Meetings

Anup Kumar (Albert-Ludwigs-Universität Freiburg) - Prioritisation of biomarkers from DNA methylation data using graph neural networks and explainable AI

Acute myeloid leukaemia (AML) is a complex disease characterized by aberrant DNA methylation. This study uses DNA methylation profiles and machine lea...

Maren Hackenberg (IMBI) - Enriching scRNA-seq analysis by adding layers of information using pre-trained language models

Abstract: Single-cell technologies generate increasingly complex and multi-layered datasets, increasing the need for analysis workflows that incorpora...

Florian Geier - DBM Basel

Abstract: I will give an overview of our work at the bioinformatics core facility of the department of biomedicine (DBM) in Basel. Based on project ex...

Anup Kumar - Histone modification marker detection using Nanopore sequences and Deep learning

Anika Erxleben - The Central Data Facility - a new service and consulting unit at Uni Freiburg

The Central Data Facility (CDF, https://uni-freiburg.de/cdf) is a new service and consulting unit at the University of Freiburg that supports research...

Johannes Hertel - Taking a deep dive into microbiome communities via constraint-based modelling

The human microbiome is key to health and disease. Yet, mapping and understanding microbiome ecology and microbiome-host interactions is a challenge d...

Cancelled

Florian Ingelfinger - CytoVI: Deep Generative Modeling of Antibody-based Single Cell Technologies

" Flow cytometry was historically the first single cell technology to measure millions of cellular states within minutes. Due to its robustness a...

Clemens Schächter - Enhancement of network architecture alignment in comparative single-cell studies

Clemens Schächter (AG Prof. Dr. Harald Binder: Knowledge Discovery Synthesis)  - Enhancement of network architecture alignment in comparative sin...

Noah Hollmann - TabPFN: A Foundation Model for Accelerating Data Analysis

Noah Hollmann (AG Hutter: Machine Learning Lab) - TabPFN: A Foundation Model for Accelerating Data Analysis Abstract "We introduce TabPFN, a...

Bas E. Dutilh - Mapping the Microverse and modelling its drivers

Bas E. Dutilh, Friedrich Schiller Universität Jena: Mapping the Microverse and modelling its drivers AbstractThe Microverse is the intricate and...

Bioinformatics Club - CANCELLED

CANCELLED

Bioinformatics Club - N. Scherer and D. Fässler

Nora Scherer and Daniel Fässler: Integrating exome-wide statistical screening and constraint based modeling to understand gene-metabolite relations vi...

Bioinformatics Club - Derek Spieler

Derek Spieler (AG Molekulare Psychosomatik): Integration of biological clock as marker of mental disorders.

Bioinformatics Club - Eva Kohnert

Eva Kohnert (IMBI): Advancing the Principles of Benchmark Studies: Validating Experimental Results with Synthetic Data for 16S Microbiome Data.Abstrac...

Bioinformatics Club - Tobias Hohl

Tobias Hohl (MPI): Sample handling in scATAC-seq and astrocytogenesis – two single-cell stories.AbstractAssay for transposase-accessible chromatin (AT...

Bioinformatics Club (additional) - Alan Rubin

Alan Rubin (Walter and Eliza Hall Institute of Medical Research, Melbourn, Australia): Analyzing and Sharing Data from High-throughput Mutagenesis Exp...

CANCELED

The meeting is canceled.

Bioinformatics Club - Niklas Brunn

Niklas Brunn (IMBI): Infusing structural assumptions into dimension reduction for single-cell RNA sequencing data to identify small gene sets.Abstract...

Bioinformatics Club - Gabi Kastenmüller

Gabi Kastenmüller (Institute of Computational Biology, Helmholtz Zentrum München): Building web-based resources for the dissemination of results from...

Bioinformatics Club - S. Haug and O. Borisov

Stefan Haug, Oleg Borisov (GenEpi): Integrating Genome Wide Association Studies with a Colocalization Framework (genepicoloc).

Bioinformatics Club - P. Zierep and E. Nasr

Paul Zierep, Engy Nasr (Bioinf): Microbial data analysis using the Galaxy framework - from a general overview to a foodborn pathogen detection use-cas...

CANCELED

CANCELED

Bioinformatics Club - Eva Kohnert

Eva Kohnert (IMBI): Employing real and synthetic data to benchmark differential abundance tools for microbiome sequencing data and to derive implicati...

Bioinformatics Club - Christopher Krolla

Christopher Krolla (IBSM): Estimation of the Tumor Microenvironment in Histology Images for PDAC.

Bioinformatics Club - E. Brombacher and J. Menger

Eva Brombacher, Jonatan Menger (IMBI): Optimizing omics analysis workflows based on data characteristics.

