Sunday, October 8, 2023
[Sunday] [Monday] [Tuesday] [Wednesday] [Thursday]
COMBINE workshop - 9:00am - 11:45am
Please consult their website for details. The tutorial on CompuCell3D will take place here at the Convention Center and is open to ICSB2023 participants.
Check-in - 12:00 PM - 3:00 PM
Workshops - 12:00 PM
- Room 12/13 Work.01 Torkel Loman: Catalyst: Fast and flexible modeling of reaction networks
- Room 11 Work.02 T.J. Sego: Biological and Biophysics Simulation in Tissue Forge: Introduction and Guided Simulation Building
Conference Opening - 3:00 PM
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Chair: Pedro Mendes Sponsored by UConn Institute for Systems Genomics |
Reception and Dinner - 5:00 PM
Open bar followed by full dinner; free to all participants.
Monday, October 9, 2023
[Sunday] [Monday] [Tuesday] [Wednesday] [Thursday]
Continental Breakfast - Mon Oct 9, 8:30am - 9:15am
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Chair: Leslie Loew Sponsored by UConn Health's Center for Cell Analysis and Modeling |
Coffee Break - 10:00am - 10:30am
Systems Immunology - 10:30 AM - Room 12/13
Chair: Kathryn Miller–Jensen
- Immun.01 Kathryn Miller–Jensen (invited): Systems analysis of intracellular and extracellular macrophage networks at single-cell resolution reveals axes of functional diversity
- Immun.02 Catera Wilder: Dynamic control of signaling networks: uncovering specificity in interferon-mediated cellular responses
- Immun.03 Nathan Manes: Data-Driven Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway
- Immun.04 Shu Wang: Using Markov Fields for predictive modeling and integration of multi-modal immune data in IV-BCG vaccinated macaques
- Immun.05 K V Venkatesh: Unravelling the Role of STAT3 in Subclinical Inflammation: A Systems Biology-Based Model Examining the Impact of Macronutrients and Lifestyle Factors on Health and Disease
- Immun.06 Corinna Holetschek: Early prediction of COVID-19 severity and multi-dimensional immune correlates in non-vaccinated versus vaccine-breakthrough patients
- Immun.07 Weihong Gu: Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells
- Immun.08 Prakrati Dangarh: Mechanistic modelling of pre-school wheezing induced by recurrent viral infections
Dynamics in Space and Time 1 - 10:30 AM - Room 14
Chair: Jae Kyoung Kim
- Dyn.01 Jae Kyoung Kim (invited): Analysis of dynamic data: from molecule to behavior
- Dyn.02 Rinat Goren: Circadian clocks control gene expression and gate cell division via an oscillatory master regulator in multicellular Anabaena
- Dyn.03 Daniel Lobo: Dynamic regulation of whole-body patterns and shape: systems biology of planarian worms
- Dyn.04 Jian-geng Chiou: A segmentation clock patterns cellular differentiation in a bacterial biofilm
- Dyn.05 Matteo Barberis: Integrative Systems and Synthetic Biology identifies a minimal molecular network that coordinates cell cycle dynamics in budding yeast
- Dyn.06 Ala Trusina: Model to Link Cell Shape and Polarity with Organogenesis
- Dyn.07 Sikao Guo: Structure of the HIV immature lattice allows for essential lattice remodeling within budded virions
Dyn.08 Martin Meier-Schellersheim: Comparative analysis of cell signaling models across non-spatial/spatial and deterministic/stochastic implementations
Computational Methods 1 - 10:30 AM - Room 15
Chair: Herbert Sauro
- Comp.01 Herbert Sauro (invited): The Past and Future in Mechanistic Modeling in Systems Biology
- Comp.02 Clemens Kreutz: Estimation of More Parameters Than Available Data Points
- Comp.04 Kevin Janes: Proteome-wide copy-number estimation from transcriptomics
- Comp.05 Daniel Paysan: Image2Reg: Linking Chromatin Images to Gene Regulation using Genetic Perturbation Screens
