Andre Sanches Ribeiro. Concluiu Física pela Universidade de Lisboa em 2000 e PhD em Engenharia Física pela Universidade Técnica de Lisboa em 2004. É Professor Associado - Tampere University of Technology. Publicou 71 artigos em revistas especializadas e 81 trabalhos em actas de eventos, possui 10 capítulos de livros e 1 livro publicados. Possui 7 softwares e outros 73 itens de produção técnica. Orientou 2 teses de doutoramento e co-orientou 2, orientou 7 dissertações de mestrado e co-orientou 4, alem de ter orientado 6 trabalhos de conclusão de curso de bach./licenciatura e 2 trabalhos de iniciação científica nas áreas de Ciências da Computação e da Informação e Ciências Biológicas. Recebeu 5 prémios e/ou homenagens. Actua nas áreas de Ciências Naturais com ênfase em Ciências Biológicas, Ciências Exactas com ênfase em Física e Ciências Exactas com ênfase em Ciências da Computação e da Informação. Nas suas actividades profissionais interagiu com 154 colaboradores em co-autorias de trabalhos científicos. No seu curriculum DeGóis os termos mais frequentes na contextualização da produção científica, tecnológica e artístico-cultural são: Emergent Behaviors, Networks e Genetic Networks.
Endereço de acesso a este CV: http://www.degois.pt/visualizador/curriculum.jsp?key=2076293572283095

Nome completo Full name	Andre Sanches Ribeiro
Nome em citações bibliográficas Quoting name	Ribeiro, Andre S.
Categoria profissional Position	Professor Associado
Domínio científico de atuação Scientific domain	Ciências Naturais-Ciências Biológicas. Ciências Exactas-Física. Ciências Exactas-Ciências da Computação e da Informação.

Endereço profissional Professional address

Tampere University of Technology Department of Signal Processing Korkeakoulunkatu 1 FI-3-3101 Tampere Finlândia Telefone: (+358)408490736 Correio electrónico: andre.ribeiro@tut.fi Homepage: http://www.cs.tut.fi/~sanchesr/

Sexo Gender

Masculino»Male

2000-2004	Doutoramento Phd
Engenharia Física (4 anos » years) . Universidade Técnica de Lisboa, Portugal.

1995-1999	Licenciatura Licentiate degree
Física (4 anos » years) . Universidade de Lisboa, Portugal.

2013-2013	Curso de curta duração Short course
Pedagogical Training. Pedagogical Skills for Teachers and Teaching Practice. Tampere University of Technology, Finlândia.

2004-2007	Pós-Doutoramento Postdoctorate
2 anos » years. University of Calgary, Canadá.

Tampere University of Technology

Jan/2015-Actual

Professor Associado

Tampere University of Technology

Fev/2012-Dez/2014

Professor Auxiliar com Agregação

Tampere University of Technology

Ago/2009-Jan/2012

Professor Auxiliar

Tampere University of Technology

Jul/2007-Jul/2009

Investigador Principal

University of Calgary

Dez/2004-Jun/2007

Outra Situação

Universidade Técnica de Lisboa

Jan/2000-Nov/2004

Outra Situação

Compreende Understandig	Português (Bem), Inglês (Bem).
Fala Speaking	Português (Bem), Inglês (Bem).
Lê Reading	Português (Bem), Inglês (Bem).
Escreve Writing	Português (Bem), Inglês (Bem).

2011	Scientific Achievement Award, Department of Signal Processing, Tampere University of Technology.
2013	Award for Teaching Activities, Department of Signal Processing , Tampere University of Technology.
2013	Best Scientific Publications of 2012, Paper: A.-B. Muthukrishnan et al, (2012) Nucl Acid Res 40(17):8472-83. Feb 2013, Managing Board of Department of Signal Processing, Tampere University of Technology.
2013	Best Scientific Publications of 2012, Paper: J. Lloyd-Price et al, (2012) Bioinformatics, 28(22):3004-5. Feb 2013, Managing Board of Department of Signal Processing, Tampere University of Technology.
2012	Adjunct Professorship, Department of Signal Processing, Tampere University of Technology, Finland.

Jan/2013 - Actual	Department of Signal Processing Teaching Development Group, TUT, Membro.
Jan/2012 - Actual	Centre of Technology and Systems (CTS), Faculty of Sciences and Technology, New University of Lisbon, External Collaborator.
Jan/2006 - Actual	Canadian Society for Systems Biology, Membro.
Jan/2001 - Actual	Portuguese Physics Society , Membro.
Jan/2013 - Dez/2014	Biotechnology Masters Programme Committee of the Degree Programme in Bioengineeering, TUT, Membro.
Jan/2013 - Dez/2013	Biotechnology Teaching Advisory Board, TUT, Membro.
Jul/2012 - Dez/2013	Board of Doctoral Studies, Institute of Biomedical Technology, UTA, Membro.
Fev/2009 - Dez/2012	Finnish Doctoral Programme in Computational Sciences (FICS), Membro.

Livros publicados/organizados ou edições Published/organized books or Editions

1.	Niiranen, Samuli; Ribeiro, Andre. eds. 2011. Information Processing and Biological Systems ed. 1, ISBN: 978-3-642-19620-1. Berlin, Heidelberg: Springer Berlin Heidelberg.

Capítulos de livros publicados Published book chapters

1.	Ribeiro, Andre S. 2015. Detecting and tracking the tips of fluorescently labeled mitochondria in U2OS cells.  In Lecture Notes in Computer Science, 363 - 372. ISBN: 978-3-319-23234-8. Genoa, Italy: Springer-Verlag.

2.	Santinha, Joao; Martins, Leonardo; Häkkinen, Antti; Lloyd-Price, Jason; Oliveira, Samuel; Gupta, Abhishekh; Annila, T; Mora, Andre; Ribeiro, Andre S; Fonseca, José M. 2015. iCellFusion – a Tool for Fusion of Time-lapsed Multimodal Microscopy images..  In Biomedical Image Analysis and Mining Techniques for Improved Health Outcomes, ed. Ahmad Taher Azar, 1 - 1. . Benha University, Egypt: IGI Global.

3.	Ribeiro, Andre S. 2013. How noisy is RNA production in Escherichia coli when seen in vivo, one event at a time.  In Recent Trends in Gene Expression, ed. SS Mandal, 13 - 46. . USA: Nova Science Publishers.

4.	Ballarini, P.; Mäkelä, Jarno; Ribeiro, Andre S. 2012. Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics.  In Computational Methods in Systems Biology, Lecture Notes in Computer Science 7605, 24 - 48. ISBN: 978-3-642-33635-5. Berlin, Heidelberg: Springer Berlin/Heidelberg.

5.	Potapov, Ilya; Mäkelä, Jarno; Yli-Harja, Olli; Ribeiro, Andre S. 2012. Sequence dependent properties of the expression dynamics of genes and gene networks.  In Computational Methods in Systems Biology, ed. David Gilbert and Monika Heiner, 307 - 321. ISBN: 978-3-642-33635-5. Berlin, Heidelberg: Springer Berlin Heidelberg .

6.	Ribeiro, Andre S; Lloyd-Price, Jason. 2011. Information Propagation in the Long-Term Behavior of Gene Regulatory Networks.  In Information Processing and Biological Systems, ed. Samuli NiiranenAndre Ribeiro, 195 - 217. ISBN: 978-3-642-19620-1. Berlin, Heidelberg: Springer Berlin Heidelberg.

7.	Ribeiro, Andre S. 2011. Delayed stochastic models of genetic switches. Noise, coupling, differentiation patterns and evolvability.  In Advances in Genetics Research, 150 - 176. . USA: Nova Science Publishers.

8.	Ribeiro, Andre S. 2010. Information Flow in Systems of Interacting Agents as a Function of Local and Global Topological Features.  In Computational Social Network Analysis, ed. Ajith AbrahamAboul-Ella HassanienVaclav Sná¿el, 155 - 187. ISBN: 978-1-84882-228-3. London: Springer London.

9.	Kesseli, Juha; Ribeiro, Andre S; Nykter, Matti. 2009. Measuring Information Propagation and Processing in Biological Systems.  In Open Information Management, ed. Samuli NiiranenJari Yli-HietanenArtur Lugmayr, 190 - 226. ISBN: 9781605662466. USA: IGI Global.

10.	Ribeiro, Andre S; Grefenstette, John J; Kauffman, Stuart A. 2009. Modeling Gene Regulatory Networks with Delayed Stochastic Dynamics.  In Handbook of Research on Computational Methodologies in Gene Regulatory Networks, ed. Sanjoy DasDoina CarageaStephen WelchWilliam H. Hsu, 198 - 218. ISBN: 9781605666853. USA: IGI Global.

11.	Ribeiro, Andre S. 2008. A Model of Genetic Networks with Delayed Stochastic Dynamics.  In Analysis of Microarray Data, ed. Frank Emmert-StreibMatthias Dehmer, 169 - 204. ISBN: 9783527622818. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA.

Artigos em revistas com arbitragem científica Papers in periodics with scientific refereeing

1.	Kislin, Mikhail; Sword, Jeremy; Fomitcheva, Ioulia V; Croom, Deborah; Pryazhnikov, Evgeny; Lihavainen, Eero; Toptunov, Dmytro; Rauvala, Heikki; Ribeiro, Andre S; Khiroug, Leonard; Kirov, Sergei A. 2017. "Reversible Disruption of Neuronal Mitochondria by Ischemic and Traumatic Injury Revealed by Quantitative Two-Photon Imaging in the Neocortex of Anesthetized Mice", The Journal of Neuroscience 37, 2: 333 - 348.

2.	Ribeiro, Andre S. 2016. "Delays as regulators of the dynamics of genetic circuits", Markov Processes and Related Fields 22, 3: 573 - 594.

3.	Zimmer, Christoph; Häkkinen, Antti; Ribeiro, Andre S. 2016. "Estimation of kinetic parameters of transcription from temporal single-RNA measurements", Mathematical Biosciences 271, 1: 146 - 153.

4.	Oliveira, Samuel M. D; Neeli-Venkata, Ramakanth; Goncalves, Nadia S. M; Santinha, João A; Martins, Leonardo; Tran, Huy; Mäkelä, Jarno; Gupta, Abhishekh; Barandas, Marilia; Häkkinen, Antti; Lloyd-Price, Jason; Fonseca, José M; Ribeiro, Andre S. 2016. " Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli ", Molecular Microbiology 99, 4: 686 - 699.

5.	Häkkinen, Antti; Ribeiro, Andre S. 2016. "Characterizing rate limiting steps in transcription from RNA production times in live cells", Bioinformatics 32, 9: 1346 - 1352.

6.	Neeli-Venkata, Ramakanth; Martikainen, Antti; Gupta, Abhishekh; Gonçalves, Nadia; Fonseca, Jose; Ribeiro, Andre S; DiRita, V. J. 2016. "Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli", Journal of Bacteriology 198, 6: 898 - 906.

7.	Lloyd-Price, Jason; Startceva, Sofia; Kandavalli, Vinodh; Chandraseelan, Jerome G; Goncalves, Nadia; Oliveira, Samuel M. D; Häkkinen, Antti; Ribeiro, Andre S. 2016. " Dissecting the stochastic transcription initiation process in live Escherichia coli ", DNA Research 23, 3: 203 - 214.

8.	Kandavalli, Vinodh K; Tran, Huy; Ribeiro, Andre S. 2016. "Effects of s factor competition are promoter initiation kinetics dependent", Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1859, 10: 1281 - 1288.

9.	Oliveira, Samuel M. D; Häkkinen, Antti; Lloyd-Price, Jason; Tran, Huy; Kandavalli, Vinodh; Ribeiro, Andre S; Przytycka, Teresa M. 2016. "Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements", PLOS Computational Biology 12, 10: e1005174 - e1005174.

