Sekerinski, E., Moreira, N., Oliveira, J.N., Ratiu, D., Guidotti, R., Farrell, M., Luckcuck, M., Marmsoler, D., Campos, J., Astarte, T., Gonnord, L., Cerone, A., Couto, L., Dongol, B., Kutrib, M., Monteiro, P., Delmas, D. (2020)
Formal Methods. FM 2019 International Workshops
Lecture Notes in Computer Science, 12232, Springer
doi:10.1007/978-3-030-54997-8

P. Pais, J. Oliveira, R. Viana, I.V. Costa, I. Sá-Correia, P.T. Monteiro, M.C. Teixeira (2022)
Prediction of Gene and Genomic Regulation in Candida Species, Using the PathoYeastract Database: A Comparative Genomics Approach in F. Devaux (editor)
Yeast Functional Genomics. Methods in Molecular Biology, 2477: 419-437, Humana Press Inc
doi:10.1007/978-1-0716-2257-5_23

M.C. Teixeira, P.T. Monteiro, I. Sá-Correia (2016)
Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis
in F. Devaux (editor)
Yeast Functional Genomics: Methods and Protocols, 1361: 391-404, Humana Press Inc
doi:10.1007/978-1-4939-3079-1_22

G. Batt, B. Besson, P.-E. Ciron, H. de Jong, E. Dumas, J. Geiselmann, R. Monte, P.T. Monteiro, M. Page, F. Rechenmann and D. Ropers (2012)
Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks
in J. van Helden, A. Toussaint and D. Thieffry (editors)
Bacterial molecular networks, 804: 439-462, Humana Press Inc
doi:10.1007/978-1-61779-361-5_22

V. Baldazzi, P.T. Monteiro, M. Page, D. Ropers, J. Geiselmann, H. de Jong (2011)
Qualitative analysis of genetic regulatory networks in bacteria
in W. Dubitzky, J. Southgate and H. Fuss (editors)
Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, 111-130, Springer-Verlag, Berlin
doi:10.1007/978-1-4419-7964-3_6

A. Lemos, F. Gouveia, P.T. Monteiro, I. Lynce (2024)
Iterative Train Scheduling under Disruption with Maximum Satisfiability
Journal of Artificial Intelligence Research, accepted

F. Cruz, P.T. Monteiro, A.S. Teixeira (2023)
Community structure in transcriptional regulatory networks of yeast species
Proc. of the International Conference on Complex Networks (CompleNet'23), Complex Networks XIV, 38-49

M.C. Teixeira, R. Viana, M. Palma, J. Oliveira, M. Galocha, M.N. Mota, D. Couceiro, M.G. Pereira, M. Antunes, I.V. Costa, P. Pais, C. Parada, C. Chaouiya, I. Sá-Correia, P.T. Monteiro (2023)
YEASTRACT+: a portal for the exploitation of global transcription regulation and metabolic model data in yeast biotechnology and pathogenesis
Nucleic Acids Research, 51(D1):D785-D791

P. Dias, P.T. Monteiro, A.S. Teixeira (2022)
Functional characterization of transcriptional regulatory networks of yeast species
Proc. of the International School and Conference on Network Science (NetSciX'22), LNCS 13197, 140-154

J. Zobolas, P.T. Monteiro, M. Kuiper, Å. Flobak (2022)
Boolean function metrics can assist modelers to check and choose logical rules
Journal of Theoretical Biology, 538:111025

C.P. Godinho, M. Palma, J. Oliveira, M.N. Mota, M. Antunes, M.C. Teixeira, P.T. Monteiro, I. Sá-Correia (2021)
The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts
FEMS Yeast Research, 21(6):foab045

J. Oliveira, M. Antunes, C.P. Godinho, M.C. Teixeira, I. Sá-Correia, P.T. Monteiro (2021)
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon
BMC Bioinformatics, 22:399

A. Lemos, P.T. Monteiro, I. Lynce (2021)
Introducing UniCorT: An Iterative University Course Timetabling Tool with MaxSAT
Journal of Scheduling, accepted

P.K. Guttula, P.T. Monteiro, M. Gupta (2021)
Prediction and Boolean logical modelling of synergistic microRNA regulatory networks during reprogramming of male germline pluripotent stem cells
BioSystems, 207:104453

J. Zobolas, P.T. Monteiro, M. Kuiper, A. Flobak (2021)
Boolean function metrics can assist modelers to check and choose logical rules
arXiv:2104.01279 [q-bio.MN]

P. Pais, J. Oliveira, V. Almeida, M. Yilmaz, P.T. Monteiro, M.C. Teixeira (2021)
Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: clues on host survival and probiotic activity based on promoter sequence variability
Genomics, 113(2): 530-539

A. Lemos, P.T. Monteiro, I. Lynce (2021)
Disruptions in Timetables: A Case Study at Universidade de Lisboa
Journal of Scheduling, 24:35-48

P.T. Monteiro^†, T. Pedreira^†, M. Galocha, M.C. Teixeira, C. Chaouiya (2020)
Assessing regulatory features of the current transcriptional network of Saccharomyces cerevisiae
Scientific Reports, 10:17744    († joint first authorship)

