PUBLICATIONS
Papers (C. elegans):
Alicea, B., Gordon, R., and Portegys, T.E. (2021). Data-theoretical Synthesis of the Early Developmental Process. Neuroinformatics, doi:10.1007/s12021-020-09508-1. Neuroinformatics SI: NeuroCommons bioRxiv OSF(code/data/infographics) Jupyter Notebooks (tutorials) 1 2 3
Alicea, B. (2020). Raising the Connectome: the emergence of neuronal activity and behavior in C. elegans. Frontiers in Cellular Neuroscience, doi:10.3389/fncel.2020.524791. Frontiers bioRxiv Github(code/data)
Alicea, B. and Gordon R. (2018). Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis. BioSystems, 173, 235-246. Biosystems PeerJ Preprint OSF (code/data) Jupyter Notebook (notes)
Alicea, B. (2017). The Emergent Connectome in Caenorhabditis elegans Embryogenesis. BioSystems, 173, 247-255. Biosystems bioRxiv Supplemental Data Github (code/data)
Alicea, B. (2016). Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans. Royal Society Open Science, 3, 160496. doi:10.1098/rsos.160496. RS Open Science Supplemental data 1 2
Alicea, B. (2016). Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans. bioRxiv, doi:10.1101/045609 bioRxiv Supplemental data 1 2 3 4 5 6
Data Repositories (C. elegans):
Alicea, B., Gordon, R., and Banerjee, A. (2018). Embryo networks and connectomes in Caenorhabditis elegans. doi:10.17605/ OSF.IO/Q9JVB. Open Science Framework
Alicea, B. (2016). Data from: Evolution in eggs and phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans. doi:10.5061/dryad.c96md Dryad
Software Releases (C. elegans):
Deb, M., Singh, U., Deb, M., and Alicea, B. (2022). DevoLearn: Machine Learning Models and Education that Enable Computational Developmental Biology. Github repo PyPi Preprint INCF (presentation)
Papers (Drosophila):
Alicea, B., Portegys, T.E., Gordon, D., and Gordon, R. (2018). Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc. BioSystems, 173, 256-265. Biosystems Open Access Supplemental data 1 2 3 4 OSF (code/data)
Data Repositories (Drosophila):
Alicea, B., Portegys, T.E. (2018). Data Repository for "Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc". doi:10.17605/OSF.IO/DAUJM, https://osf.io/daujm/. Open Science Framework
Papers (Bacillaria):
Alicea, B., Gordon, R., and Parent, J. (2023). The Psychophysical World of the Motile Diatom Bacillaria Paradoxa. In "Mathematics and Biology of Diatoms". Mathematics and Biology of Diatoms (chapter) vixra
Alicea, B., Gordon, R., Harbich, T., Singh, U., Singh, A., and Varma, V. (2021). Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology. In "Diatom Gliding Motility". Diatom Gliding Motility (Chapter) bioRxiv Github (code) OSF (data)
Papers (comparative development):
Alicea, B., Parent, J., and Singh, U. (2021). Periodicity in the Embryo: emergence of order in space, diffusion of order in time. Biosystems, 204, 104405. Biosystems bioRxiv Github (code). C. elegans and Zebrafish
Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos [invited]. Biology, 5(3), 33. SI: Beyond the Modern Evolutionary Synthesis - what have we missed? Biology (Basel) Supplemental Data C. elegans and Ciona intestinalis
Papers (in silico/theory):
Sarma, G.P., Lee, C-W., Portegys, T., Ghayoomie, V., Jacobs, T., Alicea, B., Cantarelli, M., Currie, M., Gerkin, R.C., Gingell, S., Gleeson, P., Gordon, R., Hasani, R.M., Idili, G., Khayrulin, S., Lung, D., Palyanov, A., Watts, M., Larson, S.D. (2018). OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philosophical Transactions of the Royal Society B, 373, 20170382. doi:10.1098/rstb.2017.0382. RS Proceedings B
Portegys, T.E. (2017). Morphognosis: the shape of knowledge in space and time. arXiv, 1701.02272. arXiv
Portegys, T., Pascualy, G., Gordon, R., McGrew, S., and Alicea, B. (2016). Morphozoic: cellular automata with nested neighborhoods as a metamorphic representation of morphogenesis. In “Multi-Agent Based Simulations Applied to Biological and Environmental Systems“. Multi-agent Sims (Chapter 3) ResearchGate Code (Github) Presentation
