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What is AI? Applications of artificial intelligence to dermatology.

Du-Harpur X, Watt FM, Luscombe NM, Lynch MD.

Br J Dermatol. 2020 Jan 20. doi: 10.1111/bjd.18880. [Epub ahead of print] Review.


A systems view of spliceosomal assembly and branchpoints with iCLIP.

Briese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J.

Nat Struct Mol Biol. 2019 Oct;26(10):930-940. doi: 10.1038/s41594-019-0300-4. Epub 2019 Sep 30.


Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis.

Tyzack GE, Luisier R, Taha DM, Neeves J, Modic M, Mitchell JS, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM, Patani R.

Brain. 2019 Sep 1;142(9):2572-2580. doi: 10.1093/brain/awz217.


Genome-wide reconstitution of chromatin transactions reveals that RSC preferentially disrupts H2AZ-containing nucleosomes.

Cakiroglu A, Clapier CR, Ehrensberger AH, Darbo E, Cairns BR, Luscombe NM, Svejstrup JQ.

Genome Res. 2019 Jun;29(6):988-998. doi: 10.1101/gr.243139.118. Epub 2019 May 16.


Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW; HipSci Consortium, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM.

Cell Rep. 2019 Feb 19;26(8):2078-2087.e3. doi: 10.1016/j.celrep.2019.01.094.


Publisher Correction: c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells.

Gabryšová L, Alvarez-Martinez M, Luisier R, Cox LS, Sodenkamp J, Hosking C, Pérez-Mazliah D, Whicher C, Kannan Y, Potempa K, Wu X, Bhaw L, Wende H, Sieweke MH, Elgar G, Wilson M, Briscoe J, Metzis V, Langhorne J, Luscombe NM, O'Garra A.

Nat Immunol. 2019 Mar;20(3):374. doi: 10.1038/s41590-019-0331-3.


Target-Specific Precision of CRISPR-Mediated Genome Editing.

Chakrabarti AM, Henser-Brownhill T, Monserrat J, Poetsch AR, Luscombe NM, Scaffidi P.

Mol Cell. 2019 Feb 21;73(4):699-713.e6. doi: 10.1016/j.molcel.2018.11.031. Epub 2018 Dec 13.


Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis.

Poetsch AR, Boulton SJ, Luscombe NM.

Genome Biol. 2018 Dec 7;19(1):215. doi: 10.1186/s13059-018-1582-2.


Nervous System Regionalization Entails Axial Allocation before Neural Differentiation.

Metzis V, Steinhauser S, Pakanavicius E, Gouti M, Stamataki D, Ivanovitch K, Watson T, Rayon T, Mousavy Gharavy SN, Lovell-Badge R, Luscombe NM, Briscoe J.

Cell. 2018 Nov 1;175(4):1105-1118.e17. doi: 10.1016/j.cell.2018.09.040. Epub 2018 Oct 18.


Somatic TP53 Mutations Are Detectable in Circulating Tumor DNA from Children with Anaplastic Wilms Tumors.

Treger TD, Chagtai T, Butcher R, Cresswell GD, Al-Saadi R, Brok J, Williams RD, Roberts C, Luscombe NM, Pritchard Jones K, Mifsud W.

Transl Oncol. 2018 Dec;11(6):1301-1306. doi: 10.1016/j.tranon.2018.08.006. Epub 2018 Aug 29.


Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease.

Steele AJ, Denaxas SC, Shah AD, Hemingway H, Luscombe NM.

PLoS One. 2018 Aug 31;13(8):e0202344. doi: 10.1371/journal.pone.0202344. eCollection 2018.


Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing.

Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J.

Cell. 2018 Aug 23;174(5):1067-1081.e17. doi: 10.1016/j.cell.2018.07.001. Epub 2018 Aug 2.


Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS.

Luisier R, Tyzack GE, Hall CE, Mitchell JS, Devine H, Taha DM, Malik B, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM, Patani R.

Nat Commun. 2018 May 22;9(1):2010. doi: 10.1038/s41467-018-04373-8.


c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells.

Gabryšová L, Alvarez-Martinez M, Luisier R, Cox LS, Sodenkamp J, Hosking C, Pérez-Mazliah D, Whicher C, Kannan Y, Potempa K, Wu X, Bhaw L, Wende H, Sieweke MH, Elgar G, Wilson M, Briscoe J, Metzis V, Langhorne J, Luscombe NM, O'Garra A.

Nat Immunol. 2018 May;19(5):497-507. doi: 10.1038/s41590-018-0083-5. Epub 2018 Apr 16. Erratum in: Nat Immunol. 2019 Mar;20(3):374.


Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

Turajlic S, Xu H, Litchfield K, Rowan A, Horswell S, Chambers T, O'Brien T, Lopez JI, Watkins TBK, Nicol D, Stares M, Challacombe B, Hazell S, Chandra A, Mitchell TJ, Au L, Eichler-Jonsson C, Jabbar F, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Stewart A, Xing W, Smith JC, Escudero M, Huffman A, Matthews N, Elgar G, Phillimore B, Costa M, Begum S, Ward S, Salm M, Boeing S, Fisher R, Spain L, Navas C, Grönroos E, Hobor S, Sharma S, Aurangzeb I, Lall S, Polson A, Varia M, Horsfield C, Fotiadis N, Pickering L, Schwarz RF, Silva B, Herrero J, Luscombe NM, Jamal-Hanjani M, Rosenthal R, Birkbak NJ, Wilson GA, Pipek O, Ribli D, Krzystanek M, Csabai I, Szallasi Z, Gore M, McGranahan N, Van Loo P, Campbell P, Larkin J, Swanton C; TRACERx Renal Consortium.

Cell. 2018 Apr 19;173(3):595-610.e11. doi: 10.1016/j.cell.2018.03.043. Epub 2018 Apr 12.


Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome.

Li C, Lenhard B, Luscombe NM.

Genome Res. 2018 May;28(5):676-688. doi: 10.1101/gr.231449.117. Epub 2018 Apr 4.


Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells.

Ghahramani A, Donati G, Luscombe NM, Watt FM.

Genome Biol. 2018 Jan 15;19(1):3. doi: 10.1186/s13059-017-1384-y.


Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS.

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, Patani R.

Cell Rep. 2017 May 30;19(9):1739-1749. doi: 10.1016/j.celrep.2017.05.024.


GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

Mifsud B, Martincorena I, Darbo E, Sugar R, Schoenfelder S, Fraser P, Luscombe NM.

PLoS One. 2017 Apr 5;12(4):e0174744. doi: 10.1371/journal.pone.0174744. eCollection 2017. Erratum in: PLoS One. 2017 May 3;12 (5):e0177280.


Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.

Sugimoto Y, Chakrabarti AM, Luscombe NM, Ule J.

Nat Protoc. 2017 Mar;12(3):611-637. doi: 10.1038/nprot.2016.188. Epub 2017 Feb 23.


Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.

Cakiroglu SA, Zaugg JB, Luscombe NM.

Nucleic Acids Res. 2016 Sep 30;44(17):8065-72. doi: 10.1093/nar/gkw683. Epub 2016 Aug 4.


Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications.

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, Mifsud W.

EBioMedicine. 2016 Jul;9:120-129. doi: 10.1016/j.ebiom.2016.05.029. Epub 2016 May 27.


Functional interplay between MSL1 and CDK7 controls RNA polymerase II Ser5 phosphorylation.

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, Akhtar A.

Nat Struct Mol Biol. 2016 Jun;23(6):580-9. doi: 10.1038/nsmb.3233. Epub 2016 May 16.


Inactivation of the ATMIN/ATM pathway protects against glioblastoma formation.

Blake SM, Stricker SH, Halavach H, Poetsch AR, Cresswell G, Kelly G, Kanu N, Marino S, Luscombe NM, Pollard SM, Behrens A.

Elife. 2016 Mar 17;5. pii: e08711. doi: 10.7554/eLife.08711.


Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J.

Nucleic Acids Res. 2015 Dec 2;43(21):10492-505. doi: 10.1093/nar/gkv956. Epub 2015 Sep 22.


Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

Schoenfelder S, Sugar R, Dimond A, Javierre BM, 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, Elderkin S.

Nat Genet. 2015 Oct;47(10):1179-1186. doi: 10.1038/ng.3393. Epub 2015 Aug 31.


Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

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, Osborne CS.

Nat Genet. 2015 Jun;47(6):598-606. doi: 10.1038/ng.3286. Epub 2015 May 4.


hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J.

Nature. 2015 Mar 26;519(7544):491-4. doi: 10.1038/nature14280. Epub 2015 Mar 18.


The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, 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, Fraser P.

Genome Res. 2015 Apr;25(4):582-97. doi: 10.1101/gr.185272.114. Epub 2015 Mar 9.


Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.

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 LH, Walsh CA, Shi Y.

Genes Dev. 2015 Mar 1;29(5):501-12. doi: 10.1101/gad.258483.115.


Role of histone modifications and early termination in pervasive transcription and antisense-mediated gene silencing in yeast.

Castelnuovo M, Zaugg JB, Guffanti E, Maffioletti A, Camblong J, Xu Z, Clauder-Münster S, Steinmetz LM, Luscombe NM, Stutz F.

