Publications

Selected publications

Tracing homopolymer in Oikopleura dioica's mitogenome. N Dierckxsens, K Watanabe, Y Tan, A Masunaga, MJ Mansfield, J Miao, NM Luscombe, C Plessy. Genome Biology and Evolution 2024.

Extreme genome scrambling in cryptic Oikopleura dioica species. C Plessy, MJ Mansfield, A Bliznina, A Masunaga, C West, Y Tan, AW Liu, J Grašič, MS Del Rio-Pisula, G Sánchez-Serna, M Fabrega-Torrus, A Ferrández-Roldán, V Roncalli, P Navratilova, EM Thompson, T Onuma, H Nishida, C Cañestro, NM Luscombe. Genome Research 2024.

The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe. A Masunaga, MJ Mansfield, Y Tan, AW Liu, A Bliznina, P Barzaghi, TL Hodgetts, A Ferrández-Roldán, C Cañestro, TA Onuma, C Plessy, NM Luscombe. Marine Biology 2022.

Automated phenol-cholorform extraction of high molecular weight DNA for use in long-read single-molecule sequencing. AW Liu, A Villar-Briones, NM Luscombe, C Plessy. F1000Research 2022.

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. A Bliznina, A Masunaga, MJ Mansfield, Y Tan, AW Liu, C West, T Rustagi, H-C Chien, S Kumar, J Pichon, C Plessy, NM Luscombe. BMC Genomics 2021.

H3S28P Antibody staining of Okinawan Oikopleura dioica suggests the presence of three chomosomes. AW Liu, Y Tan, A Masunaga, A Bliznina, C West, C Plessy, NM Luscombe.  F1000Research 2021.

Streamlined sampling and cultivation of the pelagic cosmopolitan larvacean, Oikopleura dioica. A Masunaga, AW Liu, Y Tan, A Scott, NM Luscombe. Journal of Visualized Experiments 2020.

Finding cell-specific expression patterns in the early Ciona embryo with single-cell RNA-seq. GR Ilsley, R Suyama, T Noda, N Satoh, NM Luscombe. Scientific Reports 2020.

Widespread use of the "ascidian" mitochondrial genetic code in tunicates. J Pichon, NM Luscombe, C Plessy. F1000Research 2019.

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis. AR Poetsch, SJ Boulton, NM Luscombe. Genome Biology 2018.

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. C Li, B Lenhard, NM Luscombe. Genome Research 2018.

 

2024

Less, but more: new insights from appendicularians on chordate Fgf evolution and the divergence of tunicate lifestyles. G Sanchez-Serna, J Badia-Ramentol, P Bujosa, A Ferrandez-Roldan, N Torres-Aguila, M Fabrega-Torrus, JN Wibisana, MJ Mansfield, C Plessy, NM Luscombe, R Albalat, C Cañestro. Molecular Biology and Evolution, accepted.

Poised PABP–RNA hubs implement signal-dependent mRNA decay in development. M Modic, K Kuret, S Steinhauser, R Faraway, EV Genderen, IRD Los Mozos, J Novljan, Z Vicic, FCY Lee, DT Berge, NM Luscombe, Jernej Ule. Nature Structural & Molecular Biology 2024.

Tracing homopolymer in Oikopleura dioica's mitogenome. N Dierckxsens, K Watanabe, Y Tan, A Masunaga, MJ Mansfield, J Miao, NM Luscombe, C Plessy. Genome Biology and Evolution 2024.

The complete mitogenome of an unidentified Oikopleura species. JN Wibisana, C Plessy, N Dierckxsens, A Masunaga, J Miao, NM Luscombe. F1000Research 2024.

Modification of clinical dental impression methods to obtain dental traits from living and whole non-mammalian vertebrates. JN Wibisana, RA Sallan, T Ota, P Puchenkov, T Kubo, L Sallan. Journal of Morpholoy, accepted. 

Extreme genome scrambling in cryptic Oikopleura dioica species. C Plessy, MJ Mansfield, A Bliznina, A Masunaga, C West, Y Tan, AW Liu, J Grašič, MS Del Rio-Pisula, G Sánchez-Serna, M Fabrega-Torrus, A Ferrández-Roldán, V Roncalli, P Navratilova, EM Thompson, T Onuma, H Nishida, C Cañestro, NM Luscombe. Genome Research 2024.

 

2023

clipplotr—a comparative visualization and analysis tool for CLIP data. AM Chakrabarti, C Capitanchik, J Ule, NM Luscombe. RNA. 2023.

Annelid functional genomics reveal the origins of bilaterian life cycles. FM Martín-Zamora, Y Liang, K Guynes, AM Carrillo-Baltodano, BE Davies, RD Donnellan, Y Tan, G Moggioli, O Seudre, M Tran. Nature. 2023.

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism. AM Chakrabarti, IA Iosub, FCY Lee, J Ule, NM Luscombe. Nucleic Acids Research. 2023.

RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis. M Rafiee, S Rohban, K Davey, J Ule, NM Luscombe. Brain. 2023.

Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity. S Rohban, M Rafiee, J Ule, N Luscombe. bioRxiv. 2023.

Extreme genome scrambling in cryptic Oikopleura dioica species. C Plessy, MJ Mansfield, A Bliznina, A Masunaga, C West, Y Tan, A Liu, J Grasic, MS del Rio Pisula, G Sanchez-Serna. bioRxiv. 2023.

