Publications


Discovering novel phenotypes with automatically inferred dynamic models: a partial melanocyte conversion in Xenopus
D. Lobo, M. Lobikin, M. Levin
Scientific Reports 7, 41339, 2017.


Modeling regenerative processes with Membrane Computing
M. García-Quismondo, M. Levin, D. Lobo
Information Sciences 381, pp. 229-249, 2017.


Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian regeneration
D. Lobo, J. Morokuma, M. Levin
Bioinformatics 32(17), pp. 2681-2685, 2016.


Computing a worm: reverse-engineering planarian regeneration
D. Lobo, M. Levin
Advances in Unconventional Computing
A. Adamatzky (ed.)
Springer 637-654, 2016.


Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form
F. Durant, D. Lobo, J. Hammelman, M. Levin
Regeneration 3(2), pp. 78-102, 2016.
(Selected for the journal cover)


MoCha: molecular characterization of unknown pathways
D. Lobo, J. Hammelman, M. Levin
Journal of Computational Biology 23(4): 291-297, 2016.


Artificial neural networks as models of robustness in development and regeneration: stability of memory during morphological remodeling
J. Hammelman, D. Lobo, M. Levin
Artificial Neural Network Modelling
S. Shanmuganathan, S. Samarasinghe (eds.)
Springer pp. 45-65, 2016.


Gap junctional blockade stochastically induces different species-specific head anatomies in genetically wild-type Girardia dorotocephala flatworms
M. Emmons-Bell, F. Durant, J. Hammelman, N. Bessonov, V. Volpert, J. Morokuma, K. Pinet, D. Adams, A. Pietak, D. Lobo, M. Levin
International Journal of Molecular Sciences 16(11), 27865-27896, 2015.
(Selected for the journal cover)


A dynamic architecture of life
B.P. Rubin, J. Brockes, B. Galliot, U. Grossniklaus, D. Lobo, M. Mainardi, M. Mirouze, A. Prochiantz, A. Steger
F1000Research 4:1288, 2015.


Serotonergic regulation of melanocyte conversion: A bioelectrically regulated network for stochastic all-or-none hyperpigmentation
M. Lobikin, D. Lobo, D.J. Blackiston, C.J. Martyniuk, E. Tkachenko, M. Levin
Science Signaling 8(397), pp. ra99, 2015.
(Reviewed in a focus paper)


Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration
D. Lobo, M. Levin
PLoS Computational Biology 11(6): e1004295, 2015.


Limbform: a functional ontology-based database of limb regeneration experiments
D. Lobo, E.B. Feldman, M. Shah, T.J. Malone, M. Levin
Bioinformatics 30(24), pp. 3598-3600, 2014.


A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration
D. Lobo, E.B. Feldman, M. Shah, T.J. Malone, M. Levin
Regeneration 1(2), pp. 37-56, 2014.


Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search
M. Budnikova, J.W. Habig, D. Lobo, N. Cornia, M. Levin, T. Andersen
BMC Bioinformatics 15:178, 2014.


A linear-encoding model explains the variability of the target morphology in regeneration
D. Lobo, M. Solano, G.A. Bubenik, M. Levin
Journal of the Royal Society Interface 30(24), pp. 3598-3600, 2014.
(Recommended by F1000Prime, Faculty of 1000, 718232471)


Planform: an application and database of graph-encoded planarian regenerative experiments
D. Lobo, T.J. Malone, M. Levin
Bioinformatics 29(8), pp. 1098-1100, 2013.


Towards a bioinformatics of patterning: a computational approach to understanding regulative morphogenesis
D. Lobo, T.J. Malone, M. Levin
Biology Open 2(2), pp. 156-169, 2013.
(Selected for the journal cover)


Behavior-finding: morphogenetic designs shaped by function
D. Lobo, J.D. Fernández, F.J. Vico
Morphogenetic Engineering: Toward Programmable Complex Systems
R. Doursat, H. Sayama, O. Michel (eds.)
Springer-Verlag pp. 441-472, 2013.


Resting potential, oncogene-induced tumorigenesis, and metastasis: the bioelectric basis of cancer in vivo
M. Lobikin, B. Chernet, D. Lobo, M. Levin
Physical Biology 9(6): 065002, 2012.
(Selected for the journal cover)


Modeling planarian regeneration: a primer for reverse-engineering the worm
D. Lobo, W.S. Beane, M. Levin
PLoS Computational Biology 8(4): e1002481, 2012.
(Selected for the journal cover)


Emergent diversity in an open-ended evolving virtual community
J.D. Fernández, D. Lobo, G.M. Martín, R. Doursat, F.J. Vico
Artificial Life 18(2), pp. 199-222, 2012.


Graph grammars with string-regulated rewriting
D. Lobo, F.J. Vico, J. Dassow
Theoretical Computer Science 412(43), pp. 6101-6111, 2011.
(Reviewed in Mathematical Reviews, American Mathematical Society, MR2883035)


Evolution of form and function in a model of differentiated multicellular organisms with gene regulatory networks
D. Lobo, F.J. Vico
BioSystems 102(2-3), pp. 112-123, 2010.


Evolutionary development of tensegrity structures
D. Lobo, F.J. Vico
BioSystems 101(3), pp. 167-176, 2010.


Reconfiguration algorithms for robotically manipulatable structures
D. Lobo, D.A. Hjelle, H. Lipson
Proceedings of the ASME/IFToMM Intern. Conf. on Reconfigurable Mechanisms and Robots
J.S. Dai, M. Zoppi, X. Kong (eds.)
ReMAR2009 pp. 13-22, London, UK, 2009.


Robust off- and online separation of intracellularly recorded up and down cortical states
Y. Seamari, J.A. Narvaez, F.J. Vico, D. Lobo, M.V. Sanchez-Vives
PLoS ONE 2(9): e888, 2007.


Mobile just-in-time training application for emergency healthcare services
F.J. Vico, V. Canteli, D. Lobo, J.D. Fernández, C. Bandera, A. García-Linares, R. Rivas, M. Rosen, B. Schlegel
Proceedings of the IADIS International Conference on Mobile Learning
I. Arnedillo-Sanchez (ed.)
IADIS2007 pp. 209-213, Lisbon, Portugal, 2007.