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Andre Sanches Ribeiro is a Professor (tenured) at Tampere University, Finland. He has a Degree in Theoretical Physics, a Ph.D. in Physics Engineering, and conducted Post-Doctoral studies in Theoretical Biology. His studies currently focus on the dynamics and regulatory mechanisms of bacterial gene expression and genetic circuits at the single-cell, single-molecule level. The aims are to understand how genes and genetic circuits are regulated and unravel their range of functionalities, thereby assisting in understanding natural transcriptional programs and in the comprehensive engineering of synthetic circuits for regulating cellular processes. Webpage: https://sites.google.com/view/andreribeirolab/home
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Identification

Personal identification

Full name
Andre Sanches Ribeiro

Citation names

  • Ribeiro, Andre S.
  • Ribeiro, A.S.

Author identifiers

Ciência ID
C016-09ED-3DC9
ORCID iD
0000-0002-7255-5211

Addresses

  • Faculty of Medicine and Health Technology Arvo Ylpön katu 34 , 33014, Tampere University, Tampere, Finland (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese (Mother tongue)
Affiliation

Science

Category
Host institution 		Employer
2012/01/01 - Current Invited Principal Investigator (Research) Centre of Technology and Systems (CTS), Faculty of Sciences and Technology, NOVA University of Lisbon, Portugal
Universidade Nova de Lisboa, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2017/07/01 - Current Full Professor (University Teacher) Tampereen yliopisto, Finland
Outputs

Publications

Journal article
  1. Bahrudeen, Mohamed N. M.; Chauhan, Vatsala; Palma, Cristina S. D.; Oliveira, Samuel M. D.; Kandavalli, Vinodh K.; Ribeiro, Andre S.. "Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry". Journal of Microbiological Methods (2019): https://publons.com/publon/27513755/.
    10.1016/J.MIMET.2019.105745
  2. Hakkinen, Antti; Oliveira, Samuel M. D.; Neeli-Venkata, Ramakanth; Ribeiro, Andre S.. "Transcription closed and open complex formation coordinate expression of genes with a shared promoter region". Journal of the Royal Society Interface (2019): https://publons.com/publon/19097586/.
    10.1098/RSIF.2019.0507
  3. Oliveira, Samuel M. D.; Goncalves, Nadia S. M.; Kandavalli, Vinodh K.; Martins, Leonardo; Neeli-Venkata, Ramakanth; Reyelt, Jan; Fonseca, Jose M.; et al. "Chromosome and plasmid-borne P-LacO3O1 promoters differ in sensitivity to critically low temperatures". Scientific Reports (2019): https://publons.com/publon/27511418/.
    10.1038/S41598-019-39618-Z
  4. Startceva, Sofia; Kandavalli, Vinodh K.; Visa, Ari; Ribeiro, Andre S.. "Regulation of asymmetries in the kinetics and protein numbers of bacterial gene expression". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (2019): https://publons.com/publon/27511415/.
    10.1016/J.BBAGRM.2018.12.005
  5. Prajapat, Mahendra Kumar; Ribeiro, Andre S.. "Added value of autoregulation and multi-step kinetics of transcription initiation". Royal Society Open Science (2018): https://publons.com/publon/2493095/.
    10.1098/RSOS.181170
  6. Goncalves, Nadia S. M.; Startceva, Sofia; Palma, Cristina S. D.; Bahrudeen, Mohamed N. M.; Oliveira, Samuel M. D.; Ribeiro, Andre S.. "Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli". Physical Biology (2018): https://publons.com/publon/12203401/.
    10.1088/1478-3975/AA9DDF
  7. Oliveira, Samuel M. D.; Bahrudeen, Mohamed N. M.; Startceva, Sofia; Ribeiro, Andre S.. "Estimating Effects of Extrinsic Noise on Model Genes and Circuits with Empirically Validated Kinetics". Communications in Computer and Information Science (2018): https://publons.com/publon/18370100/.