Bioinformatics Club - Anselm Hoppmann

Anselm Hoppmann (IBSM): Towards a harmonized NGS analysis platform.

Bioinformatics Club - Anup Kumar

Anup Kumar (Bioinf): Artificial intelligence in Galaxy Europe.

Bioinformatics Club - Krutika Pandit

Krutika Pandit (NYU Langone Health, US): Self-supervised Learning Applied to Kidney Histomorphology in Whole Slide Images.

Bioinformatics Club - Carlos Alfonso-Gonzalez

Carlos Alfonso-Gonzalez (MPI): Sites of transcription initiation drive mRNA isoform selection.

Bioinformatics Club - Jan Krumsiek

Jan Krumsiek (Weill Cornell Medicine, NY): Novel statistical approaches for the analysis of metabolomics data.

Bioinformatics Club - Sara Al-Rawi

Sara Al-Rawi (IMBI): Learning interpretable latent representations for single-cell multi-omics data.

Bioinformatics Club - Oliver Schilling

Oliver Schilling (Institute of Surgical Pathology, AG Schilling): Digging deeper into proteomics data.

Bioinformatics Club - Rolf Backofen

Rolf Backofen (Bioinf): Machine-Learning in the Context of CRISPR Research.

Bioinformatics Club - Eva Brombacher

Eva Brombacher (IMBI/MSB): Benchmarking data-independent acquisition analysis pipelines in proteomics.

Bioinformatics Club - Yidan Sun

Yidan Sun (MPI-IE):  SnakeRNAPipes: Novel nascent RNAs identification and interaction analysis.

Bioinformatics Club - Maren Hackenberg

Maren Hackenberg (IMBI): Inferring developmental trajectories and optimized dimension reduction from temporal single-cell RNA-sequencing data.

Bioinformatics Club - Matthias Wuttke

Matthias Wuttke (GenEpi): The GTEx consortium: An Atlas of of genetic regulatory effects across human tissues.

Bioinformatics Club - Daniela Zöller

Daniela Zöller (IMBI/KDS): Division Medical Data Science at IMBI: New directions.

Bioinformatics Club - Severin Dicks

Severin Dicks (IBSM): Understanding regulatory mechanisms of immune-related adverse events on a single cell level.

Bioinformatics Club - Elias Kellner

Elias Kellner (Radiologie - Medizinphysik): NORA - A Medical Imaging Platform.

Bioinformatics Club - Jochen Knaus

Jochen Knaus (IMBI):  Research Data Management - the Medical Faculty perspective and support.

Bioinformatics Club - Henrik Heiland

Henrik Heiland (Neurochirurgie): Multiomic reconstruction of spatiotemporal architecture of malignant brain tumors.

Bioinformatics Club - Grüning, Suchodoletz

Björn Grüning / Dirk von Suchodoletz (Bioinf, AG Grüning): bwSFS and de.NBI cloud: Large scale storage and compute research infrastractures.

Bioinformatics Club - Dirk von Suchodoletz

Dirk von Suchodoletz (Bioinf, AG Grüning): The past, the present and the future of Data Management in Freiburg.

Bioinformatics Club - Stefan Günther

Stefan Günther (Inst für Pharma Wiss): Automated recognition of functional compound-protein relationships in literature.

Bioinformatics Club - Francesco Ferrari

Francesco Ferrari (MPI, Bioinf): DOT1L-Dependent Epigenetic and Transcriptional Dynamics During in-vitro Neuronal Differentiation.

Bioinformatics Club - Moritz Hess

Moritz Hess (IMBI): The Pattern Extractor for Deep Learning.

Bioinformatics Club - Pascal Schlosser

Pascal Schlosser (GenEpi): The UK Biobank and what you can do with it.

Bioinformatics Club - Matthias Wuttke

Matthias Wuttke (GenEpi): Combining scRNA-seq and GWAS data to identify trait-specific cell types.

Bioinformatics Club - Geoffroy Andrieux

Geoffroy Andrieux: Detection and quantification of chromosomal aberrations derived from CRISPR-Cas activity using CAST-Seq, a novel preclinical g...

Bioinformatics Club - Stefan Lenz

Stefan Lenz: From (distributed) data to knowledge: Update on MIRACUM Use Case 2

Bioinformatics Club - Alla Bulashevska

Alla Bulashevska: Compositional analysis of high-throughput sequencing data

Bioinformatics Club - Clemens Kreutz

Clemens Kreutz: Improving Methods of Bioinformatics in Systems Biomedicine

Bioinformatics Club - Schilling, Föll

Oliver Schilling, Melanie Föll: Data Analysis in Proteomics

Bioinformatics Club - Thomas Manke

Thomas Manke: Protocols and tools for reproducible and scalable genomics analyses

Bioinformatics Club - Martin Treppner

Martin Treppner: Statistical tools for designing single-cell RNA-seq experiments.

