My research is focused on developing Systems Biology and Machine Learning studies with Life Science applications. My group conducts computational model development and experimental data analyses for various biomedical areas.
Research
My current interest is to propose original modelling techniques linked to experimental data to elucidate mechanisms governing:
- commitment of T-cell progenitors
- direct conversion of adult fibroblast cells into neurones and glia cells
- reprogramming of mouse embryonic fibroblast cells into induced pluripotent stem (iPS) cells
- 3D modelling of the neural tube development
- Machine Learning for tumour classifications and measurement
- Machine Learning for revealing cell identity genes and oncogenes from epigenetic data
Teaching
- Systems Biology - Models and Computations BERN
- Computational Physics FYTN03
- Biologiska System EXTQ20
- Computational Science: Modelling in Computational Science BERN01
People
Current – Computational Modelling
- Emil Anderson
- Paulina Ibek
- Alexander Degener
- Alice Fracchia
- Anna-Lena Hölldobler
- Enver Lee
- Guillermo Velez
Current – Wet Lab Collaborators
- Prof. Ellen Rothenberg
- Prof. Malin Parmar
- Prof. Agnete Kirkeby
- Prof. Keisuke Kaji
- Dr. Janelle Drouin-Ouellet
- Dr. Daniella Ottosson
- Prof. Malin Malmsjö
- Dr. Alin Tomoiaga
Past – Computational Modelling
- Joakim Eriksson
- Annika Lund Gade
- Cecilia Lövkvist
- Julia Nilsson
- Julia Deichmann
- Johannes Isaksson
- Mattias Sjö
- Mårten Bertenstam
- Viktor Drugge
- Adriaan Merlevede
- Max Brambach
- Ariane Ernst
- Jonas Petersson
- Fredrik Bertilsson
- Valentin Nguyen-Flor
- Daesung Cho
- Yukun Cheng
- Marc Pielies Avelli
Past – Wet Lab Collaborators
- Prof. Peter Andrews
- Prof. Tariq Enver
- Prof. Josh Brickman
Publications
Displaying of publications. Sorted by year, then title.
A distinct lineage pathway drives parvalbumin chandelier cell fate in human interneuron reprogramming
Christina A Stamouli, Alexander Degener, Efrain Cepeda-Prado, Andreas Bruzelius, Emil Andersson, et al.
(2026) Science Advances, 12
ArticleThree-dimensional co-culturing reveals human stem cell-derived somatostatin interneurons with subclass expression
Andreas Bruzelius, Christina Anastasia Stamouli, Anna Lena Hölldobler, Constanza Aretio-Medina, Efrain Cepeda-Prado, et al.
(2025) Stem Cell Reports, 20
ArticleAdvancing non-invasive melanoma diagnostics with deep learning and multispectral photoacoustic imaging
Aboma Merdasa, Alice Fracchia, Magne Stridh, Jenny Hult, Emil Andersson, et al.
(2025) Photoacoustics, 45
ArticleA spectroscopy-based machine learning framework on photoacoustic imaging data for automatic 3D delineation of melanoma tumors
Aboma Merdasa, Alice Fracchia, Magne Stridh, Jenny Hult, Emil Andersson, et al.
(2025) Progress in Biomedical Optics and Imaging - Proceedings of SPIE
Paper in conference proceedingFacilitating clinically relevant skin tumor diagnostics with spectroscopy-driven machine learning
Emil Andersson, Jenny Hult, Carl Troein, Magne Stridh, Benjamin Sjögren, et al.
(2024) iScience, 27
ArticleT-cell commitment inheritance—an agent-based multi-scale model
Emil Andersson, Ellen v. Rothenberg, Carsten Peterson, Victor Olariu
(2024) npj Systems Biology and Applications, 10
ArticleB1 SINE-binding ZFP266 impedes mouse iPSC generation through suppression of chromatin opening mediated by reprogramming factors
Daniel F. Kaemena, Masahito Yoshihara, Meryam Beniazza, James Ashmore, Suling Zhao, et al.
(2023) Nature Communications, 14 p.488
ArticleCELLoGeNe - An energy landscape framework for logical networks controlling cell decisions
Emil Andersson, Mattias Sjö, Keisuke Kaji, Victor Olariu
(2022) iScience, 25
ArticleA quantitative model of cellular decision making in direct neuronal reprogramming
Adriaan Merlevede, Emilie M. Legault, Viktor Drugge, Roger A Barker, Janelle Drouin-Ouellet, et al.
(2021) Scientific Reports, 11
ArticleNeural tube patterning : from a minimal model for rostrocaudal patterning toward an integrated 3D model
Max Brambach, Ariane Ernst, Sara Nolbrant, Janelle Drouin-Ouellet, Agnete Kirkeby, et al.
(2021) iScience, 24
ArticleMulti-scale Dynamical Modeling of T Cell Development from an Early Thymic Progenitor State to Lineage Commitment
Victor Olariu, Mary A. Yui, Pawel Krupinski, Wen Zhou, Julia Deichmann, et al.
(2021) Cell Reports, 34
ArticleKinetic models of hematopoietic differentiation
Victor Olariu, Carsten Peterson
(2019) Wiley interdisciplinary reviews. Systems biology and medicine, 11 p.e1424
Review articleDifferent reprogramming propensities in plants and mammals: Are small variations in the core network wirings responsible?
Victor Olariu, Julia Nilsson , Henrik Jönsson , Carsten Peterson
(2017) PLoS ONE
ArticleA deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths
Victor Olariu, Erica Manesso, Carsten Peterson
(2017) Royal Society Open Science, 4
ArticleNanog, Oct4 and Tet1 interplay in establishing pluripotency
Victor Olariu, Cecilia Lövkvist, Kim Sneppen
(2016) Scientific Reports, 6
ArticleA somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network.
Eduardo Anguita, Rajeev Gupta, Victor Olariu, Peter J Valk, Carsten Peterson, et al.
(2016) Developmental Biology, 411 p.277-286
ArticleDynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors
Gillian May, Shamit Soneji, Alex J. Tipping, José Teles, Simon J. McGowan, et al.
(2013) Cell Stem Cell, 13 p.754-768
ArticleProbing the role of stochasticity in a model of the embryonic stem cell - heterogeneous gene expression and reprogramming efficiency
Vijay Chickarmane, Victor Olariu, Carsten Peterson
(2012) BMC Systems Biology, 6
ArticleModeling the evolution of culture-adapted human embryonic stem cells
Victor Olariu, Neil J. Harrison, Daniel Coca, Paul J. Gokhale, Duncan Baker, et al.
(2010) Stem Cell Research, 4 p.50-56
ArticlePrepatterning in the stem cell compartment
Peter D. Tonge, Victor Olariu, Daniel Coca, Visakan Kadirkamanathan, Kelly E. Burrell, et al.
(2010) PLoS ONE, 5
ArticleModelling Stem Cells Lineages with Markov Trees
Victor Olariu, Daniel Coca, Stephen A. Billings, Visakan Kadirkamanathan
(2009) Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) , p.233-243
Paper in conference proceedingModified variational bayes EM estimation of hidden markov tree model of cell lineages
Victor Olariu, Daniel Coca, Stephen A. Billings, Peter Tonge, Paul Gokhale, et al.
(2009) Bioinformatics, 25 p.2824-2830
Article
Member of COSHE
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