Luscombe Group PublicationsThe following is a list of publications for the Luscombe group.
N.B. * denotes joint first author.
Protein-RNA interactions: new genomic technologies and perspectives.
Nature Reviews Genetics 13: 77-83.pubmed abstract full-text PDF
Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12.
Nucleic Acids Research, Epub ahead of print.pubmed abstract full-text PDF
How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.
Methods in Molecular Biology 786: 3-19pubmed abstract full-text PDF
A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast.
Genome Research 22: 84-94pubmed abstract full-text PDF
SpeCond: a method to detect condition-specific gene expression.
Genome Biology 12: R101.pubmed abstract full-text PDF
Comparative genomics suggests differential deployment of linear and branched signaling across bacteria.
Mol Biosystems 7: 3042-9pubmed abstract full-text PDF
The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
Molecular and Cellular Proteomics 10: M111.011213pubmed abstract full-text PDF
iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution.
Journal of Visualized Experiments 50; doi: 10.3791/2638.pubmed abstract full-text PDF
An overview of prokaryotic transcription factors : a summary of function and occurrence in bacterial genomes.
A Handbook of Transcriptional Factors (Hughes T.R., Editor). Springer. Subcellular Biochemistry 52: 7-23.pubmed abstract full-text PDF
Large-scale nuclear architecture and transcriptional control.
A Handbook of Transcription Factors (Hughes T.R., Editor). Springer, Subcellular Biochemistry 52: 279-95.pubmed abstract full-text PDF
A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
PLoS Biology 9: e1001046.pubmed abstract full-text PDF Press Release
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 full-text PDF
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli.
Nucleic Acids Research 39: 2073-91.pubmed abstract full-text PDF
iCLIP predicts the dual splicing effects of TIA-RNA interactions.
PLoS Biology 8: e1000530.pubmed abstract full-text PDF
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
Nature Structural and Molecular Biology 17: 909-15.pubmed abstract full-text PDF
The NSL complex is a novel transcriptional regulator in Drosophila.
Molecular Cell 38: 827-41.pubmed abstract full-text PDF
Comparative genomics of cyclic-di-GMP signalling in bacteria: post-translational regulation and catalytic activity.
Nucleic Acids Research 38:5970-81.pubmed abstract full-text PDF
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.
Nucleic Acids Research 38: 4768-77.pubmed abstract full-text PDF
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Genome Research 20: 861-73.pubmed abstract full-text PDF
Nuclear pore components Nup153 and Megator define transcriptionally active regions in the Drosophila genome.
PLoS Genetics 6: e1000846.pubmed abstract full-text PDF Epigenetics 2010
Know Your Limits: Assumptions, Constraints and Interpretation in Systems Biology.
Biochimica et Biophysica Acta 1794: 1280-7.pubmed abstract full-text PDF
A census of human transcription factors: function, expression and evolution.
Nature Reviews Genetics 10: 252-63.pubmed abstract full-text PDF website
Principles of transcriptional regulation and evolution of the metabolic system in E. coli.
Genome Research 19: 79-91.pubmed abstract full-text PDF
Genome-wide Analysis Reveals MOF as a Key Regulator of Dosage Compensation and Gene Expression in Drosophila.
Cell, 133(5): 813-828.pubmed abstract full-text PDF Press Release
Complete Genome Sequence of Uropathogenic Proteus mirabilis, a Master of both Adherence and Motility.
Journal of Bacteriology 190: 4027-4037.pubmed abstract full-text PDF
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.
Molecular Genetics and Genomics 279: 523-34.pubmed abstract full-text PDF
Transcriptional regulatory networks in bacteria: from input signals to output responses.
Current Opinions Microbiology 9: 511-519. [Epub 2006 Aug 30].pubmed abstract full-text PDF
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
Methods in Enzymology 411: 282-311.pubmed abstract full-text PDF
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
Journal of Molecular Biology 360: 213-27.pubmed abstract full-text PDF
Genome Biology 69: 344.pubmed abstract full-text PDF
GenCompass: a universal system for analysing gene expression for any genome.
Trends in Biotechnology 22(11): 552-555.pubmed abstract full-text PDF
Genomic analysis of regulatory network dynamics reveals large topological changes.
Nature 431: 308-312.pubmed abstract full-text PDF website
Structure and evolution of transcriptional regulatory networks.
Current Opinions in Structural Biology 14: 283-291.pubmed abstract full-text PDF
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome Research 14: 1107-1118.pubmed abstract full-text PDF website
CREB binds to multiple loci on human chromosome 22.
Molecular and Cellular Biology 24: 3804-3814.pubmed abstract full-text PDF
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinformatics 19: 1917-1926.pubmed abstract full-text PDF
Distribution of NF-kappaB-binding sites across human chromosome 22.
Proceedings of the National Academy of Science 100: 12247-12252.pubmed abstract full-text PDF
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
Trend in Genetics 19(8): 422-427 (2003).pubmed abstract full-text PDF website
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic Acids Research 31(13): 3477-3482.pubmed abstract full-text PDF website
The transcriptional activity of human Chromosome 22.
Genes and Development 17(4): 529-40.pubmed abstract full-text PDF
Identification of novel functional elements in the human genome.
Cold Spring Harbor Symposium in Quantitative Biology 68: 317-322.pubmed
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes and Development 16(23): 3017-3033.pubmed abstract full-text PDF
The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.
Genome Biology 3: research0040.1-0040.7.pubmed abstract full-text PDF
Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.
Journal of Molecular Biology 320(5): 991-1009.pubmed abstract full-text PDF Appendices 1 and 2 Appendix 1 Appendix 2
SNPs on human chromosomes 21 and 22 - analysis in terms of protein features and pseudogenes.
Pharmacogenomics 3: 393-402.pubmed abstract full-text PDF
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.
Nucleic Acids Research 30(11): 2515-2523.pubmed abstract full-text PDF
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.
Proceedings of the National Academy of Science 99(5): 2924-2929.pubmed abstract full-text PDF
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.
Genome Research 12: 272-280.pubmed abstract full-text PDF
Structural genomics: a new era for pharmaceutical research.
Genome Biology 3 Reports: 4004.1-4004.3.pubmed abstract full-text PDF
What is bioinformatics? An introduction and overview .
2001 International Medical Informatics Association Yearbook: 83-100.full-text PDF
Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.
Journal of Molecular Biology 313(4): 673-681.pubmed abstract full-text PDF
What is bioinformatics? A proposed definition and overview of the field.
Methods of Information in Medicine 40(4): 346-358. (Review).pubmed abstract full-text PDF
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
Genome Research 11: 1463-1468.pubmed abstract full-text PDF
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
Nucleic Acids Research 29: 2860-2874.pubmed abstract full-text PDF
Protein-RNA interactions: a structural analysis.
Nucleic Acids Research 29: 943-954.pubmed abstract full-text PDF
1996 - 2000
An overview of the structures of protein-DNA complexes.
Genome Biology 1: reviews001.1-001.37.pubmed abstract PDF: short version full-text PDF full-text PDF: Russian version
New tools and resources for analysing protein structures and their interactions.
Acta Crystallographica D54: 1132-1138.pubmed abstract
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Nucleic Acids Research 25: 4940-4945.pubmed abstract full-text PDF
Protein clefts in molecular recognition and function.
Protein Science 5: 2438-2452.pubmed abstract
N.B. * denotes joint first author.