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Luscombe Group Publications

The following is a list of publications for the Luscombe group.
N.B. * denotes joint first author.


2012

Koenig J., Zarnack K., Luscombe N.M., Ule J. (2012)
Protein-RNA interactions: new genomic technologies and perspectives.
Nature Reviews Genetics 13: 77-83.
pubmed abstract full-text PDF

Prieto A.I., Kahramanoglou C., Ali R.M., Fraser G.M., Seshasayee A.S., Luscombe N.M. (2012)
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

Vaquerizas J.M., Teichmann S.A., Luscombe N.M. (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 full-text PDF

Zaugg J.B., Luscombe N.M. (2012)
A genomic model of condition-specific nucleosome behaviour explains transcriptional activity in yeast.
Genome Research 22: 84-94
pubmed abstract full-text PDF

2011

Cavalli F.M.G., Bourgon R., Vaquerizas J.M., Luscombe N.M. (2011)
SpeCond: a method to detect condition-specific gene expression.
Genome Biology 12: R101.
pubmed abstract full-text PDF

Seshasayee A.S., Luscombe N.M. (2011)
Comparative genomics suggests differential deployment of linear and branched signaling across bacteria.
Mol Biosystems 7: 3042-9
pubmed abstract full-text PDF

Koepke J., Kaffarnik F., Haag C., Zarnack K., Luscombe N.M., Konig J., Ule J., Kellner R., Begerow D., Feldbrugge M. (2011)
The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
Molecular and Cellular Proteomics 10: M111.011213
pubmed abstract full-text PDF

Konig J., Zarnack K., Rot G., Curk T., Kayikci M., Zupan B., Turner D.J., Luscombe N.M., Ule J. (2011)
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

Seshasayee A.S.N., Sivaraman K., Luscombe N.M. (2011)
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

Vaquerizas J.M., Akhtar A., Luscombe N.M. (2011)
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

ENCODE Project Consortium [including Vaquerizas J.M. and Luscombe N.M.] (2011)
A User's Guide to the Encyclopedia of DNA Elements (ENCODE).
PLoS Biology 9: e1001046.
pubmed abstract full-text PDF Press Release

Ermakova P., Piszczek L., Luciani L., Cavalli F.M.G., Ferreira T., Farley D., Rizzo S., Paolicelli R.C., Al-Banchaabouchi M., Nerlov C., Moriggl R., Luscombe N.M., 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 full-text PDF

Kahramanoglou C.*, Seshasayee A.S.N.*, Prieto A.I., Ibberson D., Schmidt D., Zimmermann J., Benes V., Fraser G.M.*, and Luscombe N.M.* (2011)
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

2010

Wang Z.*, Kayicki M.*, Briese M., Zarnack K., Luscombe N.M., Rot G., Zupan B., Curk T., Ule J. (2010)
iCLIP predicts the dual splicing effects of TIA-RNA interactions.
PLoS Biology 8: e1000530.
pubmed abstract full-text PDF

K�nig J.*, Zarnack K.*, Rot G., Curk T., Kayikci M., Zupan B., Tuner D.J., Luscombe N.M., Ule J. (2010)
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

Raja S.J.*, Charapitsa I.*, Conrad T., Vaquerizas J.M., Gebhardt P., Holz H., Kadlec J., Fraterman S., Luscombe N.M., Akhtar A. (2010)
The NSL complex is a novel transcriptional regulator in Drosophila.
Molecular Cell 38: 827-41.
pubmed abstract full-text PDF

Seshasayee A.S.N., Fraser G., Luscombe N.M. (2010)
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

Reimand J., Vaquerizas J.M., Todd A.E., Vilo J., Luscombe N.M. (2010)
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

Jolma A., Kivioja T., Toivonen J., Cheng L., Wei G., Enge M., Taipale M., Vaquerizas J.M., Yan J., Sillanp�� M.J., Bonke M., Palin K., Talukder S., Hughes T.R., Luscombe N.M., Ukkonen E., Taipale J. (2010)
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Genome Research 20: 861-73.
pubmed abstract full-text PDF

Vaquerizas J.M.*, Suyama R.*, Kind J.*, Miura K., Luscombe N.M.*, Akhtar A*. (2010)
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

2009

Ilsley G.R., Luscombe N.M., Apweiler R. (2009)
Know Your Limits: Assumptions, Constraints and Interpretation in Systems Biology.
Biochimica et Biophysica Acta 1794: 1280-7.
pubmed abstract full-text PDF

Vaquerizas J.M., Kummerfeld S.K., Teichmann S.A., Luscombe N.M. (2009)
A census of human transcription factors: function, expression and evolution.
Nature Reviews Genetics 10: 252-63.
pubmed abstract full-text PDF website

2008

Seshasayee A.S., Fraser G.M., Babu M.M., Luscombe N.M. (2008)
Principles of transcriptional regulation and evolution of the metabolic system in E. coli.
Genome Research 19: 79-91.
pubmed abstract full-text PDF

Kind J.*, Vaquerizas J.M.*, Gebhardt P., Gentzel M., Luscombe N.M., Bertone P., Akhtar A. (2008)
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

Pearson M.M., Sebaihia M., Churcher C., Quail M.A., Seshasayee A.S., Luscombe N.M., 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 N.R., Rather P.N., Parkhill J., Mobley H.L. (2008)
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

Hancock V., Seshasayee A.S., Ussery D.W., Luscombe N.M., Klemm P. (2008)
Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.
Molecular Genetics and Genomics 279: 523-34.
pubmed abstract full-text PDF