A. Lemos, P.T. Monteiro, I. Lynce (2020)
ITC 2019: University Course Timetabling with MaxSAT
in P. De Causmaecker, E. Özcan, G.V. Berghe (editors)
Proc. of the 13th Intl. Conf. on the Practice and Theory of Automated Timetabling (PATAT'20), Volume I, 105-128
Proceedings

F. Gouveia, I. Lynce, P.T. Monteiro (2020)
ModRev - Model Revision tool for Boolean logical models of biological regulatory networks
Proc. of the 18th Intl. Conf. on Computational Methods in Systems Biology (CMSB'20), LNBI 12314, 1-10

A. Lemos, P.T. Monteiro, I. Lynce (2020)
Minimal Perturbation in University Timetabling with Maximum Satisfiability
in E. Hebrard, N. Musliu (editors)
Proc. of the 17th Intl. Conf. on Constraint Programming, Artificial Intelligence, and Operations Research (CPAIOR'20), LNCS 12296, 317-333

P.K. Guttula, P.T. Monteiro, M.K. Gupta (2020)
A Boolean Logical model for Reprogramming of Testes-derived male Germline Stem Cells into Germline pluripotent stem cells
Computer Methods and Programs in Biomedicine, 192:105473

G. Selvaggio, S. Canato, A. Pawar, P.T. Monteiro, P.S. Guerreiro, M. Manuela Brás, F. Janody, C. Chaouiya (2020)
Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors
Cancer Research, 80(11): 2407-2420

F. Gouveia, I. Lynce, P.T. Monteiro (2020)
Revision of Boolean models of regulatory networks using stable state observations
Journal of Computational Biology, 27(2): 144-155

P.T. Monteiro^†, J. Oliveira^†, P. Pais^†, M. Antunes^†, M. Palma, M. Cavalheiro, M. Galocha, C.P. Godinho, L.C. Martins, N. Bourbon, M.N. Mota, R.A. Ribeiro, R.Viana, I. Sá-Correia, M.C. Teixeira (2020)
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts
Nucleic Acids Research, 48(D1):D642-D649    († joint first authorship)   

P. Varela, P.T. Monteiro, C. Chaouiya (2019)
Impact of Changing Cell-Cell Communication Network in Models of Epithelial Pattern Formation
IFAC-PapersOnLine, 52(26):38-44
Presented at 8th Conference on Foundations of Systems Biology in Engineering (FOSBE'19)

F. Gouveia, I. Lynce, P.T. Monteiro (2019)
Model revision of Boolean regulatory networks at stable state
in Z. Cai et al. (editors)
Proc. of the 15th International Symposium on Bioinformatics Research and Applications (ISBRA'19), LNCS 11490, 1-13

A. Lemos, I. Lynce, P.T. Monteiro (2019)
Repairing Boolean logical models from time-series data using Answer Set Programming
Algorithms for Molecular Biology, 14:9

W. Abou-Jaoudé, P.T. Monteiro (2019)
On Logical Bifurcation Diagrams
Journal of Theoretical Biology, 466:39-63

J.E.R. Cury, P.T. Monteiro, C. Chaouiya (2019)
Partial Order on the set of Boolean Regulatory Functions
arXiv:1901.07623 [cs.DM]

A. Lemos, F.S. Melo, P.T. Monteiro, I. Lynce (2019)
Room Usage Optimization in Timetabling: A Case Study at Universidade de Lisboa
Operations Research Perspectives, 6:100092

P.V. Varela, C.V. Ramos, P.T. Monteiro, C. Chaouiya (2019)
EpiLog: A software for the logical modelling of epithelial dynamics [version 2; peer review: 3 approved]
F1000Research, 7:1145

N.D. Mendes, R. Henriques, E. Remy, J. Carneiro, P.T. Monteiro, C. Chaouiya (2018)
Estimating attractor reachability in asynchronous logical models
Frontiers in Physiology, 9:1161

F. Gouveia, I. Lynce, P.T. Monteiro (2018)
Model Revision of Logical Regulatory Networks Using Logic-Based Tools
in A. Dal Palu', P. Tarau, N. Saeedloei, P. Fodor (editors)
Technical Communications of the 34th International Conference on Logic Programming (ICLP 2018), OASIcs 23:1-23:10

A. Naldi, C. Hernandez, W. Abou-Jaoudé, P.T. Monteiro, C. Chaouiya, D. Thieffry (2018)
Logical modelling and analysis of cellular regulatory networks with GINsim 3.0
Frontiers in Physiology, 9:646

A. Naldi, C. Hernandez, N. Levy, G. Stoll, P.T. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé (2018)
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Frontiers in Physiology, 9:680

A.S. Teixeira, P.T. Monteiro, J.A. Carriço, F.C. Santos, A.P. Francisco (2018)
Large-scale simulations of bacterial populations over complex networks
Journal of Computational Biology, 25(8):850-861

P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2018)
Stable states of Boolean regulatory networks composed over hexagonal grids
Electronic Notes in Theoretical Computer Science, 335: 113-130
Presented at 7th International Workshop on Static Analysis and Systems Biology (SASB'16)

