Sign in

Applied Systems Biology

@appsysbio.bsky.social
1.2K followers 983 following 34 posts

Leibniz Institute: Hans Knöll Institute Jena The research group Applied Systems Biology is concerned with the mathematical modeling and computer simulation of infection processes caused by human-pathogenic fungi.

PostsRepliesMedia
Applied Systems Biology @appsysbio.bsky.social · 29/09/2026
BLUESKY IbSB 2026 was a great success! Thank you to all speakers, participants, workshop instructors, and our team for their contributions to the inspiring talks, successful workshops, discussions and networking. A few impressions from IbSB 2026. www.youtube.com/watch?v=xjyj...
youtube.com
IbSB 2026 - Conference Highlights
YouTube video by Applied Systems Biology
000
Applied Systems Biology @appsysbio.bsky.social · 25/09/2026
🎓 Congratulations to our colleague Yann Bachelot on successfully defending his PhD thesis! 👏 We’re very happy to celebrate this important milestone and wish him all the best for the next chapter of his scientific career. #PhD #HKIJena
000
Applied Systems Biology @appsysbio.bsky.social · 24/09/2026
🏆 Great news! The publication by our colleague Parastoo Akbarimoghaddam (Leibniz-HKI), Manuel Allwang (Jena University Hospital) and Maximilian Wipplinger (Jena University Hospital), has received the DMykG Stiftungspreis. 👏 Congratulations to all authors! 🔗 doi.org/10.1002/smll...
000
Applied Systems Biology @appsysbio.bsky.social · 03/09/2026
New collaborative publication! Our colleagues Anastasia Solomatina, Yann Bachelot, Carl-Magnus Svensson & Marc Thilo Figge contributed to a new study showing how neutrophil-derived vesicles can help Candida albicans evade immune clearance. 🔗 doi.org/10.1002/jev2... #CandidaAlbicans
doi.org
Host‐to‐Pathogen Transfer of Neutrophil Components via Extracellular Vesicles Shields <i>Candida albicans</i> From Immune Attack in Human Blood
Neutrophils release extracellular vesicles (EVs) in response to Candida albicans, and these EVs bind to the fungus in a complement-dependent manner while carrying neutrophil surface markers and antim...
031
Applied Systems Biology @appsysbio.bsky.social · 31/07/2026
📄 New collaborative publication in *Gut Microbes*! Congrats to co-first author Parastoo Akbarimoghaddam and our colleagues Zoltán Cseresnyés and Marc Thilo Figge. The study uses intestine-on-chip technology to investigate inflammation in ulcerative colitis. 🔗 doi.org/10.1080/1949...
doi.org
Assessing the proinflammatory potential of sterile fecal microbiome filtrate from ulcerative colitis patients using an intestine-on-chip platform and automated image analysis
Ulcerative colitis (UC) is characterized by disruptions of the gut microbiome and an exaggerated mucosal immune response in genetically susceptible individuals. Alterations in the composition of th...
010
Applied Systems Biology @appsysbio.bsky.social · 03/07/2026
📄 New collaboration publication! Congratulations to our colleagues Mounir Zerdani, Marc Thilo Figge, and Carl-Magnus Svensson on their contribution to a new study published in Colloids and Surfaces B: Biointerfaces. www.sciencedirect.com/science/arti... #Collaboration #Biomaterials #Publication
sciencedirect.com
Ethanol-Driven Structural Transitions of Human Serum Albumin and Surface-Assisted 2D Network Formation on Ti-6Al-4V: A Kinetic-Morphological Map
Ti-6Al-4V, a widely used titanium alloy for load-bearing implants, is rapidly conditioned by adsorbed proteins in vivo. Protein conditioning layers on…
120
Applied Systems Biology @appsysbio.bsky.social · 08/06/2026
📄 New publication! Congratulations to Parastoo Akbarimoghaddam, co-first author of a new study in Small. onlinelibrary.wiley.com/doi/10.1002/... #Publication #Candida #Microbiome #OrganOnChip
onlinelibrary.wiley.com
Human Colitis‐on‐Chip Model Reveals Dual Roles of Butyrate in Epithelial and Macrophage Defense Against Candida albicans Tissue Invasion
This study establishes a human immunocompetent colitis-on-chip model that mimics inflamed gut mucosa and enables quantitative analysis of Candida albicans tissue invasion under DSS-induced injury. It...
011
Applied Systems Biology @appsysbio.bsky.social · 12/05/2026
We are happy to announce the 8ᵗʰ International Symposium on Image-based Systems Biology (#IbSB2026), taking place on September 17–18, 2026 at Leibniz-HKI in Jena, Germany. Register now: asb-conference.hki-jena.de #BioimageAnalysis #SystemsBiology #Microscopy #OpenScience
110
Applied Systems Biology @appsysbio.bsky.social · 11/05/2026
📢 Deadline approaching! Apply now for the Fellows4Fungi COFUND Postdoctoral Program before May 26, 2026. 🔗 www.fellows4fungi.eu #Postdoc #FungalResearch #ScienceJobs
fellows4fungi.eu
Fellows4FungiMSCA Postdoctoral Network - Leibniz-HKI
011
Applied Systems Biology @appsysbio.bsky.social · 05/05/2026
🎉 New role in the team! Mariia continues with Applied Systems Biology as a technical assistant after completing her Bachelor’s in our group. Great to have her with us! 🚀 #NewTeamMember #Bioinformatics #ImageAnalysis #JIPipe #AI #HKIJena
020
Applied Systems Biology @appsysbio.bsky.social · 05/05/2026
🎉 Welcome to the team! Jakob Döge joins Applied Systems Biology as a PhD student in Bioinformatics, working on JIPipe and 3D bioimage analysis. Wishing him a great start! 🚀 #PhD #Bioinformatics #JIPipe #HKIJena
