Publications by authors named "Chris Holmes"

87Publications

Correction to: Graphing and reporting heterogeneous treatment effects through reference classes.

Authors:
James A Watson Chris C Holmes

Trials 2020 Oct 20;21(1):865. Epub 2020 Oct 20.

Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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October 2020

Epidemiological changes on the Isle of Wight after the launch of the NHS Test and Trace programme: a preliminary analysis.

Authors:
Michelle Kendall Luke Milsom Lucie Abeler-Dörner Chris Wymant Luca Ferretti Mark Briers Chris Holmes David Bonsall Johannes Abeler Christophe Fraser

Lancet Digit Health 2020 12 14;2(12):e658-e666. Epub 2020 Oct 14.

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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December 2020

Too noisy to sleep safely?-An observational study of noise levels and distractions during critical phases of pediatric anesthesia.

Authors:
Myles Monaghan Ahmed Abdelaal Ahmed Mahmoud M Alkhatip Chris Holmes

Paediatr Anaesth 2020 Dec 27;30(12):1402-1408. Epub 2020 Oct 27.

Department of Anesthesiology, Children's University Hospital Temple Street, Dublin, Ireland.

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December 2020

A cautionary note on the use of unsupervised machine learning algorithms to characterise malaria parasite population structure from genetic distance matrices.

Authors:
James A Watson Aimee R Taylor Elizabeth A Ashley Arjen Dondorp Caroline O Buckee Nicholas J White Chris C Holmes

PLoS Genet 2020 10 9;16(10):e1009037. Epub 2020 Oct 9.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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October 2020

Machine learning improves mortality risk prediction after cardiac surgery: Systematic review and meta-analysis.

Authors:
Umberto Benedetto Arnaldo Dimagli Shubhra Sinha Lucia Cocomello Ben Gibbison Massimo Caputo Tom Gaunt Matt Lyon Chris Holmes Gianni D Angelini

J Thorac Cardiovasc Surg 2020 Aug 10. Epub 2020 Aug 10.

Department of Translational Health Sciences, Bristol Heart Institute, University of Bristol, London, United Kingdom.

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August 2020

NRF2 metagene signature is a novel prognostic biomarker in colorectal cancer.

Authors:
Séan M O'Cathail Chieh-Hsi Wu Annabelle Lewis Chris Holmes Maria A Hawkins Tim Maughan

Cancer Genet 2020 10 21;248-249:1-10. Epub 2020 Aug 21.

Oxford Institute of Radiation Oncology, University of Oxford, United Kingdom.

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October 2020

Research Output from the Irish Paediatric Hospitals in the Field of Anaesthesia and Intensive Care Over 10 Years: A Bibliometric Analysis.

Authors:
Ahmed Abdelaal Ahmed Mahmoud M Alkhatip Mohamed Younis Chris Holmes Amr Sallam

Turk J Anaesthesiol Reanim 2020 Jun 22;48(3):223-228. Epub 2019 Oct 22.

Department of Anaesthesiology and Intensive Care, Ain Shams University Hospital, Cairo, Egypt.

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June 2020

Estimating excess 1-year mortality associated with the COVID-19 pandemic according to underlying conditions and age: a population-based cohort study.

Authors:
Amitava Banerjee Laura Pasea Steve Harris Arturo Gonzalez-Izquierdo Ana Torralbo Laura Shallcross Mahdad Noursadeghi Deenan Pillay Neil Sebire Chris Holmes Christina Pagel Wai Keong Wong Claudia Langenberg Bryan Williams Spiros Denaxas Harry Hemingway

Lancet 2020 05 12;395(10238):1715-1725. Epub 2020 May 12.

Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK.

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May 2020

Graphing and reporting heterogeneous treatment effects through reference classes.

Authors:
James A Watson Chris C Holmes

Trials 2020 May 7;21(1):386. Epub 2020 May 7.

Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.

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May 2020

Testing for dependence on tree structures.

Authors:
Merle Behr M Azim Ansari Axel Munk Chris Holmes

Proc Natl Acad Sci U S A 2020 05 22;117(18):9787-9792. Epub 2020 Apr 22.

Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom;

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May 2020

Successful Model for Guideline Implementation to Prevent Cancer-Associated Thrombosis: Venous Thromboembolism Prevention in the Ambulatory Cancer Clinic.

Authors:
Chris E Holmes Steven Ades Susan Gilchrist Daniel Douce Karen Libby Britny Rogala Emily Parenteau Mary Cushman Allison Kaigle Holm

JCO Oncol Pract 2020 Sep 8;16(9):e868-e874. Epub 2020 Apr 8.

Data Management Office, University of Vermont Health Network, Burlington, VT.

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September 2020

Machine learning and artificial intelligence research for patient benefit: 20 critical questions on transparency, replicability, ethics, and effectiveness.

Authors:
Sebastian Vollmer Bilal A Mateen Gergo Bohner Franz J Király Rayid Ghani Pall Jonsson Sarah Cumbers Adrian Jonas Katherine S L McAllister Puja Myles David Granger Mark Birse Richard Branson Karel G M Moons Gary S Collins John P A Ioannidis Chris Holmes Harry Hemingway

BMJ 2020 03 20;368:l6927. Epub 2020 Mar 20.

Health Data Research UK London, University College London, London, UK.

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March 2020

What role should the commercial food system play in promoting health through better diet?

Authors:
Martin White Emilie Aguirre Diane T Finegood Chris Holmes Gary Sacks Richard Smith

BMJ 2020 Mar 17;368:m545. Epub 2020 Mar 17.

College of Medicine and Health, University of Exeter, Exeter, UK.

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March 2020

Prospective evaluation of drug-drug interactions in ambulatory cancer patients initiated on prophylactic anticoagulation.