M.C. Teixeira^†, P.T. Monteiro^†, M. Palma, C. Costa, C.P. Godinho, P. Pais, M. Cavalheiro, M. Antunes, A. Lemos, T. Pedreira, I. Sá-Correia (2018)
YEASTRACT, an upgraded database for the analysis of transcription regulatory networks in Saccharomyces cerevisiae
Nucleic Acids Research, 46(D1): D348-D353    († joint first authorship)

F. Gouveia, P.T. Monteiro, V. Manquinho, I. Lynce (2017)
Logic-Based Encodings for Ricochet Robots
in E. Oliveira, J. Gama, Z. Vale, H. Lopes Cardoso (editors)
Proc. of the 18th EPIA Conference on Artificial Intelligence (EPIA'17), LNCS 10423, 657-669

A.S. Teixeira, P.T. Monteiro, J.A. Carriço, F.C. Santos, A.P. Francisco (2017)
Using Spark and GraphX to Parallelize Large-Scale Simulations of Bacterial Populations over Host Contact Networks
in S. Ibrahim, K.-K. Raymond Choo, Z. Yan, W. Pedrycz (editors)
Proc. of the International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP'17), LNCS 10393, 591-600

P.T. Monteiro, P. Pais, C. Costa, S. Manna, I. Sá-Correia, M.C. Teixeira (2017)
The PathoYeastract database: an information system for the analysis of gene and genomic transcription regulation in pathogenic yeasts
Nucleic Acids Research, 45(D1): D597-D603

W. Abou-Jaoudé^†, P. Traynard^†, P.T. Monteiro^†, J. Saez-Rodriguez, T. Helikar, D. Thieffry, C. Chaouiya (2016)
Logical modeling and dynamical analysis of cellular networks
Frontiers in Genetics, 7:94    († joint first authorship)

A.S. Teixeira, P.T. Monteiro, M. Ramirez, J.A. Carriço, A.P. Francisco (2015)
Not seeing the forest for the trees: Size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis
PLOS ONE, 10(3): e0119315

A. Naldi, P.T. Monteiro, C. Müssel, the Consortium for Logical Models and Tools, H.A. Kestler, D. Thieffry, I. Xenarios, J.Saez-Rodriguez, T. Helikar, C. Chaouiya (2015)
Cooperative development of logical modelling standards and tools with CoLoMoTo
Bioinformatics, 31(7): 1154-1159

W. Abou-Jaoudé^†, P.T. Monteiro^†, A. Naldi, M. Grandclaudon, V. Soumelis, C. Chaouiya, D. Thieffry (2015)
Model checking to assess T-helper cell plasticity
Frontiers in Bioengineering and Biotechnology, 2:86    († joint first authorship)

N.D. Mendes^†, P.T. Monteiro^†, J. Carneiro, E. Remy, C. Chaouiya (2014)
Quantification of reachable attractors in asynchronous discrete dynamics
arXiv:1411.3539 [cs.DM] († joint first authorship)

P.T. Monteiro, W. Abou-Jaoudé, D. Thieffry, C. Chaouiya (2014)
Model Checking Logical Regulatory Networks
IFAC Proceedings Volumes, 47(2):170-175
Presented at 12th IFAC/IEEE Workshop on Discrete Event Systems (WODES'14), 170-175

M.C. Teixeira^†, P.T. Monteiro^†, J. Guerreiro, J.P. Gonçalves, N.P. Mira, S.C. dos Santos, T.R. Cabrito, M. Palma, C. Costa, A.P. Francisco, S.C. Madeira, A.L. Oliveira, A.T. Freitas, I. Sá-Correia (2014)
The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae
Nucleic Acids Research, 42(D1): D161-D166    († joint first authorship)   

C. Chaouiya, D. Berenguier, S.M. Keating, A. Naldi, M.P. van Iersel, N. Rodriguez, A. Dräger, F. Büchel, T. Cokelaer, B. Kowal, B. Wicks, E. Gonçalves, J. Dorier, M. Page, P.T. Monteiro, A. von Kamp, I. Xenarios, H. de Jong, M. Hucka, S. Klamt, D. Thieffry, N. Le Novère, J. Saez-Rodriguez, T. Helikar (2013)
SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
BMC Systems Biology, 7:135   

D. Bérenguier, C. Chaouiya, P.T. Monteiro, A. Naldi, E. Remy, D. Thieffry and L. Tichit (2013)
Dynamical modeling and analysis of large cellular regulatory networks
Chaos: An Interdisciplinary Journal of Nonlinear Science, 23(2):025114    Most cited articles in 2014 from Chaos

A. Naldi, P.T. Monteiro and C. Chaouiya (2012)
Efficient handling of large signalling-regulatory networks by focusing on their core control
in D. Gilbert and M. Heiner (editors)
Proc. of the 10th Intl. Conf. on Computational Methods in Systems Biology (CMSB'12), LNCS 7605, Springer Verlag, 288-306

A.P. Francisco, C. Vaz, P.T. Monteiro, J. Melo-Cristino, M. Ramirez and J.A. Carriço (2012)
PHYLOViZ: Phylogenetic Inference and Data Visualization for Sequence Based Typing Methods
BMC Bioinformatics, 13:87   

