ICSB 2022: THE 21ST INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY (ICSB 2022)
PROGRAM

Days: Saturday, October 8th Sunday, October 9th Monday, October 10th Tuesday, October 11th Wednesday, October 12th

Saturday, October 8th

View this program: with abstractssession overviewtalk overview

15:00-15:15 Session 0: Opening remarks

Opening remarks by Conference Chairs Edda Klipp, Rune Linding and VP for Research at HUB Christoph Schneider.

Location: Alexander
15:15-16:00 Session K1: KEYNOTE I: Ursula Klingmüller

Abstract: The pleiotropic factor TGFbeta is a major tumor suppressor but also key regulator of epithelial to mesenchymal transition (EMT) and remodeling of the extracellular matrix (ECM) fostering tumor progression. The molecular mechanisms controlling these different functionalities remain poorly understood and it is widely believed that the cell context is decisive. In lung cancer, one of the deadliest cancer entities, increased TGFbeta levels have been associated with poor outcome and thus there is an urgent, unmet clinical need to resolve the molecular impact of TGFbeta. By a global proteomics approach, we demonstrate that the level of the TGFbeta type I and type II receptors is highly variable whereas the core components of the signaling pathway remain rather stable. Furthermore, dynamic pathway modeling of the TGFbeta induced canonical SMAD signaling cascade provides evidence that the TGFbeta receptors are the most sensitive regulatory node. Accordingly, we developed a targeted mass spectrometry-based approach and show that the amounts of the TGFbeta receptors greatly differ in lung cancer cell lines and confirm this observation in lung adeno carcinoma patients. Our results point to a critical role of the abundance of TGFbeta receptors and to an association with lung cancer recurrence.

Chair:
Location: Alexander
15:15
The Transforming Growth Factor beta Riddle – From the Cellular to the Patient Scale (abstract)
16:00-16:45 Session K2: KEYNOTE II: Chris Bowler

Abstract: The ocean is the largest ecosystem on Earth and yet we know very little about it. This is particularly true for the plankton that drift within, even though they form the base of marine food webs and are key players in Earth’s biogeochemical cycles. Ocean plankton are at least as important for the Earth system as the forests on land, but most of them are invisible to the naked eye and thus are largely uncharacterized. To increase our understanding of this underexplored world, a multidisciplinary consortium, Tara Oceans, was formed around the 36m research schooner Tara, which sampled plankton at more than 210 sites and multiple depth layers in all the major oceanic regions during expeditions from 2009-2013 (Karsenti et al. Plos Biol., 2011). This talk will summarize the foundational resources from the project, which collectively represent the largest DNA sequencing effort for the oceans (see Science special issue May 22, 2015 and Cell, Nov 14, 2019), and analyses that illustrate several aspects of the Tara Oceans’ eco-systems biology approach to address microbial contributions to ecological and evolutionary processes. The project provides unique resources for several scientific disciplines that are foundational for mapping ocean biodiversity of a wide range of organisms that are rarely studied together, exploring their interactions, and integrating biology into our physico-chemical understanding of the ocean, as well as for identifying new organisms and genes of biotechnological interest. These resources, and the scientific innovations emerging to understand them, are furthermore critical towards developing baseline ecological context and predictive power needed to track the impact of climate change on the ocean.

Location: Alexander
16:00
Tara Oceans: Eco-Systems Biology at Planetary Scale (abstract)
16:45-17:15Coffee Break
17:15-18:00 Session K3: KEYNOTE III: Robert Balderas

Abstract: As technologies in our industry advance in complexity, speed, sensitivity and ease of use, the opportunity to use multiple approaches to answer high-dimensional biological questions is changing and expanding our knowledge of immunology. To expand growth and future in our field, the combined use of high-parameter analytical and sorting flow cytometry instruments, imaging flow cytometry, advanced spectral cytometry, deep proteomic databases, and advanced single-cell multiomic tools (proteomic and genomic) will help define new functional biomarkers needed to facilitate a better understanding of the complexities of immune health and disease.

Location: Alexander
17:15
Technology advancements to enhance the future of Immune Health (abstract)
18:00-21:00 Opening Reception

Refreshments and get-together.

Location: Alexander
Sunday, October 9th

View this program: with abstractssession overviewtalk overview

09:15-10:00 Session K4: KEYNOTE IV: Peer Bork

Abstract: Environmental sequencing, that is metagenomics, has become a major driver for uncovering microbial biodiversity and increasingly also for cataloging molecular functions on our planet. The exponentially increasing metagenomes need computational tools and resources to allow researchers to access and digest these valuable data. Based on computational methods and resources, often developed in our group, but also by utilizing public resources, here I (i) introduce into our work on the gut microbiome, arguable the best-studied microbial community with its internal and environmental (host) interactions, serving as a model for other habitats. Systems approaches include large-scale perturbations by drugs of both individual strains and synthetic communities, with the aims to increase our still limited understanding, the establishment of novel diagnostics and individualized medication guidance. I (ii) further show on how to apply the underlying concepts to other habitats, like ocean and soil, to arrive at basic understanding of the underexplored microbial diversity on earth. We study, for example, how molecular function is evolving and spreading and, in analogy to microbial diagnostics and treatment for human health, prepare the grounds for bioindicators and remediation strategies in various habitats towards improving planetary health.

Chair:
Location: Alexander
09:15
Molecular eco-systems biology of microbiomes for human and planetary health (abstract)
10:00-10:30Coffee Break
10:30-12:30 Session 1: TUMOR ECOSYSTEMS

Summary: Petabyte cancer big data ranging over single cells to temporal space is changing our way of systems understanding of cancer. Various AI technologies enhanced with supercomputers and big storages are its driving force. This session focuses on the new discoveries and topics which may not be investigated with such technologies.

Location: Grenander I+II
10:30
Inferring kinase activity of a tumor from phosphoproteomic data (abstract)
PRESENTER: Kristen Naegle
10:50
XAI × Fugaku uncovered EMT mechanisms via cancer characteristic specific gene network analysis (abstract)
PRESENTER: Satoru Miyano
11:10
Are metastatic triple negative breast cancers closer to their parental tumors or primary tumors of their destination tissues? (abstract)
11:23
Unified Tumor Growth Mechanisms from Multimodel Inference and Dataset Integration (abstract)
11:36
Stochastic Model of Intra-Tumor Heterogeneity (SMITH) (abstract)
PRESENTER: Adam Streck
11:49
Vasculogenic mimicry induced by multicellular interaction in a 3D glioblastoma model-on-a-chip (abstract)
PRESENTER: Tae-Yun Kang
12:02
Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited (abstract)
12:15
Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer (abstract)
PRESENTER: Abel Szkalisity
12:18
Disentangling the internal composition of tumour activities through a hierarchical factorization model (abstract)
12:21
Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients (abstract)
PRESENTER: Michael Prummer
12:24
Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases (abstract)
PRESENTER: Claire Villette
12:25
Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state (abstract)
PRESENTER: Jonghyun Lee
12:26
Deep learning a model of cytotoxic T cell activation in the tumor microenvironment (abstract)
PRESENTER: Madison Wahlsten
12:27
Exploring the “dark proteome” in hepatocellular carcinoma (abstract)
12:28
Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model (abstract)
PRESENTER: Lina Kroehling
10:30-12:30 Session 2: IMAGING ALGORITHMS

Summary: In this session we will cover the great challenges in current imaging and imaging analysis. From deep learning to data analysis we will host talks that aim to unravel systems properties of complex biological systems including tissues. Multi-scale analysis of biological systems  demans both advanced imaging but also new algorithms and tools. Talks will include recent examples of large-scale imaging breakthroughs made possible with new algorithms. 

10:30
The Systems of Size and Shape Control (abstract)
10:50
Robust oscillations against spatial-temporal noise in intra-inter cellular kinetics (abstract)
11:03
Inference of a causal synaptic molecular network from multiplexed imaging and its perturbations in autism and schizophrenia (abstract)
PRESENTER: Reuven Falkovich
11:15
Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling (abstract)
PRESENTER: Daniel Seeler
11:27
Analyzing single-cell trajectories with augmented machine learning methods predicts cancer drugs response in live-cell microscopy assays (abstract)
PRESENTER: Marielle Péré
11:39
PolarityJaM: An image analysis toolbox for cell polarity, junction and morphology quantification (abstract)
PRESENTER: Wolfgang Giese
11:51
On multistability and constitutive relations of cell motion on Fibronectin lanes (abstract)
PRESENTER: Behnam Amiri
12:01
Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling (abstract)
PRESENTER: Kajsa Tunedal
12:04
Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning (abstract)
PRESENTER: Asma Chalabi
12:07
Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state (abstract)
PRESENTER: Matthew Lux
12:10
Morphometric analysis of macrophage populations in response to animal-derived extracellular matrices (abstract)
10:30-12:30 Session 3: SINGLE CELL MODELING

Summary: The last two decades has seen a dramatic rise in experimental approaches to characterize behaviors at the single-cell level and this has been accompanied by the development of a wide range of computational methods for both the analysis of single-cell measurements and the modeling of single-cell behavior. The single-cell modeling session broadly covers all areas of computational biology associated with the biological behaviors at the single-cell level including stochastic dynamics, gene regulation, spatiotemporal dynamics, and questions about how cells self-organize, receive, process and respond to information, and communicate with other cells. 

