The AdaLab project has produced many outputs, including:

• Public reports documenting the progress of the project.
• Major scientific deliverables from the project, including the OUK ontology and a knowledge base relating to the diauxic shift in yeast.
• Scientific papers describing the scientific outputs arising from the AdaLab project.

Journal Publications

Trejo Banos D, Trebulle P, Elati M. (2017) Integrating transcriptional activity in genome-scale models of metabolism, BMC Systems Biology 11 (Suppl. 7): 134. DOI: 10.1186/s12918-017-0507-0

Dhifli, W, Da Costa NO, Elati, M. An Evolutionary Schema for Mining Skyline Clusters of Attributed Graph Data IEEE Congress on Evolutionary Computation (2017): pp. 2102-2109 doi:10.1109/CEC.2017.7969559

Trébulle P, Nicaud J-M, Leplat Ch, Elati M, (2017) Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica, Nature npj Systems Biology and Applications 3 :21 doi:10.1038/s41540-017-0024-1

Soldano H, Santini G, and Bouthinon D. "Formal Concept Analysis of Attributed Networks", in Formal Concept Analysis in Social Network Analysis, Rokia Missaoui and Sergei Obiedkov and Sergei Kuznetsov (eds), Springer, 2017.

King RD, Costa V.Sh, Mellingwood C, and Soldatova LN. (2018) Automating science: philosophical and social dimensions. IEEE Technology and Society Magazine

Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Soldatova LN, et al. (2016) The Ontology for Biomedical Investigations. PLoS ONE 11(4): e0154556.

Njah H, Jamoussi S, Mahdi W and Elati M. (2016) A Bayesian approach to construct context-specific gene ontology. Computational Intelligence in Bioinformatics and Computational Biology, IEEE, pp. 1-6

Panov, P., Soldatova, L.N., and Dzeroski, S. (2016) Generic Ontology of Datatypes. Information Sciences Journal: 329/C, p. 900-920.

Picchetti, T.; Chiquet, J.; Elati, M.; Neuvial, P.; Nicolle, R.; Birmelé, E. (2015) A model for gene deregulation detection using expression data, BMC Systems Biology: 9 (Suppl 6): S6

Soldano, H., Santini, G., Bouthinon, D. (2016). Efficient Pattern Mining in Attributed Graphs , MARAMI

International Seminars and Conference Presentations

King, R. Robot Scientists: Automating Science Robotics and Semantic Systems for Biology (RSSB 2); Tokyo, Japan; 27 Jan 2018

King, R. The Automation of Science; 21st International SANKEN Symposium: AI Evolution in Science and Technology; Osaka, Japan; 16-17 Jan 2018

Balakirsky et al (incl. Soldatova, L.) "Towards a Robot Task Ontology Standard”; paper accepted for IEEE conference: MSEC_2017

King, R. Robot Scientists: Automating Medical Research (Keynote lecture) World Medical Robotics Conference; Shenzhen, China; Nov 25-26 2017

Elati, M.; Trejo, D.; Trébulle, P. Integrating transcriptional activity in genome-scale models of metabolism 16th International Conference on Bioinformatics; Tsinghua University, China; 20-22 Sept 2017

King, R. “AI for Biology”; Talk at the UK Embassy in Tokyo; UK-Japan AI Collaboration; March 31st 2017

Soldatova et al “Towards Reproducible Science” Birla Institute of Technology & Science; Pilani, India, 2017.

King, R. Robot Scientists: Automating Drug Design (Plenary Lecture) 3rd International Symposium for Medicinal Sciences; Sendai, Japan; 24-27 March 2017

Elati,M. “From biological network reconstruction to data analysis and visualization”. 6th Annual World DNA and Genome Day (WDD-2015) – Phase B04: Bioinformatics/Computational Tools, Big Data Analysis and Visualization, Nanjing, China

King, R. The Adam and Eve Robot Scientists for the Automated Discovery of Scientific Knowledge American Physical Society; New Orleans, USA; 17th March 2017

Soldatova et al “Reproducible Science” AAAI Fall symposium in Arlington (US), 2016

Soldatova et al ‘On Semantic Representations for Laboratory Automation’ Robotics and Semantic Systems for Biology (RSSB) Symposium; Tokyo, Japan; June 28th 2016

King, R. Automating Chemistry and Biology using Robot Scientists Robotics and Semantic Systems for Biology (RSSB) Symposium; Tokyo, Japan; June 28th 2016

King, R. Automating Chemistry and Biology using Robot Scientists Information Sciences Institute, University of Southern California, USA; November 19th 2015

Soldatova, L. On the Representation of Research Hypotheses; Information Sciences Institute, University of Southern California, USA; November 19th 2015

King, R. Robot Scientists: Automating Chemistry and Biology Argonne National Laboratory, USA; July 1st 2015

European Seminars and Conference Presentations

Elati, M. Inférence, interrogation et ingénierie de réseaux de facteurs de transcription.” Journées BIOSS- ASSTABIO, Apprentissage de réseaux à partir de données biologique. Rennes, March 2018

King, R. European Robotics Forum; Tampere, Finland; March 13-15 2018

Coutant, A., Rouveirol, C., Santini, G., Bouthinon, D., Soldano, H. Dynamic models revision for robot assisted scientific discovery, Poster, HCERES evaluation of LIPN, Feb. 2018

Elati, M. Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica” 3rd Conference of the French Research Group on Synthetic Biology, La Grand Motte, October 2017.