- Comp.06 Natasa Miskov-Zivanov: Automated model curation using LLMs: Integration of ChatGPT with the DySE framework
- Comp.07 Kemal Inecik: IDTrack: Cross-Temporal and Cross-Database Biological Identifier Mapping
- Comp.08 Dilan Pathirana: Model Selection: Standardization, Software, Algorithms, and Applications with Network-based Models
Lunch - 12:30pm - 2:15pm
Luncheon tutorials - 1:00pm - 2:00pm
- Room 12/13 Lunch.01 Rahuman Sheriff: Model of the Year Competition 2024 and results of 2023
- Room 14 Lunch.02 Ann Cowan: VCell: compartmental and spatial modeling and simulation using reactions and reaction rules
- Room 15 Lunch.03 Jürgen Pahle: Introduction to Model Analysis with COPASI
Multi-omics - 2:15 PM - Room 12/13
Chair: Jeff Chuang
- Omics.01 Jeff Chuang (invited): Spatial Dynamics of Acquired Resistance in BRAF-mutant Melanoma
- Omics.02 Mengze Li: Transcriptomic signatures of aging, extreme old age and survival identified in Long Life Family Study
- Omics.03 Iulia Lazar: The Cell-Membrane Proteome: Reshaping the Drug Target Discovery Process
- Omics.04 Alexandra Paun: Integration of transcriptomics and microbiome composition reveals ulcerative colitis endotypes
- Omics.05 Aaron Wacholder: A vast evolutionarily novel translatome participates in conserved cellular processes
- Omics.06 Sam Crowl: Merging genomic and proteomic annotations to define splicing control of post-translational modifications
- Omics.07 Gordon Broderick: Unsupervised Multi-resolution Analysis of Protein-protein Abundance Patterns in Infectious Exacerbation of COPD
- Omics.08 Anastasia Leshchyk: A Bayesian network-based approach for multi-omics integration to reveal underlying mechanisms of healthy aging.
- Omics.09 Yunfan Bai: Trans-omic analysis reveals the difference on obesity-related metabolic dysregulation between free feeding and fasting states
Microbiome and Microbial Systems Ecology - 2:15 PM - Room 14
Chair: Ayari Fuentes-Hernández
- Micro.01 Ayari Fuentes-Hernández (invited): Multi-scale modeling of syntropic microbial communities
- Micro.02 Melanie Staeubli: Towards taxon-specific growth rate prediction in microbial communities by metatranscriptomics
- Micro.03 Chen Liao: Oral Bacterial Enrichment in Feces Indicates Low Bacterial Load instead of Absolute Expansion
- Micro.04 Mohammadhassan Mirhakkak Esfahani: Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome
- Micro.05 Lillian Dillard: Competition and mutualism in the dysbiotic vaginal microbiome
- Micro.06 Jamie Lee: In silico-guided treatment design for skin damaging Staphylococcus aureus and Staphylococcus epidermidis colonisation in eczema lesions
- Micro.07 Krishna Nair: Analysing the role of gut microbiota in a south Indian cohort of healthy and obese individuals
- Micro.08 Deborah Powers: A cross-cohort comparison indicates the gut microbiome is a cohort-dependent predictor of dementia
Signaling and Mechanobiology - 2:15 PM - Room 15
Chair: Liesbet Geris
- Sign.01 Liesbet Geris (invited): Combining mechanics and biology at multiple length scale to study cartilage degeneration and regeneration
- Sign.02 Aniruddha Chattaraj: Multi-condensate state serves as a functional strategy to optimize the cell signaling output
- Sign.03 Steven Wiley: Reverse-engineering a modular reference model of the EGFR-ERK pathway using phosphoproteomics data
- Sign.04 Yozlem Bahar: Logical modeling of signaling mechanisms in early nervous system development
- Sign.05 Leslie Loew: In vitro and in silico exploration of the solubility product concept for formation of biomolecular condensates
- Sign.06 Jinsu Kim: Mathematical approaches to study how 2D and 3D liquid-liquid phase separation can be different.