Location: Alexander
10:30
Avoiding errant activation of mitophagy: dual factor authentication of the Pink1/Parkin circuit (abstract)
10:50
How do single bacterial cells make decisions? (abstract)
11:10
Dynamic fluctuations in a bacterial metabolic network (abstract)
PRESENTER: Manika Kargeti
11:28
Optimal prediction of a noisy signal (abstract)
PRESENTER: Jenny Poulton
11:40
Non-monotonic Na+ dynamics in the malaria parasite Plasmodium falciparum (abstract)
PRESENTER: Jorin Diemer
11:52
Accounting for low transcript sampling rates in scRNA-seq using the Good-Turing estimator (abstract)
12:04
Mitotic Memory as Spontaneous Symmetry Breaking in the Cell (abstract)
PRESENTER: Arran Hodgkinson
12:16
Scalable and flexible inference framework for stochastic dynamic single-cell models (abstract)
12:21
The transcriptome dynamics of single cells during the cell cycle (abstract)
PRESENTER: Daniel Schwabe
12:24
Theory of biochemical information processing with transients (abstract)
PRESENTER: Manish Yadav
12:25
Quantification of bacterial resource allocation in changining environments on the single-cell level (abstract)
PRESENTER: Antrea Pavlou
12:26
Inference and dynamical simulation of the gene-regulatory network in single cells (abstract)
PRESENTER: Patrick Stumpf
12:27
Virtual Cell Modeling and Simulation Software (abstract)
PRESENTER: Michael Blinov
12:28
Cells use molecular working memory to navigate in changing chemoattractant fields (abstract)
PRESENTER: Robert Lott
12:29
Deciphering transcriptional drivers of stem cell differentiation using causal inference (abstract)
PRESENTER: Martin Proks
12:30-13:30 Session L1: LUNCHEON I: Advancements in single cell multiomic profiling of antigen-specific T cells with dCODE Dextramer® (RiO) on the BD Rhapsody™ Single-Cell Analysis System.

Summary: The advancement of immunotherapies and drug development relies on the characterization of antigen-specific T cells. However, in many cases, detection of these cells has been difficult when their frequencies among T cells are low and their affinity to bind MHC-peptide complexes are weak. Furthermore, pairing this information with the corresponding variable (V), diversity (D), and joining (J) [V(D)J] sequences of the antigen-specific T cell receptors has also been challenging due to hurdles in sequencing these large regions, particularly at the single-cell level. Here, we demonstrate the combination of two powerful technologies, Immudex® dCODE Dextramer® (RiO) Reagents and the BD Rhapsody™ Single-Cell Analysis System, to detect and characterize low-frequency antigen-specific T cells, including the full sequences of the V(D)J gene segments of the T cell receptors, as well as profile transcriptome and protein expression.

Presenters: 

Soudabeh Rad Pour, PhD: Field Applications Specialist MultiOmics Solutions

Laurence Monnet, PhD: Senior Single Cell Solution Field Applications Scientist

Location: Alexander
12:30-13:30 Session L2: LUNCHEON II: Tutorial: Modelling with VCell

Summary: VCell (https://vcell.org/) is a comprehensive platform for modeling cell biological systems that is built on a central database and disseminated as a web application. VCell is widely used in dozens of published research projects (https://vcell.org/vcell-published-models), and for teaching at numerous universities.  The software is free with automatic installers for Windows, Mac OS and Linux. It provides a biology-based interface for inexperienced modelers and a math interface for math-inclined researchers. VCell platform may run on user’s computer or on provided remote servers enabling running complex simulations from any low-cost laptop. Models can be accessed from anywhere using the VCell database and can be shared among collaborators or made publicly available.

Location: Grenander I+II
13:30-15:30 Session 4: CLIMATE, BIOTOPES & MICROBIOMES

Summary: This session will cover biological discoveries made in a variety of biotopes - from Oceans to the Human Gut. We will be discussing the major challenges involved in systematic sampling of biotopes and also what we can learn from doing so. We also aim to put this in the context of a changing climate and how potentially systems biology can help deal with some of these challenges.

Location: Grenander I+II
13:30
An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness (abstract)
13:40
Agent-based modeling of spatiotemporal organization of bacteria in the human gut (abstract)
13:50
Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens (abstract)
PRESENTER: Nils Kurzawa
14:00
Towards identification of new life cycle-associated regions in phage genomes using deep learning (abstract)
14:10
Computationally Modeling the Human Microbiome of the Respiratory Tract (abstract)
14:20
Latent variable models of fungal growth considering the data measurement process (abstract)
PRESENTER: Tara Hameed
14:30
The metabolic community model of Staphylococcus aureus and four abundant human nasal microbes (abstract)
14:40
GuaCAMOLE: fragment GC bias-aware abundance estimation from metagenomic data increases accuracy and comparability (abstract)
PRESENTER: Laurenz Holcik
14:50
Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota (abstract)
15:00
Human host and pathogenic fungi: modeling and deciphering nested metabolic defense strategies (abstract)
15:10
Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool (abstract)
15:13
A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples (abstract)
PRESENTER: Tanja Holstein
15:16
Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity (abstract)
PRESENTER: Sascha Schaeuble
15:19
Cell Type view into tomato stem elongation in Shade avoidance response (abstract)
PRESENTER: Linge Li
15:22
Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model (abstract)
PRESENTER: Arran Hodgkinson
15:25
Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease (abstract)
PRESENTER: Emmanouil Nychas
15:26
From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496. (abstract)
15:27
Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage (abstract)
PRESENTER: Xiu Jia
15:28
In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria (abstract)
PRESENTER: Ali Navid
15:29
Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data (abstract)
PRESENTER: Levi van Doorn
13:30-15:30 Session 5: DEEP HIDDEN PHYSICS

Summary: A grand challenge with great opportunities is to develop a coherent framework that enables blending conservation laws, physical principles, and/or phenomenological behaviors expressed by differential equations with the vast data sets available in many fields of engineering, science, and technology. At the intersection of probabilistic machine learning, deep learning, and scientific computations, this work is pursuing the overall vision to establish promising new directions for harnessing the long-standing developments of classical methods in applied mathematics and mathematical physics to design learning machines with the ability to operate in complex domains without requiring large quantities of data. To materialize this vision, this work is exploring two complementary directions: (1) designing data-efficient learning machines capable of leveraging the underlying laws of physics, expressed by time dependent and non-linear differential equations, to extract patterns from high-dimensional data generated from experiments, and (2) designing novel numerical algorithms that can seamlessly blend equations and noisy multi-fidelity data, infer latent quantities of interest (e.g., the solution to a differential equation), and naturally quantify uncertainty in computations.

13:30
Continuous-time models under uncertainty (abstract)
13:50
Path Integral Stochastic Optimal Control for Sampling Transition Paths (abstract)
14:15
Posterior marginalization accelerates Bayesian inference for dynamical systems (abstract)
PRESENTER: Elba Raimundez
14:28
The Economy and Control of Balanced Cellular Growth (abstract)
PRESENTER: Hugo Dourado
14:41
Hybrid mechanistic and deep learning modeling in systems biology (abstract)
PRESENTER: Maren Philipps
14:54
Discovery of Hidden Control Variables and modeling Non-Linear Dynamical Biological Systems (abstract)
PRESENTER: Juan Munoz
15:07
Combining machine learning and ODE’s to build multiscale models for estimation of metabolic trajectories (abstract)
PRESENTER: Natal van Riel
15:20
Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations (abstract)
15:25
Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell (abstract)
15:26
Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation (abstract)
PRESENTER: Domagoj Doresic
15:27
Hybrid models for cellular signaling: meso-scale pathway identification (abstract)
15:28
On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems (abstract)
PRESENTER: Sandip Saha
15:29
Structural reduction of chemical reaction networks based on topology (abstract)
PRESENTER: Yuji Hirono
13:30-15:30 Session 6: MODELS IN SPACE AND TIME

Summary: The behavior of cells is impacted by many factors, such as  gene regulation, signaling, metabolism, transport, or mechanical forces. While studying these components in isolation can be informative, they all interact with each other and are ultimately part of the same system. The session will discuss models that capture cellular dynamics and regulation with an emphasis on the role played by the spatial organization of its components.

Location: Alexander
13:30
Directed cell migration by cortical actin and ER-PM contact site-mediated restriction of receptor signaling to the front (abstract)
PRESENTER: Tobias Meyer
13:50
Regulation of Mammalian Iron Physiology Across Scales (abstract)
14:10
Modelling how mRNA flows through subcellular compartments (abstract)
14:23
Spatio-temporal modeling reveals a layer of tunable control circuits for the distribution of cytokines in tissues. (abstract)
PRESENTER: Patrick Brunner
14:35
Real-time biochemical computations at criticality (abstract)
14:47
Stochasticity of Meiotic Entry in Xenopus Oocytes (abstract)
PRESENTER: Deniz Fettahoglu
14:59
Rhythmic protein degradation for cost-effective circadian oscillation (abstract)
PRESENTER: Junghun Chae
15:11
Model-based design of a synthetic oscillator based on an epigenetic memory system (abstract)
PRESENTER: Viviane Klingel
15:16
Advanced Modelling of Multicellular Systems in Morpheus (abstract)
PRESENTER: Jörn Starruß
15:19
Resolving Resolution Hindrances in Spatial Transcriptomics (abstract)
PRESENTER: Connor King
15:22
Inferring individual interactions in gene regulatory networks with delays from time-series experiments (abstract)
PRESENTER: Yu Wang
15:25
Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics (abstract)
PRESENTER: Ariane Ernst
15:26
Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals (abstract)
15:27
Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells (abstract)
PRESENTER: Zsófia Bujtár
15:28
A powerful modelling approach tailored to cellular signalling (abstract)
PRESENTER: Clemens Kreutz
15:29
A robust model of neural superposition sorting (abstract)
PRESENTER: Eric Reifenstein
15:30-16:00Coffee Break
16:00-16:45 Session K5: KEYNOTE V: Chris Sander

Abstract: AI and statistical learning can generate actionable predictions at the level of molecules, cells and humans.(1) EVcouplings: protein structure from experimental evolution; design of proteins for sustainability.(2) Perturbation Biology: designing targeted intervention from large-scale perturbation-response experiments.(3) CancerRiskNet: Identifying high risk of pancreatic cancer from real-world clinical records.(4) EVescape: Forecasting viral antibody escape.

