Simon Tavaré

Simon Tavaré

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Simulating the component counts of combinatorial structures.

Theor Popul Biol 2018 07 9;122:5-11. Epub 2018 Feb 9.

DAMTP, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00405809183002
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http://dx.doi.org/10.1016/j.tpb.2018.02.002DOI Listing
July 2018

Ancestral inference from haplotypes and mutations.

Theor Popul Biol 2018 07 25;122:12-21. Epub 2018 Apr 25.

DAMTP, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK.

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http://dx.doi.org/10.1016/j.tpb.2018.04.006DOI Listing
July 2018

Introduction to the Paul Joyce special issue.

Theor Popul Biol 2018 07;122:1-2

Department of Statistical Science, University of Idaho, 875 Perimeter Drive, MS 1104 Moscow, ID 83844, United States.

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http://dx.doi.org/10.1016/j.tpb.2018.07.001DOI Listing
July 2018

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.

Nat Genet 2018 05 16;50(5):682-692. Epub 2018 Apr 16.

The Institute of Cancer Research, London, UK.

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http://www.nature.com/articles/s41588-018-0086-z
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http://dx.doi.org/10.1038/s41588-018-0086-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372064PMC
May 2018

Division-independent differentiation mandates proliferative competition among stem cells.

Proc Natl Acad Sci U S A 2018 04 19;115(14):E3182-E3191. Epub 2018 Mar 19.

Department of Biological Sciences, Columbia University, New York, NY 10027;

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http://dx.doi.org/10.1073/pnas.1718646115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5889645PMC
April 2018

New Model for Estimating Glomerular Filtration Rate in Patients With Cancer.

J Clin Oncol 2017 Aug 7;35(24):2798-2805. Epub 2017 Jul 7.

Tobias Janowitz, Edward H. Williams, Stephen J. Sammut, Andy G. Lynch, Duncan I. Jodrell, Simon Tavaré, and Helena Earl, Cancer Research UK Cambridge Institute, Tobias Janowitz, Peter B. Thomas, and Duncan I. Jodrell, University of Cambridge, Addenbrooke's Hospital, Cambridge; Andrea Marshall, University of Warwick, Coventry; Nicola Ainsworth, Queen Elizabeth Hospital, King's Lynn; Scott Shepherd, Royal Marsden Hospital, London; Jeff White, NHS Greater Glasgow and Clyde; and Patrick B. Mark, Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom.

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http://dx.doi.org/10.1200/JCO.2017.72.7578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5562175PMC
August 2017

HDTD: analyzing multi-tissue gene expression data.

Bioinformatics 2016 07 7;32(14):2193-5. Epub 2016 Jun 7.

CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937203PMC
July 2016

Choline Kinase Alpha as an Androgen Receptor Chaperone and Prostate Cancer Therapeutic Target.

J Natl Cancer Inst 2016 May 11;108(5). Epub 2015 Dec 11.

Affiliations of authors:Cancer Research UK Cambridge Institute, University of Cambridge , Cambridge, UK (MA, CEM, NP, HIZ, AQ, AB, SM, BM, CE, SL, SW, VRZ, GS, RR, HM, AGL, CD, CT, AL, RS, JY, RS, JSC, JRG, ST, DEN); School of Medical Sciences, University of Aberdeen , Aberdeen, UK (FO, IJM); Department of Pathology, Addenbrooke's Hospital , Cambridge, UK (AYW, NS); Institute of Human Genetics, Jena University Hospital , Jena , Germany (ME, KL, WH, AB); Dame Roma Mitchell Cancer Research Laboratories, School of Medicine, Faculty of Health Sciences, University of Adelaide , Australia (LAS, WDT); Freemasons Foundation Centre for Men's Health, School of Medicine, Faculty of Health Sciences, University of Adelaide , Australia (LAS, WDT); Diatherix , Huntsville, AL (EG); Masonic Cancer Center, University of Minnesota , Minneapolis, MN (SMD); The Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia , Vancouver BC , Canada (PSR); Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital , Oslo , Norway (IGM); Department of Cancer Prevention, Institute of Cancer Research and Department of Urology, Oslo University Hospital , Oslo , Norway (IGM); Prostate Cancer UK/Movember Centre of Excellence, Queens University , Belfast , UK (IGM); Department of Oncology, Addenbrooke's Hospital , Cambridge, UK (MA, DEN).

