Grants per year
Personal profile
Research Interests
Professor Amaral conducts and directs research that provides insight into the emergence, evolution, and stability of complex social and biological systems. His research aims to address some of the most pressing challenges facing humanity, including the mitigation of errors in healthcare settings, the characterization of the conditions fostering innovation and creativity, or the growth limits imposed by sustainability.
Education/Academic qualification
Physics, PhD, Boston University
… → 1996
Physics, MS, University of Lisbon
Physics, BS, University of Lisbon
Research interests keywords
- Complex networks in nature
- study of innovation and creativity
- system-level modeling of biological processes
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Collaborations and top research areas from the last five years
Recent external collaboration on country/territory level. Dive into details by clicking on the dots or
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Frameworks: Born Physical, Studied Digitally (BP/SD) - An open platform for making physical archives findable, accessible, interoperable, and (re)usable
Amaral, L. A. N. (PD/PI), Stoeger, T. (Co-PD/PI) & van der Lee, S. (Co-PD/PI)
7/1/24 → 6/30/29
Project: Research project
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Successful Clinical Response In Pneumonia Therapy (SCRIPT) Systems Biology Center
Wunderink, R. G. (PD/PI), Wunderink, R. G. (PD/PI), Abdala-Valencia, H. (Co-Investigator), Abdala-Valencia, H. (Co-Investigator), Budinger, G. S. (Co-Investigator), Budinger, G. S. (Co-Investigator), Etemadi, M. (Co-Investigator), Etemadi, M. (Co-Investigator), Hartmann, E. M. (Co-Investigator), Hartmann, E. M. (Co-Investigator), Hultquist, J. F. (Co-Investigator), Hultquist, J. F. (Co-Investigator), Lorenzo Redondo, R. (Co-Investigator), Lorenzo Redondo, R. (Co-Investigator), Luo, Y. (Co-Investigator), Luo, Y. (Co-Investigator), Misharin, A. (Co-Investigator), Misharin, A. (Co-Investigator), Morales-Nebreda, L. (Co-Investigator), Morales-Nebreda, L. (Co-Investigator), Ozer, E. A. (Co-Investigator), Ozer, E. A. (Co-Investigator), Pickens, C. I. (Co-Investigator), Pickens, C. I. (Co-Investigator), Qi, C. (Co-Investigator), Qi, C. (Co-Investigator), Scholtens, D. M. (Co-Investigator), Scholtens, D. M. (Co-Investigator), Singer, B. (Co-Investigator), Singer, B. (Co-Investigator), Stoeger, T. (Co-Investigator), Stoeger, T. (Co-Investigator), Swaminathan, S. (Co-Investigator), Swaminathan, S. (Co-Investigator), Walter, J. M. (Co-Investigator), Walter, J. M. (Co-Investigator), Wunderink, R. G. (Co-Investigator), Wunderink, R. G. (Co-Investigator), Amaral, L. A. N. (Other), Amaral, L. A. N. (Other), Budinger, G. S. (Other), Budinger, G. S. (Other), Hartmann, E. M. (Other), Hartmann, E. M. (Other), Hauser, A. R. (Other), Hauser, A. R. (Other), Misharin, A. (Other), Misharin, A. (Other), Ozer, E. A. (Other), Ozer, E. A. (Other), Pickens, C. I. (Other), Pickens, C. I. (Other), Qi, C. (Other), Qi, C. (Other), Singer, B. (Other), Singer, B. (Other), Starren, J. (Other), Stoeger, T. (Other), Walter, J. M. (Other), Walter, J. M. (Other), Wunderink, R. G. (Other) & Wunderink, R. G. (Other)
National Institute of Allergy and Infectious Diseases
1/1/23 → 12/31/27
Project: Research project
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HDR DSC: Collaborative Research: The Metropolitan Chicago Data Science Corps (MCDC): Learning from Data to Support Communities
van der Lee, S. (PD/PI), van der Lee, S. (PD/PI), van der Lee, S. (PD/PI), Birkett, M. A. (Co-PD/PI), Birkett, M. A. (Co-PD/PI), Birkett, M. A. (Co-PD/PI), Goldberg, B. B. (Co-PD/PI), Goldberg, B. B. (Co-PD/PI), Goldberg, B. B. (Co-PD/PI), Schanzenbach, D. W. (Co-PD/PI), Schanzenbach, D. W. (Co-PD/PI), Schanzenbach, D. W. (Co-PD/PI), Amaral, L. A. N. (Other), Amaral, L. A. N. (Other), Amaral, L. A. N. (Other), Amato, K. R. (Other), Amato, K. R. (Other), Amato, K. R. (Other), Blomberg Stathopoulos, A. I. (Other), Blomberg Stathopoulos, A. I. (Other), Blomberg Stathopoulos, A. I. (Other), Brown, C. H. (Other), Brown, C. H. (Other), Brown, C. H. (Other), Drane, D. L. (Other), Drane, D. L. (Other), Drane, D. L. (Other), Dunn, J. B. (Other), Dunn, J. B. (Other), Dunn, J. B. (Other), Gray, K. A. (Other), Gray, K. A. (Other), Gray, K. A. (Other), Hambleton, J. P. (Other), Hambleton, J. P. (Other), Hambleton, J. P. (Other), Hammond, K. J. (Other), Hammond, K. J. (Other), Hammond, K. J. (Other), Hedges, L. V. (Other), Hedges, L. V. (Other), Hedges, L. V. (Other), Horton, D. E. (Other), Horton, D. E. (Other), Horton, D. E. (Other), Kuyper, A. M. (Other), Kuyper, A. M. (Other), Kuyper, A. M. (Other), Linna Jr., D. W. (Other), Linna Jr., D. W. (Other), Linna Jr., D. W. (Other), Miller, W. M. (Other), Miller, W. M. (Other), Miller, W. M. (Other), Packman, A. (Other), Packman, A. (Other), Packman, A. (Other), Pah, A. R. (Other), Pah, A. R. (Other), Pah, A. R. (Other), Papachristos, A. V. (Other), Papachristos, A. V. (Other), Papachristos, A. V. (Other), Phillips II, G. (Other), Phillips II, G. (Other), Phillips II, G. (Other), Rogers, J. M. (Other), Rogers, J. M. (Other), Rogers, J. M. (Other), Van Wart, S. J. (Other), Van Wart, S. J. (Other), Van Wart, S. J. (Other), Voigt, R. (Other), Voigt, R. (Other), Voigt, R. (Other), Wells, G. (Other), Wells, G. (Other), Wells, G. (Other), Youn, H. (Other), Youn, H. (Other) & Youn, H. (Other)
