J51. Evolving Neural Networks through a Reverse Encoding Tree
H. Zhang, C-H. Huck Yang, H. Zenil, N.A. Kiani, Y. Shen and J. Tegnér
submitted [preprint]

J50. On incompressible multidimensional networks
F.S. Abrahao, K. Wehmuth, H. Zenil, and A. Ziviani 
submitted [preprint]

J49. Algorithmic Probability-guided Machine Learning On Non-differentiable Spaces 
S. Hernández-Orozco, H. Zenil, J. Riedel, A. Uccello , N.A. Kiani, and J. Tegnér
​submitted [preprint]

J48. Controllability, Multiplexing, and Transfer Learning in Networks using Evolutionary Learning
R. Ooi, C.-H. Huck Yang, P.-Yu Chen, V. Eguiluz, N.A. Kiani, H. Zenil, D. Gómez-Cabrero, J. Tegnér
submitted [preprint]

J47. Immunometabolic network interactions of the kynurenine pathway in cutaneous malignant melanoma
Soudabeh Rad Pour, Hiromasa Morikawa, Narsis A. Kiani, David Gomez-Cabrera, ... Jesper Tegnér
Frontiers in Oncology-Cancer Metabolism  (accepted)

J46. Complexity of post-processing in GATE-driven X-ray spectrum
N. Gholamia, M. Mahdi Dehshibia, M. Fazlalib, Antonio Rueda-Toicen, H. Zenil, A. Adamatzky
Journal of Information Processing (accepted) [preprint]

J45. Training-free Measures Based on Algorithmic Probability Identify High Nucleosome Occupancy in DNA Sequences
H. Zenil, P. Minary
Nucleic Acids Research, gkz750, 2019. [online]

J44. Exhaustion of CD4+ t-cells mediated by the Kynurenine pathway in Melanoma
SR Pour, H Morikawa, NA Kiani, M Yang, A Azimi, G Shafi, M Shang, ...
Scientific reports 9 (1), 1-11, 2019 [online]

J43. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen 
S.M Hill, L.M. Heiser, (...) i.a. N.A. Kiani, H. Zenil (DREAM Challenge Consortium) (...), G. Stolovitzky, J. Guinney, J.R Dry, J. Saez-Rodriguez
Nature Communications, vol. 10, Article number: 2674, 2019.  [online] (NPG)

J42. MAPK pathway and B cells overactivation in multiple sclerosis revealed by phosphoproteomics and genomic analysis
E Kotelnikova, NA Kiani, D Messinis, I Pertsovskaya, V Pliaka, . . ., J Tegnér, P Villoslada
Proceedings of the National Academy of Sciences, 116 (19), 9671-9676, 2019. [online]

J41. Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg‐mediated suppression of cytokine expression
RN Joshi, SJ Fernandes, MM Shang, NA Kiani, D Gomez‐Cabrero, J Tegnér, A. Schmidt
Journal of leukocyte biology, 2019. [online]

J40. Network modules uncover mechanisms of skeletal muscle dysfunction in COPD patients
Á Tényi, I Cano, F Marabita, NA Kiani, SG Kalko, E Barreiro, P de Atauri, . . .
Journal of translational medicine 16 (1), 34, 2019. [online]

J39. Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3
A Schmidt, F Marabita, NA Kiani, CC Gross, HJ Johansson, S Éliás, ...
BMC Biology 16 (1), 47, 2018. [online]

J38. Causal Deconvolution by Algorithmic Generative Models
H. Zenil, N.A. Kiani, A. Zea, J. Tegnér
Nature Machine Intelligence, vol 1(1), pp. 58-66, 2019. [preprint]

J37. A Review of Graph and Network Complexity from an Algorithmic Information Perspective
H. Zenil, N.A. Kiani, J. Tegnér
Entropy 20(8):551, 2018. [online]

J36. Quantifying Natural and Artificial Intelligence in Robots and Natural Systems with an Algorithmic Behavioural Test
H. Zenil
In F.P. Bonsignorio, et al. (eds.), Metrics of sensory motor integration in robots and animals
Springer Cosmos Series, Cognitive Systems Monographs, Springer, 2019. [preprint]

J35. Symmetry and Correspondence of Algorithmic Complexity over Geometric, Spatial and Topological Representations
H. Zenil, N.A. Kiani and J. Tegnér
Entropy, 20(7), 534, 2018 [online]