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http://jnci.oxfordjournals.org/content/108/5/djv371.full.pdf
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http://jnci.oxfordjournals.org/lookup/doi/10.1093/jnci/djv37
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http://dx.doi.org/10.1093/jnci/djv371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849803PMC
May 2016

multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples.

Nucleic Acids Res 2015 May 26;43(9):e61. Epub 2015 Feb 26.

Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK

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http://dx.doi.org/10.1093/nar/gkv135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482059PMC
May 2015

HES5 silencing is an early and recurrent change in prostate tumourigenesis.

Endocr Relat Cancer 2015 Apr 5;22(2):131-44. Epub 2015 Jan 5.

Cancer Research UK Cambridge InstituteUniversity of Cambridge, Cambridge, CB2 0RE, UKDivision of Genetics and EpidemiologyThe Institute of Cancer Research, Sutton, UKDepartment of Biological Sciences and School of MedicineUniversity of East Anglia, Norwich, UKRoyal Marsden NHS Foundation TrustLondon and Sutton, UKDepartments of PathologyUrologySurgical OncologyAddenbrooke's Hospital, Hills Road, Cambridge, UK

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http://dx.doi.org/10.1530/ERC-14-0454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4335379PMC
April 2015

Epigenetic profile of human adventitial progenitor cells correlates with therapeutic outcomes in a mouse model of limb ischemia.

Arterioscler Thromb Vasc Biol 2015 Mar 8;35(3):675-88. Epub 2015 Jan 8.

From the Bristol Heart Institute, School of Clinical Sciences, University of Bristol, Bristol, UK (M.G., S.C.S., H.L.S., F.R., J.R., E.A., R.K., G.M., A.O., C.R., C.E., G.A., P.M.); The Institute of Cancer Research, Evolutionary Genomics and Modelling Team, Centre for Evolution and Cancer, Sutton, UK (I.S., A.S.); Imperial College, London, UK (P.C., C.E., G.A.); MultiMedica Research Institute, Milan, Italy (G.S.); Cancer Research UK Cambridge Institute, Cambridge, UK (A.T., S.T.); Centro Cardiologico Monzino, Milan, Italy (F.P., M.P.); and Austrian Institute of Technology, Vienna, Austria (M.H., V.K.).

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http://dx.doi.org/10.1161/ATVBAHA.114.304989DOI Listing
March 2015

Testing the mean matrix in high-dimensional transposable data.

Biometrics 2015 Mar 23;71(1):157-166. Epub 2015 Jan 23.

EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, U.K.

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http://dx.doi.org/10.1111/biom.12257DOI Listing
March 2015

Genetic mapping of natural variation in schooling tendency in the threespine stickleback.

G3 (Bethesda) 2015 Feb 25;5(5):761-9. Epub 2015 Feb 25.

Divisions of Basic Sciences and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109

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http://dx.doi.org/10.1534/g3.114.016519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426364PMC
February 2015

Fkh1 and Fkh2 bind multiple chromosomal elements in the S. cerevisiae genome with distinct specificities and cell cycle dynamics.

PLoS One 2014 4;9(2):e87647. Epub 2014 Feb 4.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087647PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3913637PMC
December 2014

Quantifying the impact of inter-site heterogeneity on the distribution of ChIP-seq data.

Front Genet 2014 14;5:399. Epub 2014 Nov 14.

Cancer Research UK Cambridge Institute, University of Cambridge Cambridge, UK.

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http://dx.doi.org/10.3389/fgene.2014.00399DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231950PMC
December 2014

Normalization of metabolomics data with applications to correlation maps.