A gene regulatory network for neural induction. KE Trevers, HC Lu, Y Yang, AP Thiery, AC Strobl, C Anderson, B Pálinkášová, NMM de Oliveira, IM de Almeida, MAF Khan. Elife. 2023.

nf-core/clipseq-a robust Nextflow pipeline for comprehensive CLIP data analysis. C West, C Capitanchik, C Cheshire, N Luscombe, AM Chakrabarti, J Ule. Wellcome Open Research. 2023.

RNA polymerase II-associated proteins reveal pathways affected in neural precursors with VCP mutation. M Rafiee, S Rohban, K Davey, J Ule, NM Luscombe. Brain: a journal of neurology. 2023.

scRNA-sequencing in chick suggests a probabilistic model for cell fate allocation at the neural plate border. AP Thiery, AL Buzzi, E Hamrud, C Cheshire, NM Luscombe, J Briscoe, A Streit. Elife. 2023.

Poised PABP-RNA hubs implement signal-dependent mRNA decay in development. J Ule, M Modic, K Kuret, S Steinhauser, R Faraway, E van Genderen, F Lee, IR de Los Mozos, Ž Vičič, J Novljan. Research Square. 2023.

 

2022

Speed variations of bacterial replisomes. D Bhat, S Hauf, C Plessy, Y Yokobayashi, S Pigolotti. Elife. 2022.

Meta-analysis of human and mouse ALS astrocytes reveals multi-omic signatures of inflammatory reactive states. OJ Ziff, BE Clarke, DM Taha, H Crerar, NM Luscombe, R Patani. Genome research. 2022.

m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast. RA Varier, T Sideri, C Capitanchik, Z Manova, E Calvani, A Rossi, RR Edupuganti, I Ensinck, VC Chan, H Patel. bioRxiv. 2022.

Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing. AW Liu, A Villar-Briones, NM Luscombe, C Plessy. F1000Research. 2022.

A gradient border model for cell fate decisions at the neural plate border. A Thiery, AL Buzzi, E Hamrud, C Cheshire, N Luscombe, J Briscoe, A Streit. bioRxiv. 2022.

A single-cell atlas of bobtail squid visual and nervous system highlights molecular principles of convergent evolution. D Gavriouchkina, Y Tan, F Ziadi-Künzli, Y Hasegawa, L Piovani, L Zhang, C Sugimoto, NM Luscombe, F Marlétaz, DS Rokhsar. bioRxiv. 2022.

Dissecting the cellular landscape of hidradenitis suppurativa through single-cell sequencing and spatial transcriptomics. X Du-Harpur, CGN Harun, E Rashidghamat, NM Luscombe, FM Watt, MD Lynch. BRITISH JOURNAL OF DERMATOLOGY. 2022.

The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe. A Masunaga, MJ Mansfield, Y Tan, AW Liu, A Bliznina, P Barzaghi, TL Hodgetts, A Ferrández-Roldán, C Cañestro, TA Onuma. Marine Biology. 2022.

048 The transcriptional landscape of hidradenitis suppurativa at single-cell and spatial resolution. X Du-Harpur, C Ganier, N Harun, E Rashidghamat, N Luscombe, F Watt, M Lynch. Journal of Investigative Dermatology. 2022.

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. RA Varier, T Sideri, C Capitanchik, Z Manova, E Calvani, A Rossi, RR Edupuganti, I Ensinck, VC Chan, H Patel. Elife. 2022.

2021

RNA modifications detection by comparative Nanopore direct RNA sequencing. A Leger, PP Amaral, L Pandolfini, C Capitanchik, F Capraro, V Miano, P Toolan-Kerr, T Sideri, AJ Enright. Nature communications. 2021.

Transcription levels of a noncoding RNA orchestrate opposing regulatory and cell fate outcomes in yeast. F Moretto, NE Wood, M Chia, C Li, NM Luscombe, FJ van Werven. Cell Reports. 2021.

Intergenic RNA mainly derives from nascent transcripts of known genes. F Agostini, J Zagalak, J Attig, J Ule, NM Luscombe. Genome Biology. 2021.

psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation. LM Strittmatter, C Capitanchik, AJ Newman, M Hallegger, CM Norman, SM Fica, C Oubridge, NM Luscombe, J Ule, K Nagai. Nature Communications. 2021.

Clinically relevant vulnerabilities of deep machine learning systems for skin cancer diagnosis. X Du-Harpur, C Arthurs, C Ganier, R Woolf, Z Laftah, M Lakhan, A Salam, B Wan, FM Watt, NM Luscombe. The Journal of investigative dermatology. 2021.

Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. A Bliznina, A Masunaga, MJ Mansfield, Y Tan, AW Liu, C West, T Rustagi, H Chien, S Kumar, J Pichon, NM Luscombe. BMC genomics. 2021.

High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. M Chia, C Li, S Marques, V Pelechano, NM Luscombe, FJ van Werven. Genome biology. 2021.

Cytoplasmic cleavage of IMPA1 3′ UTR is necessary for maintaining axon integrity. C Andreassi, R Luisier, H Crerar, M Darsinou, S Blokzijl-Franke, T Lenn, NM Luscombe, G Cuda, M Gaspari, A Saiardi. Cell Reports. 2021.

Reactive astrocytes in ALS display diminished intron retention. OJ Ziff, DM Taha, H Crerar, BE Clarke, AM Chakrabarti, G Kelly, J Neeves, GE Tyzack, NM Luscombe, R Patani. Nucleic Acids Research. 2021.

Aberrant cytoplasmic intron retention is a blueprint for RNA binding protein mislocalization in VCP-related amyotrophic lateral sclerosis. GE Tyzack, J Neeves, H Crerar, P Klein, OJ Ziff, DM Taha, R Luisier, NM Luscombe, R Patani. Brain. 2021.

