szymon stoma | Publications / Publications

Publications

Until the papers are not restricted by copyright of the editor they can be found here:

Journal articles

"The U2-spliceosome and its interactors regulate the levels and activity of the LDL receptor in humans" Zanoni P et al., Atherosclerosis, 2020

"AutoTube: a novel software for the automated morphometric analysis of vascular networks in tissues", Montoya J et al., Angiogenesis, 2018.

"Quantitative spatial analysis of hematopoiesis-regulating stromal cells in the bone marrow microenvironment by multiscale 3D microscopy", Gomariz A et al., Nature Comm., 2018

"VEGF-A Regulates Cellular Localization of SR-BI as Well as Transendothelial Transport of HDL but Not LDL", Velagapudi V et al., Arteriosclerosis, Thrombosis, and Vascular Biology, 2017.

"Hypoxia Induces a HIF-1-Dependent Transition from Collective-to-Amoeboid Dissemination in Epithelial Cancer Cells", Lehmann S et al., Current Biology, 2017.

"Robust Long-Term Individual Cell Tracking from Brightfield Microscopy Images of Budding Yeast", Versari C and Stoma S et al., Journal of Royal Society Interface, 2017

"In vivo imaging of the activity of CEA TCB, a novel T-cell bispecific antibody, reveals specific tumor targeting and fast induction of T-cell mediated tumor killing", Lehmann S et al., Clinical Cancer Research, 2016.

"Dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance", Bertaux F et al., PLoS Computational Biology, 2014.

"Bridging the gaps in Systems Biology", Cvijovic M et al., Molecular Genetics and Genomics, 2014.

"STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification", Stoma S and Donze A et al., PLoS Computational Biology, 2013.

"STSE: Spatio-Temporal Simulation Environment Dedicated to Biology", Stoma S et al., BMC Bioinformatics, BMC Bioinformatics, 2011.

"Flux-Based Transport Enhancement as a Plausible Unifying Mechanism for Auxin Transport in Meristem Development", Stoma S et al., PLoS Computational Biology, 2008.

Proceedings (till 2016)

Applying 3D quantitative microscopy to studyglobal topography and cellular interactions in the bone marrow, Gomariz A et al., IBSB, Jena, 2016.

"Using Signal Temporal Logics to analyze signaling pathways", Stoma S et al., Swiss Institute of Bioinformatics Open Days, Biel, 2013.

Systematic model building: modeling in space and time, Stoma S, SysteMTb – First Annual Meeting and the First Workshop on TB Biology and Modeling, Liblice, Czech Republic, March 21-24, 2011.

"Towards modeling of spatial dynamic systems based on microscopy images", Stoma S, Proceedings of 6th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, 2010.

"Spatio-Temporal Simulation Environment: A Microscopy Image Based Modelization Framework", Stoma S, Klipp E, Microscopy and Microanalysis, 16 (Suppl. 2) , pp 734-735, 2010.

"Using mechanics in the modelling of meristem morphogenesis", Stoma S, Chopard J, Godin C, Traas J: Functional-structural plant models (FSPM), Napier, New Zealand, November 4-9, 2007.

"OpenAlea: An open-source platform for the integration of heterogeneous FSPM components", S. Dufour-Kowalski et al., Functional-structural plant models (FSPM), Napier, New Zealand, November 4-9, 2007.

Other (till 2014)

"Dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance", Bertaux F, Stoma S, Drasdo D, Batt G, INRIA-Research Reaport (hal-00942885), 2014.

"STL-based analysis of TRAIL-induced apoptosis challenges the notion of type I/type II cell line classification", Stoma S, Donze A, Bertaux F, Maler O, Batt G, INRIA-Research Reaport (RR-8121), 2012.

"Defining Modeling Strategies for Systems Biology", Mats Jirstrand et al., report for the EU commission, 2011.

"Modelling development of shoot apical meristem of Arabidopsis, Stoma S, PhD thesis, Montpellier, France, February, 2009.

"Efficient and optimal pathfinding algorithm in partially unknown environment, Stoma S, Master Thesis in Computer Science, Wroclaw, Poland, 2006.

Conferences (till 2014)

"Image-based modeling of drug delivery in HeLa multicellular spheroids", Stoma et al., Image Based Systems Biology, Jena, Germany, 2014.

"Yeast Image Toolkit: A benchmark and evaluation strategy for yeast segmentation and tracking algorithms", Stoma et al., Image Bioinformatics, Leuven, Belgium, 2014.