P.T. Monteiro and C. Chaouiya (2012)
Efficient verification for logical models of regulatory networks
in M.P. Rocha, N. Luscombe, F. Fdez-Riverola and J.M. Corchado Rodriguez (editors)
Proc. of the 6th Intl. Conf. on Practical Applications on Computational Biology & Bioinformatics (PACBB'12), AISC 154, Springer Berlin / Heidelberg, 259-267    PAAMS'12 Award of Scientific Excellence

P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira and A.T. Freitas (2011)
Qualitative modeling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae
IET Systems Biology, 5(5): 308-316

P.J. Dias, C.P. Costa, I. Sá-Correia, M.C. Teixeira, P.T. Monteiro, A.L. Oliveira, A.T. Freitas (2011)
Using systems biology approaches to study a multidrug resistance network
Proc. of the 1st Portuguese meeting in Bioengineering (ENBENG'11), 1-4

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong (2011)
CTRL: Extension of CTL with Regular Expressions and Fairness Operators to Verify Genetic Regulatory Networks
Theoretical Computer Science, 412(26): 2854-2883

D. Abdulrehman, P.T. Monteiro, M.C. Teixeira, N.P. Mira, A.B. Lourenço, S.C. dos Santos, T.R. Cabrito, A.P. Francisco, S.C. Madeira, R.S. Aires, A.L. Oliveira, I. Sá-Correia and A.T. Freitas (2011)
YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface
Nucleic Acids Research, 39(suppl 1): D136-D140

M.C. Teixeira, P.J. Dias, P.T. Monteiro, A. Sala, A.L. Oliveira, A.T. Freitas and I. Sá-Correia (2010)
Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches
Molecular BioSystems, 6(12), 2471-81

G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro and H. de Jong (2010)
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
Bioinformatics, 26(18): i603-i610
Presented at European Conference on Computational Biology (ECCB'10)

P.T. Monteiro, E. Dumas, B. Besson, R. Mateescu, M. Page, A.T. Freitas and H. de Jong (2009)
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks
BMC Bioinformatics, 10:450

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong (2008)
Computation Tree Regular Logic for Genetic Regulatory Networks
in S. Cha, J.-Y. Choi, M. Kim, I. Lee and M. Viswanathan (editors)
Proc. of the 6th Intl. Symposium on Automated Technology for Verification and Analysis (ATVA'08), LNCS 5311, Springer Verlag, 48-63

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
Bioinformatics, 24(16): i227-i233
Presented at European Conference on Computational Biology (ECCB'08)

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
in M. Ghallab, C.D. Spyropoulos, N. Fakotakis and N. Avouris (editors)
Proc. of the 18th European Conference on Artificial Intelligence (ECAI'08), IOS Press, Amsterdam, 229-233

P.T. Monteiro, N. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, N.P. Mira, H. Pais, A.P. Francisco, A.M. Carvalho, A. Lourenço, I. Sá-Correia, A.L. Oliveira and A.T. Freitas (2008)
YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
Nucleic Acids Research, 36(Database issue): D132-D136

M.C. Teixeira^†, P. Monteiro^†, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
Nucleic Acids Research, 34(Database issue): D446-D451    († joint first authorship)   

P. Monteiro, M.C. Teixeira, P. Jain, S. Tenreiro, A.R. Fernandes, N. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
YEASTRACT: a database of transcription regulatory associations in Saccharomyces cerevisiae
in F.M. Couto, M.J. Silva and P. Fernandes (editors)
Proc. of Bioinformatics: Knowledge Discovery in Biology (BKDB'05), Lisbon, Portugal, 34-38
pdf

M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2005)
A Bioinformática e as Bases de Dados: o exemplo de uma Base de Dados para Análise de Mecanismos de Regulação em Levedura
Boletim de Biotecnologia, 81: 23-31

M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
YEASTRACT: a database to search for transcription regulatory associations in Saccharomyces cerevisiae
Yeast, 22(S1): S191-S195, 16-1
doi:10.1002/yea.1271

J. Graça, M. Mourão, O. Anunciação, P. Monteiro, H.S. Pinto and V. Loureiro (2005)
Ontology building process: the wine domain
in 5th Conference of the European Federation for Information Technology in Agriculture, Food and Environment (EFITA/WCCA'05), Vila Real, Portugal
pdf

A. Lemos, P.T. Monteiro, I. Lynce (2016)
Repairing Boolean regulatory networks using Answer Set Programming
Technical Report n° 5/2016, INESC-ID, Lisboa, Portugal

A.S. Teixeira, V. Ribeiro, P.T. Monteiro, J.A. Carriço, M. Ramirez, A.P. Francisco (2014)
Large scale simulation of bacterial population evolution over host contact networks
Technical Report n° 17/2014, INESC-ID, Lisboa, Portugal
pdf

P.T. Monteiro, A.P. Francisco, M. Ramirez, J.A. Carriço (2014)
Topological representation of the within-species evolutionary structure of bacterial populations: the SLV graph
Technical Report n° 16/2014, INESC-ID, Lisboa, Portugal
pdf

G. Batt, M. Page, I. Cantone, G. Goessler, P.T. Monteiro and H. de Jong (2010)
Efficient parameter search for qualitative models of regulatory networks using symbolic model checking
Research Report RR-7284, May 2010, INRIA Grenoble - Rhone-Alpes, France
pdf

