Our publicaton “Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing” is now available in Nature Communications.
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02. November 2023 The team of Melina Schuh published their paper “Mammalian oocytes store proteins for the early embryo on cytoplasmic lattices” in Cell. Congratulations to Yehor, Iina, and Juliane who collaborated with the Schuh lab on this paper.
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Wai Tuck presents at the 15th ÖGMBT Annual Meeting: Life Sciences and Cutting-edge Technologies
19. September 2023 Wai Tuck attended a conference at his alma mater, University of Salzburg in Austria. He presented his work on the Identification and Characterization of spliced peptides catalyzed by human 20S proteasomes. Wai Tuck is supported by the Marie Skłodowska-Curie Actions postdoctoral fellowship.
QSB Retreat in Portugal
26. July 2023 We held a very successful retreat in Caparica, Portugal. Days consisted of a group work, presentations by team members, and scientific discussion.
Hanna and Nyet Cheng win poster awards!!
20. July 2023 Congratulations to Hanna and Nyet Cheng who won 2 of the 3 awards for most excellent posters presented at the 5th International Caparica Conference in SPLICING 2023, Caparica, Portugal.
QSB present posters at International Caparica Conference in SPLICING
18. July 2023 Congratulations to Hanna, John, Julia, Lara, Martin, Nyet Cheng, Sahil, Wai Tuck, and Yehor who all presented posters at the 5th International Caparica Conference in SPLICING 2023, Caparica, Portugal.
QSB Presentations at International Caparica Conference in SPLICING
17. July 2023 Congratulations to Hanna, Wai Tuck, Yehor, John, and Juliane who all gave short talks at the 5th International Caparica Conference in SPLICING 2023, Caparica, Portugal. It was the first time presenting at a conference for Hanna, Yehor, and John. This work was co-funded by ERC. Wai Tuck is supported by the Marie Skłodowska-Curie Actions postdoctoral fellowship.
QSB travels to Portugal
16. July 2023 Our team is travelling to the 5th International Caparica Conference in SPLICING 2023, Caparica, Portugal at which multiple group members will give talks and present posters. After the conference, the we will remain in Caparica for a team retreat.
Wai Tuck attends 72nd Lindau Nobel Laureate Meeting
25. June 2023 Wai Tuck got nominated by the European Commission (Marie Skłodowska-Curie Actions) to attend the 72nd Lindau Nobel Laureate Meeting. Together with 600 young scientists and Nobel laureates, they spent a week (25-30th June 2023) in Lindau to foster scientific exchange among them. Wai Tuck is supported by the Marie Skłodowska-Curie Actions postdoctoral fellowship.
Hanna presents at the Francis Crick Immunology Seminar
03. Mai 2023 Hanna presented her work about “Insights into proteasome catalysis gained from in vitro experiments - the key towards understanding MHC-I epitope generation?” at the Immunology Interest Group Seminar at the Francis Crick Institute.
Welcome, Julia!
6. February 2023 We warmly welcome Julia Stachowiak to our team! Julia is a medical student and joined us for her medical doctoral thesis. She will be working on neoepitopes in oncological diseases.
John presents at the MPI-NAT Campus Seminar
12. January 2023 Congratulations to John who presented at the MPI-NAT campus seminar. John gave a talk entitled “The Search for Immunogenic Peptides: Finding Needles in Haystacks”.
10. Januar 2023 Our paper “InvitroSPI and a large database of proteasome-generated spliced and non-spliced peptides” is now available in Scientific Data.
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The Deutschlandstipendium supports talented and high-performing students. Congratulations! After her internship at QSB, Lara will continue to work with us on the proteasome as student assistant.
QSB hosts Happy Hour!
18. November 2022 We hosted a very successful edition of the institute’s Happy Hour! It was a night of music, cocktails, and good conversation as the first snow of winter came down outside.
Hanna holds online workshop on the new affinitySPI software tool.
November 4, 2022 Hanna held a workshop on the newly developed affinitySPI tool. affinitySPI identifies immunologically relevant peptides.
Hanna moved to London!