Epiblast morphogenesis is controlled by selective mRNA decay triggered by LIN28A relocation. M Modic, IR de Los Mozos, S Steinhauser, E van Genderen, S Schirge, V Bergant, J Ryan, CB Mulholland, R Faraway, FCY Lee. bioRxiv. 2021.

Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. M Rafiee, JA Zagalak, S Sidorov, S Steinhauser, K Davey, J Ule, NM Luscombe. Nucleic Acids Research. 2021.

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer. OG Wilkins, C Capitanchik, NM Luscombe, J Ule. Wellcome Open Research. 2021.

ChromWave: Deciphering the DNA-encoded competition between transcription factors and nucleosomes with deep neural networks. SA Cakiroglu, S Steinhauser, J Smith, W Xing, NM Luscombe. Available at SSRN 3816949. 2021.

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. M Hallegger, AM Chakrabarti, FCY Lee, BL Lee, AG Amalietti, HM Odeh, KE Copley, JD Rubien, B Portz, K Kuret. Cell. 2021.

RGS4 RNA secondary structure mediates staufen2 RNP assembly in neurons. SM Fernández-Moya, J Ehses, KE Bauer, R Schieweck, AM Chakrabarti, FCY Lee, C Illig, NM Luscombe, M Harner, J Ule. International Journal of Molecular Sciences. 2021.

Comparative transcriptomics reveals unique patterns of convergence in the evolution of eusociality. M Velasque, Y Tan, AW Liu, NM Luscombe, JA Denton. bioRxiv. 2021.

 

Up to 2020

Machine-driven parameter screen of biochemical reactions. S Poulain, O Arnaud, S Kato, I Chen, H Ishida, P Carninci, C Plessy. Nucleic Acids Research. 2020.

Identifying developmentally important genes with single-cell RNA-seq from an embryo. Ilsley, Garth R, Suyama, Ritsuko, Noda, Takeshi, Satoh, Nori, Luscombe, Nicholas M, Scientific reports. 2020.

RADICL-seq identifies general and cell type–specific principles of genome-wide RNA-chromatin interactions. Bonetti, Alessandro, Agostini, Federico, Suzuki, Ana Maria, Hashimoto, Kosuke, Pascarella, Giovanni, Gimenez, Juliette, Roos, Leonie, Nash, Alex J, Ghilotti, Marco, Cameron, Christopher JF, Nature Communications. 2020.

What is AI? Applications of artificial intelligence to dermatology. Du‐Harpur, X, Watt, FM, Luscombe, NM, Lynch, MD, British Journal of Dermatology. 2020.

Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome. Li, Cai, Luscombe, Nicholas M, Nature communications. 2020.

How do you identify m6 a methylation in transcriptomes at high resolution? a comparison of recent datasets. Capitanchik, Charlotte, Toolan-Kerr, Patrick, Luscombe, Nicholas M, Ule, Jernej, Frontiers in genetics. 2020.

Potential cryptic speciation in the Japanese populations of the pelagic tunicate, Oikopleura dioica. Masunaga, Aki, Bliznina, Aleksandra, Liu, Andrew, Plessy, Charles, Tan, Yongkai, Luscombe, Nicholas, Ocean Sciences Meeting 2020. 2020.

CD147 (BSG) but not ACE2 expression is detectable in vascular endothelial cells within single cell RNA sequencing datasets derived from multiple tissues in healthy individuals. Ganier, C, Du-Harpur, X, Harun, N, Wan, B, Arthurs, C, Luscombe, NM, Watt, FM, Lynch, MD, BioRxiv. 2020.

Streamlined sampling and cultivation of the pelagic cosmopolitan larvacean, Oikopleura dioica. Masunaga, Aki, Liu, Andrew W, Tan, Yongkai, Scott, Andrew, Luscombe, Nicholas M, JoVE (Journal of Visualized Experiments). 2020.

A genome database for a Japanese population of the larvacean Oikopleura dioica. Wang, Kai, Tomura, Ryo, Chen, Wei, Kiyooka, Miho, Ishizaki, Hinako, Aizu, Tomoyuki, Minakuchi, Yohei, Seki, Masahide, Suzuki, Yutaka, Omotezako, Tatsuya, Development, Growth & Differentiation. 2020.

Paraspeckle components NONO and PSPC1 are not mislocalized from motor neuron nuclei in sporadic ALS. Tyzack, Giulia E, Manferrari, Giulia, Newcombe, Jia, Luscombe, Nicholas M, Luisier, Raphaelle, Patani, Rickie, Brain. 2020.

Pervasive chromosomal instability and karyotype order in tumour evolution. Watkins, Thomas BK, Lim, Emilia L, Petkovic, Marina, Elizalde, Sergi, Birkbak, Nicolai J, Wilson, Gareth A, Moore, David A, Grönroos, Eva, Rowan, Andrew, Dewhurst, Sally M, Nature. 2020.

H3S28P antibody staining of Okinawan Oikopleura dioica suggests the presence of three chromosomes. Liu, Andrew W, Tan, Yongkai, Masunaga, Aki, Bliznina, Aleksandra, West, Charlotte, Plessy, Charles, Luscombe, Nicholas M, F1000Research. 2020.

Editor’s Choice September 2020 John Ingram. Du-Harper, X, Watt, FM, Luscombe, NM, Lynch, MD, Br J Dermatol. 2020.

