Publications - Luis M. Rocha

Latest Publications

Year	Reference
2024	J. Sánchez-Valle, R.B. Correia, M. Camacho-Artacho, R. Lepore, M.M. Mattos, L.M. Rocha, A. Valencia [2024]. "Prevalence and differences in the co-administration of drugs known to interact: an analysis of three distinct and large populations.". BMC Medicine 22: 166. doi: 10.1186/s12916-024-03384-1. PMID: 38637816.
2024	Rozum, Jordan C., and Luis M. Rocha.[2024]. "The ultrametric backbone is the union of all minimum spanning forests". arXiv:2403.12705. DOI: 10.48550/arXiv.2403.12705
2024	L.M. Rocha [2024]. Polimedicação é pior em idosos e mulheres, mas pode-se melhorar com análise de dados. Público . January 31, 2024.
2023	Paños, David Soriano, Felipe Xavier Costa, and Luis M. Rocha. [2023]. "Semi-metric topology characterizes epidemic spreading on complex networks". arXiv:2311.14817. DOI: 10.48550/arXiv.2311.14817
2023	L.M. Rocha [2023]. Jovens reduzidos a um número. Público . November 27, 2023. Longer version with additional data at Medium.
2023	Felag, J., Correia, R.B., Rocha, L.M. [2023]. "Discourse Polarization Increasing in Congressional Speeches: An Analysis from Clinton to Biden". Working Paper.
2023	K.H. Park, F.X. Costa, L.M. Rocha, R. Albert, J.C. Rozum [2023]. "Robustness of biomolecular networks suggests functional modules far from the edge of chaos". PRX Life. 1, 023009. DOI: 10.1103/PRXLife.1.023009. Preprint available at bioRxiv:2023.06.30.547297. DOI: 10.1101/2023.06.30.547297
2023	T. Parmer and L.M. Rocha. [2023]. "Dynamical Modularity in Automata Models of Biochemical Networks". arXiv:2303.16361. DOI: 10.48550/arXiv.2303.16361
2023	R.B. Correia, J.M. Almeida, Ma.J. Wyrwoll, I.Julca, D. Sobral, C.S. Misra, L.G. Guilgur, H.-C. Schuppe, N. Silva, P. Prudêncio, A. Nóvoa, A. S. Leocádio, J. Bom, M. Mallo, S. Kliesch, M. Mutwil, L.M. Rocha, F.Tüttelmann, J. D. Becker, P. Navarro-Costa [2023]. "The conserved transcriptional program of metazoan male germ cells uncovers ancient origins of human infertility". bioRxiv 2022.03.02.482557, doi: 10.1101/2022.03.02.482557.
2023	V. Dorsant-Ardon, A. B. Sanjay, L.M. Rocha, R.B. Correia, and L.G. Apostolova. [2023]. "Gene co-expression network analyses in mild cognitive impairment" Alzheimer's & Dementia. 19: e082238. DOI: 10.1002/alz.082238
2023	R.B. Correia, A. Barrat, L. M. Rocha [2023]. "Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs". PLoS Computational Biology. 19(2): e1010854. doi: 10.1371/journal.pcbi.1010854.
2023	Costa, F.X.; Rozum, J.C.; Marcus, A.M.; Rocha, L.M. [2023]. "Effective Connectivity and Bias Entropy Improve Prediction of Dynamical Regime in Automata Networks". Entropy. 25(2):374. doi: 10.3390/e25020374.
2023	A. Min, W.R. Miller, L.M. Rocha, K. Borner, R.B. Correia, and P.C. Shih. [2023]. "Understanding Contexts and Challenges of Information Management for Epilepsy Care". In: Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ’23), April 23–28, 2023, Hamburg, Germany. ACM, New York, NY, USA, 15 pages. DOI:/10.1145/3544548.3580949. Preprint Available.
2023	Cherifi, H., Mantegna, R.N., Rocha, L.M., Cherifi, C., Micciche, S. (Eds.) [2023]. Complex Networks and Their Applications XI: Proceedings of The Eleventh International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2022 Studies in Computational Intelligence Series. Vol. I and II. Springer. DOI: 10.1007/978-3-031-21127-0 and 10.1007/978-3-031-21131-7. (Two Volumes)
2023	F.X. Costa, R. B. Correia, L.M. Rocha [2023]. "The distance backbone of directed networks". In: Cherifi, H., Mantegna, R.N., Rocha, L.M., Cherifi, C., Micciche, S. (eds) Complex Networks and Their Applications XI. COMPLEX NETWORKS 2022. Studies in Computational Intelligence, vol 1078. Springer, Cham. Preprint also available:arXiv:2209.01181.
2022	Parmer, T., Rocha, L.M. & Radicchi, F. [2022]. "Influence maximization in Boolean networks". Nature Communications. 13, 3457, DOI: 10.1038/s41467-022-31066-0.
2022	L.M. Rocha [2022]. "On the feasibility of dynamical analysis of network models of biochemical regulation". Bioinformatics. btac360, DOI: 10.1093/bioinformatics/btac360. PrePrint: arXiv:2110.10821.
2022	S. Zhang, H. Wu, L. Wang, G. Zhang, L.M. Rocha, H. Shatkay, L. Li[2022]. "Translational drug–interaction corpus". Database, baac031. doi: 10.1093/database/baac031.
2022	L.M. Rocha [2022]. Ser emigrante português é ser cidadão de 10.ª classe e deixa muitos democraticamente apátridas. Público . February 22, 2022.
2022	I.B. Wood, R.B. Correia, W.R. Miller, and L.M. Rocha [2022]. "Small Cohort of Epilepsy Patients Showed Increased Activity on Facebook before Sudden Unexpected Death". Epilepsy & Behavior. 128: 108580. DOI:10.1016/j.yebeh.2022.108580. Preprint: arXiv:2201.07552.
2022	Manicka, S., M. Marques-Pita, and L.M. Rocha [2022]. Effective connectivity determines the critical dynamics of biochemical networks. Journal of the Royal Society Interface. 19(186):20210659. DOI: 10.1098/rsif.2021.0659.
2022	Benito, R.M., Cherifi, C., Cherifi, H., Moro E., Rocha, L.M., Sales-Pardo, M. (Eds.) [2022]. Complex Networks and Their Applications X: Proceedings The 10th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2021. Studies in Computational Intelligence Series. Vol. I and II. Springer. DOI: 10.1007/978-3-030-93409-5 and 10.1007/978-3-030-93413-2. (Two Volumes)
2021	Gates, A., R.B. Correia, X. Wang, and L.M. Rocha [2021]. "The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling". Proceedings of the National Academy of Sciences. 118 (12) e2022598118; DOI: 10.1073/pnas.2022598118.
2021	Sanjay, A. B., Correia, R. B., Rocha, L. M., and Apostolova, L. G. [2021]. "Transcriptomic profiling in mild cognitive impairment using peripheral blood gene co‐expression networks". Alzheimer's & Dementia, 17, e056702. DOI: 10.1002/alz.056702.
2021	Simas, T., R.B Correia and L.M. Rocha [2021]. "The distance backbone of complex networks". Journal of Complex Networks. 9 (6), cnab021. DOI: 10.1093/comnet/cnab021. Preprint at: arXiv:2103.04668
2021	A. Min, W. Miller, L.M. Rocha, K.Börner, R.B. Correia, and P.C. Shih. [2021]. "Just In Time: Challenges and Opportunities of First Aid Care Information Sharing for Supporting Epileptic Seizure Response".Proceedings of the ACM on Human-Computer Interaction.. 5, CSCW1, Article 113, pp. 1-24. DOI:10.1145/3449187.
2021	L.M. Rocha [2021]. O sexo dos anjos, ou como a complexidade das pandemias exige pensamento sistémico. Público . February 18, 2021. Longer Version at Medium.
2021	L.M. Rocha [2021]. Lixívia ideológica não resolve a pandemia. Público . January 20, 2021.
2021	Benito, R.M., Cherifi, C., Cherifi, H., Moro E., Rocha, L.M., Sales-Pardo, M. (Eds.) [2021]. Complex Networks and Their Applications IX: Proceedings The 9th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2020. Studies in Computational Intelligence Series. Vol. 943-944. Springer. DOI: 10.1007/978-3-030-65347-7 and 10.1007/978-3-030-65351-4. (Two Volumes)
2020	L.M. Rocha [2020]. Privacy apocalypse or data science for the common good? Preparing Western Nations for Pandemics to Come . Towards data science . November 22, 2020.
2020	Correia, R.B., P. Navarro-Costa, and L.M. Rocha [2020]. "Extraction of overlapping modules in networks via spectral methods and information theory". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2020	Gates, A., R.B. Correia, X. Wang, and L.M. Rocha [2020]. "The effective graph: a weighted graph that captures nonlinear logical redundancy in biochemical systems". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2020	Teixeira, A. S., J. Faskowitz, O. Sporns, and L.M. Rocha [2020]. "The Metric Backbone in the Human Connectome and across Lifespan". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2020	L.M. Rocha [2020]. Apocalípticos da privacidade vs. StayAway Covid e a ciência de dados para o bem comum. Observador . October 25, 2020.
2020	Cherifi, H., Rocha, L.M., and Wasserman, S. [2020]. "Introduction to the special issue on COMPLEX NETWORKS 2018". Network Science . 8(S1-S3). DOI: 10.1017/nws.2020.22.
2020	L.M. Rocha [2020]. É necessário mais investimento em ciência de complexidade e resiliência para lidar com pandemias. Público . March 31, 2020 Print Version. Longer version on Medium.
2020	R.B. Correia, I.B Wood, J. Bollen, L.M. Rocha [2020]. "Mining social media data for biomedical signals and health-related behavior". Annual Review of Biomedical Data Science . 3(1): 433-458. DOI: 10.1146/annurev-biodatasci-030320-040844.
2020	Cherifi, C., Gaito, S., Mendes, J.M., Moro E., Rocha, L.M. (Eds.) [2020]. Complex Networks and Their Applications VIII:. Proceedings The 8th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2019. Studies in Computational Intelligence Series. Vol. 881-882. Springer. DOI: 10.1007/978-3-030-36687-2 and 10.1007/978-3-030-36683-4. (Two Volumes)
2019	H.-Y. Wu, A. Shendre, S. Zhang, P. Zhang, L. Wang, D. Zeruesenay, L.M. Rocha, H. Shatkay, S. Quinney, X. Ning, and L. Li [2019]. Translational Knowledge Discovery between Drug Interactions and Pharmacogenetics. Clinical Pharmacology & Therapeutics . 2019 Dec 21. doi: 10.1002/cpt.1745
2019	R.B. Correia, L.P. de Araújo, M.M. Mattos, L.M. Rocha [2019]. City-wide Analysis of Electronic Health Records Reveals Gender and Age Biases in the Administration of Known Drug-Drug Interactions. NPJ Digital Medicine. 2:74.
2019	M. ten Thij, I.B. Wood, L.M. Rocha, J. Bollen [2019]. "Detecting eigenmoods in individual human emotions." 5th International Conference on Computational Social Science (IC2S2) July 17-20, 2019, University of Amsterdam, The Netherlands.
2019	A. Gates, X. Wang, R.B. Correia, L.M. Rocha [2019]. "The effective graph captures canalizing dynamics and control in Boolean network models of biochemical regulation." NetSci 2019: International School and Conference on Network Science. May 27-31, 2019, Burlington, VT, USA.
2019	A. Min, W.R. Miller, L.M. Rocha, K. Borner, R.B. Correia, P.C. Shih [2019]. "Understanding Health Information Management of People with Epilepsy and Their Caregivers." Workshop on Interactive Systems in Health Care, The ACM CHI Conference on Human Factors in Computing Systems. May 4-9, 2019, Glasgow, U.K.
2019	Aiello, L.M., Cherifi, C., Cherifi, H., Lambiotte, R., Lio, P., Rocha, L.M. (Eds.) [2019]. Complex Networks and Their Applications VII:. Proceedings The 7th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2018. Studies in Computational Intelligence Series. Vol. 812-813. Springer. DOI: 10.1007/978-3-030-05411-3 and 10.1007/978-3-030-05414-4. (Two Volumes)

