053423937&partnerID=MN8TOARS.
    10.1186/1471-2105-12-S8-S3
  24. Lourenço, A.; Conover, M.; Wong, A.; Nematzadeh, A.; Pan, F.; Shatkay, H.; Rocha, L.M.. "A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature". BMC Bioinformatics 12 SUPPL. 8 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-80053392223&partnerID=MN8TOARS.
    10.1186/1471-2105-12-S8-S12
  25. Abi-Haidar, A.; Rocha, L.M.. "Collective classification of textual documents by guided self-organization in T-Cell cross-regulation dynamics". Evolutionary Intelligence 4 2 (2011): 69-80. http://www.scopus.com/inward/record.url?eid=2-s2.0-79957643969&partnerID=MN8TOARS.
    10.1007/s12065-011-0052-5
  26. Lourenço, A.; Carreira, R.; Glez-Peña, D.; Méndez, J.R.; Carneiro, S.; Rocha, L.M.; Díaz, F.; et al. "BioDR: Semantic indexing networks for biomedical document retrieval". Expert Systems with Applications 37 4 (2010): 3444-3453. http://www.scopus.com/inward/record.url?eid=2-s2.0-71349084312&partnerID=MN8TOARS.
    10.1016/j.eswa.2009.10.044
  27. Kolchinsky, A.; Abi-Haidar, A.; Kaur, J.; Hamed, A.A.; Rocha, L.M.. "Classification of protein-protein interaction full-text documents using text and citation network features". IEEE/ACM Transactions on Computational Biology and Bioinformatics 7 3 (2010): 400-411. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955471310&partnerID=MN8TOARS.
    10.1109/TCBB.2010.55
  28. Wang, Z.; Kim, S.; Quinney, S.K.; Guo, Y.; Hall, S.D.; Rocha, L.M.; Li, L.. "Literature mining on pharmacokinetics numerical data: A feasibility study". Journal of Biomedical Informatics 42 4 (2009): 726-735. http://www.scopus.com/inward/record.url?eid=2-s2.0-67649382957&partnerID=MN8TOARS.
    10.1016/j.jbi.2009.03.010
  29. Abi-Haidar, A.; Kaur, J.; Maguitman, A.; Radivojac, P.; Rechtsteiner, A.; Verspoor, K.; Wang, Z.; Rocha, L.M.. "Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks". Genome Biology 9 SUPPL. 2 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-51049089776&partnerID=MN8TOARS.
    10.1186/gb-2008-9-s2-s11
  30. Simas, T.; Rocha, L.M.. "Stochastic model for scale-free networks with cutoffs". Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 78 6 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-58249109572&partnerID=MN8TOARS.
    10.1103/PhysRevE.78.066116
  31. Marchionini, G.; Abbasi, A.; Agichtein, E.; Ahmad, K.; Al-Maskari, A.; Amati, G.; Yahia, S.A.; et al. "TOIS reviewers January 2006 through May 2007". ACM Transactions on Information Systems 25 4 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-35348956967&partnerID=MN8TOARS.
    10.1145/1281485.1281486
  32. Huang, C.-F.; Kaur, J.; Maguitman, A.; Rocha, L.M.. "Agent-based model of genotype editing". Evolutionary Computation 15 3 (2007): 253-289. http://www.scopus.com/inward/record.url?eid=2-s2.0-35748949595&partnerID=MN8TOARS.
    10.1162/evco.2007.15.3.253
  33. Rocha, L.M.; Kaur, J.. "Genotype editing and the evolution of regulation and memory". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4648 LNAI (2007): 63-73. http://www.scopus.com/inward/record.url?eid=2-s2.0-38049027758&partnerID=MN8TOARS.
  34. Maguitman, A.G.; Rechtsteiner, A.; Verspoor, K.; Strauss, C.E.; Rocha, L.M.. "Large-scale testing of bibliome informatics using Pfam protein families". Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006 (2006): 76-87. http://www.scopus.com/inward/record.url?eid=2-s2.0-36348936988&partnerID=MN8TOARS.
  35. Verspoor K; Cohn J; Joslyn C; Mniszewski S; Rechtsteiner A; Rocha LM; Simas T. "Protein annotation as term categorization in the gene ontology using word proximity networks.". (2005): http://europepmc.org/abstract/med/15960833.