Software

I valorize my work mostly by software bringing innovation to science. Since software is usually tricky to publish I decided to list here main scientific projects I founded / supported over time:

Ongoing

founder::Essential Vision

Past

Grants

2019, Co-author of grant DEEPLAKE (SDSC), 1+m CHF, waiting
2019, Co-author of grant HINAS, 10m EUR, waiting
2019, Co-author of grant EDITH.AI, 30m EUR, waiting
2019, Co-author of grant Gameinn: CITYSTORIES, 0.75m EUR, funded
2018, Co-author of grant AQUADIG (SDSC), 0.5+m CHF, rejected
2018, Co-author of grant EXAMODE H2020, 5+m EUR, funded
2016, Co-author of grant COST European Bioimaging 2015-2020 (bioimage analysis network coordinated on EU level), > 1m Euro, funded
2015, Author of internal ScopeM grant 2015: CellStar (we propose to adapt an algorithm to microfluidics platform), 30k CHF, funded
2015, Co-author of internal ScopeM grant 2015: MOOC (we propose to establish EdX Introduction to Image Analysis course), 20k CHF, funded
2015, Author of Google Summer School of Code 2015 (we proposed to build Open Source tools supporting High content screening analysis - details are here), rejected
2013, Author of grant application for Systems Biology Model Checker (we proposed to build tools supporting model verification in Systems Biology - details are here, value: ca. 0.1 million Euro, funded
2011, Second author of Google Summer School of Code 2011 (we proposed to build tools supporting editing&visualizing pathways in the internet browser using cutting edge technologies - details are here), funded
2011, Author of individual postdoc grant @ BIOMS, reached finals, rejected
2011, First author of grant for the Deployment of New Technologies in Teaching @ Humboldt University: using Moodle platform to prepare interactive teaching materials "Python in scientific applications", rejected
2010, Author of the Foundation for Polish Science Homing Plus grant application: STSE development, cooperation between Germany and Poland, value: ca. 0.2 million Euro), finished in top 20, with average mark ,,very good application - should receive funding'', rejected

Invited talks (till 2011)

"STSE: a tool for microscopy image-based modeling", Palma, Spain, 2011
"Systematic model building: modeling in space and time", Prague, Czech Republic, 2011
"Towards modeling of spatial dynamic systems based on microscopy images", Heidelberg, Germany, 2010
"Mathematical modeling in the context of aquaporin regulation", Nijmegen, Netherlands, 2009
"Modeling of meristem development", Lyon, France, 2008

Other important roles (till 2015)

Partner in Vratis, MicroscopeIT, Histopixel
Teacher & lecturer at EXCITE 2015-now
Teacher & lecturer at ScopeM 2013-now
An external expert invited for the IMPROVER Network Verification Challenge Jamboree (Systems Biology effort to use crowd sourcing to curate bio-knowledge; project run by IBM and Phillip Morris), 2014
An external expert invited for the FutureSysBio 2010 (a coordination and support action that aim at shaping and predicting the future development of the field Systems Biology working for the European Commission), 2010
Member of the Humboldt University Recruitment Commission evaluating candidates for Junior Professorship in Biophysics, 2009
Author of the cover for PLoS Computational Biology 4(10), 2008
Reviewer for the PLoS Computational Biology, 2009-present

Organization (till 2017)

Organization of , 2017
Coordination of the european Aquaglyceroporin meeting in Berlin , (ca. 20 people, 5 countries), 2010
Co-coordination of the european Sy-stem meeting in Montpellier (ca. 40 people, 10 countries), 2008

Conference talks/posters (till 2013)

Swiss Institute of Bioinformatics Open Days, Biel, 01/2013
First Annual Meeting and Workshop on TB Biology and Modeling, Prague, Czech Republic, 03/2011
6th Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, 09/2010
Microscopy and Microanalysis, Portland, USA, 08/2010
ERAsysBio, Tenerife, Spain, 07/2010
EMBO Workshop Advanced Light Microscopy Techniques and their Applications (PO), Heidelberg, Germany, 05/2010
Aquaporins (PM), Berlin, Germany, 05/2010
Aquaporins (PM), Nijmegen, Netherlands, 12/2009
Aquaporins (PM), Goettingen, Germany, 05/2009
Aquaporins (PM) (PO), Aarhus, Denmark, 12/2008
System Biology MEET (PO), Berlin, Germany, 08/2008
IBSB (PO), Berlin, Germany, 08/2008
The understanding and modeling of auxin transport in plants, Nottingham (PO), UK, 05/2008
Sy-stem (PM), Montpellier, France, 04/2008
Functional-structural plant models (FSPM), Napier, New Zealand, 11/2007
Sy-stem (PM), Zurich, Switzerland, 12/2007
Sy-stem (PM), Ghent, Belgium, 04/2007
Sy-stem (PM), Katowice, Poland, 11/2006
Sy-stem (PM), Tubingen, Germany, 03/2006
Sy-Stem (PM) (PO), Lyon, France, 10/2005