Programme
Thursday
09:00
Registration open
10:00
Welcome
Keynote 1
10:10
Anna Poetsch (Dresden University of Technology)
DNA Language Models to Understand the Biology of Genomes
11:00
Coffee Break
Session 1 - Sequencing & genomic surveillance
11:30
Talk 1: Riko Corwin Uphoff
Fast barcode calling based on k-mer distances
(long talk)
11:50
Talk 2: Christina Kirschbaum
Imputation of Bacterial Genomes based on cgMLST Profiles
(short talk)
12:02
Talk 3: Daniel Desirò
Filling the Gaps: Combining individual and wastewater whole-genome sequencing improves SARS-CoV-2 surveillance – a case study from Germany
(short talk)
12:15
Talk 4: Jose Luis Lopez Arcondo
Highly synchronized co-evolution of codon usage patterns in functionally related genes
(short talk)
Lunch Break
12:30
Self-organized Lunch
recommendations here
Session 2 - Bioinformatics Methods & Omics Analytics
14:00
Talk 5: Fleming Kretschmer
Times are changing but order matters: Transferable prediction of small molecule liquid chromatography retention times
(long talk)
14:20
Talk 6: Ferras El-Hendi
Structural alphabets approach performance of structural alignment in remote homology detection
(long talk)
14:40
Talk 7: Singleron
Industry talk
14:52
Talk 8: Rebecca Holzschuh
Analysis of Complex Discrete Difference Data
(short talk)
15:05
Talk 9: Nikola Janakievski
A Combined Machine Learning Approach Reveals the Distinct Roles of DNA Sequence and Epigenetics in Constitutive versus Cell-Type Variable Replication Timing
(short talk)
15:20
Coffee Break
Session 3 - Functional Genomics & Precision Medicine
15:50
Talk 10: Daria Meyer
From Long-Read Epigenomics to Clinical Diagnostics: A Computational Framework for Direct Methylation-Driven Precision Medicine
(long talk)
16:10
Talk 11: Inna Lavrik
Integrative AlphaFold Modeling Reveals the Structural Blueprint of the Necrosome
(long talk)
16:30
Talk 12: Eneza Yoeli Mjema
Molecular and phenotypic footprints of climate in native Arabidopsis thaliana
(long talk)
Keynote 2
16:50
Janet Kelso (MPI for Evolutionary Anthropology Leipzig)
Archaic Genomes: insights into human history and biology
Poster Session
17:40
Session A
(see List of Posters below)
18:40
Session B
(see List of Posters below)
Friday
Keynote 3
09:00
Edda Klipp (HU Berlin)
Thermodynamically Explicit (TDE) Kinetics
Session 4 - Metabolic Modeling & Systems
09:50
Talk 13: Carolin Brune
SPECIMEN and refineGEMs: Open-Source Python Tools for Streamlined Metabolic Modelling
(short talk)
10:02
Talk 14: Dario Eltzner
Semantic Testing of Metabolic Model Predictions
(short talk)
10:15
Talk 15: Elham Gholamzadeh
Modeling microbial interaction prediction based on graph neural networks
(short talk)
10:30
Coffee Break
Session 5 - Plant & Environmental Bioinformatics
11:00
Talk 16: Chun-Han Lee
DPFlow: Systematic Image Feature Extraction and Visualization from Temporal UAV Flights for digital Phenotyping and Breeding of wheat cultivars
(long talk)
11:20
Talk 17: Maximilian Sack
Designing effective dsRNAs for RNAi-based plant protection
(long talk)
11:40
Talk 18: Marvin Behnke
ONT-only genome assembly of crop plants
(short talk)
11:52
Talk 19: David Rüscher
Integration of multi-omics data for the analysis of the biochemical and genetic diversity of 56 rosemary accessions
(short talk)
12:05
Talk 20: Rene Malsch
Fold-change-specific pathway enrichment analysis and its application to human breast cancer cells treated with a novel carbonic anhydrase inhibitor
(short talk)
Lunch Break
12:20
Self-organized Lunch
recommendations here
Keynote 4
13:50
Sebastian Böcker (FSU Jena)
Small molecule machine learning: All models are wrong
14:40
Coffee Break
Session 6 - Infection, Evolution & ML-assisted Therapeutics
15:10
Talk 21: Alejandro N. Lozada-Chavez
Genomic adaptations of self-domestication in the yellow fever mosquito Aedes aegypti
(long talk)
15:30
Talk 22: Lukas Korn
Optimizing resource allocation between biochemical defence and counter-counter defence in pathogenic and trophic interactions