010
Applied Systems Biology @appsysbio.bsky.social · 14/04/2026
Welcome to the team! We’re happy to have Johanna Hellfors (PhD) and Tim Schneider (Master’s) join Applied Systems Biology. Wishing them a great start! #NewTeamMembers #Science #HKIJena
010
Applied Systems Biology @appsysbio.bsky.social · 30/03/2026
🎉 Our 2026 JIPipe course was a great success! The enthusiasm and dedication of the participants made it especially enjoyable for us as instructors. 👏 A big thank you to all the excellent participants for their motivation and engagement! #JIPipe #Training #Science #ImageAnalysis #HKIJena
010
Applied Systems Biology @appsysbio.bsky.social · 16/03/2026
📄 New paper published! Our colleague Zoltán Cseresnyés contributed to a new study in Advanced Healthcare Materials. 🔗 advanced.onlinelibrary.wiley.com/doi/full/10.... Congrats to all authors! 👏 #Publication #Research #Biomaterials
advanced.onlinelibrary.wiley.com
Evaluating the Antiviral Efficacy of Encapsulated PKC Inhibitor BIM‐I against influenza A Virus Infection
This study explores nanoparticle delivery of the protein kinase C inhibitor bisindolylmaleimide-I (BIM-I) to combat influenza A virus infections. Encapsulation in biodegradable PLGA nanoparticles imp...
011
Applied Systems Biology @appsysbio.bsky.social · 09/03/2026
📄 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
pubs.rsc.org
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...
021
Applied Systems Biology @appsysbio.bsky.social · 09/02/2026
📄 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
link.springer.com
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...
020
Applied Systems Biology @appsysbio.bsky.social · 06/01/2026
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
advanced.onlinelibrary.wiley.com
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...
020
Reposted by Applied Systems Biology
Leibniz-HKI @leibniz-hki.de · 17/10/2025
🍁 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
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.
063
Reposted by Applied Systems Biology
Cláudia Vilhena @cvilhena.bsky.social · 17/11/2025
🧵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....
pubs.acs.org
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.
282
Applied Systems Biology @appsysbio.bsky.social · 16/10/2025
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/...
onlinelibrary.wiley.com
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...
010
Applied Systems Biology @appsysbio.bsky.social · 19/09/2025
🎉 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
120
Applied Systems Biology @appsysbio.bsky.social · 18/09/2025
🎉 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
040
Applied Systems Biology @appsysbio.bsky.social · 15/09/2025
🎓 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
microverse-cluster.de
010
Applied Systems Biology @appsysbio.bsky.social · 27/08/2025
🎉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! 🚀
010
Applied Systems Biology @appsysbio.bsky.social · 15/08/2025
🎙️ 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
010
Applied Systems Biology @appsysbio.bsky.social · 22/07/2025
📢 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
nature.com
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
030
Applied Systems Biology @appsysbio.bsky.social · 11/07/2025
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
031
Reposted by Applied Systems Biology
Applied Systems Biology @appsysbio.bsky.social · 15/04/2025
📢 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
1209
Reposted by Applied Systems Biology
Applied Systems Biology @appsysbio.bsky.social · 05/05/2025
🎓 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
164
Applied Systems Biology @appsysbio.bsky.social · 13/05/2025
📢 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
youtube.com
Applied Systems Biology
080
Applied Systems Biology @appsysbio.bsky.social · 08/05/2025
📢 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
070
Applied Systems Biology @appsysbio.bsky.social · 05/05/2025
🎓 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
164
Applied Systems Biology @appsysbio.bsky.social · 15/04/2025
📢 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
1209
Applied Systems Biology @appsysbio.bsky.social · 11/04/2025
🎉 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
1110
Applied Systems Biology @appsysbio.bsky.social · 02/04/2025
🎉 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
050
Applied Systems Biology @appsysbio.bsky.social · 10/03/2025
🦠 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
biorxiv.org
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...
062
Applied Systems Biology @appsysbio.bsky.social · 10/03/2025
🦠 New Insights into Respiratory Viral Infections 🦠 royalsocietypublishing.org/doi/10.1098/... #Science #Biotechnology #Research #Microbiome #OrganOnChip #LungHealth
royalsocietypublishing.org
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...
053
Applied Systems Biology @appsysbio.bsky.social · 05/03/2025
🚀 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
asb.hki-jena.de
Applied Systems Biology – HKI JenaContinueContinueContinue
071