10.	Neeli-Venkata, Ramakanth; Startceva, Sofia; Annila, Teppo; Ribeiro, Andre S. 2016. "Polar Localization of the Serine Chemoreceptor of Escherichia coli Is Nucleoid Exclusion-Dependent", Biophysical Journal 111, 11: 2512 - 2522.

11.	Gupta, Abhishekh; Lloyd-Price, Jason; Ribeiro, Andre S. 2015. "In silico analysis of division times of Escherichia coli populations as a function of the partitioning scheme of non-functional proteins", In Silico Biology 12, 1,2: 9 - 21.

12.	Hakkinen, A.; Ribeiro, A. S. 2015. "Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data", Bioinformatics 31, 1: 69 - 75.

13.	Oliveira, Samuel M. D; Chandraseelan, Jerome G; Häkkinen, Antti; Goncalves, Nadia S. M; Yli-Harja, Olli; Startceva, Sofia; Ribeiro, Andre S. 2015. "Single-cell kinetics of a repressilator when implemented in a single-copy plasmid", Mol. BioSyst. 11, 7: 1939 - 1945.

14.	Lihavainen, E.; KISLIN, M.; TOPTUNOV, D.; KHIROUG, L.; RIBEIRO, A.S.. 2015. "Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue", Journal of Microscopy 260, 3: 338 - 351.

15.	Tran, Huy; Oliveira, Samuel M. D; Goncalves, Nadia; Ribeiro, Andre S. 2015. "Kinetics of the cellular intake of a gene expression inducer at high concentrations", Mol. BioSyst. 11, 9: 2579 - 2587.

16.	Hakkinen, A.; KANDHAVELU, M.; Garasto, S.; Ribeiro, A. S. 2014. "Estimation of fluorescence-tagged RNA numbers from spot intensities", Bioinformatics 30, 8: 1146 - 1153.

17.	Gupta, Abhishekh; Lloyd-Price, Jason; Neeli-Venkata, Ramakanth; Oliveira, Samuel M.D.; Ribeiro, Andre S.. 2014. "In Vivo Kinetics of Segregation and Polar Retention of MS2-GFP-RNA Complexes in Escherichia coli", Biophysical Journal 106, 9: 1928 - 1937.

18.	Lloyd-Price, Jason; Tran, Huy; Ribeiro, Andre S. 2014. "Dynamics of small genetic circuits subject to stochastic partitioning in cell division", Journal of Theoretical Biology 356, 1: 11 - 19.

19.	Fukuoh, A.; Cannino, G.; Gerards, M.; Buckley, S.; Kazancioglu, S.; Scialo, F.; Lihavainen, E.; Ribeiro, A.; Dufour, E.; Jacobs, H. T. 2014. "Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase", Molecular Systems Biology 10, 6: 734 - 734.

20.	Muthukrishnan, Anantha-Barathi; Martikainen, Antti; Neeli-Venkata, Ramakanth; Ribeiro, Andre S; Cirino, Patrick C. 2014. "In Vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli Cells", PLoS ONE 9, 9: e109005 - e109005.

21.	Ribeiro, Andre S; Eales, Brenda A; Lloyd-Price, Jason; Biddle, Fred G. 2014. "Predictability and randomness of paw choices are critical elements in the behavioural plasticity of mouse paw preference", Animal Behaviour 98, 1: 167 - 176.

22.	Ribeiro, Andre S. 2013. "Kinetics of gene expression in live bacteria: from models to measurements, and back again", Canadian Journal of Chemistry 91, 7: 487 - 494.

23.	Ribeiro, A. S; Eales, Brenda; Biddle, Fred G. 2013. "Short-term and long-term memory deficits in handedness learning in mice with absent corpus callosum and reduced hippocampal commissure", Behavioural Brain Research, 245: 145 - 151.

24.	Mäkelä, Jarno; Kandhavelu, Meenakshisundaram; Oliveira, Samuel; Chandraseelan, Jerome; Lloyd-Price, Jason; Peltonen, J.; Yli-Harja, Olli; Ribeiro, A. S. 2013. "In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter", Nucleic Acids Research 41, 13: 6544 - 6552.

25.	Häkkinen, Antti; Muthukrishnan, Anantha B; Mora, Andre; Fonseca, José M; Ribeiro, Andre S. 2013. "CellAging: A tool to study segregation and partitioning in division in cell lineages of Escherichia coli", Bioinformatics  29, 13: 1708 - 1709.

26.	Häkkinen, Antti; Tran, Huy; Ingalls, B.; Ribeiro, A. S. 2013. "Effects of multimerization on the temporal variability of protein complex abundance", BMC Systems Biology 7, S1:S3: 1 - 13.

27.	Chowdhury, Sharif; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S. 2013. "Cell Segmentation by Multi-resolution Analysis and Maximum Likelihood Estimation (MAMLE)", BMC Bioinformatics  10, S10:S8: 1 - 13.

28.	Häkkinen, Antti; Tran, Huy; Yli-Harja, Olli; Ribeiro, Andre S. 2013. "Effects of Rate-Limiting Steps in Transcription Initiation on Genetic Filter Motifs", PLoS ONE 8, 8: 1 - 10.

29.	Lloyd-Price, Jason; Ribeiro, Andre S. 2013. "Bistability in a stochastic RNA-mediated gene network", Physical Review E 88, 3: 0327141 - 0327148.

30.	Chandraseelan, Jerome; Oliveira, Samuel; Potapov, Ilya; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Ribeiro, Andre S. 2013. "Temperature dependence of the LacI-TetR-CI Repressilator", Molecular BioSystems 9, 12: 3117 - 3123.

31.	CHOWDHURY, S.; KANDHAVELU, M.; YLI-HARJA, O.; RIBEIRO, A.S.. 2012. "An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy", Journal of Microscopy 245, 3: 265 - 275.

32.	Lloyd-Price, Jason; Lehtivaara, Maria; Kandhavelu, Meenakshisundaram; Chowdhury, Sharif; Muthukrishnan, Anantha-Barathi; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Probabilistic RNA partitioning generates transient increases in the normalized variance of RNA numbers in synchronized populations of Escherichia coli", Molecular BioSystems 8, 2: 565 - 565.

33.	Kandhavelu, Meenakshisundaram; Lihavainen, Eero; Muthukrishnan, Anantha B; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter", Biosystems 107, 3: 129 - 134.

34.	Lloyd-Price, J.; Hakkinen, A.; Kandhavelu, M.; Marques, I. J; Chowdhury, S.; Lihavainen, E.; Yli-Harja, O.; Ribeiro, A. S. 2012. "Asymmetric disposal of individual protein aggregates in Escherichia coli, one aggregate at a time", Journal of Bacteriology, 1: 1 - 10.

35.	Lihavainen, E.; Makela, J.; Spelbrink, J. N; Ribeiro, A. S. 2012. "Mytoe: automatic analysis of mitochondrial dynamics", Bioinformatics 28, 7: 1050 - 1051.

36.	Martins, Leonardo; Mäkelä, Jarno; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Fonseca, José M; Ribeiro, Andre S. 2012. "Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time", Journal of Theoretical Biology 301, 1: 83 - 94.

37.	Häkkinen, Antti; Ribeiro, Andre S. 2012. "Evolving kinetics of gene expression in stochastic environments", Computational Biology and Chemistry 37, 1: 11 - 16.

38.	Kandhavelu, M; Häkkinen, A; Yli-Harja, O; Ribeiro, A S. 2012. "Single-molecule dynamics of transcription of the lar promoter", Physical Biology 9, 2: 026004 - 026004.

39.	Muthukrishnan, A.-B.; Kandhavelu, M.; Lloyd-Price, J.; Kudasov, F.; Chowdhury, S.; Yli-Harja, O.; Ribeiro, A. S. 2012. "Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells", Nucleic Acids Research 40, 17: 8472 - 8483.

40.	Kandhavelu, Meenakshisundaram; Paturu, L.; Mizar, A.; Mahmudov, K.T.; Kopylovich, M. N; Karp, M.; Yli-Harja, Olli; Pombeiro, A. J. L; Ribeiro, A. S. 2012. "Synthesis, characterization and antimicrobial activity of arylhydrazones of methylene active compounds", Pharmaceutical Chemistry Journal  46, 3: 157 - 164.

41.	Emmert-Streib, Frank; Häkkinen, Antti; Ribeiro, A. S. 2012. "Detecting sequence dependent transcriptional pauses from RNA and protein number time series", BMC Bioinformatics  13, 152: 1 - 13.

42.	Lloyd-Price, Jason; Gupta, Abhishekh; Ribeiro, A. S. 2012. "Robustness and Information Propagation in Attractors of Random Boolean Networks", PLoS ONE  7, 7: 1 - 6.

43.	Potapov, Ilya; Mäkelä, Jarno; Ribeiro, A. S. 2012. "Effects of Codon Sequence on the Dynamics of Genetic Networks", Journal of Theoretical Biology, 315: 17 - 25.

44.	Lloyd-Price, Jason; Gupta, Abhishekh; Ribeiro, A. S. 2012. "SGNS2: A Compartmentalized Stochastic Chemical Kinetics Simulator for Dynamic Cell Populations", Bioinformatics 28, 22: 3004 - 3005.

45.	Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Gupta, Abhishekh; Muthukrishnan, Anantha-Barathi; Yli-Harja, Olli; Ribeiro, A. S. 2012. "Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter", FEBS Letters 586, 21: 3870 - 3875.

46.	Ribeiro, Andre S; Häkkinen, Antti; Lloyd-Price, Jason. 2012. "Effects of gene length on the dynamics of gene expression", Computational Biology and Chemistry, 41: 1 - 9.

47.	Ribeiro, Andre S; Eales, Brenda; Biddle, Fred G. 2011. "Learning of paw preference in mice is strain dependent, gradual and based on short-term memory of previous reaches", Animal Behavior 81, 1: 249 - 257.

48.	Mannerström, Henrik; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Inference of kinetic parameters of delayed stochastic models of gene expression using a Markov chain approximation", EURASIP Journal on Bioinformatics and Systems Biology, 2011: 572876 - 572876.

49.	Ribeiro, Andre S; Lloyd-Price, Jason; Chowdhury, Sharif; Yli-Harja, Olli. 2011. "Diversity of temporal correlations between genes in models of noisy and noiseless gene networks", BioSystems , 104: 136 - 144.

50.	Ribeiro, Andre S; Häkkinen, Antti. 2011. "Probing Stochastic Phenotype Switching as a Survival Strategy in Fluctuating Environments", International Journal of Computational Intelligence in Control 31, 1: 9 - 15.

51.	Mäkelä, Jarno; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Stochastic sequence-level model of coupled transcription and translation in prokaryotes", BMC Bioinformatics 2011, 12: 121 - 121.

52.	Häkkinen, Antti; Healy, Shannon; Jacobs, Howard T; Ribeiro, Andre S. 2011. "Genome wide study of NF-Y type CCAAT boxes in uni- and bi-directional promoters in human and mouse", Journal of Theoretical Biology  281, 1: 74 - 83.

53.	Smolander, Olli-Pekka; Kandhavelu, Meenakshisundaram; Mannerström, Henrik; Lihavainen, Eero; Kalaichelvan, S.; Healy, Shannon; Yli-Harja, Olli; Karp, Matti; Ribeiro, Andre S. 2011. "Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter. ", BMC Molecular Biology  2011, 12: 21 - 21.

54.	Potapov, Ilya; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Dynamics of a genetic toggle switch at the nucleotide and codon levels", Physical Review E 84, 3: 031903 - 031903.

55.	Mäkelä, Jarno; Huttunen, Heikki; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli", Bioinformatics, 27: 2714 - 2720.