    10.1007/978-3-319-78658-2_14
  8. Neeli-Venkata, Ramakanth; Oliveira, Samuel M. D.; Martins, Leonardo; Startceva, Sofia; Bahrudeen, Mohamed; Fonseca, Jose M.; Minoia, Marco; Ribeiro, Andre S.. "The precision of the symmetry in Z-ring placement in Escherichia coli is hampered at critical temperatures". Physical Biology (2018): https://publons.com/publon/1996144/.
    10.1088/1478-3975/AAC1CB
  9. Martins, Leonardo; Canelas, Pedro; Mora, Andre; Ribeiro, Andre S.; Fonseca, Jose. "Generator Platform of Benchmark Time-Lapsed Images Development of Cell Tracking Algorithms: Implementation of New Features Towards a Realistic Simulation of the Cell Spatial and Temporal Organization". Advances in Soft Computing (2018): https://publons.com/publon/12203400/.
    10.1007/978-3-319-69832-8_4
  10. Kislin, Mikhail; Sword, Jeremy; Fomitcheva, Ioulia V.; Croom, Deborah; Pryazhnikov, Evgeny; Lihavainen, Eero; Toptunov, Dmytro; et al. "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 (2017): https://publons.com/publon/27511430/.
    10.1523/JNEUROSCI.1510-16.2017
  11. Tripathi, Shailesh; Lloyd-Price, Jason; Ribeiro, Andre; Yli-Harja, Olli; Dehmer, Matthias; Emmert-Streib, Frank. "sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters". BMC Bioinformatics (2017): https://publons.com/publon/7599956/.
    10.1186/S12859-017-1731-8
  12. Makela, Jarno; Kandavalli, Vinodh; Ribeiro, Andre S.. "Rate-limiting steps in transcription dictate sensitivity to variability in cellular components". Scientific Reports (2017): https://publons.com/publon/12203402/.
    10.1038/S41598-017-11257-2
  13. Oliveira, Samuel M. D.; Hakkinen, Antti; Lloyd-Price, Jason; Huy Tran; Kandavalli, Vinodh; Ribeiro, Andre S.. "Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements". PLOS Computational Biology (2016): https://publons.com/publon/1008041/.
    10.1371/JOURNAL.PCBI.1005174
  14. Kandavalli, Vinodh K.; Huy Tran; Ribeiro, Andre S.. "Effects of sigma factor competition are promoter initiation kinetics dependent". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (2016): https://publons.com/publon/12203399/.
    10.1016/J.BBAGRM.2016.07.011
  15. Ribeiro, A. S.. "Delays as Regulators of the Dynamics of Genetic Circuits". Markov Processes and Related Fields (2016): https://publons.com/publon/12203403/.
  16. Neeli-Venkata, Ramakanth; Startceva, Sofia; Annila, Teppo; Ribeiro, Andre S.. "Polar Localization of the Serine Chemoreceptor of Escherichia coli Is Nucleoid Exclusion-Dependent". Biophysical Journal (2016): https://publons.com/publon/9366854/.
    10.1016/J.BPJ.2016.10.024
  17. Neeli-Venkata, Ramakanth; Martikainen, Antti; Gupta, Abhishekh; Goncalves, Nadia; Fonseca, Jose; Ribeiro, Andre S.. "Robustness of the Process of Nucleoid Exclusion of Protein Aggregates in Escherichia coli". Journal of Bacteriology (2016): https://publons.com/publon/9366848/.
    10.1128/JB.00848-15
  18. Hakkinen, Antti; Ribeiro, Andre S.. "Characterizing rate limiting steps in transcription from RNA production times in live cells". Bioinformatics (2016): https://publons.com/publon/12203398/.
    10.1093/BIOINFORMATICS/BTV744
  19. Zimmer, Christoph; Hakkinen, Antti; Ribeiro, Andre S.. "Estimation of kinetic parameters of transcription from temporal single-RNA measurements". Mathematical Biosciences (2016): https://publons.com/publon/12203420/.
