Welcome to the Pharmaceutical Bioinformatics research group at Uppsala University

Principal Investigator: Ola Spjuth, Professor.

Research focus: Intelligent systems with AI and machine learning in drug discovery and chemical safety

The Pharmaceutical Bioinformatics research group focuses on mathematical and statistical modeling, informatics and quantitative analysis of pharmacological systems. We develop methods, algorithms and software to study and model pharmaceutical interactions, and a key focus in the group is how artificial intelligence (AI) and machine learning can aid the drug discovery process; e.g. in drug screening and when studying drug toxicity, metabolism and resistance. We combine in silico and in vitro experiments at the cellular level, and have access to a robotized high-content imaging lab connected to a modern IT-infrastructure to manage and analyze large-scale data. We are involved in several national and international consortia and have a tight connection to the pharmaceutical industry, Uppsala University Hospital, and Science for Life Laboratory. See the Projects page for more information on our ongoing research projects.

We are an interdisciplinary team of researchers engaging in data-driven cell biology, aiming to develop autonomous biological laboratories where data drives decisions on what experiments should be done next, and where automation and AI modeling are core methodologies.

Latests Blog Posts

3 open positions: Biomedical Analyst (BMA), 1st Research Engineer and Researcher for cell profiling applications

20 Dec, 2021. Funded by an infrastructure grant from the Swedish Research Council, our research group at Uppsala University is now establishing a new node as part of the Chemical Biology Consortium Sweden, a national infrastructure for chemical biology. ...

Just published: 'A phenomics approach for antiviral drug discovery' in BMC Biology

3 Jul, 2021. Our latest work “A phenomics approach for antiviral drug discovery” has now been published at BMC Biology! Jonne Rietdijk, Marianna Tampere, Aleksandra Pettke, Polina Georgiev, Maris Lapins, Ulrika Warpman-Berglund, Ola Spjuth, Marjo-Riitt ...

Amelie Wenz joins the research group as new PhD Student

3 Jul, 2021. We welcome Amelie Wenz who recently started as a PhD Student in our group! What is your education, and what have you done earlier in your career? I started my education by studying Biological Science at the University of Konstanz in German ...

Christa Ringers receives mobility grant from Norwegian Research Council to join our team as a PostDoc for a project in functional personalized medicine for colorectal cancer

24 Jun, 2021. We are excited to announce that Christa Ringers has received a prestigious 3-year mobility grant from Norwegian Research Council to join our team at Uppsala University as a PostDoc for 2 years and then continue the project at Norwegian Univ ...

David Holmberg joins the research group as new PhD Student

3 May, 2021. We welcome David Holmberg who recently started as a PhD Student in our group! David will work in the Autonomous Phenomics project. What is your education, and what have you done earlier in your career? Alright, so I am a graduate from Lund ...

Open PhD student position in Applied Mathematics: Autonomous Decision Making in Automated Cell Profiling for Drug Discovery Applications

22 Feb, 2021. There is now an opportunity to apply for a PhD position in Applied Mathematics with a project from our group with the title: “Autonomous Decision Making in Automated Cell Profiling for Drug Discovery Applications”. The PhD stud ...

Open positions for 2 PhD students and 1 PostDoc in our lab

1 Jan, 2021. After being awarded 2 grants from the Swedish Research Council, we are now strengthening our team to work towards autonomous phenomics and precision cancer medicine.For more information about the project and research group, see https://pha ...

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Latest publications

ELIXIR and Toxicology: a community in development Martens M, Stierum R, Schymanski EL, Evelo CT, Aalizadeh R, Aladjov H, Arturi K, Audouze K, Babica P, Berka K, Bessems J, Blaha L, Bolton EE, Cases M, Damalas D, Dave K, Dilger M, Exner T, Geerke DP, Grafstrom R, Gray A, Hancock JM, Hollert H, Jeliazkova N, Jennen D, Jourdan F, Kahlem P, Klanova J, Kleinjans J, Kondic T, Kone B, Lynch I, Maran U, Martinez Cuesta S, Menager H, Neumann S, Nymark P, Oberacher H, Ramirez N, Remy S, Rocca-Serra P, Salek RM, Sallach B, Sansone SA, Sanz F, Sarimveis H, Sarntivijai S, Schulze T, Slobodnik J, Spjuth O, Tedds J, Thomaidis N, Weber RJM, van Westen GJP, Wheelock CE, Williams AJ, Witters H, Zdrazil B, Zupanic A, Willighagen EL.. F1000Research 10(ELIXIR):1129 (2021)

Learning to see colours: generating biologically relevant fluorescent labels from bright-field images Wieslander H, Gupta A, Bergman E, Hallström E, Harrison PJ. PLOS ONE 16:10 (2021)

Integrating statistical and machine-learning approach for meta-analysis of Bisphenol A-exposure datasets reveals effects on mouse gene expression within pathways of apoptosis and cell survival Lukashina N, Williams MJ, Kartysheva E, Virko E, Kudłak B, Fredriksson R, Spjuth O, Schiöth HB.. International Journal of Molecular Sciences 22:19 (2021)

An Open-Source Modular Framework for Automated Pipetting and Imaging Applications Ouyang W, Bowman R, Wang H, Bumke KE, Collins JT, Spjuth O, Carreras-Puigvert J and Diederich B. Advanced Biology 2101063: (2021)

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Latest presentations

Synergy Conformal Prediction for Regression
10th International Conference on Pattern Recognition Applications and Methods (ICPRAM 2021), . Feb 2021
A Constraint Programming Approach to Microplate Layout Design
The 19th workshop on Constraint Modelling and Reformulation, Louvain-la-Neuve, Belgium. Sep 2020
Towards automated phenotypic cell profiling with high-content imaging
Chemical Biology Seminar Series, Stockholm. Feb 2020
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Latest posters

Automating Cell Profiling of Drugs with Cell Painting
10th Pharmaceutical Profiling Symposium, Uppsala. Jan 2020
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