Program for Monday, October 10th: Talk View

PROGRAM FOR MONDAY, OCTOBER 10TH: 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

19:30

20:00

20:30

21:00

21:30

22:00

22:30

23:00

23:30

09:15-10:00

Systems Approaches to Deciphering Kinase Signaling and the Phosphoproteome: A Focus on Cancer, Inflammation, and DNA

Michael Yaffe

10:30-12:30

The metabolic and proteomic landscape of genome-scale genetic perturbation

Markus Ralser

10:30-12:30

Multi-dimensional immune correlates of early prediction of COVID-19 severe versus asymptomatic disease

Holetschek et.al

10:30-12:30

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, Andreas Dräger

10:30-12:30

Temporal Proteomics and Transcriptomics Unravels the Host-Pathogen Interaction Network of Macrophages and Corynebacterium

Luca Musella, Jens Moeller, Lisa Baeumer, Julio Vera, Andreas Burkovski

10:30-12:30

Mathematical model of the immunopathological progression of tuberculosis

E. Flores-Garza, E. Domínguez-Hüttinger, M. Zetter, R. Hernández-Pando

10:30-12:30

Proteome-scale mapping of binding sites in the intrinsically disordered regions of human and viral

Ylva Ivarsson

10:30-12:30

FAIR sharing of reproducible COVID-19 models of epidemic and pandemic forecast

Hermjakob et.al

10:30-12:30

Identification of a SARS-CoV-2 inhibitor by combining binary protein-protein interaction mapping, structure prediction and virtual

Secker et.al

10:30-12:30

A multi-strain model of immunization against influenza A viruses after infection or vaccination

Toledo Marrero et.al

10:30-12:30

Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And

Merkt et.al

10:30-12:30

COVIDpro: Database for mining protein dysregulation in patients with COVID-19

F. Zhang, A. Luna, T. Tan, Y. Chen, C. Sander, T. Guo

10:30-12:30

Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited

Goldenbogen et.al

10:30-12:30

Non-parametric model-based estimation of the effective reproduction number for SARS-CoV-2

Jacques Hermes, Christian Tönsing, Marcus Rosenblatt, Jens Timmer

10:30-12:30

Federated mathematical modelling and machine learning for a multi-national cohort of COVID-19

Manuel Huth, Jan Hasenauer, Roy Gusinow

10:30-12:30

INSIDe: Integrative modeling of the spread of serious infectious diseases

Nakonecnij et.al

10:30-12:30

Introduction

Session Chairs

10:30-12:30

Pitching for Classical modeling

Ursula Kummer

10:30-12:30

Pitching for AI / ML modeling

Trey Ideker

10:30-12:30

Pitching for hybrid/data-driven modeling

Kevin Janes

10:30-12:30

Panel Discussion

Panel Composed Of Three Invited Pitchers.

10:30-12:30

Q&A

Session Audience

10:30-12:30

Final remarks

Session Chairs

10:30-12:30

Combining multi-omics and biological knowledge to understand signaling deregulation in disease

Julio Saez-Rodriguez

10:30-12:30

Cross-inhibitory feedbacks of nucleocytoplasmic transport give rise to divergent multicellular phenotype in ERBB2-activated breast

Bishal Paudel, Lixin Wang, R Anthony McKnight, Kevin Janes

10:30-12:30

Cell-to-cell variability in JAK2/STAT5 pathway components and cytoplasmic volumes defines survival threshold in erythroid progenitor

Schilling et.al

10:30-12:30

Mechanisms of Pro- and Anti-Oncogenic Signaling Downstream of Dual Tyrosine Protein Kinases

Pau Creixell

10:30-12:30

A dynamic HIF1α-PPARγ circuit controls a paradoxical adipocyte regulatory landscape

M. Zhao, T. Kudo, K. Kovary, E. LaGory, M. Covert, M. Teruel

10:30-12:30

A Mechanistic model of EGFR and ERK signaling reveals how allostery and rewiring contribute to drug

Fabian Fröhlich, Luca Gerosa, Jeremy Muhlich, Peter Sorger

10:30-12:30

Targeted Proteomics-Driven Computational Modeling of the Mouse Macrophage Toll-like Receptor Signaling

Manes et.al

10:30-12:30

Mechanistic insights into sensitization and desensitization of the Interferon α signal transduction

