Enge lab publications

Publication list

26 original peer-reviewed publications (3 in Cell, 2 in Science, 1 in Nature), 2 software packages.

Number of citations: 7597 (Google scholar Oct 11th, 2021)

Average number of citations per publication: 292

H-index: 19 (Google scholar Oct 11th , 2021)

5-year H-index - only citations in last 5 years: 18 (Google scholar Oct 11th , 2020)

Google scholar 

Selected publications, reverse chronological order

1. An unsupervised and broadly applicable method for physical cell interaction profiling of complex tissues.

Nathanael Andrews, Jason Tyler Serviss, Natalie Geyer, Agneta Andersson, Ewa Dzwonkowska,  Rosan Heijboer, Ninib Baryawno, Marco Gerling, Martin Enge.

Nature Methods volume 18, 912–920 (2021)

2. Spinal Cord Injury Induces Permanent Re-Programming of Microglia into a Disease-Associated State which Contributes to Functional Recovery

   Hakim R, Zachariadis V, Sankavaram SR, Han J, Harris RA, Brundin L, *Enge M and *Svensson M; * corresponding authors

Journal of Neuroscience 20 August 2021, JN-RM-0860-21; 

3. A highly scalable method for joint whole genome sequencing and gene expression profiling of single cells. Vasilios Zachariadis, Huaitao Cheng, Nathanael J Andrews, Martin Enge

Molecular Cell, 80:3, 5 Nov. 2020. pp541-553.e5

4. Modeling spatial Correlation of transcripts with Application to Developing pancreas

Ruishan Liu, Marco Mignardi, Robert Jones, Martin Enge, Seung K Kim, Stephen R Quake, James 


Scientific Reports, Apr 3, 019

5. Single cell analysis of human pancreas reveals transcriptional signatures of aging and somatic 

mutation patterns.

Enge M, Arda HE, Mignardi M, Kim SK & Quake, SR. 

Cell. 2017 Oct 5;171(2):321-330.e14. doi: 10.1016/j.cell.2017.09.004.

// Notes: My main work from Stanford on pancreas biology and mutational patterns. Established 

techniques for mutation calling in low coverage and single-cell RNA-seq pipelines relevant to the 


6. DNA-dependent formation of transcription factor pairs alters their binding specificity 

Jolma A, Yin Y, Nitta KR, Dave K, Popov A, Taipale M, Enge M, Kivioja T, Morgunova E, Taipale J

Nature 527, 384–388 (19 November 2015).

7. CTCF/cohesin binding sites are frequently mutated in cancer.

Katainen R, Dave K , Pitkänen E, Palin K, Kivioja T, Välimäki N, Gylfe A, Ristolainen H, Hänninen U, 

Cajuso T, Kondelin J, Tanskanen T, Mecklin JP, Järvinen H, Renkonen--Sinisalo L, Lepistö A, 

Kaasinen E, Kilpivaara O, Tuupanen S, Enge M, Taipale J, Aaltonen L

Nature Genetics, 47, 818–821 (2015)

// Notes: My first senior author paper (after Taipale/Aaltonen as senior corresponding authors). I 

developed important parts of the groundwork in this paper for a manuscript on replication timing, and 

when I left the lab it was merged with another story to produce this paper.

8. Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor 


Yan J*, Enge M*, Whitington T, Dave K, Liu J, Sur I, Schmierer B, Jolma A, Kivioja T, Taipale M, 

Taipale J. *Equal contribution

Cell. 2013 Aug 15;154(4):801-13. doi: 10.1016/j.cell.2013.07.034.

// Notes: First author paper. Coordinated the experimental work and performed all computational 

analyses, as well as manuscript preparation.

9. DNA-Binding Specificities of Human Transcription Factors.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunova E, Enge M, Taipale M, Wei 

G, Palin K, Vaquerizas JM, Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E, 

Kivioja T, Taipale J.

Cell. 2013 Jan 17;152(1-2):327-39. doi: 10.1016/j.cell.2012.12.009.

// Notes: independently developed and applied methods to analyze experimental/computational TF 

binding patterns, an important validation experiment (Fig 2 e,f).

10. MDM2-dependent downregulation of p21 and hnRNP K provides a switch between apoptosis and 

growth arrest induced by pharmacologically activated p53.

Enge M, Bao W, Hedström E, Jackson SP, Moumen A, Selivanova G.

Cancer Cell. 2009 Mar 3;15(3):171-83.