56.	Kandhavelu, Meenakshisundaram; Mannerström, Henrik; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "In vivo kinetics of transcription initiation of the lar promoter in Escherichia coli. Evidence for a sequential mechanism with two rate limiting steps", BMC Systems Biology  2011, 5: 149 - 149.

57.	Häkkinen, Antti; Biddle, Fred G; Smolander, Olli-Pekka; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Evolutionary Dynamics of a Population of Cells with a Toxin Suppressor Gene", Lecture Notes in Computer Science, 6575: 1 - 12.

58.	Ribeiro, Andre S. 2010. "Stochastic and delayed stochastic models of gene expression and regulation", Mathematical Biosciences  223, 1: 1 - 11.

59.	Ribeiro, Andre S; Häkkinen, Antti; Mannerström, Henrik; Lloyd-Price, Jason; Yli-Harja, Olli. 2010. "Effects of the promoter open complex formation on gene expression dynamics", Physical Review E 81, 1: 011912 - 011912.

60.	Ribeiro, Andre S; Lloyd-Price, Jason; Eales, Brenda; Biddle, Fred G. 2010. "Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse", Adaptive Behavior  18, 2: 116 - 131.

61.	Rajala, Tiina; Häkkinen, Antti; Healy, Shannon; Yli-Harja, Olli; Ribeiro, Andre S. 2010. "Effects of Transcriptional Pausing on Gene Expression Dynamics", PLoS Computational Biology  6, 3: 1000704 - 1000704.

62.	Ribeiro, Andre S; Häkkinen, Antti; Healy, Shannon; Yli-Harja, Olli. 2010. "Dynamical effects of transcriptional pause-prone sites", Computational Biology and Chemistry  34, 3: 143 - 148.

63.	Chowdhury, Sharif; Lloyd-Price, Jason; Smolander, Olli-Pekka; Baici, Wayne; Hughes, Tim R; Yli-Harja, Olli; Chua, Gordon; Ribeiro, Andre S. 2010. "Information propagation within the Genetic Network of Saccharomyces cerevisiae", BMC Systems Biology  2010, 4: 143 - 143.

64.	Ribeiro, Andre S; Smolander, Olli-Pekka; Rajala, Tiina; Häkkinen, Antti; Yli-Harja, Olli. 2009. "Delayed stochastic model of transcription at the single nucleotide level", Journal of Computational Biology  16, 4: 539 - 5553.

65.	Zanotto, Ernesto; Häkkinen, Antti; Teku, Gabriel; Shen, Bairong; Ribeiro, Andre S; Jacobs, Howard T. 2009. "NF-Y influences directionality of transcription from the bidirectional Mrps12/Sarsm promoter in both mouse and human cells", Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1789, 5: 432 - 442.

66.	Ribeiro, Andre S; Dai, Xiaofeng; Yli-Harja, Olli. 2009. "Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch", Journal of Theoretical Biology 260, 1: 66 - 76.

67.	Smolander, Olli-Pekka; Ribeiro, Andre S; Yli-Harja, Olli; Karp, Matti. 2009. "Identification of ß-lactam antibiotics using bioluminescent Escherichia coli and a support vector machine classifier algorithm", Sensors and Actuators B: Chemical  141, 2: 604 - 609.

68.	Ribeiro, Andre S; Dai, Xiaofeng; Yli-Harja, Olli. 2009. "Determining the noisy attractors of a delayed stochastic Toggle Switch from multiple data sources", Bioinformatics  25, 8: 2362 - 2368.

69.	Dai, Xiaofeng; Healy, Shannon; Yli-Harja, Olli; Ribeiro, Andre S. 2009. "Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a Toggle Switch", Journal of Theoretical Biology  261, 3: 441 - 448.

70.	Ribeiro, Andre S; Kauffman, Stuart A; Lloyd-Price, Jason; Samuelsson, Bjorn; Socolar, Joshua E. 2008. "Mutual Information in Random Boolean models of regulatory networks", Physical Review E 77, 1: 011901 - 011901.

71.	Ribeiro, Andre S; Lloyd-Price, Jason; Kesseli, Juha; Häkkinen, Antti; Yli-Harja, Olli. 2008. "Quantifying Local Structure Effects in Network Dynamics", Physical Review E  78, 5: 056108 - 056108.

72.	Ribeiro, Andre S. 2008. "Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments", Physical Review E 78, 6: 061902 - 061902.

73.	Zhu, Rui; Ribeiro, Andre S; Salahub, Dennis; Kauffman, Stuart A. 2007. "Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models", Journal of Theoretical Biology 246, 4: 725 - 745.

74.	Ribeiro, Andre S; Lloyd-Price, Jason. 2007. "SGN Sim, a Stochastic Genetic Networks Simulator", Bioinformatics 23, 6: 777 - 779.

75.	Ribeiro, Andre S; Kauffman, Stuart A. 2007. "Noisy Attractors and Ergodic Sets in Models of Gene Regulatory Networks", Journal of Theoretical Biology 247, 4: 743 - 755.

76.	Ribeiro, Andre S. 2007. "Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions", Physical Review E 75, 6: 061903 - 061903.

77.	Ribeiro, Andre S; Charlebois, Daniel; Lloyd-Price, Jason. 2007. "CellLine, a stochastic cell lineage simulator", Bioinformatics 23, 24: 3409 - 3411.

78.	Ribeiro, Andre S. 2007. "Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks", Physical Review E 76, 5: 051915 - 051915.

79.	Charlebois, Daniel; Ribeiro, Andre S; Lehmussola, Antti; Lloyd-Price, Jason; Yli-Harja, Olli; Kauffman, Stuart A. 2007. "Effects of microarray noise on inference efficiency of a stochastics model of gene networks", WSEAS Transactions on Biology and Biomedicine  4, 2: 15 - 21.

80.	Ribeiro, Andre S; Almeida, Miguel. 2006. "A proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimize Efficiency and Minimize Costs", Acta Astronautica  59, 8: 1086 - 1092.

81.	Ribeiro, Andre S; Zhu, Rui; Kauffman, Stuart A. 2006. "A General Model for Gene Regulatory Networks with Stochastic Dynamics", WSEAS Transactions on Biology and Biomedicine 3, 3: 261 - 264.

82.	Ribeiro, Andre S; Este, Robert E; Lloyd-Price, Jason; Kauffman, Stuart A. 2006. "Measuring Information Propagation and Retention in Boolean Networks and its Implications to a Model of Human Organizations", WSEAS Transactions on Systems  12, 5: 2935 - 2941.

83.	Ribeiro, Andre S; Zhu, Rui; Salahub, Dennis; Kauffman, Stuart A. 2006. "A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics", Journal of Computational Biology 13, 9: 1630 - 1639.

84.	Ribeiro, Andre S; Lind, Pedro G. 2005. "Effects of lattice structure in the dynamics of coupled elements", Physica Scripta  118, 1: 165 - 167.

Trabalhos completos/resumidos em eventos com arbitragem científica Papers in conference proceedings with scientific refereeing

1.	Zare, M; Neeli-Venkata, Ramakanth; Peltonen, S; Ruotsalainen, U; Ribeiro, Andre S. 2017. "Automatic classification of Z-ring formation stages at the single cell level in Escherichia coli by Machine Learning", Trabalho apresentado em 4th International Conference on Bioimaging (BIOIMAGING 2017), In Proceedings of the 4th International Conference on Bioimaging (BIOIMAGING 2017), Porto.

2.	Bahrudeen, MNM; Ribeiro, Andre S. 2017. "Effects of extrinsic noise are promoter kinetics dependent", Trabalho apresentado em 9th International Conference on Bioinformatics and Biomedical Technology (ICBBT 2017), In Proceedings of the 9th International Conference on Bioinformatics and Biomedical Technology (ICBBT 2017), Lisbon.

3.	Startceva, Sofia; Chandraseelan, Jerome G; Visa, Ari; Ribeiro, Andre S. 2016. "Quantitative Estimation of Long-living Fluorescent Molecules from Temporal Fluorescence Intensity Data Corrupted by Nonzero-mean Noise", Trabalho apresentado em 9th International Conference on Bio-inspired Systems and Signal Processing, In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy.

4.	Annila, Teppo; Neeli-Venkata, Ramakanth; Ribeiro, Andre S. 2016. "Robustness to Sub-optimal Temperatures of the Processes of Tsr Cluster Formation and Positioning in Escherichia Coli", Trabalho apresentado em 7th International Conference on Bioinformatics Models, Methods and Algorithms, In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy.

5.	Goncalves, Nadia S. M; Martins, Leonardo; Tran, Huy; Oliveira, Samuel M. D; Neeli-Venkata, Ramakanth; Fonseca, José M; Ribeiro, Andre S. 2016. "In vivo single-molecule dynamics of transcription of the viral T7 Phi 10 promoter in Escherichia coli", Trabalho apresentado em 8th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO 2016), In Proceedings of the 8th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO 2016), Lisbon.

6.	Oliveira, Samuel M. D; Ribeiro, Andre S. 2016. "Using a synthetic probe to study the robustness of the segregation process of protein aggregates in Escherichia coli.", Trabalho apresentado em 8th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO 2016), In Proceedings of the 8th International Conference on Bioinformatics, Biocomputational Systems and Biotechnologies (BIOTECHNO 2016), Lisbon.

7.	Canelas, P; Martins, Leonardo; Mora, Andre; Ribeiro, Andre S; Fonseca, José M. 2016. "Development of an Image Generator Platform to Improve Cell Tracking Algorithms - Simulation of Objects of various Morphologies, Kinetics and Clustering", Trabalho apresentado em 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2016) , In Proceedings of the 6th International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2016), Lisbon.

8.	Goncalves, Nadia; Oliveira, Samuel M. D; Fonseca, José M; Ribeiro, Andre S. 2016. "Temperature Dependence of Leakiness of Transcription Repression Mechanisms of Escherichia coli", Trabalho apresentado em Proceedings of the 14th International Conference on Computational Methods in Systems Biology , In Proceedings of the 14th International Conference on Computational Methods in Systems Biology , Cambridge.

9.	Oliveira, Samuel M. D; Ribeiro, Andre S; Goncalves, Nadia. 2016. "Analysis of the temperature-dependence of leaky and activated transcription from the PlacO3O1 promoter in Escherichia coli.", Trabalho apresentado em International Conference on Systems Biology (ICSB 2016), In Proceedings of the International Conference on Systems Biology (ICSB 2016), Barcelona.

10.	Neeli-Venkata, Ramakanth; Startceva, Sofia; Annila, Teppo; Ribeiro, Andre S. 2016. "Polar Localization of the Serine Chemoreceptor Tsr involves a Nucleoid Exclusion phenomenon", Trabalho apresentado em International Conference on Systems Biology (ICSB 2016), In Proceedings of the International Conference on Systems Biology (ICSB 2016), Barcelona.

11.	KISLIN, M.; Sword, Jeremy; Croom, Deborah; Pryazhnikov, Evgeny; Lihavainen, E; TOPTUNOV, D.; Rauvala, Heikki; Ribeiro, Andre S; Kirov, SA; Khiroug, Leonard. 2016. "Reversible disruption of neuronal mitochondria by ischemic and traumatic injury revealed by quantitative two-photon imaging in the neocortex of anesthetized mice", Trabalho apresentado em 46th annual meeting of the Society for Neuroscience (Neuroscience 2016), In Proceedings of the 46th annual meeting of the Society for Neuroscience (Neuroscience 2016), San Diego.

12.	Oliveira, Samuel M. D; Goncalves, Nadia; Fonseca, José M; Ribeiro, Andre S. 2016. "Modeling transcription regulation from in vivo empirical data at the single molecule level", Trabalho apresentado em Portuguese Meting in Biomathematics, In Proceedings of the Portuguese Meting in Biomathematics, Beira Interior.