(long talk)
15:50
Talk 23: Alicia Hiemisch
Aligning host dependency factors of Influenza A virus with gene regulatory network dynamics in infected scRNA-seq data using a context-aware deep learning model
(short talk)
16:02
Talk 24: David Medina-Ortiz
Machine Learning–Based Strategies to Guide the Autonomous Design of Antimicrobial Peptides
(short talk)
16:15
Talk 25: Marios Miliotis
Identification and Functional Characterization of Variants in microRNA Binding Regions of BRCA Patients
(short talk)
16:30
Closing and Passing the Ring
Farewell (16:50)
List of Posters
Natalie Breidenbach
(Technische Universität Dresden)
Secure computing workflow to analyze sensitive data standardized on a shared HPC system
Homa Zarabizadeh
(IPK, Gatersleben)
Computational Dissection of Alternative Splicing Dynamics in Drought-Adapted Carthamus tinctorius (Safflower)
Mohsen Morovati
(Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben)
Image-based phenotyping reveals enhanced root morphological and anatomical traits in a safflower mutant under drought stress
Felix Moorhoff
(IPB-Halle)
SelectZyme: AI-Based Interactive Protein Space Visualization for Enzyme Discovery, Selection, and Mining
Adam El Gaf
(Technische Universität Dresden)
Genetic Predisposition of Somatic Mutagenesis in Oesophageal Adenocarcinoma through Deep Learning
Nils Alexander Haupt
(Friedrich Schiller University Jena)
Annotating small molecules from massive affinity selection libraries
Abdul Moiz Aftab
(TU Dresden)
Mapping of 5-fluorouracil-induced DNA damage reveals hierarchical DNA repair and damage accumulation
David Klemm
(Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg)
Dynamic Modeling of Starch Biosynthesis in Pisum sativum L.: Identifying Flux Control and in silico Metabolic Engineering
Andrea Pokrajčić
(Institute for Drug Discovery, Faculty of Physics and Earth System Sciences, Leipzig University)
Non-Covalent Interaction Analysis from Electron Densities: Basis-Space Approaches for Large-Scale Biomolecular Systems
Lea Morschel
(Institut für Informatik, Martin-Luther-Universität Halle-Wittenberg)
Modernizing a Long-Lived Bioinformatics Tool: Lessons from Refactoring AnnoTALE
Mozhgan Khodadadi
(Martin-Luther-Universität Halle-Wittenberg)
Transcriptomes of solitary and social halictid bees support the ovarian ground plan hypothesis as mechanistic explanation for the evolution of eusociality
Anjana Bhat
(Leibniz Institute of Plant Biochemistry, Halle)
Decoding Gene-Metabolite interactions through Integrative Bioinformatics
Adnan Jasarevic
(Technische Universität Dresden)
Predicting DNA shape parameters from sequence with an integrated deep learning approach using coarse-grained modelling and experimental structural data
Qasim Siddiqui
(IZBI, University of Leipzig)
Benchmarking Unpaired Generative Models for Virtual Staining
Tom Eulenfeld
(RNA Bioinformatics/High-Throughput Analysis, Friedrich Schiller University Jena)
How sugar can help in research and education
Lukas Buschmann
(TU Dresden, Biotec)
Much ado about nothing: Modelling amino acid replacement with predicted protein structures
Maria Schreiber
(RNA Bioinformatics & High-Throughput Analysis, FSU Jena)
How ncRNAs can shape microbial adaptation to salinity and temperature
Fionn Daire Keogh
(Universitätsklinikum Jena)
Comparing single cell sequencing data of dengue, Zika, Influenza viruses, and SARS-CoV-2 employing semantic categorizations
Kristina Müller
(University of Leipzig, Institute for Medical Informatics, Statistics and Epidemiology (IMISE))
Single-Cell Transcriptomics of Atherosclerosis and Pneumonia Infection in Mice and Humans: VAE Latent Space Analysis of Disease and Infection Interactions
Marvin Doebel
(University Medicine Halle)
Cell-Cycle-Stratified Analysis of Orthogonal Perturb-seq Screens Reveals Phase-Specific Transcriptional Rewiring
Maximilian Omlor
(ScaDS.AI Leipzig - University of Leipzig)