Bioinformatics 2014 Aug 7;30(15):2155-61. Epub 2014 Apr 7.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, SE-171 77 Stockholm, Sweden and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1093/bioinformatics/btu175DOI Listing
August 2014

The relative timing of mutations in a breast cancer genome.

PLoS One 2013 10;8(6):e64991. Epub 2013 Jun 10.

Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064991PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3677865PMC
February 2014

Flexible analysis of RNA-seq data using mixed effects models.

Bioinformatics 2014 Jan 26;30(2):180-8. Epub 2013 Nov 26.

Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK, Department of Haematology, University of Cambridge, NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, UK and Department of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal QC H3A 1A2, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt624DOI Listing
January 2014

Continuous clonal labeling reveals small numbers of functional stem cells in intestinal crypts and adenomas.

Cell Stem Cell 2013 Nov 12;13(5):626-33. Epub 2013 Sep 12.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1016/j.stem.2013.08.001DOI Listing
November 2013

Defining stem cell dynamics in models of intestinal tumor initiation.

Science 2013 Nov;342(6161):995-8

Cancer Research UK, Cambridge Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1126/science.1243148DOI Listing
November 2013

Assessing senescence in Drosophila using video tracking.

Methods Mol Biol 2013 ;965:501-16

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.

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http://dx.doi.org/10.1007/978-1-62703-239-1_33DOI Listing
June 2013

Transcriptional dynamics elicited by a short pulse of notch activation involves feed-forward regulation by E(spl)/Hes genes.

PLoS Genet 2013 3;9(1):e1003162. Epub 2013 Jan 3.

Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1003162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536677PMC
May 2013

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Proc Natl Acad Sci U S A 2013 Mar 14;110(10):4009-14. Epub 2013 Feb 14.

Department of Oncology, University of Cambridge, Cambridge CB2 2XZ, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1219747110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593922PMC
March 2013

Three-dimensional tracking and behaviour monitoring of multiple fruit flies.

J R Soc Interface 2013 Jan 3;10(78):20120547. Epub 2012 Oct 3.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1098/rsif.2012.0547DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565780PMC
January 2013

Using GFP video to track 3D movement and conditional gene expression in free-moving flies.

PLoS One 2012 19;7(7):e40506. Epub 2012 Jul 19.

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040506PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400653PMC
December 2012

High DNA methylation pattern intratumoral diversity implies weak selection in many human colorectal cancers.

PLoS One 2011 28;6(6):e21657. Epub 2011 Jun 28.

Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021657PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125304PMC
December 2011

A Bayesian approach to phylogeographic clustering.

Interface Focus 2011 Dec 5;1(6):909-21. Epub 2011 Oct 5.

Duke University, Durham, USA.

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http://dx.doi.org/10.1098/rsfs.2011.0054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262294PMC
December 2011

Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

PLoS Comput Biol 2011 May 5;7(5):e1001132. Epub 2011 May 5.

Computational Biology Group, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1001132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3088646PMC
May 2011

Sequential DNA methylation changes are associated with DNMT3B overexpression in colorectal neoplastic progression.

Gut 2011 Apr 10;60(4):499-508. Epub 2010 Nov 10.

Department of Pathology, Division of Molecular Histopathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK.

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http://dx.doi.org/10.1136/gut.2010.223602DOI Listing
April 2011

BayesPeak--an R package for analysing ChIP-seq data.

Bioinformatics 2011 Mar 17;27(5):713-4. Epub 2011 Jan 17.

Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042177PMC
March 2011

Dating primate divergences through an integrated analysis of palaeontological and molecular data.

Syst Biol 2011 Jan 4;60(1):16-31. Epub 2010 Nov 4.

School of Mathmatical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

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http://dx.doi.org/10.1093/sysbio/syq054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2997628PMC
January 2011

CNAseg--a novel framework for identification of copy number changes in cancer from second-generation sequencing data.

Bioinformatics 2010 Dec 21;26(24):3051-8. Epub 2010 Oct 21.

Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btq587DOI Listing
December 2010

The cost of reducing starting RNA quantity for Illumina BeadArrays: a bead-level dilution experiment.

BMC Genomics 2010 Oct 6;11:540. Epub 2010 Oct 6.

Department of Oncology, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2164-11-540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091689PMC
October 2010

The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans.

Nucleic Acids Res 2010 Jun 21;38(11):3780-93. Epub 2010 Feb 21.

Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Rd, Cambridge CB2 1QN, UK.

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http://dx.doi.org/10.1093/nar/gkq083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887956PMC
June 2010

CNAnova: a new approach for finding recurrent copy number abnormalities in cancer SNP microarray data.

Bioinformatics 2010 Jun 18;26(11):1395-402. Epub 2010 Apr 18.

Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq145DOI Listing
June 2010

Data analysis issues for allele-specific expression using Illumina's GoldenGate assay.

BMC Bioinformatics 2010 May 26;11:280. Epub 2010 May 26.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria, 3052, Australia.

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http://dx.doi.org/10.1186/1471-2105-11-280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2887809PMC
May 2010

Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data.

BMC Bioinformatics 2010 Apr 27;11:208. Epub 2010 Apr 27.

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1186/1471-2105-11-208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2880029PMC
April 2010

The pitfalls of platform comparison: DNA copy number array technologies assessed.

BMC Genomics 2009 Dec 8;10:588. Epub 2009 Dec 8.

Department of Oncology, University of Cambridge, Addenbrooke's Hopsital, Hills Road, Cambridge CB20XZ, UK.

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http://dx.doi.org/10.1186/1471-2164-10-588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797821PMC
December 2009

Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression.

Nucleic Acids Res 2009 Nov 10;37(20):6716-22. Epub 2009 Sep 10.

Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.

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http://dx.doi.org/10.1093/nar/gkp740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2777450PMC
November 2009

Characterisation of microRNA expression in post-natal mouse mammary gland development.

BMC Genomics 2009 Nov 20;10:548. Epub 2009 Nov 20.

Breast Cancer Functional Genomics Laboratory, Cancer Research UK Cambridge Research Institute and Department of Oncology, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2164-10-548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784809PMC
November 2009

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.

Bioinformatics 2009 Oct 6;25(19):2621-3. Epub 2009 Aug 6.

Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville Victoria 3052, Australia.

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http://dx.doi.org/10.1093/bioinformatics/btp470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752620PMC
October 2009

Hydrogen peroxide stimulates activity and alters behavior in Drosophila melanogaster.

PLoS One 2009 Oct 28;4(10):e7580. Epub 2009 Oct 28.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007580PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763216PMC
October 2009

Drosophila melanogaster p53 has developmental stage-specific and sex-specific effects on adult life span indicative of sexual antagonistic pleiotropy.

Aging (Albany NY) 2009 Oct 27;1(11):903-36. Epub 2009 Oct 27.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815744PMC
http://dx.doi.org/10.18632/aging.100099DOI Listing
October 2009

BayesPeak: Bayesian analysis of ChIP-seq data.

BMC Bioinformatics 2009 Sep 21;10:299. Epub 2009 Sep 21.

Statistical Laboratory, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, UK.

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http://dx.doi.org/10.1186/1471-2105-10-299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760534PMC
September 2009

Strategies for analyzing highly enriched IP-chip datasets.

BMC Bioinformatics 2009 Sep 22;10:305. Epub 2009 Sep 22.

Molecular and Computational Biology Program, University of Southern California, Ray Irani Hall, University Park Campus, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1471-2105-10-305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759964PMC
September 2009

Many colorectal cancers are "flat" clonal expansions.

Cell Cycle 2009 Jul 1;8(14):2187-93. Epub 2009 Jul 1.

Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145878PMC
http://dx.doi.org/10.4161/cc.8.14.9151DOI Listing
July 2009

Estimating primate divergence times by using conditioned birth-and-death processes.