Bioinformatics Club - Dilmurat Yusuf

Dilmurat Yusuf: Microglia responses to pro-inflammatory stimuli: the time series dynamics of gene expression and chromatin accessibility

Bioinformatics Club - Johannes Hertel

Johannes Hertel (University of Luxembourg): Insights for Multi-Omics Data Analyses from Merging Genome Scale Reconstructions with Population Stat...

Bioinformatics Club - Jana Naue

Jana Naue: Forensic Epigenetics: Chronological Age Prediction based on DNA Methylation Analysis and Machine Learning

Bioinformatics Club - Moritz Hess

Moritz Hess: Detection of patterns in high dimensional expression data with Deep Boltzmann Machines.

Bioinformatics Club - Patrick Metzger

Patrick Metzger: Precision Medicine - Experiences of the Molecular Tumor Board Freiburg

Bioinformatics Club - Anselm Hoppman

Anselm Hoppman: Evaluation of Tools Predicting Variant Impact on Protein Levels

Bioinformatics Club - Can Alkan

Prof. Can Alkan (Bilkent University): Characterization of genome structural variation and large inversions using high throughput sequencing

Bioinformatics Club - Peggy Sekula

Peggy Sekula: The Use of Publicly Available Omics Data to Infer Causality Using Mendelian Randomization

Bioinformatics Club - Galaxy User Conference

The Freiburg Galaxy Team organizes a local Galaxy User Conference. Date: March 15-16, 2018 Location: Lecture Hall at Otto-Krayer-Haus, Albertstr. 25,...

Bioinformatics Club - Markus List

Markus List (MPI-INF Saarbrücken): Constructing genome-wide endogenous RNA networks in a pan-cancer setting highlights novel biomarkers for precision...

Bioinformatics Club - Alla Bulashevska

Alla Bulashevska: Inferring genetic causes of immunodeficiencies using next generation sequencing data.

Bioinformatics Club - Sandra Reuter

Sandra Reuter: Bacterial whole genome sequencing for infection control and antibiotic resistance prediction

Bioinformatics Club - Boeker, Horki

MIRACUM Martin Boeker: Update on MIRACUM Petar Horki: Clinical Data Warehousing

Bioinformatics Club - Harald Binder

Harald Binder: Challenges for deep learning in omics settings.

Bioinformatics Club - Vivek Bhardwaj

Vivek Bhardwaj: Accurate detection of transcription start sites and differential gene expression using CAGE data.

Bioinformatics Club - Geoffroy Andrieux

Geoffroy Andrieux: Relapse prediction in Acute Myeloid Leukemia: A methylation based analysis

Bioinformatics Club - Jan Krumsiek

Jan Krumsiek: Methods for multi-omics data analysis

Bioinformatics Club - Osama Mahmoud

Osama Mahmoud: Improving Machine Learning from Functional Genomic Data by means of Overlapping Analysis

Bioinformatics Club - Rolf Backofen

Rolf Backofen: Evolution of CRISPS/Cas Systems

Bioinformatics Club - Pascal Schlosser

Pascal Schlosser (IMBI): Epigenome-wide Association Studies Identify DNA Methylation Associated with Kidney Function

Bioinformatics Club - Andreas Zimmer

Andreas Zimmer: Next Generation Sequencing at the Institute for Human Genetics

Bioinformatics Club - Helge Hass

Helge Hass: Mechanism-based learning connects response to growth factors with their expression in tumors

Bioinformatics Club - Oliver Schilling

Oliver Schilling: Improving protein identification and quantitation in mass-spectrometry based proteomics

Bioinformatics Club - Martin Boeker

Martin Boeker: The BMBF Förderinitiale Medizininformatik - Frameworks for the Integration of Routine and Research Data

Bioinformatics Club - Fidel Ramirez

Fidel Ramirez: Tools to study chromosome conformation

Bioinformatics Club - Matthias Wuttke

Matthias Wuttke: Digitale Patientendokumentation in der Routineversorgung mit MEONA - Potenzial zur wissenschaftlichen Sekundärnutzung der Daten (Digi...

