Nicholas M. Luscombe


BA (Hons) MA (Cantab) PhD (UCL)

Following a degree in Natural Sciences at Jesus College, University of Cambridge (1993-1996), Nick studied for a Ph.D. with Janet Thornton at UCL (1996-2000) on the basis for specificity of DNA-binding proteins. He then moved to Yale University, USA, as an Anna Fuller Postdoctoral Fellow with Mark Gerstein (2000-2005), where he shifted research focus to genomics with a particular emphasis on yeast transcriptional regulation. He was a Group Leader at the EMBL-European Bioinformatics Institute (2005-2012) in Cambridge and built a computational biology laboratory with an emphasis on genomics and gene regulation. During this time, he joined the Okinawa Institute of Science & Technology as an Adjunct Faculty to establish a small group focused on developmental regulation (2011-present). He has now recently returned to UCL as a Chair in Computational Biology in the UCL Genetics Institute and holds a joint appointment as a Senior Group Leader at the Cancer Research UK London Research Institute. His laboratory will be joining the Francis Crick Institute in 2015.



Research Career

  • University of Cambridge
  • Yale University
  • University College London
  • EMBL-European Bioinformatics Institute
  • Cancer Research UK London Research Institute

Selected Publications (*Join first author; +Joint last author)


*Conrad T, *Cavalli FC, Vaquerizas JM, +Luscombe NM, and +Akhtar A.
Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters.
Science (In press).
PubMed Journal Full-text PDF

The ENCODE Project Consortium.
An Integrated Encyclopedia of DNA Elements in the Human Genome.
Nature (In press).
PubMed Journal Full-text PDF

Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, and Luscombe NM.
m:Explorer - multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.
Genome Biology (In press).
PubMed Journal Full-text PDF

*Lam KC, *Muhlpfordt F, *Vaquerizas JM, Raja SJ, Luscombe NM, Manke, T, and Akhtar A.
The NSL complex regulates housekeeping genes in Drosophila.
PLoS Genetics (In press).
PubMed Journal Full-text PDF

Kahramanoglou C, Prieto AI, Khedar S, Haase B, Gupta A, Benes V, Fraser GM, +Luscombe NM, and +Seshasayee ASN.
Genome-scale analysis of DNA cytosine methylation in Escherichia coli K12 reveals its role in limiting stationary phase transcription.
Nature Communications (In press).
PubMed Journal Full-text PDF

Martincorena I, Seshasayee ASN, and Luscombe NM. (2012)
Evidence of non-random mutation rates suggests a risk management strategy for evolution.
Nature 485:95-8.
PubMed Journal Full-text PDF Supplementary Information

Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, +Seshasayee ASN, and +Luscombe NM. (2012)
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
Nucleic Acids Research 40:3524-37.
PubMed Journal Full-text PDF

Conrad T, Cavalli FC, Vaquerizas JM, Luscombe NM, and Akhtar A. (2012)
The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex.
Developmental Cell 22:610-24.
PubMed Journal Full-text PDF

Konig J, Zarnack K, Luscombe NM, and Ule J. (2012)
Protein-RNA interactions: new genomic technologies and perspectives.
Nature Reviews Genetics 13:77-83.
PubMed Journal Full-text PDF

Vaquerizas JM, Teichmann SA, and Luscombe NM. (2012)
How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.
Methods in Molecular Biology 786:3-19.
PubMed Journal Full-text PDF

Zaugg JB and Luscombe NM. (2012)
A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast.
Genome Research 22:84-94.
PubMed Journal Full-text PDF


Cavalli FC, Vaquerizas JM, Bourgon R, and Luscombe NM. (2011)SpeCond: a method to detect condition-specific gene expression.
Genome Biology 12:413.
PubMed Journal Full-text PDF

Seshasayee ASN and Luscombe NM. (2011)
Comparative genomics suggests differential deployment of linear and branched signalling across bacteria.
Molecular Biosystems 7:3042-9.
PubMed Journal Full-text PDF

Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, Konig J, Ule J, Kellner R, Begerow D, and Feldbrugge M. (2011)
The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
Molecular & Cellular Proteomics. 10:M111.011213.
PubMed Journal Full-text PDF

Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, and Ule J. (2011)
iCLIP - Transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.
Journal Visualized Experiments 50. pii:2638. doi:10.3791/2638.
PubMed Journal

Vaquerizas JM, Akhtar A, and Luscombe NM. (2011)
Large-scale nuclear architecture and transcriptional control.
Subcellular Biochemistry 52:279-95.
PubMed Journal Full-text PDF

Seshasayee ASN, Sivaraman K, and Luscombe NM. (2011)
An overview of prokaryotic transcription factors: a summary of function and occurrence in bacterial genomes.
Subcell Biochemistry 52:279-95.
PubMed Journal Full-text PDF