King, R. The Automation of Science. OECD – AI: Intelligent Machines, Smart Policies; Paris, France; Oct 26-27 2017.

Maikore, F.S.; Selenge, G.; Olayinka, A.; Abbott, P.; Soldatova L. OCL-SOP: an Ontology for Clinical Laboratory Standard Operating Procedures; ODLS; Bolzano, Italy; September 22, 2017

Ramon, J. Learning from partly observable time-dependent graphs. Invited presentation: ECML/PKDD workshop on Time-dependent Large-Scale Graphs; Skopje, Macedonia; September 18-22, 2017

Soldatova et al. Knowledge representation and integration for automated drug discovery. 8th SiLA Conference; Basel, Switzerland; September 14, 2017

Roper, K. Automating Glucose and Ethanol Measurement for Study of Diauxic Shift as a Model of the Warburg Effect; Poster presentation: ELRIG; Liverpool, UK; 2017

Coutant, A. and Rouveirol, C. Generative learning of dynamic structures using spanning arborescence sets. MLSB17, Eleventh International Workshop on Machine Learning in Systems Biology (Special Session); ISMB/ECCB 2017; Prague, Czech Republic; July 25, 2017

Coutant, A. and Rouveirol, C., Network Inference of Dynamic Models by the Combination of Spanning Arborescences, Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Lille, 2017

Trejo-Banos, D., Khan, S, Trebulle, P., Elati, M. Network interrogation for phenotype-genotype study of diauxic shift. ICSB 2016, Barcelona, Spain; 18th Sept 2016

King, R. Robot Scientists, the Replication Crisis, and Cancer International Symposium on Medicinal Chemistry Manchester, UK; August 30th 2016

Trejo-Banos, D. and Elati, M. Integrated metabolic-regulatory modelling for diauxic shift analysis in S. cerevisiae. “Grands Graphes et Bioinformatique”, Journées Francophones Extraction et Gestion de Connaissances, EGC Reims, 2016

Rouveirol, C. Découverte dans les réseaux biologiques hétérogènes: l'expérience Adalab, Journées BIOSS-IA 22-23 juin 2017, Gif/Yvette : Modèles logiques pour la représentation formelle des systèmes

Grzebyta, J. and Soldatova, L. Semantic data integration. Brunel University London, UK; 15th Jun 2016

Trejo-Banos, D. and Elati, M. Regulatory-metabolic study of yeast diauxic shift. Evry Spring School on advances in Systems and Synthetic Biology, 2016

Roper, K. ‘Robot Scientists as Flexible Platforms for the Investigation of Biological Problems’ The European Laboratory Research & Innovation Group, Robotics & Automation; Northampton, UK; 4th May 2016

King, R. Robot Scientists, the Replication Crisis, and Cancer. European Robotics Forum, March 21-23 2016; Ljubljana, Slovenia (Invitation from P. Courtney, member of AdaLab Scientific Advisory Board).

King, R. Computing Exponentially Faster: Implementing a Nondeterministic Universal Turing Machine using DNA; Invited talk: Josef Stefan Institute, Ljubljana. March 21st 2016

King, R. What might automation and robotics look like in the future? Automation and robotics for synthetic biology; Manchester, UK; February 25th 2016

Elati, M. Workshop co-organizer of "Grand Graphe et Bioinformatique" EGC, Reims - France, 2016.

Roper, K. Automating Biology & Chemistry Keynote talk, Cisbio’s European Lab Automation “Advances in lab automation & robotics”, Hanover 8th October 2015

King, R. Automating Chemistry and Biology using Robot Scientists Keynote talk, 38th German Conference on AI, University of Dresden, Germany; September 25th 2015

Williams, K.; Bilsland, E.; Sparkes, A.; Aubrey, W.; Young, M.; Soldatova, L. N.; De Grave, K.; Ramon, J.; de Clare, M.; Sirawaraporn, W.; Roper, K. M.; Oliver S. G.; and King R. D: Eve: Integration of machine learning with compound testing in a robot scientist. Poster presentation: ELRIG Drug Discovery Meeting; 2nd September 2015

King, R. Can a Robot do Science? Keynote talk, Summer School of Science 2015, Pozega, Croatia. July 27th 2015

Roper, K. Eve: Integration of machine learning with compound testing in a robot scientist Oral presentation: ELRIG Advances in Cell-based Screening, AZ Mölndal; 17th June 2015

Williams, K.; Bilsland, E.; Sparkes, A.; Aubrey, W.; Young, M.; Soldatova, L. N.; De Grave, K.; Ramon, J.; de Clare, M.; Sirawaraporn, W.; Roper, K. M.; Oliver S. G.; and King R. D.: Eve: Integration of machine learning with compound testing in a robot scientist. Poster presentation: ELRIG Advances in Cell Based Screening in Drug Discovery; AZ Mölndal; 17th June 2015