Volumes

Year	Reference
2023	Cherifi, H., Mantegna, R.N., Rocha, L.M., Cherifi, C., Micciche, S. (Eds.) [2023]. Complex Networks and Their Applications XI: Proceedings of The Eleventh International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS 2022 Studies in Computational Intelligence Series. Vol. I and II. Springer. DOI: 10.1007/978-3-031-21127-0 and 10.1007/978-3-031-21131-7. (Two Volumes)
2022	Benito, R.M., Cherifi, C., Cherifi, H., Moro E., Rocha, L.M., Sales-Pardo, M. (Eds.) [2022]. Complex Networks and Their Applications X:. Proceedings The 10th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2021. Studies in Computational Intelligence Series. Vol. I and II. Springer. DOI: 10.1007/978-3-030-93409-5 and 10.1007/978-3-030-93413-2. (Two Volumes)
2021	Benito, R.M., Cherifi, C., Cherifi, H., Moro E., Rocha, L.M., Sales-Pardo, M. (Eds.) [2021]. Complex Networks and Their Applications IX:. Proceedings The 9th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2020. Studies in Computational Intelligence Series. Vol. 943-944. Springer. DOI: 10.1007/978-3-030-65347-7 and 10.1007/978-3-030-65351-4. (Two Volumes)
2020	Cherifi, H., Rocha, L.M., and Wasserman, S. (Eds.) [2020]. "Special issue on COMPLEX NETWORKS 2018". Network Science . 8. DOI: 10.1017/nws.2020.22.
2020	Cherifi, C., Gaito, S., Mendes, J.M., Moro E., Rocha, L.M. (Eds.) [2020]. Complex Networks and Their Applications VIII: Proceedings The 8th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2019. Studies in Computational Intelligence Series. Vol. 881-882. Springer. DOI: 10.1007/978-3-030-36687-2 and 10.1007/978-3-030-36683-4. (Two Volumes)
2019	Aiello, L.M., Cherifi, C., Cherifi, H., Lambiotte, R., Lio, P., Rocha, L.M. (Eds.) [2019]. Complex Networks and Their Applications VII: Proceedings The 7th International Conference on Complex Networks and Their Applications COMPLEX NETWORKS 2018. Studies in Computational Intelligence Series. Vol. 812-813. Springer. DOI: 10.1007/978-3-030-05411-3 and 10.1007/978-3-030-05414-4. (Two Volumes)
2010	Bento dos Santos, L., N. Crato, A. Coutinho, J. Caraça, L.M. Rocha (Eds.) [2010]. Everything is Connected. Verbo Editora.
2009	Seabra Lopes, L.; Lau, N.; Mariano, P.; Rocha, L.M. (Eds.) [2009]. Progress in Artificial Intelligence: 14th Portuguese Conference on Artificial Intelligence (EPIA 2009). Lecture Notes in Artificial Intelligence (LNAI), 5816. Springer-Verlag. doi:10.1007/978-3-642-04686-5 (Online Fulltext Content)
2007	Almeida e Costa, F., L.M. Rocha, E. Costa, I. Harvey, A. Coutinho (Eds.) [2007]. Advances in Artificial Life: Proceedings of the 2007 European Conference on Artificial Life. Lecture Notes in Artificial Intelligence (LNAI), 4648. Springer-Verlag.
2006	Rocha, L.M., L. Yaeger, M. Bedau, D. Floreano, R. Goldstone, and A. Vespignani (Eds.) [2006]. Artificial Life 10: Tenth International Conference on the Simulation and Synthesis of Living Systems. MIT Press.
2005	Almeida e Costa, F. and Rocha, Luis M. (Eds.) [2005]. Special Issue on Embodied and Situated Cognition. Artificial Life. 11 (1-2).
2001	Rocha, Luis M. (Ed.)[2001]. The Physics and Evolution of Symbols and Codes. BioSystems Vol. 60, No. 1-3. Editorial: Biosystems Vol. 60, pp. 1-4.
1997	Rocha, Luis M. [1997]. Evidence Sets and Contextual Genetic Algorithms: Exploring Uncertainty, Context, and Embodiment in Cognitive and Biological Systems. PhD Dissertation. State University of New York at Binghamton.
1995	Rocha, Luis M. (Ed.) [1995]. Self-Reference in Biological and Cognitive Systems. Special issue of Communication and Cognition - Artificial Intelligence. Vol. 12, nos. 1-2. Contributors: Howard Pattee, Robert Rosen, George Kampis, Peter Cariani, Pedro Medina-Martins, Charles Henry, and Luis Rocha.