- Sign.07 Louis Cammarata: Adhesome Receptor Clustering is Accompanied by the Co-localization of the Associated Genes in the Cell Nucleus
- Sign.08 Luezhen Yuan: Transcription-Associated Chromatin Reorganization at Nucleus Envelope during Mechanically Induced Rejuvenation
- Sign.09 Reagan Portelance: An ODE Model to Quantify Avidity Effects in Tandem SH2 Domain Binding
Coffee Break - 4:15pm - 4:45pm
Poster Session 1 - 4:45pm - 6:00pm
Tuesday, October 10, 2023
[Sunday] [Monday] [Tuesday] [Wednesday] [Thursday]
Continental Breakfast - 8:15am - 9:00am
Single-Cell Analyses - 9:00 AM - Room 12/13
Chair: Gary Bader
- SC.01 Gary Bader (invited): Cell Cycle Dynamics Control of Gene Transcript Expression and Cell Fate
- SC.02 Purushottam Dixit: The ability to sense the environment is heterogeneously distributed in cell populations
- SC.03 Xiaolu Guo: Modeling the heterogenous NFB dynamics of single immune cells
- SC.04 Francisco Prista von Bonhorst: Differential Entropy as an indicator of the development of pluripotent murine ICM cell populations
- SC.05 Mohammed Muzamil Khan: Inhibition of -catenin/CBP Activity in Murine Oral Tumors Attenuates Stress Response
- SC.06 Ala Trusina: One-parameter tool for quantitative and statistical assessment of similarity between cell types
- SC.07 Hyun Kim: scLENS: Data-driven signal detection for unbiased scRNA-seq data analysis
- SC.08 Michael Prummer: Single-cell co-expression network analysis in immune and tumor cells of melanoma and ovarian cancer patients
- SC.09 Mark-Phillip Pebworth: MOCHA: advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human disease cohorts
Dynamics in Space and Time 2 - 9:00 AM
Chair: Ross Sozzani
- Dyn.09 Ross Sozzani (invited): The Goldilocks principle, just the right amount of growth
- Dyn.10 Torkel Loman: The mixed positive/negative feedback: a general model of bacterial stress response
- Dyn.11 Jordan Rozum: Robustness of biomolecular networks suggests functional modules far from the edge of chaos
- Dyn.12 Eric Batchelor: Entraining p53 oscillations to reduce heterogeneity of single-cell dynamics and modulate cell-fate determination
- Dyn.13 Seokjoo Chae: Spatially coordinated collective phosphorylation filters spatiotemporal noises for precise circadian timekeeping
- Dyn.14 Sven Sahle: Software für PDE-modeling of cellular processes: Spatial Model Editor/Dune-Copasi
- Dyn.15 Xiangting Li: Population overcompensation, transients, and oscillations in age-structured Lotka-Volterra models
- Canc.11 Edward Stites: Mutants, loners and bad influences
Systems Medicine - 9:00 AM - Room 15
Chair: Gary An
- Med.01 Gary An (invited): Mechanism-based Medical Digital Twins: Uses, design and development considerations, and an example of a critical illness digital twin
- Med.02 Liesbet Geris: Building an ecosystem for digital twins in healthcare
- Med.03 Hannah J. Pybus: Switch activation dynamics capture disease development of allergic asthma in early life
- Med.04 David Deritei: A Boolean model of mitochondrial dynamics reveals mechanisms underlying COPD susceptibility
- Med.05 Pradeep S: Effect of natural food and drugs on blood glucose dynamics using systems biology approaches
- Med.06 Ashoka Hadagali: Systems Biology approaches to study the effect of nutraceuticals and in combination with metformin on fasting blood glucose in type 2 diabetic patients
- Med.07 Ruth Hauptman: Using the Gut Microbiome to Predict a Future Symptom in Inflammatory Bowel Disease
- Med.08 Olga Krebs: FAIR data management for collaborative Systems Medicine projects : from Instruments to Publication.
- Med.09 Hayley Hassler: Dynamic model sheds light on C. difficile infections: insights into antibiotic treatment and fecal microbiota transplantation
Coffee Break - 11:00am - 11:30am
Poster Session 2 - 11:30am - 1:00pm
Lunch - 1:00pm - 1:30pm
Social Activities - Tue Oct 10 1:30pm - 6:00pm
Participants can chose one of three options. Details for selection will reach you by email.