M. Rosenblatt, F. Kok, M. Teusel, M. Schilling, U. Klingmüller, J. Timmer

10:30-12:30

Information Processing by Homo-Oligomeric Proteins: From First Principles to Cardiac Disease

Daniel Koch

10:30-12:30

Periodic Forcing of the ERK pathway

Nguyen Tran, Andrew Clayton

10:30-12:30

Coordination of p53 and MAPK dynamics controls heterogeneous responses to genotoxic agents in single

Eric Batchelor

10:30-12:30

Dynamic single cell analysis of a MAPK signaling cascade and its impact on transcriptional output

Guilaume Lieb

10:30-12:30

Deciphering dysregulation in Erythroleukemia to design intervention strategies

Abdullah, Bang, Li, Motzfeldt, Helm, Gjertsen, Schilling, Timmer, Klingmüller

10:30-12:30

Building the knowledge base to understand cellular signal transduction in different inflammatory

Marcus Krantz, Robert Kruse, Eva Särndahl, Katarina Persson

10:30-12:30

Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level (EXCEPTION -

Shubhank Sherekar, Ganesh Viswanathan

12:30-13:30 LUNCHEON III: BioModels: Model of the year competition

12:30-13:30 LUNCHEON IV: JIPipe Workshop

13:30-15:30

System Pathology of Cancer

Peter J. Wild

13:30-15:30

Advantages of Ensemble CNN’s in Computational Pathology.

Nadine Flinner

13:30-15:30

Artificial Intelligence in Digital Pathology Research - Where do we come from and where do we go?

Hannah Sophie Muti

13:30-15:30

EMPAIA - Harmonizing Access to Clinical-Grade AI Algorithms in Pathology

Rasmus Kiehl

13:30-15:30

Computational Pathology of Kidney Disease

Peter Boor

13:30-15:30

Latent Dirichlet Allocation for Double Clustering (LDA-DC): Discovering patients phenotypes and cell populations within a single Bayesian

Elie-Julien El Hachem, Nataliya Sokolovska, Hédi Soula

13:30-15:30

Reconstructing a quantitative measure of disease dynamics for discovery and clinical benefit

Amit Frishberg, Neta Milman, Joachim Schultze, Shai Shen-Orr, Fabian Theis

13:30-15:30

Lineage plasticity in prostate cancer depends on FGFR and JAK/STAT inflammatory signaling

Chan et.al

13:30-15:30

Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer

Casado, Szabo, Farago, Launonen, Anttila, Lin, Elias, Sorger, Färkkilä

13:30-15:30

3D reconstruction and mathematical modelling of whole slide images to elucidate resistance to the targeted therapy in

Arslan et.al

13:30-15:30

Automated detection and regional classification of Cerebral Amyloid Angiopathy in digital whole slide

Minaud et.al

13:30-15:30

Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population

H. Mi, S. Sivagnanam, C. Betts, S. Liudahl, E. Jaffee, L. Coussens, A. Popel

13:30-15:30

Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer

B. Arora, A. Kulkarni, F. Ramos, P. Ströbel, F. Alves, A. Markus

13:30-15:30

Rapid parallel model inference and on-the-fly tiling of digital pathology images

Sina Ghandian, Lise Minaud, Brittany Dugger, Michael Keiser

13:30-15:30

Single-cell spatial atlas of high-grade serous ovarian cancer

Perez-Villatoro et.al

13:30-15:30

Become an ICSB - an Interdisciplinary Champion of Systems & Biology

Olaf Wolkenhauer

13:30-15:30

How to find good problems with collaborators!

Jaekyoung Kim

13:30-15:30

From bench to scientific publishing

Maria Polychronidou

13:30-15:30

From Academic Research to Pharmaceutical R&D and Back

Jana Wolf

13:30-15:30

Thinking of a career in big pharma? Here is what you need to know.

Bernhard Steiert

13:30-15:30

Q&A and Open Discussion

Thomas Lemberger

13:30-15:30

Mapping Genetic and Chemical Genetic Interaction Networks in Yeast and Human Cells

Charles Boone

13:30-15:30

Formatting Biological Big Data to Enable Systems Pharmacology

Patrick Aloy

13:30-15:30

Dissecting the principles underlying transcriptional heterogeneity

Francesc Posas

13:30-15:30

CRISPRi meets metabolomics: a platform for rapid functional annotation of compound libraries