Authors:
Hank K Ng Britny G Rogala Steven Ades Joanna R Schwartz Takamaru Ashikaga Pamela Vacek Chris E Holmes

J Oncol Pharm Pract 2020 Oct 11;26(7):1637-1642. Epub 2020 Feb 11.

Hematology and Oncology Division, University of Vermont Cancer Center, Burlington, VT, USA.

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October 2020

Machine learning analysis plans for randomised controlled trials: detecting treatment effect heterogeneity with strict control of type I error.

Authors:
James A Watson Chris C Holmes

Trials 2020 Feb 10;21(1):156. Epub 2020 Feb 10.

Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.

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February 2020

Interferon lambda 4 impacts the genetic diversity of hepatitis C virus.

Authors:
M Azim Ansari Elihu Aranday-Cortes Camilla Lc Ip Ana da Silva Filipe Siu Hin Lau Connor Bamford David Bonsall Amy Trebes Paolo Piazza Vattipally Sreenu Vanessa M Cowton J Ball E Barnes G Burgess G Cooke J Dillon G Foster C Gore N Guha R Halford C Holmes E Hudson S Hutchinson W Irving S Khakoo P Klenerman N Martin T Mbisa J McKeating J McLauchlan A Miners A Murray P Shaw P Simmonds S Smith C Spencer E Thomson P Troke P Vickerman N Zitzmann Emma Hudson Rory Bowden Arvind H Patel Graham R Foster William L Irving Kosh Agarwal Emma C Thomson Peter Simmonds Paul Klenerman Chris Holmes Eleanor Barnes Chris Ca Spencer John McLauchlan Vincent Pedergnana

Elife 2019 09 3;8. Epub 2019 Sep 3.

Wellcome Centre Human Genetics, University of Oxford, Oxford, United Kingdom.

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September 2019

Risk factors for cancer-associated venous thromboembolism: The venous thromboembolism prevention in the ambulatory cancer clinic (VTE-PACC) study.

Authors:
Daniel R Douce Chris E Holmes Mary Cushman Charles D MacLean Steven Ades Neil A Zakai

J Thromb Haemost 2019 12 22;17(12):2152-2159. Epub 2019 Sep 22.

Departments of Medicine and Pathology & Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA.

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December 2019

Successful management of refractory bleeding in liver failure with tranexamic acid: Case report and literature review.

Authors:
Saranya Kodali Chris E Holmes Eswar Tipirneni Christina R Cahill Andrew J Goodwin Mary Cushman

Res Pract Thromb Haemost 2019 Jul 26;3(3):424-428. Epub 2019 Apr 26.

Division of Hematology Oncology, Department of Medicine Larner College of Medicine at the University of Vermont Burlington Vermont.

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July 2019

Regional variation and cost implications of prescribed extended half-life factor concentrates among U.S. Haemophilia Treatment Centres for patients with moderate and severe haemophilia.

Authors:
Stacy E Croteau Dunlei Cheng Alice J Cohen Chris E Holmes Lynn M Malec Michael Silvey Courtney D Thornburg Allison P Wheeler Peter A Kouides Leslie J Raffini Ellis J Neufeld

Haemophilia 2019 Jul 17;25(4):668-675. Epub 2019 Apr 17.

St. Jude Children's Research Hospital, Memphis, Tennessee.

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July 2019

Saving sevoflurane: Automated gas control can reduce consumption of anesthetic vapor by one-third in pediatric anesthesia.

Authors:
Peter Moran David Barr Chris Holmes

Paediatr Anaesth 2019 04 7;29(4):310-314. Epub 2019 Mar 7.

Department of Anesthesia, Children's University Hospital, Dublin, Ireland.

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April 2019

GWAS identifies 14 loci for device-measured physical activity and sleep duration.

Authors:
Aiden Doherty Karl Smith-Byrne Teresa Ferreira Michael V Holmes Chris Holmes Sara L Pulit Cecilia M Lindgren

Nat Commun 2018 12 10;9(1):5257. Epub 2018 Dec 10.

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, OX3 7LF, UK.

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December 2018

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration.

Authors:
Zeya Wang Shaolong Cao Jeffrey S Morris Jaeil Ahn Rongjie Liu Svitlana Tyekucheva Fan Gao Bo Li Wei Lu Ximing Tang Ignacio I Wistuba Michaela Bowden Lorelei Mucci Massimo Loda Giovanni Parmigiani Chris C Holmes Wenyi Wang

iScience 2018 Nov 2;9:451-460. Epub 2018 Nov 2.

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address:

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November 2018

STAC3 variants cause a congenital myopathy with distinctive dysmorphic features and malignant hyperthermia susceptibility.

Authors:
Irina T Zaharieva Anna Sarkozy Pinki Munot Adnan Manzur Gina O'Grady John Rendu Eduardo Malfatti Helge Amthor Laurent Servais J Andoni Urtizberea Osorio Abath Neto Edmar Zanoteli Sandra Donkervoort Juliet Taylor Joanne Dixon Gemma Poke A Reghan Foley Chris Holmes Glyn Williams Muriel Holder Sabrina Yum Livija Medne Susana Quijano-Roy Norma B Romero Julien Fauré Lucy Feng Laila Bastaki Mark R Davis Rahul Phadke Caroline A Sewry Carsten G Bönnemann Heinz Jungbluth Christoph Bachmann Susan Treves Francesco Muntoni

Hum Mutat 2018 12 11;39(12):1980-1994. Epub 2018 Oct 11.

Dubowitz Neuromuscular Centre, UCL Great Ormond Street Institute of Child Health, London, UK.

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December 2018

Principles of Bayesian Inference Using General Divergence Criteria.

Authors:
Jack Jewson Jim Q Smith Chris Holmes

Entropy (Basel) 2018 Jun 6;20(6). Epub 2018 Jun 6.