    10.1016/J.MBS.2015.10.001
  20. Lloyd-Price, Jason; Startceva, Sofia; Kandavalli, Vinodh; Chandraseelan, Jerome G.; Goncalves, Nadia; Oliveira, Samuel M. D.; Hakkinen, Antti; Ribeiro, Andre S.. "Dissecting the stochastic transcription initiation process in live Escherichia coli". DNA Research (2016): https://publons.com/publon/1008044/.
    10.1093/DNARES/DSW009
  21. Oliveira, Samuel M. D.; Neeli-Venkata, Ramakanth; Goncalves, Nadia S. M.; Santinha, Joao A.; Martins, Leonardo; Huy Tran; Makela, Jarno; et al. "Increased cytoplasm viscosity hampers aggregate polar segregation in Escherichia coli". Molecular Microbiology (2016): https://publons.com/publon/1008045/.
    10.1111/MMI.13257
  22. Hakkinen, Antti; Ribeiro, Andre S.. "Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data". Bioinformatics (2015): https://publons.com/publon/12203418/.
    10.1093/BIOINFORMATICS/BTU592
  23. Lihavainen, E.; Kislin, M.; Toptunov, D.; Khiroug, L.; Ribeiro, A. S.. "Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue". Journal of Microscopy (2015): https://publons.com/publon/12203421/.
    10.1111/JMI.12301
  24. Oliveira, Samuel M. D.; Chandraseelan, Jerome G.; Hakkinen, Antti; Goncalves, Nadia S. M.; Yli-Harja, Olli; Startceva, Sofia; Ribeiro, Andre S.. "Single-cell kinetics of a repressilator when implemented in a single-copy plasmid". Molecular Omics (2015): https://publons.com/publon/9374640/.
    10.1039/C5MB00012B
  25. Martins, Leonardo; Fonseca, Jose; Ribeiro, Andre. "'miSimBa' - A Simulator of Synthetic Time-Lapsed Microscopy Images of Bacterial Cells". IEEE 4TH PORTUGUESE MEETING ON BIOENGINEERING (ENBENG) (2015): https://publons.com/publon/12203419/.
  26. Tran, Huy; Oliveira, Samuel M. D.; Goncalves, Nadia; Ribeiro, Andre S.. "Kinetics of the cellular intake of a gene expression inducer at high concentrations". Molecular Omics (2015): https://publons.com/publon/9374639/.
    10.1039/C5MB00244C
  27. Ribeiro, Andre S.; Eales, Brenda A.; Lloyd-Price, Jason; Biddle, Fred G.. "Predictability and randomness of paw choices are critical elements in the behavioural plasticity of mouse paw preference". Animal Behaviour (2014): https://publons.com/publon/1008046/.
    10.1016/J.ANBEHAV.2014.10.008
  28. Gupta, Abhishekh; Lloyd-Price, Jason; Neeli-Venkata, Ramakanth; Oliveira, Samuel M. D.; Ribeiro, Andre S.. "In Vivo Kinetics of Segregation and Polar Retention of MS2-GFP-RNA Complexes in Escherichia coli". Biophysical Journal (2014): https://publons.com/publon/1008049/.
    10.1016/J.BPJ.2014.03.035
  29. Muthukrishnan, Anantha-Barathi; Martikainen, Antti; Neeli-Venkata, Ramakanth; Ribeiro, Andre S.. "In Vivo Transcription Kinetics of a Synthetic Gene Uninvolved in Stress-Response Pathways in Stressed Escherichia coli Cells". Plos One (2014): https://publons.com/publon/9366849/.
    10.1371/JOURNAL.PONE.0109005
  30. Fukuoh, Atsushi; Cannino, Giuseppe; Gerards, Mike; Buckley, Suzanne; Kazancioglu, Selena; Scialo, Filippo; Lihavainen, Eero; et al. "Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase". Molecular Systems Biology (2014): https://publons.com/publon/12203363/.
