Johan Henriksson (Group leader)

Computational jack of all trades, with a recent love for the pipette.

Got an MSc in mechanical engineering from Chalmers, aimed at taking over family business, but the studies derailed. Ended up getting degrees in mathematics and computer science, among other, in addition. Somewhat randomly ended up with a hobby project on speciation and realized biology was the place to be if you are computational. Did a PhD working on microscopy for C.elegans at the Karolinska Institut. Realized this wasn’t the most efficient approach and went to learn single-cell RNA-seq at the Sanger Institute as a postdoc. Decided it was time to also do wet lab work. Was working on single-cell methodology but got stuck on a CRISPR-related project; this became the new speciality, with a focus on T cells. Still didn’t have enough of the academic experience and decided T cells would be a good model system of choice to go back and do regulatory modelling – full circle back to the speciation project, just completely different equations!

On the spare-time, only have the hobby of collecting hobbies (including now for example dancing, sawing, cooking, playing guitar and other typically Swedish macho male pastimes). General provider of banter, irony and dad humour.

ORCID 0000-0002-7745-2844, Github account

Ira Yakovenko (postdoc) – details to follow

Martin Selinger (postdoc) – Email

Molecular biologist/virologist trying to uncover the secrets of Python. Working on CRISPR screens in human T-cells for identification of helper genes, which might be useful in CAR T-cell design. As a typical Czech guy, loves beer and good food.

Sebastian Mihai (Moist project assistant) – Email

Biologist, now doing 50/50 wet-dry work (“moist”), because learning just one side was too simple.

Likes driving. Deploys robotic minions.

MR ROBOT (Pipetting robot)

Highly equipped OT-2 system

Does the work while the rest are off drinking coffee or hacking on new algorithms. Has a particular appetite for 96-well plates but considers the 384-diet. Does up to 200ul volumes on a regular basis, especially when 80% ethanol is involved, but otherwise works down to 5ul. Less if needed. Doesn’t have much patience and usually goes with the 8-channel pipette. Though 1-channel pipettes available for all our cherry-picking or normalization needs.

Happy to also play with other groups at MIMS and Umeå University, as long they feed me well!

Friends of mine in the lab includes, among other, a Mantis dispenser, and several single-cell library prep systems.

Students / Internships:

Current:

2023 – Agata Jasna; master thesis on high-throughput bacteria genome sequencing
2023 – Sarang Chafle; intership on T cells
2023 – Henrietta Hellberg; master thesis on NLP
2023 – Ebba Hellberg; master thesis on NLP

2022 – Hien Minh To; master thesis on CRISPR screening
2022 – Mara Blanco Arauzo; master thesis on CRISPR screening
2022 – Jan Hoffman; master thesis on CRISPR screening methods development
2022 – Iqra Nazir; master thesis on padlock probes for CRISPR screening
2022 – Angele Ahebla; master thesis on polycomb regulation of T cell activation

Past:

2022 – Linnea Borg; project work on padlock probes for CRISPR screening
2022 – Iqra Nazir; master thesis on padlock probes for CRISPR screening
2022 – Willem de Chateau; master thesis on how well the T cell transcriptome correspond chromatin accessibility
2022 – Oliwia Mruk; project work on hypoxia
2022 – Sarah Narrowe Danielsson; master thesis on VAEs
2022 – Filippe Seiz De Filippi; master thesis on mutiomic data integration
2022 – Arek Sahal; master thesis on mutiomic data integration
2022 – Enzo Giacopino; master thesis on CRISPR screening methods development

2021 – Kristina Krank; internship on CRISPR screening methods development
2021 – Hayoung Lee; master thesis on CRISPR screening methods development
2021 – William Rosenbaum; mixed wet-dry lab master thesis on microRNA regulation of CD4+ T cells
2021 – Nagham Saleh; master thesis in single-cell analysis
2021 – Annica Pedersen; single-cell internship – Forskaraspiranterna
2021 – Eleonora Hedin; single-cell internship
2021 – Illia Simutin; single-cell internship
2021 – Johan Lehto, Mathias Jonsson, Agata Jasna, Tiam Fitoon, Johan Lundberg & Elsa Renström – DBT2021 project students; automating SPRI cleaning on the OT2-robot
2021 – Anna Münch; rotation project on single-cell analysis and advanced CRISPR screening
2021 – Jonathan Persson; thesis project on machine learning
2021 – Laura Plutowski; rotation project on single-cell analysis
2021 – Mattias Wassbjer; thesis project on machine learning. Prediction of RNA levels given gene sequence
2021 – Fanny Gustavsson; summer course on padlock probes / isothermal amplification
2021 – Yanka Rabelo; thesis project on lentivirus production for gene perturbation
2021 – Lisabeth Emilius; thesis project on ATAC-seq wet lab implementation and analysis

2020 – Zinzou Maëva; Single-cell analysis, CellPhoneDB
2020 – Hanna Olsson, Leonardo Monrroy Perez, Rasmus Burge & Yanka Rabelo – DBT2019 project students; predicting RNA binding protein activity from RNA-seq data.

Alumni:

Debojyoti Das (Computational postdoc)

Sarah Narrowe Danielsson (Computational project assistant)

Nicolò Lazzaro (Computational project assistant)

Luisa F. Corredor-Arias (Postdoc / Wetlab guru)

Anton Björk (Computational project assistant)