13.	Chandraseelan, Jerome; Oliveira, Samuel; Häkkinen, Antti; Startceva, Sofia; Ribeiro, Andre S. 2015. "Synchrony between genetic repressilators in sister cells in different temperatures", Trabalho apresentado em International Conference on Computational and Molecular Systems Biology , In Proceedings of the International Conference on Computational and Molecular Systems Biology (ICCMSB 2015), Zurich.

14.	Santinha, J; Goncalves, N; Mora, Andre; Ribeiro, Andre S; Fonseca, José M. 2015. "Detection and Segmentation of nucleoids based on Gradient Path Labelling", Trabalho apresentado em 2nd International Conference on Biomedical and Pharmaceutical Engineering, In 2nd International Conference on Biomedical and Pharmaceutical Engineering, Warsaw.

15.	Santinha, J; Goncalves, N; Mora, Andre; Ribeiro, Andre S; Fonseca, José M. 2015. "A cell cycle phase-independent nucleoid segmentation method", Trabalho apresentado em 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), In 4th Portuguese Meeting on Bioengineering, Porto.

16.	Martins, L; Ribeiro, Andre S; Fonseca, José M. 2015. "‘MISIMBA’ – A simulator of synthetic time-lapse microscopy images of Escherichia coli.", Trabalho apresentado em 2015 IEEE 4th Portuguese Meeting on Bioengineering (ENBENG), In 4th Portuguese Meeting on Bioengineering, Porto.

17.	Lihavainen, Eero; Mäkelä, Jarno; Spelbrink, J. N; Ribeiro, Andre S. 2015. "Detecting and tracking the tips of fluorescently labeled mitochondria in U2OS cells", Trabalho apresentado em 18th International Conference on Image Analysis and Processing, ICIAP 2015, In 18th International Conference on Image Analysis and Processing, Genova.

18.	Tran, Huy; Ribeiro, Andre S. 2015. "An estimation method of the kinetic rates of transcription initiation by Es70 and Es38 from measurements of individual RNA productions", Trabalho apresentado em 3rd International Conference on Biological and Medical Sciences (ICBMS 2015) , In Proceedings of the 3rd International Conference on Biological and Medical Sciences (ICBMS 2015), Shanghai.

19.	Kandavalli, Vinodh K; Tran, Huy; Chandraseelan, Jerome G; Ribeiro, Andre S. 2015. "Promoter initiation kinetics determines its sensitivity to changes in s factor numbers in Escherichia coli", Trabalho apresentado em Congress of Microbiology and Biotechnology (MicroBiotech 15), In Proceedings of Congress of Microbiology and Biotechnology (MicroBiotech 15), Evora.

20.	Muthukrishnan, A.-B.; Ribeiro, Andre S. 2015. "Implications of in vivo single-molecule analysis for Bioprocess monitoring and control.", Trabalho apresentado em 3rd Annual conference of Bioprocessing, In Proceedings of the 3rd Annual conference of Bioprocessing, Madras.

21.	Martikainen, Antti; Venkata, Ramakanth N; Goncalves, N; Ribeiro, Andre S. 2014. "Effects of the nucleoid’s structural plasticity on the robustness of retention of unwanted protein aggregates at the cell poles in Escherichia coli", Trabalho apresentado em Lyon SysBio 2014, In Conference Proceedings of Lyon SysBio 2014, Lyon.

22.	Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Gupta, Abhishekh; Ribeiro, Andre S. 2012. "Probing the in vivo transcription initiation dynamics of unidirectional promoters at the single molecule level", Trabalho apresentado em IUBMB FEBS, From single molecules to Systems Biology, In IUBMB FEBS, From single molecules to Systems Biology, Sevilla.

23.	Muthukrishnan, Anantha-Barathi; Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Kudasov, Fedor; Chowdhury, S.; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Effect of temperature on the in vivo kinetics of transcription initiation by the tetA promoter in Escherichia coli", Trabalho apresentado em Proceedings of the Select Biosciences conference on Single cell Analysis Europe, In Proceedings of the Select Biosciences conference on Single cell Analysis Europe, Edinburgh.

24.	Lloyd-Price, Jason; Kandhavelu, Meenakshisundaram; Gupta, Abhishekh; Ribeiro, Andre S. 2012. "Transcription initiation at the lar promoter is a two-step stochastic process that allows independent regulation of noise and RNA mean levels", Trabalho apresentado em 2nd SMTDA2012 International Conference, In 2nd SMTDA2012, Chania.

25.	Gupta, Abhishekh; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Attractor robustness does not restrict information propagation in critical random Boolean networks", Trabalho apresentado em 9th International Workshop on Computational Systems Biology (WCSB 2012), In 9th International Workshop on Computational Systems Biology (WCSB 2012), Ulm.

26.	Oliveira, Samuel; Mäkelä, Jarno; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Single-Molecule Dynamics of the Bidirectional Arabinose Promoter", Trabalho apresentado em 9th International Workshop on Computational Systems Biology (WCSB 2012), In 9th International Workshop on Computational Systems Biology (WCSB 2012), Ulm.

27.	Tran, Huy; Häkkinen, Antti; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Effects of rate limiting steps in transcription initiation on the behavior of small genetic motifs", Trabalho apresentado em 9th International Workshop on Computational Systems Biology (WCSB 2012), In 9th International Workshop on Computational Systems Biology (WCSB 2012), Ulm.

28.	Ribeiro, Andre S; Lloyd-Price, Jason; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Marques, I. J; Chowdhury, Sharif; Lihavainen, Eero; Yli-Harja, Olli. 2012. "In vivo kinetics of asymmetric disposal of individual protein aggregates in E. coli, one aggregate at a time.", Trabalho apresentado em 9th International Workshop on Computational Systems Biology (WCSB 2012), In 9th International Workshop on Computational Systems Biology (WCSB 2012), Ulm.

29.	Martins, Leonardo; Mäkelä, Jarno; Häkkinen, Antti; Ribeiro, Andre S; Fonseca, José M. 2012. "Stochastic model of transcription initiation of closely spaced promoters in Escherichia coli", Trabalho apresentado em CIBB - Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, In CIBB - Ninth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Houston.

30.	Queimadelas, C.; Rodrigues, J.; Muthukrishnan, A.-B.; Mora, Andre; Ribeiro, Andre S; Fonseca, José M. 2012. "Protein measurements from combined DIC/Fluorescence images", Trabalho apresentado em 5th Int. Conf. MEDSIP, Advances in Medical Signal and Information Processing,, In 5th Int. Conf. MEDSIP, Advances in Medical Signal and Information Processing,, Liverpool.

31.	Häkkinen, Antti; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Evolving the kinetics of single gene expression", Trabalho apresentado em SocBiN Bioinformatics 2011, In SocBiN Bioinformatics 2011, Helsinki.

32.	Potapov, Ilya; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Dynamics of the genetic toggle switch at single nucleotide and codon levels", Trabalho apresentado em 8th International Workshop on Computational Systems Biology , In 8th International Workshop on Computational Systems Biology , Zurich.

33.	Smolander, Olli-Pekka; Kandhavelu, Meenakshisundaram; Mannerström, Henrik; Lihavainen, Eero; Kalaichelvan, S.; Healy, Shannon; Yli-Harja, Olli; Karp, Matti; Ribeiro, Andre S. 2011. "Dynamics of gene expression under tetracycline inducible promoters", Trabalho apresentado em 8th International Workshop on Computational Systems Biology, In 8th International Workshop on Computational Systems Biology, Zurich.

34.	Chowdhury, Sharif; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "A new autofocus algorithm for time-lapse imaging in confocal microscope", Trabalho apresentado em 8th International Workshop on Computational Systems Biology, In 8th International Workshop on Computational Systems Biology, Zurich.

35.	Lihavainen, Eero; Mäkelä, Jarno; Yli-Harja, Olli; Jacobs, Howard T; Spelbrink, J. N; Ribeiro, Andre S. 2011. "A method for quantitative analysis of mitochondrial motion and morphology from confocal microscope images", Trabalho apresentado em 8th International Workshop on Computational Systems Biology , In 8th International Workshop on Computational Systems Biology , Zurich.

36.	Lloyd-Price, Jason; Gupta, Abhishekh; Mäkelä, Jarno; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Efficient stochastic simulation of dynamically compartmentalized chemical reaction systems", Trabalho apresentado em ICIAM 2011, In ICIAM 2011, Vancouver.

37.	Kandhavelu, Meenakshisundaram; Mannerström, Henrik; Lihavainen, Eero; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Detection of Mg2+ regulated transcription events by single-molecule imaging in living cells", Trabalho apresentado em EMBO conference on Intracellular RNA Localization and localized Translation, In EMBO conference on Intracellular RNA Localization and localized Translation, Barga.

38.	Havela, Rikka; Lihavainen, Eero; Mäkelä, Jarno; Spelbrink, J. N; Jacobs, Howard T; Ribeiro, Andre S. 2011. "Using Automated Analysis of the Mithocondrial Structure for an Objective Assessment of Phenotype Abnormalities", Trabalho apresentado em SocBiN 2011, In SocBiN 2011, Helsinki.

39.	Muthukrishnan, Anantha-Barathi; Kandhavelu, Meenakshisundaram; Lihavainen, Eero; Chowdhury, Sharif; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Dynamics of transcription controlled by tetracycline inducible promoter in Escherichia coli.", Trabalho apresentado em Functional Genomics and Systems Biology 2011, In Functional Genomics and Systems Biology 2011, Cambridge.

40.	Gupta, Abhishekh; Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Häkkinen, Antti; Yli-Harja, Olli; Ribeiro, Andre S. 2011. "Mechanisms of control of the in vivo expression of the lar promoter in Escherichia coli", Trabalho apresentado em Biomeditech Research Day, In Biomeditech Research Day, Tampere.

41.	Ribeiro, Andre S; Häkkinen, Antti; Healy, Shannon; Rajala, Tiina; Yli-Harja, Olli. 2010. "Dynamical effects of transcriptional pause sites", Trabalho apresentado em Seventh International Workshop on Computational Systems Biology, In Seventh International Workshop on Computational Systems Biology, Luxembourg.

42.	Smolander, Olli-Pekka; Karp, Matti; Yli-Harja, Olli; Ribeiro, Andre S. 2010. "Characterizing the activity of a gene driven by a Tet-promoter at the population and at the single cell levels", Trabalho apresentado em Seventh International Workshop on Computational Systems Biology, In Seventh International Workshop on Computational Systems Biology, Luxembourg.

43.	Lloyd-Price, Jason; Mäkelä, Jarno; Yli-Harja, Olli; Ribeiro, Andre S. 2010. "Detailed model of transcription and translation at the single nucleotide level", Trabalho apresentado em Seventh International Workshop on Computational Systems Biology, In Seventh International Workshop on Computational Systems Biology, Luxembourg.

44.	Kandhavelu, Meenakshisundaram; Mannerström, Henrik; Yli-Harja, Olli; Ribeiro, Andre S. 2010. "Emulation of the Delayed Stochastic Simulation Algorithm with higher order Markov Chains", Trabalho apresentado em Seventh International Workshop on Computational Systems Biology, In Seventh International Workshop on Computational Systems Biology, Luxembourg.

45.	Kandhavelu, Meenakshisundaram; Lihavainen, Eero; Healy, Shannon; Lloyd-Price, Jason; Chowdhury, Sharif; Häkkinen, Antti; Yli-Harja, Olli; Ribeiro, Andre S. 2010. "Riboswitch is a regulator of the noise in mRNA levels", Trabalho apresentado em Current Opinion in Cellular Host-Pathogen Interactions , In Current Opinion in Cellular Host-Pathogen Interactions , Holland.