Journal Papers

Year	Reference
2024	J. Sánchez-Valle, R.B. Correia, M. Camacho-Artacho, R. Lepore, M.M. Mattos, L.M. Rocha, A. Valencia [2024]. "Prevalence and differences in the co-administration of drugs known to interact: an analysis of three distinct and large populations.". BMC Medicine 22: 166. doi: 10.1186/s12916-024-03384-1. PMID: 38637816.
2024	Rozum, Jordan C., and Luis M. Rocha.[2024]. "The ultrametric backbone is the union of all minimum spanning forests". arXiv:2403.12705. DOI: 10.48550/arXiv.2403.12705
2023	Paños, David Soriano, Felipe Xavier Costa, and Luis M. Rocha. [2023]. "Semi-metric topology characterizes epidemic spreading on complex networks". arXiv:2311.14817. DOI: 10.48550/arXiv.2311.14817
2023	Felag, J., Correia, R.B., Rocha, L.M. [2023]. "Discourse Polarization Increasing in C
2023	K.H. Park, F.X. Costa, L.M. Rocha, R. Albert, J.C. Rozum [2023]. "Robustness of biomolecular networks suggests functional modules far from the edge of chaos". PRX Life. 1, 023009. DOI: 10.1103/PRXLife.1.023009. Preprint available at bioRxiv:2023.06.30.547297. DOI: 10.1101/2023.06.30.547297
2023	V. Dorsant-Ardon, A. B. Sanjay, L.M. Rocha, R.B. Correia, and L.G. Apostolova. [2023]. "Gene co-expression network analyses in mild cognitive impairment" Alzheimer's & Dementia. 19: e082238. DOI: 10.1002/alz.082238
2023	T. Parmer and L.M. Rocha. [2023]. "Dynamical Modularity in Automata Models of Biochemical Networks". arXiv:2303.16361. DOI: 10.48550/arXiv.2303.16361
2023	R.B. Correia, J.M. Almeida, Ma.J. Wyrwoll, I.Julca, D. Sobral, C.S. Misra, L.G. Guilgur, H.-C. Schuppe, N. Silva, P. Prudêncio, A. Nóvoa, A. S. Leocádio, J. Bom, M. Mallo, S. Kliesch, M. Mutwil, L.M. Rocha, F.Tüttelmann, J. D. Becker, P. Navarro-Costa [2023]. "The conserved transcriptional program of metazoan male germ cells uncovers ancient origins of human infertility". bioRxiv 2022.03.02.482557, doi: 10.1101/2022.03.02.482557.
2023	R.B. Correia, A. Barrat, L. M. Rocha [2023]. "Contact networks have small metric backbones that maintain community structure and are primary transmission subgraphs". PLoS Computational Biology. 19(2): e1010854. doi: 10.1371/journal.pcbi.1010854.
2023	Costa, F.X.; Rozum, J.C.; Marcus, A.M.; Rocha, L.M. [2023]. "Effective Connectivity and Bias Entropy Improve Prediction of Dynamical Regime in Automata Networks". Entropy. 25(2):374. doi: 10.3390/e25020374.
2022	Parmer, T., Rocha, L.M. & Radicchi, F. [2022]. "Influence maximization in Boolean networks". Nature Communications. 13, 3457, DOI: 10.1038/s41467-022-31066-0.
2022	L.M. Rocha [2022]. "On the feasibility of dynamical analysis of network models of biochemical regulation". Bioinformatics. btac360, DOI: 10.1093/bioinformatics/btac360. PrePrint: arXiv:2110.10821.
2022	S. Zhang, H. Wu, L. Wang, G. Zhang, L.M. Rocha, H. Shatkay, L. Li[2022]. "Translational drug–interaction corpus". Database, baac031. doi: 10.1093/database/baac031.
2022	I.B. Wood, R.B. Correia, W.R. Miller, and L.M. Rocha [2022]. "Small Cohort of Epilepsy Patients Showed Increased Activity on Facebook before Sudden Unexpected Death". Epilepsy & Behavior. 128: 108580. DOI:10.1016/j.yebeh.2022.108580. Preprint: arXiv:2201.07552.
2022	Manicka, S., M. Marques-Pita, and L.M. Rocha [2022]. Effective connectivity determines the critical dynamics of biochemical networks. Journal of the Royal Society Interface. 19(186):20210659. DOI: 10.1098/rsif.2021.0659.
2021	Gates, A., R.B. Correia, X. Wang, and L.M. Rocha [2021]. "The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling". Proceedings of the National Academy of Sciences. 118 (12) e2022598118; DOI: 10.1073/pnas.2022598118.
2021	Simas, T., R.B Correia and L.M. Rocha [2021]. "The distance backbone of complex networks". Journal of Complex Networks. 9 (6), cnab021. DOI: 10.1093/comnet/cnab021. Preprint at: arXiv:2103.04668
2021	Sanjay, A. B., Correia, R. B., Rocha, L. M., and Apostolova, L. G. [2021]. "Transcriptomic profiling in mild cognitive impairment using peripheral blood gene co‐expression networks". Alzheimer's & Dementia, 17, e056702. DOI: 10.1002/alz.056702.
2020	R.B. Correia, I.B Wood, J. Bollen, L.M. Rocha [2020]. "Mining social media data for biomedical signals and health-related behavior". Annual Review of Biomedical Data Science . 3(1): 433-458. DOI: 10.1146/annurev-biodatasci-030320-040844.
2020	Cherifi, H., Rocha, L.M., and Wasserman, S. [2020]. "Introduction to the special issue on COMPLEX NETWORKS 2018". Network Science . 8(S1-S3). DOI: 10.1017/nws.2020.22.
2019	H.-Y. Wu, A. Shendre, S. Zhang, P. Zhang, L. Wang, D. Zeruesenay, L.M. Rocha, H. Shatkay, S. Quinney, X. Ning, and L. Li [2020]. Translational Knowledge Discovery between Drug Interactions and Pharmacogenetics. Clinical Pharmacology & Therapeutics . In Press. doi: 10.1002/cpt.1745
2019	R.B. Correia, L.P. de Araújo, M.M. Mattos, L.M. Rocha [2019]. City-wide Analysis of Electronic Health Records Reveals Gender and Age Biases in the Administration of Known Drug-Drug Interactions. NPJ Digital Medicine. 2:74.
2018	R.B. Correia, A.J. Gates, X. Wang, L.M. Rocha [2018]. CANA: A python package for quantifying control and canalization in Boolean Networks. Frontiers in Physiology. 9: 1046. DOI: 10.3389/fphys.2018.01046
2017	I.B Wood, P.L. Varela, J. Bollen, L.M. Rocha, J. Gonçalves-Sá [2017]. "Human Sexual Cycles are Driven by Culture and Match Collective Moods". Scientific Reports. 7: 17973 DOI: 10.1038/s41598-017-18262-5.
2016	A. Gates and L.M. Rocha. [2016] "Control of complex networks requires both structure and dynamics." Scientific Reports 6, 24456. doi: 10.1038/srep24456.
2015	A. Kolchinsky, A. Gates and L.M. Rocha. [2015] "Modularity and the spread of perturbations in complex dynamical systems." Phys. Rev. E Rapid Communications. 92, 060801(R).