Alicea, B., Portegys, T.E., and Gordon, R. (2016). Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages. bioRxiv, doi:10.1101/062539 bioRxiv Supplemental Data 1 2 3
Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., and Watts, M. (2014). DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, doi:10.1101/009993 bioRxiv Dataset and code (Github)
Working Papers (in silico/theory):
Alicea, B. Hypergraphs Demonstrate Anastomoses During Divergent Integration. ResearchGate. paper
Alicea, B. Game Theory of Developmental Processes. ResearchGate. paper
Posters:
Alicea, B. Mathematics of DevoWorm. Find Your Inner Modeler V (2022), University of Illinois-Chicago (virtual). Poster
Alicea, B. Game Theory of Developmental Processes. Dynamics Days 2022, Atlanta, GA (virtual). 2-minute Video Poster
Alicea, B., Deb, M., Deb, M., Katyal, K., and Parent, J. Neuromorphogenetic Patterns and the Theory of Deep Learning. 2021 NetNeuro Satellite, Networks Conference, Virtual. 2-minute Video Poster
Gleeson, P., Alicea, B., Cantarelli, M., Ghayoomie, V., Idili, G., Khayrulin, S., Palyanov, A., Watts, M. and Larson, S.D. The OpenWorm Project: progress update, available resources and future plans. 2021 International C. elegans Conference, Virtual. Poster
Alicea, B. A New Kind of Developmental Biology. Find Your Inner Modeler III (2019), University of Alabama-Birmingham, Birmingham, AL. doi:10.6084/m9.figshare.8257046. Poster
Alicea, B. and Gordon, R. Network Architecture of Embryo Developmental Regulation. 2015 Network Frontiers Workshop (Northwestern University) and 2016 Midwest Regenerative Medicine Conference (Washington U -- St. Louis). Poster Extended abstract Presentation
Alicea, B., Larson, S., McGrew, S., and Gordon, R. DevoWorm: raising the worm on datapoints, trees, and matrices. 20th International C. elegans Conference (2015). Los Angeles, CA. Poster
Infographics:
The Emergent Worm in Heat Map Form. Figshare, doi:10.6084/m9.figshare.3791970. Figshare
Developmental connectome during embryogenesis (Caenorhabditis elegans). ResearchGate, doi:10.13140/RG.2.2.20933.65765/1 YouTube
Blogposts:
Google Summer of Code 2022 in the OpenWorm Community (DevoWorm) Synthetic Daisies blog, June 15, 2022.
OpenWorm Annual Meeting 2021 (DevoWorm update) Synthetic Daisies blog, September 29, 2021.
DevoLearn (Open-source) Maintenance and Evangelism Synthetic Daisies blog, May 2, 2021.
OpenWorm Annual Meeting Slides Synthetic Daisies blog, September 30, 2020.
Welcome to DevoLearn! Synthetic Daisies blog, August 24, 2020.
Open Data Day 2020 Synthetic Daisies blog, March 5, 2020.
Pre-trained Models for Developmental Biology Synthetic Daisies blog, October 30, 2019.
Open Data Day 2019: DevoZoo is Live! Synthetic Daisies blog, March 2, 2019.
January is DevoWorm Month! Synthetic Daisies blog, January 1, 2019.
Finding Your Inner Modeler (Part II) Synthetic Daisies blog, September 30, 2018.
OpenWorm: Royal Society B special issue now live! Synthetic Daisies blog, September 10, 2018.
Things that Just Happened in London..... Synthetic Daisies blog, February 1, 2018.
"Hello World", project version. Synthetic Daisies blog, June 5, 2017.
OpenWorm Blog: announcing the OpenWorm Open House 2016. Synthetic Daisies blog, October 20, 2016.
Upcoming Update on DevoWorm Project to OpenWorm. Synthetic Daisies blog, April 6, 2016.
Posters at the International C. elegans Meeting. Synthetic Daisies blog, June 30, 2015.
C. elegans as an Evolutionary Model. Synthetic Daisies blog, October 26, 2014.
Upcoming DevoWorm talk to the OpenWorm group. Synthetic Daisies blog, September 10, 2014.
Now Announcing the DevoWorm Project. Synthetic Daisies blog, June 3, 2014.
Grant Proposals:
Providing 4D Structure to the Human Cell Atlas via the Human Differentiation Tree. Chan-Zuckerberg Foundation (April 2017).
Quantifying New Variables for C. elegans Integrative Biology. NCSA, University of Illinois Urbana-Champaign (February, 2015).
DynamicWorm. General Proposal (December 2014).