Theor Popul Biol 2009 Jun 6;75(4):278-85. Epub 2009 Mar 6.

Department of Probability and Statistics, University of Sheffield, Hicks Building, Sheffield, United Kingdom.

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http://dx.doi.org/10.1016/j.tpb.2009.02.003DOI Listing
June 2009

Autophagy mediates the mitotic senescence transition.

Genes Dev 2009 Apr 11;23(7):798-803. Epub 2009 Mar 11.

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Cambridge, United Kingdom.

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http://dx.doi.org/10.1101/gad.519709DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666340PMC
April 2009

Simultaneous tracking of movement and gene expression in multiple Drosophila melanogaster flies using GFP and DsRED fluorescent reporter transgenes.

BMC Res Notes 2009 Apr 17;2:58. Epub 2009 Apr 17.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA.

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http://dx.doi.org/10.1186/1756-0500-2-58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679045PMC
April 2009

Older individuals appear to acquire mitotically older colorectal cancers.

J Pathol 2009 Mar;217(4):483-8

Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1002/path.2506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418435PMC
March 2009

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers.

Proc Natl Acad Sci U S A 2009 Mar 4;106(12):4828-33. Epub 2009 Mar 4.

Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1073/pnas.0810276106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651202PMC
March 2009

Population genetic inference from resequencing data.

Genetics 2009 Jan 3;181(1):187-97. Epub 2008 Nov 3.

Department of Oncology, University of Cambridge, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1534/genetics.107.080630DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2621167PMC
January 2009

A screen of apoptosis and senescence regulatory genes for life span effects when over-expressed in Drosophila.

Aging (Albany NY) 2009 Jan 30;1(2):191-211. Epub 2009 Jan 30.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806004PMC
http://dx.doi.org/10.18632/aging.100018DOI Listing
January 2009

Simultaneous tracking of fly movement and gene expression using GFP.

BMC Biotechnol 2008 Dec 16;8:93. Epub 2008 Dec 16.

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1186/1472-6750-8-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2625341PMC
December 2008

O fly, where art thou?

J R Soc Interface 2008 Oct;5(27):1181-91

Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, USA.

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http://dx.doi.org/10.1098/rsif.2007.1333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3226990PMC
October 2008

Species-specific transcription in mice carrying human chromosome 21.

Science 2008 Oct 11;322(5900):434-8. Epub 2008 Sep 11.

Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1126/science.1160930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717767PMC
October 2008

Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae.

Genes Dev 2008 Jul;22(14):1906-20

Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA.

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http://dx.doi.org/10.1101/gad.1660408DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492737PMC
July 2008

Hidden copy number variation in the HapMap population.

Proc Natl Acad Sci U S A 2008 Jul 15;105(29):10067-72. Epub 2008 Jul 15.

Department of Oncology, Computational Biology Group, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0711252105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481329PMC
July 2008

Inferring relative numbers of human leucocyte genome replications.

Br J Haematol 2008 Jun 10;141(6):862-71. Epub 2008 Apr 10.

Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA.

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http://dx.doi.org/10.1111/j.1365-2141.2008.07142.xDOI Listing
June 2008

Spike-in validation of an Illumina-specific variance-stabilizing transformation.

BMC Res Notes 2008 Jun 4;1:18. Epub 2008 Jun 4.

Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1186/1756-0500-1-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518281PMC
June 2008

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

Genome Biol 2007 ;8(10):R215

Breast Cancer Functional Genomics, Cancer Research UK Cambridge Research Institute and Department of Oncology University of Cambridge, Li Ka-Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1186/gb-2007-8-10-r215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246289PMC
May 2008

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

Genome Biol 2007 ;8(10):R228

Computational Biology Group, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, UK.

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http://dx.doi.org/10.1186/gb-2007-8-10-r228DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2246302PMC
May 2008

Statistical issues in the analysis of Illumina data.

BMC Bioinformatics 2008 Feb 6;9:85. Epub 2008 Feb 6.

Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1186/1471-2105-9-85DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2291044PMC
February 2008