Identifying extrinsic versus intrinsic drivers of variation in cell behavior in human iPSC lines from healthy donors. Vigilante, Alessandra, Laddach, Anna, Moens, Nathalie, Meleckyte, Ruta, Leha, Andreas, Ghahramani, Arsham, Culley, Oliver J, Kathuria, Annie, Hurling, Chloe, Vickers, Alice, Cell reports. 2019.

Target-specific precision of CRISPR-mediated genome editing. Chakrabarti, Anob M, Henser-Brownhill, Tristan, Monserrat, Josep, Poetsch, Anna R, Luscombe, Nicholas M, Scaffidi, Paola, Molecular cell. 2019.

Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes. Cakiroglu, Aylin, Clapier, Cedric R, Ehrensberger, Andreas H, Darbo, Elodie, Cairns, Bradley R, Luscombe, Nicholas M, Svejstrup, Jesper Q, Genome Research. 2019.

Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Tyzack, Giulia E, Luisier, Raphaelle, Taha, Doaa M, Neeves, Jacob, Modic, Miha, Mitchell, Jamie S, Meyer, Ione, Greensmith, Linda, Newcombe, Jia, Ule, Jernej, Brain. 2019.

Widespread use of the “ascidian” mitochondrial genetic code in tunicates. Pichon, Julien, Luscombe, Nicholas M, Plessy, Charles, F1000Research. 2019.

A systems view of spliceosomal assembly and branchpoints with iCLIP. Briese, Michael, Haberman, Nejc, Sibley, Christopher R, Faraway, Rupert, Elser, Andrea S, Chakrabarti, Anob M, Wang, Zhen, König, Julian, Perera, David, Wickramasinghe, Vihandha O, Nature structural & molecular biology. 2019.

Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells. Ghahramani, Arsham, Donati, Giacomo, Luscombe, Nicholas M, Watt, Fiona M, Genome biology. 2018.

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis. Poetsch, Anna R, Boulton, Simon J, Luscombe, Nicholas M, Genome biology. 2018.

Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Li, Cai, Lenhard, Boris, Luscombe, Nicholas M, Genome research. 2018.

Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease. Steele, Andrew J, Denaxas, Spiros C, Shah, Anoop D, Hemingway, Harry, Luscombe, Nicholas M, PloS one. 2018.

Generative adversarial networks uncover epidermal regulators and predict single cell perturbations. Ghahramani, Arsham, Watt, Fiona M, Luscombe, Nicholas M, BioRxiv. 2018.

Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing. Attig, Jan, Agostini, Federico, Gooding, Clare, Chakrabarti, Anob M, Singh, Aarti, Haberman, Nejc, Zagalak, Julian A, Emmett, Warren, Smith, Christopher WJ, Luscombe, Nicholas M, Cell. 2018.

c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells. Gabryšová, Leona, Alvarez-Martinez, Marisol, Luisier, Raphaëlle, Cox, Luke S, Sodenkamp, Jan, Hosking, Caroline, Pérez-Mazliah, Damián, Whicher, Charlotte, Kannan, Yashaswini, Potempa, Krzysztof, Nature immunology. 2018.

Data science issues in studying protein–RNA interactions with CLIP technologies. Chakrabarti, Anob M, Haberman, Nejc, Praznik, Arne, Luscombe, Nicholas M, Ule, Jernej, Annual Review of Biomedical Data Science. 2018.

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. Luisier, Raphaelle, Tyzack, Giulia E, Hall, Claire E, Mitchell, Jamie S, Devine, Helen, Taha, Doaa M, Malik, Bilal, Meyer, Ione, Greensmith, Linda, Newcombe, Jia, Nature communications. 2018.

Somatic TP53 mutations are detectable in circulating tumor DNA from children with anaplastic Wilms tumors. Treger, Taryn D, Chagtai, Tasnim, Butcher, Robert, Cresswell, George D, Al-Saadi, Reem, Brok, Jesper, Williams, Richard D, Roberts, Chrissy, Luscombe, Nicholas M, Jones, Kathy Pritchard, Translational oncology. 2018.

Nervous system regionalization entails axial allocation before neural differentiation. Metzis, Vicki, Steinhauser, Sebastian, Pakanavicius, Edvinas, Gouti, Mina, Stamataki, Despina, Ivanovitch, Kenzo, Watson, Thomas, Rayon, Teresa, Gharavy, S Neda Mousavy, Lovell-Badge, Robin, Cell. 2018.

Deterministic evolutionary trajectories influence primary tumor growth: TRACERx renal. Turajlic, Samra, Xu, Hang, Litchfield, Kevin, Rowan, Andrew, Horswell, Stuart, Chambers, Tim, O’Brien, Tim, Lopez, Jose I, Watkins, Thomas BK, Nicol, David, Cell. 2018.

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein. Sugimoto, Yoichiro, Chakrabarti, Anob M, Luscombe, Nicholas M, Ule, Jernej, Nature Protocols. 2017.

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. Mifsud, Borbala, Martincorena, Inigo, Darbo, Elodie, Sugar, Robert, Schoenfelder, Stefan, Fraser, Peter, Luscombe, Nicholas M, PloS one. 2017.

Progressive motor neuron pathology and the role of astrocytes in a human stem cell model of VCP-related ALS. Hall, Claire E, Yao, Zhi, Choi, Minee, Tyzack, Giulia E, Serio, Andrea, Luisier, Raphaelle, Harley, Jasmine, Preza, Elisavet, Arber, Charlie, Crisp, Sarah J, Cell reports. 2017.

Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation. Blake, Sophia M, Stricker, Stefan H, Halavach, Hanna, Poetsch, Anna R, Cresswell, George, Kelly, Gavin, Kanu, Nnennaya, Marino, Silvia, Luscombe, Nicholas M, Pollard, Steven M, Elife. 2016.

Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation. Chlamydas, Sarantis, Holz, Herbert, Samata, Maria, Chelmicki, Tomasz, Georgiev, Plamen, Pelechano, Vicent, Dündar, Friederike, Dasmeh, Pouria, Mittler, Gerhard, Cadete, Filipe Tavares, Nature Structural & Molecular Biology. 2016.

Intra-tumor genetic heterogeneity in Wilms tumor: clonal evolution and clinical implications. Cresswell, George D, Apps, John R, Chagtai, Tasnim, Mifsud, Borbala, Bentley, Christopher C, Maschietto, Mariana, Popov, Sergey D, Weeks, Mark E, Olsen, Øystein E, Sebire, Neil J, EBioMedicine. 2016.

Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. Cakiroglu, S Aylin, Zaugg, Judith B, Luscombe, Nicholas M, Nucleic Acids Research. 2016.
Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Murn, Jernej, Zarnack, Kathi, Yang, Yawei J, Durak, Omer, Murphy, Elisabeth A, Cheloufi, Sihem, Gonzalez, Dilenny M, Teplova, Marianna, Curk, Tomaž, Zuber, Johannes, Genes & development. 2015.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Schoenfelder, Stefan, Furlan-Magaril, Mayra, Mifsud, Borbala, Tavares-Cadete, Filipe, Sugar, Robert, Javierre, Biola-Maria, Nagano, Takashi, Katsman, Yulia, Sakthidevi, Moorthy, Wingett, Steven W, Genome research. 2015.

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Sugimoto, Yoichiro, Vigilante, Alessandra, Darbo, Elodie, Zirra, Alexandra, Militti, Cristina, D’Ambrogio, Andrea, Luscombe, Nicholas M, Ule, Jernej, Nature. 2015.

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Mifsud, Borbala, Tavares-Cadete, Filipe, Young, Alice N, Sugar, Robert, Schoenfelder, Stefan, Ferreira, Lauren, Wingett, Steven W, Andrews, Simon, Grey, William, Ewels, Philip A, Nature genetics. 2015.

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome. Schoenfelder, Stefan, Sugar, Robert, Dimond, Andrew, Javierre, Biola-Maria, Armstrong, Harry, Mifsud, Borbala, Dimitrova, Emilia, Matheson, Louise, Tavares-Cadete, Filipe, Furlan-Magaril, Mayra, Nature genetics. 2015.

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Tajnik, Mojca, Vigilante, Alessandra, Braun, Simon, Hänel, Heike, Luscombe, Nicholas M, Ule, Jernej, Zarnack, Kathi, König, Julian, Nucleic acids research. 2015.

Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop. Kiselev, Vladimir Yu, Juvin, Veronique, Malek, Mouhannad, Luscombe, Nicholas, Hawkins, Phillip, Novère, Nicolas Le, Stephens, Len, Nucleic acids research. 2015.

GOTHiC, a simple probabilistic model to resolve complex biases and to identify real interactions in Hi-C data. Mifsud, Borbala, Martincorena, Inigo, Darbo, Elodie, Sugar, Robert, Schoenfelder, Stefan, Fraser, Peter, Luscombe, Nicholas M, bioRxiv. 2015.

Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements. Harding, Joanne L, Horswell, Stuart, Heliot, Claire, Armisen, Javier, Zimmerman, Lyle B, Luscombe, Nicholas M, Miska, Eric A, Hill, Caroline S, Genome research. 2014.
Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast. Castelnuovo, Manuele, Zaugg, Judith B, Guffanti, Elisa, Maffioletti, Andrea, Camblong, Jurgi, Xu, Zhenyu, Clauder-Münster, Sandra, Steinmetz, Lars M, Luscombe, Nicholas M, Stutz, Francoise, Nucleic acids research. 2014.

Non‐random mutation: the evolution of targeted hypermutation and hypomutation. Martincorena, Iñigo, Luscombe, Nicholas M, Bioessays. 2013.

DNA-binding specificities of human transcription factors. Jolma, Arttu, Yan, Jian, Whitington, Thomas, Toivonen, Jarkko, Nitta, Kazuhiro R, Rastas, Pasi, Morgunova, Ekaterina, Enge, Martin, Taipale, Mikko, Wei, Gonghong, Cell. 2013.

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements. Zarnack, Kathi, König, Julian, Tajnik, Mojca, Martincorena, Iñigo, Eustermann, Sebastian, Stévant, Isabelle, Reyes, Alejandro, Anders, Simon, Luscombe, Nicholas M, Ule, Jernej, Cell. 2013.

Response to comments on “Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters”. Vaquerizas, Juan M, Cavalli, Florence MG, Conrad, Thomas, Akhtar, Asifa, Luscombe, Nicholas M, Science. 2013.

Response to No gene-specific optimization of mutation rate in Escherichia coli. Martincorena, Inigo, Luscombe, Nicholas M, arXiv preprint arXiv:1305.1436. 2013.

Cellular resolution models for even skipped regulation in the entire Drosophila embryo. Ilsley, Garth R, Fisher, Jasmin, Apweiler, Rolf, DePace, Angela H, Luscombe, Nicholas M, Elife. 2013.

Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Ilik, Ibrahim Avsar, Quinn, Jeffrey J, Georgiev, Plamen, Tavares-Cadete, Filipe, Maticzka, Daniel, Toscano, Sarah, Wan, Yue, Spitale, Robert C, Luscombe, Nicholas, Backofen, Rolf, Molecular cell. 2013.
A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast. Zaugg, Judith B, Luscombe, Nicholas M, Genome Research. 2012.

