10th Conference on
Constraint-Based
Reconstruction and Analysis
(COBRA2026)

March 17, 2026 to March 19, 2026
Seminaris Seehotel Potsdam | Germany

About The Event

COBRA 2026 invites all established and new members of the COBRA community to discuss the latest development in Constraint-Based Reconstruction and Analysis. COBRA2026 will focus on constraint-based modelling at the interface of AI and plant science, while offering a forum for exchanges in advances in other areas of constraint-based modeling.

COBRA 2026 aims to attract and gather early-career as well as established researchers from computational biology, machine learning / AI, metabolomics, building a dialogue that can widen the applications of constraint-based modelling in agriculture and crop breeding. COBRA2026 keeps the emphasis on constraint-based modelling applications in microbiology, metabolic engineering, synthetic biology, and medicine, while establishing stronger relations with advances in machine learning, AI, and data science.

Day 1 – Interface between constraint-based modelling and AI in microbiology and biotechnology

Day 2 – Hybrid constraint-based modelling and AI for advances in plant sciences

Day 3 – Interface between constraint-based modelling and AI in medical applications

Each of these days will include three sessions on: (i) method / model development, (ii) applications, as well as (iii) challenges and new frontiers. This organization of the conference will foster cross-discipline interactions and will result in establishing new collaborations.

Where

Seminaris Seehotel Potsdam
An der Pirschheide 40 | 14471 Potsdam

When

17-19 March, 2026 Tuesday to Thursday

Program

Topic: Interface between constraint-based modelling and AI in microbiology and biotechnology.

09:00 – 09:15	Welcome
Methods \| model development \| Chair: Eivind Almaas
09:15 – 10:00	Daniel Zielinski	University of California San Diego	Facilitating complex simulations via efficient multi-scale constraint-based modeling
10:00 – 10:30	Patrick Victor Phaneuf	Technical University of Denmark, Denmark	Harnessing Pangenomes for Microbial Discovery and Engineering
10:30 – 11:00	Zahra Razaghi-Moghadam	University of Potsdam, Germany	Metabolite-informed prediction of flux distributions in genome-scale metabolic networks
11:00 – 11:30	Daniel Machado	Norwegian University of Science and Technology, Norway	Reconstruction and simulation of microbial community models for sustainable biotechnology applications
11:30 – 12:00	Nicola Claire Hallmann	ETH Zurich, Switzerland	Multiobjective design of growth media with genome-scale metabolic models and Bayesian optimization
Lunch break
Applications \| Chair: Anika Küken
13:30 – 14:00	Jason Papin	University of Virginia, USA	Metabolic network analysis of probiotics to guide selection for therapeutic development
14:00 – 14:30	Andreas Dräger	Martin Luther University Halle-Wittenberg, Germany	From Host-Associated Communities to Industrial Biocatalysts: Integrative Constraint-Based Modeling across Biological Scales
14:30 – 15:15	Anastasia Santo	University of Padova, Italy	Multi-stage Modeling of Microbial Resilience in Power-to-Gas Systems: An Integrated dFBA and Genetic Algorithm Approach
15:00 – 15:30	Ameneh Mehrjerd	University medicine Greifswald, Germany	Fluxome-based biological age-scores derived by prior fitted neural networks trained on COBRA microbiome community models highlight sex-specific microbiome functional aging patterns
Coffee break
Challenges and new frontiers \| Chair: Steffen Klamt
16:15 – 17:00	Ines Thiele	University of Galway, Ireland	Keynote
17:00 – 17:30	Supriya Shivanna	University of Toronto, Canada	Growth Environment Reshapes the Dose - Response of Transcription-Factor Biosensors Across Nutrient Conditions
17:30 – 17:45	Group Photo
Opening Reception with Poster session (from 18:00)

Topic: Hybrid constraint-based modelling and AI for advances in plant sciences.