Mattia Zampieri

13:30-15:30

Dynamic metabolome profiling uncovers potential TOR signaling genes

Holbrook-Smith, Reichling, Doubleday, Germade, Bergmann, Loewith, Sauer

13:30-15:30

Mapping metabolic regulation in E. coli with a metabolism-wide CRISPRi library

A. Alvarado, A. Verhuelsdonk, N. Farke, T. Glatter, H. Link

13:30-15:30

A new platform for deep multiplexed metabolomics with a DNA barcode readout

Andy Fraser, June Tan, Maria Mercado

13:30-15:30

Dynamics of growth and ribosome level in batch cultures of S. cerevisiae

Yu Huo, Xiao Wang, Jack W. Thomson, Peter S. Swain

13:30-15:30

An optimal RNA growth law and its relationship with genome organization in bacteria

Xiao-Pan Hu, Martin Lercher

13:30-15:30

A model of RNA repair to study antibiotic tolerance

Hollie Hindley, Andrea Weiße, Meriem El Karoui

13:30-15:30

Gene-essentiality based drug signature helps repurposing non-cancer drugs

Wenyu Wang, Jing Tang

13:30-15:30

Towards rational design of antibiotic combination therapies

Elena Pascual Garcia, Andrea Weiße, Charlotte Kloft, Wilhelm Huisinga

13:30-15:30

Patterns of differentially essential genetic interactions characterize functional modules across cancer

Lukas Annerer-Walcher, Ulrich Stelzl

13:30-15:30

Identification of causal genes at GWAS loci with pleiotropic gene regulatory effects using instrumental variable

Mariyam Khan, Adriaan Ludl, Sean Bankier, Tom Michoel

13:30-15:30

A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer

K. Taoma, M. Liangruksa, M. Ruengjitchatchawalya, T. Laomettachit

13:30-15:30

Tissue-specific codon usage: from systems to synthetic biology

Xavier Hernandez-Alias, Hannah Benisty, Luis Serrano, Martin H. Schaefer

13:30-15:30

Interrogating the effect of enzyme kinetics on metabolism using differentiable constraint-based

St. Elmo Wilken, Oliver Ebenhöh

13:30-15:30

Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics

T.D. Rose, N. Köhler, L. Falk, L. Klischat, O.E. Lazareva, J.K. Pauling

13:30-15:30

Structural proteomics evidence for a predicted glycolytic metabolon

Elsässer, Marulli, Gollub, Doerig, Leitner, Stelling, Picotti

13:30-15:30

From System Biology to Pharmacology: Identifying what is important

Wilhelm Huisinga

13:30-15:30

Optimization of functional efficiency in key tissues constrains protein rate of evolution in multicellular

Dinara Usmanova, German Plata, Dennis Vitkup

13:30-15:30

Universally valid reduction of multiscale stochastic biochemical systems with simple non-elementary

Yun Min Song, Hyukpyo Hong, Jae Kyoung Kim

13:30-15:30

A physiologically-structured population model for pharmacokinetics of orally inhaled drugs

Niklas Hartung

13:30-15:30

When cells decide to give up on repairing DNA damage

A. Sadeghi, R. Dervey, V. Gligorovski, M. Labagnara, S.J. Rahi

13:30-15:30

Quasi-Entropy Closure: A Fast and Reliable Approach to Close the Moment Equations of the Chemical Master

Nicole Radde, Vincent Wagner

13:30-15:30

GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations

Yusuf Roohani, Kexin Huang, Jure Leskovec

13:30-15:30

Bias and reproducibility in a Computational Neurobiology PhD’s journey

S. Roman Garcia, M. Stefan, D. Sterratt, N. Romano, M. Sharan, C. Fischer

13:30-15:30

Learning synthetic cell classifier designs with genetic algorithms and logic programming

Melania Nowicka, Heike Siebert

13:30-15:30

Predicting metabolite accumulation in cancerous metabolic network

Tin Yau Pang, Martin Lercher

13:30-15:30

Nonstationary Biomedical Signal Feature Extraction

Sri Krishnan

13:30-15:30

Using multi-omics data and machine learning to unravel alternative splicing regulation

Ulf Schmitz, Veronika Petrova, Justin J.-L. Wong, John E.J. Rasko

16:00-16:45

Elucidating functions of microbial dark matter

Jörg Overmann

16:45-19:30

Manatee invariants entailing signal transduction pathways in Petri nets of signaling networks

Marius Kirchner, Jörg Ackermann, Ina Koch

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

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

Machine learning-based sepsis risk prediction modeling using electronic health records of cancer