Alicea, B., Gordon, R., and Portegys, T.E. (2021). Data-theoretical Synthesis of the Early Developmental Process. Neuroinformatics, doi:10.1007/s12021-020-09508-1. Neuroinformatics SI: NeuroCommons bioRxiv OSF(code/data/infographics) Jupyter Notebooks (tutorials) 1 2 3
Alicea, B. (2020). Raising the Connectome: the emergence of neuronal activity and behavior in C. elegans. Frontiers in Cellular Neuroscience, doi:10.3389/fncel.2020.524791. Frontiers bioRxiv Github(code/data)
Alicea, B. and Gordon R. (2018). Cell Differentiation Processes as Spatial Networks: identifying four-dimensional structure in embryogenesis. BioSystems, 173, 235-246. Biosystems PeerJ Preprint OSF (code/data) Jupyter Notebook (notes)
Alicea, B. (2017). The Emergent Connectome in Caenorhabditis elegans Embryogenesis. BioSystems, 173, 247-255. Biosystems bioRxiv Supplemental Data Github (code/data)
Alicea, B. (2016). Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans. Royal Society Open Science, 3, 160496. doi:10.1098/rsos.160496. RS Open Science Supplemental data 1 2
Alicea, B. (2016). Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans. bioRxiv, doi:10.1101/045609 bioRxiv Supplemental data 1 2 3 4 5 6
Data Repositories (C. elegans):
Alicea, B., Gordon, R., and Banerjee, A. (2018). Embryo networks and connectomes in Caenorhabditis elegans. doi:10.17605/ OSF.IO/Q9JVB. Open Science Framework
Alicea, B. (2016). Data from: Evolution in eggs and phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans. doi:10.5061/dryad.c96md Dryad
Software Releases (C. elegans):
Deb, M., Singh, U., Deb, M., and Alicea, B. (2022). DevoLearn: Machine Learning Models and Education that Enable Computational Developmental Biology. Github repo PyPi Preprint INCF (presentation)
Papers (Drosophila):
Alicea, B., Portegys, T.E., Gordon, D., and Gordon, R. (2018). Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc. BioSystems, 173, 256-265. Biosystems Open Access Supplemental data 1 2 3 4 OSF (code/data)
Data Repositories (Drosophila):
Alicea, B., Portegys, T.E. (2018). Data Repository for "Morphogenetic processes as data: Quantitative structure in the Drosophila eye imaginal disc". doi:10.17605/OSF.IO/DAUJM, https://osf.io/daujm/. Open Science Framework
Papers (Bacillaria):
Alicea, B., Gordon, R., and Parent, J. (2023). The Psychophysical World of the Motile Diatom Bacillaria Paradoxa. In "Mathematics and Biology of Diatoms". Mathematics and Biology of Diatoms (chapter) vixra
Alicea, B., Gordon, R., Harbich, T., Singh, U., Singh, A., and Varma, V. (2021). Towards a Digital Diatom: image processing and deep learning analysis of Bacillaria paradoxa dynamic morphology. In "Diatom Gliding Motility". Diatom Gliding Motility (Chapter) bioRxiv Github (code) OSF (data)
Papers (comparative development):
Alicea, B., Parent, J., and Singh, U. (2021). Periodicity in the Embryo: emergence of order in space, diffusion of order in time. Biosystems, 204, 104405. Biosystems bioRxiv Github (code). C. elegans and Zebrafish
Alicea, B. and Gordon, R. (2016). Quantifying Mosaic Development: Towards an Evo-Devo Postmodern Synthesis of the Evolution of Development Via Differentiation Trees of Embryos [invited]. Biology, 5(3), 33. SI: Beyond the Modern Evolutionary Synthesis - what have we missed? Biology (Basel) Supplemental Data C. elegans and Ciona intestinalis
Papers (in silico/theory):
Sarma, G.P., Lee, C-W., Portegys, T., Ghayoomie, V., Jacobs, T., Alicea, B., Cantarelli, M., Currie, M., Gerkin, R.C., Gingell, S., Gleeson, P., Gordon, R., Hasani, R.M., Idili, G., Khayrulin, S., Lung, D., Palyanov, A., Watts, M., Larson, S.D. (2018). OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans. Philosophical Transactions of the Royal Society B, 373, 20170382. doi:10.1098/rstb.2017.0382. RS Proceedings B
Portegys, T.E. (2017). Morphognosis: the shape of knowledge in space and time. arXiv, 1701.02272. arXiv
Portegys, T., Pascualy, G., Gordon, R., McGrew, S., and Alicea, B. (2016). Morphozoic: cellular automata with nested neighborhoods as a metamorphic representation of morphogenesis. In “Multi-Agent Based Simulations Applied to Biological and Environmental Systems“. Multi-agent Sims (Chapter 3) ResearchGate Code (Github) Presentation
