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Chen M, Xiao K, Zhao T, Zhou Y, Zhang Q, Aires-de-Sousa J. "Exploration of automatic learning to establish relationships between the molecular structure of chiral ionic liquids and the specific optical rotation". Journal of Molecular Liquids 2018, 254, 231-240.

Fernandes, SS, Herbivo C, Aires-de-Sousa J, Comel A, Belsley M, Raposo MM. "Theoretical and experimental studies of aryl-bithiophene based push-pull p-conjugated heterocyclic systems bearing cyanoacetic or rhodanine-3-acetic acid acceptors for SHG nonlinear optical applications". Dyes and Pigments 2018, 149, 566-573.

Binev Y, Peixoto D, Pereira F, Rodrigues I, Cavaco S, Lobo AM, Aires-de-Sousa J. "NavMol 3.0: enabling the representation of metabolic reactions by blind users". Bioinformatics 2018, 34(1), 120-121.

Soares A, S Estevao M, MB Marques M, Kovalishyn V, ARS Latino D, Aires-de-Sousa J, Ramos J, Viveiros M, Martins F. 
"Synthesis and Biological Evaluation of Hybrid 1,5- and 2,5-Disubstituted Indoles as Potentially New Antitubercular Agents". Medicinal Chemistry 2017, 13(5), 439-447.

Pereira F, Xiao K, Latino DA, Wu C, Zhang Q, J. Aires-de-Sousa, "Machine Learning Methods to Predict Density Functional Theory B3LYP Energies of HOMO and LUMO Orbitals",  J. Chem. Inf. Model. 2017, 57(1), 11-21.

Aires-de-Sousa, Joao; Cardoso, M. Margarida; Ferreira, Luisa M.; Lima, Joao C.; Noronha, Joao P.; Nunes, Ana V.M.; Nunes da Ponte, Manuel. "Team-Based Learning in Chemistry Courses with Laboratory Sessions". 3rd International Conference on Higher Education Advances, HEAd’17,Valencia, Spain, June 21–23, 2017. DOI:

Ian Rodrigues; Ricardo Teixeira; Sofia Cavaco; Vasco D. B. Bonifácio; Daniela Peixoto; Yuri Binev; Florbela Pereira; Ana Lobo; João Aires-de-Sousa. "2D Spatial Audio in a Molecular Navigator/Editor for Blind and Visually Impaired Users". Proceedings of the 20th International Conference on Digital Audio Effects (DAFx-17), Edinburgh, UK, September 5–9, 2017.

Zhang Q, Zheng F, Zhao T, Qu X, Aires-de-Sousa J, "Machine Learning Estimation of Atom Condensed Fukui Functions", Molecular Informatics 2016, 35, 62–69.

Marcou G, Aires de Sousa J, Latino DA, de Luca A, Horvath D, Rietsch V, Varnek A, "Expert system for predicting reaction conditions: the Michael reaction case",  J. Chem. Inf. Model. 2015, 55(2), 239-250.

Q.-Y. Zhang, F. Zheng, R.P.S. Fartaria, D. A. R. S. Latino, X. Qu, T. Campos, T. Zhao, J. Aires-de-Sousa, "A QSPR approach for the fast estimation of DFT/NBO partial atomic charges", Chemom. Intell. Lab. Syst. 2014, 134, 158-163.

D.A.R.S. Latino, J. Aires-de-Sousa, "Automatic NMR-Based Identification of Chemical Reaction Types in Mixtures of Co-Occurring Reactions", PloS One 2014, 9.2: e88499.

F. Martins, S. Santos, C. Ventura, R. Elvas-Leitão, L. Santos, S. Vitorino, M. Reis, V. Miranda, H.F. Correia, J. Aires-de-Sousa, V. Kovalishyn, D.A.R.S. Latino, J. Ramos, M. Viveiros, "Design, synthesis and biological evaluation of novel isoniazid derivatives with potent antitubercular activity", Eur. J. Med. Chem. 2014, 81, 119-138.

X. Qu, D.A.R.S. Latino, J. Aires-de-Sousa, "A big data approach to the ultra-fast prediction of DFT-calculated bond energies", J. Cheminform. 2013, 5(1), 34.

F. Pereira, J.C. Ponte-e-Sousa, V.D. Bonifácio, P. Mata, J. Aires-de-Sousa, A.M. Lobo, "Sonified Infrared Spectra and Their Interpretation by Blind and Visually Impaired Students", J. Chem. Educ. 2013, 90(8), 1028–1031.

R.P.S. Fartaria, F. Pereira, V.D.B. Bonifácio, P. Mata, J. Aires-de-Sousa, A.M. Lobo, "NavMol 2.0 – A Molecular Structure Navigator/Editor for Blind and Visually Impaired Users", Eur. J. Org. Chem. 2013, 8, 1415–1419.

