Program for Tuesday, October 11th: Talk View

PROGRAM FOR TUESDAY, OCTOBER 11TH: TALK VIEW

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View: with abstracts session overview

9:30

10:00

10:30

11:00

11:30

12:00

12:30

13:00

13:30

14:00

14:30

15:00

15:30

16:00

16:30

17:00

17:30

18:00

18:30

19:00

09:15-10:00

The workings and impact of AlphaFold

Alex Pritzel

10:30-12:30

Integrating cellular and physiologically-based pharmacokinetic (PBPK) modelling

Ursula Kummer

10:30-12:30

A Novel and Robust Molecular Switch Actuating the Quantitative Model of Eukaryotic Cell Cycle

Matteo Barberis

10:30-12:30

More BANG for the buck: how to distribute measurements to optimize information gain for mathematical

Severin Bang, Jens Timmer

10:30-12:30

A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics

Baishakhi Tikader, Samir K. Maji, Sandip Kar

10:30-12:30

Unraveling the role of network motifs to decipher the origin of robust decision-making in biological

Amitava Giri, Sandip Kar

10:30-12:30

Geometric programming to Solve Optimal Concentrations of Metabolites and Enzymes in Constraint-based

Sabine Peres, Marc Dinh, Vincent Fromion

10:30-12:30

Multi-Omics Regulatory Network Inference in the Presence of Missing Data

Henao, Lauber, Azevedo, Grekova, Theis, List, Ogris, Schubert

10:30-12:30

BioCypher: an ontology-driven framework for flexible harmonisation of large-scale biomedical knowledge

Sebastian Lobentanzer, Dénes Türei, Julio Saez-Rodriguez

10:30-12:30

Fast parameter estimation for ODE-based models of heterogeneous cell populations

Yulan van Oppen, Andreas Milias-Argeitis

10:30-12:30

Statistical estimation of enzyme kinetics and pathway cost predicts overflow metabolism

Mattia Gollub, Thierry Backes, Hans-Michael Kaltenbach, Joerg Stelling

10:30-12:30

Integrating 13C labeling and thermodynamic data for thermodynamically consistent Bayesian Metabolic Flux Analysis

Johann F. Jadebeck, Mattia G. Gollub, Axel Theorell, Katharina Nöh

10:30-12:30

Simulation Based Metabolic Flux Inference

Thomas Diederen, Nicola Zamboni

10:30-12:30

BioSimulations: integrated models, model languages, model repositories, simulation experiments, simulation tools and data

B. Shaikh, L. Smith, M. Blinov, H. Sauro, J. Karr, I. Moraru

10:30-12:30

Systematic inference identifies a major source of heterogeneity in non-Markovian cell signaling dynamics: the rate-limiting step

Hyukpyo Hong, Dae Wook Kim, Jae Kyoung Kim

10:30-12:30

FAIR assessment of biosimulation models - a cross-community project

Balaur, Welter, Nickerson, Sheriff, König, Hermjakob, Satagopam, Waltemath

10:30-12:30

FLOVELO - Pushing Boundaries of Cell Dynamics Inference with Maximum Flow Networks

Julia Naas, Arndt von Haeseler

10:30-12:30

Exact Confidence Regions for Non-Linear Models

Rafael Arutjunjan, Björn Malte Schäfer, Clemens Kreutz

10:30-12:30

Transcription start site signal profiling improves transposable element RNA expression analysis at

Natalia Savytska, Peter Heutink, Vikas Bansal

10:30-12:30

Combined multiple transcriptional repression mechanisms generate ultrasensitivity and oscillations

Eui Min Jeong, Yun Min Song, Jae Kyoung Kim

10:30-12:30

DUNE-COPASI: Multi-Compartment Diffusion-Reaction solver for Cell Biology

S. Ospina De Los Rios, P. Bastian, L. Keegan, U. Kummer, S. Sahle

10:30-12:30

Gene expression heterogeneity arises from signaling networks

Mariko Okada

10:30-12:30

Systematic elucidation and pharmacological targeting of non-oncogene dependencies at the single cell

Andrea Califano

10:30-12:30

Digital Twin models for the precision diagnosis and therapy of cancer

Walter Kolch

10:30-12:30

Model ensembling as a tool to form interpretable multi-omic predictors of cancer pharmacosensitivity

Sebastien De Landtsheer, Apurva Badkas, Dagmar Kulms, Thomas Sauter

10:30-12:30

MultiOmics Network Embedding for SubType Analysis

Giovanni Scala, Luigi Ferraro, Majello Barbara, Michele Ceccarelli

10:30-12:30

Flow Cytometry Combined with Systems Biology Modelling Reveals Heterogeneous “NFkB Fingerprints” in