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome. Vaquerizas, Juan M, Teichmann, Sarah A, Luscombe, Nicholas M, Gene Regulatory Networks: Methods and Protocols. 2012.

Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Prieto, Ana I, Kahramanoglou, Christina, Ali, Ruhi M, Fraser, Gillian M, Seshasayee, Aswin SN, Luscombe, Nicholas M, Nucleic acids research. 2012.

Protein–RNA interactions: new genomic technologies and perspectives. König, Julian, Zarnack, Kathi, Luscombe, Nicholas M, Ule, Jernej, Nature Reviews Genetics. 2012.

The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Conrad, Thomas, Cavalli, Florence MG, Holz, Herbert, Hallacli, Erinc, Kind, Jop, Ilik, Ibrahim, Vaquerizas, Juan M, Luscombe, Nicholas M, Akhtar, Asifa, Developmental cell. 2012.

Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Martincorena, Iñigo, Seshasayee, Aswin SN, Luscombe, Nicholas M, Nature. 2012.

Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription. Kahramanoglou, Christina, Prieto, Ana I, Khedkar, Supriya, Haase, Bettina, Gupta, Ankur, Benes, Vladimir, Fraser, Gillian M, Luscombe, Nicholas M, Seshasayee, Aswin SN, Nature communications. 2012.
The NSL complex regulates housekeeping genes in Drosophila. Lam, Kin Chung, Muehlpfordt, Friederike, Vaquerizas, Juan M, Raja, Sunil Jayaramaiah, Holz, Herbert, Luscombe, Nicholas M, Manke, Thomas, Akhtar, Asifa, PLoS genetics. 2012.

m: Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. Reimand, Jüri, Aun, Anu, Vilo, Jaak, Vaquerizas, Juan M, Sedman, Juhan, Luscombe, Nicholas M, Genome biology. 2012.

Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters. Conrad, Thomas, Cavalli, Florence MG, Vaquerizas, Juan M, Luscombe, Nicholas M, Akhtar, Asifa, Science. 2012.
Gene loops enhance transcriptional directionality. Tan-Wong, Sue Mei, Zaugg, Judith B, Camblong, Jurgi, Xu, Zhenyu, Zhang, David W, Mischo, Hannah E, Ansari, Aseem Z, Luscombe, Nicholas M, Steinmetz, Lars M, Proudfoot, Nick J, Science. 2012.

Response to Horizontal gene transfer may explain variation in theta_s. Martincorena, Inigo, Luscombe, Nicholas M, arXiv preprint arXiv:1211.0928. 2012.

An integrated encyclopedia of DNA elements in the human genome. ENCODE Project Consortium, Nature. 2012.

Small-molecule-mediated Signalling in Bacteria. Seshasayee, Aswin Sai Narain, Luscombe, Nicholas M, . 2012.

Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Kahramanoglou, Christina, Seshasayee, Aswin SN, Prieto, Ana I, Ibberson, David, Schmidt, Sabine, Zimmermann, Jurgen, Benes, Vladimir, Fraser, Gillian M, Luscombe, Nicholas M, Nucleic acids research. 2011.

Sensitized phenotypic screening identifies gene dosage sensitive region on chromosome 11 that predisposes to disease in mice. Ermakova, Olga, Piszczek, Lukasz, Luciani, Luisa, Cavalli, Florence MG, Ferreira, Tiago, Farley, Dominika, Rizzo, Stefania, Paolicelli, Rosa Chiara, Al‐Banchaabouchi, Mumna, Nerlov, Claus, EMBO molecular medicine. 2011.

Large-scale nuclear architecture and transcriptional control. Vaquerizas, Juan M, Akhtar, Asifa, Luscombe, Nicholas M, A Handbook of Transcription Factors. 2011.

An overview of prokaryotic transcription factors: a summary of function and occurrence in bacterial genomes. Seshasayee, Aswin Sai Narain, Sivaraman, Karthikeyan, Luscombe, Nicholas M, A handbook of transcription factors. 2011.

iCLIP-transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Konig, Julian, Zarnack, Kathi, Rot, Gregor, Curk, Tomaz, Kayikci, Melis, Zupan, Blaz, Turner, Daniel J, Luscombe, Nicholas M, Ule, Jernej, JoVE (Journal of Visualized Experiments). 2011.

Comparative genomics suggests differential deployment of linear and branched signaling across bacteria. Seshasayee, Aswin Sai Narain, Luscombe, Nicholas M, Molecular BioSystems. 2011.

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Koepke, Janine, Kaffarnik, Florian, Haag, Carl, Zarnack, Kathi, Luscombe, Nicholas M, König, Julian, Ule, Jernej, Kellner, Ronny, Begerow, Dominik, Feldbrügge, Michael, Molecular & cellular proteomics. 2011.

SpeCond: a method to detect condition-specific gene expression. Cavalli, Florence MG, Bourgon, Richard, Vaquerizas, Juan M, Luscombe, Nicholas M, Genome Biology. 2011.

A user's guide to the encyclopedia of DNA elements (ENCODE). ENCODE Project Consortium, PLoS biology. 2011.

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. König, Julian, Zarnack, Kathi, Rot, Gregor, Curk, Tomaž, Kayikci, Melis, Zupan, Blaž, Turner, Daniel J, Luscombe, Nicholas M, Ule, Jernej, Nature structural & molecular biology. 2010.

Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. Vaquerizas, Juan M, Suyama, Ritsuko, Kind, Jop, Miura, Kota, Luscombe, Nicholas M, Akhtar, Asifa, PLoS genetics. 2010.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Jolma, Arttu, Kivioja, Teemu, Toivonen, Jarkko, Cheng, Lu, Wei, Gonghong, Enge, Martin, Taipale, Mikko, Vaquerizas, Juan M, Yan, Jian, Sillanpää, Mikko J, Genome research. 2010.

The nonspecific lethal complex is a transcriptional regulator in Drosophila. Raja, Sunil Jayaramaiah, Charapitsa, Iryna, Conrad, Thomas, Vaquerizas, Juan M, Gebhardt, Philipp, Holz, Herbert, Kadlec, Jan, Fraterman, Sven, Luscombe, Nicholas M, Akhtar, Asifa, Molecular cell. 2010.

Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity. Seshasayee, Aswin SN, Fraser, Gillian M, Luscombe, Nicholas M, Nucleic acids research. 2010.
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Reimand, Jüri, Vaquerizas, Juan M, Todd, Annabel E, Vilo, Jaak, Luscombe, Nicholas M, Nucleic acids research. 2010.

iCLIP predicts the dual splicing effects of TIA-RNA interactions. Wang, Zhen, Kayikci, Melis, Briese, Michael, Zarnack, Kathi, Luscombe, Nicholas M, Rot, Gregor, Zupan, Blaž, Curk, Tomaž, Ule, Jernej, PLoS biology. 2010.

A census of human transcription factors: function, expression and evolution. Vaquerizas, Juan M, Kummerfeld, Sarah K, Teichmann, Sarah A, Luscombe, Nicholas M, Nature Reviews Genetics. 2009.

Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Seshasayee, Aswin SN, Fraser, Gillian M, Babu, M Madan, Luscombe, Nicholas M, Genome research. 2009.

Know your limits: assumptions, constraints and interpretation in systems biology. Ilsley, Garth R, Luscombe, Nicholas M, Apweiler, Rolf, Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics. 2009.

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Kind, Jop, Vaquerizas, Juan M, Gebhardt, Philipp, Gentzel, Marc, Luscombe, Nicholas M, Bertone, Paul, Akhtar, Asifa, cell. 2008.

Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. Pearson, Melanie M, Sebaihia, Mohammed, Churcher, Carol, Quail, Michael A, Seshasayee, Aswin S, Luscombe, Nicholas M, Abdellah, Zahra, Arrosmith, Claire, Atkin, Becky, Chillingworth, Tracey, Journal of bacteriology. 2008.

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972. Hancock, Viktoria, Seshasayee, Aswin S, Ussery, David W, Luscombe, Nicholas M, Klemm, Per, Molecular Genetics and Genomics. 2008.

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. Balaji, Sai, Babu, M Madan, Iyer, Lakshminarayan M, Luscombe, Nicholas M, Aravind, Lakshminarayan, Journal of molecular biology. 2006.

Transcriptional regulatory networks in bacteria: from input signals to output responses. Seshasayee, Aswin SN, Bertone, Paul, Fraser, Gillian M, Luscombe, Nicholas M, Current opinion in microbiology. 2006.

Extrapolating Traditional DNA Microarray Statistics to Tiling and Protein Microarray Technologies. Royce, Thomas E, Rozowsky, Joel S, Luscombe, Nicholas M, Emanuelsson, Olof, Yu, Haiyuan, Zhu, Xiaowei, Snyder, Michael, Gerstein, Mark B, Methods in enzymology. 2006.

Analytical evolutionary model for protein fold occurrence in genomes, accounting for the effects of gene duplication, deletion, acquisition and selective pressure. Koonin, Eugene V, Wolf, Yuri I, Karev, Georgy P, Kamal, Michael, Luscombe, Nicholas M, Qian, Jiang, Gerstein, Mark, Power Laws, Scale-Free Networks and Genome Biology. 2006.

Transcriptional networking. Teichmann, Sarah A, Bornberg-Bauer, Erich, Luscombe, Nicholas M, Genome Biology. 2005.

Genomic analysis of regulatory network dynamics reveals large topological changes. Luscombe, Nicholas M, Madan Babu, M, Yu, Haiyuan, Snyder, Michael, Teichmann, Sarah A, Gerstein, Mark, Nature. 2004.

Structure and evolution of transcriptional regulatory networks. Babu, M Madan, Luscombe, Nicholas M, Aravind, L, Gerstein, Mark, Teichmann, Sarah A, Current opinion in structural biology. 2004.

Annotation transfer between genomes: protein–protein interologs and protein–DNA regulogs. Yu, Haiyuan, Luscombe, Nicholas M, Lu, Hao Xin, Zhu, Xiaowei, Xia, Yu, Han, Jing-Dong J, Bertin, Nicolas, Chung, Sambath, Vidal, Marc, Gerstein, Mark, Genome research. 2004.

CREB binds to multiple loci on human chromosome 22. Euskirchen, Ghia, Royce, Thomas E, Bertone, Paul, Martone, Rebecca, Rinn, John L, Nelson, F Kenneth, Sayward, Fred, Luscombe, Nicholas M, Miller, Perry, Gerstein, Mark, Molecular and cellular biology. 2004.

GenCompass: a universal system for analysing gene expression for any genome. Luscombe, Nicholas M, Babu, M Madan, Trends in biotechnology. 2004.

Distribution of NF-κB-binding sites across human chromosome 22. Martone, Rebecca, Euskirchen, Ghia, Bertone, Paul, Hartman, Stephen, Royce, Thomas E, Luscombe, Nicholas M, Rinn, John L, Nelson, F Kenneth, Miller, Perry, Gerstein, Mark, Proceedings of the National Academy of Sciences. 2003.