Jimin Kim

Numerical approaches for the rapid analysis of prophylactic efficacy against HIV

Lanxin Zhang, Junyu Wang, Max von Kleist

A Boolean Modeling Framework for Drug Synergy Prediction in Breast Cancer

K. Taoma, M. Liangruksa, M. Ruengjitchatchawalya, T. Laomettachit

Fast and scalable machine learning approach for dynamic metabolic engineering

Charlotte Merzbacher, Diego Oyarzún

Reinforcement learning and Monte-Carlo tree search in gene expression enable the entire gene regulation in a

Tomoyuki Yamaguchi

Timelapse of Single Cell Lipidomics

Paul Jonas Jost, Klaus Wunderling, Christoph Thiele, Jan Hasenauer

Efficient brute-force model selection by iterative elimination of less useful model subspaces

J. Vanhoefer, A. Körner, D. Doresic, J. Hasenauer, D. Pathirana

Candida expansion in the human gut is associated with an ecological signature that supports growth under dysbiotic

Bastian Seelbinder, Zoltan Lohinai, Gianni Panagiotou

Variance of filtered signals: characterization for linear reaction networks and application to neurotransmission

Ariane Ernst, Christof Schütte, Stephan Sigrist, Stefanie Winkelmann

Analyzing human E3 ligome for efficient design of PROTACs

Arghya Dutta, Alberto Cristiani, Jonathan Eisert, Ramachandra M. Bhaskara

Mechanistic modeling of patient-specific response to hormone therapy and CDK inhibitors in breast

Leonard Schmiester, Alvaro Köhn-Luque, Arnoldo Frigessi

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

A training strategy for hybrid models to break the curse of dimensionality: An application in mortality estimation for cohorts of COVID-19

M. E. Samadi, S. Kiefer, S. Fritsch, J. Bickenbach, A. Schuppert

Deep insight into SABIO-RK data via visualization

Dorotea Dudas, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller

Improving drug-induced transcriptional descriptors and their biological connectivity

Elena Pareja-Lorente, Adrià Fernández-Torras, Patrick Aloy

Dynamics of growth and ribosome level in batch cultures of S. cerevisiae

Yu Huo, Xiao Wang, Jack W. Thomson, Peter S. Swain

Biological-informed multi-modality integration of unmatched single-cell-omics datasets to provide a multi-dimensional

Lea Seep, Yannik Schälte, Jan Hasenauer

Hybrid cellular automaton representation of the influence of mechanical stimulation on the development of bone

Claire Villette, Liesbet Geris

A framework for predicting the effect of multiple factors on HIV protection from heterosexual transmission through truvada-based pre-exposure prophylaxis (PrEP) in

Sara Iannuzzi

Investigating antagonistic chromatin remodeling by the Swi-Snf and Tup1-Cyc8 (Ssn6) complexes in

Mohamed Alhussain, Nicole Byrne, Nicholas Kent, Atif Bamagoos, Alastair Fleming

Theory of biochemical information processing with transients

Manish Yadav, Aneta Koseska

An optimal RNA growth law and its relationship with genome organization in bacteria

Xiao-Pan Hu, Martin Lercher

Decrypting drug actions and protein modifications by dose- and time-resolved proteomics

F.P. Bayer, J. Zecha, S. Wiechmann, T.T. Tum Team, B. Kuster

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

Elisa Gomez de Lope, Enrico Glaab

Modeling the tumor microenvironment in patient-derived organoid culture

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

Accelerating whole-cell modelling with surrogate machine learning models

I. Gherman, Z. Abdallah, W. Pang, T. Gorochowski, C. Grierson, L. Marucci

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

Predicting developmental states in zebrafish using transfer learning

Gaurav Jumde

Expanding the disease network of Glioblastoma Multiforme via topological analysis

Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter

Single cell pseudo-time inference based on copy number variants for identifying a tumor transition

Jonghyun Lee, Najung Lim, Minwoo Kim, Juyeon Cho, Dongkwan Shin

Single cell analysis of a breast pre-cancerous state to explore critical tumor microenvironment

Juyeon Cho, Jonghyun Lee, Dongkwan Shin

Uncovering cell-type specific mechanisms across an arbitrary number of cell-types by adapting the clustered LASSO to differential equation