Chair:
Location: Alexander
16:00
Machine learning for hard biological problems (abstract)
16:45-19:30 Session P1: POSTER SESSION I (Odd Submission Numbers)

ODD NUMBERED POSTERS (1, 3, 5, ...;)

Location: All Grenanders
FitMultiCell: Simulating and parameterizating computational models of multi-cellular processes (abstract)
PRESENTER: Emad Alamoudi
Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells (abstract)
Benchmarking of analysis strategies for data-independent acquisition proteomics data (abstract)
PRESENTER: Eva Brombacher
A generic framework to coarse-grain stochastic reaction networks by Abstract Interpretation (abstract)
PRESENTER: Albin Salazar
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection (abstract)
PRESENTER: Tongta Sae-Ong
Tissue-specific codon usage: from systems to synthetic biology (abstract)
A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair (abstract)
Impact of Amyloid-Beta Induced Disruption on Ca2+ Homeostasis in a Simple model of Neuronal Activity (abstract)
Improving Our Understanding of ADPKD: Computational Analysis of Metabolome Data (abstract)
Molecular principles governing substrate specificity of human SUMO E3 Ligases (abstract)
A mechanistic model for endocrine profiles of female puberty maturation (abstract)
Advanced Modelling of Multicellular Systems in Morpheus (abstract)
PRESENTER: Jörn Starruß
Resistant starch decreases intrahepatic triglycerides in NAFLD patients via the gut microbiome contribution to the branched-chain amino acids pool (abstract)
Data-driven mathematical modeling of human skin aging and its application for natural compound screening (abstract)
PRESENTER: Masatoshi Haga
Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease (abstract)
Modeling the adaptive immune response of a lymph node as Petri net (abstract)
PRESENTER: Sonja Scharf
Resolving Resolution Hindrances in Spatial Transcriptomics (abstract)
PRESENTER: Connor King
Digital twins and hybrid modelling for simulation of physiological variables and stroke risk (abstract)
PRESENTER: Tilda Herrgårdh
Dynamical basis of cellular sensing and responsiveness to spatial-temporal signals (abstract)
Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets (abstract)
PRESENTER: Mariyam Khan
A model of RNA repair to study antibiotic tolerance (abstract)
PRESENTER: Hollie Hindley
Insights on hemodynamic changes in hypertension and T2D through non-invasive cardiovascular modeling (abstract)
PRESENTER: Kajsa Tunedal
COVRECON: Combining Genome-scale Metabolic Network Reconstruction and Data-driven Inverse Modeling to Reveal Causal Biochemical Regulations (abstract)
PRESENTER: Jiahang Li
Lipid metabolic reprogramming extends beyond histological tumor demarcations in human operable pancreatic cancer (abstract)
PRESENTER: Abel Szkalisity
Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2 (abstract)
PRESENTER: Jacques Hermes
Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients (abstract)
PRESENTER: Manuel Huth
Integrative analysis on comorbid signatures in psychotic disorders using multi-rank non-negative matrix factorization based graph approach (abstract)
PRESENTER: Youcheng Zhang
The pharmaco-epigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity (abstract)
Manually curated genome-scale metabolic reconstructions of the multi-drug resistant Gram-negative pathogens A. baumannii and K. pneumoniae (abstract)
PRESENTER: Nantia Leonidou
Single cell analysis of colorectal cancers with familial adenomatous polyposis for revealing differential pre-malignant programs (abstract)
PRESENTER: Najung Lim
A deep learning-based approach for counting ovarian follicles (abstract)
PRESENTER: Misbah Razzaq
Modeling disease progression in spinocerebellar ataxias (abstract)
Computational modeling of the Hes1 oscillator for the self-renewal of muscle stem cells (abstract)
PRESENTER: Zsófia Bujtár
Learning synthetic cell classifier designs with genetic algorithms and logic programming (abstract)
PRESENTER: Melania Nowicka
Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II) (abstract)
PRESENTER: Jeff Didier
M4-health: digital twins that follow you throughout your health journey (abstract)
PRESENTER: Gunnar Cedersund
Multi-platform model training reduces bias in translational drug sensitivity models for cancer patients (abstract)
Quantify the role of DMT1 endocytosis, IRPs activity, and FT iron sequestration in duodenal enterocyte iron regulation (abstract)
PRESENTER: Joseph Masison
Periodic Forcing of the ERK pathway (abstract)
PRESENTER: Nguyen Tran
Jinkō Knowledge: An integrated knowledge management tool prior to in silico multiscale model development (abstract)
PRESENTER: Shiny Martis B
Deciphering dysregulation in Erythroleukemia to design intervention strategies (abstract)
PRESENTER: Yomn Abdullah
The insidious trappings of gene set enrichments (abstract)
Predicting metabolite accumulation in cancerous metabolic network (abstract)
PRESENTER: Tin Yau Pang
Patient-specific modeling of the TP53 pathway in endometrial carcinoma patients (abstract)
The abundance and cross-talk of EGFR and MET receptors in lung cancer cell lines is critical for the efficacy of tyrosine kinase inhibitors (abstract)
PRESENTER: Dario Lucas Frey
Alterations in hepatocyte growth factor induced signal transduction in fatty liver disease foster cancer development (abstract)
Inferring individual interactions in gene regulatory networks with delays from time-series experiments (abstract)
PRESENTER: Yu Wang
Multilevel approach characterizing the progression of fatty liver disease (abstract)
PRESENTER: Ina Biermayer
A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics (abstract)
Dynamic fluctuations in a bacterial metabolic network (abstract)
PRESENTER: Manika Kargeti
The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data (abstract)
PRESENTER: Thomas Stiehl
Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway (abstract)
Fast parameter estimation for ODE-based models of heterogeneous cell populations (abstract)
PRESENTER: Yulan van Oppen
Dynamic analysis framework to detect cell division and cell death in live-cell imaging, using signal processing and machine learning (abstract)
PRESENTER: Asma Chalabi
Quantification of bacterial resource allocation in changining environments on the single-cell level (abstract)
PRESENTER: Antrea Pavlou
A robust model of neural superposition sorting (abstract)
PRESENTER: Eric Reifenstein
Decoding cellular deformation from pseudo-simultaneously observed RhoGTPase activities (abstract)
PRESENTER: Katsuyuki Kunida
Amino Acid Impact on Protein Secretion in B. subtilis: an RBA Approach (abstract)
PRESENTER: Rafael Moran
Phylogeny and artificial neural networks (abstract)
Discovery of Robust and Highly Specific Microbiome Signatures for Non-Alcoholic Fatty Liver Disease (abstract)
PRESENTER: Emmanouil Nychas
Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes (abstract)
PRESENTER: Marcus Krantz
Macroecological Laws Naturally Arise from Complex Chaotic Dynamics of Gut Microbiota (abstract)
Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM) (abstract)
Frequency preference in miRNA-mRNA interaction models: competition and cooperativity effects (abstract)
PRESENTER: Candela Szischik
Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells (abstract)
Explainable Machine Learning in Mass Spectrometry-based Proteomics (abstract)
PRESENTER: Tom Altenburg
Logical modeling of signaling mechanisms in early development (abstract)
PRESENTER: Yozlem Bahar
Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course (abstract)
Hybrid models for cellular signaling: meso-scale pathway identification (abstract)
Gene-essentiality based drug signature helps repurposing non-cancer drugs (abstract)
PRESENTER: Jing Tang
Elucidating the role of TAS2R43 in HGT-1 cells – an integrated omics approach (abstract)
PRESENTER: Juergen Behr
Dynamics of the circadian clock in models of cancer and its potential for treatment (abstract)
PRESENTER: Carolin Ector
Identification of personalised driver gene panels in Melanoma (abstract)
Inference of differential gene regulatory networks from gene expression data using boosted differential trees (abstract)
PRESENTER: Gihanna Galindez
Initial source of heterogeneity in a model for cell fate decision in the early mammalian embryo (abstract)
Exact Confidence Regions for Non-Linear Models (abstract)
Towards rational design of antibiotic combination therapies (abstract)
Combining single-cell imaging techniques to probe surface-adhesion-dependent morphological features of disease state (abstract)
PRESENTER: Matthew Lux
Network-based Stratification of Cancer Drugs (abstract)
PRESENTER: Nurcan Tuncbag
Deep learning a model of cytotoxic T cell activation in the tumor microenvironment (abstract)
PRESENTER: Madison Wahlsten
Lactobacillus rhamnosus colonisation antagonizes Candida albicans by forcing metabolic adaptations that compromise pathogenicity (abstract)
PRESENTER: Sascha Schaeuble
Nonstationary Biomedical Signal Feature Extraction (abstract)
Reconstruction of regulatory networks driving patterned expression in the Drosophila embryo based on spatially resolved single-cell sequencing data​ (abstract)
Improving our Mechanistic Understanding of Cell Cycle Dynamics (abstract)
PRESENTER: Paul Lang
A graph-based approach to analyze signal transduction involving cytokines and the JAK-STAT pathway in hepatocytes using Petri nets (abstract)
PRESENTER: Marcus Keßler
A Reproducibility Scorecard for Self-checking of Systems Biology Models (abstract)
BioModels: an open repository of mathematical models of the biological and biomedical processes (abstract)
Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning (abstract)
Model-based design of a synthetic oscillator based on an epigenetic memory system (abstract)
PRESENTER: Viviane Klingel
Structural reduction of chemical reaction networks based on topology (abstract)
PRESENTER: Yuji Hirono
Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations (abstract)
PRESENTER: Eui Min Jeong
Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity (abstract)
PRESENTER: Luigi Ferraro
DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology (abstract)
Computational modeling of DLBCL predicts response to BH3-mimetics (abstract)
PRESENTER: Simon Mitchell
Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images (abstract)
PRESENTER: Lise Minaud
Cell type-specific gene co-expression modules define tumor heterogeneity in melanoma patients (abstract)
PRESENTER: Michael Prummer
Universality of form: The case of retinal cone photoreceptor mosaics (abstract)
Dimethyl fumarate shifts CSF protein profile in relapsing remitting MS: a proteomics approach for biomarker discovery (abstract)
PRESENTER: Sara Hojjati
Automated improvement of genome-scale models using a first-order logical model of metabolism (abstract)
PRESENTER: Alexander Gower
The potential of PBI for high resolution lung imaging in patients (abstract)
Cohort-specific Boolean models highlight different regulatory modules during disease progression (abstract)
PRESENTER: Ahmed Hemedan
A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation (abstract)
A comprehensive mechanistic model of adipocyte signaling with layers of confidence (abstract)
PRESENTER: William Lövfors
Hierarchical gene function prediction using a novel topology-based threshold and comparing 6 correlation metrics. Study case: Rice (abstract)
Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level (abstract)
PRESENTER: Roberta Bursi
Deciphering transcriptional drivers of stem cell differentiation using causal inference (abstract)
PRESENTER: Martin Proks
In silico analysis of metabolic capabilities in a synthetic community of phycosphere bacteria (abstract)
PRESENTER: Ali Navid
GO Term-based Comparative Functional Genomics in Plants (abstract)
Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing (abstract)
PRESENTER: Marie Coutelier
Comparative analysis of molecular fingerprints in prediction of drug combination effects (abstract)
PRESENTER: Bulat Zagidullin
Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis (abstract)
PRESENTER: Julia Åkesson
Linking models of biochemical dynamics via mass-constrained neural ordinary differential equations (abstract)
Data-driven modeling of mitochondrial metabolism (abstract)
Quantitative Impacts of Bumble Bee Ecology on Foraging Behaviour: An Economic Model (abstract)
PRESENTER: Arran Hodgkinson
Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output (abstract)
Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway (abstract)
PRESENTER: Nathan Manes
Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework (abstract)
Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks (abstract)
PRESENTER: Avlant Nilsson
Agent-based modeling of spatiotemporal organization of bacteria in the human gut (abstract)
Scalable and flexible inference framework for stochastic dynamic single-cell models (abstract)
Stochastic Model of Intra-Tumor Heterogeneity (SMITH) (abstract)
PRESENTER: Adam Streck
Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. (abstract)
PRESENTER: Luca Musella
Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling (abstract)
PRESENTER: Joseph Chan
Efficient parameter estimation for ODE models with semi-quantitative data using spline approximation (abstract)
PRESENTER: Domagoj Doresic
Monday, October 10th

