PubMed

Know your limits: assumptions, constraints and interpretation in systems biology.

Ilsley GR, Luscombe NM, Apweiler R.

Biochim Biophys Acta. 2009 Sep;1794(9):1280-7. Epub 2009 May 9. Review.PMID: 19439202 [PubMed - indexed for MEDLINE]Related articles

A census of human transcription factors: function, expression and evolution.

Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM.

Nat Rev Genet. 2009 Apr;10(4):252-63.PMID: 19274049 [PubMed - indexed for MEDLINE]Related articles

Principles of transcriptional regulation and evolution of the metabolic system in E. coli.

Seshasayee AS, Fraser GM, Babu MM, Luscombe NM.

Genome Res. 2009 Jan;19(1):79-91. Epub 2008 Oct 3.PMID: 18836036 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila.

Kind J, Vaquerizas JM, Gebhardt P, Gentzel M, Luscombe NM, Bertone P, Akhtar A.

Cell. 2008 May 30;133(5):813-28.PMID: 18510926 [PubMed - indexed for MEDLINE]Related articles

Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility.

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, Mobley HL.

J Bacteriol. 2008 Jun;190(11):4027-37. Epub 2008 Mar 28.PMID: 18375554 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

Hancock V, Seshasayee AS, Ussery DW, Luscombe NM, Klemm P.

Mol Genet Genomics. 2008 May;279(5):523-34.PMID: 18317809 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional regulatory networks in bacteria: from input signals to output responses.

Seshasayee AS, Bertone P, Fraser GM, Luscombe NM.

Curr Opin Microbiol. 2006 Oct;9(5):511-9. Epub 2006 Aug 30. Review.PMID: 16942903 [PubMed - indexed for MEDLINE]Related articles

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.

Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB.

Methods Enzymol. 2006;411:282-311. Review.PMID: 16939796 [PubMed - indexed for MEDLINE]Related articles

Use of [14C]-sodium bicarbonate/urea to measure total energy expenditure in overweight men and women before and after low calorie diet induced weight loss.

Luscombe ND, Tsopelas C, Bellon M, Clifton PM, Kirkwood I, Wittert GA.

Asia Pac J Clin Nutr. 2006;15(3):307-16.PMID: 16837421 [PubMed - indexed for MEDLINE]Related articles

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast.

Balaji S, Babu MM, Iyer LM, Luscombe NM, Aravind L.

J Mol Biol. 2006 Jun 30;360(1):213-27. Epub 2006 May 3.PMID: 16762362 [PubMed - indexed for MEDLINE]Related articles

Transcriptional networking.

Teichmann SA, Bornberg-Bauer E, Luscombe NM.

Genome Biol. 2005;6(9):344. Epub 2005 Aug 31. No abstract available. PMID: 16168097 [PubMed - indexed for MEDLINE]Related articlesFree article

Use of [14C]-sodium bicarbonate/urea to measure physical activity induced increases in total energy expenditure in free-living healthy males.

Roffey DM, Luscombe ND, Byrne NM, Hills AP, Bellon M, Tsopelas C, Kirkwood ID, Wittert GA.

Asia Pac J Clin Nutr. 2005;14(1):83-90.PMID: 15734713 [PubMed - indexed for MEDLINE]Related articles

GenCompass: a universal system for analysing gene expression for any genome.

Luscombe NM, Babu MM.

Trends Biotechnol. 2004 Nov;22(11):552-5.PMID: 15491796 [PubMed - indexed for MEDLINE]Related articles

Genomic analysis of regulatory network dynamics reveals large topological changes.

Luscombe NM, Babu MM, Yu H, Snyder M, Teichmann SA, Gerstein M.

Nature. 2004 Sep 16;431(7006):308-12.PMID: 15372033 [PubMed - indexed for MEDLINE]Related articles

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, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M.

Cold Spring Harb Symp Quant Biol. 2003;68:317-22. No abstract available. PMID: 15338632 [PubMed - indexed for MEDLINE]Related articles

Ghrelin and measures of satiety are altered in polycystic ovary syndrome but not differentially affected by diet composition.

Moran LJ, Noakes M, Clifton PM, Wittert GA, Tomlinson L, Galletly C, Luscombe ND, Norman RJ.

J Clin Endocrinol Metab. 2004 Jul;89(7):3337-44.PMID: 15240612 [PubMed - indexed for MEDLINE]Related articlesFree article

Structure and evolution of transcriptional regulatory networks.

Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA.

Curr Opin Struct Biol. 2004 Jun;14(3):283-91. Review.PMID: 15193307 [PubMed - indexed for MEDLINE]Related articles

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.

Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M.

Genome Res. 2004 Jun;14(6):1107-18.PMID: 15173116 [PubMed - indexed for MEDLINE]Related articlesFree article

CREB binds to multiple loci on human chromosome 22.

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M.

Mol Cell Biol. 2004 May;24(9):3804-14.PMID: 15082775 [PubMed - indexed for MEDLINE]Related articlesFree article

Ghrelin and measures of satiety are altered in polycystic ovary syndrome but not differentially affected by diet composition.

Moran LJ, Noakes M, Clifton PM, Wittert G, Tomlinson L, Galletly C, Luscombe N, Tomlinson L, Norman RJ.

Asia Pac J Clin Nutr. 2003;12 Suppl:S52.PMID: 15023670 [PubMed - in process]Related articles

Long-term effects of a high-protein, low-carbohydrate diet on weight control and cardiovascular risk markers in obese hyperinsulinemic subjects.

Brinkworth GD, Noakes M, Keogh JB, Luscombe ND, Wittert GA, Clifton PM.

Int J Obes Relat Metab Disord. 2004 May;28(5):661-70. Erratum in: Int J Obes Relat Metab Disord. 2004 Sep;28(9):1187. PMID: 15007396 [PubMed - indexed for MEDLINE]Related articles

Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.

Qian J, Lin J, Luscombe NM, Yu H, Gerstein M.

Bioinformatics. 2003 Oct 12;19(15):1917-26.PMID: 14555624 [PubMed - indexed for MEDLINE]Related articlesFree article

Distribution of NF-kappaB-binding sites across human chromosome 22.

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

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3.PMID: 14527995 [PubMed - indexed for MEDLINE]Related articlesFree article

Genomic analysis of gene expression relationships in transcriptional regulatory networks.

Yu H, Luscombe NM, Qian J, Gerstein M.

Trends Genet. 2003 Aug;19(8):422-7.PMID: 12902159 [PubMed - indexed for MEDLINE]Related articles

ExpressYourself: A modular platform for processing and visualizing microarray data.

Luscombe NM, Royce TE, Bertone P, Echols N, Horak CE, Chang JT, Snyder M, Gerstein M.

Nucleic Acids Res. 2003 Jul 1;31(13):3477-82.PMID: 12824348 [PubMed - indexed for MEDLINE]Related articlesFree article

Effect of a high-protein, energy-restricted diet on body composition, glycemic control, and lipid concentrations in overweight and obese hyperinsulinemic men and women.

Farnsworth E, Luscombe ND, Noakes M, Wittert G, Argyiou E, Clifton PM.

Am J Clin Nutr. 2003 Jul;78(1):31-9.PMID: 12816768 [PubMed - indexed for MEDLINE]Related articlesFree article

Effect of a high-protein, energy-restricted diet on weight loss and energy expenditure after weight stabilization in hyperinsulinemic subjects.

Luscombe ND, Clifton PM, Noakes M, Farnsworth E, Wittert G.

Int J Obes Relat Metab Disord. 2003 May;27(5):582-90.PMID: 12704402 [PubMed - indexed for MEDLINE]Related articles

The transcriptional activity of human Chromosome 22.

Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.

Genes Dev. 2003 Feb 15;17(4):529-40.PMID: 12600945 [PubMed - indexed for MEDLINE]Related articlesFree article

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae.

Horak CE, Luscombe NM, Qian J, Bertone P, Piccirrillo S, Gerstein M, Snyder M.

Genes Dev. 2002 Dec 1;16(23):3017-33.PMID: 12464632 [PubMed - indexed for MEDLINE]Related articlesFree article

The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties.

Luscombe NM, Qian J, Zhang Z, Johnson T, Gerstein M.

Genome Biol. 2002 Jul 25;3(8):RESEARCH0040. Epub 2002 Jul 25.PMID: 12186647 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity.

Luscombe NM, Thornton JM.

J Mol Biol. 2002 Jul 26;320(5):991-1009.PMID: 12126620 [PubMed - indexed for MEDLINE]Related articles

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.

Balasubramanian S, Harrison P, Hegyi H, Bertone P, Luscombe N, Echols N, McGarvey P, Zhang Z, Gerstein M.

Pharmacogenomics. 2002 May;3(3):393-402.PMID: 12052146 [PubMed - indexed for MEDLINE]Related articles

Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes.