Methods \| model development \| Chair: Caroline Baroukh
09:00 – 09:45	Douglas Allan	Danforth Plant Science Center	Synergies and Counterintuitive Cycles that Define Architecture and Metabolism in Plants and Algae
09:45 – 10:15	Philipp Wendering	University of Potsdam, Germany	Metabolic modeling identifies determinants of thermal growth responses in Arabidopsis thaliana
10:15 – 10:45	Sophie Colombié	INRAE, France
10:45 – 11:15	Nadine Töpfer	University of Cologne, Germany	Metabolic modelling of a synthetic maize root microbiome using genome-scale constraint-based approaches
11:15 – 11:45	Martina Feierabend	University of Cologne, Germany	Pan-genome-scale metabolic modeling to understand metabolic functions of plant-associated microbes
Lunch break
Applications \| Chair: Daniel Machado
13:30 – 14:00	Steffen Klamt	Max Planck Institute Magdeburg, Germany	COBRA-k: a powerful framework bridging constraint-based and kinetic metabolic modeling
14:00 – 14:30	Michael Predl	University of Vienna, Austria	A Geometric View of Community Metabolism
14:30 – 15:00	Mariana Monteiro	Imperial College London, UK	CellTarget: A convex optimisation approach to discover cellular objectives
15:00 – 15:30	Evelyn Gonzalez	University of Luxembourg, Luxembourg	scFASTCORMICS 2.0: Fast and Scalable Context-Specific Metabolic Modeling from Single-Cell RNA-seq Data of the Tumor Microenvironment
15:30 – 15:45	Sponsor presentations
Coffee break
Challenges and new frontiers \| Chair: Alia Benkahla
16:15 – 17:00	Jean-Loup Faulon	University of Manchester and INRAE	Neural–Mechanistic Methods for Learning Constraints in Genome-Scale Models
17:00 – 17:30	Samuel Seaver	Argonne National Laboratory, USA	Interpreting Metabolic Imbalance in Hybrid ML-Constraint-Based Models of Plant Plastids
17:30 – 18:30	Poster Session (all posters)
18:30	Joint trip to Barberini
Reception at the Barbarini Museum (from 19:00)

Topic: Interface between constraint-based modelling and AI in medical applications.

Methods \| model development \| Chair: Thomas Sauter
09:00 – 09:45	Rajib Saha	University of Nebraska-Lincoln	From Feasibility to Mechanism: Constraint-Guided Learning for Inference in Biomedicine
09:45 – 10:15	Hyun Uk Kim	KAIST, South Korea	Metabolic modeling and AI approaches to predict drug targets and drug responses
10:15 – 10:45	Eduard Kerkhoven	Chalmers University of Technology, Schweden	Human-GEM and beyond: improving model accuracy and coverage through LLM-assisted curation and dark metabolism mining
10:45 – 11:15	Xinmeng Liao	KTH Royal Institute of Technology, Sweden	ENCORE: an end-to-end pipeline to reconstruct enzyme-constrained community metabolic models and identify reporter metabolites from metagenomes
11:15 – 11:45	Connor Moore	University of Virginia, USA	Metabolic network analysis of Crohn’s disease reveals sex- and age-specific cellular phenotypes
Lunch break
Applications \| Chair: Nadine Töpfer
13:30 – 14:00	L. Safak Yilmaz	Umass Chan Medical School, USA	sciMAT++: Quantitative, Network-Level Flux Maps at Cell-Type Resolution from scRNA-seq
14:00 – 14:30	Maria Zimmermann	European Molecular Biology Laboratory, Germany	Combining metabolic modelling and machine learning to unravel microbial metabolic functions and microbe-host interactions
14:45 – 15:00	Zita Soons	University Hospital RWTH Aachen, Germany	Integrative Multi-Omics Metabolic Modeling Reveals Mechanisms of Drug-Induced Liver Toxicity
15:00 – 15:30	Takeyuki Tamura	Kyoto University, Japan	Predicting Growth-Coupled Gene Deletion Strategies Using Neural Networks in Constraint-Based Metabolic Models
Coffee break
Challenges and new frontiers \| Chair: Zoran Nikoloski
16:15 – 17:00	Vassily Hatzimanikatis	École Polytechnique Fédérale de Lausanne, Switzerland	From Genome-Scale Models to Translational and Precision Medicine: Methodological Challenges and Lessons Learned
17:00 – 17:30	Handan Cetin	University of Virginia, USA	Multi-scale Network Topology Analysis Reveals Metabolic Reprogramming and Therapeutic Vulnerabilities in the Tumor Microenvironment
Closing remarks

Deadline for registration & abstract submission: we accept late registrations and poster abstract submission.
The final conference program and instructions for poster presentations will be shared by Monday, 16.02.2026.