    10.15252/MSB.20145117
  31. Gupta, Abhishekh; Lloyd-Price, Jason; Oliveira, Samuel M. D.; Yli-Harja, Olli; Muthukrishnan, Anantha-Barathi; Ribeiro, Andre S.. "Robustness of the division symmetry in Escherichia coli and functional consequences of symmetry breaking". Physical Biology (2014): https://publons.com/publon/1008048/.
    10.1088/1478-3975/11/6/066005
  32. Hakkinen, Antti; Kandhavelu, Meenakshisundaram; Garasto, Stefania; Ribeiro, Andre S.. "Estimation of fluorescence-tagged RNA numbers from spot intensities". Bioinformatics (2014): https://publons.com/publon/9946576/.
    10.1093/BIOINFORMATICS/BTT766
  33. Lloyd-Price, Jason; Huy Tran; Ribeiro, Andre S.. "Dynamics of small genetic circuits subject to stochastic partitioning in cell division". Journal of Theoretical Biology (2014): https://publons.com/publon/1008047/.
    10.1016/J.JTBI.2014.04.018
  34. Haekkinen, Antti; Muthukrishnan, Anantha-Barathi; Mora, Andre; Fonseca, Jose M.; Ribeiro, Andre S.. "CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli". Bioinformatics (2013): https://publons.com/publon/9253409/.
    10.1093/BIOINFORMATICS/BTT194
  35. Chowdhury, Sharif; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S.. "Cell segmentation by multi-resolution analysis and maximum likelihood estimation (MAMLE)". BMC Bioinformatics (2013): https://publons.com/publon/9946580/.
    10.1186/1471-2105-14-S10-S8
  36. Makela, Jarno; Kandhavelu, Meenakshisundaram; Oliveira, Samuel M. D.; Chandraseelan, Jerome G.; Lloyd-Price, Jason; Peltonen, Juha; Yli-Harja, Olli; Ribeiro, Andre S.. "In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter". Nucleic Acids Research (2013): https://publons.com/publon/1008051/.
    10.1093/NAR/GKT350
  37. Chandraseelan, Jerome G.; Oliveira, Samuel M. D.; Hakkinen, Antti; Huy Tran; Potapov, Ilya; Sala, Adrien; Kandhavelu, Meenakshisundaram; Ribeiro, Andre S.. "Effects of temperature on the dynamics of the LacI-TetR-CI repressilator". Molecular Omics (2013): https://publons.com/publon/9374642/.
    10.1039/C3MB70203K
  38. Hakkinen, Antti; Huy Tran; Yli-Harja, Olli; Ribeiro, Andre S.. "Effects of Rate-Limiting Steps in Transcription Initiation on Genetic Filter Motifs". Plos One (2013): https://publons.com/publon/12203383/.
    10.1371/JOURNAL.PONE.0070439
  39. Annila, Teppo; Lihavainen, Eero; Marques, Ines J.; Williams, Darren R.; Yli-Harja, Olli; Ribeiro, Andre. "ZebIAT, an image analysis tool for registering zebrafish embryos and quantifying cancer metastasis". BMC Bioinformatics (2013): https://publons.com/publon/3803502/.
    10.1186/1471-2105-14-S10-S5
  40. Sala, A.; Ribeiro, A. S.; Kandhavelu, M.. "Study of the kinetics of transcription as a function of the cell growth phase". The FEBS Journal (2013): https://publons.com/publon/12203387/.
  41. Ribeiro, Andre S.; Eales, Brenda A.; Biddle, Fred G.. "Short-term and long-term memory deficits in handedness learning in mice with absent corpus callosum and reduced hippocampal commissure". Behavioural Brain Research (2013): https://publons.com/publon/12203396/.
    10.1016/J.BBR.2013.02.021
  42. Lloyd-Price, Jason; Ribeiro, Andre S.. "Bistability in a stochastic RNA-mediated gene network". Physical Review E (2013): https://publons.com/publon/1008050/.