Connecticut River Cruise in a Mississippi-style riverboat 2.5 hour cruise of the largest river in New England, hopefully with the background of the wonderful Fall foliage colors. (Drinks available for purchase)
Follow instructions to board Bus |
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Guided tour of the Mark Twain House The Mark Twain House & Museum has restored the author’s Hartford, Connecticut, home, where the author and his family lived from 1874 to 1891. Twain wrote his most important works during the years he lived there.
Find your own way to 351 Farmington Av., Hartford, CT 06105 |  |
Sampling tour of local breweries Learn about different styles of brewing and experience all-inclusive service to 3 local CT breweries.
Tour will be by minivan in 3 different groups |  |
Conference Dinner - 7:00pm - 10:30pm
Takes place at the The Society Room of Hartford, within walking distance of the Convention Center. (requires ticket purchased at registration)
Wednesday, October 11, 2023
[Sunday] [Monday] [Tuesday] [Wednesday] [Thursday]
Continental Breakfast - Wed Oct 11, 8:30am - 9:15am
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Chair: Ion Moraru Sponsored by Dell Technologies |
Coffee Break - 10:00am - 10:30am
Cancer Systems Biology 1 - 10:30 AM - Room 12/13
Chair: Emmanuel Barillot
- Canc.01 Emmanuel Barillot (invited): Multimodal modeling of tumors
- Canc.02 Meera Prasad: An interplay of motility and adhesion drives mechanical transitions from healthy to tumor in multicellular context
- Canc.03 Elizabeth Brunk: Towards a Functional Understanding of Extrachromosomal DNA (ecDNA)
- Canc.04 Jorge Gomez Tejeda Zanudo: Mathematical modeling and genomics of cancer networks: applications to drug resistance and transcriptional reprogramming
Canc.05 Saran Pankaew: Personalize Boolean model at the single-cell level to investigate colorectal cancer (CRC) response to CHK1 inhibitor
- Canc.06 Ida Larsson: Reconstructing the regulatory programs underlying the phenotypic plasticity of neural cancers
- Canc.07 Luisa Quesada: Differentiation state-specific patterns of histone modifications uncover new epigenetic vulnerabilities in melanoma
- Canc.08 Chen-Hsiang Yeang: An integrated analysis of the cancer genome atlas data discovers a hierarchical association structure across thirty three cancer types
Network Biology - 10:30 AM - Room 14
Chair: Rachel O'Neill
- Net.01 Yuji Hirono: Complete characterization of robust perfect adaptation in biochemical reaction networks
- Net.02 Gaoxiang Zhou: Unraveling the Dynamics of Complex Systems through Element-Based Approaches
- Net.03 Jacques Hermes: Inositol pyrophosphate fluxomics disentagled via mathemical modeling: A case of model reduction
- Net.04 Luis Rocha: Redundancy in the Causal Logic of Interactions Shapes the Dynamics of Biochemical Networks
- Net.05 Lauren Marazzi Hinson: Reframing Cell Fate in Static Networks with Control Theory and a Dynamical Systems Framework
- Net.06 Reuven Falkovich: Functional, dynamic and generalizable subcellular molecular network inference from multiplexed and multimodal imaging
- Net.07 G Broderick: Knowledge-based inference of regional brain regulation in Explosive Ordnance Disposal Veterans using disparate data
- Net.08 J Page: Constraint Satisfaction for Hypothesis Generation in Neurotoxic Injury Using Sparsely Sampled Data
Gene Regulatory Networks - 10:30 AM - Room 15
Chair: Michael Guertin
- GRN.01 Michael Guertin (invited): Kinetic networks and compartment modeling reveal mechanistic functions of transcription factors
- GRN.02 Yusuke Hiki: Inference of gene regulatory network overcoming low performance for real world data
- GRN.03 Ruihao Li: Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