View this program: with abstractssession overviewtalk overview

09:15-10:00 Session K6: KEYNOTE VI: Michael Yaffe

Abstract: Major advances in phosphoproteomic technologies have led to the discovery of over 100,000 sites of protein phosphorylation in the human proteome. Connecting these phosphorylation sites to the protein kinases and signaling networks responsible for their creation and regulation has been the major bottleneck in deciphering how phosphorylation at these sites contributes to specific cellular phenotypes in health and disease. I will present ongoing work from the Cantley, Turk, Linding, and Yaffe laboratories aimed at conquering this ‘dark phosphoproteome’ by determining the motifs for the complete human serine/threonine kinome using solution phase oriented peptide library screening. Computational analysis of large public phosphoproteomic datasets using these motifs identifies distinct signaling pathways and networks that are up- or down-regulated in response to particular stimuli, and provides insights into complex biological responses that are mediated through cross-network signaling. Secondly, I will present ongoing work examining the control of cell senescence in cancer cells following DNA damage, revealing unexpected roles for MAP kinases in controlling the decision between senescence and proliferation in response to genotoxic stress.

Location: Alexander
09:15
Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA Damage (abstract)
10:00-10:30Coffee Break
10:30-12:30 Session 7: PREVENTING FUTURE PANDEMICS

Summary: This session covers pressing questions about the biology and epidemiology of the COVID-19 disease such as understanding disease systems and mechanisms, mapping infection, and distinguishing susceptibity and resilience. Recent systems biology and epidemiological data will be highlighted to discuss actionable paths towards SARS-CoV2 infection prevention and resilience. 

Location: Grenander I+II
10:30
The metabolic and proteomic landscape of genome-scale genetic perturbation (abstract)
10:50
Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease course (abstract)
11:03
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells (abstract)
PRESENTER: Nantia Leonidou
11:16
Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium diphtheriae. (abstract)
PRESENTER: Luca Musella
11:28
Mathematical model of the immunopathological progression of tuberculosis (abstract)
11:40
Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral proteomes (abstract)
11:52
FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast (abstract)
12:02
Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual screening (abstract)
12:14
A multi-strain model of immunization against influenza A viruses after infection or vaccination (abstract)
PRESENTER: Lara Bruezière
12:17
Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community (abstract)
PRESENTER: Simon Merkt
12:20
COVIDpro: Database for mining protein dysregulation in patients with COVID-19 (abstract)
PRESENTER: Augustin Luna
12:23
Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination (abstract)
12:26
Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2 (abstract)
PRESENTER: Jacques Hermes
12:27
Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19 patients (abstract)
PRESENTER: Manuel Huth
12:28
INSIDe: Integrative modeling of the spread of serious infectious diseases (abstract)
10:30-12:30 Session 8: YOUNG SCIENTIST FORUM

Summary: Artificial intelligence (AI), with its ability to propose decisions for world-wide threats, generate realistic videos and imitate human thought processes, is rapidly making its way into many domains of science and everyday life. At the same time, certain spectacular failings of this technology require an intervention by well contextualised human knowledge. In systems biology, AI is now complementing classical modeling approaches (ODE and Boolean models, for example) and is part of new hybrid modeling approaches. Three panel members, representing three modeling approaches, will discuss their benefits and drawbacks in the context of systems biology, a field with its own specific issues in data acquisition and knowledge representation. We open the discussion to topics of current limitations and possible future goals in the field, as well as the role of systems biology in the broader social context. We invite the audience to challenge the panel members with questions they would like to see addressed by the community.

10:30
Introduction
10:35
Pitching for Classical modeling
10:45
Pitching for AI / ML modeling
10:55
Pitching for hybrid/data-driven modeling
11:05
Panel Discussion
12:05
Q&A
12:25
Final remarks
10:30-12:30 Session 9: SIGNAL TRANSDUCTION

Summary: Responsiveness to signals influencing cell phenotypic behaviors is a key characteristic of living organisms. Processing of encoded information through cellular signal transduction networks triggers the expression of genes and modulation of protein activities in metabolism and cytoskeleton, culminating in either "all-or-nothing" or “graded" cellular decisions. These decisions are affected by the heterogeneity in protein expression and cell size and in multicellular organisms link cellular processes to tissue effects. This session covers advances in technologies such as proteomics and life cell imaging that allow to monitor dynamic behavior at high temporal resolution and quantitative accuracy. Likewise advances in mathematical modelling approaches potentially linking the cell population scale to the tissue or single cell level will be covered. Synergies of AI based modeling and mechanistic modelling provide novel avenues to unravel principle mechanism that determine dynamic behavior at multiple scales. 

Location: Alexander
10:30
Combining multi-omics and biological knowledge to understand signaling deregulation in disease (abstract)
10:50
Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast epithelia (abstract)
PRESENTER: Bishal Paudel
11:05
Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor cells (abstract)
PRESENTER: Marcel Schilling
11:20
Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases (abstract)
11:34
A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape (abstract)
PRESENTER: Michael Zhao
11:47
A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug resistance (abstract)
PRESENTER: Fabian Fröhlich
11:59
Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling Pathway (abstract)
PRESENTER: Nathan Manes
12:11
Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction pathway (abstract)
12:16
Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease (abstract)
12:19
Periodic Forcing of the ERK pathway (abstract)
PRESENTER: Nguyen Tran
12:22
Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single cells (abstract)
12:25
Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output (abstract)
12:28
Deciphering dysregulation in Erythroleukemia to design intervention strategies (abstract)
PRESENTER: Yomn Abdullah
12:29
Building the knowledge base to understand cellular signal transduction in different inflammatory phenotypes (abstract)
PRESENTER: Marcus Krantz
12:30
Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION - ZOOM) (abstract)
12:30-13:30 Session L3: LUNCHEON III: BioModels: Model of the year competition

Summary: BioModels’s Model of the year is a new competition for early career researchers, including but not limited to PhD students and postdocs, to applaud emerging leaders in the area of systems biology modelling. This competition aims to recognize exciting modelling research as well as promote reproducibility and good modelling practice among early career researchers. The competition will be officially launched at ICSB2022. Details on the application process, eligibility criteria, guidance to submit reproducible models (required as part of application) to enter this competition will be discussed during this luncheon workshop. More details are available at https://www.ebi.ac.uk/biomodels/competition/model-of-the-year-2022

Location: Grenander I+II
12:30-13:30 Session L4: LUNCHEON IV: JIPipe Workshop

Summary: The continuous development of new microscopy techniques is tracked by the emergence of new or improved image analysis software that can provide the necessary means of quantification. A stalwart amongst these tools is ImageJ, which has served the increasingly demanding needs of the image analysis community for decades. Despite the large community support behind ImageJ that has been keeping the platform up to date, ImageJ is still hindered by the lack of a versatile visual programming language (VPL) that would allow simple creation of fully reproducible and readily expandable workflows of all levels of complexity according to the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. Here we designed a new VPL, termed Java Image Processing Pipeline (JIPipe, www.JIPipe.org), which provides over 1000 functionalities of ImageJ in a fully visual format. Main features of JIPipe include full reproducibility of the algorithmic procedure, a standardized project- and results format, automatic scalability towards batch analysis, parallel processing, GPU support via CLIJ2, an integration of Cellpose, as well as support for Python and R scripting. JIPipe is fully equipped to be the new tool of choice for both expert and beginner image analysts and can function as a convenient tool where analysis and quantification ideas can be easily cast into visual workflows. These are easy adaptable and adjustable even by experimentalists, thus bridging the gap between image analysts and experimentalists. In this workshop, we will introduce the main features of JIPipe in interactive sessions, where the details of the main graphical user interface will be demonstrated, and a simple but representative image analysis workflow will be built together with the participants. The structure of the individual image operations, as well as of JIPipe’s backbone data structure will be explored with respect to how batch processing and implementation of the FAIR principles are achieved. More complex examples will follow, where the highly sophisticated data annotation system of JIPipe will be introduced via easy-to-follow examples. Projects will include the tracking of nematodes, the quantification of pathogen uptake by immune cells, deep learning-based segmentation tasks, as well as light sheet microscopy data analysis of the kidney.