    10.1103/PHYSREVE.88.032714
  43. Chandraseelan, J. G.; Oliveira, S. M. D.; Ribeiro, A. S.. "Dynamics of the Elowitz et al. synthetic repressilator as a function of temperature". The FEBS Journal (2013): https://publons.com/publon/9374641/.
  44. Hakkinen, Antti; Huy Tran; Yli-Harja, Olli; Ingalls, Brian; Ribeiro, Andre S.. "Effects of multimerization on the temporal variability of protein complex abundance". BMC Systems Biology (2013): https://publons.com/publon/12203385/.
    10.1186/1752-0509-7-S1-S3
  45. Ribeiro, Andre S.. "Kinetics of gene expression in bacteria - From models to measurements, and back again". Canadian Journal of Chemistry (2013): https://publons.com/publon/12203393/.
    10.1139/CJC-2012-0409
  46. Lloyd-Price, Jason; Gupta, Abhishekh; Ribeiro, Andre S.. "Robustness and Information Propagation in Attractors of Random Boolean Networks". Plos One (2012): https://publons.com/publon/1008052/.
    10.1371/JOURNAL.PONE.0042018
  47. Hakkinen, Antti; Ribeiro, Andre S.. "Evolving kinetics of gene expression in stochastic environments". Computational Biology and Chemistry (2012): https://publons.com/publon/12203397/.
    10.1016/J.COMPBIOLCHEM.2012.02.002
  48. Potapov, Ilya; Makela, Jarno; Yli-Harja, Olli; Ribeiro, Andre S.. "Effects of codon sequence on the dynamics of genetic networks". Journal of Theoretical Biology (2012): https://publons.com/publon/9399072/.
    10.1016/J.JTBI.2012.08.029
  49. Muthukrishnan, Anantha-Barathi; Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Kudasov, Fedor; Chowdhury, Sharif; Yli-Harja, Olli; Ribeiro, Andre S.. "Dynamics of transcription driven by the tetA promoter, one event at a time, in live Escherichia coli cells". Nucleic Acids Research (2012): https://publons.com/publon/1008054/.
    10.1093/NAR/GKS583
  50. Lloyd-Price, Jason; Hakkinen, Antti; Kandhavelu, Meenakshisundaram; Marques, Ines J.; Chowdhury, Sharif; Lihavainen, Eero; Yli-Harja, Olli; Ribeiro, Andre S.. "Asymmetric Disposal of Individual Protein Aggregates in Escherichia coli, One Aggregate at a Time". Journal of Bacteriology (2012): https://publons.com/publon/1008053/.
    10.1128/JB.06500-11
  51. Chowdhury, S.; Kandhavelu, M.; Yli-Harja, O.; Ribeiro, A. S.. "An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy". Journal of Microscopy (2012): https://publons.com/publon/9946563/.
    10.1111/J.1365-2818.2011.03568.X
  52. Kandhavelu, M.; Hakkinen, A.; Yli-Harja, O.; Ribeiro, A. S.. "Single-molecule dynamics of transcription of the lar promoter". Physical Biology (2012): https://publons.com/publon/9946578/.
    10.1088/1478-3975/9/2/026004
  53. Lihavainen, Eero; Makela, Jarno; Spelbrink, Johannes N.; Ribeiro, Andre S.. "Mytoe: automatic analysis of mitochondrial dynamics". Bioinformatics (2012): https://publons.com/publon/1802606/.
    10.1093/BIOINFORMATICS/BTS073
  54. Kandhavelu, Meenakshisundaram; Lihavainen, Eero; Muthukrishnan, Anantha Barathi; Yli-Harja, Olli; Ribeiro, Andre Sanches. "Effects of Mg2+ on in vivo transcriptional dynamics of the lar promoter". BioSystems (2012): https://publons.com/publon/9946560/.