2006

Seshasayee A.S., Bertone P., Fraser G.M., Luscombe N.M. (2006)
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

Royce T.E., Rozowsky J.S., Luscombe N.M., Emanuelsson O., Yu H., Zhu X., Snyder M., Gerstein M.B. (2006)
Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.
Methods in Enzymology 411: 282-311.
pubmed abstract full-text PDF

Balaji S., Babu M.M., Iyer L.M., Luscombe N.M., Aravind L. (2006)
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.
Journal of Molecular Biology 360: 213-27.
pubmed abstract full-text PDF



2005

Teichmann S.A., Bornberg-Bauer E., Luscombe N.M. (2005)
Transcriptional networking.
Genome Biology 69: 344.
pubmed abstract full-text PDF



2004

Luscombe NM & Babu MM (2004)
GenCompass: a universal system for analysing gene expression for any genome.
Trends in Biotechnology 22(11): 552-555.
pubmed abstract full-text PDF

Luscombe NM*, Babu MM*, Yu H, Snyder M, Teichmann SA & Gerstein M (2004)
Genomic analysis of regulatory network dynamics reveals large topological changes.
Nature 431: 308-312.
pubmed abstract full-text PDF website

Babu MM*, Luscombe NM*, Aravind L, Gerstein M & Teichmann SA (2004)
Structure and evolution of transcriptional regulatory networks.
Current Opinions in Structural Biology 14: 283-291.
pubmed abstract full-text PDF

Yu H, Luscombe NM, Lu H, Zhu X, Xia Y, Han J, Bertin N, Chung S, Goh C, Vidal M & Gerstein M (2004)
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
Genome Research 14: 1107-1118.
pubmed abstract full-text PDF website

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S & Snyder M (2004)
CREB binds to multiple loci on human chromosome 22.
Molecular and Cellular Biology 24: 3804-3814.
pubmed abstract full-text PDF



2003

Qian J, Lin J, Luscombe NM, Yu H & Gerstein M (2003)
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.
Bioinformatics 19: 1917-1926.
pubmed abstract full-text PDF

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S & Snyder M (2003)
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

Yu H*, Luscombe NM*, Qian J & Gerstein M
Genomic analysis of gene expression relationships in transcriptional regulatory networks.
Trend in Genetics 19(8): 422-427 (2003).
pubmed abstract full-text PDF website

Luscombe NM*, Royce TE*, Bertone P, Echols N, Horak CE, Chang JT, Snyder M & Gerstein M (2003)
ExpressYourself: A modular platform for processing and visualizing microarray data.
Nucleic Acids Research 31(13): 3477-3482.
pubmed abstract full-text PDF website

Rinn JL , Euskirchen G, Bertone P, Martone, R , Luscombe NM, Hartman S , Harrison PM, Nelson ,FK , Miller P , Gerstein M , Weissman S & Snyder M (2003)
The transcriptional activity of human Chromosome 22.
Genes and Development 17(4): 529-40.
pubmed abstract full-text PDF

Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe NM, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M (2003)
Identification of novel functional elements in the human genome.
Cold Spring Harbor Symposium in Quantitative Biology 68: 317-322.
pubmed



2002

Horak CE , Luscombe, NM , Qian J , Bertone P , Piccirrillo S , Gerstein M & Snyder M (2002)
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.
Genes and Development 16(23): 3017-3033.
pubmed abstract full-text PDF

Luscombe, NM , Qian J, Zhang Z , Johnson T & 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: research0040.1-0040.7.
pubmed abstract full-text PDF

Luscombe NM & Thornton JM (2002)
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

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

Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z & Gerstein M (2002)
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

Horak CE, Mahajan M, Luscombe NM, Gerstein M, Weissman S & 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 Science 99(5): 2924-2929.
pubmed abstract full-text PDF

Harrison PM, Hegyi H, Balisubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T & Gerstein M (2002)
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

Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison PM, Zhang Z & Gerstein M (2002)
Structural genomics: a new era for pharmaceutical research.
Genome Biology 3 Reports: 4004.1-4004.3.
pubmed abstract full-text PDF



2001

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

Qian J*, Luscombe NM* & Gerstein MB (2001)
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

Luscombe NM, Greenbaum D & Gerstein M (2001)
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

Greenbaum D, Luscombe NM, Jansen R, Qian J & Gerstein MB (2001)
Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.
Genome Research 11: 1463-1468.
pubmed abstract full-text PDF

Luscombe NM, Roman A Laskowski & Thornton JM (2001)
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

Jones S, Daley DTA, Luscombe NM, Berman HM & Thornton JM (2001)
Protein-RNA interactions: a structural analysis.
Nucleic Acids Research 29: 943-954.
pubmed abstract full-text PDF



1996 - 2000

Luscombe NM, Austin SE, Berman H M & Thornton JM (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

Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou & Thornton JM (1998)
New tools and resources for analysing protein structures and their interactions.
Acta Crystallographica D54: 1132-1138.
pubmed abstract

Luscombe NM, Laskowski RA & Thornton JM (1997)
NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.
Nucleic Acids Research 25: 4940-4945.
pubmed abstract full-text PDF

Laskowski RA, Luscombe NM, Swindells MB, Thornton JM (1996)
Protein clefts in molecular recognition and function.
Protein Science 5: 2438-2452.
pubmed abstract


N.B. * denotes joint first author.
































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