Retrospect - 2023
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
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
Title: Lachnospiraceae-related bacteria trigger MS-like disease in germfree transgenic mice
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
Human adipocytes at scale
13.06.2023 | 4 pm
Phil Kubitz
Venue:
Zoom.
Please contact geschaeftsstelle.ziel[at]tum.de, if you are interested in the link.
Host: Prof. Hans Hauner
Non-penetrance in patients with monogenetic inborn errors of immunity
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
Co-regulators of the glucocorticoid receptor in macrophages
27.06.2023 | 4 pm
Benjamin Strickland
Venue:
Zoom. Please contact geschaeftsstelle.ziel[at]tum.de if you are interested in the link.
Host: Prof. Henriette Uhlenhaut
Title coming soon
18.07.2023 | 4 pm
Shen Jin
Venue:
Zoom.
Please contact geschaeftsstelle.ziel[at]tum.de, if you are interested in the link.
Host: Dr. Melanie Schirmer
Modelling Cancer-Microbiome interactions with Organoids and Organ Chips
12.09.2023 | 4 pm
Dr. Jens Puschhof
Epithelium Microenvironment Interaction Laboratory
Microbiome and Cancer Division (F220)
Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
69120 Heidelberg
Venue:
Auditorium, TranslaTUM, Einsteinstr. 25, 81675 München
Host: Prof. Dr. Dieter Saur
Title: Lymphatic vessel obstruction underlies the pathology of ileal Crohn’s disease and murine ileitis driven by the TNFdeltaARE mutation
05.10.2023 | 4 pm
Gwendalyn J. Randolph, PhD
Emil R. Unanue Distinguished Professor
Department of Pathology & Immunology
Washington University School of Medicine
Saint Louis, Missouri 63110 USA
Venue:
Zoom. Please request the link here: sfb1371.ziel@tum.de
Host: Dirk Haller
Title: Unleashing the potential of metaproteomics for understanding host-microbe functional dynamics
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:
Room 2.98, Gregor-Mendel-Str. 2, 85354 Freising
Host: Dirk Haller
Title: Gut Microbial Metabolism of Dietary Polyphenols in Health and Disease
17.10.2023 | 4 pm
PhD Jan Claesen
Department of Cardiovascular and Metabolic Sciences
Cleveland Clinic Lerner College of Medicine, CWRU
9500 Euclid Avenue | Cleveland
Venue: Zoom. Please request link here: sfb1371.ziel[at]tum.de
Host: Dirk Haller
Title: The nuclear receptors TR2 and TR4 drive hepatic fibrosis
07.11.2023 | 4 pm
Marion Schweiger
Venue:
online (Zoom)
Host:
Prof. Uhlenhaut
Initiation of immune responses by surveillance of homeostasis perturbations
28.11.2023 | 4 pm
Luis Ferreira Moita, M.D.
Innate Immunity and Inflammation Laboratory
Instituto Gulbenkian de Ciência
Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal
Venue:
DG01 iGZW, Gregor-Mendel-Str. 4, 3. OG, 85354 Freising
Host: Dr. Dirk Haller