Adrian Lukas Hauber, Marcus Rosenblatt, Jens Timmer

A physiology-based model of bile acid metabolism in mice

Kister et.al

Analysis of the impact of MYCN on the energy metabolism in neuroblastoma using metabolomics data and mathematical

Mareike Simon, Katharina Baum, Uwe Benary, Alexander Schramm, Jana Wolf

Modelling mutations in B-cell malignancies reveals how mutations synergise to contribute to aggressive

Richard Norris, Simon Mitchell

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

Maria Krantz, Oliver Niggemann

Moving Horizon Estimation for Patient-Specific Optimal Control of Blood Glucose in Intensive Care

Dilan Pathirana, Jan Hasenauer

A multi-strain model of immunization against influenza A viruses after infection or vaccination

Toledo Marrero et.al

BlotIt - Optimal alignment of Western blot and qPCR experiments

Svenja Kemmer, Severin Bang, Marcus Rosenblatt, Jens Timmer, Daniel Kaschek

A probabilistic graphical model for taxonomic profiling of viral and microbiome proteome samples

Tanja Holstein, Pieter Verschaffelt, Lennart Martens, Thilo Muth

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

Studying conformational transitions of selected proteins using UNRES coarse-grained replica exchange molecular dynamics simulations with Lorentzian

Iga Biskupek, Cezary Czaplewski, Artur Giełdoń

Connecting the Neurovascular coupling and Electrophysiological signaling – a modeling approach

Henrik Podéus, Gunnar Cedersund, Salvador Dura-Bernal

Computational Models of Heterogeneous Mutations in Diffuse Large B-cell Lymphoma.

Arran Pack, Simon Mitchell

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

Le Yuan, Feiran Li, Jens Nielsen, Eduard Kerkhoven

A bottom-up investigation of emergence in a self-organizing model of embryonic pattern formation

Michael Zhao, Jan Rombouts, Alexander Aulehla, Anna Erzberger

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

Julia Naas, Arndt von Haeseler

A powerful modelling approach tailored to cellular signalling

Rafael Arutjunjan, Emilia Neuwirt, Svenja Wöhrle, Olaf Groß, Clemens Kreutz

Integrational approaches for cross-species analysis of lung pathologies at single-cell resolution.

Pennitz et.al

Development of a mass-spectrometry based clinical proteomics pipeline allows absolute quantification of pathway components and provides insights in pathway

Frey et.al

Ionizing radiation triggers differential signaling dynamics of p-p53 and p-ERK1/2 in sensitive and resistant HNSCC cell

Astaburuaga-García, Mutlu, Sell, Branz, Sieber, Klinger, Lauber, Blüthgen

Defining Design Rules for Next-Generation Snakebite Antivenoms

Natalie Morris, Johanna Blee, Sabine Hauert

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

Microbial compound bioactivity descriptors enable large-scale prediction of small molecule impact on microbiota species and

Nils Kurzawa, Patrick Aloy

Development of a geometric blood vessel model to quantify morphological changes of endothelial cells in 3D during vascular

Seeler, Grdseloff, Rödel, Kloft, Abdelilah-Seyfried, Huisinga

Delivering Virtual Reality and Gaming Technologies to the Field of Systems Biology

Eliott Jacopin, Yuki Sakamoto, Kozo Nishida, Kazunari Kaizu, Koichi Takahashi

Inference and dynamical simulation of the gene-regulatory network in single cells

Stumpf, Meyer, Valeanu, Kiefer, Krishnan, Schaub, Grohe, Schuppert

The transcriptome dynamics of single cells during the cell cycle

D. Schwabe, S. Formichetti, J.P. Junker, M. Falcke, N. Rajewsky

Non-linear mixed effects modeling of the T cell response in individuals infected with SARS-CoV-2

Peiter et.al

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

Diana Széliová, Stefan Müller, Jürgen Zanghellini

Extracting knowledge from multi-omics and clinical datasets using graph machine learning

Ferdinand Popp, Nektarios A. Valous, Pornpimol Charoentong, Inka Zörnig

Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory

Nataša Puzović, Tanvi Madaan, Julien Y. Dutheil

Mathematical modeling of cytokine interplay in human monocytes during LPS stimulation

Nikaein et.al

Mutually Antagonistic Protein Pairs of Cancer

Ertugrul Dalgic, Merve Vural, Ozlen Konu

Virtual Cell Modeling and Simulation Software

Michael Blinov, Ion Moraru, Leslie Loew, James Schaff

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

Daniel Koch

Discovery of potential functional paths by integration of phospho-proteomics data in the PPI network using a RWR

