News of 2022

Welcome, Lara!

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.
Wai Tuck is awarded the Marie Sklodowska-Curie Actions fellowship!
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. more

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!

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

John holds internal online workshop on the rescoring tool Caravan

25 Feb 2022 Caravan 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.
We published!
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
Hanna receives PhD studentship from Wellcome Trust UK!
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. more

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.

Collaborator's websites:
https://www.uu.nl/staff/EJAMSijts
https://www.kcl.ac.uk/research/mishto-lab

Kamil obtains SINGA PhD scholarship!

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

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!

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

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.

Collaborator's websites:
https://medicine.nus.edu.sg/mbio/about-us/our-people/academic-staff/liu-haiyan.html
https://www.kcl.ac.uk/research/mishto-lab
Two out of three poster awards at Horizons go to QSB!
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!

Click here to see the posters. more
Hanna holds hands-on workshop on invitroSPI tool

Hanna holds hands-on workshop on invitroSPI tool

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!

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!

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!

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!

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!
Hanna obtains stipend by Manfred Eigen Förderstiftung!
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! more
Yehor and his team win at Dataethics pilot school!
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! more
We published!
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. more
Sarah holds introductory Python course
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/] more

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.
We published!
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. more
We have been awarded an ERC Starting Grant!
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] more
Welcome, Kamil!

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!

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.

Collaborator's websites:
http://shepherd-group.ismb.lon.ac.uk/
https://www.kcl.ac.uk/research/mishto-lab

 News of 2020

We cracked the case!

We cracked the case!

05 November 2020 Online gathering for a Sherlock Holmes Escape Room
Sarah holds modelling course
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!

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!

Hanna was accepted to Max Planck School!

27 April 2020 Hanna Rötschke was accepted to join the Max Planck School "Matter of Life Undergraduate Research Opportunities”. Congratulations Hanna!

News of 2019

 

We published!
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. more
We published!
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 patients was published in Frontiers in Immunology. more
Juliane gives seminar in Melbourne

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

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

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!

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

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

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.
We published!
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. more

Sarah wins best student talk at MASAMB!
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! more
Welcome, Sophie-Asako!

Welcome, Sophie-Asako!

April 2019 We welcome Sophie-Asako Xerri to our team!
Yehor stays for his PhD

Yehor stays for his PhD

01 April 2019 Yehor will do his PhD with us on multi-omics integration for immune epitope prediction.
We published!
20 March 2019 Our paper on modelling the dynamics of the extracellular proteasome osteopontin circuit in Multiple Sclerosis is out in Cells. more

Welcome, Gerd!

Welcome, Gerd!

05 March 2019 We welcome Gerd Specht to our team! Gerd will join us to work on his Bachelor thesis.

 

Welcome, Debdas!

Welcome, Debdas!

01 February 2019 Debdas Paul joins our team as postdoc. Welcome Debdas! He will work on machine learning approaches in immunology.
 

We published!
January 2019 Our paper showing the frequency and characteristics of spliced peptides in cancer cell lines is now published in Cancer Immunology Research. more

News of 2018


 

Juliane gives talk at KCL about in silico methods

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!

Welcome, Yehor!

01 October 2018 We welcome Yehor Horokhovskyi in our team! Yehor will join us to work on his MSc Thesis.

 

Horizons 2018

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!

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

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

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!

Our first retreat!

06-08 June 2018 The departments Jahn and Urlaub 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.

 


We published!
30 May 2018: The two sides of proteases - our new review is published in Current Opinion Immunology. more

 

We are in the News!
21 May 2018 The May issue of the MPIbpc News published a portrait about our group. more
Welcome, Sarah!

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.

News of 2017

We published!
07 December 2017 Our experimental design paper is now published in Bioinformatics. more

Welcome, Artem!

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.

 


We published!
17 August 2017 New review published in Trends in Immunology. more

 


We published!
01 August 2017 Our paper highlighting the role of spliced peptides in infection is now published in Cell Reports. more

 

QSB is launched!

QSB is launched!

March 2017 Dr. Juliane Liepe starts research group "Quantitative and Systems Biology" at the Max Planck Institute for Biophysical Chemistry
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