Eleanor Jayawant, Andrea Pepper, Chris Pepper, Simon Mitchell

10:30-12:30

Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data

Bengi Ruken Yavuz, Chung-Jung Tsai, Ruth Nussinov, Nurcan Tuncbag

10:30-12:30

Improving our Mechanistic Understanding of Cell Cycle Dynamics

Paul Lang, David Penas, Julio Banga, Daniel Weindl, Bela Novak

10:30-12:30

Modeling the tumor microenvironment in patient-derived organoid culture

Jennifer von Schlichting, Stefan Peidli, Markus Morkel, Nils Blüthgen

10:30-12:30

Transcriptional fluctuations govern the serum dependent cell cycle duration heterogeneities in Mammalian

Vinodhini Govindaraj, Subrot Sarma, Atharva Karulkar, Rahul Purwar, Sandip Kar

10:30-12:30

Model Predictive Control of Cancer Cellular Dynamics: A New Strategy For Therapy Design

Benjamin Smart, Lucia Marucci, Ludovic Renson, Irene de Cesare

10:30-12:30

Harnessing cancer heterogeneity for the systematic discovery of treatable cancer-driver exons with

Miquel Anglada-Girotto, Samuel Miravet-Verde, Sarah A. Head, Luis Serrano Pubul

10:30-12:30

Expanding the disease network of Glioblastoma Multiforme via topological analysis

Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter

10:30-12:30

Mutually Antagonistic Protein Pairs of Cancer

Ertugrul Dalgic, Merve Vural, Ozlen Konu

10:30-12:30

A disease network-based deep learning approach for characterizing melanoma

X. Lai, J. Zhou, A. Wessely, M. Heppt, A. Maier, C. Berking, J. Vera, L. Zhang

10:30-12:30

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

Mingjie He, Xuelian Li, Melissa Mang, Zhi Li, Uwe Ludewig, Waltraud Schulze

10:30-12:30

A modular concept for modeling of plant lipid metabolism

Sandra Correa, Hao Tong, Feng Zhu, Asdrubal Burgos, Zoran Nikoloski

10:30-12:30

Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana

Hao Tong, Roosa A. E. Laitinen, Zoran Nikoloski

10:30-12:30

Stress Knowledge Map: A knowledge resource for modeling of plant stress responses

C. Bleker, Z. Ramsak, V. Podpecan, M. Zagorščak, Š. Baebler, K. Gruden

10:30-12:30

Topological properties accurately predict cell division events and organization of Arabidopsis thaliana’s shoot apical

T.W. Matz, Y. Wang, R. Kulshreshtha, A. Sampathkumar, Z. Nikoloski

10:30-12:30

Computational analysis of cambium activity during plant radial growth

Lebovka, Hay Mele, Liu, Zakieva, Schlamp, Gursanscky, Merks, Großeholz, Greb

10:30-12:30

Metabolome-wise analysis of plants exposed to abiotic stress conditions to identify potential metabolites inducers of cross-tolerance to biotic

Antoni Garcia-Molina, Cristian Vicent, Victor Flors, Victoria Pastor

10:30-12:30

Deep convolutional neural networks capture the relationship between genetic variation and gene expression in

Fritz Forbang Peleke, Jedrzej Jakub Szymanski

10:30-12:30

PlantEd - a serious game about plant growth that aims to support metabolic modeling with citizen

Daniel Koch

10:30-12:30

From Plants to Plants and Beyond: How Modeling Strategies from the Engineering Field Could Benefit Systems

Maria Krantz, Oliver Niggemann

12:30-13:30 LUNCHEON V: ICSB Conference Organizers/Community Discussion

12:30-13:30 LUNCHEON VI: Workshop on gene set enrichment

13:30-15:30

Can we trust genome-wide metabolic models?

Chiara Damiani

13:30-15:30

The limit on dry mass density is an organizing principle for cellular physiology

Martin Lercher, Hugo Dourado

13:30-15:30

How can we unleash the potentials of whole-cell modelling?

Yin Hoon Chew

13:30-15:30

Analyzing Optimal and Non-Optimal Resource Allocations in Whole-Cell Models

Diana Széliová, Stefan Müller, Jürgen Zanghellini

13:30-15:30

The E. coli Whole-Cell Modeling Project: Vision and Progress

Markus W. Covert

13:30-15:30

Building a synthetic cell: search for the minimal requirements for robust, sustainable, and tunable cell

Qiong Yang

13:30-15:30

FROG Analysis - a community standard to foster reproducibility and curation of constraint-based

Raman et.al

13:30-15:30

A low-granularity model integrating metabolism, growth and cell cycle: towards multi-level whole cell modeling of budding