C. Muller, G. Marcou, D. Horvath, J. Aires-de-Sousa, A. Varnek, "Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms", J. Chem. Inf. Model. 2012, 52(12), 3116-3122.

D. A. R. S. Latino, J. Aires-de-Sousa, "Automatic Perception of Chemical Similarities Between Metabolic Pathways", Molecular Informatics 2012, 31, 135–144.

M. J. Cabrita, J. Aires-de-Sousa, M. D. R. Gomes da Silva, F. Rei, A. M. Costa Freitas, "Multivariate Statistical Approaches for Wine Classification Based on Low Molecular Weight Phenolic Compounds", Australian Journal of Grape and Wine Research 201218(12), 138-146.

Sushko, I.; Novotarskyi, S.; Körner, R.; Pandey, A. K.; Rupp, M.; Teetz, W.; Brandmaier, S.; Abdelaziz, A.; Prokopenko, V. V.; Tanchuk, V. Y.; Todeschini, R.; Varnek, A.; Marcou, G.; Ertl, P.; Potemkin, V.; Grishina, M.; Gasteiger, J.; Schwab, C.; Baskin, I. I.; Palyulin, V. A.; Radchenko, E. V.; Welsh, W. J.; Kholodovych, V.; Chekmarev, D.; Cherkasov, A.; Aires-de-Sousa, J.; Zhang, Q.-Y.; Bender, A.; Nigsch, F.; Patiny, L.; Williams, A.; Tkachenko; V.; Tetko, I. V.; "Online Chemical Modeling Environment (OCHEM): Web Platform for Data Storage, Model Development and Publishing of Chemical Information",  J. Comput.-Aided Mol. Des. 2011, 25(6), 533-554.

F. Pereira, D. A. R. S. Latino, J. Aires-de-Sousa, "Estimation of Mayr Electrophilicity with a Quantitative Structure-Property Relationship Approach Using Empirical and DFT Descriptors", J. Org. Chem. 2011, 76(22), 9312-9319.

F. Pereira, J. Aires-de-Sousa, V. D. B. Bonifacio, P. Mata, A. M. Lobo, "MOLinsight: A Web Portal for the Processing of Molecular Structures by Blind Students", J. Chem. Educ. 2011, 88(3), 361–362.

V. Kovalishyn, J. Aires-de-Sousaa, C. Ventura, R. E. Leitão, F. Martins, "QSAR modeling of antitubercular activity of diverse organic compounds", Chemom. Intell. Lab. Syst. 2011, 107(1), 69-74.

Carrera, G. V. S. M.; Frade, R. F. M.; Aires-de-Sousa, J.; Afonso, C. A. M.; Branco, L. C. "Synthesis and Properties of New Functionalized Guanidinium Based Ionic Liquids as Non-toxic Versatile Organic Materials", Tetrahedron 2010, 66(45), 8785-8794.

Gómez-Carracedo, M. P.; Andrade, J. M.; Carrera, G. V. S. M.; Aires-de-Sousa, J.; Carlosena, A.; Prada, D. "Combining Kohonen Neural Networks and Variable Selection by Classification Trees to Cluster Road Soil Samples", Chemom. Intell. Lab. Syst. 2010, 102(1), 20-34.

Borges, C.; Gómez-Carracedo, M. P.; Andrade, J. M.; Duarte, M. F.; Biscaya, J. L.; Aires-de-Sousa, J. "Geographical Classification of Weathered Crude Oil Samples with Unsupervised Self-Organizing Maps and a Consensus Criterion", Chemom. Intell. Lab. Syst. 2010, 101(1), 43-55.

D. A. R. S. Latino, J. Aires-de-Sousa, "Assignment of EC Numbers to Enzymatic Reactions with MOLMAP Reaction Descriptors and Random Forests", J. Chem. Inf. Model. 2009, 49 (7), 1839–1846.

D. A. R. S. Latino, R. P. S. Fartaria, F. F. M. Freitas, J. Aires-de-Sousa, F. M. S. Silva Fernandes, "Approach to potential energy surfaces by neural networks. A review of recent work", Int. J. Quantum Chem. 2009, 110(2), 432-445.

G. Carrera, S. Gupta, J. Aires-de-Sousa, "Machine learning of chemical reactivity from databases of organic reactions", J. Comput. Aided Mol. Des. 2009, 23, 419–429.

D. A. R. S. Latino, Q.-Y. Zhang, J. Aires-de-Sousa, "Genome-scale classification of metabolic reactions and assignment of EC numbers with self-organizing maps", Bioinformatics 2008, 24(19), 2236-2244.