Department of Statistics, University of Oxford, Oxford OX1 3LB, UK.

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June 2018

Statistical machine learning of sleep and physical activity phenotypes from sensor data in 96,220 UK Biobank participants.

Authors:
Matthew Willetts Sven Hollowell Louis Aslett Chris Holmes Aiden Doherty

Sci Rep 2018 05 21;8(1):7961. Epub 2018 May 21.

Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.

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May 2018

High-throughput mouse phenomics for characterizing mammalian gene function.

Authors:
Steve D M Brown Chris C Holmes Ann-Marie Mallon Terrence F Meehan Damian Smedley Sara Wells

Nat Rev Genet 2018 06;19(6):357-370

MRC Harwell Institute, Harwell, UK.

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June 2018

Comparing two sequential Monte Carlo samplers for exact and approximate Bayesian inference on biological models.

Authors:
Aidan C Daly Jonathan Cooper David J Gavaghan Chris Holmes

J R Soc Interface 2017 09;14(134)

Department of Statistics, University of Oxford, Oxford, UK.

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September 2017

Characterization of purine-rich element binding protein B as a novel biomarker in acute myelogenous leukemia prognostication.

Authors:
Robert J Kelm Gurpreet S Lamba Jamie E Levis Chris E Holmes

J Cell Biochem 2018 02 18;119(2):2073-2083. Epub 2017 Oct 18.

Division of Hematology/Oncology, Department of Medicine, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont.

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February 2018

Artemether-Lumefantrine and Dihydroartemisinin-Piperaquine Exert Inverse Selective Pressure on Drug Sensitivity-Associated Haplotypes in Uganda.

Authors:
Aimee R Taylor Jennifer A Flegg Chris C Holmes Philippe J Guérin Carol H Sibley Melissa D Conrad Grant Dorsey Philip J Rosenthal

Open Forum Infect Dis 2017 25;4(1):ofw229. Epub 2016 Oct 25.

Department of Medicine, University of California, San Francisco.

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October 2016

The nature and nurture of cell heterogeneity: accounting for macrophage gene-environment interactions with single-cell RNA-Seq.

Authors:
Quin F Wills Esther Mellado-Gomez Rory Nolan Damien Warner Eshita Sharma John Broxholme Benjamin Wright Helen Lockstone William James Mark Lynch Michael Gonzales Jay West Anne Leyrat Sergi Padilla-Parra Sarah Filippi Chris Holmes Michael D Moore Rory Bowden

BMC Genomics 2017 01 7;18(1):53. Epub 2017 Jan 7.

Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, OX3 7BN, UK.

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January 2017

A note on statistical repeatability and study design for high-throughput assays.

Authors:
George Nicholson Chris Holmes

Stat Med 2017 02 24;36(5):790-798. Epub 2016 Nov 24.

Department of Statistics, University of Oxford, 24-29 St Giles, Oxford, OX1 3LB, U.K.

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February 2017

Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures.

Authors:
Sarah Filippi Chris C Holmes Luis E Nieto-Barajas

Electron J Stat 2016 Nov;10(2):3338-3354

Department of Statistics, University of Oxford, England.

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November 2016

When Clinical Trial Participation Is Not an Option in the Era of Personalized Medicine: The Case of Two Patients.

Authors:
Claire F Verschraegen Hibba Rehman Bhargavi Pulluri James DeKay Maura Barry Edmund Folefac Kim Dittus Chris Holmes Julian Sprague Steve Ades Pam C Gibson

Oncology 2017 8;92(1):55-60. Epub 2016 Nov 8.

University of Vermont Cancer Center, Burlington, Vt., USA.

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January 2017

A multidisciplinary quality improvement program increases the inferior vena cava filter retrieval rate.

Authors:
John P Winters Christopher S Morris Chris E Holmes Patricia Lewis Anant D Bhave Kenneth E Najarian Joseph T Shields William Charash Mary Cushman

Vasc Med 2017 02 3;22(1):51-56. Epub 2016 Nov 3.

1 Thrombosis and Hemostasis Program, Division of Hematology - Oncology, Department of Medicine, and Cardiovascular Research Institute of Vermont, Larner College of Medicine, University of Vermont, Burlington, VT, USA.

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February 2017

Platelet phenotype changes associated with breast cancer and its treatment.

Authors:
Chris E Holmes Jamie E Levis David J Schneider Nadia M Bambace Deva Sharma Inder Lal Marie E Wood Hyman B Muss

Platelets 2016 Nov 2;27(7):703-711. Epub 2016 May 2.

e University of North Carolina Lineberger Comprehensive Cancer Center , Chapel Hill , NC , USA.

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November 2016

Plasma composition distribution in cancer: Discrimination by thrombin and factor Xa generation.

Authors:
Matthew Gissel Chris Holmes Richard Branda Lauren Ferris Kathleen Brummel-Ziedins

Thromb Res 2016 Oct 20;146:56-58. Epub 2016 Aug 20.

University of Vermont, Department of Biochemistry, Colchester, VT, United States. Electronic address:

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October 2016

Scalable Bayesian nonparametric regression via a Plackett-Luce model for conditional ranks.

Authors:
Tristan Gray-Davies Chris C Holmes François Caron

Electron J Stat 2016 Jul;10(2):1807-1828

Department of Statistics, University of Oxford.

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July 2016

Spinal Cord Infarction in a Patient with Hereditary Spherocytosis: A Case Report and Discussion.

Authors:
Waqar Waheed Anjali L Varigonda Chris E Holmes Christopher Trevino Neil M Borden W Pendlebury

Case Rep Neurol Med 2016 14;2016:7024120. Epub 2016 Mar 14.

Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT 05401, USA.

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April 2016

Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods.