2015	G.L. Ciampaglia, P. Shiralkar, L.M. Rocha, J. Bollen, F. Menczer, A. Flammini [2015]. “Computational fact checking from knowledge networks.” PLoS One. 10(6): e0128193. doi:10.1371/journal.pone.0128193.
2015	A. Kolchinsky, A. Lourenço, H. Wu, L. Li, L.M. Rocha [2015]. "Extraction of Pharmacokinetic Evidence of Drug-drug Interactions from the literature.". PLoS One 10(5): e0122199. doi:10.1371/journal.pone.0122199.
2015	T. Simas and L.M. Rocha [2015]."Distance Closures on Complex Networks". Network Science, 3(2):227-268. doi:10.1017/nws.2015.11.
2014	A. Kolchinsky, M. P. Van Den Heuvel, A. Griffa, P. Hagmann, L.M. Rocha, O. Sporns, J. Goni [2014]. "Multi-scale Integration and Predictability in Resting State Brain Activity". Frontiers in Neuroinformatics, 8:66. doi: 10.3389/fninf.2014.00066.
2013	M. Marques-Pita and L.M. Rocha [2013]. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster". PLoS ONE, 8(3): e55946. doi:10.1371/journal.pone.0055946.
2013	Wu, Hengyi, S. Karnik, A. Subhadarshini, Z. Wang, S. Philips, X. Han, C. Chiang, L. Liu, M. Boustani, L.M. Rocha, S.K. Quinney, D.A. Flockhart and L. Li [2013]. "An Integrated Pharmacokinetics Ontology and Corpus for Text Mining. BMC Bioinformatics. 14:35. DOI:10.1186/1471-2105-14-35. (Highly Accessed)
2011	A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha [2011]."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):S12.
2011	M. Krallinger, et al [2011]."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):S3.
2011	A. Abi-Haidar and L.M. Rocha [2011]. "Collective Classification of Textual Documents by Guided Self-Organization in T-Cell Cross-Regulation Dynamics". Evolutionary Intelligence. 4(2):69-80.
2010	A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed and L.M. Rocha [2010]. "Classification of protein-protein interaction full-text documents using text and citation network features." IEEE/ACM Transactions On Computational Biology And Bioinformatics, 7(3):400-411. DOI: doi.ieeecomputersociety.org/10.1109/TCBB.2010.55
2009	A. Lourenço; R.C. Carreira; D. Glez-Peña; J.R. Méndez; S.A. Carneiro; L.M. Rocha; F. Díaz; E.C. Ferreira; I.P. Rocha; F. Fdez-Riverola; M. Rocha [2009]. "BioDR: Semantic Indexing Networks for Biomedical Document Retrieval." Expert Systems with Applications, 37, 3444ñ3453.
2009	Z. Wang, S. Kim, S.K. Quinney, Y. Guo, S.D. Hall, L.M. Rocha, and L. Li [2009]. "Literature mining on pharmacokinetics numerical data: A feasibility study". Journal of Biomedical Informatics. 42 (4): 726-735.
2008	T. Simas and L.M. Rocha [2008]."Stochastic model for scale-free networks with cutoffs". Physical Review E, 78(6):066116.
2008	A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha [2008]. Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks". Genome Biology. 9(Suppl 2):S11
2007	C. Huang, J. Kaur, A. Maguitman, L.M. Rocha[2007]."Agent-Based Model of Genotype Editing". Evolutionary Computation, 15(3): 253-89.
2005	Almeida e Costa, F. and Rocha, Luis M. [2005]. "Embodied and Situated Cognition". Artificial Life. 11 (1-2), pp. 5 - 11
2005	Rocha, Luis M. and W. Hordijk [2005]. "Material Representations: From the Genetic Code to the Evolution of Cellular Automata". Artificial Life. 11 (1-2), pp. 189 - 214
2005	Verspoor, K., J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L.M. Rocha, T. Simas [2005]. "Protein Annotation as Term Categorization in the Gene Ontology using Word Proximity Networks". BMC Bioinformatics, 6(Suppl 1):S20. doi:10.1186/1471-2105-6-S1-S20
2004	Challacombe, J,, A. Rechtsteiner, G. Gottardo, L.M. Rocha, E.P. Brown, T. Shenk, M. Altherr, T. Brettin [2004]. "Evaluation of the host transcriptional response to human cytomegalovirus infection". Physiol. Genomics (April 6, 2004). 10.1152/physiolgenomics.00155.2003. In Press.
2004	Rocha, Luis M. and A. Rechtsteiner [2004]. "Review of Bioinformatics for Geneticists." Clinical Chemistry 50 (9), pp. 2471 - 2472. CLINCHEM/2003/020909.
2001	Rocha, Luis M. [2001]. "Evolution with material symbol systems". Biosystems. Vol. 60, pp. 95-121.
2001	Rocha, Luis M. [2001]. "Adaptive Recommendation and Open-Ended Semiosis". Kybernetes. Vol. 30, No. 5-6.
1999	Rocha, Luis M. [1999]." Evidence Sets: Modeling Subjective Categories." In: International Journal of General Systems. Vol. 27, pp. 457-494.
1998	Joslyn, Cliff and Luis Rocha [1998] "Towards a Formal Taxonomy of Hybrid Uncertainty Representations" (pdf). Information Sciences. Vol. 110, pp. 255-277
1998	Rocha, Luis M. [1998]." Where is the progress?. " Cybernetics and Human Knowing. Vol.5, No. 4, pp. 86-90.
1998	Rocha, Luis M. and Cliff Joslyn [1998]." "Simulations of Evolving Embodied Semiosis: Emergent Semantics in Artificial Environments" Simulation Series; Vol. 30, (2), pp. 233-238.
1997	Rocha, Luis M. [1997]." Relative Uncertainty and Evidence Sets: A Constructivist Framework." In: International Journal of General Systems. Vol. 26. (1-2), pp. 35-61.
1997	Rocha, Luis M. (Ed.) [1997]. "Obituary for Professor Gordon Pask." In: International Journal of General Systems. Vol. 26, no. 3, pp. 219-222.
1996	Rocha, Luis M., V. Kreinovich, and R. Kearfott[1996]. " Computing Uncertainty in Interval Based Sets." Applied Optimization. Vol. 3, pp. 337-380. Also appears In: Applications of Interval Computation. R.B. Kearfott and V. Kreinovich (Eds.). Kluwer Academic Press. pp. 337-380.
1996	Henry, Charles and Luis Rocha [1996] "Language Theory: Consensual Selection of Dynamics". Cybernetics and Systems: An International Journal. Vol. 27, pp. 541-553. Winner of the best paper award of the EMCSR96 and the Gordon Pask Memorial Award.
1996	Rocha, Luis M. [1996]." Eigenbehavior and symbols." In: Systems Research Vol. 13, No 3, pp. 371-384.
1995	Rocha, Luis M. [1995]. " Artificial semantically closed objects." Communication and Cognition - Artificial Intelligence. Vol. 12, nos. 1-2 ( Rocha [1995a]). pp. 63-90.

