Research@TUM4224
Die Seminarreihe Research@TUM 4224 bietet Doktorand*innen und Postdocs die Möglichkeit, die eigene Doktorarbeit oder Wissenschaft einem größeren Publikum vorzustellen und in diesem Rahmen zu diskutieren. Dieses Format fördert darüber hinaus die Vernetzung und das Wissen über die Wissenschaft im eigenen Gebäude. Research@TUM4224 wird terminlich mit der Seminarreihe des SFB 1371 (Dienstagnachmittags 16:00, 30 Minuten Vortrag, 15 Minuten Diskussion; Moderation durch Betreuende) verknüpft.
Title: TBD
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
Title: TBD
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
Title: TBD
18.07.2023 | 4 pm
Shen Jin
Venue:
online (Zoom)
Host:
Dr. Schirmer
Title: TBD
27.06.2023 | 4 pm
Benjamin Stickland
Venue:
online (Zoom)
Host:
Prof. Uhlenhaut
Title: TBD
13.06.2023 | 4 pm
Phil Kubitz
Venue:
online (Zoom)
Host:
Prof. Hauner
Title: TBD
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
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
Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients
17.01.2023 | 4 pm
Dr. Heather Armstrong
Assistant Professor; Department of Internal Medicine
Manitoba Centre for Proteomics and Systems Biology; University of Manitoba
Venue:
virtual via Zoom
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel@tum.de
Host:
Kolja Siebert
Past lectures in 2022
Impact of a dietary fiber intervention on plasma TMAO-level : “Meatmark” – a human intervention study
13.12.2022 | 4 pm
Melanie Haas
Venue:
Seminar room 1.48 | Gregor-Mendel Str 2 | Freising
Host:
Prof. Skurk
Exploring the role of the gut microbiota during early life development
18.01.2022 | 4 pm
Prof. Dr. Lindsay Hall
Venue:
virtual
Members of the Research@TUM4224 receive link in advance. Other interested persons, please request link at geschaeftsstelle.ziel@tum.de
Of mice and Popeye - microbial sulfur metabolism in the gut
01.02.2022 | 4 pm
Univ.-Prof. Dr. Alexander Loy
University of Vienna
Centre for Microbiology and Environmental Systems Science
Division of Microbial Ecology
Venue:
virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel@tum.de
Host:
Bärbel Stecher
Paper presentation organized by PhD candidates
Microbe-host-immune interactions at the gut mucosal-luminal interface
15.02.2022 | 4 pm
Dr. rer. nat. Jianbo Zhang
Swammerdam Institute for Life Sciences
University of Amsterdam
Venue:
virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel@tum.de
Host:
Paper presentation organized by PhD candidates
Esther Wortmann
Alexandra von Strempel
Host-microbiome interactions in the context of recent human evolution
22.02.2022 | 4 pm
Mathieu Groussin, PhD and/or Mathilde Poyet, PhD
Massachusetts Institute of Technology, United States of America
Venue:
virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel@tum.de
Host:
Thomas Clavel
Mitochondrial perturbation of the epithelium causes microbial dysbiosis
05.04.2022 | 4 pm
Elisabeth Urbauer, PhD
Chair of Nutrition and Immunology
Prof. Dr. Dirk Haller
Venue:
virtual
Members of the Research@TUM4224 receive link in advance. Other interested persons, please request link at geschaeftsstelle.ziel@tum.de
Host:
Prof. Dr. Dirk Haller
Chair of Nutrition and Immunology
On the limitations of cancer subtyping with gene expression signatures
17.05.2022 | 4 pm
Manuela Lautizi, PhD
Chair of Experimental Bioinformatics
Institute of General and Surgical Pathology
Venue:
virtual
Members of the Research@TUM4224 receive link in advance. Other interested persons, please request link at geschaeftsstelle.ziel@tum.de
Host:
Dr. Markus List
Chair of Experimental Bioinformatics
Regulation of metabolic health by delta-9 desaturases
31.05.2022 | 4 pm
Harini Sampath, Ph.D.
Assistant Professor, Departrment of Nutritional Sciences
Director of Lipidomics, New Jersey Institute for Food, Nutrition and Health
Rutgers University, New Brunswick, New Jersey, USA
Venue:
virtual
CRC1371 members receive link in advance. Other interested persons, please request link at sfb1371.ziel@tum.de
Host:
Prof. Dr. Klaus-Peter Janssen
Altered lipid metabolism in ATF6-mediated colon tumorigenesis
28.06.2022 | 4 pm
Miriam Ecker, PhD
Chair of Nutrition and Immunology
Prof. Dr. Dirk Haller
Venue:
virtual
Members of the Research@TUM4224 receive link in advance. Other interested persons, please request link at geschaeftsstelle.ziel@tum.de
Host:
Prof. Dr. Dirk Haller
Chair of Nutrition and Immunology
Food & You: Pilot study tracking dietary intake, physical activity, blood glucose levels, and gut microbiota in healthy volunteers
19.07.2022 | 4 pm
Sebastian Gimpfl, M.Sc.
AG Public Health Nutrition
Venue:
virtual
Members of the Research@TUM4224 receive link in advance. Other interested persons, please request link at geschaeftsstelle.ziel@tum.de
Host:
Prof. Dr. Kurt Gedrich