Authors:
Aidan C Daly David J Gavaghan Chris Holmes Jonathan Cooper

R Soc Open Sci 2015 Dec 23;2(12):150499. Epub 2015 Dec 23.

Department of Computer Science University of Oxford Oxford, UK.

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December 2015

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

Authors:
Martin Hrabě de Angelis George Nicholson Mohammed Selloum Jacqui White Hugh Morgan Ramiro Ramirez-Solis Tania Sorg Sara Wells Helmut Fuchs Martin Fray David J Adams Niels C Adams Thure Adler Antonio Aguilar-Pimentel Dalila Ali-Hadji Gregory Amann Philippe André Sarah Atkins Aurelie Auburtin Abdel Ayadi Julien Becker Lore Becker Elodie Bedu Raffi Bekeredjian Marie-Christine Birling Andrew Blake Joanna Bottomley Mike Bowl Véronique Brault Dirk H Busch James N Bussell Julia Calzada-Wack Heather Cater Marie-France Champy Philippe Charles Claire Chevalier Francesco Chiani Gemma F Codner Roy Combe Roger Cox Emilie Dalloneau André Dierich Armida Di Fenza Brendan Doe Arnaud Duchon Oliver Eickelberg Chris T Esapa Lahcen El Fertak Tanja Feigel Irina Emelyanova Jeanne Estabel Jack Favor Ann Flenniken Alessia Gambadoro Lilian Garrett Hilary Gates Anna-Karin Gerdin George Gkoutos Simon Greenaway Lisa Glasl Patrice Goetz Isabelle Goncalves Da Cruz Alexander Götz Jochen Graw Alain Guimond Wolfgang Hans Geoff Hicks Sabine M Hölter Heinz Höfler John M Hancock Robert Hoehndorf Tertius Hough Richard Houghton Anja Hurt Boris Ivandic Hughes Jacobs Sylvie Jacquot Nora Jones Natasha A Karp Hugo A Katus Sharon Kitchen Tanja Klein-Rodewald Martin Klingenspor Thomas Klopstock Valerie Lalanne Sophie Leblanc Christoph Lengger Elise le Marchand Tonia Ludwig Aline Lux Colin McKerlie Holger Maier Jean-Louis Mandel Susan Marschall Manuel Mark David G Melvin Hamid Meziane Kateryna Micklich Christophe Mittelhauser Laurent Monassier David Moulaert Stéphanie Muller Beatrix Naton Frauke Neff Patrick M Nolan Lauryl Mj Nutter Markus Ollert Guillaume Pavlovic Natalia S Pellegata Emilie Peter Benoit Petit-Demoulière Amanda Pickard Christine Podrini Paul Potter Laurent Pouilly Oliver Puk David Richardson Stephane Rousseau Leticia Quintanilla-Fend Mohamed M Quwailid Ildiko Racz Birgit Rathkolb Fabrice Riet Janet Rossant Michel Roux Jan Rozman Ed Ryder Jennifer Salisbury Luis Santos Karl-Heinz Schäble Evelyn Schiller Anja Schrewe Holger Schulz Ralf Steinkamp Michelle Simon Michelle Stewart Claudia Stöger Tobias Stöger Minxuan Sun David Sunter Lydia Teboul Isabelle Tilly Glauco P Tocchini-Valentini Monica Tost Irina Treise Laurent Vasseur Emilie Velot Daniela Vogt-Weisenhorn Christelle Wagner Alison Walling Bruno Weber Olivia Wendling Henrik Westerberg Monja Willershäuser Eckhard Wolf Anne Wolter Joe Wood Wolfgang Wurst Ali Önder Yildirim Ramona Zeh Andreas Zimmer Annemarie Zimprich Chris Holmes Karen P Steel Yann Herault Valérie Gailus-Durner Ann-Marie Mallon Steve Dm Brown

Nat Genet 2015 Sep 27;47(9):969-978. Epub 2015 Jul 27.

MRC Harwell, Medical Research Council, Harwell, UK.

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September 2015

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.

Authors:
Jenny C Taylor Hilary C Martin Stefano Lise John Broxholme Jean-Baptiste Cazier Andy Rimmer Alexander Kanapin Gerton Lunter Simon Fiddy Chris Allan A Radu Aricescu Moustafa Attar Christian Babbs Jennifer Becq David Beeson Celeste Bento Patricia Bignell Edward Blair Veronica J Buckle Katherine Bull Ondrej Cais Holger Cario Helen Chapel Richard R Copley Richard Cornall Jude Craft Karin Dahan Emma E Davenport Calliope Dendrou Olivier Devuyst Aimée L Fenwick Jonathan Flint Lars Fugger Rodney D Gilbert Anne Goriely Angie Green Ingo H Greger Russell Grocock Anja V Gruszczyk Robert Hastings Edouard Hatton Doug Higgs Adrian Hill Chris Holmes Malcolm Howard Linda Hughes Peter Humburg David Johnson Fredrik Karpe Zoya Kingsbury Usha Kini Julian C Knight Jonathan Krohn Sarah Lamble Craig Langman Lorne Lonie Joshua Luck Davis McCarthy Simon J McGowan Mary Frances McMullin Kerry A Miller Lisa Murray Andrea H Németh M Andrew Nesbit David Nutt Elizabeth Ormondroyd Annette Bang Oturai Alistair Pagnamenta Smita Y Patel Melanie Percy Nayia Petousi Paolo Piazza Sian E Piret Guadalupe Polanco-Echeverry Niko Popitsch Fiona Powrie Chris Pugh Lynn Quek Peter A Robbins Kathryn Robson Alexandra Russo Natasha Sahgal Pauline A van Schouwenburg Anna Schuh Earl Silverman Alison Simmons Per Soelberg Sørensen Elizabeth Sweeney John Taylor Rajesh V Thakker Ian Tomlinson Amy Trebes Stephen Rf Twigg Holm H Uhlig Paresh Vyas Tim Vyse Steven A Wall Hugh Watkins Michael P Whyte Lorna Witty Ben Wright Chris Yau David Buck Sean Humphray Peter J Ratcliffe John I Bell Andrew Om Wilkie David Bentley Peter Donnelly Gilean McVean

Nat Genet 2015 Jul 18;47(7):717-726. Epub 2015 May 18.

Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.

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July 2015

Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications.

Authors:
Katherine E Pinnick George Nicholson Konstantinos N Manolopoulos Siobhán E McQuaid Philippe Valet Keith N Frayn Nathan Denton Josine L Min Krina T Zondervan Jan Fleckner Mark I McCarthy Chris C Holmes Fredrik Karpe

Diabetes 2014 Nov 19;63(11):3785-97. Epub 2014 Jun 19.

Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, U.K. National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University Hospitals Trust, Oxford, U.K.

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November 2014

Estimation of malaria haplotype and genotype frequencies: a statistical approach to overcome the challenge associated with multiclonal infections.

Authors:
Aimee R Taylor Jennifer A Flegg Samuel L Nsobya Adoke Yeka Moses R Kamya Philip J Rosenthal Grant Dorsey Carol H Sibley Philippe J Guerin Chris C Holmes

Malar J 2014 Mar 17;13:102. Epub 2014 Mar 17.

WorldWide Antimalarial Resistance Network (WWARN), Oxford, UK.

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March 2014

Efficacy of a short course of complex lymphedema therapy or graduated compression stocking therapy in the treatment of post-thrombotic syndrome.

Authors:
Chris E Holmes Nadia M Bambace Patricia Lewis Peter W Callas Mary Cushman

Vasc Med 2014 Feb;19(1):42-8

Department of Medicine, University of Vermont, Burlington, VT, USA.

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February 2014

Platelets in tumor progression: a host factor that offers multiple potential targets in the treatment of cancer.

Authors:
Deva Sharma Kathleen E Brummel-Ziedins Beth A Bouchard Chris E Holmes

J Cell Physiol 2014 Aug;229(8):1005-15

Department of Medicine, University of Vermont, Burlington, Vermont.

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August 2014

Integrative network-based Bayesian analysis of diverse genomics data.

Authors:
Wenting Wang Veerabhadran Baladandayuthapani Chris C Holmes Kim-Anh Do

BMC Bioinformatics 2013 1;14 Suppl 13:S8. Epub 2013 Oct 1.

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May 2014

Initiation of aspirin therapy modulates angiogenic protein levels in women with breast cancer receiving tamoxifen therapy.

Authors:
Chris E Holmes Jagoda Jasielec Jamie E Levis Joan Skelly Hyman B Muss

Clin Transl Sci 2013 Oct 15;6(5):386-90. Epub 2013 May 15.

Department of Medicine, University of Vermont, Burlington, Vermont, USA.

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October 2013

Platelets, coagulation and fibrinolysis in breast cancer progression.

Authors:
Inder Lal Kim Dittus Chris E Holmes

Breast Cancer Res 2013 ;15(4):207

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December 2014

Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments.

Authors:
Quin F Wills Kenneth J Livak Alex J Tipping Tariq Enver Andrew J Goldson Darren W Sexton Chris Holmes

Nat Biotechnol 2013 Aug 21;31(8):748-52. Epub 2013 Jul 21.

Department of Statistics, University of Oxford, Oxford, UK.

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August 2013

Associations between arterial stiffness and platelet activation in normotensive overweight and obese young adults.

Authors:
Jennifer N Cooper Rhobert W Evans Maria Mori Brooks Linda Fried Chris Holmes Emma Barinas-Mitchell Kim Sutton-Tyrrell

Clin Exp Hypertens 2014 8;36(3):115-22. Epub 2013 May 8.

Department of Epidemiology, Graduate School of Public Health .

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December 2014

A novel test for gene-ancestry interactions in genome-wide association data.

Authors:
Joanna L Davies Jean-Baptiste Cazier Malcolm G Dunlop Richard S Houlston Ian P Tomlinson Chris C Holmes

PLoS One 2012 6;7(12):e48687. Epub 2012 Dec 6.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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May 2013

Methods for qPCR gene expression profiling applied to 1440 lymphoblastoid single cells.

Authors:
Kenneth J Livak Quin F Wills Alex J Tipping Krishnalekha Datta Rowena Mittal Andrew J Goldson Darren W Sexton Chris C Holmes

Methods 2013 Jan 16;59(1):71-9. Epub 2012 Oct 16.

Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA.

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January 2013

GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.

Authors:
Jean-Baptiste Cazier Chris C Holmes John Broxholme

Bioinformatics 2012 Nov 8;28(22):2981-2. Epub 2012 Sep 8.

Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, OX3 7BN and Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG, Oxford, UK.

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November 2012

Bayesian sparsity-path-analysis of genetic association signal using generalized t priors.

Authors:
Anthony Lee Francois Caron Arnaud Doucet Chris Holmes

Stat Appl Genet Mol Biol 2012 Jan 6;11(2). Epub 2012 Jan 6.

Oxford-Man Institute and Department of Statistics, University of Oxford, UK.

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January 2012

Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes.

Authors:
Josine L Min George Nicholson Ingileif Halgrimsdottir Kristian Almstrup Andreas Petri Amy Barrett Mary Travers Nigel W Rayner Reedik Mägi Fredrik H Pettersson John Broxholme Matt J Neville Quin F Wills Jane Cheeseman Maxine Allen Chris C Holmes Tim D Spector Jan Fleckner Mark I McCarthy Fredrik Karpe Cecilia M Lindgren Krina T Zondervan

PLoS Genet 2012 23;8(2):e1002505. Epub 2012 Feb 23.