13:30-15:30 Session 10: COMPUTATIONAL PATHOLOGY

Summary: The digitization of the diagnostics of tissue sections offers interesting application possibilities for patients, doctors and researchers. Not only the digitization process with the viewing software is one of the advantages, but also the possibility to apply decision support systems in the form of artificial intelligence (machine learning). Structured pathological diagnoses, digital histological multiplex images, molecular pathological data as well as known interactions between gene alterations and drugs are the basis for personalized medicine, where individual predictions can be made for each patient.

Location: Grenander I+II
13:30
System Pathology of Cancer (abstract)
13:50
Advantages of Ensemble CNN’s in Computational Pathology. (abstract)
14:00
Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go? (abstract)
14:10
EMPAIA - Harmonizing Access to Clinical-Grade AI Algorithms in Pathology (abstract)
14:20
Computational Pathology of Kidney Disease (abstract)
14:40
Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian framework (abstract)
14:45
Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit (abstract)
PRESENTER: Amit Frishberg
14:50
Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling (abstract)
PRESENTER: Joseph Chan
14:55
Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer (abstract)
PRESENTER: Julia Casado
15:00
3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in melanoma (abstract)
PRESENTER: Janan Arslan
15:05
Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide images (abstract)
PRESENTER: Lise Minaud
15:10
Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures (abstract)
PRESENTER: Haoyang Mi
15:15
Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues (abstract)
PRESENTER: Bharti Arora
15:20
Rapid parallel model inference and on-the-fly tiling of digital pathology images (abstract)
PRESENTER: Sina Ghandian
15:25
Single-cell spatial atlas of high-grade serous ovarian cancer (abstract)
13:30-15:30 Session 11: CAREER FORUM

Summary: The two most important aspects for a career in science? Publications and Grants. Taking an interdisciplinary career path with systems biology approaches, should one focus on data science methodologies, experimental technologies, or biological/medical questions to reach a professorship? The session will combine short presentations with an interactive debate about career development. We invite experienced scientists to share their views and advice, and we welcome younger scientists who we will try to support with advice about a career centred around systems biology approaches. We also will be giving practical advice regarding grant writing, publications and personal development.

 

13:30
Become an ICSB - an Interdisciplinary Champion of Systems & Biology (abstract)
13:40
How to find good problems with collaborators! (abstract)
13:55
From bench to scientific publishing (abstract)
14:10
From Academic Research to Pharmaceutical R&D and Back (abstract)
14:25
Thinking of a career in big pharma? Here is what you need to know. (abstract)
14:40
Q&A and Open Discussion
13:30-15:30 Session 12: CHEMICAL & GENETIC SYSTEMS BIOLOGY

Summary: The inherent complexity of biological systems has fostered the implementation of large-scale experimental screenings to synthesize a deeper understanding of cellular responses to genetic and chemical perturbations. In this session, we will explore novel methodological approaches to integrate and analyze this data to understand the general principles of the wiring of living cells and its context-dependent variations. We thus welcome submissions in the fields of genetic interactions, including synthetic lethal and genetic suppression, context-specific dependency mappings and drug-induced cell responses, as well as computational methods to interpret the corresponding large-scale data sets.

Location: Alexander I+II
13:30
Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells (abstract)
13:51
Formatting Biological Big Data to Enable Systems Pharmacology (abstract)
14:12
Dissecting the principles underlying transcriptional heterogeneity (abstract)
14:32
CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries (abstract)
14:45
Dynamic metabolome profiling uncovers potential TOR signaling genes (abstract)
14:58
Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library (abstract)
PRESENTER: Hannes Link
15:11
A new platform for deep multiplexed metabolomics with a DNA barcode readout (abstract)
PRESENTER: Andy Fraser
15:19
Dynamics of growth and ribosome level in batch cultures of S. cerevisiae (abstract)
PRESENTER: Yu Huo
15:20
An optimal RNA growth law and its relationship with genome organization in bacteria (abstract)
PRESENTER: Xiao-Pan Hu
15:21
A model of RNA repair to study antibiotic tolerance (abstract)
PRESENTER: Hollie Hindley
15:22
Gene-essentiality based drug signature helps repurposing non-cancer drugs (abstract)
PRESENTER: Jing Tang
15:23
Towards rational design of antibiotic combination therapies (abstract)
15:24
Patterns of differentially essential genetic interactions characterize functional modules across cancer types (abstract)
15:25
Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable sets (abstract)
PRESENTER: Mariyam Khan
15:26
A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer (abstract)
PRESENTER: Kittisak Taoma
13:30-15:30 Session 17A: WILDCARDS *.* [Part I]

Summary: This session will entail talks across any hot topic or landmark work selected by all session chairs and organizers of ICSB 2022. They can be from any field of systems biology or associated fields. We will consider both contributed wildcard talks and approach researchers who has or is conducting exciting groundbreaking work.

Location: Alexander III
13:30
Tissue-specific codon usage: from systems to synthetic biology (abstract)
13:40
Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based models (abstract)
PRESENTER: St. Elmo Wilken
13:50
Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data (abstract)
PRESENTER: Nikolai Köhler
14:00
Structural proteomics evidence for a predicted glycolytic metabolon (abstract)
14:10
From System Biology to Pharmacology: Identifying what is important (abstract)
14:20
Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular species (abstract)
PRESENTER: Dinara Usmanova
14:30
Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary propensities (abstract)
PRESENTER: Yun Min Song
14:40
A physiologically-structured population model for pharmacokinetics of orally inhaled drugs (abstract)
14:50
When cells decide to give up on repairing DNA damage (abstract)
15:00
Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master Equation (abstract)
PRESENTER: Nicole Radde
15:10
GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations (abstract)
PRESENTER: Yusuf Roohani
15:13
Bias and reproducibility in a Computational Neurobiology PhD’s journey (abstract)
15:16
Learning synthetic cell classifier designs with genetic algorithms and logic programming (abstract)
PRESENTER: Melania Nowicka
15:17
Predicting metabolite accumulation in cancerous metabolic network (abstract)
PRESENTER: Tin Yau Pang
15:18
Nonstationary Biomedical Signal Feature Extraction (abstract)
15:19
Using multi-omics data and machine learning to unravel alternative splicing regulation (abstract)
PRESENTER: Ulf Schmitz
15:30-16:00Coffee Break
16:00-16:45 Session K7: HFSP sponsored KEYNOTE: Jörg Overmann

Abstract: Current estimates of the global bacterial diversity exceed 1 billion species. By comparison, the number of bacterial species that are described and available for direct physiological and biochemical characterization in the laboratory amounts to less than 19,000. Microbes offer insights into novel biology, drive biogeochemical transformations and are key sources of biochemical innovation. Therefore their functions and interactions need to be better resolved. Insights from state-of-the-art, culture-independent studies of bacteria in their environment can guide the development of novel cultivation approaches that better mimic their natural niche, e.g., natural substrate conditions, growth in biofilms, or exploiting signal compounds and biotic interactions. A combination with high throughput, automated methods that allow multifactorial testing of a large variety of such cultivation conditions (“culturomics”) are particularly promising. These approaches have begun to return novel types of bacteria of interest for research and applications. A currently almost untapped source for novel insights is the wealth of molecular, environmental, and phenotypic data on microorganisms that are principally available but highly dispersed, heterogenous, and non-standardized. Recent integrative database projects address these challenges, render data accessible for semantic searches and artificial intelligence analyses, and thereby offer new, digital gateways to biodiscovery.

Location: Alexander
16:00
Elucidating functions of microbial dark matter (abstract)
16:45-19:30 Session P2: POSTER SESSION II (Even Submission Numbers)

EVEN NUMBERED POSTERS (2, 4, 6, ...;)

