Applied Systems Biology

Mapping the nonribosomal specificity code through promiscuity-guided A-domain engineering Nonribosomal peptide synthetases (NRPSs) assemble bioactive peptides from various building blocks. The binding pocket residues governing building block specificity have allowed prediction of NRPS prod...

📄 New paper accepted!

Our colleague Carl-Magnus Svensson co-authored a study on engineering NRPS specificity to design new bioactive peptides.

🔗 pubs.rsc.org/en/Content/A...

#NRPS #SyntheticBiology #Publication

From Observation to Mechanistic Insight: Image-based Systems Biology of Human Pathogenic Fungi - Current Clinical Microbiology Reports Purpose of Review Human pathogenic fungi are increasingly recognized as major threats to human health, yet their complex biology and interactions with the host remain poorly understood. This review hi...

📄 New review published!

From Observation to Mechanistic Insight: Image-based Systems Biology of Human Pathogenic Fungi

Image-based modeling reveals how fungal growth, immune evasion & host responses shape infection.

🔗 link.springer.com/article/10.1...

#SystemsBiology #Fungi #Publication

Generation of an Induced Pluripotent Stem Cell‐Derived Alveolar Type II In Vitro Model to Study Influenza A Virus Infection and Drug Treatments Patient-specific induced pluripotent stem cells (iPSCs) can be differentiated into alveolar type II cells (iAT2s), expanded as 3D alveolospheres, and grown at physiologically relevant air–liquid inte...

New paper accepted in Advanced Healthcare Materials!

Our colleague Yann Bachelot co-authored a study on an iPSC-derived alveolar type II model for influenza A infection and drug testing.

Congrats to all authors! 👏

advanced.onlinelibrary.wiley.com/doi/10.1002/...

#Influenza #StemCells

Zoltán Cseresnyés, an older man with short gray hair and a friendly smile, stands indoors beside a long office table. He is wearing a light blue short-sleeved shirt, gray trousers, and brown shoes. He holds a small potted bonsai tree in both hands. On the table next to him are a large potted plant, a green watering can, and a book. The background shows a bright modern room with white walls and wooden flooring. In the upper left, a colorful speech bubble contains the text: “I am an image analyst. I help biologists and chemists to analyze their image data and get information and quantification out of microscopy images, thus allowing them to modify or plan experiments.” The Leibniz-HKI logo appears in blue at the bottom left, and an orange arrow points to the right.

Colorful calendar page for October 2025 from the Leibniz-HKI Calendar. The background fades from blue on the left to purple on the right. The word 'OCTOBER' appears in bold orange letters. Below it, the name 'Zoltán Cseresnyés' is written in large green text. At the bottom left, small black text reads 'Leibniz-HKI Calendar 2025' with the blue Leibniz-HKI logo beneath it. On the right side, the word 'SWIPE' is written in black uppercase letters next to an orange arrow pointing right.

A close-up photo shows the back of a man’s head as he looks at a computer monitor displaying a complex network of colorful lines and nodes on a dark background – microscopy data visualization. The desk below the monitor holds papers, computer accessories, and cables. In the top left, a colorful speech bubble contains the text: “The real highlight was being there at the very beginning of super-resolution microscopy.” The Leibniz-HKI logo appears in blue at the bottom left, and an orange arrow points to the right.

Zoltán Cseresnyés and a younger woman with dark hair, one of his colleagues, sit side by side at a table in a bright office. Zoltán, wearing a light blue short-sleeved shirt, gestures with his hand while explaining something on a laptop screen. The woman listens attentively, wearing a patterned blouse and a wristwatch. Behind them, large windows with blinds fill the room with natural light. A colorful speech bubble above them contains the text: “It is crucial to remain flexible and open – both in mind and in career.” The Leibniz-HKI logo appears in blue at the bottom left of the image.