The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

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February 2013

nEASE: a method for gene ontology subclassification of high-throughput gene expression data.

Authors:
Thomas W Chittenden Eleanor A Howe Jennifer M Taylor Jessica C Mar Martin J Aryee Harold Gómez Razvan Sultana John Braisted Sarita J Nair John Quackenbush Chris Holmes

Bioinformatics 2012 Mar 13;28(5):726-8. Epub 2012 Jan 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA.

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March 2012

MicroRNA expression in abdominal and gluteal adipose tissue is associated with mRNA expression levels and partly genetically driven.

Authors:
Mattias Rantalainen Blanca M Herrera George Nicholson Rory Bowden Quin F Wills Josine L Min Matt J Neville Amy Barrett Maxine Allen Nigel W Rayner Jan Fleckner Mark I McCarthy Krina T Zondervan Fredrik Karpe Chris C Holmes Cecilia M Lindgren

PLoS One 2011 15;6(11):e27338. Epub 2011 Nov 15.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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May 2012

Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.

Authors:
Bernet S Kato George Nicholson Maja Neiman Mattias Rantalainen Chris C Holmes Amy Barrett Mathias Uhlén Peter Nilsson Tim D Spector Jochen M Schwenk

Proteome Sci 2011 Nov 17;9:73. Epub 2011 Nov 17.

Department of Twin Research and Genetic Epidemiology, King's College London, St, Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, UK.

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November 2011

Application of a novel score test for genetic association incorporating gene-gene interaction suggests functionality for prostate cancer susceptibility regions.

Authors:
Julia Ciampa Meredith Yeager Kevin Jacobs Michael J Thun Susan Gapstur Demetrius Albanes Jarmo Virtamo Stephanie J Weinstein Edward Giovannucci Walter C Willett Geraldine Cancel-Tassin Olivier Cussenot Antoine Valeri David Hunter Robert Hoover Gilles Thomas Stephen Chanock Chris Holmes Nilanjan Chatterjee

Hum Hered 2011 11;72(3):182-93. Epub 2011 Nov 11.

Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852, USA.

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May 2012

Accounting for control mislabeling in case-control biomarker studies.

Authors:
Mattias Rantalainen Chris C Holmes

J Proteome Res 2011 Dec 8;10(12):5562-7. Epub 2011 Nov 8.

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom.

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December 2011

A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.

Authors:
George Nicholson Mattias Rantalainen Jia V Li Anthony D Maher Daniel Malmodin Kourosh R Ahmadi Johan H Faber Amy Barrett Josine L Min N William Rayner Henrik Toft Maria Krestyaninova Juris Viksna Sudeshna Guha Neogi Marc-Emmanuel Dumas Ugis Sarkans Peter Donnelly Thomas Illig Jerzy Adamski Karsten Suhre Maxine Allen Krina T Zondervan Tim D Spector Jeremy K Nicholson John C Lindon Dorrit Baunsgaard Elaine Holmes Mark I McCarthy Chris C Holmes

PLoS Genet 2011 Sep 8;7(9):e1002270. Epub 2011 Sep 8.

Department of Statistics, University of Oxford, Oxford, United Kingdom.

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September 2011

Human metabolic profiles are stably controlled by genetic and environmental variation.

Authors:
George Nicholson Mattias Rantalainen Anthony D Maher Jia V Li Daniel Malmodin Kourosh R Ahmadi Johan H Faber Ingileif B Hallgrímsdóttir Amy Barrett Henrik Toft Maria Krestyaninova Juris Viksna Sudeshna Guha Neogi Marc-Emmanuel Dumas Ugis Sarkans The Molpage Consortium Bernard W Silverman Peter Donnelly Jeremy K Nicholson Maxine Allen Krina T Zondervan John C Lindon Tim D Spector Mark I McCarthy Elaine Holmes Dorrit Baunsgaard Chris C Holmes

Mol Syst Biol 2011 Aug 30;7:525. Epub 2011 Aug 30.

Department of Statistics, University of Oxford, Oxford, UK.

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August 2011

Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array.

Authors:
Niall Cardin Chris Holmes Peter Donnelly Jonathan Marchini

Genet Epidemiol 2011 Sep 18;35(6):536-48. Epub 2011 Jul 18.

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, United Kingdom.

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September 2011

Hierarchical Bayesian nonparametric mixture models for clustering with variable relevance determination.

Authors:
Christopher Yau Chris Holmes

Bayesian Anal 2011 Jul;6(2):329-352

Department of Statistics, University of Oxford, Oxford, U.K.,

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July 2011

Therapeutic implications of GIPC1 silencing in cancer.

Authors:
Thomas W Chittenden Jane Pak Renee Rubio Hailing Cheng Kristina Holton Niall Prendergast Vladimir Glinskii Yi Cai Aedin Culhane Stefan Bentink Mathew Schwede Jessica C Mar Eleanor A Howe Martin Aryee Razvan Sultana Anthony A Lanahan Jennifer M Taylor Chris Holmes William C Hahn Jean J Zhao J Dirk Iglehart John Quackenbush

PLoS One 2010 Dec 30;5(12):e15581. Epub 2010 Dec 30.

Functional Genomics and Computational Biology Group, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States America.

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December 2010

An association between anti-platelet drug use and reduced cancer prevalence in diabetic patients: results from the Vermont Diabetes Information System Study.

Authors:
Chris E Holmes Maria E Ramos-Nino Benjamin Littenberg

BMC Cancer 2010 Jun 15;10:289. Epub 2010 Jun 15.

Hematology and Oncology, University of Vermont, Given Building Second Floor, Burlington, VT 05401, USA.

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June 2010

Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls.