Location: All Grenanders
Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks (abstract)
PRESENTER: Marius Kirchner
Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design (abstract)
PRESENTER: Benjamin Smart
Machine learning-based sepsis risk prediction modeling using electronic health records of cancer patients (abstract)
Numerical approaches for the rapid analysis of prophylactic efficacy against HIV (abstract)
PRESENTER: Lanxin Zhang
A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer (abstract)
PRESENTER: Kittisak Taoma
Fast and scalable machine learning approach for dynamic metabolic engineering (abstract)
Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a cell (abstract)
Timelapse of Single Cell Lipidomics (abstract)
PRESENTER: Paul Jonas Jost
Efficient brute-force model selection by iterative elimination of less useful model subspaces (abstract)
PRESENTER: Dilan Pathirana
Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic conditions (abstract)
Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission dynamics (abstract)
PRESENTER: Ariane Ernst
Analyzing human E3 ligome for efficient design of PROTACs (abstract)
PRESENTER: Arghya Dutta
Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast cancer (abstract)
Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter (abstract)
A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients (abstract)
PRESENTER: Moein E. Samadi
Deep insight into SABIO-RK data via visualization (abstract)
PRESENTER: Dorotea Dudas
Improving drug-induced transcriptional descriptors and their biological connectivity (abstract)
Dynamics of growth and ribosome level in batch cultures of S. cerevisiae (abstract)
PRESENTER: Yu Huo
Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional view (abstract)
PRESENTER: Lea Seep
Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone metastases (abstract)
PRESENTER: Claire Villette
A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in women (abstract)
Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in yeast (abstract)
Theory of biochemical information processing with transients (abstract)
PRESENTER: Manish Yadav
An optimal RNA growth law and its relationship with genome organization in bacteria (abstract)
PRESENTER: Xiao-Pan Hu
Decrypting drug actions and protein modifications by dose- and time-resolved proteomics (abstract)
PRESENTER: Florian P Bayer
Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease (abstract)
Modeling the tumor microenvironment in patient-derived organoid culture (abstract)
Accelerating whole-cell modelling with surrogate machine learning models (abstract)
PRESENTER: Ioana Gherman
A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis (abstract)
PRESENTER: Rebekka Fendt
Predicting developmental states in zebrafish using transfer learning (abstract)
Expanding the disease network of Glioblastoma Multiforme via topological analysis (abstract)
PRESENTER: Apurva Badkas
Single cell pseudo-time inference based on copy number variants for identifying a tumor transition state (abstract)
PRESENTER: Jonghyun Lee
Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment interactions (abstract)
PRESENTER: Juyeon Cho
Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation models (abstract)
A physiology-based model of bile acid metabolism in mice (abstract)
PRESENTER: Bastian Kister
Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical modeling (abstract)
PRESENTER: Mareike Simon
Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive disease. (abstract)
PRESENTER: Richard Norris
From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology (abstract)
PRESENTER: Maria Krantz
Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care Units (abstract)
PRESENTER: Dilan Pathirana
A multi-strain model of immunization against influenza A viruses after infection or vaccination (abstract)
PRESENTER: Lara Bruezière
BlotIt - Optimal alignment of Western blot and qPCR experiments (abstract)
PRESENTER: Jens Timmer
A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples (abstract)
PRESENTER: Tanja Holstein
Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes (abstract)
PRESENTER: Wilhelm Neubert
Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian restraints. (abstract)
PRESENTER: Iga Biskupek
Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach (abstract)
PRESENTER: Henrik Podéus
Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma. (abstract)
PRESENTER: Arran Pack
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (abstract)
PRESENTER: Le Yuan
A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation (abstract)
PRESENTER: Michael Zhao
FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks (abstract)
PRESENTER: Julia Naas
A powerful modelling approach tailored to cellular signalling (abstract)
PRESENTER: Clemens Kreutz
Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution. (abstract)
PRESENTER: Peter Pennitz
Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway activation (abstract)
PRESENTER: Barbara Helm
Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones (abstract)
Defining Design Rules for Next-Generation Snakebite Antivenoms (abstract)
PRESENTER: Natalie Morris
Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize (abstract)
PRESENTER: Mingjie He
Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and pathogens (abstract)
PRESENTER: Nils Kurzawa
Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular remodeling (abstract)
PRESENTER: Daniel Seeler
Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology (abstract)
PRESENTER: Eliott Jacopin
Inference and dynamical simulation of the gene-regulatory network in single cells (abstract)
PRESENTER: Patrick Stumpf
The transcriptome dynamics of single cells during the cell cycle (abstract)
PRESENTER: Daniel Schwabe
Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2 (abstract)
PRESENTER: Clemens Peiter
Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models (abstract)
PRESENTER: Diana Széliová
Extracting knowledge from multi-omics and clinical datasets using graph machine learning (abstract)
PRESENTER: Ferdinand Popp
Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks (abstract)
PRESENTER: Nataša Puzović
Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation (abstract)
PRESENTER: Niloofar Nikaein
Mutually Antagonistic Protein Pairs of Cancer (abstract)
PRESENTER: Ertugrul Dalgic
Virtual Cell Modeling and Simulation Software (abstract)
PRESENTER: Michael Blinov
PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science (abstract)
Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR framework (abstract)
PRESENTER: Christine Brun
On the relation between input and output distributions of scRNA-seq experiments (abstract)
PRESENTER: Daniel Schwabe
Investigating brain development using tissue and single-cell gene expression data (abstract)
INSIDe: Integrative modeling of the spread of serious infectious diseases (abstract)
Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And Community (abstract)
PRESENTER: Simon Merkt
Disentangling the internal composition of tumour activities through a hierarchical factorization model (abstract)
Patient- and cell line-specific modeling of diffuse large B-cell lymphoma (abstract)
PRESENTER: Fabian Konrath
Neural Circuits Underlying Autism Spectrum Disorders (abstract)
PRESENTER: Jon Chang
From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus LEU18496. (abstract)
Using graph theory and recurrent neural network models to investigate the anxiety circuit (abstract)
Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling (abstract)
PRESENTER: Enes Sefa Ayar
TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion syndrome (abstract)
GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations (abstract)
PRESENTER: Yusuf Roohani
MeDaX - our vision for bioMedical Data eXploration (abstract)
PRESENTER: Judith Wodke
Using multi-omics data and machine learning to unravel alternative splicing regulation (abstract)
PRESENTER: Ulf Schmitz
An interconnected multi-level mechanistic model of the human brain (abstract)
On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological systems (abstract)
PRESENTER: Sandip Saha
Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level (abstract)
PRESENTER: Natalia Savytska
COVIDpro: Database for mining protein dysregulation in patients with COVID-19 (abstract)
PRESENTER: Augustin Luna
Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer (abstract)
PRESENTER: Julia Casado
SynBioSuite: Web-based modeling and analysis of biological systems (abstract)
PRESENTER: Lukas Buecherl
A robust clustering strategy for patient stratification in complex diseases (abstract)
PRESENTER: Sara Palomino
Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl (abstract)
A disease network-based deep learning approach for characterizing melanoma (abstract)
PRESENTER: Xin Lai
Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction (abstract)
PRESENTER: Laura Sudupe
Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed efficiency (abstract)
PRESENTER: Haja Kadarmideen
Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited Vaccination (abstract)
Exploring the “dark proteome” in hepatocellular carcinoma (abstract)
Cells use molecular working memory to navigate in changing chemoattractant fields (abstract)
PRESENTER: Robert Lott
Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq Data (abstract)
PRESENTER: Mahdi Alshoyokh
New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers (abstract)
Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage (abstract)
PRESENTER: Xiu Jia
Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+ (abstract)
PRESENTER: Balazs Erdos
Towards a Computational Toolkit for Cell Fate Decision Detection (abstract)
PRESENTER: Ali Balubaid
FISHing for Correlation (abstract)
Patterns of differentially essential genetic interactions characterize functional modules across cancer types (abstract)
Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells (abstract)
Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer tissues (abstract)
PRESENTER: Bharti Arora
Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model (abstract)
PRESENTER: Lina Kroehling
Bias and reproducibility in a Computational Neurobiology PhD’s journey (abstract)
MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL data (abstract)
PRESENTER: Hendrik de Weerd
Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data (abstract)
PRESENTER: Levi van Doorn
Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion modes. (abstract)
Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq (abstract)
PRESENTER: Leon Strenger
Cell Type view into tomato stem elongation in Shade avoidance response (abstract)
PRESENTER: Linge Li
Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a fed-batch (abstract)
Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks (abstract)
Evaluation of methods to compute quasi-potential functions and their use as systems biology models (abstract)
PRESENTER: Subash Balsamy
Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with GotEnzymes (abstract)
PRESENTER: Mihail Anton
Single-cell spatial atlas of high-grade serous ovarian cancer (abstract)
Mitotic Memory as Spontaneous Symmetry Breaking in the Cell (abstract)
PRESENTER: Arran Hodgkinson
Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity (abstract)
PRESENTER: Zita Soons
BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs (abstract)
Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems (abstract)
PRESENTER: Amitava Giri
Latent variable models of fungal growth considering the data measurement process (abstract)
PRESENTER: Tara Hameed
Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems (abstract)
PRESENTER: Stephan Grein
Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population Architectures (abstract)
PRESENTER: Haoyang Mi
Tuesday, October 11th

View this program: with abstractssession overviewtalk overview

09:15-10:00 Session K8: KEYNOTE VIII: Alexander Pritzel

Abstract:

Location: Alexander
09:15
The workings and impact of AlphaFold (abstract)
10:00-10:30Coffee Break
10:30-12:30 Session 13: INTEGRATION OF COMPUTATIONAL APPROACHES

Summary: In recent years, more and more studies are appearing where different computational approaches and methodologies are combined to address biological phenomena. On one hand, integration of different methodologies poses problems regarding the definition of the respective interface, for example when combining agent-based models with ordinary differential equations, or Boolean with genome-scale metabolic models. On the other hand, the successful combination offers the opportunity to answer biological questions not easily addressable otherwise. This session will present success cases where the combination of different computational methodologies and approaches has shed light on mechanisms underlying emergent properties of biological systems. 