    10.1186/1471-2105-6-S1-S20
  36. Rocha, L.M.; Hordijk, W.. "Material representations: From the genetic code to the evolution of cellular automata". Artificial Life 11 1-2 (2005): 189-214. http://www.scopus.com/inward/record.url?eid=2-s2.0-15444379171&partnerID=MN8TOARS.
    10.1162/1064546053278964
  37. Almeida e Costa, F.; Rocha, L.M.. "Introduction to the special issue: Embodied and situated cognition". Artificial Life 11 1-2 (2005): 5-11. http://www.scopus.com/inward/record.url?eid=2-s2.0-15444366725&partnerID=MN8TOARS.
    10.1162/1064546053279035
  38. Huang, C.-F.; Rocha, L.M.. "A systematic study of genetic algorithms with genotype editing". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3102 (2004): 1233-1245. http://www.scopus.com/inward/record.url?eid=2-s2.0-35048824396&partnerID=MN8TOARS.
  39. Challacombe, J.F.; Rechtsteiner, A.; Gottardo, R.; Rocha, L.M.; Browne, E.P.; Shenk, T.; Altherr, M.R.; Brettin, T.S.. "Evaluation of the host transcriptional response to human cytomegalovirus infection". Physiological Genomics 18 (2004): 51-62. http://www.scopus.com/inward/record.url?eid=2-s2.0-4243169338&partnerID=MN8TOARS.
    10.1152/physiolgenomics.00155.2003
  40. Rocha, L.M... "The physics and evolution of symbols and codes: Reflections on the work of Howard Pattee". BioSystems 60 1-3 (2001): 1-4. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035038115&partnerID=MN8TOARS.
    10.1016/S0303-2647(01)00103-4
  41. Rocha, L.M.. "Adaptive recommendation and open-ended semiosis". Kybernetes 30 5-6 (2001): 821-851. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035640002&partnerID=MN8TOARS.
    10.1108/03684920110392093
  42. Rocha, L.M.. "Evolution with material symbol systems". BioSystems 60 1-3 (2001): 95-121. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035037993&partnerID=MN8TOARS.
    10.1016/S0303-2647(01)00110-1
  43. Rocha, L.M.. "Syntactic autonomy: Why there is no autonomy without symbols and how self-organizing systems might evolve them". Annals of the New York Academy of Sciences 901 (2000): 207-223. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034059262&partnerID=MN8TOARS.
  44. Rocha, L.M.. "Evidence sets: Modeling subjective categories". International Journal of General Systems 27 6 (1999): 457-494. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032671796&partnerID=MN8TOARS.
  45. Rocha, Luis Mateus. "Syntactic autonomy". IEEE International Symposium on Intelligent Control - Proceedings (1998): 706-711. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032292082&partnerID=MN8TOARS.
  46. Joslyn, C.; Rocha, L.. "Towards a formal taxonomy of hybrid uncertainty representations". Information Sciences 110 3-4 (1998): 255-277. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032188417&partnerID=MN8TOARS.
  47. Rocha, L.M.. "Relative uncertainty and evidence sets: A constructive framework". International Journal of General Systems 26 1-2 (1997): 35-61. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030692880&partnerID=MN8TOARS.
  48. Henry, C.; Rocha, L.M.. "Language theory: Consensual selection of dynamics". Cybernetics and Systems 27 6 (1996): 541-553. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030286811&partnerID=MN8TOARS.
  49. Rocha, L.M.. "Eigenbehavior and symbols". Systems Research and Behavioral Science 13 3 (1996): 371-384. http://www.scopus.com/inward/record.url?eid=2-s2.0-0000353379&partnerID=MN8TOARS.
Newspaper article
  1. Luis M. Rocha. "Mining social media data for biomedical signals and health-related behavior", Annual Review of Biomedical Data Science, 2020
    10.1146/annurev-biodatasci-030320-040844