    10.1016/J.BIOSYSTEMS.2011.11.001
  55. Kandhavelu, M.; Paturu, L.; Mizar, A.; Mahmudov, K. T.; Kopylovich, M. N.; Karp, M.; Yli-Harja, O.; Pombeiro, A. J. L.; Ribeiro, A. S.. "Synthesis, characterization and antimicrobial activity of arylhydrazones of methylene active compounds". Pharmaceutical Chemistry Journal (2012): https://publons.com/publon/9946579/.
    10.1007/S11094-012-0751-Y
  56. Lloyd-Price, Jason; Gupta, Abhishekh; Ribeiro, Andre S.. "SGNS2: a compartmentalized stochastic chemical kinetics simulator for dynamic cell populations". Bioinformatics (2012): https://publons.com/publon/1008057/.
    10.1093/BIOINFORMATICS/BTS556
  57. Emmert-Streib, Frank; Hakkinen, Antti; Ribeiro, Andre S.. "Detecting sequence dependent transcriptional pauses from RNA and protein number time series". BMC Bioinformatics (2012): https://publons.com/publon/7599979/.
    10.1186/1471-2105-13-152
  58. Kandhavelu, Meenakshisundaram; Lloyd-Price, Jason; Gupta, Abhishekh; Muthukrishnan, Anantha-Barathi; Yli-Harja, Olli; Ribeiro, Andre S.. "Regulation of mean and noise of the in vivo kinetics of transcription under the control of the lac/ara-1 promoter". FEBS Letters (2012): https://publons.com/publon/1008055/.
    10.1016/J.FEBSLET.2012.09.014
  59. Martins, Leonardo; Makela, Jarno; Hakkinen, Antti; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Fonseca, Jose M.; Ribeiro, Andre S.. "Dynamics of transcription of closely spaced promoters in Escherichia coli, one event at a time". Journal of Theoretical Biology (2012): https://publons.com/publon/3663283/.
    10.1016/J.JTBI.2012.02.015
  60. Ribeiro, Andre S.; Hakkinen, Antti; Lloyd-Price, Jason. "Effects of gene length on the dynamics of gene expression". Computational Biology and Chemistry (2012): https://publons.com/publon/1008058/.
    10.1016/J.COMPBIOLCHEM.2012.10.002
  61. Ribeiro, Andre S.; Eales, Brenda A.; Biddle, Fred G.. "Learning of paw preference in mice is strain dependent, gradual and based on short-term memory of previous reaches". Animal Behaviour (2011): https://publons.com/publon/12203382/.
    10.1016/J.ANBEHAV.2010.10.014
  62. Smolander, Olli-Pekka; Kandhavelu, Meenakshisundaram; Mannerstrom, Henrik; Lihavainen, Eero; Kalaichelvan, Shanmugapriya; Healy, Shannon; Yli-Harja, Olli; Karp, Matti; Ribeiro, Andre S.. "Cell-to-cell diversity in protein levels of a gene driven by a tetracycline inducible promoter". BMC Molecular Biology (2011): https://publons.com/publon/9946562/.
    10.1186/1471-2199-12-21
  63. Makela, Jarno; Huttunen, Heikki; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Ribeiro, Andre S.. "Automatic detection of changes in the dynamics of delayed stochastic gene networks and in vivo production of RNA molecules in Escherichia coli". Bioinformatics (2011): https://publons.com/publon/1255023/.
    10.1093/BIOINFORMATICS/BTR471
  64. Potapov, Ilya; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S.. "Dynamics of a genetic toggle switch at the nucleotide and codon levels". Physical Review E (2011): https://publons.com/publon/1008061/.
    10.1103/PHYSREVE.84.031903
  65. Makela, Jarno; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S.. "Stochastic sequence-level model of coupled transcription and translation in prokaryotes". BMC Bioinformatics (2011): https://publons.com/publon/1008062/.