Palumbo, Busti, Teusink, Wortel, Papa, Airoldi, Alberghina, Vanoni

13:30-15:30

Multi-scale modeling of B-cell fate decisions required for antibody generation

Alexander Hoffmann

13:30-15:30

Circadian and cell cycle control of terminal cell differentiation

Mary Teruel

13:30-15:30

Individualized modules and models of enterovirus infection in host cells

Kevin Janes

13:30-15:30

Predicting pathogenicity of TPM1 variants using multi-scale models

Stuart Campbell

13:30-15:30

Multimodal perception links cellular state to decision making in single cells

Bernhard Kramer, Jacobo Sarabia del Castillo, Lucas Pelkmans

13:30-15:30

Understanding Stem Cell Growth Dynamics in Human Cerebral Organoids

S. Haendeler, C. Esk, D. Lindenhofer, F. Pflug, A. von Haeseler, J. A. Knoblich

13:30-15:30

Computational modeling for the elucidation of cell fate decisions in early development

Jana Wolf

13:30-15:30

Physiologically based pharmacokinetic (PBPK) models for metabolic phenotyping and evaluation of liver

Matthias König, Jan Grzegorzewski

13:30-15:30

A Systems Biology Approach To Study The Spatiotemporal Dynamics Of Senescent Cells In Wound Healing And Tissue

Sharmilla Chandrasegaran

13:30-15:30

Modeling the adaptive immune response of a lymph node as Petri net

S. Scharf, P. Wurzel, H. Schäfer, J. Ackermann, M.-L. Hansmann, I. Koch

13:30-15:30

Digital twins and hybrid modelling for simulation of physiological variables and stroke risk

T. Herrgårdh, E. Hunter, K. Tunedal, J.D. Kelleher, G. Cedersund

13:30-15:30

Multiscale Modeling of Dyadic Structure-Function Relation in Ventricular Cardiac Myocytes

F.G. Cosi, W. Giese, W. Neubert, S. Luther, N. Chamakuri, U. Parlitz, M. Falcke

13:30-15:30

Multilevel approach characterizing the progression of fatty liver disease

Biermayer et.al

13:30-15:30

An interconnected multi-level mechanistic model of the human brain

Sundqvist et.al

13:30-15:30

Clemens Schmitt

13:30-15:30

The genotype-phenotype nexus: uncovering causal mechanisms in neurodegenerative disease with experimental and theoretical

Erich Wanker

13:30-15:30

Precision machine-learning identifies a new paradigm for therapeutic discovery in Huntington’s disease: remodeling stress response to re-instate neuronal health and

Megret et.al

13:30-15:30

Multiple-omics based metabolic modelling reveals effects of drug-induced liver toxicity

Zita Soons, Henrik Cordes, Lars Kuepfer, Hecatos Consortium

13:30-15:30

The role of the kynurenine metabolism in chronic graft-versus-host-disease: Insights from computational modeling and patient

T. Stiehl, L. Orsatti, R. Speziale, P. Di Pasquale, E. Monteagudo, T. Luft

13:30-15:30

Personalized Treatment of Anemia in Lung Carcinoma

Rodriguez Gonzalez et.al

13:30-15:30

Transomic network analysis of glucose metabolism and its dysfunction associated with obesity

Shinya Kuroda

13:30-15:30

The Mixed Meal Model; quantifying metabolic resilience in overweight and obesity

Shauna O'Donovan, Ilja Arts, Lydia Afman, Natal van Riel

13:30-15:30

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human

Sae-Ong, Barber, Kang, Seelbinder, Li, Walther, Kurzai, Panagiotou

13:30-15:30

Machine learning based pathway deregulation analysis of metabolomics data for Parkinson's Disease

Elisa Gomez de Lope, Enrico Glaab

13:30-15:30

A systems pharmacology approach reveals robust drug metabolism and altered glucuronide disposition in a mouse model of liver

Fendt, Ghallab, Hofmann, Schlender, Myllys, Hassan, Hengstler, Kuepfer

13:30-15:30

Machine learning-based prediction of frailty in elderly people - Data from the Berlin Aging Study-II

Didier, De Landtsheer, Pires Pacheco, Kishk, Schneider, Demuth, Sauter

13:30-15:30

M4-health: digital twins that follow you throughout your health journey

Gunnar Cedersund, Henrik Podéus

13:30-15:30

Defining Design Rules for Next-Generation Snakebite Antivenoms

Natalie Morris, Johanna Blee, Sabine Hauert

13:30-15:30

Neural Circuits Underlying Autism Spectrum Disorders

Jon Chang, Jiayao Wang, Dennis Vitkup

13:30-15:30

MeDaX - our vision for bioMedical Data eXploration

Judith Wodke, Ron Henkel, Dagmar Waltemath

13:30-15:30

Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction

Sudupe et.al

16:00-16:45

Bacterial therapy for pulmonary infectious diseases

Luis Serrano

16:45-19:00 Excursion

10:00-10:30 Coffee Break

15:30-16:00 Coffee Break