Other

Other output
  1. The distance backbone of complex networks. 2021. Luis M. Rocha.
    10.1093/comnet/cnab021
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/03/11 The effective graph: a weighted graph that captures nonlinear logical redundancy in biochemical systems Network Science for Fluid Mechanics Seminar Series
Network Science for Fluid Mechanics Seminar Series (Los Angeles, United States)
2021/10/03 Towards Causal Explanation and Control of Complex (Biochemical) Systems Center for Collective Dynamics of Complex Systems Colloquium Series
Center for Collective Dynamics of Complex Systems (Binghamton, United States)
2021/07/28 Redundancy in the Structure and Dynamics of Complex Systems the PhD programme in Physics and Chemistry of Biological Systems Colloquium Series
Scuola Internazionale Superiore di Studi Avanzati (Trieste, Italy)
2021/07/26 Bias as a limitation of modeling the World Data Analytics, a tool for Development: Technical, Ethical, and Legal Complexities Session
International Conference on Robot Ethics and Standards series (Troy, United States)
2021/04/14 Sex and Gender perspective in the future of Personalized Medicine GENDER BIAS IN ARTIFICIAL INTELLIGENCE AND HEALTH: Building a Future for Equality
Barcelona Supercomputing Center (Barcelona, Spain)
2021/04/01 Redundancy in Structure and Dynamics of Complex Systems Northeast Regional Conference on Complex Systems 2021
Northeast Regional Conference on Complex Systems (Binghamton, United States)
2020/11/30 Towards Control of Complex Biomedical Systems 5th European Conference on Translational Bioinformatics: Biomedical Big Data Supporting Precision Medicine
Spanish National Cancer Research Center (Madrid, Spain)
2020/09/18 Writing an Interdisciplinary Training Grant with Systems Thinking CISE NRT Writing a Winning Proposal Workshop
National Science Foundation (Alexandria, United States)
2020/07/14 Actionable Models of Control in Complex Systems for the Biomedical Domain Artificial Intelligence Talk Series
Indiana University, Bloomington (Bloomington, United States)
2020/01/23 Actionable models of control in complex systems for the biomedical domain Artificial Intelligence, HPC and Biomedicine: implicit biases, scientific, technical and ethical challenges
Barcelona Supercomputing Center (Barcelona, Spain)
2019/12/03 Towards understanding biosocial complexity of human health with actionable models Data and Network Science for Social Good, Complex Networks Satellite 2019
NOVA Business School (Carcavelos, Portugal)
2019/10/22 Interdisciplinarity, Data Science and Complex Systems 1st Workshop on Modeling Complex Systems
Post-graduate program in complex systems modeling (PPG-SCX), University of São Paulo (São Paulo, Brazil)
2019/09/12 Smart cities ecosystem in a changing environment Schréder Hyperion inauguration ceremony
Nova School of Business and Economics (Carcavelos, Portugal)
2019/06/25 Towards understanding biosocial complexity of human health with network and data science Joint Sorbonne Université and Indiana University Symposium on A.I.
Sorbonne Université (Paris, France)
2019/05/15 Representation and measurement of complex systems Complex Systems @ Purdue
Purdue University (West Laffayete, United States)
2019/05 Redundancy in Complex Brain Networks How systems learn, change, and self-organize: Insights from network science workshop
Indiana University (Bloomington, Spain)
2018/11 Complex Systems from Cybernetics to Network Science: Modeling Multilevel Human Complexity Computer Science Lecture Series Speaker
Universidad Nacional del Sur (Bahia Blanca, Argentina)
2018/07/04 Redundancy in the Structure and Dynamics of Complex Networks Instituto de Sistemas e Robotica Colloquium Series
Instituto Superior Tecnico (Lisboa, Portugal)
2018/06/23 Towards understanding biosocial complexity in human health: from biochemical control to social factors in DDI and reproduction Frontières du Vivant PhD program Sorbonne Paris University Retreat
Frontières du Vivant PhD program Sorbonne Paris University (Sesimbra, Portugal)
2018/06/11 Towards understanding biosocial complexity in human health: from control of biochemical regulation of disease to social factors in drug-interaction and human reproduction Network Medicine (NetMed18): Personalized Medicine in the Era of Big Data. NetSci 2018 Satellite symposium
NetSci 2018 (Paris, France)
2018/04/19 Towards understanding the multi-level complexity of human health: from control of biochemical regulation of disease to social factors in drug-interaction Clinical Seminar
Fundação Champalimaud (Lisboa, Portugal)
2018/02/01 Towards understanding the multi-level complexity of human health: from drug-interaction to human reproduction cycles 2nd Week of Complexity Sciences
Centro de Ciencias de la Complejidad C3, Universidad Nacional Autonoma de México (Mexico City, Mexico)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2021/01 - 2021/12 Complex Networks 2021: 10th Int. Conference on Complex Networks & Their Applications, Madrid, Spain, November 30 - December 2, 2021, (Program Chair) (2021/11/30 - 2021/12/02)
Conference (Member of the Organising Committee)
2020/01/01 - 2020/12/03 Complex Networks 2020: 9th Int. Conference on Complex Networks & Their Applications (2020/12/01 - 2020/12/03)
Conference (President of the Organising Committee)
2019 - 2019 Complex Networks 2019: 8th Int. Conference on Complex Networks & Their Applications (2019 - 2019)
Conference (President of the Organising Committee)
 Fundação Calouste Gulbenkian, Portugal
2019 - 2019 Charting interdisciplinary research opportunities between data and life sciences, Instituto Gulbenkian de Ciência, Oeiras and ISI Foundation, Turin. (2019 - 2019)
Meeting (President of the Organising Committee)
 Instituto Gulbenkian de Ciência, Portugal
2018 - 2018 Complex Networks 2018: 7th Int. Conference on Complex Networks & Their Applications (2018 - 2018)
Congress (Member of the Scientific Committee)
 University of Cambridge Queens' College, United Kingdom