9/1/21 → 8/31/25
Project: Research project
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Assessing SARS-CoV-2 Variant Evolution in Patients
Wunderink, R. G. (PD/PI), Achenbach, C. J. (Co-PD/PI), Hultquist, J. F. (Co-PD/PI), Ison, M. G. (Co-PD/PI), Lorenzo Redondo, R. (Co-PD/PI), Ozer, E. A. (Co-PD/PI), Qi, C. (Co-PD/PI), Scholtens, D. M. (Co-PD/PI), Amaral, L. A. N. (Other), Hauser, A. R. (Other) & Misharin, A. (Other)
National Institute of Allergy and Infectious Diseases
7/29/21 → 12/31/22
Project: Research project
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Integrative Multi-Scale Systems Analysis of Gene-Expression-Driven Aging Morbidity
Amaral, L. A. N. (PD/PI) & Stoeger, T. (PD/PI)
9/15/20 → 10/31/23
Project: Research project
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Artificial intelligence needs a scientific method-driven reset
Nunes Amaral, L. A., Apr 2024, In: Nature Physics. 20, 4, p. 523-524 2 p.Research output: Contribution to journal › Comment/debate › peer-review
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Energy metabolism modulates the regulatory impact of activators on gene expression
Qiao, S., Bernasek, S., Gallagher, K. D., Connell, J. O., Yamada, S., Bagheri, N., Amaral, L. A. N. & Carthew, R. W., Jan 2024, In: Development (Cambridge). 151, 1, dev201986.Research output: Contribution to journal › Article › peer-review
Open Access -
Meta-Research: Understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results
Richardson, R., Tejedor Navarro, H., Nunes Amaral, L. A. & Stoeger, T., Mar 2024, In: eLife. 12, RP93429.Research output: Contribution to journal › Article › peer-review
Open Access3 Scopus citations -
On the improvement of handwritten text line recognition with octave convolutional recurrent neural networks
Castro, D., Zanchettin, C. & Amaral, L. A. N., 2024, (Accepted/In press) In: International Journal on Document Analysis and Recognition.Research output: Contribution to journal › Article › peer-review
1 Scopus citations -
A new approach for extracting information from protein dynamics
Liu, J., Amaral, L. A. N. & Keten, S., Feb 2023, In: Proteins: Structure, Function and Bioinformatics. 91, 2, p. 183-195 13 p.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations
Datasets
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Appendix A. Homogeneity calculations.
Guimera, R. (Contributor), Stouffer, D. B. (Contributor), Sales-Pardo, M. (Contributor), Leicht, E. A. (Contributor), Newman, M. E. J. (Contributor) & Amaral, L. A. N. (Contributor), figshare, 2016
DOI: 10.6084/m9.figshare.3549900, https://wiley.figshare.com/articles/dataset/Appendix_A_Homogeneity_calculations_/3549900
Dataset
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Supplementary material from "A novel framework for evaluating the performance of codon usage bias metrics"
Liu, S. S. (Creator), Hockenberry, A. J. (Creator), Jewett, M. C. (Creator) & Amaral, L. A. N. (Creator), figshare, 2018
DOI: 10.6084/m9.figshare.c.3986280, https://figshare.com/collections/Supplementary_material_from_A_novel_framework_for_evaluating_the_performance_of_codon_usage_bias_metrics_/3986280
Dataset
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Appendix C. The generalized niche model.
Guimera, R. (Contributor), Stouffer, D. B. (Contributor), Sales-Pardo, M. (Contributor), Leicht, E. A. (Contributor), Newman, M. E. J. (Contributor) & Amaral, L. A. N. (Contributor), wiley, 2016
DOI: 10.6084/m9.figshare.3549894, https://wiley.figshare.com/articles/dataset/Appendix_C_The_generalized_niche_model_/3549894
Dataset
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Additional file 1 of The first step is recognizing there is a problem: a methodology for adjusting for variability in disease severity when estimating clinician performance
Bechel, M. (Creator), Pah, A. R. (Creator), Persell, S. D. (Creator), Weiss, C. H. (Creator) & Nunes Amaral, L. A. (Creator), figshare, 2022
DOI: 10.6084/m9.figshare.19373452, https://springernature.figshare.com/articles/dataset/Additional_file_1_of_The_first_step_is_recognizing_there_is_a_problem_a_methodology_for_adjusting_for_variability_in_disease_severity_when_estimating_clinician_performance/19373452
Dataset
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Appendix E. Compartment properties for the niche model.
Guimera, R. (Contributor), Stouffer, D. B. (Contributor), Sales-Pardo, M. (Contributor), Leicht, E. A. (Contributor), Newman, M. E. J. (Contributor) & Amaral, L. A. N. (Contributor), wiley, 2016
DOI: 10.6084/m9.figshare.3549888, https://wiley.figshare.com/articles/dataset/Appendix_E_Compartment_properties_for_the_niche_model_/3549888
Dataset