Publications by authors named "Daniel Lobo"

28Publications

Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus.

Biotechnol Bioeng 2020 Aug 24. Epub 2020 Aug 24.

Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA.

View Article and Find Full Text PDF
August 2020

Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.

Nucleic Acids Res 2020 07;48(W1):W427-W435

Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA.

View Article and Find Full Text PDF
July 2020

Rendering of Constraints With Underactuated Haptic Devices.

IEEE Trans Haptics 2020 Oct-Dec;13(4):699-708. Epub 2020 Dec 25.

View Article and Find Full Text PDF
December 2020

Curation and annotation of planarian gene expression patterns with segmented reference morphologies.

Bioinformatics 2020 05;36(9):2881-2887

Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.

View Article and Find Full Text PDF
May 2020

Continuous Dynamic Modeling of Regulated Cell Adhesion: Sorting, Intercalation, and Involution.

Biophys J 2019 12 31;117(11):2166-2179. Epub 2019 Oct 31.

Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland; Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, Maryland; Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland. Electronic address:

View Article and Find Full Text PDF
December 2019

Cross-inhibition of Turing patterns explains the self-organized regulatory mechanism of planarian fission.

J Theor Biol 2020 01 12;485:110042. Epub 2019 Oct 12.

Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States; Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, United States. Electronic address:

View Article and Find Full Text PDF
January 2020

Discovering novel phenotypes with automatically inferred dynamic models: a partial melanocyte conversion in Xenopus.

Sci Rep 2017 01 27;7:41339. Epub 2017 Jan 27.

Allen Discovery Center at Tufts University, and Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.

View Article and Find Full Text PDF
January 2017

Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form.

Regeneration (Oxf) 2016 Apr 28;3(2):78-102. Epub 2016 Apr 28.

Department of Biology, Allen Discovery Center at Tufts University, Tufts Center for Regenerative and Developmental Biology Tufts University MA 02155 USA.

View Article and Find Full Text PDF
April 2016

Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian regeneration.

Bioinformatics 2016 09 10;32(17):2681-5. Epub 2016 May 10.

Center for Regenerative and Developmental Biology Department of Biology, Tufts University, Medford, MA 02155, USA.

View Article and Find Full Text PDF
September 2016

MoCha: Molecular Characterization of Unknown Pathways.

J Comput Biol 2016 Apr 7;23(4):291-7. Epub 2016 Mar 7.

2 Center for Regenerative and Developmental Biology, and Department of Biology, Tufts University , Medford, Massachusetts.

View Article and Find Full Text PDF
April 2016

Gap Junctional Blockade Stochastically Induces Different Species-Specific Head Anatomies in Genetically Wild-Type Girardia dorotocephala Flatworms.

Int J Mol Sci 2015 Nov 24;16(11):27865-96. Epub 2015 Nov 24.

Center for Regenerative and Developmental Biology and Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.

View Article and Find Full Text PDF
November 2015

Serotonergic regulation of melanocyte conversion: A bioelectrically regulated network for stochastic all-or-none hyperpigmentation.

Sci Signal 2015 Oct 6;8(397):ra99. Epub 2015 Oct 6.

Biology Department and Center for Regenerative and Developmental Biology, Tufts University, Medford, MA 02155, USA.

View Article and Find Full Text PDF
October 2015

Inferring regulatory networks from experimental morphological phenotypes: a computational method reverse-engineers planarian regeneration.

PLoS Comput Biol 2015 Jun 4;11(6):e1004295. Epub 2015 Jun 4.

Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, Medford, Massachusetts, United States of America.

View Article and Find Full Text PDF
June 2015

A bioinformatics expert system linking functional data to anatomical outcomes in limb regeneration.

Regeneration (Oxf) 2014 Apr;1(2):37-56

Center for Regenerative and Developmental Biology, and Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, U.S.A.

View Article and Find Full Text PDF
April 2014

A dynamic architecture of life.

F1000Res 2015 18;4:1288. Epub 2015 Nov 18.

Institute of Theoretical Computer Science, ETH Zurich, Zurich, 8092, Switzerland.

View Article and Find Full Text PDF
March 2016

Limbform: a functional ontology-based database of limb regeneration experiments.

Bioinformatics 2014 Dec 27;30(24):3598-600. Epub 2014 Aug 27.

Center for Regenerative and Developmental Biology, Department of Biology, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.

View Article and Find Full Text PDF
December 2014

Design of a flexible component gathering algorithm for converting cell-based models to graph representations for use in evolutionary search.

BMC Bioinformatics 2014 Jun 10;15:178. Epub 2014 Jun 10.

Department of Computer Science, Boise State University, 1910 University Drive, Boise, ID 83725, USA.

View Article and Find Full Text PDF
June 2014

A linear-encoding model explains the variability of the target morphology in regeneration.

J R Soc Interface 2014 Mar 8;11(92):20130918. Epub 2014 Jan 8.

Department of Biology, Center for Regenerative and Developmental Biology, Tufts University, , 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.

View Article and Find Full Text PDF
March 2014