🍁 Meet our #October #calendar 2025 feature: Zoltán Cseresnyés, imaging specialist at our @appsysbio.bsky.social research group. From 1980s Hungary to super-resolution microscopy at Cambridge, he now helps researchers unlock insights from complex images. 🔬🌌
lmy.de/LsPim

#FacesOfScience #LeibnizHKI

Mechanistic Insights into the Role of Extracellular Vesicles at the Bacterial–Host Interface Bacterial and human cells produce extracellular vesicles (EVs) in response to diverse stimuli, e.g., toxins, oxidative stress, nutrient depletion, or high cell density. Here, we describe a cocultivation platform that allows recovery of mixed extracellular vesicles (mix-EVs) produced simultaneously by both cell types. We investigated interactions between Gram-positive and Gram-negative bacteria (Streptococcus pyogenes, Staphylococcus aureus, Escherichia coli, and Neisseria meningitidis) and human peripheral blood mononuclear cells (PBMCs). The production of the mix-EVs population decreased with higher bacterial concentrations. Exposing PBMCs to mix-EVs repressed the general transcriptomic signature, in contrast with a significant upregulation generated by single bacterial-EVs. However, mix-EVs-derived IL-1β upregulation was confirmed at the protein level. Inhibition experiments showed that IL-1β production involved TLR2 and TLR4 signaling, acting through IRAK-1 and TRAF6 related pathways. This approach provides a new platform for the study of EVs at the pathogen–host interface and presents mechanistic insights into the effect of EVs on an infected host.

🧵1/2- So so happy to share our very first publication from the #BIDlab! 🥳 🎉 🙏

A huge thanks to our super talented PhD student Miriana Battista and our amazing collaborators @appsysbio.bsky.social and Christoph Saffer for the work and support 👌 🙏

⏩ pubs.acs.org/doi/full/10....

Selective Activation of Dynamics in Kinetically Frozen Supramolecular Polymer Bottlebrush Assemblies Static at rest—dynamic on demand: Although supramolecular polymers are known for their dynamic nature, this study investigates the dynamics of amphiphilic assemblies based on polymer-modified benzene...

New publication:
"Selective activation of dynamics in kinetically frozen supramolecular polymer bottlebrush assemblies"

#hki-Jena #BioimageAnalysisTools #SupramolecularPolymers
#PolymerChemistry #Biomaterials #Nanotechnology #DrugDelivery #SoftMatter

onlinelibrary.wiley.com/doi/10.1002/...

🎉 SBMI 2025 was an inspiring experience!
It has been an enriching experience, discussions, and new collaborations
Thanks to all participants for their contributions. 🙏
✈️ Wishing everyone a safe journey home, see you at the next IbSB2026!

#MicrobialInfections #ScientificCommunity#HKIJena

🎉 We’re excited to kick off SBMI 2025 in Jena!
Scientists meet to discuss microbiology, immunology & systems biology.

🔗 asb-conference.hki-jena.de

#SBMI2025 #SystemsBiology #Conference

🎓 PhD position available!
Automated image processing of immune interactions in organ-on-chip models @ Microverse Cluster (Prof. Figge, HKI Jena).

🗓️ Apply by Oct 5, 2025
🔗 www.microverse-cluster.de/files/conten...

#PhDPosition #Microverse #BioimageAnalysis

🎉Exciting news from Applied Systems Biology @ HKI 🎉
We’re welcoming three new members:

• Lennart Köhler — Technical Assistant
• Behnaz Asiabanha — Master student and Assistant
• Mariia Kolchanova — Master student and Assistant

Great to have you on board! 🚀

🎙️ Excited to welcome Prof. Somenath Bakshi (University of Cambridge) as an invited speaker at SBMI 2025!
www.bakshilab.net

Early Bird Registration extended!
Reduced registration fee until:
🗓️ 20 August 2025 at 23:59 (CEST)
asb-conference.hki-jena.de

#SBMI2025 #SystemsBiology #Conference

Complex-mediated evasion: modeling defense against antimicrobial peptides with application to human-pathogenic fungus Candida albicans - npj Systems Biology and Applications npj Systems Biology and Applications - Complex-mediated evasion: modeling defense against antimicrobial peptides with application to human-pathogenic fungus Candida albicans

📢 New article from our team!

A model of neutrophil transendothelial migration at single-cell resolution has just been published in npj Systems Biology & Applications.

🔗 www.nature.com/articles/s41...

#SystemsBiology #Publication#Neutrophils #ComputationalModeling #AppliedSystemsBiology #HKIJena

Final call for abstracts!!

