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.