21. October 2022 Hanna graduated from her BSc studies in Biochemistry and moved to the Molecular Immunobiology group of Dr. Michele Mishto at Kings College London to conduct her PhD studies. We are happy that Hanna will remain a team member of QSB through extended research stays (Front to back: Hanna Rötschke, Hassnae Afrache, Connie Fourny, KCL).
Wai Tuck and Nyet Cheng arrive in London!
21. October 2022 To learn new techniques and collect data for their projects Wai Tuck and Nyet Cheng are currently on a research stay for 10 weeks hosted by the Molecular Immunobiology group of Dr. Michele Mishto at the Francis Crick institute in London (left to right: Ying Thong (Crick), Nyet Cheng Chiam (QSB), Wai Tuck Soh (QSB) and Bei Fang Teo (Crick)).
20. October 2022 Our paper “inSPIRE: An open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction” is now available in Molecular & Cellular Proteomics.
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From Göttingen to London and back.
15. October 2022 To further increase interaction and exchange between 'wet' and 'dry' labs, we have weekly joint group meetings between QSB and the Molecular Immunobiology group of Dr. Michele Mishto at King's College and the Francis Crick Institute in London.
03. October 2022 Our paper “iBench: A ground truth approach for advanced validation of mass spectrometry identification method” is now available in Proteomics.
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Welcome Martin!
October 01. 2022 A warm welcome to Martin Pašen! Martin started as a PhD student in our team. His project will focus on on quantitative and statistical approaches to modelling the APP (antigen processing and presentation) pathway.
John presents poster at the Horizons in Molecular Biology Symposium
15. September 2022 John presented a poster on “iBench & inSPIRE: Getting peptide sequences right” at the 19th Horizons in Molecular Biology Symposium.
31. July 2022 Wai Tuck took part the 14th Advanced Proteomics Summer School. At the conference, he presented a poster on Characterization of the Antigen Processing by Proteasomes.
Sarah Graduates!
04. July 2022 We warmly congratulate Dr. Sarah Henze, who received her PhD at QSB. Sarah was awarded her PhD for her research into absolute quantification of peptides with a computational approach using Bayesian inference.
Welcome Iina!
01. June 2022 We warmly welcome Iina Takala to our team! Iina has joined our team after completing her masters at the University of Turku. She is working on multi-omics analysis of proteasome subtype expression effects.
Welcome Sahil!
01. June 2022 A warm welcome to Sahil Khan! Sahil has started as a PhD student on our team. His project will focus on developing a mechanistic model for APP (Antigen Processing and Presentation) pathway.
Welcome, Lara!
02 May 2022 Lara has joined our team, welcome! Lara is doing a 3-months internship before starting her BSc studies in Biochemistry in October. During her time here she will get introduced to enzyme biochemistry, experimental work e.g. pipetting and computer-based data analysis.
Artem Graduates!
20. April 2022 We warmly congratulate Dr. Artem Mansurkhodzhaev who was awarded his PhD. Artem earned his PhD for his research into the role of proteasome generated spliced peptides in the adaptive immune response, immune evasion by pathogens and autoimmunity.
21 Mar 2022 We congratulate Wai Tuck for being awarded the Marie Sklodowska-Curie Actions fellowship by the European Commission! The project is about PROTAC-driven Protein degradation by Proteasome during Antigen Processing and Presentation (ProAPP) and will be funded for 24 months.
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Welcome, Vera!
14 Mar 2022 We welcome Vera Subrakova to our team! Vera studies Biotechnology at AgroParisTech University Paris and joins us for a 6-month master project. She is interested in anti-cancer drug development and with us she will work on the prediction of peptide splicing in order to identify possible cancer-specific spliced peptides.
Welcome, Nyet Cheng!
01 March 2022 A warm welcome to Nyet Cheng Chiam, who joins our team as postdoc! Nyet Cheng is a trained molecular biologist and she will work experimentally on proteasome-mediated antigen processing and MHC-1 presentation.
John holds internal online workshop on the rescoring tool Caravan
25 Feb 2022Caravan uses Percolator and Prosit tools to generate high confidence peptide-spectrum matches from mass spectrometry search results using recent advances in spectral prediction.
