Nicholas Luscombe: Publications

  • Hall, CE; Yao, Z; Choi, M; Tyzack, GE; Serio, A; Luisier, R; Harley, J; Preza, E; Arber, C; Crisp, SJ; Watson, PMD; Kullmann, DM; Abramov, AY; Wray, S; Burley, R; Loh, SHY; Martins, LM; Stevens, MM; Luscombe, NM; Sibley, CR; Lakatos, A; Ule, J; Gandhi, S and Patani, R (2017)
    Progressive motor neuron pathology and the role of astrocytes in a human stem cell model of VCP-related ALS.
    Cell Reports 19, 1739-1749 PubMed abstract
  • Kar, G; Kim, JK; Kolodziejczyk, AA; Natarajan, KN; Torlai Triglia, E; Mifsud, B; Elderkin, S; Marioni, JC; Pombo, A and Teichmann, SA (2017)
    Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
    Nature Communications 8, 36 PubMed abstract
  • Mifsud, B; Martincorena, I; Darbo, E; Sugar, R; Schoenfelder, S; Fraser, P and Luscombe, NM (2017)
    GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.
    PLOS ONE 12, e0174744 PubMed abstract
  • Sugimoto, Y; Chakrabarti, AM; Luscombe, NM and Ule, J (2017)
    Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
    Nature Protocols 12, 611-637 PubMed abstract
  • Blake, SM; Stricker, SH; Halavach, H; Poetsch, AR; Cresswell, G; Kelly, G; Kanu, N; Marino, S; Luscombe, NM; Pollard, SM and Behrens, A (2016)
    Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation.
    eLife 5, e08711 PubMed abstract
  • Cakiroglu, SA; Zaugg, JB and Luscombe, NM (2016)
    Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.
    Nucleic Acids Research 44, 8065-8072 PubMed abstract
  • Chlamydas, S; Holz, H; Samata, M; Chelmicki, T; Georgiev, P; Pelechano, V; Dündar, F; Dasmeh, P; Mittler, G; Cadete, FT; Ramírez, F; Conrad, T; Wei, W; Raja, S; Manke, T; Luscombe, NM; Steinmetz, LM and Akhtar, A (2016)
    Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.
    Nature Structural & Molecular Biology 23, 580-589 PubMed abstract
  • Cresswell, GD; Apps, JR; Chagtai, T; Mifsud, B; Bentley, CC; Maschietto, M; Popov, SD; Weeks, ME; Olsen, ØE; Sebire, NJ; Pritchard-Jones, K; Luscombe, NM; Williams, RD and Mifsud, W (2016)
    Intra-tumor genetic heterogeneity in Wilms tumor: clonal evolution and clinical implications.
    EBioMedicine 9, 120-129 PubMed abstract
  • Curry, S; Rohn, J and Steele, A (2016)
    UK research reform: protest now.
    Nature 539, 357 PubMed abstract
  • Kiselev, VY; Juvin, V; Malek, M; Luscombe, N; Hawkins, P; Le Novère, N and Stephens, L (2015)
    Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.
    Nucleic Acids Research 43, 9663-9679 PubMed abstract
  • Mifsud, B; Tavares-Cadete, F; Young, AN; Sugar, R; Schoenfelder, S; Ferreira, L; Wingett, SW; Andrews, S; Grey, W; Ewels, PA; Herman, B; Happe, S; Higgs, A; LeProust, E; Follows, GA; Fraser, P; Luscombe, NM and Osborne, CS (2015)
    Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.
    Nature Genetics 47, 598-606 PubMed abstract
  • Murn, J; Zarnack, K; Yang, YJ; Durak, O; Murphy, EA; Cheloufi, S; Gonzalez, DM; Teplova, M; Curk, T; Zuber, J; Patel, DJ; Ule, J; Luscombe, NM; Tsai, L-H; Walsh, CA and Shi, Y (2015)
    Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.
    Genes & Development 29, 501-512 PubMed abstract
  • Schoenfelder, S; Furlan-Magaril, M; Mifsud, B; Tavares-Cadete, F; Sugar, R; Javierre, B-M; Nagano, T; Katsman, Y; Sakthidevi, M; Wingett, SW; Dimitrova, E; Dimond, A; Edelman, LB; Elderkin, S; Tabbada, K; Darbo, E; Andrews, S; Herman, B; Higgs, A; LeProust, E; Osborne, CS; Mitchell, JA; Luscombe, NM and Fraser, P (2015)
    The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.
    Genome Research 25, 582-597 PubMed abstract