Authors:
Nick Craddock Matthew E Hurles Niall Cardin Richard D Pearson Vincent Plagnol Samuel Robson Damjan Vukcevic Chris Barnes Donald F Conrad Eleni Giannoulatou Chris Holmes Jonathan L Marchini Kathy Stirrups Martin D Tobin Louise V Wain Chris Yau Jan Aerts Tariq Ahmad T Daniel Andrews Hazel Arbury Anthony Attwood Adam Auton Stephen G Ball Anthony J Balmforth Jeffrey C Barrett Inês Barroso Anne Barton Amanda J Bennett Sanjeev Bhaskar Katarzyna Blaszczyk John Bowes Oliver J Brand Peter S Braund Francesca Bredin Gerome Breen Morris J Brown Ian N Bruce Jaswinder Bull Oliver S Burren John Burton Jake Byrnes Sian Caesar Chris M Clee Alison J Coffey John M C Connell Jason D Cooper Anna F Dominiczak Kate Downes Hazel E Drummond Darshna Dudakia Andrew Dunham Bernadette Ebbs Diana Eccles Sarah Edkins Cathryn Edwards Anna Elliot Paul Emery David M Evans Gareth Evans Steve Eyre Anne Farmer I Nicol Ferrier Lars Feuk Tomas Fitzgerald Edward Flynn Alistair Forbes Liz Forty Jayne A Franklyn Rachel M Freathy Polly Gibbs Paul Gilbert Omer Gokumen Katherine Gordon-Smith Emma Gray Elaine Green Chris J Groves Detelina Grozeva Rhian Gwilliam Anita Hall Naomi Hammond Matt Hardy Pile Harrison Neelam Hassanali Husam Hebaishi Sarah Hines Anne Hinks Graham A Hitman Lynne Hocking Eleanor Howard Philip Howard Joanna M M Howson Debbie Hughes Sarah Hunt John D Isaacs Mahim Jain Derek P Jewell Toby Johnson Jennifer D Jolley Ian R Jones Lisa A Jones George Kirov Cordelia F Langford Hana Lango-Allen G Mark Lathrop James Lee Kate L Lee Charlie Lees Kevin Lewis Cecilia M Lindgren Meeta Maisuria-Armer Julian Maller John Mansfield Paul Martin Dunecan C O Massey Wendy L McArdle Peter McGuffin Kirsten E McLay Alex Mentzer Michael L Mimmack Ann E Morgan Andrew P Morris Craig Mowat Simon Myers William Newman Elaine R Nimmo Michael C O'Donovan Abiodun Onipinla Ifejinelo Onyiah Nigel R Ovington Michael J Owen Kimmo Palin Kirstie Parnell David Pernet John R B Perry Anne Phillips Dalila Pinto Natalie J Prescott Inga Prokopenko Michael A Quail Suzanne Rafelt Nigel W Rayner Richard Redon David M Reid Renwick Susan M Ring Neil Robertson Ellie Russell David St Clair Jennifer G Sambrook Jeremy D Sanderson Helen Schuilenburg Carol E Scott Richard Scott Sheila Seal Sue Shaw-Hawkins Beverley M Shields Matthew J Simmonds Debbie J Smyth Elilan Somaskantharajah Katarina Spanova Sophia Steer Jonathan Stephens Helen E Stevens Millicent A Stone Zhan Su Deborah P M Symmons John R Thompson Wendy Thomson Mary E Travers Clare Turnbull Armand Valsesia Mark Walker Neil M Walker Chris Wallace Margaret Warren-Perry Nicholas A Watkins John Webster Michael N Weedon Anthony G Wilson Matthew Woodburn B Paul Wordsworth Allan H Young Eleftheria Zeggini Nigel P Carter Timothy M Frayling Charles Lee Gil McVean Patricia B Munroe Aarno Palotie Stephen J Sawcer Stephen W Scherer David P Strachan Chris Tyler-Smith Matthew A Brown Paul R Burton Mark J Caulfield Alastair Compston Martin Farrall Stephen C L Gough Alistair S Hall Andrew T Hattersley Adrian V S Hill Christopher G Mathew Marcus Pembrey Jack Satsangi Michael R Stratton Jane Worthington Panos Deloukas Audrey Duncanson Dominic P Kwiatkowski Mark I McCarthy Willem Ouwehand Miles Parkes Nazneen Rahman John A Todd Nilesh J Samani Peter Donnelly

Nature 2010 Apr;464(7289):713-20

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April 2010

The effect of P2Y-mediated platelet activation on the release of VEGF and endostatin from platelets.

Authors:
Nadia M Bambace Jamie E Levis Chris E Holmes

Platelets 2010 ;21(2):85-93

Department of Medicine, University of Vermont, Burlington, Vermont, USA.

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May 2010

Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknown.

Authors:
Joanna L Davies Jotun Hein Chris C Holmes

Genet Epidemiol 2010 May;34(4):299-308

Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, United Kingdom.

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May 2010

A boosting approach to structure learning of graphs with and without prior knowledge.

Authors:
Shahzia Anjum Arnaud Doucet Chris C Holmes

Bioinformatics 2009 Nov 20;25(22):2929-36. Epub 2009 Aug 20.

Medical Research Council, Harwell, UK.

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November 2009

A novel association between a chronic subdural hematoma and a fibrinolytic pathway defect: case report.

Authors:
Anand I Rughani Chris E Holmes Paul L Penar

Neurosurgery 2009 Jun;64(6):E1192; discussion E1192

Division of Neurosurgery, University of Vermont, Burlington, Vermont 05401, USA.

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June 2009

Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency.

Authors:
Jochen W Klingelhoefer Loukas Moutsianas Chris Holmes

Bioinformatics 2009 Jul 6;25(13):1594-601. Epub 2009 May 6.