J34.  Coding-theorem Like Behaviour and Emergence of the Universal Distribution from Resource-bounded Algorithmic Probability 
H. Zenil*, L. Badillo, S. Hernández-Orozco and F. Hernandez-Quiroz
International Journal of Parallel Emergent and Distributed Systems, 2018  [online, preprint]
(Taylor & Francis)

J33. Data Dimensionality Reduction and Network Sparsification By Minimal Algorithmic Information Loss
H. Zenil, N.A. Kiani, A. Rueda-Toicen, ​A. Zea, J. Tegnér 
submitted [preprint]

J32. An Algorithmic Refinement of Maxent Induces a Thermodynamic-like Behaviour in the Reprogrammability of Generative Mechanisms
H. Zenil, N.A. Kiani, J. Tegnér
Entropy, 21(6), 560, 2019  [online]

J31. An Algorithmic Information Calculus for Causal Discovery and Reprogramming Systems
H. Zenil, N.A. Kiani, F. Marabita, Y. Deng, S. Elias, A. Schmidt, G. Ball, J. Tegnér
​iScience (in press) [preprint, video]

J30. Algorithmically probable mutations reproduce aspects of evolution such as convergence rate, genetic memory, and modularity
S. Hernández-Orozco, H. Zenil and N.A. Kiani
Royal Society Open Science, 5:180399, 2018 [online]

J29. Algorithmic Information Dynamics of Emergent, Persistent, and Colliding Particles in the Game of Life
H. Zenil, N.A. Kiani and J. Tegnér
In A. Adamatzky (ed), From Parallel to Emergent Computing
Taylor & Francis / CRC Press, 2019. [preprint]

J28. A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity
H. Zenil, S. Hernández-Orozco, N.A. Kiani, F. Soler-Toscano, A. Rueda-Toicen
Entropy 20(8), 605, 2018. [online]

J27. HiDi: An Efficient Reverse Engineering Schema for Large Scale Dynamic Regulatory Network Reconstruction Using Adaptive Differentiation
Y. Deng, H. Zenil, J. Tegnér and N.A. Kiani
Bioinformatics, btx501, 2017. [preprint, online] 

J26. Dynamics and Heterogeneity of Brain Damage in Multiple Sclerosis
E. Kotelnikova, N.A. Kiani, E. Abad, E.H Martinez-Lapiscina, M. Andorra, I. Zubizarreta, I. Pulido-Valdeolivas, I. Pertsovskaya, L. Alexopoulos, T. Olsson, R. Martin, J. Tegner, F. Paul, J. Garcia-Ojalvo, P. Villoslada
PLoS Comput Biol, 13(10): e1005757 [online]

J25. Low Algorithmic Complexity Entropy-deceiving Graphs
H. Zenil, N.A. Kiani and Jesper Tegnér
Phys Rev. E 96. 012308, 2017 [online]

J24. A Minimal Unified Model of Disease Trajectories Captures Hallmarks of Multiple Sclerosis
V. Kannan, N.A. Kiani, F. Piehl, J. Tegnér
Mathematical Biosciences 289, 1-8, 2017 [online]

J23. Human Behavioral Complexity Peaks at Age 25 
N. Gauvrit, H. Zenil, F. Soler-Toscano, J.-P. Delahaye, P. Brugger
PLoS Comput Biol, 13(4): e1005408, 2017 [online]

J22. Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems
A. Adams, H. Zenil, P.W.C. Davies and S.I. Walker
Scientific Reports 7, Article number: 997, 2017 [online]

J21. Systems Toxicology: Systematic Approach to Predict Toxicity
N.A. Kiani, M.M. Shang and J. Tegnér
Current Pharmaceutical Design, 2016 (online ahead of print) [online]

J20. Perspective on Bridging Scales and Design of Models using Low-Dimensional Manifolds & Data-driven Model Inference
J. Tegner, H. Zenil, N.A. Kiani, G. Ball and D. Gomez-Cabrero
Philosophical Transactions of the Royal Society A, volume 374, issue 2080,  2016 [online]

J19. Flow of Information in Biological Systems (editorial to special issue)
A. Masoudi-Nejad and H. Zenil
Seminars in Cell and Developmental Biology, vol. 51 pp 1-2, 2016 [online]

J18. Empirical assessment of causal network learning through a community-based effort
i.a. H. Zenil (DREAM Challenge Consortium)
Nature Methods  13, pp. 310–318, 2016 [online]