Nucleic Acids Res. 2014 Apr;42(7):4348-62. doi: 10.1093/nar/gku100. Epub 2014 Feb 4.


Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements.

Harding JL, Horswell S, Heliot C, Armisen J, Zimmerman LB, Luscombe NM, Miska EA, Hill CS.

Genome Res. 2014 Jan;24(1):96-106. doi: 10.1101/gr.144469.112. Epub 2013 Sep 24.


Cellular resolution models for even skipped regulation in the entire Drosophila embryo.

Ilsley GR, Fisher J, Apweiler R, De Pace AH, Luscombe NM.

Elife. 2013 Aug 6;2:e00522. doi: 10.7554/eLife.00522.


Response to Comments on "Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters".

Vaquerizas JM, Cavalli FM, Conrad T, Akhtar A, Luscombe NM.

Science. 2013 Apr 19;340(6130):273. doi: 10.1126/science.1232874.


Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.

Zarnack K, König J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J.

Cell. 2013 Jan 31;152(3):453-66. doi: 10.1016/j.cell.2012.12.023.


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.


Non-random mutation: the evolution of targeted hypermutation and hypomutation.

Martincorena I, Luscombe NM.

Bioessays. 2013 Feb;35(2):123-30. doi: 10.1002/bies.201200150. Epub 2012 Dec 20. Review.


Gene loops enhance transcriptional directionality.

Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ.

Science. 2012 Nov 2;338(6107):671-5. doi: 10.1126/science.1224350. Epub 2012 Sep 27.


Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters.

Conrad T, Cavalli FM, Vaquerizas JM, Luscombe NM, Akhtar A.

Science. 2012 Aug 10;337(6095):742-6. doi: 10.1126/science.1221428. Epub 2012 Jul 19.


The NSL complex regulates housekeeping genes in Drosophila.

Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A.

PLoS Genet. 2012;8(6):e1002736. doi: 10.1371/journal.pgen.1002736. Epub 2012 Jun 14.


m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence.

Reimand J, Aun A, Vilo J, Vaquerizas JM, Sedman J, Luscombe NM.

Genome Biol. 2012 Jun 21;13(6):R55. doi: 10.1186/gb-2012-13-6-r55.


Genomics of DNA cytosine methylation in Escherichia coli reveals its role in stationary phase transcription.

Kahramanoglou C, Prieto AI, Khedkar S, Haase B, Gupta A, Benes V, Fraser GM, Luscombe NM, Seshasayee AS.

Nat Commun. 2012 Jun 6;3:886. doi: 10.1038/ncomms1878.


Evidence of non-random mutation rates suggests an evolutionary risk management strategy.

Martincorena I, Seshasayee AS, Luscombe NM.

Nature. 2012 May 3;485(7396):95-8. doi: 10.1038/nature10995.


The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex.

Conrad T, Cavalli FM, Holz H, Hallacli E, Kind J, Ilik I, Vaquerizas JM, Luscombe NM, Akhtar A.

Dev Cell. 2012 Mar 13;22(3):610-24. doi: 10.1016/j.devcel.2011.12.016.


Protein-RNA interactions: new genomic technologies and perspectives.

König J, Zarnack K, Luscombe NM, Ule J.

Nat Rev Genet. 2012 Jan 18;13(2):77-83. doi: 10.1038/nrg3141. Review. Erratum in: Nat Rev Genet. 2012 Mar;13(3):220.


Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.

Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee AS, Luscombe NM.

Nucleic Acids Res. 2012 Apr;40(8):3524-37. doi: 10.1093/nar/gkr1236. Epub 2011 Dec 17.


SpeCond: a method to detect condition-specific gene expression.

Cavalli FM, Bourgon R, Vaquerizas JM, Luscombe NM.

Genome Biol. 2011 Oct 18;12(10):R101. doi: 10.1186/gb-2011-12-10-r101. Erratum in: Genome Biol. 2011;12(12):413. Huber, Wolfgang [removed].


How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.

Vaquerizas JM, Teichmann SA, Luscombe NM.

Methods Mol Biol. 2012;786:3-19. doi: 10.1007/978-1-61779-292-2_1. Review.


A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast.

Zaugg JB, Luscombe NM.

Genome Res. 2012 Jan;22(1):84-94. doi: 10.1101/gr.124099.111. Epub 2011 Sep 19.


Comparative genomics suggests differential deployment of linear and branched signaling across bacteria.

Seshasayee AS, Luscombe NM.

Mol Biosyst. 2011 Nov;7(11):3042-9. doi: 10.1039/c1mb05260h. Epub 2011 Aug 30.


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