Preprints are published on bioRxiv. Find publications on PubMed and Google Scholar.
(* Joint first author, + Joint last author)

bioRxiv preprints

Attig J, Agostini F, Gooding C, Singh A, Chakrabarti AM, Haberman N, Emmett W, Smith CWJ, Luscombe NM, Ule J.
Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing.
bioRxiv 297853; doi:

Ghahramani A, Watt FM, Luscombe NM.
Generative adversarial networks uncover epidermal regulators and predict single cell perturbations.
bioRxiv 262501; doi:

Steele AJ, Cakiroglu SA, Shah AD, Denaxas SC, Hemingway H, Luscombe NM.
Machine learning models in electronic health records can outperform conventional survival models for predicting patient mortality in coronary artery disease.
bioRxiv 256008; doi:

Metzis V, Steinhauser S, Pakanavicius E, Gouti M, Stamataki D, Lovell-Badge R, Luscombe NM, Briscoe J.
Regionalization of the nervous system requires axial allocation prior to neural lineage commitment.
bioRxiv 229203; doi:

Chakrabarti AM, Haberman N, Praznik A, Luscombe NM, Ule J.
Data Science Issues in Understanding Protein-RNA Interactions.
bioRxiv 208124; doi:

Ilsley GR, Suyama R, Noda T, Satoh N, and Luscombe NM.
Identifying developmentally important genes with single-cell RNA-seq from an embryo.
bioRxiv 197699; doi:

Andreassi C, Luisier R, Crerar H, Franke S, Luscombe NM, Cuda G, Gaspari M, and Riccio A.
3′ UTR Remodelling of Axonal Transcripts in Sympathetic Neurons.
bioRxiv 170100; doi:

Poetsch AR, Boulton SJ+, and Luscombe NM+.
Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis.
bioRxiv 168153; doi:


Luisier R*, Tyzack GE*, Hall CE, Mitchell JS, Devine H, Taha DM, Malik B, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM+, and Patani+.
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS.
Nat Comm. In Press.


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. (2018).
c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells.
Nat Immunol. 19:497-507

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. (2018).
Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.
Cell. 173:595-610.e11.

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

Ghahramani A, Donati G, Luscombe NM+, and Watt FM+. (2018).
Epidermal Wnt signalling regulates transcriptome heterogeneity and proliferative fate in neighbouring cells.
Genome Biol. 19:3.


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 Rep. 19:1739-1749. 

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. 

Sugimoto Y, Chakrabarti AM, Luscombe NM, and Ule J. (2017).
Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
Nat Protoc. 12:611-637. 


Cakiroglu SA, Zaugg JB+, and Luscombe NM+. (2016).
Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation.
Nucleic Acids Res. 44:8065-72. 

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. 9:120-9.

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.
Nat Struct Mol Biol. 23:580-9. .

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.


Kiselev VY, Juvin V, Malek M, Luscombe N, Hawkins P, Le Novère N, Stephens L. (2015). 
Perturbations of PIP3 signalling trigger a global remodelling of mRNA landscape and reveal a transcriptional feedback loop.
Nucleic Acids Res. 43:9663-79.

Tajnik M*, Vigilante A*, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J. (2015).
Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.
Nucleic Acids Res. 43:10492-10505.

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. (2015).
Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.
Nat Genet. 47:1179-1186.

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 Genet. 47:598-606.

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+, and Peter Fraser+. (2015).
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.
Genome Res. 25:582-597.

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.

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. (2015).
Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.
Genes Dev. 29:501-512.

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 Res 42:4348-62.

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 Res 24:96-106.

Ilsley GR, Fisher J, Apweiler R, DePace AH, and Luscombe NM. (2013)
Cellular resolution models for even skipped regulation in the entire Drosophila embryo.
eLife 340:273.

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.
Mol Cell 51:156-73.

Vaquerizas JM, Cavalli FM, 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.

Martincorena I and Luscombe NM. (2013)
Non-random mutation: the evolution of targeted hypermutation and hypomutation.
BioEssays 35:123-30.

*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 uncontrolled exonization of Alu elements. 
Cell 152:453-66.

Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P, Morgunoca 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 152:327-39.

*Tan-Wong SM, *Zaugg JB, *Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari ZA, Luscombe NM, Steinmetz LM, and Proudfoot NJ. (2012)
Gene loops enhance transcriptional directionality. 
Science 338:671-5.

The ENCODE Project Consortium. (2012)
An Integrated Encyclopedia of DNA Elements in the Human Genome.
Nature 489:57-74.

*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 337:742-6.

*Lam KC, *Muhlpfordt F, *Vaquerizas JM, Raja SJ, Luscombe NM, Manke, T, and Akhtar A. (2012)
The NSL complex regulates housekeeping genes in Drosophila.
PLoS Genetics 8:e1002736.

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.