Conference Proceedings

Year	Reference
2023	V. Dorsant-Ardon, A. B. Sanjay, L.M. Rocha, R.B. Correia, and L.G. Apostolova. [2023]. "Gene co-expression network analyses in mild cognitive impairment" In: Alzheimer's Association International Conference (AAIC ’23), Jul 16 - 20, 2023, Amsterdam, The Netherlands.
2023	A. Min, W.R. Miller, L.M. Rocha, K. Borner, R.B. Correia, and P.C. Shih. [2023]. "Understanding Contexts and Challenges of Information Management for Epilepsy Care". In: Proceedings of the 2023 CHI Conference on Human Factors in Computing Systems (CHI ’23), April 23–28, 2023, Hamburg, Germany. ACM, New York, NY, USA, 15 pages. DOI:/10.1145/3544548.3580949. Preprint Available.
2023	F.X. Costa, R. B. Correia, L.M. Rocha [2023]. "The distance backbone of directed networks". In: Cherifi, H., Mantegna, R.N., Rocha, L.M., Cherifi, C., Micciche, S. (eds) Complex Networks and Their Applications XI. COMPLEX NETWORKS 2022. Studies in Computational Intelligence, vol 1078. Springer, Cham. Preprint also available:arXiv:2209.01181.
2021	Sanjay, A.B., Correia, R.B., Rocha, L.M. and Apostolova, L.G.[2021]. "Transcriptomic profiling in Mild Cognitive Impairment using peripheral blood gene co-expression networks". In 2021 Alzheimer's Association International Conference. ALZ.
2021	A. Min, W. Miller, L.M. Rocha, K.Börner, R.B. Correia, and P.C. Shih. [2021]. "Just In Time: Challenges and Opportunities of First Aid Care Information Sharing for Supporting Epileptic Seizure Response".Proceedings of the ACM on Human-Computer Interaction.. 5, CSCW1, Article 113, pp. 1-24. DOI:10.1145/3449187.
2020	Correia, R.B., P. Navarro-Costa, and L.M. Rocha [2020]. "Extraction of overlapping modules in networks via spectral methods and information theory". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2020	Gates, A., R.B. Correia, X. Wang, and L.M. Rocha [2020]. "The effective graph: a weighted graph that captures nonlinear logical redundancy in biochemical systems". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2020	Teixeira, A. S., J. Faskowitz, O. Sporns, and L.M. Rocha [2020]. "The Metric Backbone in the Human Connectome and across Lifespan". Complex Networks 2020. The 9th International Workshop on Complex Networks and Their Applications. Dec. 1-3, 2020, Madrid, Spain (Online).
2019	M. ten Thij, I.B. Wood, L.M. Rocha, J. Bollen [2019]. "Detecting eigenmoods in individual human emotions." 5th International Conference on Computational Social Science (IC2S2) July 17-20, 2019, University of Amsterdam, The Netherlands.
2019	A. Gates, X. Wang, R.B. Correia, L.M. Rocha [2019]. "The effective graph captures canalizing dynamics and control in Boolean network models of biochemical regulation." NetSci 2019: International School and Conference on Network Science. May 27-31, 2019, Burlington, VT, USA.
2019	A. Min, W.R. Miller, L.M. Rocha, K. Borner, R.B. Correia, P.C. Shih [2019]. "Understanding Health Information Management of People with Epilepsy and Their Caregivers." Workshop on Interactive Systems in Health Care, The ACM CHI Conference on Human Factors in Computing Systems. May 4-9, 2019, Glasgow, U.K.
2018	R.B. Correia, N. Ratkiewicz, A. Barrat, L.M. Rocha [2018]. The Metric Backbone of Contact Networks in Epidemic Spread Models. Paper and Materials presented at NetSci 2018: International School and Conference on Network Science.
2017	Correia, R.B, Gates, A., Manicka, S., M. Marques-Pita, X. Wang, and L.M. Rocha [2017]. "The effective structure of complex networks: Canalization in the dynamics of complex networks drives dynamics, criticality and control". Complex Networks 2017. The 6th International Workshop on Complex Networks & Their Applications. Nov. 29 - Dec. 01, 2017, Lyon, pp. 354-355
2016	Gates, A., Manicka, S., M. Marques-Pita, L.M. Rocha [2016]. The effective structure of complex networks drives dynamics, criticality and control. Complex Networks 2016. The 5th International Workshop on Complex Networks & Their Applications. Nov. 30 - Dec. 02, 2016, Milan, pp. 107-109.
2016	R.B. Correia, L. Li, L.M. Rocha [2016]. "Monitoring potential drug interactions and reactions via network analysis of Instagram user timeliness". Pacific Symposium on Biocomputing. 21:492-503.
2015	Correia, Rion B., K. N. Chan, & L.M. Rocha [2015]. "Polarization in the US Congress." The 8th Annual Conference of the Comparative Agendas Project (CAP). Lisbon, Portugal, June 23-24, 2015. Preprint Available
2014	A. Gates and L.M. Rocha [2014]. "Structure and dynamics affect the controllability of complex systems: a Preliminary Study". Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems: 429-430, MIT Press.
2014	M.R. Francisco, I. Wood, S. Sabanovic and L.M. Rocha [2014]. "Designing a minimalist socially aware robotic agent for the home". Artificial Life 14: Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems: 876-883, MIT Press.
2013	A. Kolchinsky, A. Lourenço, L. Li, L.M. Rocha [2013]. "Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions". Pacific Symposium on Biocomputing 18:409-420.
2012	T. Simas and L.M. Rocha [2012]."Semi-metric networks for recommender systems". 2012 IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology, pp. 175-179.
2012	J. Goni, A. Kolchinsky, M. Van den Heuvel, A. Griffa, L. M. Rocha, O. Sporns [2012]. "Information, Space and Structure in the Human Brain Resting State". In: Physics, Computation, and the Mind, 12th Granada Seminar, September 17-21, 2012.
2011	A. Kolchinsky, and L.M. Rocha [2011]."Prediction and modularity in complex dynamical systems" (pdf). In: Proc. of the 8th Int. Conf. on Complex Systems. June 26 - July 1, 2011, Quincy, MA, USA. In Press.
2011	S. Karnik, A. Subhadarshini, Z. Wang, L.M. Rocha, and L. Li [2011]."Extraction of drug-drug interactions using all paths graph kernel." (pdf). In: Proceedings of the 1st Challenge task on Drug-Drug Interaction Extraction. I. Segura-Bedmar, P. MartÌnez, D. S·nchez. September, 7th, 2011, Huelva, Spain, pp. 83-88.
2011	A. Kolchinsky, and L.M. Rocha [2011]."Prediction and Modularity in Dynamical Systems". In: Advances in Artificial Life, Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 2011). August 8 ñ 12, 2011, Paris, France,. MIT Press, pp. 423-430.