  • Schoenfelder, S; Sugar, R; Dimond, A; Javierre, B-M; Armstrong, H; Mifsud, B; Dimitrova, E; Matheson, L; Tavares-Cadete, F; Furlan-Magaril, M; Segonds-Pichon, A; Jurkowski, W; Wingett, SW; Tabbada, K; Andrews, S; Herman, B; LeProust, E; Osborne, CS; Koseki, H; Fraser, P; Luscombe, NM and Elderkin, S (2015)
    Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.
    Nature Genetics 47, 1179-1186 PubMed abstract
  • Sugimoto, Y; Vigilante, A; Darbo, E; Zirra, A; Militti, C; D'Ambrogio, A; Luscombe, NM and Ule, J (2015)
    hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
    Nature 519, 491-494 PubMed abstract
  • Tajnik, M; Vigilante, A; Braun, S; Hänel, H; Luscombe, NM; Ule, J; Zarnack, K and König, J (2015)
    Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.
    Nucleic Acids Research 43, 10492-10505 PubMed abstract
  • Castelnuovo, M; Zaugg, JB; Guffanti, E; Maffioletti, A; Camblong, J; Xu, Z; Clauder-Münster, S; Steinmetz, LM; Luscombe, NM and Stutz, F (2014)
    Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.
    Nucleic Acids Research 42, 4348-4362 PubMed abstract
  • Harding, JL; Horswell, S; Heliot, C; Armisen, J; Zimmerman, LB; Luscombe, NM; Miska, EA and Hill, CS (2014)
    Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.
    Genome Research 24, 96-106 PubMed abstract
  • Ilik, IA; Quinn, JJ; Georgiev, P; Tavares-Cadete, F; Maticzka, D; Toscano, S; Wan, Y; Spitale, RC; Luscombe, N; Backofen, R; Chang, HY and Akhtar, A (2013)
    Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila.
    Molecular Cell 51, 156-173 PubMed abstract
  • Ilsley, GR; Fisher, J; Apweiler, R; De Pace, AH and Luscombe, NM (2013)
    Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
    eLife 2, e00522 PubMed abstract
  • 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 and Taipale, J (2013)
    DNA-binding specificities of human transcription factors.
    Cell 152, 327-339 PubMed abstract
  • Martincorena, I and Luscombe, NM (2013)
    Non-random mutation: the evolution of targeted hypermutation and hypomutation.
    Bioessays 35, 123-130 PubMed abstract
  • Vaquerizas, JM; Cavalli, FMG; Conrad, T; Akhtar, A and Luscombe, NM (2013)
    Response to comments on "Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters".
    Science 340, 273-e PubMed abstract
  • Zarnack, K; König, J; Tajnik, M; Martincorena, I; Eustermann, S; Stévant, I; Reyes, A; Anders, S; Luscombe, NM and Ule, J (2013)
    Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.
    Cell 152, 453-466 PubMed abstract
  • Conrad, T; Cavalli, FMG; Holz, H; Hallacli, E; Kind, J; Ilik, I; 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, 610-624 PubMed abstract
  • Conrad, T; Cavalli, FMG; Vaquerizas, JM; Luscombe, NM and Akhtar, A (2012)
    Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters.
    Science 337, 742-746 PubMed abstract
  • ENCODE Project Consortium (2012)
    An integrated encyclopedia of DNA elements in the human genome.
    Nature 489, 57-74 PubMed abstract
  • Kahramanoglou, C; Prieto, AI; Khedkar, S; Haase, B; Gupta, A; Benes, V; Fraser, GM; Luscombe, NM and Seshasayee, ASN (2012)
    Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.
    Nature Communications 3, 886 PubMed abstract
  • König, J; Zarnack, K; Luscombe, NM and Ule, J (2012)
    Protein-RNA interactions: new genomic technologies and perspectives.
    Nature Reviews Genetics 13, 77-83 PubMed abstract
  • Lam, KC; Mühlpfordt, F; Vaquerizas, JM; Raja, SJ; Holz, H; Luscombe, NM; Manke, T and Akhtar, A (2012)
    The NSL complex regulates housekeeping genes in Drosophila.