Location: Grenander I+II
10:30
Integrating cellular and physiologically-based pharmacokinetic (PBPK) modelling (abstract)
10:50
A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle Control (abstract)
11:10
More BANG for the buck: how to distribute measurements to optimize information gain for mathematical models (abstract)
PRESENTER: Severin Bang
11:25
A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics (abstract)
11:30
Unraveling the role of network motifs to decipher the origin of robust decision-making in biological systems (abstract)
PRESENTER: Amitava Giri
11:35
Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based modelling (abstract)
PRESENTER: Sabine Peres
11:40
Multi-Omics Regulatory Network Inference in the Presence of Missing Data (abstract)
PRESENTER: Juan Henao
11:45
BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge graphs (abstract)
11:50
Fast parameter estimation for ODE-based models of heterogeneous cell populations (abstract)
PRESENTER: Yulan van Oppen
11:55
Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism (abstract)
PRESENTER: Mattia Gollub
12:00
Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis (T13C-MFA) (abstract)
12:05
Simulation Based Metabolic Flux Inference (abstract)
PRESENTER: Thomas Diederen
12:10
BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualization (abstract)
PRESENTER: Ion Moraru
12:15
Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step number (abstract)
PRESENTER: Hyukpyo Hong
12:20
FAIR assessment of biosimulation models - a cross-community project (abstract)
PRESENTER: Dagmar Waltemath
12:25
FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks (abstract)
PRESENTER: Julia Naas
12:26
Exact Confidence Regions for Non-Linear Models (abstract)
12:27
Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level (abstract)
PRESENTER: Natalia Savytska
12:28
Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations (abstract)
PRESENTER: Eui Min Jeong
12:29
DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology (abstract)
10:30-12:30 Session 15: CANCER SYSTEMS BIOLOGY

Summary: Over the last decade, a large amount of data has been collected and made publicly available in cancer research. This has enabled development of new approaches in cancer research, ranging from predicting the functional nature of genetic alterations and assessing the effect of genetic and pharmacologic perturbations to predicting patient sensitivity to specific drugs and adaptive response in cancer cells. These methodologies represent critical contribution to the field of precision cancer medicine and support increasing clinical translational of computational and systems biology approaches to the clinic. This session will present some of the latest development in both basic and translational research using mathematical modeling, network- and deep learning-based, for the prediction of biological mechanisms, drug responses and personalized cancer medicine.

Location: Alexander
10:30
Gene expression heterogeneity arises from signaling networks (abstract)
10:50
Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell level. (abstract)
11:10
Digital Twin models for the precision diagnosis and therapy of cancer (abstract)
11:25
Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity (abstract)
11:37
MultiOmics Network Embedding for SubType Analysis (abstract)
PRESENTER: Giovanni Scala
11:49
Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in DLBCL (abstract)
PRESENTER: Eleanor Jayawant
12:01
Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data (abstract)
PRESENTER: Nurcan Tuncbag
12:11
Improving our Mechanistic Understanding of Cell Cycle Dynamics (abstract)
PRESENTER: Paul Lang
12:21
Modeling the tumor microenvironment in patient-derived organoid culture (abstract)
12:24
Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian cells (abstract)
12:25
Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design (abstract)
PRESENTER: Benjamin Smart
12:26
Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with spotter (abstract)
12:27
Expanding the disease network of Glioblastoma Multiforme via topological analysis (abstract)
PRESENTER: Apurva Badkas
12:28
Mutually Antagonistic Protein Pairs of Cancer (abstract)
PRESENTER: Ertugrul Dalgic
12:29
A disease network-based deep learning approach for characterizing melanoma (abstract)
PRESENTER: Xin Lai
10:30-12:30 Session 20: PLANT SYSTEMS BIOLOGY

Summary: A rapidly changing environment challenges our understanding of plant metabolism, growth and development. It has become evident that application of systems biology approaches essentially supports the quantitative analysis of plant-environment interactions, plant resilience against diverse stressors and plant performance. This conference session will focus on methods, theories, and approaches in the field of plant systems biology comprising experimental omics analysis, flux analysis, network analysis, mathematical modelling, and bioinformatics.

10:30
Co-expression analysis of transcriptome and proteome identifies LRR-VIII-1 kinase and MAPK-kinase (MEK1) regulatory modules associated with P-deficiency adaptation and P use efficiency in maize (abstract)
PRESENTER: Mingjie He
10:42
A modular concept for modeling of plant lipid metabolism (abstract)
PRESENTER: Sandra Correa
10:54
Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana (abstract)
PRESENTER: Hao Tong
11:06
Stress Knowledge Map: A knowledge resource for modeling of plant stress responses (abstract)
PRESENTER: Kristina Gruden
11:18
Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical meristem (abstract)
PRESENTER: Timon W. Matz
11:30
Computational analysis of cambium activity during plant radial growth (abstract)
PRESENTER: Ruth Großeholz
11:42
Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic stressors (abstract)
11:54
Deep convolutional neural networks capture the relationship between genetic variation and gene expression in plants (abstract)
12:06
PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen science (abstract)
12:18
From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems Biology (abstract)
PRESENTER: Maria Krantz
12:30-13:30 Session L5: LUNCHEON V: ICSB Conference Organizers/Community Discussion

Summary: Discussion of ICSB future and next meetings etc.

Location: Grenander I+II
12:30-13:30 Session L6: LUNCHEON VI: Workshop on gene set enrichment

Summary: Gene set enrichments (GSEs) remain an important tools to link statistical results of high throughput data sets with biological reality. While the principle is simple, there is a substantial number of variations and special applications, such as combining GSEs with correlation analysis, multivariate modelling or applying to non-standard data sets (such as OLINK, Nanostring, ATAC-Seq or ChIP-Seq as well as metabolic profiling). There is a substantial number of algorithms and packages for GSEs. These are not redundant, but rather suitable for different applications. In this tutorial, I will show simple yet effective strategies for gene set enrichment analysis in several different scenarios, including metabolomic profiling, multivariate analyses, single cell RNA-Seq, small gene universes, the strengths and weaknesses of different GSE packages and many tips and tricks. To fully take advantage of the workshop, a very basic command of the R programming language is recommended.

13:30-15:30 Session 14: WHOLE CELL MODELING

Summary: The challenge of whole cell-modeling is indeed one of the most important ones in computational biology. In metabolism, there has been a series of genome scale modeling studies which we aim to involve in the session in addition to topics such as signaling and  regulation.

13:30
Can we trust genome-wide metabolic models? (abstract)
13:50
The limit on dry mass density is an organizing principle for cellular physiology (abstract)
PRESENTER: Martin Lercher
14:03
How can we unleash the potentials of whole-cell modelling? (abstract)
14:16
Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models (abstract)
PRESENTER: Diana Széliová
14:26
The E. coli Whole-Cell Modeling Project: Vision and Progress (abstract)
14:46
Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell cycles (abstract)
14:56
FROG Analysis - a community standard to foster reproducibility and curation of constraint-based models (abstract)
15:06
A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding yeast (abstract)
PRESENTER: Marco Vanoni
15:16
Multi-scale modeling of B-cell fate decisions required for antibody generation (abstract)
13:30-15:30 Session 16: MULTISCALE MODELS

Summary: Systems-biology principles emerge across many orders of magnitude in length and time. This session will highlight leading research that tackles multiscale questions in biology through the integration of models and quantitative experiments. Topics will include the coupling of fast and slow processes, the extrapolation of molecular networks–modules to broader populations of cells and organisms, and the fusion of single-cell mechanisms with tissue-level phenomena.

Location: Grenander I+II
13:30
Circadian and cell cycle control of terminal cell differentiation (abstract)
13:50
Individualized modules and models of enterovirus infection in host cells (abstract)
14:10
Predicting pathogenicity of TPM1 variants using multi-scale models (abstract)
14:30
Multimodal perception links cellular state to decision making in single cells (abstract)
PRESENTER: Bernhard Kramer
14:42
Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids (abstract)
PRESENTER: Simon Haendeler
14:54
Computational modeling for the elucidation of cell fate decisions in early development (abstract)
15:04
Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver function (abstract)
PRESENTER: Matthias König
15:14
A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue Repair (abstract)
15:17
Modeling the adaptive immune response of a lymph node as Petri net (abstract)
PRESENTER: Sonja Scharf
15:20
Digital twins and hybrid modelling for simulation of physiological variables and stroke risk (abstract)
PRESENTER: Tilda Herrgårdh
15:23
Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes (abstract)
PRESENTER: Wilhelm Neubert
15:26
Multilevel approach characterizing the progression of fatty liver disease (abstract)
PRESENTER: Ina Biermayer
15:29
An interconnected multi-level mechanistic model of the human brain (abstract)
13:30-15:30 Session 18: CLINICAL IMPACT AND CHALLENGES OF SYSTEMS BIOLOGY

Summary: In this session we will be covering the challenges associated with delivering real impact in the clinic using systems biology. What are some of the open major challenges currently facing clinicians that could benefit from systems biology? We will host talks that cover recent examples of how systems approaches can be powerfully integrated into clinical research and problem solving flows. 

Location: Alexander
13:30
Therapy-related senescence signatures in lymphoma (abstract)
13:50
The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical approaches (abstract)
14:10
Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and resilience. (abstract)
PRESENTER: Lucile Megret
14:25
Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity (abstract)
PRESENTER: Zita Soons
14:37
The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient data (abstract)
PRESENTER: Thomas Stiehl
14:49
Personalized Treatment of Anemia in Lung Carcinoma (abstract)
15:01
Transomic network analysis of glucose metabolism and its dysfunction associated with obesity (abstract)
15:11
The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity (abstract)
PRESENTER: Shauna O'Donovan
15:21
Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection (abstract)
PRESENTER: Tongta Sae-Ong
15:22
Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease (abstract)
15:23
A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver cirrhosis (abstract)
PRESENTER: Rebekka Fendt
15:24
Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II (BASE-II) (abstract)
PRESENTER: Jeff Didier
15:25
M4-health: digital twins that follow you throughout your health journey (abstract)
PRESENTER: Gunnar Cedersund
15:26
Defining Design Rules for Next-Generation Snakebite Antivenoms (abstract)
PRESENTER: Natalie Morris
15:27
Neural Circuits Underlying Autism Spectrum Disorders (abstract)
PRESENTER: Jon Chang
15:28
MeDaX - our vision for bioMedical Data eXploration (abstract)
PRESENTER: Judith Wodke
15:29
Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction (abstract)
PRESENTER: Laura Sudupe
15:30-16:00Coffee Break
16:00-16:45 Session K9: KEYNOTE IX: Luis Serrano

Abstract: Alternative splicing shapes the regulatory and functional diversity in the cell. Cancer cells tend to select alternative splicing programs involved in tumor progression. However, while therapies based on targeting splicing events have been developed to treat cancer and other diseases, the systematic prioritization of potential disease-driver targets still remains unaddressed. Here, by using publicly available gene-level cancer dependencies from RNAi viability screens across 713 cancer cell lines, we define 140,310 exon-level linear models using splicing profiles and mRNA levels. We then identified cancer-driver exons as the ensemble of models that best prioritized experimental cancer dependencies across individual samples, which we call spotter. The 1,073 selected models corresponded to exons that mostly disrupt their gene's ORF or create new isoforms. These exons belong to genes related to the splicing machinery and cell proliferation and show a low rate of aberrant mutations. Interestingly, our ensemble model inferred the effects of single and multiple splicing perturbations on cell proliferation. Integrating pharmacological screens with our predicted splicing-level dependencies, we uncovered cancer-driver exons that mechanistically mediate drug sensitivity and synergize with drug effects. In patients, our ensemble model can not only aid the systematic prioritization of splicing targets across 14 different types of cancer but also identify putative splicing events driving patient response upon drug treatment or pinpoint susceptible splicing events at single-patient resolution. Taken together, in silico RNA isoform screening with spotter sheds light on the weak spots of cancer samples at the splicing level and holds the potential to be implemented for personalizing treatments.