- GRN.04 Reza Mousavi Jafarabad: Designing gene regulatory mechanisms for spatial patterns with an automated machine learning framework
- GRN.05 Ataur Katebi: Context-Specific Gene Regulatory Networks: Inference and Modeling
- GRN.06 Tian Hong: Non-Modular Biochemical Oscillator and Switch without Imposed Feedback
- GRN.07 Michele Gentili: Modeling the regulatory role of miRNAs in COPD
- GRN.08 Jacques Hermes: Embryonic Gen Expression in Zebrafish: Rise of the Mini-Models
Lunch - 12:30pm - 2:15pm
Luncheon tutorials - 1:00pm - 2:00pm
- Room 12/13 Lunch.04 Eran Agmon: Integrative Multiscale Models with Vivarium
- Room 14 Lunch.05 H Steven Wiley: Integrating and normalizing multi-omics data for modeling
- Room 15 Lunch.06 Michael Blinov: Advanced spatial modeling using VCell, BioNetGen, and SpringSalad
Machine Learning 1 - 2:15 PM - Room 12/13
Chair: Carlos Lopez
- ML.01 Carlos Lopez (invited): Model certainty in biochemical reaction networks calibrated to multiple data types
- ML.02 Juan Diaz: Bridging Normal Form Dynamical Systems with Foundational Machine Learning Techniques
- ML.03 Masato Tsutsui: Deep Learning-Based Framework for Capturing Prognostic Signaling Dynamics in Cancer: Generating Interpretable Features from Patient-Specific Models
- ML.04 Haiqi Zhu: Advancing Systems Biology Approaches for Precision Medicine in Complex Diseases
- ML.06 Kwonmoo Lee: Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery
- ML.07 Takashi Morikura: Automatic quantitative evaluation for the performance of in vitro testis tissues using anomaly detection-based ensemble model with error-correcting output codes
Synthetic Biology - 2:15 PM - Room 14
Chair: Irene Otero-Muras
- Synth.01 Irene Otero-Muras (invited): Towards Enhanced Predictability in Synthetic Biology: harnessing uncertainty and noise for Precision Biocircuit Engineering
Synth.02 Anastasiya Malyshava: Developing the Principles for Designing Custom Genomes Using the Yeast Minimal Cell Cycle
- Synth.03 Egils Stalidzans: Sustainable metabolic engineering: application in the microbial strain design
- Synth.04 Connor King: Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production
- Synth.05 Douglas McCloskey: An Automated Platform for Multiomics Screening To Enable Faster and Better Design-Build-Test-Learn Cycles
- Synth.06 Qirun Wang: A mechanistic model of mRNA buffering
- Synth.07 Aleksej Zelezniak: Leveraging Machine Learning for Precision Control in Synthetic Biology
Multi-scale Biology - 2:15 PM - Room 15
Chair: Peter Hunter
- MS.01 Peter Hunter (invited): Multiscale Modelling with Bond Graphs
- MS.02 Carla Kumbale: Multiscale Systems Analysis through Template-and-Anchor Modeling Permits Personalized Health Risk Assessments
- MS.03 Eran Agmon: Process Bigraph Schema: A Framework for Integrative, Multiscale Modeling
- MS.04 Josiah Kratz: Nonoptimal growth physiology increases bacterial survival in time-varying antibiotic stress
- MS.05 Eunbi Park: Multicellular Modeling of Human Induced Pluripotent Stem Cell Colonies Informs Control over Phenotypes and Spatial Organization during Early Differentiation
- MS.06 Marco Ruscone: Multiscale model of the different modes of cancer cell invasion
- MS.07 Mingtao Xia: Kinetic theories of generation-dependent cellular proliferation models
Coffee Break - Wed Oct 11, 4:00pm - 4:30pm
Cancer Systems Biology 2 - 4:30 PM - Room 12/13
Chair: Matteo Barberis
- Canc.09 Hanieh Mazloom Farsibaf: Data-driven computational model of membrane geometry controlling Ras oncogenic signaling
- Canc.10 Chinmaya Joisa: Inhibition State of the Kinome is Predictive of Cancer Responses
- Canc.12 Amir Mahari: A computational model of crosstalk between MAPK signaling and store-operated calcium entry in melanoma cells
- Canc.13 Cara Abecunas: Systematic analysis reveals metabolic state-specific gene vulnerabilities through conditional synthetic lethality