J17. Methods of Information Theory and Algorithmic Complexity for Network Biology
H. Zenil, N.A. Kiani and J. Tegnér
Seminars in Cell and Developmental Biology  vol. 51, pp. 32-43, 2016 [online, preprint]
​​
J16. Quantifying Loss of Information in Network-based Dimensionality Reduction Techniques
H. Zenil, N.A. Kiani and J. Tegnér
Journal of Complex Networks, vol. 4:(3) pp. 342-362, 2016 [online, preprint]

J15. Evaluating Network Inference Methods in Terms of Their Ability to Preserve the Topology and Complexity of Genetic Networks
N.A. Kiani, H. Zenil, J. Olczak and J. Tegnér
Seminars in Cell and Developmental Biology, vol. 51, pp. 44-52, 2016 [online, preprint]

P14. Undecidability and Irreducibility Conditions for Open-Ended Evolution and Emergence
S. Hernández-Orozco, F. Hernández-Quiroz and H. Zenil
15th International Conference on the Synthesis and Simulation of Living Systems, Artificial Life Conference (ALIFE), MIT Press, 2016 [online,preprint]

P13. Causality, Information and Biological Computation
H. Zenil, A. Schmidt and J. Tegnér
In S I. Walker, P.C.W. Davies and G. Ellis (eds.), Information and Causality: From Matter to Life,
Cambridge University Press, pp. 244-279, 2017 [preprint]

P12. Algorithmic Data Analytics, Small Data Matters and Correlation versus Causation
H. Zenil
In M. Ott, W. Pietsch, J. Wernecke (eds.), Berechenbarkeit der Welt? Philosophie und Wissenschaft im Zeitalter von Big Data (Computability of the World? Philosophy and Science in the Age of Big Data)
Springer Verlag, pp 453-475, 2016 [preprint]
​
P11. Asymptotic Intrinsic Universality and Reprogrammability by Behavioural Emulation
H. Zenil and J. Riedel
Invited contribution in Advances in Unconventional Computation. A. Adamatzky (ed)
​Springer Verlag, pp. 205-220, 2016 [preprint]

P10. Topological Evaluation of Methods for Reconstruction of Genetic Regulatory Networks
J. Olczak, N.A. Kiani, H. Zenil and J. Tegnér
Proceedings of the IEEE Workshop on Complex Networks, SITIS, Bangkok 2015. [online program]

J9. Two-Dimensional Kolmogorov Complexity and Validation of the Coding Theorem Method by Compressibility
H. Zenil, F. Soler-Toscano, J.-P. Delahaye and N. Gauvrit
PeerJ Computer Science, 1:e23, 2015 [online]

P8. The Information-theoretic and Algorithmic Approach to Human, Animal and Artificial Cognition
N. Gauvrit, H. Zenil and J. Tegnér
In G. Dodig-Crnkovic and R. Giovagnoli (Eds.) Representation and reality : Humans, animals and machines.
pp. 117-139, Springer, 2017 [preprint]

P7. Numerical Investigation of Graph Spectra and Information Interpretability of Eigenvalues
H. Zenil, N.A. Kiani and J. Tegnér
In F. Ortuño & I. Rojas (Eds.): 3rd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO) 2015, Part II,  LNCS 9044, pp. 395--405. Springer, 2015. [preprint, online]

J6. Dynamic Probabilistic Threshold Networks to Infer Signaling Pathways from Time-Course Perturbation Data
N.A. Kiani and L. Kaderali
BMC Bioinformatics 15(1):250, 2014

J5 Signaling networks in MS: A systems-based approach to developing new pharmacological therapies
i.a. N.A. Kiani
Multiple Sclerosis Journal, 21(2), 2014

J4. Algorithmicity and Programmability in Natural Computing with the Game of Life as an In Silico Case Study
H. Zenil
Journal of Experimental & Theoretical Artificial Intelligence, Volume 27, Issue 1, pp. 109-121, 2015 [online]

J3 Systems Medicine: From molecular features and models to the clinic in COPD
i.a. N.A. Kiani
Journal of Translational Medicine 12(Suppl 2), 2014

J2 Laplace transform formula on fuzzy nth-order derivative and its application in fuzzy ordinary differential equations
M. Barkhordari Ahmadi, N.A. Kiani and N. Mikaeilvand
Soft Computing 18(12), 2014

J1. Correlation of Automorphism Group Size and Topological Properties with Program-size Complexity Evaluations of Graphs and Complex Networks
H. Zenil, F. Soler-Toscano, K. Dingle and A. Louis
Physica A: Statistical Mechanics and its Applications, vol. 404, pp. 341–358, 2014 [online, preprint]