Publications
Mechanistic regulation of planarian shape during growth and degrowth
J.M. Ko, W. Reginato, A. Wolff, D. Lobo
Development 151 (9): dev202353, 2024.
(Highlighted and interviewed)
Automatic design of gene regulatory mechanisms for spatial pattern formation
R. Mousavi, D. Lobo
NPJ Systems Biology and Applications 10, 35, 2024.
mergem: merging, comparing, and translating genome-scale metabolic models using universal identifiers
A. Hari, A. Zarrabi, D. Lobo
NAR Genomics and Bioinformatics 6(1), lqae010, 2024.
Mechanistic regulation of planarian shape during growth and degrowth
J.M. Ko, W. Reginato, D. Lobo
bioRxiv doi:10.1101/2023.09.15.557968, 2023.
mergem: merging and comparing genome-scale metabolic models using universal identifiers
A. Hari, D. Lobo
bioRxiv doi:10.1101/2022.07.14.499633, 2022.
In situ probe and inhibitory RNA synthesis using streamlined gene cloning with Gibson assembly
A. Wolff, C. Wagner, J. Wolf, D. Lobo
STAR Protocols 3, 101458, 2022.
Formalizing phenotypes of regeneration
D. Lobo
Whole-Body Regeneration
S. Blanchoud, B. Galliot (eds.)
Springer pp. 663-679, 2022.
Automatic generation of interactive multidimensional phase portraits
O.O. Ogunsan, D. Lobo
bioRxiv doi:10.1101/2022.02.23.481676, 2022.
Inference of dynamic spatial GRN models with multi-GPU evolutionary computation
R. Mousavi, S.H. Konuru, D. Lobo
Briefings in Bioinformatics 22(5), bbab104, 2021.
Computational systems biology of morphogenesis
J.M. Ko, R. Mousavi, D. Lobo
Computational Systems Biology in Medicine and Biotechnology
S. Cortassa, M.A. Aon (eds.)
Springer pp. 343-365, 2021.
Kinetic modeling of microbial growth, enzyme activity, and gene deletions: an integrated model of β-glucosidase function in Cellvibrio japonicus
J. Hwang, A. Hari, R. Cheng, J.G. Gardner, D. Lobo
Biotechnology and Bioengineering 117, pp. 3876-3890, 2020.
Fluxer: a web application to compute, analyze, and visualize genome-scale metabolic flux networks
A. Hari, D. Lobo
Nucleic Acids Research 48, pp. 427-435, 2020.
Curation and annotation of planarian gene expression patterns with segmented reference morphologies
J. Roy, E. Cheung, J. Bhatti, A. Muneem, D. Lobo
Bioinformatics 36(9), pp. 2881-2887, 2020.
Continuous dynamic modeling of regulated cell adhesion: sorting, intercalation, and involution
J.M. Ko, D. Lobo
Biophysical Journal 117(11), pp. 2166-2179, 2019.
Cross-inhibition of Turing patterns explains the self-organized regulatory mechanism of planarian fission
S. Herath, D. Lobo
Journal of Theoretical Biology 485, 110042, 2019.
Continuous dynamic modeling of regulated cell adhesion
J.M. Ko, D. Lobo
bioRxiv 582429, 2019.
Modeling regenerative processes with Membrane Computing
M. García-Quismondo, M. Levin, D. Lobo
Information Sciences 381, pp. 229-249, 2017.
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.
Computing a worm: reverse-engineering planarian regeneration
D. Lobo, M. Levin
Advances in Unconventional Computing: Emergence, Complexity and Computation
A. Adamatzky (ed.)
Springer pp. 637-654, 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.
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.