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

Deyong Zhu


Simon Jakobsen

PhD student

Andreas Møller

PhD Student

Maja Brask

Master student


Valentina Hekimova

Master's student

Felix Pedersen

ISA student

Join us!

We welcome enquiries from highly interdisciplinary, motivated and ambitious candidates.

Postdocs candidates with strong background and interest in areas of single-cell genomics, computational biology and machine learning are welcome to enquire informally on lab projects. We encourage and support applications to Danish and international funding agencies. Please email a tailored cover letter, CV, publication record and details of two references

Interested PhD students are also welcome to enquire about applying for funding. The lab accepts 1-2 students (Masters, ISA and Bachelors) every year. Please email directly.



TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data.

Kim J, Jakobsen ST, Natarajan KN# and Won KJ#
Published in: Nucleic Acid Research.

Predicting gene regulatory networks from cell atlases

Moeller AF and Natarajan KN#
Published in: Life Science Alliance.

SBML Level 3: an extensible format for the exchange and reuse of biological models

Keating SM, Waltemath D, et al., and SBML Level 3 Community members
Published in: Molecular Systems Biology.

Transcriptional dynamics of hepatic sinusoid‐associated cells after liver injury.

Terkelsen MK, Bendixen SM, Hansen D, Scott EAH, Moeller AF, Nielsen R, Mandrup S, Schlosser A, Andersen TL, Sorensen GL, Krag A, Natarajan KN, Detlefsen S, Dimke H, Ravnskjaer K
Published in: Hepatology.

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.

Cuomo SE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O.
Published in: Nature Communications.

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

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


The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle.

Howick VM, Russell AJC, Andrews T, Heaton H, Reid AJ, Natarajan K, Butungi H, Metcalf T, Verzier LH, Rayner JC, Berriman M, Herren JK, Billker O, Hemberg M, Talman AM, Lawniczak MKN.
Published in: Science.

Comparative analysis of sequencing technologies for single-cell transcriptomics.

Natarajan KN*#, Miao Z*, Jiang M*, Huang X, Zhou H, Xie J, Wang C, Qin S, Zhao Z, Wu L, Yang N, Li B, Hou Y, Liu S, Teichmann SA#.
Published in: Genome Biology.

Single-Cell Tagged Reverse Transcription (STRT-Seq).

Natarajan KN#.
Published in: Methods in Molecular Biology.


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

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

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 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.


  • (2018) Welcome to Natarajan Lab!

    The Natarajan laboratory officially starts at Functional Genomics Unit at SDU. We look forward to setting up setting up single-cell experimental and computational capabilities for stem cells and single-cell genomics.

  • (2018) Welcome Valentina, Maja, Simon and Andreas!

    September: Valentina Hekimova and Andreas Møller are starting their Masters thesis projects. Maja Brask starts her individual study assignment (ISA) and Simon Jakobsen is starting his PhD.
    Welcome Valentina, Andreas, Maja and Simon

  • (2019) Natarajan lab receives external funding!

    The Natarajan lab was awarded the NNF Bioscience and Basic Biomedicine project grant and Villum Young Investigator award. Congratulations!!!

  • (2019) Congratulations Valentina and Andreas!

    Valentina Hekimova and Andreas Møller both succesfully defended their Masters thesis. Valentina will be changing fields and pursuing her interests in software design and consulting. We wish you best!!
    Andreas will re-join the lab as PhD student. Welcome back!

  • (2019) Natarajan lab receives collaborative grant!

    The Natarajan lab was awarded the NNF Synergy grant along with Brewer (SDU), Sedzinski (KU) and Kutter (KU) labs. Congratulations to all!!!

  • (2020) Congratulation Andreas !

    Andreas Møller received Sino Danish Centre funding to begin his PhD in the lab and also published his first author paper
    Double Congratulations !!

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Our research is possible due to generous support form:

Contact Us

We are based at Functional Genomics Unit , within Department of Biochemistry and Molecular Biology at the University of Southern Denmark.

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