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Understand

We have expertise in advanced data integration using statistical, bioinformatic, machine learning, and modeling approaches.

Modeling includes risk-assessment models, genome-scale and whole cell models, protein structure modeling and biomolecular simulation, virtual ligand-docking screens, and dynamic modeling of specific pathways.

While each of these methods have their merits, these approaches should be combined to provide better mechanistic understanding of trends and patterns in data (called explainable AI), as well as advanced biomarker discovery. This is an exciting scientific frontier where AIMMS can be a partner with data and computer scientists.

Methods

  • Bioinformatics

  • Theoretical chemistry

  • Systems biology

  • Evolutionary biology

  • Toxicology

Data stewardship, analysis and modeling

  • Advanced data integration using statistical, bioinformatic, machine learning, and modeling approaches 
  • Knowledge database development 
  • Genome-scale and whole cell models 
  • Protein structure modeling and biomolecular simulation
  • Multi-scale modeling
  • Dynamic modeling of specific pathways

Bioinformatics

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Theoretical chemistry

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Techniques

Mass spec-based methods

We have advanced analytical methods for metabolomics, proteomics and glycomics for the analysis of human fluids, intracellular metabolites, tissues and cell culture media. We hyphen separation techniques as HPLC, CE and GC with high-end (tandem) mass spectrometry (high-resolution, ion mobility and UVPD/IRMPD). We also have MS-based imaging facilities.

Contacts: Pim Leonards, Govert Somsen, Sofia Moco

NMR and crystallography

We have 300 – 600 MHz NMR machines for compound identification and analysis of complex fluids for metabolite quantification. 

For protein structure determination, the workflow includes liquid handling for sample crystallization, optimizing crystals, crystal handling including cryo-protection and storage. Diffraction analysis and data collection is done on an in-house, state of the art Bruker D8 Quest X-ray source attached to an cutting edge PhotonII detector including downstream software suits for structure determination. 

Contact: Elwin Janssen (nmr.beta@vu.nl).

Techniques

MIMETAS OrganoPlate® Challenge Winner Selected

| Challenges | No Comments
Congratulations to Elisabeth Naderlinger, Lenya de Brouwer, and Olivia Klatt for winning the MIMETAS-AIMMS VU OrganoPlate® Platform Proposal Contest! 🎉 The idea for the MIMETAS-AIMMS…

Kickstarting the animal to plant protein transition

| Challenges, Food, Human health & food | No Comments
When ten bright minds come together for two full days, innovation is bound to prosper! The first AIMMS hackathon revolved all around finding alternative protein…

Systems biology

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Single-cell

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Evolutionary biology

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Toxicology

Even the all-powerful Pointing has no control about the blind texts it is an almost unorthographic life One day however a small line of blind text by the name of Lorem Ipsum decided to leave for the far World of Grammar. The Big Oxmox advised her not to do so, because there were thousands of bad Commas, wild Question Marks and devious Semikoli.

Sample projects

Meet the Scientist: Thomas Hansen

| Meet the Scientist | No Comments
Thomas Hansen Assistant Professor in the Synthetic Organic Chemistry & Catalysis Group "People with different personal, cultural, and scientific backgrounds bring unique insights...the beauty of…
Sofia discussing metabolism with PhD candidate Victoria Pozo Photo credit: David Poole III

Meet the Scientist: Sofia Moco

| Meet the Scientist | No Comments
Sofia Moco PI at the Chemistry and Pharmaceutical Sciences department of the VU. Birthplace:  Portugal "I was always curious about how things work, and somehow…

Do NMR Experiments with AIMMS

| Equipment hire, Research | No Comments
Interested in using our NMR equipment? Nuclear Magnetic Resonance (NMR) spectroscopy is widely used to determine the structure of organic molecules and is closely tied to…

Using metabolomics to study the dynamics of metabolism

| Fermentation, Food, Research | No Comments
Dysregulation of metabolism is closely linked to the development of various diseases and lifetime changes, including metabolic disorders, cancer, and ageing. Understanding the nuances of…

AIMMS researchers win €5M NWO Perspective Grant for the plant-based fermentation proposal

| Fermentation, Food, Research | No Comments
This week The Netherlands Organisation for Scientific Research (NWO) granted the FERMI Perspective proposal led by Herwig Bachmann from the Systems Biology Lab. The project…

Stringing Science Together: Bead-azzling Macrocyclization for Biochemistry Bling!

| Research | No Comments
Imagine making a necklace. You start with various colors and shapes of beads, and you decide which specific beads you want to connect to form…