R. Mateescu, P.T. Monteiro, E. Dumas and H. de Jong (2008)
Computation Tree Regular Logic for Genetic Regulatory Networks
Research Report RR-6521, May 2008, INRIA Grenoble - Rhône-Alpes, France
pdf

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
Research Report RR-6470, Mar 2008, INRIA Grenoble - Rhône-Alpes, France
pdf

A. Ramalho and P.T. Monteiro (2003)
Avaliação de métodos computacionais para a detecção de estruturas em genomas
Technical Report n° 3/2003, INESC-ID, Lisboa, Portugal

J. Castanheira, A.S. Teixeira, S.C. Madeira, P.T. Monteiro (2022)
Predicting blood donor return in Portugal: the role of demographics
Working notes of the 13th INForum - Simpósio de Informática (INForum'22), Guarda, Portugal

F. Cruz, P.T. Monteiro, A.S. Teixeira (2022)
Community detection for the characterization of transcriptional regulatory networks of yeast species
Working notes of the 13th INForum - Simpósio de Informática (INForum'22), Guarda, Portugal

A. Lemos, P.T. Monteiro, I. Lynce (2020)
ITC-2019: A MaxSAT approach to solve university timetabling problems
Working notes of the International Timetabling Competition (ITC 2019)
[ pdf ]

P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2016)
SAT-based identification of stable states in composed Boolean regulatory networks
Working notes of the International Workshop on Static Analysis and Systems Biology (SASB 2016), Edinburgh, UK

P.L. Varela, I. Lynce, V. Manquinho, C. Chaouiya, P.T. Monteiro (2016)
SAT-based identification of stable states in composed Boolean regulatory networks
Working notes of the 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2014)
Logical modeling of T-helper cell differentiation and plasticity
Working notes of the Logical Modelling and Analysis of Cellular Networks Workshop (LMACN-ECCB'14), Strasbourg, France

A. Fauré, B.M.I. Vreede, P.L. Varela, P.T. Monteiro, E. Sucena, C. Chaouiya (2014)
A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects
Working notes of the Logical Modelling and Analysis of Cellular Networks Workshop (LMACN-ECCB'14), Strasbourg, France

P.L. Varela, N.D. Mendes, P.T. Monteiro, A. Fauré, C. Chaouiya (2013)
EpiLog: a novel tool for the qualitative modelling of epithelial patterning
Working notes of the 5th INForum - Simpósio de Informática (INForum'13), Évora, Portugal

A.S. Teixeira, P.T. Monteiro, J.A. Carriço, M. Ramirez, A. P. Francisco (2013)
Spanning edge betweenness
Working notes of the Mining and Learning with Graphs - Knowledge Discovery and Data Mining (MLG-KDD'13), Chicago, US
[ pdf ]

C. Chaouiya, A. Naldi, L. Spinelli, P.T. Monteiro, D. Berenguier, L. Grieco, A. Mbodj, S. Collombet, A. Niarakis, L. Tichit, E. Remy, D. Thieffry (2012)
Logical modelling of cellular decision processes with GINsim
Working notes of the Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM'12), Rennes, France

P.T. Monteiro and C. Chaouiya (2011)
Logical modelling of biological regulatory networks: turning automatic verification effective
Working notes of the 3rd INForum - Simpósio de Informática (INForum'11), Coimbra, Portugal

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
Temporal Logic Patterns for Querying Qualitative Models of Genetic Regulatory Networks
in Elizabeth Bradley, Louise Travé-Massuyès, eds., Working notes of the 22nd International Workshop on Qualitative Reasoning (QR'08), 102-7, Boulder, CO, USA

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas and H. de Jong (2008)
Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks
in Jacques van Helden, Yves Moreau, eds., Working notes of the Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM'08), 71-6, Lille, France

A. Ramalho and P. Monteiro (2003)
PoeTA III - Poetry Teaching Agent III
Working notes of the Workshop of Introduction to Autonomous Agents (WIAA'03), Lisboa, Portugal

Dual PhD Thesis, P.T. Monteiro (2010)
Towards an integrative approach for the modeling and formal verification of biological regulatory networks
Instituto Superior Técnico - Technical University of Lisbon, Portugal
Université Claude Bernard Lyon 1, France
[ pdf ]

MSc Thesis, P.T. Monteiro (2005)
Sistema de gestão da informação associada à regulação da transcrição da Saccharomyces cerevisiae
Instituto Superior Técnico - Technical University of Lisbon, Portugal
[ pdf ]

Diploma Thesis, A. Ramalho and P. Monteiro (2003)
Avaliação de métodos computacionais para a detecção de estruturas em genomas
Instituto Superior Técnico - Technical University of Lisbon, Portugal

D. Couceiro, M. Pereira, C. Parada, R. Viana, M.C. Teixeira, P.T. Monteiro (2023)
Aiming at the Automation of Genome-wide Regulatory Network Inference in Yeast
Abstract and Poster at Congress of Microbiology and Biotechnology (MicroBiotec'23), Covilhãa, Portugal