Bioinformatics Club - Silke Laßmann

Prof. Dr. Laßmann: Up-date on NGS in molecular pathology

Bioinformatics Club - Sekula, Li

Peggy Sekula, Yong Li: Metabolomic GWAS (mGWAS) in a CKD cohort

Bioinformatics Club - Bodo Grimbacher

Bodo Grimbacher: Ethical implications of conducting research on patient samples

Bioinformatics Club - Anselm Hoppmann

Anselm Hoppmann (IMBI): GenTos

Bioinformatics Club - Bodo Grimbacher

Bodo Grimbacher: Next generation sequencing at the CCI

Bioinformatics Club - Alla Bulashevska

Alla Bulashevska: Inferring the role of microbiota in CVID enteropathy using 16S rRNA sequencing data

Bioinformatics Club - Kristin Ohneberg

Kristin Ohneberg, Martin Wolkewitz, Jan Beyersmann, Martin Schumacher: Nested case-control and case-cohort sampling designs: A powerful and economical...

Bioinformatics Club - Daniel Maticzka

Daniel Maticzka: Studying Protein-RNA-Interactions and Analysis of uvCLAP Data

Bioinformatics Club - Dominic Grün

Dominic Grün (MPI): De novo prediction of stem cell identity using single-cell transcriptome data.

Bioinformatics Club - Schwab, Eskandarian

Charlotte Schwab, Zoya Eskandarian: Approaches for the identification of modifiers in monogenetic diseases - CTLA4 and TACI

Bioinformatics Club - Ward Deboutte

Ward Deboutte (MPI): EBF1 primes B-lymphoid enhancers and limits the myeloid bias in murine.

Bioinformatics Club - Mohammad Lotfollahi

Mohammad Lotfollahi (TU Munich): Machine learning to understand single-cell biology: from cells to patients.

Bioinformatics Club - Stefan Haug

Stefan Haug (GenEpi): Comparing kidney cortex and medulla with an integrative analysis of RNA-seq, ATAC-seq and HiC data.

Bioinformatics Club - Severin Dicks

Severin Dicks (IBSM): Accelerating scRNA-Seq analysis using GPU Computing.

Bioinformatics Club - Eva Brombacher

Eva Brombacher (IMBI/MSB): Benchmarking of analysis strategies for data-independent acquisition proteomics data.

Bioinformatics Club - Maren Hackenberg

Maren Hackenberg (IMBI): Combining deep learning and modeling für time-series single-cell RNA-sequencing data.

Bioinformatics Club - Virginie Stanislas

Virginie Stanislas (Inst. for Prevention and Cancer Epidemiology): Design and analysis of diet-microbiome epidemiological studies.

Bioinformatics Club - Sebastian Preissl

Sebastian Preissl (Inst. of Experimental and Clinical Pharmacology and Toxicology): Uncovering cell type-specific gene regulatory programs and interpr...

Bioinformatics Club - Peter Kohl

Peter Kohl: Systems Biology of the Heart: Model or Muddle?

Bioinformatics Club - Regina Brinster

Regina Brinster: Multiple statistical testing - Approaches and methods to control the type 1 error

Bioinformatics Club - Björn Grüning

Björn Grüning: RNA Bioinformatics and the German Network for Bioinformatics Infrastructure

Bioinformatics Club - Alla Bulashevska

Alla Bulashevska: GenoMetric Query Language toolkit for large-scale genomic data management

Bioinformatics Club - Fidel Ramirez

Fidel Ramirez: Tools developed at the Max Planck for Immunobiology and Epigenetics for studying ChIP and Hi-C sequencing data

Bioinformatics Club - Lübbert, Schlosser

Prof. Lübbert, Pascal Schlosser: DECIDER: An AML (acute myeloid leukemia) trial with an epigenetic treatment - lessons learned and challenges to solve

Bioinformatics Club - Björn Grüning

Björn Grüning: Exome sequencing & Galaxy

Bioinformatics Club - Jörg Dengjel

Jörg Dengjel: Mass spectrometry-based proteomics

Bioinformatics Club - Stefanie Hieke

Stefanie Hieke: Statistical strategies for clinical cohort RNA-Seq data: component wise boosting vs. univariate testing

Bioinformatics Club - Anne-Sophie Stöhlker

Anne-Sophie Stölker: Huang, Sherman and Lempicki (2009) "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large...

Bioinformatics Club - Anna Köttgen

Jochen Knaus (IMBI): short presentation of the new homepage of the club Anna Köttgen (IMBI): about the paper Personal Omics Profiling Reveals Dynamic...

Bioinformatics Club - Martin Treppner

Martin Treppner (IMBI): scVIDE - Single Cell Variational Inference for Designing Experiments.

Bioinformatics Club - Said el Bouhaddani

Said el Bouhaddani (UMC Utrecht, NL): Statistical integration of multiple omics datasets with probabilistic PLS methods.