Bioinformatics career story: Dimitris Konstantopoulos

Patience and excellent communication skills – these are the two most crucial qualities in bioinformatics, according to Dr. Dimitris Konstantopoulos, our Scientific Project Manager. With a background in computer science and over a decade of experience in various molecular biology labs, he now excels as a single-cell analysis expert at Genevia Technologies.

Journey to Bioinformatics

A career in bioinformatics wasn’t an obvious choice for Dimitris Konstantopoulos. Nearing the end of his Bachelor's degree in computer science, he found himself feeling uninspired by the field and its current trends, leading him to reconsider his academic choices. However, discussions with university faculty members opened up two new potential avenues for him: astroinformatics and bioinformatics.

Ultimately, Dimitris chose to pursue a Master's degree in bioinformatics in Athens, Greece, where he still resides. His interest in biology, which began in high school, and the belief that bioinformatics offered more opportunities and a larger community than astroinformatics, guided his decision. He immediately found the studies engaging and joined a bioinformatics lab in his first year.

– My research career began with de novo microRNA identification and microRNA target prediction. Although the lab primarily focused on transcription regulation in vertebrates, my project centered on Ceratitis capitata, the Mediterranean fruit fly. The goal was to control its population by sterilizing the fly with a bacterium, Dimitris explains.

While he enjoyed this work, the research group moved to another institution, and Dimitris began to look for a new lab. He joined BSRC Alexander Fleming as a bioinformatician, eventually becoming a PhD student and then a postdoctoral researcher. His new research focus was on transcriptional and chromatin dynamics in human skin cells during disease perturbations.

– I studied basic mechanisms of the transcription cycle and the elongation rate of RNA polymerase II, for example, and the effects of UV exposure on healthy cells and cells unable to repair themselves, he elaborates.

As one of the few bioinformaticians in Greece at the time, Dimitris became well-known in his field. His expertise grew through collaborations, covering a range of NGS data types. His projects varied from studying autoimmune diseases in humans and mouse models, like lupus erythematosus, multiple sclerosis, and rheumatoid arthritis, to cutaneous squamous cell carcinoma research, building on his previous skin cell studies. He worked with data from a diverse range of common and less common NGS assays, including RNA-Seq, ATAC-Seq, ChIP-Seq, and Gro-seq.

Dimitris's interest gradually shifted towards single-cell analysis, drawn by its higher resolution and the opportunity to develop novel analytical concepts. He gained valuable experience during an EMBO scholarship project at KU Leuven, working with a renowned group in single-cell analysis tool development. He also became the leader of the Single Cell Analysis Unit at BSRC Alexander Fleming, offering single-cell analysis services within the institution, while simultaneously continuing his research.

– Currently, I'm most intrigued by the dynamic inference of gene regulatory networks using multimodal single-cell NGS data, like scRNA-Seq and scATAC-Seq. I’m really into single-cell analysis but I still like projects with bulk assays as well. Ten years in bioinformatics exposes you to a lot of interesting data types and analyses, he says with a smile.

– What I particularly enjoy about bioinformatics are two things. Firstly, receiving a new dataset is always exciting; it contains hidden information and insight, which motivates me to start analyzing it. Secondly, I love the moment when things start making sense, especially discussing and interpreting results with the researcher who conceived the initial idea and hypothesis. This might be the most rewarding part of the job.

Joining Genevia Technologies

Dimitris joined Genevia Technologies as a Scientific Project Manager two years ago. He values the multidisciplinary work environment and the continuous learning opportunities. His single-cell expertise has been vital, and he has explored new areas, like neuroscience. He likes the team and the way everything is organized, which facilitates navigating between different projects.

– These two years have been wonderful. We constantly acquire new clients and projects. I've worked with many scientists, each with unique personalities and interests, fostering a multidisciplinary environment that encourages personal growth and improvement. I enjoy integrating ideas from my projects into new ones, optimizing my approach continuously, he describes.

– Choosing my favorite project at Genevia is challenging, as I'm partial to single-cell projects. However, the two neuroscience projects and a recent spatial transcriptomics project on kidney cells stand out. They've been particularly engaging and challenging, keeping me highly motivated.

Outside of work, Dimitris has various hobbies. He enjoys traveling, especially to mountains and islands, attending concerts, staying active with workouts and basketball, and cooking. He particularly relished a recent company cooking class featuring Finnish cuisine.

So, what makes a good bioinformatician? Speaking from experience, Dimitris highlights two qualities: patience and communication.

– Patience is essential for dealing with unexpected analysis challenges and finding the right pipelines for unique datasets. Equally important is the ability to communicate effectively in this interdisciplinary field. Some scientists lean more towards 'informatics,' while others are closer to 'bio.' It's crucial to bridge these areas through clear communication, ensuring that insights are properly understood and interpreted by all team members. Of course, motivation and hard work are given, but patience and communication truly stand out as the most vital skills in bioinformatics.

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Antti Ylipää
Antti Ylipää CEO, co-founder Genevia Technologies Oy +358 40 747 7672