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2021/09 Computationally Modeling Roman Domestic Art and Architecture
Supervisor
 Kelly McClinton (PhD)
Indiana University Bloomington, United States
2020/06 Canalization in Stochastic Boolean Networks
Supervisor
 Sikander Khare (Master)
Indiana University, United States
2019 Prediction of Drug Interaction and Adverse Reactions, with data from Electronic Health Records, Clinical Reporting, Scientific Literature, and Social Media, using Complexity Science Methods
Supervisor
 Rion Brattig Correia (PhD)
Indiana University Bloomington, United States
2019 Neural Correlates of Adaptive Behavior: Structure, Dynamics, and Information Processing
Supervisor
 Steven Williams (PhD)
Indiana University Bloomington, United States
2017 The anatomical and effective structure of complex systems
Supervisor
 Alexander Gates (PhD)
Indiana University Bloomington, United States
2017 The Role of Canalization in the Spreading of Perturbations in Boolean Networks
Supervisor
 Santosh Manicka (PhD)
Indiana University Bloomington, United States
2015 Measuring Scales: Integration and Modularity in Complex Systems
Supervisor
 Artemy Kolchinsky (PhD)
Indiana University Bloomington, United States
2012 Stochastic Models and Transitivity In Complex Networks
Supervisor
 Tiago Simas (PhD)
Indiana University Bloomington, United States
2012 Biomedical Literature Mining for Pharmacokinetics Numerical Parameter Collection
Supervisor
 Zhiping Wang (PhD)
Indiana University Bloomington, United States
2011 An adaptive document classifier inspired by T-Cell cross-regulation in the immune system
Supervisor
 Alaa Abi-Haidar (PhD)
Indiana University Bloomington, United States
2011 Reverse Engineering the Mechanisms and the Dynamical Behavior of Complex Biochemical Pathways
Supervisor
 Marcio Mourão (PhD)
Indiana University Bloomington, United States
2008 Análise e Simulação do Processo da Inovação Segundo uma Perspectiva Evolucionária
Supervisor
 Humberto Santos (PhD)
Universidade da Beira Interior, Portugal
2004 Multivariate Analysis of Gene Expression Data and Functional Information: Automated Methods for Functional Genomics.
Supervisor
 Andreas Rechtsteiner (PhD)
Portland State University, United States
2001 A cognitive model of adaptive web design and navigation
Supervisor
 Johan Bollen (PhD)
Université Libre de Bruxelles Campus de la Plaine, Belgium

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2022/01/18 - Current Bio-inspired Computing end Evolutionary Systems Systems Science (Graduado) Binghamton University Thomas J Watson School of Engineering and Applied Science, United States
2012 - 2021 Complex Systems Seminar I Informatics (Doctor of Philosophy) Indiana University Bloomington, United States
2008 - 2017 Intro to Informatics Informatics (Doctor of Philosophy) Indiana University Bloomington, United States
2005 - 2015 Bio-inspired Computing Informatics (Bachelor) Indiana University Bloomington, United States
2010 - 2012 Intro to Complex Systems Informatics (Doctor of Philosophy) Indiana University Bloomington, United States
2008 - 2011 Complex Systems Seminar II Informatics (Doctor of Philosophy) Indiana University Bloomington, United States
2005 - 2007 Introduction to Informatics Informatics (Bachelor) Indiana University Bloomington, United States

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2008 - Current Member of Review Panels for NSF: Computer & Information Science & Engineering, 2006; Cyber-Enabled Discovery, 2008; IIS-Biomedical Career awards 2008; Computing and Communication Foundations (CCF): Core Programs 2010; Networks, Synthetic Biology and Evolution 2011, Networks and Regulation Cluster; Science and Technology Centers: Directorate for Biological Sciences, 2014, 2018.
Evaluator
 National Science Foundation, United States
2000 - Current Member of Review Panels for FCT: Computer Engineering, 2007; Ciência Viva 2008; Chair of Robotics, Intelligent and Information Systems Review Panel, 2000, 2003, 2004; Bilateral Scientific Cooperation Agreements 2011.
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal
2018 - 2018 Member of External Review Committee of the Center for the Study of Complex Systems in the College of Literature, Science, and the Arts at the University of Michigan
Evaluator
 University of Michigan, United States
Distinctions

Award

2019 Research Excellence Award
Indiana University Bloomington, United States
2015 Teaching Award
Indiana University Bloomington, United States
2006 Teaching Award
Indiana University Bloomington, United States

Title

2016 Fulbright Scholar