46.	Rajala, Tiina; Häkkinen, Antti; Smolander, Olli-Pekka; Yli-Harja, Olli; Ribeiro, Andre S. 2009. "Effect of Pauses on Transcriptional Noise", Trabalho apresentado em BioSysBio 2009, Synthetic Biology, Systems Biology and Bioinformatics, In BioSysBio 2009, Synthetic Biology, Systems Biology and Bioinformatics, Cambridge.

47.	Smolander, Olli-Pekka; Karp, Matti; Yli-Harja, Olli; Ribeiro, Andre S. 2009. "Stochastic model of bacterial bioluminescence at the single cell, single molecule level", Trabalho apresentado em Sixth International Workshop on Computational Systems Biology, In Sixth International Workshop on Computational Systems Biology, Aarhus .

48.	Häkkinen, Antti; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2009. "Effects of transcriptional time delays on gene expression dynamics", Trabalho apresentado em Sixth International Workshop on Computational Systems Biology, In Sixth International Workshop on Computational Systems Biology, Aarhus.

49.	Socolar, Joshua E; Ribeiro, Andre S; Samuelsson, Bjorn; Lloyd-Price, Jason; Kauffman, Stuart A. 2008. "Mutual Information in Random Boolean models of regulatory networks", Trabalho apresentado em APS March Meeting, In APS March Meeting, New Orleans.

50.	Ribeiro, Andre S; Grefenstette, J.J.; Cloud, Daniel; Häkkinen, Antti; Rajala, Tiina; Yli-Harja, Olli. 2008. "Selective Advantages of Stochastic Phenotypic determination in unpredictable Environments", Trabalho apresentado em Fifth International Workshop on Computational Systems Biology, WCSB 2008, In Fifth International Workshop on Computational Systems Biology, Leipzig.

51.	Emmert-Streib, Frank; Ribeiro, Andre S. 2008. "Optimize Observational Time Points to Maximize the Inferability of Gene Networks", Trabalho apresentado em ICANN, 18th International Conference on Artificial Neural Networks, In 18th International Conference on Artificial Neural Networks, Prague.

52.	Männinen, T.; Ribeiro, Andre S; Lloyd-Price, Jason; Linne, M-L; Ruohonen, K; Yli-Harja, Olli; Kauffman, Stuart A. 2007. "Reverse Engineering of Firefly Luciferase Pathway Model", Trabalho apresentado em 5th IEEE International Workshop on Genomic Signal Processing and Statistics , In 5th IEEE International Workshop on Genomic Signal Processing and Statistics , Tuusula.

53.	Charlebois, Daniel; Ribeiro, Andre S; Lehmussola, Antti; Lloyd-Price, Jason; Kauffman, Stuart A; Yli-Harja, Olli. 2007. "Effects of microarray noise on inference capability from time series of gene expression of a stochastic model of gene networks", Trabalho apresentado em 7th Int. Conf. Canadian Proteomics Initiative, In 7th Int. Conf. Canadian Proteomics Initiative, Ottawa.

54.	Ribeiro, Andre S; Lehmussola, Antti; Lloyd-Price, Jason; Kauffman, Stuart A; Yli-Harja, Olli; Charlebois, Daniel; Chan, William; Bratland, Murray. 2007. "Two noise models’ effects on IADGRN’s inference of stochastic gene network models from simulated noisy microarray data", Trabalho apresentado em 6th Annual Conference on Computational Systems Bioinformatics, In 6th Annual Conference on Computational Systems Bioinformatics, San Diego.

55.	Ribeiro, Andre S; Zhu, Rui; Kauffman, Stuart A. 2006. "A General Model for Gene Regulatory Networks with Stochastic Dynamics", Trabalho apresentado em WSEAS International Conference on Mathematical Biology and Ecology , In Proceedings of the WSEAS International Conference on Mathematical Biology and Ecology , Miami.

56.	Ribeiro, Andre S; Charlebois, Daniel; Lloyd-Price, Jason; Kauffman, Stuart A. 2006. "IADGRN: Inferring gene regulatory networks from time series of genes activity. Increasing the scope of efficiency to more general interaction functions between genes and more complex time series", Trabalho apresentado em 6th Int. Conference of the Canadian Proteomics Initiative,, In Proceedings of the 6th Int. Conference of the Canadian Proteomics Initiative, Edmonton.

57.	Ribeiro, Andre S; Lloyd-Price, Jason; Chan, William; Bratland, Murray; Zhu, Rui; Andrecut, Mircea; Este, Robert E; Kauffman, Stuart A. 2006. "Unraveling the Gene Regulatory Network: Boolean Modeling and inferring, Stochastic Modeling, Spatial Modeling, Searching for attractors and Information propagation", Trabalho apresentado em iCORE 2006 Banff Summit, In iCORE 2006 Banff Summit Proceedings, Banff.

58.	Ribeiro, Andre S; Este, Robert E; Kauffman, Stuart A. 2006. "A Measure of Efficiency of Orientation Systems in Building Structures", Trabalho apresentado em 1st Iberian Conference on Information Systems and Technologies, In Proceedings of the 1st Iberian Conference on Information Systems and Technologies, Esposende.

59.	Ribeiro, Andre S; Kauffman, Stuart A. 2006. "Modeling Strategies of Gene Regulatory Networks", Trabalho apresentado em IBI / IBM Systems Biology Workshop, In IBI / IBM Systems Biology Workshop, New York.

60.	Ribeiro, Andre S; Este, Robert E; Lloyd-Price, Jason; Kauffman, Stuart A. 2006. "Measuring Information Propagation and Retention in Boolean Networks and its Implications to a Model of Human Organizations", Trabalho apresentado em 6th WSEAS Int. Conf. on Simulation, Modeling and Optimization, In 6th WSEAS Int. Conf. on Simulation, Modeling and Optimization, Lisbon.

61.	Ribeiro, Andre S; Lloyd-Price, Jason; Bratland, Murray; Chan, William; Noskov, Serguei; Charlebois, Daniel; Kauffman, Stuart A. 2006. "Models of Gene Regulatory Networks", Trabalho apresentado em Progress in Sys. Biology, In Progress in Sys. Biology, Ottawa.

62.	Real, Eduardo C; Ribeiro, Andre S; Andre, Sonia; Batel, S.; Lisboa, C.; Rosa, Carlos. 2005. "Pre-design of signage and orientation systems in Portuguese hospitals", Trabalho apresentado em 5th International Space Syntax Symposium, In Proceedings of the 5th International Space Syntax Symposium, Delft.

63.	Kauffman, Stuart A; Ribeiro, Andre S; Lloyd-Price, Jason. 2005. "Inferring Dynamical Gene Regulatory Networks Subject to Noise", Trabalho apresentado em Third Annual Rocky Mountain Regional Bioinformatics Meeting, In Proceedings of the Third Annual Rocky Mountain Regional Bioinformatics Meeting, Aspen.

64.	Ribeiro, Andre S. 2003. "Is Extra-terrestrial intelligence possible? An approach using complex systems theory on the computation of the probability for the emergence of intelligence", Trabalho apresentado em Workshop on Soft Computing and Complex Systems, In Proceedings of Workshop on Soft Computing and Complex Systems, Coimbra.

65.	Andre, Sonia; Real, Eduardo C; Ribeiro, Andre S; Rosa, Carlos; Simoes, Vitor. 2003. "Interdisciplinary analysis of Sign Systems and Guidance Systems in Hospitals", Trabalho apresentado em 4th Inter. Space Syntax Symp., In Proceedings of the 4th Inter. Space Syntax Symp., London.

66.	Ribeiro, Andre S; Almeida, Miguel. 2003. "A proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimize Efficiency and Minimize Costs", Trabalho apresentado em 5th IAA Int. Conf. Low-Cost Planetary Missions, In Proceedings of 5th IAA Int. Conf. Low-Cost Planetary Missions, Noordwijk.

67.	Ribeiro, Andre S; Lind, Pedro G. 2003. "Geometry Effects on synchronization between Coupled Elements", Trabalho apresentado em 1st Int. Meeting on Applied Physics, In Proceedings of the 1st Int. Meeting on Applied Physics, Badajoz.

68.	Rodrigues, Fernando C; Ribeiro, Andre S. 2002. "Calculation of Energy Consumption and Storage Capacity of Information in Complex Systems", Trabalho apresentado em XIII Conferencia Nacional de Física, In Proceedings of the XIII Conferencia Nacional de Física, Évora.

69.	Ribeiro, Andre S. 2002. "Humanity, Transition of the local to the planetarium. The importance of Portugal in the emergence of a global village", Trabalho apresentado em Jornadas do Mar 2002, In Jornadas do Mar 2002, Lisbon.

Artigos em revistas sem arbitragem científica Papers in periodics without scientific refereeing

1.	Annila, T; Lihavainen, E; MArques, IJ; Williams, DR; Yli-Harja, O; Ribeiro, AS. 2013. "ZebIAT, an image analysis tool for registering zebra fish embryos and quantifying cancer metastasis", BMC Bioinformatics 14, S10-S5: 1 - 9.

Trabalhos completos/resumidos em eventos sem arbitragem científica Papers in conference proceedings without scientific refereeing

1.	Goncalves, N; Venkata, Ramakanth N; Martikainen, A; Santinha, J; Fonseca, José M; Ribeiro, Andre S. 2014. "Effects of stress on the in vivo dynamics of non-stress-responsive genes in Escherichia coli", Trabalho apresentado em 11th International Workshop on Computational Systems Biology (WCSB 2014), In Proceedings of the 11th International Workshop on Computational Systems Biology (WCSB 2014), Lisboa.

2.	Martins, Leonardo; Fonseca, José M; Ribeiro, Andre S. 2014. "Generator of synthetic time-lapsed, phase-contrast microscopy images of growing E. coli cell populations", Trabalho apresentado em 11th International Workshop on Computational Systems Biology (WCSB 2014), In Proceedings of the 11th International Workshop on Computational Systems Biology (WCSB 2014), Lisbon.

3.	Santinha, J; Häkkinen, Antti; Gupta, Abhishekh; Annila, T; Lloyd-Price, Jason; Ribeiro, Andre S; Fonseca, José M. 2014. "Image Alignment and Lineage construction tool to study segregation and partitioning in division of unwanted protein aggregates in Escherichia coli", Trabalho apresentado em 11th International Workshop on Computational Systems Biology (WCSB 2014), In Proceedings of the 11th International Workshop on Computational Systems Biology (WCSB 2014), Lisboa.

4.	Chandraseelan, Jerome; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2014. "Estimating the duration of the open complex formation from in vivo measurements", Trabalho apresentado em 11th International Workshop on Computational Systems Biology (WCSB 2014), In Proceedings of the 11th International Workshop on Computational Systems Biology (WCSB 2014), Lisboa.

5.	Oliveira, Samuel; Chandraseelan, Jerome; Häkkinen, Antti; Yli-Harja, Olli; Ribeiro, Andre S. 2014. "Analysis of the Robustness of a Single Copy Repressilator", Trabalho apresentado em 11th International Workshop on Computational Systems Biology (WCSB 2014), In Proceedings of the 11th International Workshop on Computational Systems Biology (WCSB 2014), Lisboa.

6.	Venkata, Ramakanth N; Goncalves, N; Martikainen, A; Ribeiro, Andre S. 2014. "Mechanisms of in vivo polar retention of protein aggregates in Escherichia coli", Trabalho apresentado em Molecular Genetics of Bacteria and Phages meeting, In Proceedings of the Molecular Genetics of Bacteria and Phages meeting, Madison.