Welcome, Lorenz!
21 Feb 2022 We welcome Lorenz Mammen to our team! Lorenz is currently doing his undergraduate studies in biology and maths at the University of Tuebingen. He joins us for an internship of six weeks. During his stay, he will work on modelling of the antigen presenting pathway.
20 Feb 2022 Our paper “Database search engines and target database features impinge upon the identification of post-translationally cis-spliced peptides in HLA class I immunopeptidomes” was published in Proteomics.more
31 Jan 2022 Hanna receives a PhD studentship from the Wellcome Trust in UK. Congratuations, Hanna! She will join the Neuro-Immune Interactions in Health & Disease Programme at King's College London in September.
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News of 2021
Internal proteogenomics workshop
14 December 2021 Yehor, Kamil and Iga gave a workshop on proteogenomics.
First joint group meeting with Sijts and Mishto labs
04 November 2021 Today we had our first joint group meeting online with the group of Alice Sijts at Utrecht University and members of the Molecular Immunobiology lab at King's College and The Francis Crick Institute in London. We discussed experimental and modelling approaches to investigate the antigen presentation pathway.
October 2021 Kamil obtained the SINGA PhD scholarship to work on aging at NUS! The National University of Singapore (NUS) is among the top 25 best universities in the world according to the Times Higher Education ranking. The SINGA scholarship is only awarded to 3-4% of all applicants. Congratulations, Kamil!
3rd Retreat of the IMPRS Genome Science
14 October 2021 This year, the IMPRS-GS retreat took place in short form in Göttingen.
Welcome, Ali!
01 October 2021 Ali Salehzadeh-Yazdi joins our team as Postdoc. Welcome Ali! He will work on mechanistic modeling of proteasome dynamics.
First joint group meeting with Liu and Mishto labs
23 September 2021 Today we had our first joint group meeting online with Prof. Liu Haiyan from the Department of Microbiology and Immunology at National University of Singapore and members of the Molecular Immunobiology lab at King's College and The Francis Crick Institute in London. We discussed experimental and computational approaches to investigate the role and function of the extracellular proteasome.
16 September 2021 Artem, Hanna and Sarah presented their projects at the online symposium "18th Horizons in Molecular Biology". Hanna and Sarah won poster prizes, congratulations!
08 September 2021 Hanna Roetschke held an online workshop on her new tool invitroSPI. Title: "Identification of spliced and non-spliced peptides from in vitro experiments via mass spectrometry - An introduction to the invitroSPI tool including a hands-on training session"
Wai Tuck holds online lecture on allergies in Malaysia
07 September 2021 Wai Tuck was invited to give a virtual lecture at the School of Foundation studies, INTI International University, Malaysia! Title: Allergies and Immune systems. It is an introductory lecture to Pre-university/A-level students on allergy and scientific approaches used in the study of allergens.
Welcome, John!
01 September 2021 John Cormican joins our team as PhD candidate. Welcome John! He will work on search strategies and improvements to tools used in the identification of non-conventional peptides in the immunopeptidome.
Welcome, Iga!
01 September 2021 Iga Niemiec joins our team for her PhD. Welcome Iga! She will work on multi-omics integration of the antigen processing and presentation pathway.
Welcome, Szabolcs!
01 June 2021 Szabolcs Elias joins our team as Postdoc. Welcome, Szabolcs! He will work on machine learning methods in immunology.
Welcome, Wai Tuck!
01 June 2021 Wai Tuck Soh joins our team as Postdoc. Welcome Wai Tuck! He is a molecular biologist and his work with us will focus on the proteasome-mediated antigen processing and MHC-I presentation.
Jaspreet goes to Israel!
June 2021 Jaspreet got accepted into the Master's Program of Tel Aviv University (Israel) with a full scholarship. Congratulations!
April 2021 Hanna obtained the "Principles of Cancer Research - Stipend for an exceptional, independently working young scientist" of the Manfred Eigen Förderstiftung for her work on ”Prediction and characterisation of proteasome-catalysed spliced peptides”. Congratulations, Hanna!
