Bioinformatics career story: Fredrik Salmén
Scientific Project Manager Dr. Fredrik Salmén is our transcriptomics specialist, with an impressive background in developing and applying spatial and single-cell transcriptomics methods. At Genevia, he thrives on combining his computational expertise with interdisciplinary communication skills to solve complex data analysis challenges for clients across both academic research and industry.
A Non-Linear Path to Bioinformatics
Bioinformatics wasn’t an obvious choice for Dr. Fredrik Salmén. Until the last six months of his Master’s in biotechnology at KTH Royal Institute of Technology in Stockholm, Sweden, academic research wasn’t even on his radar. That all changed during his Master’s thesis project, which happened to involve spatial transcriptomics: a field that immediately captured his interest and set him on a new course.
– To be honest, before I started my thesis, I had absolutely no idea what I wanted to do. But during that project, I realized I really wanted to pursue a PhD, he recalls.
Dr. Fredrik Salmén
Fredrik’s PhD officially began 1.5 years later, after initially working on the project under scholarship funding. The work was a collaboration between Prof. Joakim Lundeberg at KTH and Prof. Jonas Frisén and Dr. Patrik Ståhl at the Karolinska Institute. Building on his thesis, Fredrik contributed to a major success: together with colleagues, he developed a spatial transcriptomics technology that later caught the attention of 10x Genomics and was eventually commercialized as Visium.
The technology involves placing tissue sections onto a slide embedded with oligonucleotides with positional barcodes. After permeabilizing the tissue and applying reverse-transcription reagents, cDNA is synthesized directly on the surface. This spatially barcoded cDNA is sequenced, enabling the mapping of gene expression patterns across the tissue while preserving the original spatial context.
– We worked for this project for six years–it was tough, but also a lot of fun, Fredrik says.
Engineering Spatial Transcriptomics—From Lab to Laptop
Fredrik’s PhD began with a focus on wet lab work, but as the project progressed and sequencing data started coming in, his curiosity about the computational side grew.
– I didn’t like being limited to only one part of the project: I had no say–and didn’t understand–what was happening computationally, so I started learning it. I took a Python course and picked up R on my own, and most importantly, asked a lot of questions from people around me. That’s how I got into bioinformatics and became a hybrid researcher doing both lab work and data analysis, he explains.
His academic focus remained on method development, leaning more toward molecular technologies than biology itself.
– During my PhD, I felt like my brain didn’t have the capacity for biology on top of everything else, he laughs.
Despite the repetitive nature of lab work, Fredrik values the skills he gained—especially the moments when collaborative brainstorming led to breakthroughs. One such moment stands out clearly:
– I was in a meeting with my PI, Joakim Lundeberg, and we were wondering how to prove RNA could be captured and converted to cDNA on the surface. Joakim asked whether it would be possible to somehow mark the RNA or cDNA, and I got the idea: why don’t we use fluorescent nucleotides for the cDNA synthesis?
That’s what they did, and after just two tries, a fluorescent pattern appeared in the perfect shape of a mouse olfactory bulb (part of the mouse brain).
– That was the moment we all knew it would work, and even people who had doubted the project were finally convinced. It is so fascinating how these kinds of ideas come together: it’s rarely one person inventing the whole thing from scratch, but rather a process where bits and pieces suddenly click.
The team spent time trying to create high-resolution chips with spatial barcodes, but persistent quality issues led them to switch to microarray-style printing using high-quality oligos from a trusted supplier. This enabled spatial transcriptomics at a "mini-bulk" resolution of 10–100 cells.
– We tested countless reagents and conditions, so it was very satisfying to finally see it work—even without achieving single-cell resolution.
The developed spatial transcriptomics method was published in 2016 in Science.
From Spatial to Single-Cell Transcriptomics
After completing his PhD, Fredrik was ready for a change and moved to Utrecht, Netherlands, joining the lab of Professor Alexander van Oudenaarden. Given creative freedom to develop a new project, he devised a single-cell technology that became VASA-seq, a method for full-transcriptome single-cell RNA sequencing.
– I wanted to apply it to FFPE samples, but Alexander wisely suggested starting with regular single cells. I modified an existing method, CEL-seq, and built from there. That’s often how development works—rethinking what already exists.