7.	Tran, Huy; Oliveira, Samuel; Yli-Harja, Olli; Ribeiro, Andre S. 2014. "Inducer intake kinetics under high extracellular concentrations in live Escherichia coli", Trabalho apresentado em 13th European Conference on Computational Biology, In Proceedings of ECCB'14, 13th European Conference on Computational Biology, Strasbourg.

8.	Mäkelä, Jarno; Yli-Harja, Olli; Ribeiro, Andre S. 2014. "Variability of single RNA production dynamics in monoclonal Escherichia coli clusters", Trabalho apresentado em 20th International Workshop on Single Molecule Spectroscopy and Ultra-Sensitive Analysis in the Life Sciences, In 20th International Workshop on Single Molecule Spectroscopy and Ultra-Sensitive Analysis in the Life Sciences, Berlim.

9.	Lihavainen, E; Kislin, M; Khirug, L; Ribeiro, Andre S. 2014. "Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue", Trabalho apresentado em 13th European Conference on Computational Biology, In Proceedings of ECCB'14, 13th European Conference on Computational Biology, Strasbourg.

10.	Annila, T; Muthukrishnan, Anantha B; Gupta, Abhishekh; Venkata, Ramakanth N; Ribeiro, Andre S. 2014. "Properties of the spatial organization of Tsr protein clusters in live Escherichia coli cells", Trabalho apresentado em 13th European Conference on Computational Biology, In Proceedings of ECCB'14, 13th European Conference on Computational Biology, Strasbourg.

11.	Kandavalli, V; Tran, Huy; Chandraseelan, Jerome; Ferreira, C; Fonseca, José M; Ribeiro, Andre S. 2014. "The role of different sigma factors in the dynamics of transcription during the exponential growth phase", Trabalho apresentado em Symposium on Views into Nuclear Function, In Proceedings of the Symposium on Views into Nuclear Function, Patras.

12.	Ribeiro, Andre S. 2014. "Modelling Polar Retention of Complexes in Escherichia Coli", Trabalho apresentado em Computational Methods in Systems Biology, In Computational Methods in Systems Biology, Manchester.

13.	Ribeiro, Andre S. 2014. "Finding Metastable States in Stochastic Gene Regulatory Networks", Trabalho apresentado em International BioMS Workshop Modeling Cellular Systems, In International BioMS Workshop Modeling Cellular Systems, Heidelberg.

14.	Ribeiro, Andre S. 2014. "Single-cell kinetics of a single-copy genetic Repressilator", Trabalho apresentado em 2nd International Conference on Systems Biology, In 2nd International Conference on Systems Biology, Lausanne.

15.	Ribeiro, Andre S. 2014. "Inference of transcription initiation dynamics from RNA production intervals in live Escherichia coli", Trabalho apresentado em EMBL Conference: From Functional Genomics to Systems Biology, In EMBL Conference: From Functional Genomics to Systems Biology, Heidelberg.

16.	Gupta, Abhishekh; Lloyd-Price, Jason; Kandhavelu, Meenakshisundaram; Oliveira, Samuel; Ribeiro, Andre S. 2013. "Cell division asymmetries in Escherichia coli when in sub-optimal conditions", Trabalho apresentado em 10th International Workshop on Computational Systems Biology, In WCSB 2013, Tampere.

17.	Sala, Adrien; Garasto, S; Kandhavelu, Meenakshisundaram; Ribeiro, Andre S. 2013. "Study of in vivo transcription dynamics of lac promoter at single cell level", Trabalho apresentado em 10th International Workshop on Computational Systems Biology, In WCSB 2013, Tampere.

18.	Venkata, Ramakanth N; Gupta, Abhishekh; Muthukrishnan, Anantha B; Yli-Harja, Olli; Ribeiro, Andre S. 2013. "Effect of environmental stress on the in vivo kinetics of segregation of unwanted protein aggregates in E. coli, at single cell, single event level", Trabalho apresentado em 10th International Workshop on Computational Systems Biology, In WCSB 2013, Tampere.

19.	Chandraseelan, Jerome; Oliveira, Samuel; Ribeiro, Andre S. 2013. "The Dynamics of the Genetic Repressilator for varying temperatures", Trabalho apresentado em 10th International Workshop on Computational Systems Biology, In WCSB 2013, Tampere.

20.	Chandraseelan, Jerome; Oliveira, Samuel; Ribeiro, Andre S. 2013. "Dynamics of the Elowitz et al synthetic Repressilator as a function of temperature", Trabalho apresentado em FEBS CONGRESS 2013, Mechanisms in Biology, In FEBS CONGRESS 2013, Mechanisms in Biology, São Petersburgo.

21.	Lloyd-Price, Jason; Ribeiro, Andre S. 2013. "Stability of a small RNA mediated Toggle Switch", Trabalho apresentado em 35th Annual Int. IEEE EMBS Conf. of the IEEE Engineering in Medicine and Biology Society, In 35th Annual Int. IEEE EMBS Conf. of the IEEE Engineering in Medicine and Biology Society, Osaka.

22.	Gupta, Abhishekh; Lloyd-Price, Jason; Ribeiro, Andre S. 2013. "Modeling partitioning in cell division and subsequent aging in Bacteria", Trabalho apresentado em Int. Conf. on Computational Cell Biology, In Int. Conf. on Computational Cell Biology, Blacksburg.

23.	Sala, Adrien; Ribeiro, Andre S; Kandhavelu, Meenakshisundaram. 2013. "Study of the kinetics of transcription as a function of the cell growth phase", Trabalho apresentado em FEBS CONGRESS 2013 “Mechanisms in Biology” , In FEBS CONGRESS 2013 “Mechanisms in Biology” , St. Petersburg.

24.	Annila, T; Lihavainen, E; Ribeiro, Andre S. 2013. "Quantification of cancer metastasis processes by image analysis of Zebrafish embryos at early stages of development", Trabalho apresentado em Second International Symposium on In Vivo Microscopy, In Second International Symposium on In Vivo Microscopy, Helsinki.

25.	Muthukrishnan, Anantha B; Venkata, Ramakanth N; Gupta, Abhishekh; Mäkelä, Jarno; Ribeiro, Andre S. 2013. "Real time monitoring of effect of stress on the in vivo kinetics of transcription initiation in Escherichia coli, at single cell, single molecule level", Trabalho apresentado em Molecular Genetics of Bacteria and Phage Meeting, In Molecular Genetics of Bacteria and Phage Meeting, Madison.

26.	Ribeiro, Andre S; Tran, Huy; Gupta, Abhishekh; Annila, T; Mäkelä, Jarno; Lloyd-Price, Jason; Chandraseelan, Jerome; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram; Oliveira, Samuel. 2013. "In vivo transcription dynamics of bacterial promoters in optimal and sub-optimal temperatures", Trabalho apresentado em 14th International Conference on Systems Biology (ICSB), In 14th International Conference on Systems Biology (ICSB), Copenhagen.

27.	Tran, Huy; Ribeiro, Andre S. 2013. "Effects of inducer intake kinetics on the dynamics of gene expression", Trabalho apresentado em Advances in Artificial Life, ECAL 2013, In Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems, Taormina.

28.	Potapov, Ilya; Mäkelä, Jarno; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Sequence dependent properties of the expression dynamics of genes and gene networks", Trabalho apresentado em CMSB 2012 10th International Conference on Computational Methods in Systems Biology , In Computational Methods in Systems Biology, Lecture Notes in Computer Science 307-321, Londres.

29.	Ballarini, P.; Mäkelä, Jarno; Ribeiro, Andre S. 2012. "Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics", Trabalho apresentado em CMSB 2012 10th International Conference on Computational Methods in Systems Biology, In Computational Methods in Systems Biology, Lecture Notes in Computer Science , Londres.

30.	Chandraseelan, Jerome; Gupta, Abhishekh; Muthukrishnan, Anantha B; Ribeiro, Andre S; Kandhavelu, Meenakshisundaram. 2012. "Role of thermal stress in the kinetics of intermediate steps in transcription initiation of Escherichia coli", Trabalho apresentado em RNA: a key to coordination of gene expression, In RNA: a key to coordination of gene expression, Roscoff.

31.	Muthukrishnan, Anantha B; Kandhavelu, Meenakshisundaram; Gupta, Abhishekh; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S. 2012. "Plasticity of in vivo RNA production under the control of tetA promoter in individual Escherichia coli cells", Trabalho apresentado em The Complex Life of mRNA, In The Complex Life of mRNA, EMBL Heidelberg, Heidelberg.

Textos em jornais ou revistas Texts in newspapers or magazines

1.	Ribeiro, Andre S. 16 nov. 2010. "Effects of Transcriptional Delays on Gene Expression Dynamics" Virtual Journal of Biological Physics Research, 1 - 9.

2.	Ribeiro, Andre S. 02 dez. 2008. "Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments" Virtual Journal of Biological Physics Research , 0619021 - 0619029.

3.	Ribeiro, Andre S. 28 nov. 2008. "Quantifying Local Structure Effects in Network Dynamics" Virtual Journal of Biological Physics Research , 0561081 - 05610810.

4.	Ribeiro, Andre S. 20 nov. 2007. "Mutual Information in Random Boolean models of regulatory networks" Virtual Journal of Biological Physics Research, 1 - 11.

5.	Ribeiro, Andre S. 20 nov. 2007. "Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks" Virtual Journal of Biological Physics Research , 0519151 - 05191514.

6.	Ribeiro, Andre S. 04 jun. 2007. "Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions" Virtual Journal of Biological Physics Research, 0619031 - 06190312.

7.	Ribeiro, Andre S. 16 set. 2004. "Emergence of Intelligence in Systems" Lisbon Academy of Sciences, 1 - 3.

8.	Ribeiro, Andre S. 24 jul. 2003. "A Proposed Model for Small-World Structural Organization of Mission Teams and Tasks in order to Optimize Efficiency and Minimize Costs" SP-542 ESA Bulletin Magazine, 149 - 155.

9.	Ribeiro, Andre S. 28 out. 2002. "Walking on Flames" Magazine of IADE, 12 - 13.

10.	Ribeiro, Andre S. 24 nov. 2001. "Loss of Societal Cohesion due to HIV/AIDS Epidemics" Scientific Annals of UnI , 1 - 1.

11.	Ribeiro, Andre S. 01 set. 2001. "Limitations of Science: concerning the Recent Presidential elections in USA" Scientific Annals of UnI , 2 - 2.

12.	Ribeiro, Andre S. 01 set. 2001. "The Cost in Energy and in Time of the Intelligence" Scientific Annals of UnI , 1 - 1.

13.	Ribeiro, Andre S. 05 jun. 2001. "Quantity of Information in Portuguese Architecture" Age of Image 2, 1 - 1.

14.	Ribeiro, Andre S. 02 maio 2001. "Quantidade de Informação na Arquitectura Portuguesa (1050-1950)" Memorias da Academia de Ciências de Lisboa, 1 - 2.

Software sem registo ou patente Software without patent or official record

1.	Ribeiro, Andre S; Häkkinen, Antti. RateLimit (Tool to identify rate limiting steps in transcription from RNA production times in live cells),2016.

2.	Ribeiro, Andre S; Häkkinen, Antti. RNANumbers (Tool for Estimation of fluorescence-tagged RNA numbers from spot intensities),2014.

4.	Ribeiro, Andre S. CellAging (A tool to study segregation and partitioning in division in cell lineages of Escherichia coli),2013.

5.	Ribeiro, Andre S. MAMLE, Cell Segmentation Tool (Tool for image analysis of E. coli and other bacteria),2013.

3.	Ribeiro, Andre S. ZebIAT (Tool for image analysis of zebrafish embryos),2013.

6.	Ribeiro, Andre S. Mytoe (Software for image analysis of mitochondria),2012.

7.	Ribeiro, Andre S. SGNS2 (Simulator of delayed stochastic genetic circuits. Version 2, which includes transient compartmentalization of reactions),2012.