    PLOS Genetics 8, e1002736 PubMed abstract
  • Martincorena, I; Seshasayee, ASN and Luscombe, NM (2012)
    Evidence of non-random mutation rates suggests an evolutionary risk management strategy.
    Nature 485, 95-98 PubMed abstract
  • 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, 3524-3537 PubMed abstract
  • Reimand, J; Aun, A; Vilo, J; Vaquerizas, JM; Sedman, J and Luscombe, NM (2012)
    m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.
    Genome Biology 13, R55 PubMed abstract
  • Tan-Wong, SM; Zaugg, JB; Camblong, J; Xu, Z; Zhang, DW; Mischo, HE; Ansari, AZ; Luscombe, NM; Steinmetz, LM and Proudfoot, NJ (2012)
    Gene loops enhance transcriptional directionality.
    Science 338, 671-675 PubMed abstract
  • 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 abstract
  • Zaugg, JB and Luscombe, NM (2012)
    A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.
    Genome Research 22, 84-94 PubMed abstract
  • Cavalli, FMG; Bourgon, R; Vaquerizas, JM and Luscombe, NM (2011)
    SpeCond: a method to detect condition-specific gene expression.
    Genome Biology 12, R101 PubMed abstract
  • ENCODE Project Consortium (2011)
    A user's guide to the encyclopedia of DNA elements (ENCODE).
    PLOS Biology 9, e1001046 PubMed abstract
  • Ermakova, O; 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 3, 50-66 PubMed abstract
  • Kahramanoglou, C; Seshasayee, ASN; 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, 2073-2091 PubMed abstract
  • Koepke, J; Kaffarnik, F; Haag, C; Zarnack, K; Luscombe, NM; König, J; Ule, J; Kellner, R; Begerow, D and Feldbrügge, M (2011)
    The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
    Molecular & Cellular Proteomics 10, M111.011213 PubMed abstract
  • König, 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 of Visualized Experiments 50, e2638 PubMed abstract
  • Seshasayee, ASN and Luscombe, NM (2011)
    Comparative genomics suggests differential deployment of linear and branched signaling across bacteria.
    Molecular BioSystems 7, 3042-3049 PubMed abstract
  • Seshasayee, ASN; Sivaraman, K and Luscombe, NM (2011)
    An overview of prokaryotic transcription factors : a summary of function and occurrence in bacterial genomes.
    Subcellular Biochemistry 52, 7-23 PubMed abstract
  • Vaquerizas, JM; Akhtar, A and Luscombe, NM (2011)
    Large-scale nuclear architecture and transcriptional control.
    Subcellular Biochemistry 52, 279-295 PubMed abstract
  • 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, 861-873 PubMed abstract
  • 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, 909-915 PubMed abstract
  • 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, 827-841 PubMed abstract
  • 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, 4768-4777 PubMed abstract
  • Seshasayee, ASN; 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, 5970-5981 PubMed abstract
  • 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 abstract
  • 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 abstract

[Page last updated 1 Aug 2017]

Nicholas Luscombe

nicholas.luscombe@crick.ac.uk
+44 (0)20 379 61132

  • Qualifications and history
  • 2000 PhD from University College London, UK
  • 2004 Postdoctoral Fellow, Yale University, USA
  • 2005 Group Leader, EMBL-European Bioinformatics Institute, Cambridge, UK.
  • 2012 Established lab London Research Institute, Cancer Research UK, Professor of Computational Biology, University College London, UK
  • 2011 Adjunct Faculty, Okinawa Institute of Science & Technology, Japan
  • 2015 Winton Group Leader, the Francis Crick Institute, London, UK