    10.1186/1471-2105-12-121
  66. Kandhavelu, Meenakshisundaram; Mannerstrom, Henrik; Gupta, Abhishekh; Hakkinen, Antti; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S.. "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): https://publons.com/publon/1008064/.
    10.1186/1752-0509-5-149
  67. Hakkinen, Antti; Healy, Shannon; Jacobs, Howard T.; Ribeiro, Andre S.. "Genome wide study of NF-Y type CCAAT boxes in unidirectional and bidirectional promoters in human and mouse". Journal of Theoretical Biology (2011): https://publons.com/publon/7507761/.
    10.1016/J.JTBI.2011.04.027
  68. Ribeiro, Andre S.; Lloyd-Price, Jason; Chowdhury, Sharif; Yli-Harja, Olli. "Diversity of temporal correlations between genes in models of noisy and noiseless gene networks". BioSystems (2011): https://publons.com/publon/1008059/.
    10.1016/J.BIOSYSTEMS.2011.02.003
  69. Ribeiro, Andre S.; Lloyd-Price, Jason; Eales, Brenda A.; Biddle, Fred G.. "Dynamic Agent-Based Model of Hand-Preference Behavior Patterns in the Mouse". Adaptive Behavior (2010): https://publons.com/publon/1008065/.
    10.1177/1059712309339859
  70. Ribeiro, Andre S.. "Stochastic and delayed stochastic models of gene expression and regulation". Mathematical Biosciences (2010): https://publons.com/publon/12203384/.
    10.1016/J.MBS.2009.10.007
  71. Ribeiro, Andre S.; Hakkinen, Antti; Healy, Shannon; Yli-Harja, Olli. "Dynamical effects of transcriptional pause-prone sites". Computational Biology and Chemistry (2010): https://publons.com/publon/12203388/.
    10.1016/J.COMPBIOLCHEM.2010.04.003
  72. Ribeiro, Andre S.; Hakkinen, Antti; Mannerstrom, Henrik; Lloyd-Price, Jason; Yli-Harja, Olli. "Effects of the promoter open complex formation on gene expression dynamics". Physical Review E (2010): https://publons.com/publon/1008063/.
    10.1103/PHYSREVE.81.011912
  73. Rajala, Tiina; Hakkinen, Antti; Healy, Shannon; Yli-Harja, Olli; Ribeiro, Andre S.. "Effects of Transcriptional Pausing on Gene Expression Dynamics". PLOS Computational Biology (2010): https://publons.com/publon/12203386/.
    10.1371/JOURNAL.PCBI.1000704
  74. Chowdhury, Sharif; Lloyd-Price, Jason; Smolander, Olli-Pekka; Baici, Wayne C. V.; Hughes, Timothy R.; Yli-Harja, Olli; Chua, Gordon; Ribeiro, Andre S.. "Information propagation within the Genetic Network of Saccharomyces cerevisiae". BMC Systems Biology (2010): https://publons.com/publon/1008067/.
    10.1186/1752-0509-4-143
  75. Ribeiro, Andre S.; Dai, Xiaofeng; Yli-Harja, Olli. "Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch". Journal of Theoretical Biology (2009): https://publons.com/publon/12203390/.
    10.1016/J.JTBI.2009.05.025
  76. Smolander, Olli-Pekka; Ribeiro, Andre S.; Yli-Harja, Olli; Karp, Matti. "Identification of beta-lactam antibiotics using bioluminescent Escherichia coli and a support vector machine classifier algorithm". Sensors and Actuators B: Chemical (2009): https://publons.com/publon/12203389/.
    10.1016/J.SNB.2009.06.019
  77. Dai, Xiaofeng; Yli-Harja, Olli; Ribeiro, Andre S.. "Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources". Bioinformatics (2009): https://publons.com/publon/12203391/.
    10.1093/BIOINFORMATICS/BTP411
  78. Ribeiro, Andre S.; Smolander, Olli-Pekka; Rajala, Tiina; Hakkinen, Antti; Yli-Harja, Olli. "Delayed Stochastic Model of Transcription at the Single Nucleotide Level". Journal of Computational Biology (2009): https://publons.com/publon/12203394/.