Chair:
Location: Alexander
16:00
Bacterial therapy for pulmonary infectious diseases (abstract)
Wednesday, October 12th

View this program: with abstractssession overviewtalk overview

09:00-11:00 Session 17B: WILDCARDS *.* [Part II]

Summary: This session will entail talks across any hot topic or landmark work selected by all session chairs and organizers of ICSB 2022. They can be from any field of systems biology or associated fields. We will consider both contributed wildcard talks and approach researchers who has or is conducting exciting groundbreaking work.

09:00
Data-driven modeling of cell-cell communication networks (abstract)
PRESENTER: Philipp Burt
09:15
Modelling of Pharmacokinetics and Pharmacodynamics for first-in-man dose selection of targeted alpha therapy (abstract)
PRESENTER: Andrea Gruber
09:35
A quantum circuit model for inferring gene regulatory networks with application to single-cell transcriptomic data (abstract)
PRESENTER: James Cai
09:45
Foundations for a theory of IP3 induced Ca2+ signalling - re-inventing a classic. (abstract)
PRESENTER: Martin Falcke
09:55
What are the functions of the short open reading frame-encoded peptides in monocytes? An interactomic approach. (abstract)
10:05
Reconstruction of a catalogue of enzyme constrained models of metabolism using GECKO 2.0 and its applications to eukaryote metabolism (abstract)
PRESENTER: Iván Domenzain
10:15
The COmputational MOdeling in BIology NEtwork in 2022: Evolving needs in standardisation and model reuse (abstract)
PRESENTER: David Nickerson
10:25
Spatially-Coordinated Collective Protein Behaviors Enable Robust Circadian Timekeeping (abstract)
PRESENTER: Seokjoo Chae
10:35
A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools (abstract)
10:45
Mathematical modelling of the regulatory mechanisms of keratinocyte differentiation for epidermal homeostasis (abstract)
10:50
Numerical approaches for the rapid analysis of prophylactic efficacy against HIV (abstract)
PRESENTER: Lanxin Zhang
10:53
Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (abstract)
PRESENTER: Le Yuan
10:56
Exploring the missing heritability in SPG7 heterozygous carriers with Whole Genome Sequencing (abstract)
PRESENTER: Marie Coutelier
10:57
Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq (abstract)
PRESENTER: Leon Strenger
10:58
Evaluation of methods to compute quasi-potential functions and their use as systems biology models (abstract)
PRESENTER: Subash Balsamy
09:00-11:00 Session 19: MACHINE LEARNING / ARTIFICIAL INTELLIGENCE

Summary: This session covers the exciting recent advances that are emerging at the intersection of machine learning and systems biology. An example is in formulation of predictive machine learning models, in which model structure and/or selection of parameters can be effectively guided by reference maps of biological structures and their functional state transitions. Such calibration is a critical component of formulating biological models, including models of molecular structures, pathways, cells, tissues, and human populations. Calibration requires not only in-depth understanding of the applied model and phenomena but also application of proper optimization algorithms, where the long-term goal is to find avenues for incorporating and applying methods of machine learning and artificial intelligence. 

Location: Grenander I+II
09:00
Hypergraph for predicting adverse drug reactions (abstract)
09:21
Building a Mind for Cancer (abstract)
09:43
Prediction of enzyme kinetic parameters and substrate scopes using artificial intelligence (abstract)
PRESENTER: Alexander Kroll
09:56
DeepCellRegMap: An interpretable deep learning framework for mapping genetic effects at cell subtype resolution using large-scale single-cell sequencing data (abstract)
PRESENTER: Danai Vagiaki
10:09
A novel drug response network analysis on supercomputers uncovered gastric cancer drug sensitivity mechanism (abstract)
PRESENTER: Heewon Park
10:19
LipiDetective: a Deep Learning Model for the Detection of Lipid Species in Mass Spectra (abstract)
PRESENTER: Vivian Würf
10:29
NETISCE: A dynamical systems and control theory approach to cell reprogramming (abstract)
10:39
Fast and scalable machine learning approach for dynamic metabolic engineering (abstract)
10:42
Efficient brute-force model selection by iterative elimination of less useful model subspaces (abstract)
PRESENTER: Dilan Pathirana
10:45
The insidious trappings of gene set enrichments (abstract)
10:48
Inference of differential gene regulatory networks from gene expression data using boosted differential trees (abstract)
PRESENTER: Gihanna Galindez
10:51
Metabolic profile predictions using efficient and interpretable data descriptors generated with relational learning (abstract)
10:54
Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks (abstract)
10:57
A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19 patients (abstract)
PRESENTER: Moein E. Samadi
10:58
Predicting developmental states in zebrafish using transfer learning (abstract)
10:59
New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust classifiers (abstract)
09:00-11:00 Session 21: NETWORK BIOLOGY & PRECISION MEDICINE

Summary: Network biology is a fundamental branch of systems biology, which views, represents, and analyzes biological processes as networks of interacting components. Examples of these networks are protein-protein interaction networks, metabolic networks and gene regulatory networks. In this session, we will cover innovative large-scale network biology approaches involving single and multi’omics technologies that reveal novel interactions and regulatory mechanisms that control the phenotypes of normal and diseased cells.  We will showcase how applications of this concept in the field of precision medicine can be used to guide personalized therapeutic approaches. 

Location: Alexander
09:00
Proteomes in 3D: Structural proteome snapshots as a new functional ‘omics readout (abstract)
09:20
Cancer cell fate decisions (abstract)
PRESENTER: Lani Wu
09:40
Disentangling Proliferation Signaling in Breast Cancer Subtypes based on an integrative modeling approach (abstract)
PRESENTER: Svenja Kemmer
09:52
Combinatorial effects of ligands are predicted by a genome-scale model of signaling based on artificial neural networks (abstract)
PRESENTER: Avlant Nilsson
10:04
Implementation of multiplexed single cell proteomics for the investigation of cellular heterogeneity in mammalian cell lines (abstract)
PRESENTER: Craig Barry
10:16
DecryptM: decrypting drug actions and protein modification by dose- and time-resolved proteomics (abstract)
PRESENTER: Matthew The
10:26
Computational modeling of DLBCL predicts response to BH3-mimetics (abstract)
PRESENTER: Simon Mitchell
10:36
Data-driven mathematical modeling of human skin aging and its application for natural compound screening (abstract)
PRESENTER: Masatoshi Haga
10:39
Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell clones (abstract)
10:42
Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks (abstract)
PRESENTER: Nataša Puzović
10:45
Multi-Omics Visible Drug Activity prediction, interpreting the biological processes underlying drug sensitivity (abstract)
PRESENTER: Luigi Ferraro
10:48
Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells (abstract)
10:51
Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+ (abstract)
PRESENTER: Balazs Erdos
10:52
FISHing for Correlation (abstract)
10:53
Personalized medicine for Multiple Sclerosis treatment strategies at the individual and population level (abstract)
PRESENTER: Roberta Bursi
10:54
Comparative analysis of molecular fingerprints in prediction of drug combination effects (abstract)
PRESENTER: Bulat Zagidullin
10:55
Proteomics profiling revealed a combination of protein biomarkers for predicting disease trajectory of multiple sclerosis (abstract)
PRESENTER: Julia Åkesson
10:56
Data-driven modeling of mitochondrial metabolism (abstract)
11:00-11:25Coffee Break
11:25-12:00 Session K10: CLINICAL KEYNOTE: Leif Erik Sander

Abstract: Growing population density and -mobility, urbanization, decreasing biodiversity and changing ecosystems substantially contribute to an elevated risk of epidemic or pandemic outbreaks. COVID-19, and more recently the global MPX (monkeypox) outbreak, have demonstrated the high pandemic potential of zoonotic pathogens. Vaccine induced population immunity plays a major role in preventing and limiting pandemics and their detrimental medical and socioeconomic impact. Here I will review recent advances in developing protective vaccines, their mechanisms of action and future directions for transmission reducing vaccines for respiratory pathogens.

Chair:
Location: Alexander
11:25
Preventing & limiting pandemics through vaccination: what have we learned from COVID-19 and MPX? (abstract)
12:00-12:45 Session K11: KEYNOTE XI: Eske Willerslev

Abstract: The field of ancient genomics has transformed our understanding of human history by uncovering how we obtained our present-day genetic diversity through past migrations and admixture events. It has also changed our understanding of ecosystem change in space and time by providing plant and animal ancient DNA directly from past environments and pathogen evolution by reconstructing the genomes of infectious diseases of the past . One future direction of the field is to understand the emergence of differences in disease risk across human populations. In this talk, I will cover these topics by providing research examples from Centre for GeoGenetics.

Location: Alexander
12:00
What we can learn from ancient genomics? Human history, ecosystem change, infectious disease, and disease susceptibility. (EXCEPTION - ZOOM) (abstract)