- Canc.14 Kyeong Beom Jo: Exploring Drivers of Chemotherapeutic resistance through a novel overexpression screening Platform
- Canc.15 Paola Vera-Licona: Constructing an Encyclopedia of Cancer Cell Reversion Mechanisms
Computational Methods 2 - 4:30 PM - Room 14
Chair: Ion Moraru
- Comp.09 Hannah Dromiack: Xenomics: Method for Extracting Calcium Signaling Data from Xenopus Tissue
- Comp.10 Natasa Miskov-Zivanov: ACCORDION: An expert system for knowledge selection and model recommendation
- Comp.11 Mingyang Lu: A method for building gene regulatory circuit models from single-cell gene expression dynamics
- Comp.13 Salil Bhate: De novo decipherment of genetic architecture enabled by its consistency with phenotypic geometry and genomic syntax
- Comp.14 Jason Vailionis: Metabolic modeling of the hyperthermophilic archaeon, Pyrococcus furiosus
- Comp.15 Gaoxiang Zhou: A Novel Node Influence Metric for Complex Networks with Semantic Knowledge
Machine Learning 2 - 4:30 PM - Room 15
Chair: Ion Mandoiu
- ML.08 Bartosz Prokop: Data-driven discovery of oscillator models: Towards the application on experimental data in biology
- ML.09 Carl Herrmann: From black to grey boxes: an interpretable variational autoencoder allows predictive modelling of biological perturbations
- ML.10 Xinyi Zhang: Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization during DCIS progression
- ML.11 Hyeontae Jo: Density Physics-Informed Neural Network: Inferring Sources of Cell-to-Cell Heterogeneity in Intracellular Signaling Dynamics
- ML.12 Taichi Kanazawa: Design and implementation of four-dimensional bright-field microscopy image segmentation algorithm of mouse embryos
- ML.13 Rahuman S Malik Sheriff: Building FAIR and Reproducible Collection of Machine Learning and Systems Biology Models in BioModels Repository
Thursday, October 12, 2023
[Sunday] [Monday] [Tuesday] [Wednesday] [Thursday]
Continental Breakfast - 8:30am - 9:15am
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Chair: Pedro Mendes Sponsored by United Therapeutics |
Coffee Break - 10:00am - 10:30am
Systems Pharmacology - 10:30 AM - Room 12/13
Chair: Matthew Riggs
- Pharm.01 Matthew Riggs (invited): Quantitative Systems Pharmacology in Model-Informed Drug Development
- Pharm.02 Julien Olivet: Interactome editing with small molecules: from networks to hot spots
- Pharm.03 Ginte Kutkaite: Systematic identification of pan-cancer single-gene expression biomarkers in drug high-throughput screens
- Pharm.04 Jacques Hermes: Opening up new strategies for personalized Interferon (IFN) treatment governed by a mechanistic understanding of pathway sensitization in IFN signaling.
- Pharm.06 K V Venkatesh: Pharmacokinetic-Pharmacodynamic Modeling of Nutraceutical Combinations for Managing Subclinical Inflammation: A Systems Biology Approach
- Pharm.07 Yun Min Song: Accurate Prediction of Drug Interactions Through Cytochrome P450 Induction
Miscellaneous - 10:30 AM - Room 11
Chair: Paola Vera-Licona
- Misc.01 Eraj Khokhar: From noise to signal: quantifying stochasticity in mRNA splicing
- Misc.06 Tin Yau Pang: Optimization of cytosolic density in bacterial cells
- Misc.03 Amelia Palermo: Systems biology of metabolism unveils the impact of a ketogenic diet on SARS-CoV-2 systemic reprogramming and inflammation
- Misc.04 Anastasia Baryshnikova: Global analysis of the yeast knock-out phenome
- Misc.05 Diogo Pellegrina: Effect of comorbidities, behaviour, and other clinical data on population polymorphisms that interfere with human phospho-signaling networks altered by SARS-CoV-2 infection.
- Comp.03 Maren Philipps: Semi-Mechanistic Modeling with Neural UDEs
Closing - 12:15pm - Room 12/13
A pack lunch will be available for those who request it (free)