Submit your abstracts for (SBMI 2025) by:
🗓️ July 15, 2025 at 23:59 (CEST

Take advantage of Early Bird Registration until:
🗓️ July 31, 2025 at 23:59 (CEST)

🔗 asb-conference.hki-jena.de

#SBMI2025 #CallForAbstracts #SystemsBiology

📢 SBMI 2025
Join us at the 8th International Symposium "Systems Biology of Microbial Infection", Sept 18–19, 2025 in Jena

Submit your abstract & consider applying for a Tandem-Talk!

Info & speakers: asb-conference.hki-jena.de

#SystemsBiology #InfectionBiology #BioimageAnalysisTools

🎓 Are you a Bachelor or Master students?
📢 SBMI 2025 is free of charge for you!

Join us at the 8th International Symposium "Systems Biology of Microbial Infection",
📅 September 18–19, 2025 in Jena 🇩🇪
🔗 More info: lnkd.in/ej7w9MwH

#SystemsBiology #BioimageAnalysis #InfectionBiology

Applied Systems Biology

📢 New JIPipe tutorials now on YouTube!🎥

Learn how to build and analyze visual pipelines for bioimage data.
👉 www.youtube.com/@appliedsyst...
Feel free to share your feedback and questions!

#JIPipe #BioimageAnalysis #OpenSource

📢 Excited to welcome Liliana Angeles Martinez to our team at Applied Systems Biology!
Her expertise in cell–cell interactions and spatio-temporal modeling brings valuable new perspectives to our research.

#SystemsBiology #CellInteractions #SpatioTemporalModeling #HKIJena #AppliedSystemsBiology

🎓 Are you a Bachelor or Master students?
📢 SBMI 2025 is free of charge for you!

Join us at the 8th International Symposium "Systems Biology of Microbial Infection",
📅 September 18–19, 2025 in Jena 🇩🇪
🔗 More info: lnkd.in/ej7w9MwH

#SystemsBiology #BioimageAnalysis #InfectionBiology

📢 SBMI 2025
Join us at the 8th International Symposium "Systems Biology of Microbial Infection", Sept 18–19, 2025 in Jena

Submit your abstract & consider applying for a Tandem-Talk!

Info & speakers: asb-conference.hki-jena.de

#SystemsBiology #InfectionBiology #BioimageAnalysisTools

🎉 Girl's and Boy's Day 2025

This year we were delighted to take part in the Forsche Schüler Tag/Boys' and Girls' Day by introducing five interested ninth graders (15-16 years old) to the exciting world of systems biology. 🧪🔬

#STEM #JIPipe #SystemsBiology #ScienceEducation

🎉 Congrats to our colleague Simone Piccioni for winning a Poster Prize at the Joint Annual Meeting 2025 of FungiNet and IMIHM XV in Würzburg! 🏆
A big shoutout for this amazing achievement! 👏

#Science #FungiNet #IMIHM #PosterPrize #InfectionResearch #BioImageAnalysis

Convergent evolution of a fungal effector enabling phagosome membrane penetration The ability of pathogens to evade phagosomal killing is critical for their pathogenicity. Previously, we had identified the HscA effector protein in the clinically important fungal pathogen Aspergillu...

🦠 Fungal Pathogens & Phagosome Evasion 🦠

New research explores how convergent evolution has shaped fungal effectors to penetrate host phagosomal membranes.

www.biorxiv.org/content/10.1...

#Microbiology #FungalPathogens #InfectionBiology #Research #PathogenicFungi

Deciphering respiratory viral infections by harnessing organ-on-chip technology to explore the gut–lung axis | Open Biology The lung microbiome has recently gained attention for potentially affecting respiratory viral infections, including influenza A virus, respiratory syncytial virus (RSV) and SARS-CoV-2. We will discuss...

🦠 New Insights into Respiratory Viral Infections 🦠

royalsocietypublishing.org/doi/10.1098/...

#Science #Biotechnology #Research #Microbiome #OrganOnChip #LungHealth

🚀 We are now on Bluesky!

We are the Applied Systems Biology research group, specializing in mathematical modeling and computer simulation of infection processes. 📊🦠

🌍 Website: asb.hki-jena.de

💻 GitHub: github.com/applied-syst...

#ImageAnalysis #BlueskyScience #BioimageAnalysisTools