These Are

Our Speakers

Chemical Engineering & Bioengineering

Chemical & Bimolecular Engineering

Gene regulation & metabolism

Building & Scaling SynBio Solutions

Molecular Systems Physiology

additional invited speakers are:

Patrick Victor Phaneuf, Jason Papin, Zahra Razaghi-Moghadam, Andreas Dräger, Sophie Colombie, Nadine Töpfer, Safak Yilmaz, Philipp Wendering, Maria Zimmermann, Hyun Uk Kim

About The Event Organizer

COBRA2026 is shaped by Prof. Dr. Zoran Nikoloski and the core group of the organizing committee with world-renowned experts in plant science, AI, and metabolic modelling, including: University of Potsdam / Max Planck Institute of Molecular Plant Physiology, Germany, University of San Diego, California, USA, and King’s College London, UK.

The organizing committee views COBRA2026 as a forum where methodological advances are discussed in parallel with industrial developments that bridge microbial and plant biotechnology. The strong emphasis on AI will also prioritize topics related to the access and use of curated high-throughput phenotyping data. Therefore, COBRA 2026 is also expected to stimulate exchange with the German research data infrastructure (NFDI) in life sciences and other similar international efforts.

Co-organizers

Anika Kueken (University of Potsdam, Germany)
Alia Benkhala (BIMS, Tunisa)
Caroline Baroukh (INRA, France)
Eivind Almaas (NTNU, Norway)
Paul Jensen (University of Michigan, USA)
Adil Mardinoglu (King’s College London, UK)
Sang Yup Lee (KAIST, South Korea)
Bernhard Palsson (UCSD, USA)

Contact

For general questions regarding the conference or questions about submitting contributions, please use the corresponding address below.

Book Your Participation Now!

Be part of the 10th Conference on Constraint-Based Reconstruction and Analysis (COBRA2026). This landmark event will bring together leading scientists and emerging researchers to advance the field of constraint-based modeling. Expect cutting-edge presentations, vibrant discussions, and valuable networking opportunities across disciplines. The deadline for registration & abstract submission: we accept late registrations and poster abstract submissions. Registration for participation is possible until the first day of the event.

Please note: Registration and event sign-up are two separate steps. Creating a ConfTool account (registration on the platform) is only the first step. To actually take part in COBRA2026, you also need to log in and select “Register as Participant” within ConfTool. Your participation is only confirmed once both steps have been successfully completed.

Venue

The conference venue, the SeeHotel Potsdam is unique in many ways: Located just outside Potsdam, nestled in the charming forest and lake landscape of Pirschheide, in the immediate vicinity of the famous world heritage Sanssouci Park and directly on Lake Templin, the hotel impresses with its modern flair, innovation, and meticulous attention to detail. A tram and bus stop and the Pirschheide train station, with connections to the city center and Potsdam Central Station, are just a few meters away.

A number of rooms could be reserved for the conference participants at a reasonable rate – please use the following reservation form for further details.

We strongly urge all interested participants to book rooms way in advance, preferably till January 2026.

Directions

Arrival BER airport Berlin (~35min): Take the regional train RB22 directly from BER Airport to Potsdam Pirschheide. From there, use the exit “An der Pirschheide” and follow the clearly signposted path to the hotel (about 10 minutes walk).

Arrival Potsdam Hauptbahnhof (Potsdam main station ~30min): Take tram line 91 or 98 toward Pirschheide and get off at“Pirschheide Bahnhof”. From the tram stop, walk to the regional train station and use the exit “An der Pirschheide”. From there, follow the clearly signposted path to the hotel. The walk takes about 10 minutes.