M.C. Teixeira, R. Viana, M. Palma, J. Oliveira, M. Galocha, M.N. Mota, D. Couceiro, M.G. Pereira, M. Antunes, I.V. Costa, P. Pais, C. Parada, C. Chaouiya, I. Sá-Correia, P.T. Monteiro (2023)
The YEASTRACT+ database to explore the transcription regulation and metabolic model data in yeasts
Abstract at 15th International Conference on Culture Collections (ICCC'15), Braga, Portugal

A.P. Francisco, P.T. Monteiro, G. Ribeiro, A.S. Teixeira (2022)
On edge significance in large phylogenetic (spanning) trees
Abstract at 24th International Conference on Computational Statistics (COMPSTAT'22), Bologna, Italy

A.S. Teixeira, P.T. Monteiro, J. Carriço, M. Ramirez, F.C. Santos, A.P. Francisco (2022)
Link Significance in Phylogenetic Analysis and Networked Systems
Abstract at International School and Conference on Network Science (NetSciX), Porto, Portugal

P. Dias, P.T. Monteiro, A.S. Teixeira (2021)
A multilayer network approach to map functional clusters between yeast species
Abstract and oral presentation at International Conference on Complex Networks (Complenet), Online

P. Dias, P.T. Monteiro, A.S. Teixeira (2021)
Mapping functional clusters between yeast species using a multilayer network approach
Abstract and oral presentation at Networks, Washington D.C., USA

J.S. Oliveira, P. Pais, M. Antunes, M. Palma, M. Galocha, C.P. Godinho, I.V. Costa, R. Viana, I. Sá-Correia, M.C. Teixeira, P.T. Monteiro (2021)
Towards an automatic cross-species comparative genomics portal
Abstract and oral presentation at Bioinformatic Open Days'21, Braga, Portugal

M. Yilmaz, P. Pais, V. Almeida, M. Cavalheiro, J. Oliveira, P.T. Monteiro, M.C. Teixeira (2019)
New clues on the probiotic activity of Saccharomyces boulardii, obtained from global gene promoter analysis
Abstract at Neuroscience, Bioinformatics, Microbiome and Beyond International Conference, Bachinovo, Bulgaria

A. Naldi, C. Hernandez, N. Levy, G. Stoll, P. Monteiro, C. Chaouiya, T. Helikar, A. Zinovyev, L. Calzone, S. Cohen-Boulakia, D. Thieffry, L. Paulevé (2019)
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Abstract at Basel Computational Biology Conference ([BC]2), Basel, Switzerland

P. Varela, C. Chaouiya, P.T. Monteiro (2019)
Logical modelling to explore communication network features influencing pattern formation
Abstract and Poster at SysMod Computational Modeling of Biological Systems (COSI) at European Conference on Computational Biology (ISMB/ECCB), Basel, Switzerland

J.S. Oliveira, V. Pinheiro, I. Sá-Correia, M.C. Teixeira, P.T. Monteiro (2019)
YEASTRACT+: a comparative genomics cool platform for the analysis of transcriptional regulatory networks in yeast species
Abstract and demo presentation at Cool Tools for Science, Lisbon, Portugal

A. Fonseca, P.T. Monteiro, M.C. Teixeira, C. Chaouiya (2019)
Genome-Scale Logical Regulatory Models for S. cerevisiae, C. albicans and C. glabrata
Poster at Advanced Lecture Course on Computational Systems Biology (CompSysBio), Aussois, France

J.S. Oliveira, P. Pais, M.Antunes, M. Palma, M. Galocha, C.P. Godinho, M. Cavalheiro, M. Yilmaz, R. Viana, I. Sá-Correia, M.C. Teixeira, P.T. Monteiro (2019)
YEASTRACT+: a comparative genomics platform for the analysis of transcriptional regulatory networks in yeast species
Abstract and oral presentation at Bioinformatic Open Days'19, Braga, Portugal

R. Schwieger, P. Monteiro, C. Chaouiya (2018)
Investigation of Boolean model pools: Which components should be measured to distinguish models and behaviors?
Abstract and oral presentation at 11th European Conference on Mathematical and Theoretical Biology (ECMTB'18), Lisboa, Portugal

T. Pedreira, P.T. Monteiro, M.C. Teixeira, C. Chaouiya (2018)
Reconstruction and analysis of the global transcriptional regulatory network in yeast
Poster at 11th European Conference on Mathematical and Theoretical Biology (ECMTB'18), Lisboa, Portugal

P.V. Varela, C. Chaouiya, P.T. Monteiro (2018)
Logical Modelling To Explore Communication Network Features Influencing Pattern Formation
Poster at 11th European Conference on Mathematical and Theoretical Biology (ECMTB'18), Lisboa, Portugal

C. Chaouiya, L. Calzone, T. Helikar, C. Hernandez, P. Monteiro, A. Naldi, D. Thieffry, D Waltemath (2017)
Standardisation effort from the Consortium for Logical Models and Tools (CoLoMoTo)
Poster and oral presentation at COMBINE 2017, Milan, Italy

T. Pedreira, P.T. Monteiro, M.C. Teixeira, C. Chaouiya (2017)
Reconstruction and analysis of the global transcriptional regulatory network in yeast
Poster at 13th Basel Computational Biology Conference ([BC]2'17), Basel, Switzerland

