Bioinformatics Seminar & Journal Club @ RöttgerLab

General Information

Welcome the Bioinformatic Seminar series and journal club. We are meeting once a month to listen to exciting talks in an informal atmosphere. The Seminar talks are mostly held by PhD students and they are presenting their latest results, challenging problems, or also give a lecture like introduction into various Bioinformatic topics.

The Journal Club is bi-weekly, and we are discussing hot papers in the realm of Bioinformatics. One student is preparing a short 15-min talk which then forms the basis for an open-ended discussion. We are flexible and curious, wandering between different topics and discussing the latest trends.

If this sounds interesting to you and, you want to participate, please feel free to join at any time by shooting a quick Email to Richard and be included into the mailing list, so you won’t miss a session.

Corona Information: Given the current status of the pandemic, the Journal Club as well as the Seminar are held in hybrid format. The zoom link will be sent around over the mailing list.

Spring 2022

Date Type Speaker Topic
14.06.2022 JC TBA TBA
07.06.2022 Seminar Muhammad Irfan Malik Lifelong Machine Learning for Text Data Analysis
07.06.2022 Seminar Jiawei Zhao VIEW-SC+ webtool for protein bioinformatics & Identifying a fine genomic structure across Ashkenazic Jews
17.05.2022 JC TBA TBA
03.05.2022 Seminar Tim Kacprowski Data Science in Biomedicine
03.05.2022 Seminar Gunnar Klau Understanding genomic alterations in cancer using genetic and protein interactions
19.04.2022 Seminar Anne Federated Unsupervised Machine Learning
05.04.2022 JC Tobias R. PROCAL: A Set of 40 Peptide Standards for Retention Time Indexing, Column Performance Monitoring, and Collision Energy Calibration
22.03.2022 JC Anne Federated learning for predicting clinical outcomes in patients with COVID-19
08.03.2022 JC Mathias Multi-domain translation between single-cell imaging and sequencing data using autoencoders
22.02.2022 JC Juan ADNet: Attention-Guided Deformable Convolutional Network for High Dynamic Range Imaging
08.02.2022 JC Tobias F. Privacy Preserving RNA-Model Validation Across Laboratories

Fall 2021

Date Type Speaker Topic
30.11.2021 Seminar Pawel Characterization of Atomically-Thin Transition Metal Dichalcogenides
16.11.2021 Seminar Tobias MS2AI bridges the gap between MS data and AI applications
02.11.2021 JC Anne The Specious Art of Single-Cell Genomics
12.10.2021 JC TBA CoCoNet, an effecient deep learning tool for viral meta genome binning

Spring 2021

Date Type Speaker Topic
22.06.2021 JC Tobias TBA
08.06.2021 Seminar Maria & Johannes Antibody Maturation: factors increasing or limiting the diversity
25.05.2021 JC Juan Enhancing Photorealism Enhancement
18.05.2021 JC Zsofia Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways
27.04.2021 JC Tobias MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data
20.04.2021 JC Johannes Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks
13.04.2021 JC Anne Adversarial generation of gene expression data
23.03.2021 Seminar Vasileios Community Projects in Computational Proteomics: EuBIC Developer's meeting
16.03.2021 JC Niklas High-quality MS/MS spectrum prediction for data-dependent and data-independent acquisition data analysis
02.03.2021 JC Mathias Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
23.02.2021 Seminar Juan Generative adverserial Neural Networks
16.02.2021 JC Alexander The pros and cons of peptide-centric proteomics
26.01.2021 Seminar Philipp TBA
19.01.2021 JC Tobias Making proteomics data accessible and reusable: current state of proteomics databases and repositories

Fall 2020

Date Type Speaker Topic
15.12.2020 JC Tobias Sinitcyn, Pavel, Jan Daniel Rudolph, and Jürgen Cox. 'Computational methods for understanding mass spectrometry–based shotgun proteomics data.' Annual Review of Biomedical Data Science 1 (2018): 207-234.
08.12.2020 JC Louise Aebersold, Ruedi, and Matthias Mann. 'Mass-spectrometric exploration of proteome structure and function.' Nature 537.7620 (2016): 347-355.
01.12.2020 Seminar Zsofia Predicting exon vulnerability using empirical data.
17.11.2020 JC Mathias Eraslan, Gökcen, et al. 'Single-cell RNA-seq denoising using a deep count autoencoder.' Nature communications 10.1 (2019): 1-14.
10.11.2020 JC Anne Buettner, Florian, et al. 'Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.' Nature biotechnology 33.2 (2015): 155-160.
03.11.2020 JC Johannes Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. 'Validation of noise models for single-cell transcriptomics.' Nature methods 11.6 (2014): 637-640.
27.10.2020 JC Maria Haque, Ashraful, et al. 'A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.' Genome medicine 9.1 (2017): 1-12.
20.10.2020 Seminar Tobias Big Data, privacy and disease
06.10.2020 Seminar Vikas Studies of membrane transport in biology

Spring 2020

Date Type Speaker Topic
08.07.2020 Seminar All Virtual Recomb Session.
04.06.2020 Seminar Andreas Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis
04.06.2020 Seminar Katharina VulExMap - Detection Of Constitutive Vulnerable Exons
30.04.2020 Seminar Tobias MS2 prediction based on MS1 data.
30.04.2020 Seminar Dominika Differentially evolutionary-conserved regions in populations
02.04.2020 Seminar Konrad Looking for therapeutic antibodies in next generation sequencing datasets.
02.04.2020 Seminar Anne Federated analysis of gene expression data
05.03.2020 JC Richard Lonsdale, Andrew, et al. 'Ten simple rules for a bioinformatics journal club.' (2016): e1004526.