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April 2021 Yehor participated in the online school "Data Ethics - Ethical considerations in interpretation and handling of Biomedical Big Data" of the Medical University of Innsbruck, Austria. His team won the first place award for a case study! Congratulations!
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15 April 2021 The paper “Potential Mimicry of Viral and Pancreatic β Cell Antigens Through Non-Spliced and cis-Spliced Zwitter Epitope Candidates in Type 1 Diabetes” by Mishto M., Mansurkhodzhaev A., Rodriguez-Calvo T. and Liepe J. was published in Frontiers in Immunology! The paper highlights in silico identification of putative spliced peptides derived from viruses associated with Type 1 Diabetes could trigger CD8+ T cell mediated immunity via molecular mimicry to self.
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29 March - 01 April 2021 Florian Jochheim (Cramer lab) and Sarah Henze give an introductory course to programming in Python. Mo: Introduction to Python Di-Do: Introduction to Data Science with Python The course will be held online and is offered as GGNB methods course to fellow PhD students.
[Image source: https://www.python.org/community/logos/]
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Welcome, Jaspreet!
01 March 2021 Jaspreet Ishar joins our team remotely for an internship. Welcome Jaspreet! She will work on predicting conversion factors for quantitative proteomics using classical machine learning approaches.
24 February 2021 Artems first author paper “Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8+ T Cell Tolerance” was published in Frontiers in Immunology. The paper describes a computational analysis of the impact of proteasome generated spliced peptides on the immune evasion of viruses via molecular mimicry of MHC class I presented peptides to self and formation of subsequent gaps in CD8+ T cell mediated immunity.
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01 February 2021 We are very happy to announce that our project, IMAP, will be funded by the European Research Council!
[Image source: Von Europäischer Forschungsrat - http://erc.europa.eu, Logo, https://de.wikipedia.org/w/index.php?curid=9020693]
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Welcome, Kamil!
01 February 2021 We welcome Kamil Pabis to our team! He will work with us on understanding sequencing information in the MHC-I antigen presentation pathway.
Welcome, Andrew!
15 January 2021 Andrew Graham joined our team. Welcome Andrew! Andrew is a first year Wellcome Trust PhD student and part of the Neuro-Immune Interaction in Health and Disease programme at Kings College London. He joined our team to work on his project “Investigating the influence of the proteasome and its inducible isoform (immunoproteasome) on neuroinflammation in Alzheimer’s Disease” in collaboration with Michele Mishto and Maria Jimenez Sanchez.
First joint group meeting with Shepherd and Mishto labs
14 January 2021 Today we had our first joint group meeting with members of the Computational Biology group at Birkbeck University London and the Molecular Immunobiology lab at King's College and The Francis Crick Institute in London. We discussed the role of spliced neoepitopes in solid cancer.
16-17 September 2020 Sarah offers a GGNB methods course with the title "Introduction to Mechanistic Modelling in Systems Biology". The course will take place online. more
We published!
15 May 2020 We generated a large database of proteasome generated spliced and non-spliced peptides, which is now published in Scientific Data.
Hanna was accepted to Max Planck School!
27 April 2020Hanna Rötschke was accepted to join the Max Planck School "Matter of Life Undergraduate Research Opportunities”. Congratulations Hanna!
15 November 2019 Our paper on the effect of ER-aminopeptidase 1 on the processing and presentation of immunotherapy-relevant melanoma epitopes is now published in the European Journal of Immunology.
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15 November 2019 Our paper introducing an in silico—in vitro pipeline identifying an HLA-A*02:01+ KRAS G12V+ spliced epitope candidate for a broad tumor-immune response in cancer patientswas published in Frontiers in Immunology.
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Juliane gives seminar in Melbourne
23 October 2019 Juliane Liepe gives a seminar on “Systems Biology of the MHC-I antigen presentation pathway" at Melbourne Integrative Genomics Center, University of Melbourne(Melbourne, Australia).
Hanna stays as research assistent
01 October 2019 Hanna will continue to work with us on characterisation and prediction of proteasome-catalysed peptide splicing using Deep Learning.