D. A. R. S. Latino, R. P. S. Fartaria, F. F. M. Freitas, J. Aires-de-Sousa, F. M. S. Silva Fernandes, "Mapping Potential Energy Surfaces by Neural Networks. The Ethanol/Au(111) interface.", J. Electroanal. Chem. 2008, 624(1-2), 109-120.

G. Carrera, L.C. Branco, J. Aires-de-Sousa, C.M. Afonso, "Exploration of quantitative structure-property relationships (QSPR) for the design of new guanidinium ionic liquids", Tetrahedron 2008, 64(9), 2216-2224.

Y. Binev, M.M. Marques, J. Aires-de-Sousa, "Prediction of 1H NMR coupling constants with associative neural networks trained for chemical shifts", J. Chem. Inf. Model. 2007, 47(6), 2089-2097.

D. A. R. S. Latino, F. F. M. Freitas, J. Aires-de-Sousa, F. M. S. Silva Fernandes, "Neural networks to approach potential energy surfaces: Application to a molecular dynamics simulation", Int. J. Quantum Chem. 2007, 107 (11), 2120-2132.

S. Gupta, J. Aires-de-Sousa, "Comparing the chemical spaces of metabolites and available chemicals: models of metabolite-likeness", Mol. Divers. 2007, 11(1), 23-36.

D. A. R. S. Latino, J. Aires-de-Sousa, "Linking Databases of Chemical Reactions to NMR Data: an Exploration of 1H NMR-Based Reaction Classification", Anal. Chem. 2007, 79(3), 854-862.

Q.-Y. Zhang, J. Aires-de-Sousa, "Random Forest Prediction of Mutagenicity from Empirical Physicochemical Descriptors"J. Chem. Inf. Model. 2007, 47(1), 1-8.

Q.-Y. Zhang, J. Aires-de-Sousa, "Physicochemical Stereodescriptors of Atomic Chiral Centers", J. Chem. Inf. Model. 2006, 46(6), 2278-2287.

D. A. R. S. Latino, J. Aires-de-Sousa, "Genome-Scale Classification of Metabolic Reactions: A Chemoinformatics Approach", Angew. Chem. Int. Ed. 2006, 45 (13), 2066-2069.

A. M. Fonseca, J. L. Biscaya, J. Aires-de-Sousa, A. M. Lobo,"Geographical classification of crude oils by Kohonen self-organizing maps", Anal. Chim. Acta 2006, 556 (2), 374-382.

S. Gupta, S. Mathew,  P. M. Abreu, J. Aires-de-Sousa, "QSAR analysis of phenolic antioxidants using MOLMAP descriptors of local properties", Bioorg. Med. Chem. 2006, 14 (4), 1199-1206.

Q.-Y. Zhang, J. Aires-de-Sousa, "Structure-based classification of chemical reactions without assignment of reaction centers", J. Chem. Inf. Model. 2005, 45(6), 1775-1783.

S. Caetano, J. Aires-de-Sousa, M. Daszykowski, Y. Vander Heyden, "Prediction of enantioselectivity using chirality codes and Classification and Regression Trees", Anal. Chim. Acta 2005, 544(1-2), 315-326.

Q.-Y. Zhang, G. Carrera, M. J. S. Gomes, J. Aires-de-Sousa, "Automatic assignment of absolute configuration from 1D NMR data", J. Org. Chem. 2005, 70(6), 2120-2130.

J. Aires-de-Sousa, J. Gasteiger, "Prediction of Enantiomeric Excess in a Combinatorial Library of Catalytic Enantioselective Reactions", J. Comb. Chem. 2005, 7(2), 298-301.

G. Carrera, J. Aires-de-Sousa, "Estimation of melting points of pyridinium bromides ionic liquids with decision trees and neural networks", Green Chemistry 2005, 7(1), 20-27.

F. B. Da Costa, Y. Binev, J. Gasteiger, J. Aires-de-Sousa, "Structure-based predictions of 1H NMR chemical shifts of sesquiterpene lactones using neural networks", Tetrahedron Lett. 2004, 45(37), 6931-6935.

J. Aires-de-Sousa, J. Gasteiger, I. Gutman, D. Vidović, "Chirality Codes and Molecular Structure", J. Chem. Inf. Comput. Sci., 2004, 44(3); 831-836.

Y. Binev, M. Corvo, J. Aires-de-Sousa, "The Impact of Available Experimental Data on the Prediction of 1H NMR Chemical Shifts by Neural Networks", J. Chem. Inf. Comp. Sci. 2004, 44(3); 946-949.

Y. Binev, J. Aires-de-Sousa, "Structure-Based Predictions of 1H NMR Chemical Shifts Using Feed-Forward Neural Networks", J. Chem. Inf. Comp. Sci. 200444(3); 940-945.