8.	Ribeiro, Andre S. SGNSim (Simulator of delayed stochastic genetic circuits),2007.

9.	Ribeiro, Andre S. CellLine (Simulator of genetic circuits within cell lineages),2007.

Apresentação oral de trabalho Oral work presentation

1.	Ribeiro, Andre S. Modelling, Predicting, and Validating the Mechanics of a Gene Regulatory Mechanism,Annual meeting of the BioCity research program for Computational and Molecular Methodologies for Life Science,Turku,2016 (Comunicação).

2.	Ribeiro, Andre S. Promoter sensitivity to s factor numbers in Escherichia coli,Seminars of ITQB, Dept. Life Sciences,Lisbon,2016 (Seminário).

3.	Ribeiro, Andre S. How Escherichia coli introduces selectivity in the s factors global regulatory mechanism,Department of Signal Processing Coffee Seminars,Tampere,2016 (Seminário).

4.	Ribeiro, Andre S. Modelling, Analysis, and Validation of a Gene Regulatory Mechanism,Visiting lecturer at University of Helsinki course "Modelling and Analysis in Bioinformatics",Helsinki ,2016 (Comunicação).

5.	Venkata, Ramakanth N; Martikainen, A; Goncalves, N; Gupta, Abhishekh; Fonseca, José M; Ribeiro, Andre S. Robustness of the mechanisms of in vivo polar retention of protein aggregates in Escherichia coli,2015 (Seminário).

6.	Tran, Huy; Oliveira, Samuel; Ribeiro, Andre S. Kinetics of the cellular intake of a gene expression inducer at high concentrations in the media,2015 (Conferência ou palestra).

7.	Ribeiro, Andre S. Live transcription dynamics in bacteria at the single RNA level,Symposium on Single Cell Transcriptomics,Helsinki,2015 (Simpósio).

8.	Ribeiro, Andre S. The role of the nucleoid on the spatial organization of protein aggregates in Escherichia coli,Seminars of the Department of Bioengineering,Lisbon,2015 (Seminário).

9.	Ribeiro, Andre S. Laboratory of Biosystem Dynamics,2015 (Comunicação).

10.	Ribeiro, Andre S. Sequential delays as a means to regulate the fluctuations in the transcription process,Workshop on Inhomogeneous Random Systems (IRS),Paris,2014 (Conferência ou palestra).

11.	Lloyd-Price, Jason; Ribeiro, Andre S. Predictability and randomness of paw usage in mice,Biomeditech Research Day,Tampere,2014 (Comunicação).

12.	Ribeiro, Andre S. Effects of stress on the in vivo dynamics of non-stress-responsive genes in Escherichia coli,11th International Workshop on Computational Systems Biology (WCSB 2014),Lisboa,2014 (Conferência ou palestra).

13.	Canino, G; Sriram, A; Annila, T; Ribeiro, Andre S; Jacobs, HT; Sanz, A; Dufour, E. Mitochondrial maintenance throughout the cell cycle,2014 (Seminário).

14.	Ribeiro, Andre S. Delays as regulators of the dynamics of genetic circuits,2014 (Outra).

15.	Ribeiro, Andre S. In vivo single-molecule kinetics of activation and subsequent activity of bacterial promoters,Workshop on Statistical Mechanics of Biological Cooperativity,Mariehamn,2013 (Conferência ou palestra).

16.	Ribeiro, Andre S. Single Cell Signal Processing,2013 (Outra).

17.	Muthukrishnan, Anantha B; Venkata, Ramakanth N; Ribeiro, Andre S. Spatial distribution of Tsr clusters in Escherichia coli,BMT/IBT Research Day 2013,Tampere,2013 (Seminário).

18.	Ribeiro, Andre S. Kinetics of cellular aging by segregation of unwanted substances,2013 (Outra).

19.	Ribeiro, Andre S. My Way To Tenure Track,2013 (Outra).

20.	Ribeiro, Andre S. Dynamics of Genetic Networks,Invited lecture,2012 (Conferência ou palestra).

21.	Ribeiro, Andre S. In vivo Gene Expression Dynamics in Escherichia coli,2012 (Outra).

22.	Ribeiro, Andre S. Dynamics of Gene Expression,Tampere,2012 (Comunicação).

23.	Ribeiro, Andre S. Dynamics of Gene Expression in Escherichia Coli: models and measurements at the single event level,Invited talk,Trento,2011 (Comunicação).

24.	Ribeiro, Andre S. Phenotypic Diversity in Escherichia coli at the single molecule level,Invited talk,2011 (Conferência ou palestra).

25.	Ribeiro, Andre S. Dynamics of transcription and translation in Escherichia coli at the single cell, single molecule level,ICIAM minisymposium on stochasticity in gene expression,Vancouver,2011 (Simpósio).

26.	Ribeiro, Andre S. Dynamics of Gene Expression in Escherichia Coli: models and measurements at the single event level,Invited talk,Seattle,2011 (Comunicação).

27.	Ribeiro, Andre S. Dynamics of Genetic Networks,Johdatus biotekniikkaan,2011 (Comunicação).

28.	Ribeiro, Andre S. Regulatory Mechanisms of Cell to Cell Phenotypic Diversity in Escherichia coli,Invited Talk,Lisbon,2011 (Conferência ou palestra).

29.	Ribeiro, Andre S. Molecular models of genetic networks allow better understanding of cellular malfunction and differentiation,DataDriven Medicine,Tampere,2011 (Conferência ou palestra).

30.	Ribeiro, Andre S. Evidence for stringent control of noise in expression of the lar promoter in the regimes of weak and medium induction,8th International Workshop on Computational Systems Biology,Zurich,2011 (Comunicação).

31.	Ribeiro, Andre S. Molecular models of genetic circuits,Biotechnology Research Seminars 2010-11,Tampere,2011 (Conferência ou palestra).

32.	Ribeiro, Andre S. Dynamics of Gene Regulatory Networks,2011 (Comunicação).

33.	Ribeiro, Andre S. Dynamics of Gene Networks,Science Lectures,2010 (Comunicação).

34.	Ribeiro, Andre S. Dynamics of Gene Networks,Science Lectures,2010 (Comunicação).

35.	Ribeiro, Andre S. Studies on the Dynamics of Genetic Networks,Basic science course,2010 (Comunicação).

36.	Ribeiro, Andre S. Laboratory of Biosystem Dynamics,2010 (Comunicação).

37.	Ribeiro, Andre S; Smolander, Olli-Pekka. Dynamics of Gene Regulatory Networks,Johdatus biotekniikkaan BIO-1300,2010 (Comunicação).

38.	Ribeiro, Andre S. Dynamics of transcription and translation in Escherichia coli at the single cell, single molecule level,Roland Roth Seminars,2010 (Comunicação).

39.	Ribeiro, Andre S. Dynamics of Gene Networks,Tampere University of Tampere Science Seminars,2010 (Seminário).

40.	Ribeiro, Andre S. Dynamics of Gene Networks,Science Lectures,2010 (Conferência ou palestra).

41.	Ribeiro, Andre S. Dynamics and Information flow within Delayed Stochastic Gene Regulatory Networks,Basic Science Course,2009 (Comunicação).

42.	Ribeiro, Andre S; Yli-Harja, Olli. Dynamics of Gene Regulatory Networks,Kauffman’s 70th birthday IBI Symposium on Biocomplexity,Calgary,2009 (Comunicação).

43.	Ribeiro, Andre S; Smolander, Olli-Pekka. Dynamics of Gene Regulatory Networks,Johdatus biotekniikkaan BIO-1300,2009 (Comunicação).

44.	Ribeiro, Andre S. Gene Regulatory Networks, Structure and Dynamics,RekomBIOnaatio,2009 (Comunicação).

45.	Ribeiro, Andre S; Häkkinen, Antti; Smolander, Olli-Pekka; Rajala, Tiina; Antikainen, Aku; Yli-Harja, Olli. Delayed Stochastic Models of Gene Regulatory Networks: Internal dynamics and interactions with the environment,CoE seminar in Signal Processing,Tampere,2008 (Comunicação).

46.	Ribeiro, Andre S. Dynamics of Delayed Stochastic Models of Gene Regulatory Networks interacting with the environment,HUT-TUT Fall DSP Seminar 2008 “Advanced applications of signal processing”,2008 (Conferência ou palestra).

47.	Ribeiro, Andre S. A Model of Gene Regulatory Networks with Delayed Stochastic Dynamics,Institute for Signal Processing Seminars,2007 (Comunicação).

48.	Ribeiro, Andre S. From Stochastic Gene Regulatory Networks to Phenotypes,Seminars of the Institute for Signal Processing,2007 (Comunicação).

49.	Ribeiro, Andre S. Gene Regulatory Networks: Structure, Dynamics and Inference,Seminars, Dept. Physics & Astronomy Seminars,Calgary,2006 (Comunicação).

50.	Ribeiro, Andre S. Artificial Gene Regulatory Networks: from noisy Boolean networks to stochastic dynamics. Inference algorithms from time series of gene activity,Seminars of the Centre for Computational Physics,2006 (Comunicação).

51.	Ribeiro, Andre S. A flux based self regulated traffic lights control system,5ª Seminars series on Complexity,2005 (Comunicação).

52.	Ribeiro, Andre S. Inference Algorithm for Dynamical Gene Regulatory Networks,Biocomplexity Institute Seminars,2005 (Comunicação).

53.	Kauffman, Stuart A; Ribeiro, Andre S; Lloyd-Price, Jason. JAS-ARACNE Inference Engine of Gene Regulatory Networks,1st Conference on Biocomplexity of the Institute for Biocomplexity and Informatics,Calgary,2005 (Comunicação).

54.	Rodrigues, Fernando C; Ribeiro, Andre S. Intelligence Emergence in Systems,Comunicacao,2004 (Comunicação).

55.	Ribeiro, Andre S. Characterizing the evolution of biological neural networks,Seminar ,Lisbon,2004 (Comunicação).

56.	Ribeiro, Andre S. Using Complex Systems Theory on the Computation of the Probability for the Emergence of Intelligence,4ª Série dos Seminários sobre Complexidade,2003 (Comunicação).

57.	Ribeiro, Andre S; Rodrigues, Fernando C. Humanity: from the local to the planetarium. The importance of Portugal in the creation of the global village,Talk,2003 (Comunicação).

Curso de curta duração lecionado Taught short course

1.	Ribeiro, Andre S. Winter School Erasmus Mundus master's programme in Systems Biology (euSYSBIO), 2013 (Extensão), promovido por Institute Superior Tecnico, Technical Univ., Lisbon, Portugal.