Yehor presents poster at ICSA in Athens
12 September 2019 Yehor presented his work "Characterization of MHC-I immunopeptidome to eradicate senescent lymphoma cells after Doxorubicin chemotherapy” on a poster at the ICSA (Cellular senescence - The bright & dark side) in Athens.
Welcome, Hanna!
01 August 2019 Hanna Rötschke joined our team. Welcome, Hanna! Hanna is doing a summer internship with us, before starting her BSc studies in Biochemistry at the University of Göttingen. She will work with our team on the systems biology of the MHC-I antigen presentation pathway.
Away Day
19 June 2019 Our group went on a hiking trip to the Harz mountains. We visited the Unicorn Cave and the ruins of Schwarzfels near Herzberg.
2nd Retreat of the IMPRS Genome Science
13-15 June 2019 The second IMPRS-GS retreat took place in Volpriehausen. All students of the program presented their work, networked and exchanged ideas. Sarah gave a talk and Artem and Yehor presented their work on posters.
10 May 2019 Our work on the differences between the 20S thymoproteasome and immunoproteasome and the effect on the processing of antigens associated to tumors and autoimmune diseases is published in Journal of Biological Chemistry.
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26 April 2019: Sarah presented her work on "Bayesian statistical inference based on MCMC facilitates the analysis of protease dynamics using tandem mass spectrometry measurements" at the workshop MASAMB 2019 at EMBL-EBI in Cambridge. She won a prize for giving the best student talk. Congratulations Sarah!
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Welcome, Sophie-Asako!
April 2019 We welcome Sophie-Asako Xerri to our team!
Yehor stays for his PhD
01 April 2019 Yehor will do his PhD with us on multi-omics integration for immune epitope prediction.
January 2019 Our paper showing the frequency and characteristics of spliced peptides in cancer cell lines is now published in Cancer Immunology Research.
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News of 2018
Juliane gives talk at KCL about in silico methods
03 October 2018 Juliane talks at Kings College London (UK) about the usefulness of in silico methods to study the adaptive immune system.
Welcome, Yehor!
01 October 2018 We welcome Yehor Horokhovskyi in our team! Yehor will join us to work on his MSc Thesis.
Horizons 2018
September 2018 Artem and Sarah presented their projects on the "15th Horizons in Molecular Biology" in Göttingen.
Poster titles: Artem: The mechanisms of peptide bond cleavage and Proteasome- Catalysed Peptide Splicing in Humans Sarah: Kinetic analysis of signaling cascades involved in the adaptive immune response
We published!
09 September 2018 Our chapter "ABC in Systems Biology" is now published in Handbook of Approximate Bayesian Computation.
Artem presents a poster in Vienna
17 July 2018 Artem presents his work on kinetic analysis of the proteasome at the 2018 EuPA School on Practical Proteomics in Vienna.
1st Retreat of the IMPRS Genome Science
14-16 June 2018 The first IMPRS-GS retreat took place in Berlin. What a great opportunity to present and discuss projects and to get to know each other. Artem and Sarah presented their work on posters.
Poster titles: Artem: "The impact of proteasome-catalysed peptide splicing on the occurence of gaps in T-cell immunity" Sarah: "Kinetic analysis of signaling cascades in the adaptive immune response"
Our first retreat!
06-08 June 2018 The departments Jahn andUrlaub kindly invited us to join them on their retreat to Ringberg castle at the Tegernsee. A great opportunity to network and learn about each other's research. Both Artem and Sarah presented their work.
21 May 2018 The May issue of the MPIbpc News published a portrait about our group.
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Welcome, Sarah!
01 March 2018 We welcome our new team member Sarah Henze, who joins us as a PhD student for the next years. She will work on parameter estimation in immunology.
07 December 2017 Our experimental design paper is now published in Bioinformatics.
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Welcome, Artem!
01 November 2017 We welcome our new team member Artem Mansurkhodzhaev, who joins us as a PhD student for the next years. He will work on the investigation of the alternative mechanism of generation of peptides by proteasome - proteasome generated spliced peptides, and their immunological relevance in context of the MHC class I presentation pathway.