As in his PhD, Fredrik again played a dual role in both lab work and data analysis. Towards the end of the project, he also got the opportunity to collaborate with highly skilled computational scientists, gaining valuable insights that continued to support his learning even afterward.
The VASA-seq method was published in 2022 in Nature Biotechnology.
Taking a Break and Finding His Way to Genevia
After four years in the Netherlands, Fredrik needed a break. He relocated to Cyprus—where he’s still based—and began working as an Airbnb host.
– Honestly, it was a lazy and boring job, he laughs.
– But it gave my brain a chance to rest.
After a year, he re-entered science, working remotely as an R&D consultant for Single-Cell Discoveries, a contract research organization focused on single-cell sequencing. Unfortunately, budget cuts ended the collaboration after 1.5 years.
That’s when he discovered Genevia Technologies on LinkedIn.
– I wasn’t sure if I should apply—I’d never been a full-time bioinformatician. I contacted a recruiter on LinkedIn who helped me: she was familiar with Genevia and sent my CV their way.
Fredrik recalls his first interview with Genevia’s CEO Antti Ylipää fondly:
– It was relaxed and warm. Antti seemed to be evaluating my communication skills more than my technical ones. It was very encouraging when Antti sent me to the second interview almost immediately, Fredrik says.
The second round involved a technical presentation, which Fredrik prepared with help from friends.
– I couldn’t answer every question, but I was honest. Thankfully, they appreciated that, and I was thrilled to get the offer soon after.
A Happy Return to Spatial Transcriptomics
At Genevia, Fredrik works on diverse projects, but his specialties remain spatial, single-cell, and bulk transcriptomics.
– For years, I wanted nothing to do with spatial transcriptomics. But now I’m back, and I’m really enjoying it. The field is still young—there’s no one ‘best’ technology, but each has their strengths and weaknesses. For instance, brain tissue works nicely for all of the technologies, but muscle is more challenging due to its length and tendency to dry quickly. Tumor samples can yield interesting spatial information, but it can be quite chaotic: there are invasive cells and infiltrating immune cells, for example.
He especially appreciates projects with strong client collaboration. One highlight was a CosMx project that overcame early hurdles to deliver impactful results. Another involved studying transcription factors in cardiac development—a topic he found rewarding to explore.
– Sometimes I even feel like part of the client’s team. Sharing results that make them happy—that’s the best part. Of course, I love data analysis, but it’s the human connection that makes it truly fulfilling.
Although Fredrik felt pressure when he first joined Genevia, that quickly faded.
– As a newcomer, you want to prove yourself. But after a few months, the stress eased. What I really appreciate is Genevia’s flexibility: as long as you communicate, do your hours, and deliver, you can also take time off when needed – the company trusts and respects us, which reduces a lot of stress.
– Also, it’s important to keep in mind that no one can work at 100% every minute of the day without burning out.
Life Beyond Science
Outside of work, Fredrik’s passions include surfing, motorcycles, caring for his two cats, and—most importantly—spending time with his 6-year-old son.
– I love being a dad. My son is so fun to be around and listen to; he has such creative ideas and questions I’d never think of.
Reflecting on alternate career paths, Fredrik says psychology might have been his second choice.
– I took a class during an exchange year in the US and really enjoyed it. Interestingly, I now do some sales and marketing at Genevia, which involves a lot of psychology. We’re encouraged to pursue self-development here, so I chose to focus on that area. It’s great to have the opportunity to explore beyond just analysis.
– Then of course, there could be work related to surfing or motorcycles, but I think it’s important to keep some things just as hobbies, to ensure that the joy in them remains.
For aspiring bioinformaticians, Fredrik has a piece of advice:
– A PhD is a good foundation, even if you don’t want to stay in academia. It teaches problem-solving and stress management. But only do it if you really want to—honestly, it’s going to be stressful. Also, if you’re focused on bioinformatics, try to get some lab experience: do some pipetting and run some experiments, to understand what’s happening there and how it affects what you see on the computer. Likewise, if you’re a lab scientist, try to learn at least some basic bioinformatics. Understanding both sides of the workflow is incredibly valuable.
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