J. Aires-de-Sousa, L. Aires-de-Sousa, “Representation of DNA sequences with virtual potentials (SEQREP) and their processing by Kohonen self-organizing maps”, Bioinformatics 2003, 19(1), 30-36. [Abstract][Supplementary Information

J. Aires-de-Sousa, J. Gasteiger, “Prediction of enantiomeric selectivity in chromatography. Application of conformation-dependent and conformation-independent descriptors of molecular chirality”, J. Molec. Graphics and Model. 2002, 20 (5), 373-388. [Abstract]

J. Aires-de-Sousa, "JATOON: Java Tools for Neural Networks", Chemometrics and Intelligent Laboratory Systems 2002, 61(1-2), 167-173. [Abstract]

J. Aires-de-Sousa, M. Hemmer, J. Gasteiger, “Prediction of 1H NMR Chemical Shifts Using Neural Networks”, Analytical Chemistry 2002, 74(1), 80-90. [Abstract]

J. Aires-de-Sousa, S. Prabhakar, A. M. Lobo, A. M. Rosa, M. J. S. Gomes, M. C. Corvo, D. J. Williams, and A. J. P. White, “Chiral Synthesis of N-Aryl Aziridines”, Tetrahedron: Asymmetry  2002, 12 (24), 3349-3365. [Abstract]

J. Aires-de-Sousa, J. Gasteiger, "New Description of Molecular Chirality and its Application to the Prediction of the Preferred Enantiomer in Stereoselective Reactions", J. Chem. Inf. Comp. Sci. 2001, 41 (2), 369-375. [Abstract]

J. Aires-de-Sousa, "An Electronic Discussion Forum for Organic Chemistry - the ORGLIST Case", Internet Journal of Chemistry 1999, 2. [Abstract]

J. Aires-de-Sousa, "Verifying Wine Origin: A Neural Network Approach", American Journal of Enology and Viticulture 1996, 47 (4), 410-414.

J. Aires-de-Sousa, A.M. Lobo, S. Prabhakar, "A New Enantioselective Synthesis of N-arylaziridines by Phase-Transfer Catalysts" , Tetrahedron Letters 1996, 37 (18), 3183-3186.

Book chapters:

Aires-de-Sousa, J. "Processing of SMILES, InChI, and Hashed Fingerprints". In Tutorials in Chemoinformatics, Varnek, A., Ed.; John Wiley & Sons: Hoboken, NJ, 2017, 75-81.

Aires-de-Sousa, J. Data "Visualization and Analysis Using Kohonen Self-Organizing Maps". In Tutorials in Chemoinformatics, Varnek, A., Ed.; John Wiley & Sons: Hoboken, NJ, 2017, 119-126.

Aires-de-Sousa, J. "Descriptors Generation Using the CDK Toolkit and Web Services". In Tutorials in Chemoinformatics, Varnek, A., Ed.; John Wiley & Sons: Hoboken, NJ, 2017, 129-134.

D. A. R. S. Latino, J. Aires-de-Sousa, "Classification of Chemical Reactions and Chemoinformatics Approaches to Enzymatic Transformations", in Chemoinformatics and Computational Chemical Biology, Methods in Molecular Biology, vol. 672, Ed. Jürgen Bajorath, Humana Press (Springer), 2011, 325-340.

J. Aires-de-Sousa, "Chirality Descriptors", in Chemoinformatics - A Textbook, eds. Johnann Gasteiger and Thomas Engel, Wiley-VCH, 2003, 418-427.

M. Hemmer, J. Aires-de-Sousa, "Structure-Spectra Correlations", in Chemoinformatics - A Textbook, eds. Johnann Gasteiger and Thomas Engel, Wiley-VCH, 2003515-541.

J. Aires-de-Sousa, "Representation of Molecular Chirality", in Handbook of Chemoinformatics, ed. Johnann Gasteiger, Wiley-VCH, 2003, 1062-1078.

Chinese publications

Zhang Q. Y., Li J. Y., Aires-de-Sousa J., Xu L., Leng J. Y. "Conformation-Dependent Chirality Code Based on Electronegativity and its Applications", Chinese Journal of Analytical Chemistry 2011, 39(2), 257-260.

Zhang Q. Y., Aires-de-Sousa J., Xu L. "Chirality codes and applications", Computers and Applied Chemistry 2008, 25(6), 733-736.

PhD Thesis

"Síntese de N-Arilaziridinas Quirais", Universidade Nova de Lisboa, Lisboa, 1997.

Other selected publications:

J. Aires-de-Sousa, "Química na Internet", Química 1996, 61, 16-20.

J. Aires-de-Sousa, "Quimio-informática. Conteúdos que Urge Ensinar", Química 2002, 84, 55-59.