The ENCODE Project Consortium. (2011)
A user’s guide to the Encyclopedia of DNA Elements (ENCODE).
PLoS Biology 9:e1001046.
PubMed Journal Full-text PDF

Ermakova P, Piszczek L, Luciani L, Cavalli FMG, Ferreira T, Farley D, Rizzo S, Paolicelli RC, Al-Banchaabouchi M, Nerlov C, Moriggl R, Luscombe NM, and Gross C. (2011)
Sensitized Phenotypic Screening Identifies Gene Dosage Sensitive Region on Chromosome 11 that Predisposes to Disease in Mice.
EMBO Molecular Medicine 1:50-66.
PubMed Journal Full-text PDF

*Kahramanoglou C, *Seshasayee AS, Prieto AI, Ibberson D, Schmidt S, Zimmermann J, Benes V, Fraser GM, and Luscombe NM. (2011)
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.
Nucleic Acids Research 39:2073-91.
PubMed Journal Full-text PDF


Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, and Ule J. (2010)iCLIP predicts the dual splicing effects of TIA-RNA interactions.
PLoS Biology 8:e1000530.
PubMed Journal Full-text PDF

Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, Holz H, Kadlec J, Fraterman S, Luscombe NM, and Akhtar A. (2010)
The nonspecific lethal complex is a transcriptional regulator in Drosophila.
Molecular Cell 38:827-41.
PubMed Journal Full-text PDF

*König J, *Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, and Ule J. (2010)
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Nature Structural & Molecular Biology 17:909-15.
PubMed Journal Full-text PDF

Seshasayee AS, Fraser GM, and Luscombe NM. (2010)
Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity.
Nucleic Acids Research 38:5970-81.
PubMed Journal Full-text PDF

Reimand J, Vaquerizas JM, Todd AE, Vilo J, and Luscombe NM. (2010)
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.
Nucleic Acids Research 38:4768-77.
PubMed Journal Full-text PDF

Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, Bonke M, Palin K, Talukder S, Hughes TR, Luscombe NM, Ukkonen E, and Taipale J. (2010)
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Genome Research 20:861-73.
PubMed Journal Full-text PDF

*Vaquerizas JM, *Suyama R, *Kind J, Miura K, +Luscombe NM, and +Akhtar A. (2010)
Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome.
PLoS Genetics 6:e1000846.
PubMed Journal Full-text PDF


Ilsley GR, Luscombe NM, and Apweiler R. (2009)Know your limits: assumptions, constraints and interpretation in systems biology.
Biochimica et Biophysica Acta 1794:1280-7.
PubMed Journal Full-text PDF

Vaquerizas JM, Kummerfeld SK, Teichmann SA, and Luscombe NM. (2009)
A functional census of human transcription factors.
Nature Reviews Genetics 10:252-63.
PubMed Journal Full-text PDF

Seshasayee AS, Fraser GM, Babu MM, and Luscombe NM. (2009)
Principles of transcriptional regulation and evolution of the metabolic system in E. coli.
Genome Research 19:79-91.
PubMed Journal Full-text PDF


*Kind J, *Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, and Akhtar A. (2008)
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.
Cell 133:813-28.
PubMed Journal Full-text PDF

Pearson MM, Sebaihia M, Churcher C, Quail MA, Seshasayee AS, Luscombe NM, Abdellah Z, Arrosmith C, Atkin B, Chillingworth T, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Walker D, Whithead S, Thomson NR, Rather PN, Parkhill J, and Mobley HL. (2008)
Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.
Journal of Bacteriology 190:4027-4037.
PubMed Journal Full-text PDF

Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, and Klemm P. (2008)
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.
Molecular Genetics & Genomics 279:523-34.
PubMed Journal Full-text PDF


Seshasayee AS, Bertone P, Fraser GM, and Luscombe NM. (2006) Transcriptional regulatory networks in bacteria: from input signals to output responses.
Current Opinions in Microbiology 9:511-519.
PubMed Journal Full-text PDF

Royce TE, Luscombe NM, Bertone P, Yu H, Rozowsky JS, Emanuelsson O, Zhu X, Chang JT, Snyder M, and Gerstein M. (2006)
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
Methods in Enzymology. 411:282-311.
PubMed Journal Full-text PDF

Balaji S, Babu MM, Iyer LM, Luscombe NM, and Aravind L. (2006)
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
Journal of Molecular Biology 360:213-217.
PubMed Journal Full-text PDF

Kamal M, Luscombe NM, Qian J, and Gerstein M. (2006)
Analytical evolutionary model for protein fold occurrence in genomes: accounting for the effects of gene duplication, acquisition and selective pressure.
In “Power laws, scale-free networks and genome biology” edited by Eugene V Koonin. Springer, New York. 2006.
Journal Full-text PDF


Teichmann SA, Bornberg-Bauer E, and Luscombe NM. (2005)Transcriptional networking.
Genome Biology 6:344.
PubMed Journal Full-text PDF