Jérémie Perrin, Olivier Destaing, Christine Brun

On the relation between input and output distributions of scRNA-seq experiments

Daniel Schwabe, Martin Falcke

Investigating brain development using tissue and single-cell gene expression data

Sathish Periyasamy, Pierre Youssef, Bryan Mowry

INSIDe: Integrative modeling of the spread of serious infectious diseases

Nakonecnij et.al

Seroepidemiology And Modeling Of SARS-CoV-2 In Ethiopia: Longitudinal Cohort Study Among Front-line Health-care Workers And

Merkt et.al

Disentangling the internal composition of tumour activities through a hierarchical factorization

J. Carbonell-Caballero, A. López-Quílez, D. Conesa, J. Dopazo, A. Valencia

Patient- and cell line-specific modeling of diffuse large B-cell lymphoma

Fabian Konrath, Jens Löber, Björn Chapuy, Jana Wolf

Neural Circuits Underlying Autism Spectrum Disorders

Jon Chang, Jiayao Wang, Dennis Vitkup

From genome sequencing to the first draft of the genome scale metabolic model of the symbiont fungus Leucoagaricus gongylophorus

Castillo Alfonso et.al

Using graph theory and recurrent neural network models to investigate the anxiety circuit

Veronica Porubsky

Leveraging the Molecular Signatures of Cancer for Dynamic Network Modeling

Enes Sefa Ayar, Nurcan Tuncbag

TREAT-SGS - a multi-omics approach to treat the rare neuro-developmental disorder Schinzel–Giedion

Marc-Daniel Hagel, Patrick Simon Stumpf

GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations

Yusuf Roohani, Kexin Huang, Jure Leskovec

MeDaX - our vision for bioMedical Data eXploration

Judith Wodke, Ron Henkel, Dagmar Waltemath

Using multi-omics data and machine learning to unravel alternative splicing regulation

Ulf Schmitz, Veronika Petrova, Justin J.-L. Wong, John E.J. Rasko

An interconnected multi-level mechanistic model of the human brain

Sundqvist et.al

On data-driven learning of an effective energy landscape from trajectories of nonlinear dynamical biological

S. Saha, S. A. Khan, A. O. Balubaid, D. Gomez-Cabrero, N. A. Kiani, J. N. Tegner

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

Natalia Savytska, Peter Heutink, Vikas Bansal

COVIDpro: Database for mining protein dysregulation in patients with COVID-19

F. Zhang, A. Luna, T. Tan, Y. Chen, C. Sander, T. Guo

Tribus reveals the single-cell tumor architecture and effect of chemotherapy in ovarian cancer

Casado, Szabo, Farago, Launonen, Anttila, Lin, Elias, Sorger, Färkkilä

SynBioSuite: Web-based modeling and analysis of biological systems

Z. Sents, T. Stoughton, L. Buecherl, P.J. Thomas, P. Fontanarrosa, C.J. Myers

A robust clustering strategy for patient stratification in complex diseases

Palomino et.al

Composing and perturbing large-scale constraint-based metabolic models with COBREXA.jl

M. Kratochvíl, S.E. Wilken, L. Heirendt, R. Schneider, C. Trefois, W. Gu

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

Characterization of cardiac fibroblast remodeling dynamics after myocardial infarction

Sudupe et.al

Genome-wide analysis of genetic variants affecting metabolomic abundance in pigs divergent for feed

Xiao Wang, Haja Kadarmideen

Control of COVID-19 Outbreaks under Stochastic Community Dynamics, Bimodality, or Limited

Goldenbogen et.al

Exploring the “dark proteome” in hepatocellular carcinoma

Polenkowski, Burbano de Lara, Allister, Saborowski, Vogel, Tran

Cells use molecular working memory to navigate in changing chemoattractant fields

Robert Lott, Aneta Koseska

Inferring Gene Networks Rewiring of Naive and Primed Human Embryonic Stem Cells During Cellular Reprogramming Using Single-Cell RNA-seq

M. Alshoyokh, A. Zia, A. Balubaid, D. Gomez-Cabrero, N.A. Kiani, J. Tegner

New data-driven gene representations using deep autoencoders at multiple omics to identify candidate disease genes and robust

David Martínez-Enguita, Sanjiv Dwivedi, Mika Gustafsson

Effect of dispersal by inundation on soil bacterial communities depends on soil developmental stage