Desenvolvimento de material didáctico ou pedagógico Didactic and pedagogic material development

1.	Ribeiro, Andre S. Methods in Single Cell Biology,2016.

2.	Ribeiro, Andre S. Special Topics in Signal Processing,2014.

3.	Ribeiro, Andre S. Processing of Biosignals,2013.

4.	Ribeiro, Andre S. Laboratory course in Information Technology for Health and Biology,2012.

5.	Ribeiro, Andre S. Computational Modeling in Biomedical Problems,2012.

6.	Ribeiro, Andre S. Techniques in Molecular Biology and Applications to Gene Expression,2012.

7.	Ribeiro, Andre S. Graduate Seminar on Signal Processing for Systems Biology,2012.

8.	Ribeiro, Andre S. Introduction to Information Technology for Health and Biology,2012.

9.	Ribeiro, Andre S. Biology of the Cell,2012.

10.	Ribeiro, Andre S. International Doctoral Seminar in Signal Processing,2012.

11.	Kandhavelu, Meenakshisundaram; Ribeiro, Andre S. Cell culturing, microscopy and cell image analysis,2012.

12.	Ribeiro, Andre S. Computational Models in Complex Systems,2012.

13.	Ribeiro, Andre S; Kandhavelu, Meenakshisundaram. Introduction to Biology of the Cell,2011.

14.	Ribeiro, Andre S. Computational Systems Biology ,2011.

15.	Ribeiro, Andre S. Models of Gene Networks,2008.

16.	Ribeiro, Andre S. Statistics for Management,2003.

17.	Ribeiro, Andre S. Statistics Applied to Psychology,2003.

18.	Ribeiro, Andre S. Applied Sciences for Design II,2001.

19.	Ribeiro, Andre S. Applied Sciences for Design I,2001.

20.	Ribeiro, Andre S. Basic Physics,2000.

21.	Ribeiro, Andre S. General and Experimental Physics,2000.

Organização de evento Event organization

1.	Ribeiro, Andre S. Techniques for Microscopic Image Analysis,2016 (Seminário).

2.	Ribeiro, Andre S. 11th International Workshop on Computational Systems Biology (WCSB14),2014 (Oficina).

3.	Ribeiro, Andre S. 10th International Workshop on Computational Systems Biology (WCSB 2013),2013 (Oficina).

4.	Ribeiro, Andre S. Laboratory Safety,2013 (Encontro).

5.	Ribeiro, Andre S. 9th International Workshop on Computational Systems Biology (WCSB 2012),2012 (Oficina).

6.	Ribeiro, Andre S. Introduction to Computer Graphics,2012 (Seminário).

7.	Ribeiro, Andre S. Bacterial Genetics Horizontal Gene Transfer,2012 (Seminário).

8.	Ribeiro, Andre S. 8th International Workshop on Computational Systems Biology (WCSB 2011),2011 (Oficina).

9.	Ribeiro, Andre S. Biotechnology Researcher Seminar 2010,2010 (Seminário).

10.	Ribeiro, Andre S. Biotechnology Researcher Seminar 2009,2009 (Seminário).

11.	Ribeiro, Andre S. Critical Phenomena and Local Dynamics on Complex Networks,2009 (Outro).

12.	Ribeiro, Andre S. Identification and Reconstruction of a Gene Network that Regulates Learning and Memory in Mouse Behavior,2009 (Outro).

13.	Ribeiro, Andre S. Biotechnology Researcher Seminar 2008,2008 (Seminário).

14.	Jacobs, Howard T; Ribeiro, Andre S. Murikka Summer School on Cell signaling and its transcriptional readout,2008 (Seminário / Outra).

15.	Ribeiro, Andre S. Genetics of Learning and Memory in Mice,2008 (Outro).

Programa de rádio ou TV Radio or TV show

1.	Ribeiro, Andre S. Interview conducted by Tuuli Laukkanen, Communications Manager, Tampere University of Technology,2016 (Entrevista).

2.	Ribeiro, Andre S. Nanokoneet tarkkailevat elimiston terveytta tampereella tahdataan alan huipulle katso kuvat,2013 (Entrevista).

3.	Ribeiro, Andre S. Destined to become a scientist,2011 (Entrevista).

4.	Ribeiro, Andre S. Destined to become a scientist,2011 (Entrevista).

Orientações Orientations

Participação no júri de Graus Académicos Academic Degrees jury participation

Participação editorial em revistas Magazine editorial participation

Orientações Orientations

Tese de Doutoramento Phd Thesis

Concluídas Completed

1.	J Mäkelä, Image analysis algorithms for single-cell study in systems biology, 2016. Bolseiro(a) de Tampere University of Technology (Orientador).

2.	H Tran, Environment-sensing Mechanisms of Gene Expression and their Effects on the Dynamics of Genetic Circuits across Cell Generations, 2016. (Orientador).

3.	A Häkkinen, Quantifying Transcriptional Dynamics and Their Effects on Genetic Motifs from Live Cell Fluorescence Microscopy, 2016. (Orientador).

4.	S Chowdhury, Image analysis algorithms for single-cell study in systems biology, 2016. (Co-orientador).

5.	E Lihavainen, Image Analysis Methods for the Characterization of Mitochondrial Morphology and Dynamics, 2016. (Orientador).

6.	J Lloyd-Price, Dynamics of Genetic Circuits with Molecule Partitioning Errors in Cell Division and RNA-RNA Interactions, 2015. Bolseiro(a) de Tampere University of Technology (Orientador).

7.	JG Chandraseelan, Synthetic Genetic Circuits: Plasticity and Robustness., 2015. (Orientador).

8.	A Gupta, Effects of intracellular and partitioning asymmetries in Escherichia coli, 2015. (Orientador).

9.	A.-B. Muthukrishnan, Studies of the plasticity of transcription in Escherichia coli using single-molecule, in vivo detection techniques, 2014. (Orientador).

10.	Ilya Potapov, Switching and Oscillatory Dynamics of Genetic Networks, 2013. (Orientador).

11.	Olli-Pekka Smolander, Data Fusion Methods and Applications on Exploration of Gene Regulatory Mechanisms, 2011. (Co-orientador).

12.	Xiaofeng Dai, Data Fusion Methods and Applications on Exploration of Gene Regulatory Mechanisms, 2010. (Co-orientador).

Dissertação de Mestrado Master degree dissertation

Concluídas Completed

1.	M Zare, Single cell analysis of Z ring formation in Escherichia coli using machine learning methods, 2016. (Co-orientador).

2.	A Martikainen, Segregation of protein aggregates in Escherichia coli, 2015. (Orientador).

3.	T Annila, Detection of Fluorescently Labeled Particles in Escherichia coli, 2015. (Orientador).

4.	Samuel MD Oliveira, In vivo single-cell kinetics of the repressilator as a function of its intracellular copy numbers, 2014. (Orientador).

5.	C Ferreira, Study of the influence of s factors on the kinetics of RNA production, 2014. (Co-orientador).

6.	H Tran, Sequence-dependent noise filtering in small genetic motifs, 2013. (Orientador).

7.	S Garasto, A Mixture Model to Estimate Numbers of Fluorescence-tagged Molecules Using Their Intensity Distributions, 2013. (Co-orientador).

8.	A. Gupta, Stochastic processes as a source of cell to cell diversity and cellular ageing, 2012. Dissertação (Faculty of Computing and Electrical Engineering) - Tampere University of Technology (Orientador).

9.	Antti Häkkinen, Simulating Evolutionary Processes of Stochastic Genetic Networks in Volatile Environments, 2012. (Orientador).

10.	C.C.A. Queimadelas, Automated segmentation, tracking and evaluation of bacteria in microscopy images, 2012. (Co-orientador).

11.	L. P. V. Martins, Stochastic model of transcription initiation at the nucleotide level of Escherichia coli bidirectional promoters, 2011. (Co-orientador).

12.	Jason Lloyd-Price, Simulating Stochastic Chemical Kinetics with Dynamics Compartmentalization at Runtime, 2011. (Orientador).

13.	Eero Lihavainen, Analysis of Mitochondrial motion and structure in confocal time-lapse microscopy, 2011. (Orientador).

14.	Jarno Mäkelä, Dynamics of stochastic sequence-level models of transcription and translation in prokaryotes, 2011. (Orientador).

Trabalho de conclusão de curso de Bacharelato/Licenciatura Bachelor/Licenciate degree conclusion work

Concluídas Completed

1.	J Smolander, Lambda-Phage PRM Promoter Dynamics, 2013. (Orientador).

2.	T Annila, Registration of zebrafish images using thin plate splines, 2012. (Orientador).

3.	SMD Oliveira, Single-Molecule Dynamics of the Bidirectional Arabinose Promoter, 2012. (Co-orientador).

4.	Elahe Moradi, Analysis of the Dynamics of Transcription of the Arabinose promoter in Escherichia coli, 2011. (Orientador).

5.	Antti Häkkinen, DNA-sekvenssien Etmininen ja löydösten merkitysen analysointi, 2008. (Orientador).

6.	D. Charlesboi, Modeling the P53 network, 2007. (Orientador).

Iniciação científica Scientific initiation

Concluídas Completed

1.	Meenakshisundaram Kandhavelu, Post-Doctoral Work, 2012. (Orientador).

2.	Shannon Healy, Post-doctoral work, 2010. (Orientador).

Participação no júri de Graus Académicos Academic Degrees jury participation

Doutoramento Phd

1.	Ribeiro, Andre S.. Participação no júri de H.X. Ta. Computational Approaches to Biological Network Inference and Modeling in Systems Biology, 2012.

2.	Ribeiro, Andre S.. Participação no júri de Ines J. Marques. Disease Models in Vertebrates: from hypoxia to cancer, 2011.

3.	Ribeiro, Andre S.. Participação no júri de Juha Kesseli. Annealed Approximation and Boolean Network Dynamics, 2007.

Mestrado Master degree

1.	Ribeiro, Andre S.. (S Muhammad) Analysis of time lapse microscopy images to understand real time gene expression kinetics during the cell cycle, 2015.

2.	Ribeiro, Andre S.. (A Vishwanathan) Chemical stress in bacteria: Analysis of the cellular dynamics, sub-lethal injury and cell death, 2015.

3.	Ribeiro, Andre S.. (A Sala) Elucidating the transcriptional regulatory mechanisms at the single cell level, 2015.

4.	Ribeiro, Andre S.. Participação no júri de J. de C.B. Aleixo. O Impacto das Tecnologias da Informacao na Guerra Assimetrica, 2005.

5.	Ribeiro, Andre S.. Participação no júri de J.M.C. Ribeiro. Mecanismos de Seguranca de Sistemas Operativos, 2005.

6.	Ribeiro, Andre S.. Participação no júri de J.A.T. Amaro. A Quantidade de Informacao e a Teoria das Catastrofes, 2005.

7.	Ribeiro, Andre S.. Participação no júri de D.H. Sereno. Principios de Auditoria de Seguranca de sistemas de informacao, 2005.

8.	Ribeiro, Andre S.. Participação no júri de P.M. Jesus. Principios da Criptografia Quantica, 2005.

Participação editorial em revistas Magazine editorial participation

1.	Ribeiro, Andre S.. In Silico Biology, Função ou tipo de participação: Corpo editorial.
2.	Ribeiro, Andre S.. BMC Bioinformatics, de 2012/01/01 até 2014/06/24, Função ou tipo de participação: Corpo editorial.

Produção científica Scientific production

Produção técnica Technical production

Dados complementares data

Total

Produção científica Scientific production

211

Livros e capítulos Books and book chapters

12

Livros publicados ou organizados Published or organized books

1

Capítulos de livros publicados Published book chapters

11

Artigos científicos em revistas Papers in periodics

85

Com arbitragem científica With scientific refereeing

84

Sem arbitragem científica Without scientific refereeing

1

Trabalhos em eventos Papers in conference proceedings

100

Com arbitragem científica With scientific refereeing

69

Sem arbitragem científica Without scientific refereeing

31

Textos em jornais ou revistas Texts in journals or magazines

14

Revistas Magazines

14

Total

Produção técnica Technical production

107

Software

9

Software sem registo ou patente Software without patent or official record

9

Outros tipos de produção técnica Other technical production

98

Total

Dados complementares (Additional data)

47

Orientações Orientations

34

Participação no Júri de Graus Académicos Academic Degrees jury participation

11

Participação editorial em revistas Magazine editorial participation

2

	André Teixeira Bento Damas Mora
	José Manuel Matos Ribeiro da Fonseca
	Leonardo Pedro Donas-Boto de Vilhena Martins
	Nádia Solange Moreira Gonçalves
	Pedro Gonçalves Lind