Natarajan Laboratory
Exploring the single-cell interplay between cell cycle and gene expression during embryonic development.
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Our research

The Natarajan laboratory investigates the fundamental process of cell cycle during embryonic development at single-cell level. We focus on understanding how the crosstalk between cell cycle and gene expression influences cell-state and fate decisions in embryonic stem cells.

We apply and develop a wide variety of experimental and computational tools to study mechanisms involved in stem cells state and during their differentiation. These bulk and single-cell approaches include advanced molecular biology, state-of-art imaging, Flow cytometry, genome editing and variety of single-cell functional genomics methods. Our research aims to gain a deeper ‘system biology’ single-cell view of biological systems.

"Simply, we study how a single fertilized cell divides, scales and generates an incredible complexity and numbers of cell types, tissues and organs during embryonic development."

Areas of research

Cell cycle control of transcriptional regulation

We study how transcriptional regulation is governed globally during cell cycle and across phases in embryonic stem cells at single-cell level.
We utilise FUCCI cell cycle sensors combined with candidate gene perturbation and single-cell profiling to understand different mechanisms involved in cell cycle regulation of pluripotency.

Cell cycle dynamics during differentiation

Distinct cell cycle changes accompany stem cell differentiation and can drive cell-fate responses.
We combine state-of-art single-cell methods to investigate how underlying single-cell gene expression dynamics contribute to cell-fate decisions.

New methods for single-cell biology

We have a strong interest in development, extension and utilisation of new experimental and computational methods for single-cell biology.
Working closely with collaborators, we develop new computational tools that integrate measurements from several single-cell technologies.

Our Team

Kedar Natarajan

Group Leader

Simon Jakobsen

PhD student

Valentina Hekimova

Master's student

Maja Brask

Bachelor student

Andreas Møller

Master’s student

Felix Pedersen

Master’s student

Join us!

We are always interested in passionate, talented and inquisitive students (Bachelors, ISA, Masters and PhD), Post-doctoral fellows and visitors interested in single-cell, systems and developmental biology, computational modelling and big data analysis to join our team.
If you are interested in our lab, please email a tailored cover letter, highlighting your specific interest and motivation to Kedar Natarajan (



A rapid and robust method for single cell chromatin accessibility profiling.

Chen X, Miragaia RJ, Natarajan KN, Teichmann SA.
Published in: Nat Communications.

Comparative analysis of sequencing technologies platforms for single-cell transcriptomics.

Natarajan KN, Zhichao M, Jiang M, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Li B, Hou Y, Liu S, Teichmann SA.
Published in: bioRxiv.

Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.

Pramanik J, Chen X, Kar G, Henriksson J, Gomes T, Park JE, Natarajan K, Meyer KB, Miao Z, McKenzie ANJ, Mahata B, Teichmann SA.
Published in: Genome Medicine.

Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.

Tuck AC, Natarajan KN, Rice GM, Borawski J, Mohn F, Rankova A, Flemr M, Wenger A, Nutiu R, Teichmann SA, Bühler M
Published in: Life Science Alliance.

Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development.

Oatley M, Bolukbasi OV, Valentine Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV , Milchevskaya V, Foteva V, Natarajan KN, Baying B, Benes B, Patil KR, Teichmann SA, Lancrin C.
Published in: bioRxiv.

The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.

Pramanik J, Chen X, Gozde K, Gomes T, Henriksson J, Miao Z, Natarajan KNN, McKenzie ANJ, Mahata B, Teichmann SA.
Published in: bioRxiv.


Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.

Natarajan KN#, Teichmann SA, Kolodziejczyk AA.
Published in: Current Opinion of Genetics and Development .

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA
Published in: Nature Communications.

SC3: consensus clustering of single-cell RNA-seq data

Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M.
Published in: Nature Methods.

Cell biology: tracking a cell’s cycle

Natarajan KN and Teichmann SA (Journalistic feature)
Published in: Nature methods.

Postdocs: What would you tell your younger self.

Natarajan KN (Special feature comment)
Published in: Cell.

Power analysis of single-cell RNA-sequencing experiments.

Svensson V*, Natarajan KN*, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA.
Published in: Nature Methods.


Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T, Svensson V, Pramanik J, Natarajan KN, Zhai W, Zhang X, Donati G, Kayikci M, Kotar J, McKenzie AN, Montandon R, Billker O, Woodhouse S, Cicuta P, Nicodemi M, Teichmann SA.
Published in: Genome Biology.

The systems biology format converter.

Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N.
Published in: BMC Biology.


Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA
Published in: Cell Stem Cell.

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F
Published in: Methods.

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Buettner F*, Natarajan KN*, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O.
Published in: Nature Biotechnology.


BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C
Published in: Nucleic Acid Research.


The System Biology Format Converter.

Jalowicki G, Rodriguez N, Kutmon M, Pettit JB, Li L, Henry A, Natarajan KN, Laibe C, Evelo CT, Novere NL
Published in: Nature Precedings.


  • Welcome to Natarajan Lab!

    The Natarajan laboratory officially starts at Functional Genomics and Metabolism Unit. In the coming months, we will set up experimental capabilities for stem cell work, single-cell genomics and computational analysis of single-cell data.

  • Welcome Valentina!

    Valentina Hekimova is starting in the lab from September 2018 for a year to pursue her Master’s thesis. She is currently studying Masters in Computational Biomedicine at SDU and has a background in software development. Valentina will be working on computational analysis of single-cell omics datasets

  • Welcome Maja!

    Maja Brask joins the lab from September 2018 for an ISA project. Maja currently studies Biochemistry and Molecular Biology at SDU and is interested in functional genomics, CRISPR and stem cell biology.

  • Welcome Simon!

    Simon Jakobsen is starting as a PhD student in the lab. Simon is an molecular biologist with interest in innovative usages of Next Generation Sequencing and data-science.

  • Welcome Andreas!

    Andreas Møller joins the lab from September 2018 for a joint Master's project with Grøntved Lab. Andreas is currently pursuing his studies at Sino Danish Center, and he is interested in computational analysis of single-cell RNA-seq data.

  • Welcome Felix!

    Felix Boel Pedersen will be starting in the lab from February 2019 for his Master’s project and thesis. Felix is currently studying Masters in Computational Biomedicine at SDU and has a strong interest in gene editing methods. He will be working on CRISPR-based gene targeting methods and single-cell transcriptomics.

  • Natarajan lab receives NNF Project Grant

    The Natarajan lab was awarded the Novo Nordisk Foundation Project grant in Bioscience and Basic Biomedicine 2018. Congratulations!!!

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Our research is possible due to generous support form:

Contact Us

We are based in the Functional Genomics and Metabolism Unit , within Department of Biochemistry and Molecular Biology at the University of Southern Denmark, which is a great place to start and progress a scientific career in science. We are an interdisciplinary team where we learn and integrate both experimental and computational approaches to address fundamental biological questions.

Natarajan Laboratory
Functional Genomics and Metabolism Unit,
Department of Biochemistry and Molecular Biology
University of Southern Denmark
Campusvej 55, 5230 Odense, Denmark
+45 6550 8929