mdAnnotator: From Isolated Expert Analysis to Collaborative Shared Intelligence in MD Simulations
Carina Keuters
(Martin-Luther-Universität Halle-Wittenberg)
Metabolomics based GWAS analysis in Conyza canadensis
Silver A. Wolf
(Genome Competence Centre (MF1), Robert Koch Institute, Berlin)
Establishing the bioinformatics toolkit for the integrated genomic surveillance of bacterial pathogens in Germany
Torsten Houwaart
(MF1 Genome Competence Center, Robert Koch Institute, Berlin)
Variability of allelic distance estimates with different cgMLST software across bacterial pathogens
Caroline Roschek
(Robert Koch-Institut)
Structural Variant Detection and Evaluation of Their Impact on cgMLST Genotyping in German Mycobacterium tuberculosis Samples
Marie Lataretu
(Robert Koch Institute, Berlin)
Virus genome reconstruction for the integrated genomic surveillance in Germany using Nextflow
Jonah Reiner
(Department MFI, Robert Koch Institute, Berlin)
Subtype-agnostic genome reconstruction of the human metapneumovirus using long reads
Guillaume Patoine
(Leibniz Institute of Plant Biochemistry)
Towards MetFamily 2.0 - A tandem mass spectrometry toolbox for untargeted metabolite discovery
Alexandra Baumann
(University of Rostock)
Associations Between Epigenetic Age Acceleration and Survival Across Cancer Types
Michael Richter
(Leibniz-HKI)
Human RNA editing patterns reveal disrupted mRNA splicing upon Rhizopus arrhizus stimulation
Tushar Patel
(Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))
An improved epigenetic age estimation with TFMethyl clock reveals DNA methylation changes in transcription factor binding sites during aging
Tobias Pfennig
(Leibniz Institute of Plant Genetics and Crop Plant Research (IPK))
Looking behind the sequence: Using machine learning to investigate plant gene regulation
Zhipeng Deng
(Interdisciplinary Centre for Bioinformatics (IZBI), University of Leipzig)
LivKid: An End-to-End Deep Learning Toolchain for Liver and Kidney WSIs Segmentation
Anton Vlasov
(Biomedical Genomics, Technische Universität Dresden)
Sequence-Based Inference of Nucleosome Positions in the Human Genome
Muhammad Yasir Ateeque
(Institute for Drug Discovery, Medical Faculty, Leipzig University)
Beyond Static Predictions: Integrating Targeted Molecular Dynamics to Resolve AI Limitations in Helicase Conformational Transitions
Elina Wiechens
(Leibniz institute on aging - Fritz Lipmann Institute)
Beyond Negative Binomial: Differential ATAC-seq Peak Calling Using the Generalized Discrete Laplace Distribution
Valentin Wesp
(Friedrich-Schiller-Universität Jena)
Strong correlation between amino acid frequency and codon number in genetic codes among all domains of life
Valentin Wesp
(Friedrich-Schiller-Universität Jena)
Proteomic study for the prediction of μCT imaging with iodine
Atakan Ayden
(Leibniz Institute on Aging – Fritz Lipmann Institute (FLI) Jena)
Enhancer state shifts in aged hematopoietic stem cells
Norman Storz
(MLU Halle, IPB Halle)
Metabolomics and MS/MS based GWAS analysis in Arabidopsis Thaliana
Yvonne Poeschl
(Martin-Luther-Universität Halle-Wittenberg)
The long and the short of it: The wild barley pangenome creates an inventory of structural variations
Maren Maruschewski
(Department of Genetics, Martin Luther University Halle-Wittenberg)
Discovering alternative polyadenylation in plant transcriptomes from 3'end sequencing data
Jonas Emmert
(Max Planck Institute for Chemical Ecology)
Scripting metabolite annotation in R and Python with the SIRIUS API
Jan Grau
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Improved reconstruction of transcripts and coding sequences from RNA-seq data
Christina Kuhn
(Fraunhofer IZI Leipzig)
CERTOMICS: Trusted Single-Cell Multiomics Pipeline for High-Resolution Profiling of Adaptive Cellular Immunotherapies
Irma Junk
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Is Peroxisomal Protein Transport Vulnerable to SNPs in the PTS1 Signal in Arabidopsis thaliana?