Echols N, Harrison P, Balasubramanian S, Luscombe NM, Bertone P, Zhang Z, Gerstein M.

Nucleic Acids Res. 2002 Jun 1;30(11):2515-23.PMID: 12034841 [PubMed - indexed for MEDLINE]Related articlesFree article

Effects of energy-restricted diets containing increased protein on weight loss, resting energy expenditure, and the thermic effect of feeding in type 2 diabetes.

Luscombe ND, Clifton PM, Noakes M, Parker B, Wittert G.

Diabetes Care. 2002 Apr;25(4):652-7.PMID: 11919120 [PubMed - indexed for MEDLINE]Related articlesFree article

Effect of a high-protein, high-monounsaturated fat weight loss diet on glycemic control and lipid levels in type 2 diabetes.

Parker B, Noakes M, Luscombe N, Clifton P.

Diabetes Care. 2002 Mar;25(3):425-30.PMID: 11874925 [PubMed - indexed for MEDLINE]Related articlesFree article

GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.

Horak CE, Mahajan MC, Luscombe NM, Gerstein M, Weissman SM, Snyder M.

Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2924-9. Epub 2002 Feb 26.PMID: 11867748 [PubMed - indexed for MEDLINE]Related articlesFree article

Structural genomics: a new era for pharmaceutical research.

Liu Y, Luscombe NM, Alexandrov V, Bertone P, Harrison P, Zhang Z, Gerstein M.

Genome Biol. 2002;3(2):REPORTS4004. Epub 2002 Jan 14. No abstract available. PMID: 11864367 [PubMed - indexed for MEDLINE]Related articlesFree article

Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22.

Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, Johnson T, Gerstein M.

Genome Res. 2002 Feb;12(2):272-80.PMID: 11827946 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model.

Qian J, Luscombe NM, Gerstein M.

J Mol Biol. 2001 Nov 2;313(4):673-81.PMID: 11697896 [PubMed - indexed for MEDLINE]Related articles

What is bioinformatics? A proposed definition and overview of the field.

Luscombe NM, Greenbaum D, Gerstein M.

Methods Inf Med. 2001;40(4):346-58. Review.PMID: 11552348 [PubMed - indexed for MEDLINE]Related articles

Interrelating different types of genomic data, from proteome to secretome: 'oming in on function.

Greenbaum D, Luscombe NM, Jansen R, Qian J, Gerstein M.

Genome Res. 2001 Sep;11(9):1463-8.PMID: 11544189 [PubMed - indexed for MEDLINE]Related articlesFree article

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.

Luscombe NM, Laskowski RA, Thornton JM.

Nucleic Acids Res. 2001 Jul 1;29(13):2860-74.PMID: 11433033 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein-RNA interactions: a structural analysis.

Jones S, Daley DT, Luscombe NM, Berman HM, Thornton JM.

Nucleic Acids Res. 2001 Feb 15;29(4):943-54.PMID: 11160927 [PubMed - indexed for MEDLINE]Related articlesFree article

An overview of the structures of protein-DNA complexes.

Luscombe NM, Austin SE, Berman HM, Thornton JM.

Genome Biol. 2000;1(1):REVIEWS001. Epub 2000 Jun 9. Review.PMID: 11104519 [PubMed - indexed for MEDLINE]Related articlesFree article

Diets high and low in glycemic index versus high monounsaturated fat diets: effects on glucose and lipid metabolism in NIDDM.

Luscombe ND, Noakes M, Clifton PM.

Eur J Clin Nutr. 1999 Jun;53(6):473-8.PMID: 10403584 [PubMed - indexed for MEDLINE]Related articles

New tools and resources for analysing protein structures and their interactions.

Luscombe NM, Laskowski RA, Westhead DR, Milburn D, Jones S, Karmirantzou M, Thornton JM.

Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 1):1132-8.PMID: 10089489 [PubMed - indexed for MEDLINE]Related articles

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions.

Luscombe NM, Laskowski RA, Thornton JM.

Nucleic Acids Res. 1997 Dec 15;25(24):4940-5.PMID: 9396800 [PubMed - indexed for MEDLINE]Related articlesFree article

Protein clefts in molecular recognition and function.

Laskowski RA, Luscombe NM, Swindells MB, Thornton JM.

Protein Sci. 1996 Dec;5(12):2438-52.PMID: 8976552 [PubMed - indexed for MEDLINE]Related articlesFree article