2011	M. Marques-Pita and L.M. Rocha [2011]. "Schema Redescription in Cellular Automata: Revisiting Emergence in Complex Systems". In: The 2011 IEEE Symposium on Artificial Life, at the IEEE Symposium Series on Computational Intelligence 2011. April 11 ñ 15, 201, Paris, France,. IEEE Press, pp: 233-240.
2010	A. LourenÁo, M. Conover, A. Wong, F. Pan, Alaa Abi-Haidar, A. Nematzadeh, H. Shatkay, and L.M. Rocha [2010]."Testing Extensive Use of NER tools in Article Classification and a Statistical Approach for Method Interaction Extraction in the Protein-Protein Interaction Literature" (pdf). Proceedings of the BioCreative III Workshop 2010, Bethesda, Maryland, September 13-15, 2010.
2010	A. Abi-Haidar and L.M. Rocha [2010]. "Collective Classification of Biomedical Articles using T-Cell Cross-regulation". In: Artificial Life XII: Twelfth International Conference on the Simulation and Synthesis of Living Systems. H. Fellermann et al et al (Eds.). MIT Press, pp. 706-713.
2010	A. Abi-Haidar and L.M. Rocha [2010]. "Biomedical Article Classification Using an Agent-Based Model of T-Cell Cross-Regulation". In: Artificial Immune Systems: 9th International Conference, (ICARIS 2010). E. Hart, C. McEwan, J. Timmis, and A. Hone (Eds.) Lecture Notes in Computer Science. Springer-Verlag, 6209: 237-249. Recipient of Best Paper Award. for ICARIS 2010
2010	A. Lourenço, L.M. Rocha, and H. Shatkay [2010]. " Establishing an evaluation baseline for document classifiers in biomedical curation". Biolink@ISMB, Washington DC, September, 2010.
2009	A. Kolchinsky, A. Abi-Haidar, J. Kaur, A.A. Hamed and L.M. Rocha [2009]."Classification of protein-protein interaction documents using text and citation network features". Proceedings of the BioCreative II.5 Workshop 2009: Special Session on Digital Annotations, Madrid, Spain, October 7-9, 2009. pp 34.
2009	A. Lourenço, S. Carneiro, E.C. Ferreira, R. Carreira, L.M. Rocha, D. Glez-Peña, J.R. Méndez, F. Fdez-Riverola, F. Diaz, I. Rocha and M. Rocha [2009]. "Biomedical Text Mining Applied To Document Retrieval and Semantic Indexing.". In: Proc. of the 3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB'09). Lecture Notes in Computer Science. Springer-Verlag, 5518: 954-963.
2008	M. Marques-Pita, M. Mitchell, and L.M. Rocha [2008]. "The Role of Conceptual Structure in Learning Cellular Automata to Perform Collective Computation". In: Unconventional Computation: 7th International Conference (UC 2008). Lecture Notes in Computer Science. Springer-Verlag, 5204: 146-163.
2008	A. Abi-Haidar and L.M. Rocha [2008]. Adaptive Spam Detection Inspired by a Cross-Regulation Model of Immune Dynamics: A Study of Concept Drift". In: Artificial Immune Systems: 7th International Conference, (ICARIS 2008). Bentley, Peter; Lee, Doheon; Jung, Sungwon (Eds.) Lecture Notes in Computer Science. Springer-Verlag, 5132: 36-47.
2008	M. Marques-Pita and L.M. Rocha [2008]. "Conceptual Structure in Cellular Automata: The Density Classification Task". In: Artificial Life XI: Eleventh International Conference on the Simulation and Synthesis of Living Systems. S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.). MIT Press, pp. 390-397.
2008	A. Abi-Haidar and L.M. Rocha [2008]. Adaptive Spam Detection Inspired by the Immune System". In: Artificial Life XI: Eleventh International Conference on the Simulation and Synthesis of Living Systems. S. Bullock, J. Noble, R. A. Watson, and M. A. Bedau (Eds.). MIT Press, pp. 1-8.
2007	L.M. Rocha and J. Kaur [2007]."Genotype Editing and the Evolution of Regulation and Memory". Proceedings of the 9th European Conference on Artificial Life. Lecture Notes in Artificial Intelligence (LNAI), 4648: 63-73 (Springer-Verlag).
2007	A. Abi-Haidar, J. Kaur, A. Maguitman, P. Radivojac, A. Retchsteiner, K. Verspoor, Z. Wang, and L.M. Rocha [2007]."Uncovering Protein-Protein Interactions in the Bibliome". Proceedings of the Second BioCreative Challenge Evaluation Workshop (ISBN 84-933255-6-2), pp.247-255.
2006	Rechtsteiner, A., Luinstra, J., Rocha, L.M., Strauss, C.E., [2006]. "Use of Text Mining for Protein Structure Prediction and Functional Annotation in Lack of Sequence Homology". In: Joint BioLINK and Bio-Ontologies Meeting 2006 (ISMB Special Interest Group).In Press.
2006	Rocha, L.M., A. Maguitman, C. Huang, J. Kaur, and S. Narayanan. [2006].""An Evolutionary Model of Genotype Editing". In: Artificial Life 10: Tenth International Conference on the Simulation and Synthesis of Living SystemsL.M.Rocha, L. Yaeger, M. Bedau, D. Floreano, R. Goldstone, and A. Vespignani (Eds.). MIT Press, pp. 105-111.
2006	Maguitman, A. G., Rechtsteiner, A., Verspoor, K., Strauss, C.E., Rocha, L.M. [2006]. "Large-Scale Testing Of Bibliome Informatics Using Pfam Protein Families". In: Pacific Symposium on Bioinformatics 2006. In Press.
2005	Huang, Chien-Feng and Luis M. Rocha [2005]. "Tracking Extrema in Dynamic Environments using a Coevolutionary Agent-based Model of Genotype Edition". In: Genetic and Evolutionary Computation Conference: GECCO 2005. ACM Press, pp. 545-552.
2005	Rocha, L.M., T. Simas, A. Rechtsteiner, M. DiGiacomo, R. Luce [2005]. "MyLibrary@LANL: Proximity and Semi-metric Networks for a Collaborative and Recommender Web Service". In: Proc. 2005 IEEE/WIC/ACM International Conference on Web Intelligence (WI'05), IEEE Press, pp. 565-571.
2004	Huang, Chien-Feng and Luis M. Rocha [2004]. "A Systematic Study of Genetic Algorithms with Genotype Editing". In: Genetic and Evolutionary Computation: GECCO 2004. Lecture Notes in Computer Science Vol. 3102, pp.1233 - 1245. Springer-Verlag.
2004	Rocha, Luis M. [2004]. "Evolving Memory: Logical Tasks for Cellular Automata". Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9). Boston, Massachusetts, September 12-15th 2004.
2004	Rocha, Luis M. and Chien-feng Huang [2004]. "The Role of RNA Editing in Dynamic Environments". In: Ninth International Conference on the Simulation and Synthesis of Living Systems (ALIFE9). Boston, Massachusetts, September 12-15th 2004.