Kahramanoglou C, Prieto AI, Khedar S, Haase B, Gupta A, Benes V, Fraser GM, +Luscombe NM, and+Seshasayee ASN. (2012)
Genome-scale analysis of DNA cytosine methylation in Escherichia coli K12 reveals its role in limiting stationary phase transcription. 
Nature Communications 3:886.

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.

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.

Conrad T, Cavalli FMG, 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.

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

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. 

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

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

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

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.

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. 

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

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.

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

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.

*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.

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. 

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.

*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. 

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.

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. 

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. 

*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. 

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.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, and Luscombe NM. (2009)
A census of human transcription factors: function, expression, and evolution. 
Nature Reviews Genetics 10:252-63.

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.

*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.

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.

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.

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.

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.

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.

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. 

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

Luscombe NM and Babu MM. (2004)
GenCompass: a universal system for analysing gene expression for any genome. 
Trends in Biotechnology 22:552-5.

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, and Gerstein M. (2004)
Genomic analysis of regulatory network dynamics reveals large topological changes. 
Nature 431:308-12.

*Babu MM, *Luscombe NM, Aravind L, Gerstein M, and Teichmann SA. (2004)
Structure and evolution of transcriptional regulatory networks. 
Current Opinions in Structural Biology 14:283-91.

Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, and Gerstein M. (2004)
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. 
Genome Research 14:1107-18.

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, and Snyder M. (2004)
CREB binds to multiple loci on human chromosome 22.
Molecular & Cellular Biology 24:3804-14.

Qian J, Lin J, Luscombe NM, Yu H, and Gerstein M. (2003)
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. 
Bioinformatics 19:1917-26.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, and Snyder M. (2003)
Distribution of NF-kB-binding sites across human chromosome 22. 
Proceedings of the National Academy of Sciences USA 100:12247-52.

*Yu H, *Luscombe NM, Qian J, and Gerstein M. (2003)
Genomic analysis of gene expression relationships in transcriptional regulatory networks. 
Trends in Genetics 19:422-7.

Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, and Gerstein M. (2003)
ExpressYourself: A modular platform for processing and visualizing microarray data. 
Nucleic Acids Research 31:3477-82.

*Rinn JL, *Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, and Snyder M. (2003)
The transcriptional activity of human chromosome 22. 
Genes & Development 17:529-40.

Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, and Snyder M. (2003)
Identification of novel functional elements in the human genome. 
Cold Spring Harbor Symposia on Quantitative Biology 68:317-22.

Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, and Snyder M. (2002)
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae
Genes & Development 16:3017-33.

Luscombe NM, Qian J, Zhang Z, Johnson T, and Gerstein M. (2002)
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. 
Genome Biology 3:RESEARCH0040.

Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, and Gerstein M. (2002)
SNPs on human chromosomes 21 and 22 - analysis in terms of protein features and pseudogenes. 
Pharmacogenomics 3:393-402.

Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, and Gerstein M. (2002)
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. 
Nucleic Acids Research 30:2515-23.

Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, and Snyder M. (2002)
GATA-1 binding sites mapped in the beta-globin locus by using mammalian ChIp-chip analysis. 
Proceedings of the National Academy of Sciences USA 99:2924-9.

Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, and Gerstein M. (2002)
Structural genomics: a new era for pharmaceutical research. 
Genome Biology 3:REPORTS4004.

Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, and Gerstein M. (2002)
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. 
Genome Research 12:272-80.

Luscombe NM and Thornton JM. (2002)
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Journal of Molecular Biology 320:991-1009.

*Qian J, *Luscombe NM, and Gerstein M. (2001)
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. 
Journal of Molecular Biology 313:673-81.

Luscombe NM, Greenbaum D, and Gerstein M. (2001)
What is bioinformatics? A proposed definition and overview of the field. 
Methods of Information in Medicine 40:346-58.

Luscombe NM, Greenbaum D, and Gerstein M. (2001)
What is bioinformatics? An introduction and overview. 
International Medical Informatics Yearbook 2001:83-100.

Greenbaum D, Luscombe NM, Jansen R, Qian J, and Gerstein M. (2001)
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function. 
Genome Research 11:1463-8.

Luscombe NM, Laskowski RA, and Thornton JM. (2001)
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. 
Nucleic Acids Research 29:2860-74.

Jones S, Daley DT, Luscombe NM, Berman HM, and Thornton JM. (2001)
Protein-RNA interactions: a structural analysis. 
Nucleic Acids Research. 29:943-54.

Luscombe NM, Austin SE, Berman HM, and Thornton JM. (2000)
An overview of the structures of protein-DNA complexes. 
Genome Biology 1:REVIEWS001.

Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, and Thornton JM. (1998)
New tools and resources for analysing protein structures and their interactions.
Acta Crystallografica D 54:1132-8.

Luscombe NM, Laskowski RA, and Thornton JM. (1997)
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions. 
Nucleic Acids Research. 25:4940-5.

Laskowski RA, Luscombe NM, Swindells MB, and Thornton JM. (1996)
Protein clefts in molecular recognition and function. 
Protein Science 5:2438-52.