S. Fueyo, P.T. Monteiro, A. Naldi, J. Dorier, E. Remy, C. Chaouiya (2017)
Reversed dynamics to uncover basins of attraction of asynchronous logical models
Poster and oral presentation at ISMB/ECCB, Prague, Czech Republic [F1000Posters]

P. Fernandes, J. Borbinha, A. Canário, J. Cardoso, I. Chaves, I. Sá-Correia, B. Costa, C. Cox, D. Faria, A.T. Freitas, C. Miguel, P.T. Monteiro, G. De Moro, A. Oliveira, D. Sobral, M.C. Teixeira, M.J. Silva (2017)
ELIXIR Portugal: Platforms, Use Cases and Services
Poster and oral presentation at Bioinformatic Open Days'17, Braga, Portugal [doi:10.6084/m9.figshare.4708603.v1 ]

C. Ramos, P.L. Varela, P.T. Monteiro, C. Chaouiya (2016)
Patterning in proliferating epithelia, a modelling approach
Poster at 17th International Conference on Systems Biology (ICSB'16), Barcelona, Spain

C. Ramos, P.L. Varela, P.T. Monteiro, C. Chaouiya (2016)
Patterning in proliferating epithelia, a modelling approach
Poster and oral presentation at 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

A. Lemos, P.T. Monteiro, I. Lynce (2016)
Repairing Boolean regulatory networks using Answer Set Programming
Poster and oral presentation at 8th INForum - Simpósio de Informática (INForum'16), Lisboa, Portugal

Monteiro P.T., Cury J.E.R., Chaouiya C. (2016)
On the number and structure of Boolean functions compatible with a regulatory network topology
Abstract and oral presentation at 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Nottingham, UK

Fueyo S., Monteiro P.T., Naldi A., Remy A., Chaouiya C. (2016)
Reversing Boolean gene regulatory networks
Abstract and oral presentation at 10th European Conference on Mathematical and Theoretical Biology (ECMTB), Nottingham, UK

Teixeira A.S., Monteiro P.T., Francisco A.P., Carriço J.A. (2016)
Large scale simulation of bacterial populations evolution over host contact networks
Poster at 8th International Conference on Discrete Models of Complex Systems, Aveiro, Portugal

I. Chaves, N.D. Mendes, C. Vaz, C. Miguel, Monteiro P.T. (2016)
Plant Experimental Assay Ontology
Abstract and oral presentation at Plant Biology Europe EPSO/FESPB, Prague, Czech Republic

Dias P.J., Machado A., Zhang K., Blake T., Monteiro P.T., Sá-Correia I. (2015)
Yeast Drug:H+ antiporters: comparative genomic and phylogenetic analyses and design and implementation of a dedicated database
Poster at Congress of Microbiology and Biotechnology (MicroBiotec'15), Évora, Portugal

W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2015)
Predicting T-helper cell differentiation and plasticity using logical modelling and model-checking
Poster at 4th European Congress of Immunology (ECI'15), Vienna, Austria

P.L. Varela, A. Fauré, C. Chaouiya, P.T. Monteiro (2015)
A computational framework for the logical modelling of epithelial patterning
Presentation and poster at 12th Basel Computational Biology Conference ([BC]2'15), Basel, Switzerland

W. Abou-Jaoudé, M. Grandclaudon, P.T. Monteiro, A. Naldi, C. Chaouiya, V. Soumelis, D. Thieffry (2015)
Logical modeling of T-helper cell differentiation and plasticity
Poster at 6th Young Researchers in Life Sciences Conference (YRLS'15), Paris, France

A. Naldi, P.T. Monteiro, D. Thieffry, C. Chaouiya (2014)
GINsim: a software tool for the modelling and analysis of logical regulatory networks
Poster at 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France

P.L. Varela, P.T. Monteiro, Nuno Mendes, Adrien Fauré, C. Chaouiya (2014)
EpiLog, a computational tool for the logical modelling of epithelial pattern formation
Poster at 13th European Conference on Computational Biology (ECCB'14), Strasbourg, France [F1000Posters]

N.D. Mendes, P.T. Monteiro, C. Vaz, I. Chaves (2014)
Towards a Plant Experimental Assay Ontology
Poster at 10th International Conference on Data Integration in the Life Sciences (DILS'14), Lisbon, Portugal

F. Rebelo, I. Chaves, N.D. Mendes, P.T. Monteiro, J. Borbinha (2014)
A Repository for Biological Data applied to the Woody Plants Domain
Poster at 10th International Conference on Data Integration in the Life Sciences (DILS'14), Lisbon, Portugal

P.T. Monteiro, M.C. Teixeira, A.P. Francisco, I. Sá-Correia (2014)
YEASTRACT-NET: extracting and visualizing transcription regulatory networks in S. cerevisiae
Poster and oral presentation at XX Jornadas de leveduras Professor Nicolau van Uden, Lisbon, Portugal

A.S. Teixeira, A.P. Francisco, P.T. Monteiro, R. Oliveira, M. Ramirez, J.A. Carriço (2013)
NetPopSim - a population simulator for microbial allelic profiles for simulating spread and evolution within social networks
Poster at 10th International Meeting on Microbial Epidemiological Markers (IMMEM), Paris, France