The transcriptional activity of human Chromosome 22. Rinn, John L, Euskirchen, Ghia, Bertone, Paul, Martone, Rebecca, Luscombe, Nicholas M, Hartman, Stephen, Harrison, Paul M, Nelson, F Kenneth, Miller, Perry, Gerstein, Mark, Genes & development. 2003.

Genomic analysis of gene expression relationships in transcriptional regulatory networks. Yu, Haiyuan, Luscombe, Nicholas M, Qian, Jiang, Gerstein, Mark, TRENDS in Genetics. 2003.

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Qian, Jiang, Lin, Jimmy, Luscombe, Nicholas M, Yu, Haiyuan, Gerstein, Mark, Bioinformatics. 2003.

ExpressYourself: A modular platform for processing and visualizing microarray data. Luscombe, Nicholas M, Royce, Thomas E, Bertone, Paul, Echols, Nathaniel, Horak, Christine E, Chang, Joseph T, Snyder, Michael, Gerstein, Mark, Nucleic Acids Research. 2003.

Identification of novel functional elements in the human genome. Lian, Z, Euskirchen, G, Rinn, J, Martone, R, Bertone, P, Hartman, S, Royce, T, Nelson, K, Sayward, F, Luscombe, N, Cold Spring Harbor symposia on quantitative biology. 2003.

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Horak, Christine E, Luscombe, Nicholas M, Qian, Jiang, Bertone, Paul, Piccirrillo, Stacy, Gerstein, Mark, Snyder, Michael, Genes & development. 2002.

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Harrison, Paul M, Hegyi, Hedi, Balasubramanian, Suganthi, Luscombe, Nicholas M, Bertone, Paul, Echols, Nathaniel, Johnson, Ted, Gerstein, Mark, Genome research. 2002.

GATA-1 binding sites mapped in the β-globin locus by using mammalian chIp-chip analysis. Horak, Christine E, Mahajan, Milind C, Luscombe, Nicholas M, Gerstein, Mark, Weissman, Sherman M, Snyder, Michael, Proceedings of the National Academy of Sciences. 2002.

Protein–DNA interactions: amino acid conservation and the effects of mutations on binding specificity. Luscombe, Nicholas M, Thornton, Janet M, Journal of molecular biology. 2002.

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Luscombe, Nicholas M, Qian, Jiang, Zhang, Zhaolei, Johnson, Ted, Gerstein, Mark, Genome Biol. 2002.

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Echols, Nathaniel, Harrison, Paul, Balasubramanian, Suganthi, Luscombe, Nicholas M, Bertone, Paul, Zhang, Zhaolei, Gerstein, Mark, Nucleic acids research. 2002.

SNPs on human chromosomes 21 and 22–analysis in terms of protein features and pseudogenes. Balasubramanian, Suganthi, Harrison, Paul, Hegyi, Hedi, Bertone, Paul, Luscombe, Nicholas, Echols, Nathaniel, McGarvey, Patrick, Zhang, ZhaoLei, Gerstein, Mark, Pharmacogenomics. 2002.

Structural genomics: a new era for pharmaceutical research. Liu, Yang, Luscombe, Nicholas M, Alexandrov, Vadim, Bertone, Paul, Harrison, Paul, Zhang, Zhaolei, Gerstein, Mark, . 2002.

Amino acid–base interactions: a three-dimensional analysis of protein–DNA interactions at an atomic level. Luscombe, Nicholas M, Laskowski, Roman A, Thornton, Janet M, Nucleic acids research. 2001.
Protein–RNA interactions: a structural analysis. Jones, Susan, Daley, David TA, Luscombe, Nicholas M, Berman, Helen M, Thornton, Janet M, Nucleic acids research. 2001.

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. Qian, Jiang, Luscombe, Nicholas M, Gerstein, Mark, Journal of molecular biology. 2001.

What is bioinformatics? A proposed definition and overview of the field. Luscombe, Nicholas M, Greenbaum, Dov, Gerstein, Mark, Methods of information in medicine. 2001.

Interrelating different types of genomic data, from proteome to secretome:'oming in on function. Greenbaum, Dov, Luscombe, Nicholas M, Jansen, Ronald, Qian, Jiang, Gerstein, Mark, Genome research. 2001.

What is bioinformatics? An introduction and overview. Luscombe, Nicholas M, Greenbaum, Dov, Gerstein, Mark, Yearbook of medical informatics. 2001.

An overview of the structures of protein-DNA complexes. Luscombe, Nicholas M, Austin, Susan E, Berman, Helen M, Thornton, Janet M, Genome biology. 2000.

New tools and resources for analysing protein structures and their interactions. Luscombe, Nicholas M, Laskowski, Roman A, Westhead, David R, Milburn, Duncan, Jones, Susan, Karmirantzou, Maria, Thornton, Janet M, Acta Crystallographica Section D: Biological Crystallography. 1998.

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. Luscombe, Nicholas M, Laskowski, Roman A, Thornton, Janet M, Nucleic acids research. 1997.

Protein clefts in molecular recognition and function.. Laskowski, Roman A, Luscombe, Nicholas M, Swindells, Mark B, Thornton, Janet M, Protein science: a publication of the Protein Society. 1996.

A Moonlighting Function of Aldh18a1 Supports Pausing RNA Polymerase II in Promoter-Proximal Regions. Rafiee, Mahmoud-Reza, Rohban, Sara, Davey, Karen, Steinhauser, Sebastian, Krijgsveld, Jeroen, Ule, Jernej, Luscombe, Nicholas M, Available at SSRN 4087712. 2022.