2004	Verspoor, K., J. Cohn, C. Joslyn, S. Mniszewski, A. Rechtsteiner, L.M. Rocha, T. Simas [2004]. "Protein Annotation as Term Categorization in the Gene Ontology". EMBO Workshop: A critical assessment of text mining methods in molecular biology, Granada, Spain, March 28-31, 2004.
2004	Rechtsteiner, A. and L.M. Rocha [2004]. "MeSH Key Terms for Validation and Annotation of Gene Expression Clusters" (pdf). Currents in Computational Molecular Biology. Proceedings of the Eight Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004), San Diego, CA, March 2004. A. Gramada and Philip E. Bourne (Eds). pp. 212-213.
2003	Rechtsteiner, A., R. Gottardo, L.M. Rocha, and M.E. Wall [2003]. "Singular Value Decomposition for Analysis of Gene Expression" (pdf). Currents in Computational Molecular Biology. Proceedings of the The Seventh Annual International Conference on Research in Computational Molecular Biology (RECOMB 2003), Berlin, April 10-13, 2003. R. Spang, P.Beziat and M. Vingron (Eds).pp. 275-276
2003	Rechtsteiner, A., R. Gottardo, L.M. Rocha, M.E. Wall and T. Brettin [2003]. "Three Algorithms for Filtering and Analysis of Gene Expression Data". Poster at Pacific Symposium on Biocomputing 2003.
2003	Rocha Luis M. [2003]. "Extraction and Semi-metric Analysis of Social and Biological Networks". Poster at Networks: Structure, Dynamics and Function, May 12 - 16, 2003, Santa Fe, New Mexico, USA.
2003	Rocha, Luis M. and Andreas Rechtsteiner [2003]. "Fast Cheap and Synthetic Oracle (FACSO): Proximity Measures to capture Expert Knowledge in the Bibliome". Poster at Pacific Symposium on Biocomputing 2003.
2003	Huang, Chien-Feng and Luis M. Rocha [2003]. "Exploration of RNA Editing and Design of Robust Genetic Algorithms". 2003 IEEE Congress on Evolutionary Computation (CEC), Canberra, Australia, December 2003. R.Sarker et al (Eds). IEEE Press, pp. 2799-2806.
2002	Rocha, Luis M. [2002]. "Combination of Evidence in Recommendation Systems Characterized by Distance Functions". In: Proceedings of the 2002 World Congress on Computational Intelligence: FUZZ-IEEE'02. Honolulu, Hawaii, May 2002. IEEE Press, pp. 203-208. LAUR 02-154.
2001	Rocha, Luis M. [2001]. "Adaptive Webs for Heterarchies with Diverse Communities of Users". Paper prepared for the workshop From Intelligent Networks to the Global Brain: Evolutionary Social Organization through Knowledge Technology, Brussels, July 3-5, 2001. LAUR 005173.
2000	Joslyn, Cliff and Luis M. Rocha [2000]. "Towards Semiotic Agent-Based Models of† Socio-Technical Organizations." Proc. AI, Simulation and Planning in High Autonomy Systems (AIS 2000) Conference, Tucson, Arizona, USA. ed. HS Sarjoughian et al., pp. 70-79.
2000	Bollen, Johan, Luis M. Rocha [2000]. "An Adaptive Systems Approach to the Implementation and Evaluation of Digital Library Recommendation Systems." In: Research and Advanced Technology for Digital Libraries: 4th European Conference, ECDL 2000. Lectures Notes in Computer Science, Springer-Verlag, pp.356-359.
1999	Bollen, Johan, Hebert Van de Sompel, and Luis M. Rocha [1999]. ìMining associative relations from website logs and their application to context-dependent retrieval using spreading activation (adobe pdf). Workshop on Organizing Web Space (WOWS), ACM Digital Libraries 99, August 1999, Berkeley, California.
1999	Rocha, Luis M. [1999]. "TalkMine and the Adaptive Recommendation Project". In: the Proceedings of the Association for Computing Machinery (ACM) - Digital Libraries 99. U.C. Berkely, August 1999. pp. 242-243.
1998	Johnson, Norman, Steen Rasmussen, Cliff Joslyn, Luis Rocha, Steven Smith, and Marianna Kantor [1998] " Symbiotic intelligence: self-organizing knowledge on distributed networks, driven by human interaction"(postscript), (pdf). Proceedings of the Sixth International Conference on Artificial Life, C. Adami, R. K. Belew, H. Kitano, C. E. Taylor (Eds.), MIT Press, pp. 403-407.
1998	Rocha, Luis M. [1998]. "Syntactic autonomy". In: Proceedings of the Joint Conference on the Science and Technology of Intelligent Systems (ISIC/CIRA/ISAS 98). National Institute of Standards and Technology, Gaithersburg, MD, September 1998. IEEE Press, pp. 706-711.
1997	Rocha, Luis M. [1997]. "Evidence Sets: Contextual Categories". In: Proceedings of the meeting on Control Mechanisms for Complex Systems, Physical Science Laboratory, New Mexico State University, Las Cruces, New Mexico, January 1997. M. Coombs (ed.). NMSU Press, pp. 339-357.
1996	Rocha, Luis M. [1996]." "Relative Uncertainty: Measuring Uncertainty in Discrete and Nondiscrete Domains". " In: Proceedings of the NAFIPS'96. M. Smith et al (Eds). IEEE Press, pp. 551-555.
1995	Rocha, Luis M. [1995]." Contextual Genetic Algorithms: Evolving Developmental Rules ." In: Advances in Artificial Life: Proceedings of the European Conference on Artificial Life (ECAL 2005) . F. Moran, A. Moreno, J.J. Merelo, and P. Chacon (Eds.). Series: Lecture Notes in Artificial Intelligence, Springer-Verlag. pp. 368-382.
1995	Rocha, Luis M. [1995]." Interval Based Evidence Sets." In: Proceedings of the ISUMA-NAFIPS'95. B. Ayyub (Ed.). IEEE Press. pp.624-629.
1994	Rocha, Luis M. [1994]."Von Foerster's cognitive tiles: semantically closed building blocks for AI and Alife." In: Cybernetics and Systems ' 94. Robert Trappl (Ed.). Vol. 1, pp 621-628. World Scientific Press.
1994	Rocha, Luis M. [1994]." Cognitive Categorization revisited: extending interval valued fuzzy sets as simulation tools for concept combination ." In: Proceedings of the 1994 International Conference of NAFIPS/IFIS/NASA. IEEE. pp 400-404.
1994	Medina-Martins, Pedro R., Luis Rocha, et al [1994]."Metalogues: an essay on computers' psychology - from childhood to adulthood." In: Cybernetics and Systems 94. R, Trappl (Ed.). World Scientific Press. pp. 565-572.
1992	Medina-Martins, Pedro R. and Luis Rocha [1992]."The in and the out: an evolutionary approach." In: Cybernetics and Systems Research '92. Robert Trappl. World Scientific Press. pp 681-689.
1991	Rocha, Luis M. [1991]."Fuzzification of Conversation Theory (pdf)." In: Principia Cybernetica Conference, Free University of Brussels, Brussels, June 1991. Ed. Francis Heylighen.