Department of Biochemistry, University of Oxford, Oxford, UK.

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July 2009

Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture.

Authors:
Jacob E Lemieux Natalia Gomez-Escobar Avi Feller Celine Carret Alfred Amambua-Ngwa Robert Pinches Felix Day Sue A Kyes David J Conway Chris C Holmes Chris I Newbold

Proc Natl Acad Sci U S A 2009 May 17;106(18):7559-64. Epub 2009 Apr 17.

Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, United Kingdom.

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May 2009

Correlates of anemia in American blacks and whites: the REGARDS Renal Ancillary Study.

Authors:
Neil A Zakai Leslie A McClure Ronald Prineas George Howard William McClellan Chris E Holmes Britt B Newsome David G Warnock Paul Audhya Mary Cushman

Am J Epidemiol 2009 Feb 9;169(3):355-64. Epub 2008 Dec 9.

Department of Medicine, University of Vermont, Burlington, VT, USA.

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February 2009

Phylogenetic inference under recombination using Bayesian stochastic topology selection.

Authors:
Alex Webb John M Hancock Chris C Holmes

Bioinformatics 2009 Jan 20;25(2):197-203. Epub 2008 Nov 20.

Department of Statistics, Oxford, UK.

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January 2009

The trends in prostate specific antigen usage amongst United Kingdom urologists--a questionnaire based study.

Authors:
Helena P Burden Chris R Davis Sophie Tate Raj Persad Chris H Holmes Kate Whittington

BMC Urol 2008 Nov 20;8:17. Epub 2008 Nov 20.

Urology Speciality Registrar, Derriford, Plymouth, UK.

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November 2008

Key issues in conducting a meta-analysis of gene expression microarray datasets.

Authors:
Adaikalavan Ramasamy Adrian Mondry Chris C Holmes Douglas G Altman

PLoS Med 2008 Sep 2;5(9):e184. Epub 2008 Sep 2.

Centre for Statistics in Medicine, University of Oxford, Oxford, United Kingdom.

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September 2008

The clinical diagnosis of heparin-induced thrombocytopenia in patients receiving continuous renal replacement therapy.

Authors:
Chris E Holmes Joe C Huang Carina Cartelli Alan Howard Jeffrey Rimmer Mary Cushman

J Thromb Thrombolysis 2009 May 17;27(4):406-12. Epub 2008 May 17.

Department of Medicine, Division of Hematology & Oncology, University of Vermont College of Medicine, Burlington, VT 05401, USA.

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May 2009

Tamoxifen and aromatase inhibitors differentially affect vascular endothelial growth factor and endostatin levels in women with breast cancer.

Authors:
Chris E Holmes Joe C Huang Thomas R Pace Alan B Howard Hyman B Muss

Clin Cancer Res 2008 May;14(10):3070-6

Department of Medicine, University of Vermont, Burlington, Vermont, USA.

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May 2008

Functional classification analysis of somatically mutated genes in human breast and colorectal cancers.

Authors:
Thomas W Chittenden Eleanor A Howe Aedin C Culhane Razvan Sultana Jennifer M Taylor Chris Holmes John Quackenbush

Genomics 2008 Jun 22;91(6):508-11. Epub 2008 Apr 22.

Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115-6084, USA.

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June 2008

Agricultural intensity and landscape structure: influences on the macroinvertebrate assemblages of small streams in northern Germany.

Authors:
Carola A Schriever Maria Hansler Ball Chris Holmes Steve Maund Matthias Liess

Environ Toxicol Chem 2007 Feb;26(2):346-57

Helmholtz Centre for Environmental Research-UFZ, Department of System Ecotoxicology (OEKOTOX), Permoserstrasse 15, 04318 Leipzig, Germany.

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February 2007

How does crop type influence risk from pesticides to the aquatic environment?

Authors:
Colin D Brown Chris Holmes Ryan Williams Sabine Beulke Wendy van Beinum Emma Pemberton Claire Wells

Environ Toxicol Chem 2007 Sep;26(9):1818-26

Environment Department, University of York, York, United Kingdom.

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September 2007

Influence of preparative procedures on assay of platelet function and apparent effects of antiplatelet agents.

Authors:
Nathaniel J Madsen Chris E Holmes Feliciano A Serrano Burton E Sobel David J Schneider

Am J Cardiol 2007 Aug 26;100(4):722-7. Epub 2007 Jun 26.

Cardiology Unit, Department of Medicine, University of Vermont, Burlington, Vermont, USA.

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August 2007

Contributions of young platelets and of previously activated platelets to platelet reactivity in patients with coronary artery disease.

Authors:
David J Schneider Chris E Holmes Heidi S Taatjes-Sommer Burton E Sobel

Thromb Res 2008 1;121(4):455-62. Epub 2007 Aug 1.

Cardiology Unit, Department of Medicine, University of Vermont, Burlington, Vermont, USA.

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April 2008

Modulation of the BK channel by estrogens: examination at single channel level.

Authors:
Heidi De Wet Marcus Allen Chris Holmes Michelle Stobbart Jonathan D Lippiat Richard Callaghan

Mol Membr Biol 2006 Sep-Oct;23(5):420-9

School of Pharmacy and Biomolecular Sciences, University of Brighton, Oxford, UK.

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January 2007

All systems GO for understanding mouse gene function.

Authors:
Chris Holmes Steve D M Brown

J Biol 2004 17;3(5):20. Epub 2004 Dec 17.

MRC Mammalian Genetics Unit, Harwell OX11 0RD, UK.

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September 2006

Diagnosis and treatment of breast cancer in the elderly.

Authors:
Chris E Holmes Hyman B Muss

CA Cancer J Clin 2003 Jul-Aug;53(4):227-44

Department of Medicine, University of Vermont, Burlington, VT, USA.

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September 2003