    10.1089/CMB.2008.0153
  79. Zanotto, Ernesto; Hakkinen, Antti; Teku, Gabriel; Shen, Bairong; Ribeiro, Andre S.; Jacobs, Howard T.. "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 (2009): https://publons.com/publon/7507805/.
    10.1016/J.BBAGRM.2009.05.001
  80. Dai, Xiaofeng; Healy, Shannon; Yli-Harja, Olli; Ribeiro, Andre S.. "Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch". Journal of Theoretical Biology (2009): https://publons.com/publon/12203392/.
    10.1016/J.JTBI.2009.08.024
  81. Ribeiro, Andre S.; Lloyd-Price, Jason; Kesseli, Juha; Haekkinen, Antti; Yli-Harja, Olli. "Quantifying local structure effects in network dynamics". Physical Review E (2008): https://publons.com/publon/1008066/.
    10.1103/PHYSREVE.78.056108
  82. Ribeiro, Andre S.; Kauffman, Stuart A.; Lloyd-Price, Jason; Samuelsson, Bjoern; Socolar, Joshua E. S.. "Mutual information in random Boolean models of regulatory networks". Physical Review E (2008): https://publons.com/publon/1008069/.
    10.1103/PHYSREVE.77.011901
  83. Ribeiro, Andre S.. "Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments". Physical Review E (2008): https://publons.com/publon/12203407/.
    10.1103/PHYSREVE.78.061902
  84. Ribeiro, Andre S.; Lloyd-Price, Jason. "SGN Sim, a stochastic genetic networks simulator". Bioinformatics (2007): https://publons.com/publon/1008070/.
    10.1093/BIOINFORMATICS/BTM004
  85. Ribeiro, Andre S.. "Effects of coupling strength and space on the dynamics of coupled toggle switches in stochastic gene networks with multiple-delayed reactions". Physical Review E (2007): https://publons.com/publon/12203411/.
    10.1103/PHYSREVE.75.061903
  86. Zhu, Rul; Ribeiro, Andre S.; Salahub, Dennis; Kauffman, Stuart A.. "Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models". Journal of Theoretical Biology (2007): https://publons.com/publon/12203405/.
    10.1016/J.JTBI.2007.01.021
  87. Ribeiro, Andre S.; Kauffman, Stuart A.. "Noisy attractors and ergodic sets in models of gene regulatory networks". Journal of Theoretical Biology (2007): https://publons.com/publon/12203406/.
    10.1016/J.JTBI.2007.04.020
  88. Ribeiro, Andre S.; Charlebois, Daniel A.; Lloyd-Price, Jason. "CellLine, a stochastic cell lineage simulator". Bioinformatics (2007): https://publons.com/publon/1008068/.
    10.1093/BIOINFORMATICS/BTM491
  89. Ribeiro, Andre S.. "Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks". Physical Review E (2007): https://publons.com/publon/12203404/.
    10.1103/PHYSREVE.76.051915
  90. Ribeiro, Andre S.; Almeida, Miguel. "A proposed model for small-world structural organization of mission teams and tasks in order to optimize efficiency and minimize costs". Acta Astronautica (2006): https://publons.com/publon/12203417/.
    10.1016/J.ACTAASTRO.2005.07.056
  91. Ribeiro, Andre; Zhu, Rui; Kauffman, Stuart A.. "A general modeling strategy for gene regulatory networks with stochastic dynamics". Journal of Computational Biology (2006): https://publons.com/publon/12203415/.
    10.1089/CMB.2006.13.1630
  92. Ribeiro, AS; Lind, PG. "Effects of lattice structure in the dynamics of coupled elements". Physica Scripta (2005): https://publons.com/publon/6293264/.
    10.1238/PHYSICA.TOPICAL.118A00165