Book Chapters

Year	Reference
2003	Rocha, L.M. [2003]. "Automatic Conversation Driven by Uncertainty Reduction and Combination of Evidence for Recommendation Agents ". In: Systematic Organization of Information in Fuzzy Systems. NATO Science Series. P. Melo-Pinto, H.N. Teodorescu and T. Fukuda (Eds.) IOS Press, pp 249-265.
2003	Wall, Michael E., Andreas Rechtesteiner, and Luis M. Rocha [2003]. "Singular Value Decomposition and Principal Component Analysis ". In: A Practical Approach to Microarray Data Analysis. D. P. Berrar, W. Dubitzky, and M. Granzow (Eds.). Kluwer Academic Publishers, pp. 91-109.
2002	Rocha, Luis M. [2002]. "Semi-metric Behavior in Document Networks and its Application to Recommendation Systems". In: Soft Computing Agents: A New Perspective for Dynamic Information Systems. V. Loia (Ed.) International Series Frontiers in Artificial Intelligence and Applications. IOS Press, pp. 137-163..
2001	Rocha, Luis M. and Johan Bollen. [2001]. Biologically Motivated Distributed Designs for Adaptive Knowledge Management". In: Design Principles for the Immune System and other Distributed Autonomous Systems. L. Segel and I. Cohen (Eds.) Santa Fe Institute Series in the Sciences of Complexity. Oxford University Press, pp. 305-334.
2001	Rocha, Luis M. [2001]. "TalkMine: a Soft Computing Approach to Adaptive Knowledge Recommendation". In: Soft Computing Agents: New Trends for Designing Autonomous Systems. Vincenzo Loia and Salvatore Sessa (Eds.). Series on Studies in Fuzziness and Soft Computing. Physica-Verlag, Springer, pp. 89-116
2000	Rocha, Luis M. [2000]. "Syntactic autonomy, cellular automata, and RNA editing: or why self-organization needs symbols to evolve and how it might evolve them". In: Closure: Emergent Organizations and Their Dynamics. Chandler J.L.R. and G, Van de Vijver (Eds.) Annals of the New York Academy of Sciences. Vol. 901, pp 207-223.
1998	Rocha, Luis M. [1998]." Selected Self-Organization and the Semiotics of Evolutionary Systems." In: Evolutionary Systems: Biological and Epistemological Perspectives on Selection and Self-Organization. S. Salthe, G. Van de Vijver, and M. Delpos (eds.). Kluwer Academic Publishers, pp. 341-358.

Media Writings

Year	Reference
2024	L.M. Rocha [2024]. Polimedicação é pior em idosos e mulheres, mas pode-se melhorar com análise de dados. Público . January 31, 2024.
2023	L.M. Rocha [2023]. Jovens reduzidos a um número. Público . November 27, 2023. Longer version with additional data at Medium.
2022	L.M. Rocha [2022]. Ser emigrante português é ser cidadão de 10.ª classe e deixa muitos democraticamente apátridas. Público . February 22, 2022.
2021	L.M. Rocha [2021]. O sexo dos anjos, ou como a complexidade das pandemias exige pensamento sistémico. Público . February 18, 2021. Longer Version at Medium.
2021	L.M. Rocha [2021]. Lixívia ideológica não resolve a pandemia. Público . January 20, 2021.
2020	L.M. Rocha [2020]. Privacy apocalypse or data science for the common good? Preparing Western Nations for Pandemics to Come . Towards data science . November 22, 2020.
2020	L.M. Rocha [2020]. Apocalípticos da privacidade vs. StayAway Covid e a ciência de dados para o bem comum. Observador . October 25, 2020.
2020	L.M. Rocha [2020]. É necessário mais investimento em ciência de complexidade e resiliência para lidar com pandemias. Público . March 31, 2020 Print Version. Longer version on Medium.
2014	L.M. Rocha [2014]. "Ciência 2.0: do elitismo à decisão coletiva". Expresso. 8 Fevereiro, 2014, pp. 35.
2014	L.M. Rocha [2014]. "Get in Sync". Herald Times, Bloomington, IN. August 7, 2014. Reprint available.
2013	L.M. Rocha [2013]. "Summer Education". Herald Times, Bloomington, IN. August 29, 2013.
2008	L.M. Rocha [2008]."The Logical Mechanisms of Life". In: Complex Biological Systems. Icfai University Press, 2008.
2007	L.M. Rocha [2007]."Reality is Stranger than Fiction: What can Artificial Life do about Advances in Biology?". Invited presentation for the "Biocomplexity" discussion section at the 9th European Conference on Artificial Life, September 12, 2007 in Lisbon, Portugal. Reprinted in: Complex Biological Systems. Icfai University Press, 2008.
2002	Rocha, Luis M. [2002]. Partnership of Fools. Wired Magazine, (Rants and Raves) April 2002.
2002	Rocha, Luis M. [2002]. Path to Enlightenment?. New York Times Book Review, (Letters) pp. 4, June 23.
1999	Rocha, Luis M. [1999]. "Complex Systems Modeling: Using Metaphors From Nature in Simulation and Scientific Models". BITS: Computer and Communications News. Computing, Information, and Communications Division. Los Alamos National Laboratory. November 1999.

Blogs

Name	Epoch	Address
Medium	2018 - Present	medium.com/@lmrocha
Sciber	2008 - Present	http://sciber.blogspot.com/
Life Inspired	2007 - Present	http://life-inspired.blogspot.com/
Hey City Zen	2008 - Present	http://hey-city-zen.blogspot.com/
InfoPort	2004 - 2008	http://infoport.blogspot.com/

Electronic Publications

Year	Reference
n/a	L.M. Rocha. Biologically-inspired computing Lecture Notes (pdf document), Lecture notes for course taught at Indiana University.
2005,2006	Rocha, Luis M. and S. Schnell [2005,2006]. "Introduction to Informatics", Lecture notes for course taught at Indiana University.
2002	Rocha, Luis M. [2002] .Introduction to Bioinformatics. Lecture notes for PhD course at the Instituto Gulbenkian da Ciencia, Oeiras, Portugal.
2000	L.M. Rocha [2000]. "O Caminho de Santa Fe."
1999	Rocha, Luis M. [1999]. From Artificial Life to Semiotic Agent Models: Review and Research Directions. Los Alamos National Laboratory Internal Report. LAUR-99-5475.
1999	Rocha, Luis M. [1995]. " Evolutionary Systems and Artificial Life. Lecture Notes for the course taught at the Department of Systems Science and Industrial Engineering at the State University of New York at Binghamton.

Translations

Year	Reference
2003	Varela F., E. Thompson and E. Rosch [1998]. A Mente Corporea: Ciência Cognitiva e Experiencia Humana.. Editora Piaget. Translation and Scientific Editing by Luis M. Rocha from the original "The Embodied Mind".

Installations and Creative Productions

Year	Reference
2016	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2016]. Morfogénese Musical ("Musical Morphogenesis"). In Dia D – Ligações ("D Day – Conections"). Museu da Fundação Gulbenkian (Gulbenkian Museum), Lisbon, October 9, 2016.
2016	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2016-2017]. Morfogénese Musical ("Musical Morphogenesis"). Museu da Fundação Gulbenkian (Gulbenkian Museum), Lisbon, 2016-2017.
2016	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2016]. A "Morfogénese musical" na Semana da Ciência e Tecnologia ("Musical Morphogenesis" in the Science and Technology Week). Museu da Eletricidade (Electricity Museum), Lisbon, November 21, 2016
2016	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2016]. Musical Morphogenesis: Open Day at the Instituto Gulbenkian de Ciência - Science in Zoom, Oeiras, October 1, 2016. Also on Facebook.
2016	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2016]. Morfogénese musical: Visita-instalação interativa (Musical Morphogenesis: Interactive Installation). Belém Art Fest, Museu de Marinha, Lisbon, May 6-7, 2016. Also on Facebook.
2014	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2014]. At the faire: Morfogénese Musical. In Maker Faire Lisbon. Lisbon, September 13, 2014.
2013,2014	Marques Pita, M., S. Costa, A. Paio, M.J. Oliveira, S. Oliveira, Luis M. Rocha [2013-2014]. Morfogênese musical: Visita-instalação interativa (Musical Morphogenesis: Interactive Installation). Opening: Fundação Calouste Gulbenkian Museum, Lisbon, October 5th, 2013. Also on Facebook.

Last Modified: April 19, 2024

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