Giulio Pacchiarotti
(SECAI, School of Embedded Composite AI, University of Leipzig)
Paths to integrating prior knowledge into transformer-based architectures for applications in single-cell biology
Stefan Schuster
(Universität Jena, Lehrstuhl für Bioinformatik)
The One Twist to Rule Them All: Explaining the Right-Handed Bias of β-Sheets
Vincent Kreuziger
(prefrontal cortex GmbH)
From Table to Parametric Artwork
Marlene Mertens
(University Leipzig, IZBI, Scads.AI)
Knowledge-driven Neural Networks for Small Medical Image Datasets
Alexander Cherkasov
(Leibniz Institute on Aging - Fritz Lipmann Institute (FLI))
Molecular Trajectories of Aging in the Mouse Hippocampus
Patrick König
(Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK))
Navigating the Pan-Proteomic Landscape: A Visual Analytics Framework for the Barley Pan-Proteom based on Protein Language Model Embeddings and Dimensionality Reduction
Aman Nalakath, Dario Eltzner
(Martin-Luther-Universität Halle-Wittenberg)
An end-to-end pipeline for the Transcriptomics-Based Specialization of Genome-Scale Metabolic Models
Leopold Brinkmann
(Friedrich-Schiller-Universität Jena)
Mitigating Data Leakage in Drug Discovery via MCES Clustering
Antonia Schmidt
(Martin-Luther-Universität Halle-Wittenberg)
Engineering DNA Barcode Calling with Unknown Error Probabilities
Toni Oestereich
(Institute for Drug Discovery, Leipzig University Medical School)
InterAktioNN – An AI-Accelerated QM-Level Model for Biomolecular Non-Covalent Interaction Energies
Camila Castillo-Vilcahuaman
(Institute of Biodiversity, Ecology, and Evolution, Friedrich Schiller University Jena)
ViroFrac for weighted similarity-aware distances between viral communities
Andreas Kröpelin
(University Hospital Jena)
PointCloudRegistration.jl: A Julia package for rigid and non-rigid registration of point clouds
Vincent Messow
(Microscopic Image Analysis Group, Jena University Hospital)
Zelll: a fast, framework-free, and flexible implementation of the cell lists algorithm for the Rust programming language
Lucas Ringleben
(University of Applied Sciences Jena)
A Common Mathematical Structure of Mechanistic Photosynthesis Light-Response Models
Stefan Kranz
(Institute for Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg)
Reinventing genome visualization – a retrospective view of the developments
Rene Malsch
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Gene expression and pathway enrichment analyses of human breast cancer cells treated by carbonic anhydrase inhibitors
Johnny Alexander Jimenez Siegert
(Leipzig University)
Scalable and Energy-Efficient Ultra-Large Library Screening on a SpiNNaker2 Neuromorphic Chip
Andrés Martínez Bilesio
(Friedrich-Schiller-Universität Jena, Lehrstuhl Bioinformatik Jena)
Systematic comparison of Collision-Induced Dissociation (CID) and Electron-Induced Dissociation (EID) spectra reveals complementary chemical class-specific fragmentation information in LC–MS/MS Metabolomics
Michael Wenk
(IPB Halle)
Sherlock - A Free and Open-Source System for the Computer-Assisted Structure Elucidation of Organic Compounds from NMR
Johannes Schwerdt
(Martin Luther University Halle-Wittenberg)
Replexer: A rule-based system for Demultiplexing and Trimming Long-Read Sequencing Data
Marios Miliotis
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Predicting Transcription Factor Binding Sites in Arabidopsis thaliana using the Multi-Motif Machine Learning Approach MEX-ArChIPelago
Stavros Panagiotis Giannoukakos
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Arabidopsis Transcription Factor–DNA Interaction Atlas
Christian Mathias Richter
(Institute of Computer Science, Martin Luther University Halle-Wittenberg)
Interactive visualisation of fold-change-specific pathway enrichment
Shahram Saghaei
(Friedrich-Schiller-Universität Jena)
VirJenDB: A Scalable Data Engineering Platform for Harmonised Virus Genomics and Metadata
Andrés Martínez Bilesio
(Friedrich-Schiller-Universität Jena, Lehrstuhl Bioinformatik)
Interlaboratory standardization and validation of LC–MS/MS metabolomics data using semi-automated annotation workflows and SIRIUS-based cross-platform evaluation
Organizers
IPB Halle
MLU Halle
MLU Halle
MLU Halle
IPB Halle
MLU Halle
MLU Halle
Contact
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