Xiu Jia, Cas Cornet, Joana Falcão Salles

Analysis of multivariate longitudinal metabolomics data from meal challenges using RM-ASCA+

Erdos, Westerhuis, Adriaens, O'Donovan, Xie, Singh-Povel, Smilde, Arts

Towards a Computational Toolkit for Cell Fate Decision Detection

A. Balubaid, S. Balsamy, R. Lehmann, D. Gómez-Cabrero, N. Kiani, J. Tegner

FISHing for Correlation

Schreiber et.al

Patterns of differentially essential genetic interactions characterize functional modules across cancer

Lukas Annerer-Walcher, Ulrich Stelzl

Molecular regulators of catecholamine response in human pulmonary microvascular endothelial cells

A. Lopez Garcia de Lomana, A.I. Vilhjálmsson, P.I. Johansson, Ó. Rolfsson

Quantification of imaging biomarkers in the extracellular matrix of left and right sided colon cancer

B. Arora, A. Kulkarni, F. Ramos, P. Ströbel, F. Alves, A. Markus

Analysis of Heterogeneity in the Tumor Microenvironment in the 4NQO HNSCC Mouse Model

L. Kroehling, M.M. Khan, M. Kukuruzinska, X. Varelas, M. Bias, S. Monti

Bias and reproducibility in a Computational Neurobiology PhD’s journey

S. Roman Garcia, M. Stefan, D. Sterratt, N. Romano, M. Sharan, C. Fischer

MODalyseR—a novel software for inference of disease module hub regulators identified a putative multiple sclerosis regulator supported by independent eQTL

Hendrik de Weerd, Julia Åkesson, Mika Gustafsson, Zelmina Lubovac

Benchmarking Phage-Host Prediction Tools using Real Metagenomics Data

van Doorn, Wu, Hauptfield, Carillo, Grozdani, Pappas, Dutilh

Characterizing all feasible metabolic conversions of individual cells and microbial communities with elementary conversion

B. A.Buchner, M. Mansouri, T. J. Clement, D. H. de Groot, J. Zanghellini

Dissecting the Developing Mouse Brain at Spatial Single-Cell Resolution Using PASTA-seq

Strenger, Karaiskos, Licha, Pentimalli, Schott, Splendiani, Macino, Rajewsky

Cell Type view into tomato stem elongation in Shade avoidance response

Linge Li, Ticho Helming, Chrysoula K. Pantazopoulou, Ronald Pierik, Kaisa Kajala

Amino acid metabolism of Chinese Hamster Ovary cells: Comparison of growth and production phases in a

Štor, Ruckerbauer, Széliová, Sacco, Young, Borth, Zanghellini

Construction and Decomposition of Cellular Energy Landscapes using Hopfield Neural Networks

Juan P. Bernal-Tamayo, David Gomez-Cabrero, Narsis Kiani, Jesper N. Tegner

Evaluation of methods to compute quasi-potential functions and their use as systems biology models

Balsamy et.al

Metabolic Atlas - extending metabolic networks for model organisms with enzyme turnover predictions with

Li, Chen, Anton, Shu, Hyltander, Klang, Huang, Svensson, Nielsen

Single-cell spatial atlas of high-grade serous ovarian cancer

Perez-Villatoro et.al

Mitotic Memory as Spontaneous Symmetry Breaking in the Cell

A. Hodgkinson, M. Bellec, M. Douaihy, A. Devenyi, M. Lagha, O. Radulescu

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

Zita Soons, Henrik Cordes, Lars Kuepfer, Hecatos Consortium

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

Sebastian Lobentanzer, Dénes Türei, Julio Saez-Rodriguez

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

Amitava Giri, Sandip Kar

Latent variable models of fungal growth considering the data measurement process

Tara Hameed, Natasha Motsi, Elaine Bignell, Reiko J. Tanaka

Web-based analysis of indirect calorimetric data arising from metabolic phenotyping systems

Grein, Bruder, Stromeyer, Heine, Klingenspor, Herren, Hasenauer

Quantitative Spatial Profiling Reveals Tumor Microenvironment Heterogeneity and Prognostic Biomarkers Associated with Immune Population

H. Mi, S. Sivagnanam, C. Betts, S. Liudahl, E. Jaffee, L. Coussens, A. Popel

20:00-23:59 Conference Dinner

10:00-10:30 Coffee Break

15:30-16:00 Coffee Break