Lecture series 2023
17.01.2023 - Dr. Heather Armstrong
Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients
17.01.2023 | 4 pm
Dr. Heather Armstrong
Manitoba Centre for Proteomics and Systems Biology
University of Manitoba
Winnipeg, Canada
Venue:
virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel[at]tum.de
Host: Kolja Siebert
21.03.2023 - Prof. Dr. Julien Gagneur
Title: Recent algorithms from the TUM chair of Computational Molecular Medicine with relevance for microbial signatures research
21.03.2023 | 4 pm
Prof. Dr. Julien Gagneur
Technical University of Munich
Chair for Computational Molecular Medicine
Boltzmannstr. 3/I
85748 Garching b. München
Venue:
Room 2.98, Gregor-Mendel-Str. 2, 85354 Freising
Host: Dirk Haller
Abstract:
This talk aims to give an overview of methodological advancements from my lab with potential utility for microbial signatures research. I will touch on 3 topics relevant to metagenomics, metaproteomics, and host genetics.
We developed a method that can leverage large genome datasets to identify conserved elements without sequence alignment [1]. We leverage masked language modeling – a pivotal technique in natural language processing – i.e. our model is trained to recover nucleotides artificially masked in the input. We trained the model on over 800 fungal species and demonstrated its utility for sequence motif detection and for deriving state-of-the-art performance predictors for a range of gene regulatory prediction tasks.
Second, I will present Spectralis, an algorithm for de novo peptide sequencing, i.e. reference-free identification of peptides from tandem mass spectrometry data [2]. Significant progress is being made on this long-standing problem thanks to deep learning. Spectralis surpassed 40% sensitivity at 90% precision on spectra for which database search provided a ground truth, nearly doubling state-of-the-art sensitivity.
Third, I will give an overview of methodologies to pinpoint the genetic cause of inherited rare disorders using RNA-seq as a complement to genome sequencing [3-5]. Our tools have helped to improve the diagnostic rate of rare disorders by as much as 15% for certain disorders and are now used by multiple rare-disease consortia.
1. Gankin, Karollus et al. Species-aware DNA language modeling. bioRxiv, 2023
2. Klaproth-Andrade et al. Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing. bioRxiv, 2023
3. Kremer, Bader et al. Genetic diagnosis of Mendelian disorders via RNA sequencing, Nature communications, 2017
4. Yépez et al. Detection of aberrant events in RNA-seq data. Nature Protocols, 2021
5. Wagner, Çelik, et al. Aberrant splicing prediction across human tissues, Nature genetics, in press
16.05.2023 - Prof. Anneli Peters
Title: coming soon
16.05.2023 | 4 pm
Dr. Anneli Peters
Ludwig-Maximilians-Universität München
Biomedical Center Munich
Adaptive immune responses in CNS autoimmunity
Geschwister-Scholl-Platz 1
80539 Munich
Venue:
DG01 iGZW, Gregor-Mendel-Str. 4, 3. OG, 85354 Freising
Host: Dirk Haller
20.06.2023 - Prof. Dr. Bodo Grimbacher
Title coming soon
20.06.2023 | 4 pm
Prof. Dr. Bodo Grimbacher
Universitätsklinikum Freiburg
Institute for Immunodeficiency
Centrum für Chronische Immundefizienz (CCI)
Venue:
Zoom
if you want to join online, please request link at sfb1371.ziel[at]tum.de
CRC members will receive the link in advance
Host: Prof. Dirk Haller
25.07.2023 - Prof. Dr. Jörg Vogel
The promises and challenges of programmable RNA antibiotics
25.07.2023 | 4 pm
Prof. Dr. Jörg Vogel
Julius-Maximilians-Universität Würzburg
Institute for Molecular Infection Biology
Venue:
iGZW, DG01, Gregor-Mendel-Str. 4, 85354 Freising
and virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel[at]tum.de
Host: Prof. Dr. Dirk Haller
26.09.2023 - Prof. Dr. Gianni Panagiotou
Title coming soon
26.09.2023 | 4 pm
Prof. Dr. Gianni Panagiotou
Department of Microbiome Dynamics, Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie
Hans-Knöll-Institut, Jena
Venue:
DG01 iGZW, Gregor-Mendel-Str. 4, 3. OG, 85354 Freising
Host: Dr. Markus List
10.10.2023 - PhD David Gomez Varela
Title: coming soon
10.10.2023 | 4 pm
PhD David Gomez Varela
Systems Biology of Pain
Division of Pharmacology & Toxicology
Department of Pharmaceutical Sciences
University of Vienna
Josef-Holaubek-Platz 2, 1090 Vienna, Austria
Venue:
DG01 iGZW, Gregor-Mendel-Str. 4, 3. OG, 85354 Freising
Host: Dirk Haller
21.11.2023 - Prof. Vincenzo Barnbara
Title: coming soon
21.11.2023 | 4 pm
Prof. Vincenzo Barnaba
Sapienza University of Rome
Department of Clinical Internal, Anesthesiological and Cardiovascular Sciences
Piazzale Aldo Moro, 5, 00185 Roma, Italy
Venue:DG01, iGZW, Gregor-Mendel-Str. 4, 85354 Freising
Zoom link will also be available.
Host: Dietmar Zehn