Alicea, B., Portegys, T.E., and Gordon, R. (2016). Information Isometry Technique Reveals Organizational Features in Developmental Cell Lineages. bioRxiv, doi:10.1101/062539 bioRxiv Supplemental Data 1 2 3
Alicea, B., McGrew, S., Gordon, R., Larson, S., Warrington, T., and Watts, M. (2014). DevoWorm: differentiation waves and computation in C. elegans embryogenesis. bioRxiv, doi:10.1101/009993 bioRxiv Dataset and code (Github)
Working Papers (in silico/theory):
Alicea, B. Hypergraphs Demonstrate Anastomoses During Divergent Integration. ResearchGate. paper
Alicea, B. Game Theory of Developmental Processes. ResearchGate. paper
Posters:
Alicea, B. Mathematics of DevoWorm. Find Your Inner Modeler V (2022), University of Illinois-Chicago (virtual). Poster
Alicea, B. Game Theory of Developmental Processes. Dynamics Days 2022, Atlanta, GA (virtual). 2-minute Video Poster
Alicea, B., Deb, M., Deb, M., Katyal, K., and Parent, J. Neuromorphogenetic Patterns and the Theory of Deep Learning. 2021 NetNeuro Satellite, Networks Conference, Virtual. 2-minute Video Poster
Gleeson, P., Alicea, B., Cantarelli, M., Ghayoomie, V., Idili, G., Khayrulin, S., Palyanov, A., Watts, M. and Larson, S.D. The OpenWorm Project: progress update, available resources and future plans. 2021 International C. elegans Conference, Virtual. Poster
Alicea, B. A New Kind of Developmental Biology. Find Your Inner Modeler III (2019), University of Alabama-Birmingham, Birmingham, AL. doi:10.6084/m9.figshare.8257046. Poster
Alicea, B. and Gordon, R. Network Architecture of Embryo Developmental Regulation. 2015 Network Frontiers Workshop (Northwestern University) and 2016 Midwest Regenerative Medicine Conference (Washington U -- St. Louis). Poster Extended abstract Presentation
Alicea, B., Larson, S., McGrew, S., and Gordon, R. DevoWorm: raising the worm on datapoints, trees, and matrices. 20th International C. elegans Conference (2015). Los Angeles, CA. Poster
Infographics:
The Emergent Worm in Heat Map Form. Figshare, doi:10.6084/m9.figshare.3791970. Figshare
Developmental connectome during embryogenesis (Caenorhabditis elegans). ResearchGate, doi:10.13140/RG.2.2.20933.65765/1 YouTube
Blogposts:
Google Summer of Code 2022 in the OpenWorm Community (DevoWorm) Synthetic Daisies blog, June 15, 2022.
OpenWorm Annual Meeting 2021 (DevoWorm update) Synthetic Daisies blog, September 29, 2021.
DevoLearn (Open-source) Maintenance and Evangelism Synthetic Daisies blog, May 2, 2021.
OpenWorm Annual Meeting Slides Synthetic Daisies blog, September 30, 2020.
Welcome to DevoLearn! Synthetic Daisies blog, August 24, 2020.
Open Data Day 2020 Synthetic Daisies blog, March 5, 2020.
Pre-trained Models for Developmental Biology Synthetic Daisies blog, October 30, 2019.
Open Data Day 2019: DevoZoo is Live! Synthetic Daisies blog, March 2, 2019.
January is DevoWorm Month! Synthetic Daisies blog, January 1, 2019.
Finding Your Inner Modeler (Part II) Synthetic Daisies blog, September 30, 2018.
OpenWorm: Royal Society B special issue now live! Synthetic Daisies blog, September 10, 2018.
Things that Just Happened in London..... Synthetic Daisies blog, February 1, 2018.
"Hello World", project version. Synthetic Daisies blog, June 5, 2017.
OpenWorm Blog: announcing the OpenWorm Open House 2016. Synthetic Daisies blog, October 20, 2016.
Upcoming Update on DevoWorm Project to OpenWorm. Synthetic Daisies blog, April 6, 2016.
Posters at the International C. elegans Meeting. Synthetic Daisies blog, June 30, 2015.
C. elegans as an Evolutionary Model. Synthetic Daisies blog, October 26, 2014.
Upcoming DevoWorm talk to the OpenWorm group. Synthetic Daisies blog, September 10, 2014.
Now Announcing the DevoWorm Project. Synthetic Daisies blog, June 3, 2014.
Grant Proposals:
Providing 4D Structure to the Human Cell Atlas via the Human Differentiation Tree. Chan-Zuckerberg Foundation (April 2017).
Quantifying New Variables for C. elegans Integrative Biology. NCSA, University of Illinois Urbana-Champaign (February, 2015).
DynamicWorm. General Proposal (December 2014).
