Welcome to the Pharmaceutical Bioinformatics research group at Uppsala University

Principal Investigator: Ola Spjuth

Research focus: Data-intensive and translational bioinformatics

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 predictive modeling, large-scale calculations and modern e-infrastructure (such as high-performance and cloud computing) can aid the drug discovery process; e.g. when studying drug toxicity, metabolism and resistance. 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.

Open position: PhD student in bioinformatics with focus on machine learning on large-scale image data

22 Jun, 2017

Our group is participating in the HASTE project (Hierarchical Analysis of Temporal and Spatial Image Data) which is recruiting two PhD students. One of the positions will be placed in our lab with focus on machine-learning with quantifiable ...
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Pharmb.io running team 'Metab elite' completes Blodomloppet race

19 Jun, 2017

On 2017-05-18, the pharmb.io running team ‘Metab elite’ were able to complete the Blodomloppet race over 10 km! When enjoying the well-deserved picnic after the finish line, the team was looking ahead to future races… Re ...
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Open position: Postdoc/Researcher in Bioinformatics with focus on Machine Learning and Image Analysis

8 May, 2017

Our group is participating in the HASTE project (Hierarchical Analysis of Temporal and Spatial Image Data) which is recruiting up to three postdocs or researchers in Computerized Image Analysis, Scientific Computing and Bioinformatics. One ...
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Paper published: E-Science technologies in a workflow for personalized medicine using cancer screening as a case study

24 Apr, 2017

After 3 years, our paper on e-Science in cancer screening is finally published by J Am Med Inform Assoc (JAMIA). Abstract Objective: We provide an e-Science perspective on the workflow from risk factor discovery and classification of disea ...
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New supercomputers at Uppsala University and SciLifeLab enables data-intensive bioinformatics on sensitive data

20 Apr, 2017

Today the two supercomputers Bianca and Rackham are inaugurated at Uppsala University. Read the news article at SciLifeLab, interviewing Ola Spjuth in his role as Head of Compute and Storage facility at SciLifeLab. See also the Inauguration ...
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Marco Capuccini and Stephanie Herman presenting on PhenoMeNal Workflow Workshop, 4-5 April, in Halle, Germany

4 Apr, 2017

Marco Capuccini and Stephanie Herman presented at the “PhenoMeNal Workflow Workshop”, 4-5 April, in Halle, Germany. The presentation covered a lot of the work that has been going on in the Uppsala team on workflows in “Phe ...
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Ola Spjuth presented at CloudBeer 2017: 'The case for cloud computing in Life Sciences'

30 Mar, 2017

Ola Spjuth held a presentation “The case for cloud computing in Life Sciences” at CloudBeer 2017 on March 23rd: The case for cloud computing in the life sciences There is a recording from the event available (also embedded belo ...
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Our paper: Large-scale virtual screening on public cloud resources with Apache Spark, got published in the Journal of Cheminformatics

7 Mar, 2017

Abstract Background Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, h ...
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Video from Marco Capuccinis talk at Spark Summit now online

14 Feb, 2017

As we have posted before, our colleague Marco Capuccini has been presenting at Spark Summit East 2017, with the title “EasyMapReduce: Leverage the power Of Spark And Docker To scale scientific tools In MapReduce fashion“ (click ...
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Our project: 'Hierarchical Analysis of Temporal and Spatial Image Data' will receive funding by SSF

9 Feb, 2017

Ola Spjuth is co-PI in the project ‘Hierarchical Analysis of Temporal and Spatial Image Data’ that received 29 MSEK from SSF for the period 2017-2021. Press release from Uppsala University Press release from SSF Abstract from th ...
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Presentation 'Analyzing Big Data in Medicine with Virtual Research Environments and Microservices' by Ola Spjuth on Uppsala University official YouTube Channel

26 Jan, 2017

This presentation was given by Ola Spjuth in the ‘Current Challenges in Biomedical Information Technology - Big Data in Medicine’ symposium series at the IT-department at Uppsala University. The slides are available from “ ...
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The 6th Symposium on Conformal and Probabilistic Prediction with Applications (COPA 2017)

24 Jan, 2017

14-16 June, 2017, Karolinska Institutet, Stockholm, Sweden. Ola Spjuth is local organizer of the event with the conference website: clrc.rhul.ac.uk/copa2017 Symposium Theme: Quantifying the uncertainty of the predictions produced by classif ...
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Marco Capuccini to present at Spark Summit East 2017

20 Dec, 2016

Marco Capuccini will present at Spark Summit East 2017: “EasyMapReduce: Leverage the power Of Spark And Docker To scale scientific tools In MapReduce fashion” Abstract: High-throughput methods in various scientific fields produc ...
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