Publications

Selected peer-reviewed publications.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes
J Markowski , Alexander Kukalev , C Robens , CJ Thieme , A Streck , H Mao , KM Parsi , R Maehr , Ana Pombo , RF Schwarz
bioRxiv (2026)
URL
BibTeX 
@article{Markowski2026,
  title={Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes},
  author={Markowski J, Kukalev A, Robens C, Thieme CJ, Streck A, Mao H, Parsi KM, Maehr R, Pombo A, Schwarz RF},
  year={2026}
}
Specialised super-enhancer networks in stem cells and neurons.
Izabela Harabula , L Speakman , F Musella , L Forillo , Luna Zea Redondo , Alexander Kukalev , RA Beagrie , KJ Morris , L Fernandes , Ibai Irastorza-Azcarate , AM Fernandes , S Carvalho , Dominik Szabo , C Ferrai , M Nicodemi , L Welch , Ana Pombo
bioRxiv (2026)
URL
BibTeX 
@article{Harabula2026,
  title={Specialised super-enhancer networks in stem cells and neurons.},
  author={Harabula I, Speakman L, Musella F, Forillo L, Zea-Redondo L, Kukalev A, Beagrie RA, Morris KJ, Fernandes L, Irastorza-Azcarate I, Fernandes AM, Carvalho S, Szabo D, Ferrai C, Nicodemi M, Welch L, Pombo A.},
  year={2026}
}
Extensive folding variability between homologous chromosomes in mammalian cells.
Ibai Irastorza-Azcarate , Alexander Kukalev , R Kempfer , CJ Thieme , G Mastrobuoni , J Markowski , G Loof , TM Sparks , E Brookes , KN Natarajan , S Sauer , AG Fisher , M Nicodemi , B Ren , RF Schwarz , S Kempa , Ana Pombo
Mol Syst Biol (2025)
URL
BibTeX 
@article{Irastorza2025,
  title={Extensive folding variability between homologous chromosomes in mammalian cells.},
  author={Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A.},
  year={2025}
}
A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons
Dominik Szabo , V Franke , S Bianco , MY Batiuk , EJ Paul , Alexander Kukalev , UG Pfisterer , Ibai Irastorza-Azcarate , AM Chiariello , S Demharter , Luna Zea Redondo , JP Lopez-Atalaya , M Nicodemi , A Akalin , K Khodosevich , MA Ungless , Warren Winick-Ng , Ana Pombo
bioRxiv (2024)
URL
BibTeX 
@article{Szabo2024,
  title={A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons},
  author={Szabo D, Franke V, Bianco S, Batiuk MY, Paul EJ, Kukalev A, Pfisterer UG, Irastorza-Azcarate I, Chiariello AM, Demharter S, Zea-Redondo L, Lopez-Atalaya JP, Nicodemi M, Akalin A, Khodosevich K, Ungless MA, Winick-Ng W, Pombo A.},
  year={2024}
}
SRRM2 splicing factor modulates cell fate in early development
S Carvalho , Luna Zea Redondo , TCC Tang , P Stachel-Braum , D Miller , P Caldas , Alexander Kukalev , S Diecke , S Grosswendt , AR Grosso , Ana Pombo
Biol Open (2024)
URL
BibTeX 
@article{Carvalho2024,
  title={SRRM2 splicing factor modulates cell fate in early development},
  author={Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A.},
  year={2024}
}
SRRM2 splicing factor modulates cell fate in early development
S Carvalho , Luna Zea Redondo , TCC Tang , P Stachel-Braum , D Miller , P Caldas , Alexander Kukalev , S Diecke , S Grosswendt , AR Grosso , Ana Pombo
Biol Open (2024)
URL
BibTeX 
@article{Carvalho2024,
  title={SRRM2 splicing factor modulates cell fate in early development},
  author={Carvalho S, Zea-Redondo L, Tang TCC, Stachel-Braum P, Miller D, Caldas P, Kukalev A, Diecke S, Grosswendt S, Grosso AR, Pombo A.},
  year={2024}
}
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
RA Beagrie , CJ Thieme , C Annunziatella , C Baugher , Y Zhang , M Schueler , Alexander Kukalev , R Kempfer , AM Chiariello , S Bianco , Y Li , T Davis , A Scialdone , LR Welch , M Nicodemi , Ana Pombo
Nat Methods (2023)
URL
BibTeX 
@article{Beagrie2023,
  title={Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C},
  author={Beagrie RA, Thieme CJ, Annunziatella C, Baugher C, Zhang Y, Schueler M, Kukalev A, Kempfer R, Chiariello AM, Bianco S, Li Y, Davis T, Scialdone A, Welch LR, Nicodemi M, Pombo A.},
  year={2023}
}
Cell-type specialization is encoded by specific chromatin topologies.
Warren Winick-Ng , Alexander Kukalev , Izabela Harabula , Luna Zea Redondo , Dominik Szabo , M Meijer , L Serebreni , Y Zhang , S Bianco , AM Chiariello , Ibai Irastorza-Azcarate , CJ Thieme , TM Sparks , S Carvalho , L Fiorillo , F Musella , E Irani , E Torlai Triglia , AA Kolodziejczyk , A Abentung , G Apostolova , EJ Paul , V Franke , R Kempfer , A Akalin , SA Teichmann , G Dechant , MA Ungless , M Nicodemi , L Welch , G Castelo-Branco , Ana Pombo
Nature (2021)
URL
BibTeX 
@article{Winick-Ng2021,
  title={Cell-type specialization is encoded by specific chromatin topologies.},
  author={Winick-Ng W, Kukalev A, Harabula I, Zea-Redondo L, Szabo D, Meijer M, Serebreni L, Zhang Y, Bianco S, Chiariello AM, Irastorza-Azcarate I, Thieme CJ, Sparks TM, Carvalho S, Fiorillo L, Musella F, Irani E, Torlai Triglia E, Kolodziejczyk AA, Abentung A, Apostolova G, Paul EJ, Franke V, Kempfer R, Akalin A, Teichmann SA, Dechant G, Ungless MA, Nicodemi M, Welch L, Castelo-Branco G, Pombo A.},
  year={2021}
}
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