Hoffecker Lab

Back for more action after an eventful summer! Ian attended the Statphys Satellite meeting in Lviv, Ukraine (Statphys Lviv article) - building important connections and learning about the latest ideas in statistical physics, and Ian and Joel debuted our work on DNA-based data storage at the DBDS meeting in Prague this year. Simon's paper on hidden networks was accepted to Nature Communications - congrats! And Voluminex collaborators Martin Weigt and Federico Scarpati visited Stockholm for a graph theory hackathon together with Ian and David. Link to DBDS webpage

Collaborators of the Voluminex project, coordinated by the Hoffecker group and KTH, arrive in Stockholm for the official project kickoff. In this 5 year international project, we will develop a network based imaging technology for 3D mapping of molecules in organoids. Link to project webpage

Exciting announcement - our group at KTH/SciLifeLab will be coordinating a big cross-Europe project over the next 5 years to develop a 3D spatial molecular imaging technology from networks. The project will be conducted together with partners Erik Benson at Karolinska/SciLifeLab Stockholm, Stockholm-based sequencing technology company Single Technologies AB led by CEO Johan Strömqvist, biologists Benedetta Artegiani and Delilah Hendriks at Princess Maxima Center for Pediatric Oncology in Utrecht, Netherlands, and physicist Martin Weigt at Sorbonne University in Paris. We're funded by the EU through the EIC Pathfinder program. Read more about it here: News article link

This autumn, Ian, David, and Simon attended an exciting DNA30 conference in Baltimore where we learned about the latest breakthroughs in the molecular programming field. David and Simon presented the results of their recent research on finding hidden spatial information in DNA barcode networks. We were also honored to host a talk here at SciLifeLab by Joshua Weinstein, a pioneer in the field of spatial inference from molecular networks, who presented to our community the exciting work he is doing in this field. This autumn also marked the second iteration of the popular KTH master's/doctoral course Machine Learning for Biotechnology - co-taught with Anniina Vihervaara. Great to listen to the student presentations at the end! Earlier this month, Ian traveled to Japan and gave a talk on spatial molecular networks at Kyoto University's Institute for Frontier Life and Medical Sciences (LiMe) hosted by Professor Hirofumi Shintaku. And Ian is now on Bluesky - Follow and connect here! Lastly, we recently admitted Krzysztof Mrosik to our ranks who will conduct his Master's thesis with us on the informatics and computational processing of information contained in DNA barcodes. Welcome Krzysztof!

This spring, we welcomed new member, experienced postdoctoral researcher Joel Spratt. Joel did his PhD in Oxford, and did a postdoc at Karolinska Institutet prior to joining us, where he will be working on developing new sequencing-based technologies. This spring we also published 2 preprints. Check them out here: Dahlberg SK, Bonet DF, Franzén L, Ståhl PL, Hoffecker IT. Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction. bioRxiv. 2024:2024-06. and here: Bonet DF, Blumenthal JI, Lang S, Dahlberg SK, Hoffecker IT. Spatial coherence of DNA barcode networks. bioRxiv. 2024:2024-05.

🍂 Autumn greetings! 🍂 A warm welcome to two new lab members. Dr. Anastassia Runina is joining us as a postdoc. Anastassia, with background in real-time PCR, microarrays and next gen sequencing product development, and STI detection, will be developing novel biotechnologies related to next gen sequencing with us. Johanna Blumenthal, from the Molecular Techniques in the Life Sciences Scilifelab Master program, is joining us for her Project and Master's thesis. Welcome Anastassia and Johanna! In other news, Ian is in the final weeks of a new Master's course CB206V on Machine Learning in Biotechnology, co-organized with Gene Technology Department colleague Anniina Vihervaara. Check out the recorded lectures on Youtube.

Warm welcome to KI student Salomé Hahne! She has recently joined us as part of the Biomedicine Master's program's rotation. Ian taught a 2 day statistics and programming workshop for the Scilifelab Master's program this month. Video lectures can be found on youtube.

We're proud to announce our latest contribution to the emerging field of DNA sequencing-based microscopy. The work was led by newly enrolled doctoral student David Fernandez Bonet. Check out the full preprint.

Congratulations to lab members Simon Kolmodin Dahlberg and David Fernandez Bonet on successful graduation and completion of their M.Sc. programs including successful defenses! We welcome them now as doctoral students. We wish you courage, strength, and good luck on your coming journey!

New paper out on the stochastic modeling of antibody multivalent binding: nature.com/articles/s43588-022-00218-z Check out our research briefing on the topic, and KTH news item for a reader-friendly explanation!

We are welcoming three new members: Dr. Erik Benson has joined us for a postdoc after previously being at Oxford as an MSCA Fellow. Shuai Lang who was previously a Master's student at Karolinska Institutet will begin his doctoral studies with us. And KTH M.Sc. student Simon Kolmodin Dahlberg has joined us now for his thesis. Welcome!

A warm welcome and thanks to our first generation of students. KTH students David Fernández Bonet and Simon Kolmodin Dahlberg will each do their Master's thesis with us. And a belated welcome to KI Master's student Li Ma who has worked over the summer and this autumn, establishing the first experiments and infrastructure of our new lab. Amazing job!

The Hoffecker Lab has set up shop in the amazing Gene Technology department at KTH/SciLifeLab. It is a huge honor to be among this stellar group of internationally recognized researchers.

The Hoffecker Lab will officially launch from May 1st 2021 as a new member in the Gene Technology Department, at KTH Royal Institute of Technology on the SciLifeLab campus in Stockholm. The funding making this possible comes from an ERC Starting grant , a starting grant from the Swedish Research Council (VR), co-financing from KTH's School of Engineering Sciences in Chemistry Biotechnology and Health (CBH), central funding from KTH, and a project grant from the Åke Wiberg Foundation.