P.L. Varela, N.D. Mendes, P.T. Monteiro, A. Fauré, C. Chaouiya (2013)
Epilog: a software for the logical modelling of epithelial patterning
Poster at Bioinformatic Open Days'13, Braga, Portugal

A.P. Francisco, C. Vaz, P.T. Monteiro, M. Ramirez, J. Carriço (2011)
Fooled by trees: when simple can be misleading
Poster at Congresso Nacional MicroBiotec'11, Braga, Portugal

P.J. Dias, P.T. Monteiro, A.L. Oliveira, A.T. Freitas, I. Sá-Correia, M.C. Teixeira (2011)
Insights into the transcription regulatory network controlling the multidrug resistance gene FLR1: a systems biology approach
Poster at 25th International Conference on Yeast Genetics and Molecular Biology, Olsztyn-Kortowo, Poland

P.T. Monteiro, A.T. Freitas, D. Ropers, R. Mateescu, H. de Jong (2010)
Modeling and formal verification of biological regulatory networks: an integrative approach
Poster at IEEE International Conference on Bioinformatics & Biomedicine (BIBM'10), Hong Kong, China

P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, I. Sá-Correia, M.C. Teixeira, A.T. Freitas (2010)
Computational modeling and analysis of the yeast FLR1 regulatory network in mancozeb-challenged cells
Poster at 11th International Conference on Systems Biology (ICSB'10), Edinburgh, Scotland, UK

G. Batt, M. Page, P. Monteiro, G. Goessler, Hidde de Jong (2010)
Design of synthetic gene networks: symbolic model checking of PADE models
Poster at Systems Biology of Microorganisms'10, Paris, France

P.T. Monteiro, P.J. Dias, D. Ropers, A.L. Oliveira, A.T. Freitas, I. Sá-Correia, M.C. Teixeira (2009)
The regulatory network underlying the transcriptional up-regulation of the FLR1 gene in mancozeb stressed yeast cells: qualitative modeling and simulation
Abstract at Congresso Nacional MicroBiotec'09, Vilamoura, Portugal

P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, H. de Jong (2008)
Temporal logic patterns for querying dynamic models of cellular interaction networks
Poster at Forum Português de Biologia Computacional (FPBC'08), Oeiras, Portugal

M.C. Teixeira, P.T. Monteiro, N.P. Mira, P.M. Santos, A.T. Freitas, A.L. Oliveira, I. Sá-Correia (2008)
The YEASTRACT database and its exploitation in Toxicogenomics: the Yeast response to the herbicide 2,4-D
Poster at Forum Português de Biologia Computacional (FPBC'08), Oeiras, Portugal

M.C. Teixeira, P. Monteiro, S. Tenreiro, N.P. Mira, A.B. Lourenço, A.M. Carvalho, N. Mendes, S. d'Orey, H. Pais, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2007)
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
Extended abstract at 3rd Conference on Physiology of Yeasts and Filamentous Fungi, S245: 52, Helsinki, Finland [pdf]

P. Monteiro, N. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, N.P. Mira, H. Pais, A.P. Francisco, A.M. Carvalho, A.B. Lourenço, I. Sá-Correia, A.L. Oliveira and A.T. Freitas (2007)
Analysis of new and known DNA-binding site motifs in Saccharomyces cerevisiae using the YEASTRACT-DISCOVERER tools
Poster and Extended abstract at Congresso Nacional MicroBiotec'07, Lisboa, Portugal
Sartorius award - Inovation in Microbiology/Biotechnology

M.C. Teixeira, P. Monteiro, S. Tenreiro, N. Mira, A.M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
Poster at Yeast Genetics and Molecular Biology Meeting, Book of Abstracts 529A, Princeton, USA [www]

M.C. Teixeira, P. Monteiro, S. Tenreiro, N.P. Mira, A.M. Carvalho, N. Mendes, A. Casimiro, C. Nogueira, C. Oliveira, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2006)
Analysis of transcription regulatory associations in Saccharomyces cerevisiae using the YEASTRACT database
Poster at 2nd FEMS Congress of European Microbiologists, Book of Abstracts W12.4-P.COM.3, Madrid, Spain

M.C. Teixeira, P. Monteiro, N.P. Mira, S. Tenreiro, A.T. Freitas, A.L. Oliveira and Isabel Sá-Correia (2006)
The YEASTRACT database: application to the analysis of Saccharomyces cerevisiae genome-wide expression data
Extended abstract at XVth National Congress of Biochemistry, 1(SA1): 30, Aveiro, Portugal

M.C. Teixeira, P. Monteiro, P. Jain, S. Tenreiro, A.R. Fernandes, N.P. Mira, M. Alenquer, A.B. Lourenço, A.T. Freitas, A.L. Oliveira and I. Sá-Correia (2005)
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
Poster at Congresso Nacional MicroBiotec'05, Book of Abstracts OC28, Póvoa do Varzim, Portugal

P. Monteiro, A. Ramalho, A.T. Freitas and A.L. Oliveira (2005)
DECIDE: A Gene Finding Evaluation Tool
Poster at Bioinformatics: Knowledge Discovery in Biology BKDB'05