Daniela Witten

Daniela Witten

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Daniela Witten

Daniela Witten

Publications by authors named "Daniela Witten"

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Discussion on Covariate-assisted ranking and screening for large-scale two-sample inference.

J R Stat Soc Series B Stat Methodol 2019 Apr 18;81(2):229-231. Epub 2019 Mar 18.

University of Washington, Seattle.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6553469PMC
April 2019

Data-adaptive additive modeling.

Stat Med 2019 Feb 16;38(4):583-600. Epub 2018 Jul 16.

Departments of Biostatistics and Statistics, University of Washington, Seattle, WA, USA.

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http://dx.doi.org/10.1002/sim.7859DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335202PMC
February 2019

Are clusterings of multiple data views independent?

Biostatistics 2019 Feb 8. Epub 2019 Feb 8.

Department of Biostatistics, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA and Department of Statistics, University of Washington, B313 Padelford Hall, West Stevens Way Northeast, Seattle, WA 98105, USA.

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http://dx.doi.org/10.1093/biostatistics/kxz001DOI Listing
February 2019

Fast nonconvex deconvolution of calcium imaging data.

Biostatistics 2019 Feb 8. Epub 2019 Feb 8.

Department of Statistics, University of Washington, Seattle, WA 98195, USA and Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy083DOI Listing
February 2019

CADD: predicting the deleteriousness of variants throughout the human genome.

Nucleic Acids Res 2019 Jan;47(D1):D886-D894

Berlin Institute of Health (BIH), 10178 Berlin, Germany.

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http://dx.doi.org/10.1093/nar/gky1016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323892PMC
January 2019

SCALPEL: EXTRACTING NEURONS FROM CALCIUM IMAGING DATA.

Ann Appl Stat 2018 Dec 13;12(4):2430-2456. Epub 2018 Nov 13.

Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA, Departments of Biostatistics and Statistics, University of Washington, Seattle, Washington 98195, USA,

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https://projecteuclid.org/euclid.aoas/1542078051
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http://dx.doi.org/10.1214/18-AOAS1159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6269150PMC
December 2018

EXACT SPIKE TRAIN INFERENCE VIA ℓ OPTIMIZATION.

Ann Appl Stat 2018 Dec 13;12(4):2457-2482. Epub 2018 Nov 13.

Departments of Statistics and Biostatistics, University of Washington, Seattle, Washington 98195, USA,

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http://dx.doi.org/10.1214/18-AOAS1162DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322847PMC
December 2018

Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.

Authors:
Joshua C Bis Xueqiu Jian Brian W Kunkle Yuning Chen Kara L Hamilton-Nelson William S Bush William J Salerno Daniel Lancour Yiyi Ma Alan E Renton Edoardo Marcora John J Farrell Yi Zhao Liming Qu Shahzad Ahmad Najaf Amin Philippe Amouyel Gary W Beecham Jennifer E Below Dominique Campion Camille Charbonnier Jaeyoon Chung Paul K Crane Carlos Cruchaga L Adrienne Cupples Jean-François Dartigues Stéphanie Debette Jean-François Deleuze Lucinda Fulton Stacey B Gabriel Emmanuelle Genin Richard A Gibbs Alison Goate Benjamin Grenier-Boley Namrata Gupta Jonathan L Haines Aki S Havulinna Seppo Helisalmi Mikko Hiltunen Daniel P Howrigan M Arfan Ikram Jaakko Kaprio Jan Konrad Amanda Kuzma Eric S Lander Mark Lathrop Terho Lehtimäki Honghuang Lin Kari Mattila Richard Mayeux Donna M Muzny Waleed Nasser Benjamin Neale Kwangsik Nho Gaël Nicolas Devanshi Patel Margaret A Pericak-Vance Markus Perola Bruce M Psaty Olivier Quenez Farid Rajabli Richard Redon Christiane Reitz Anne M Remes Veikko Salomaa Chloe Sarnowski Helena Schmidt Michael Schmidt Reinhold Schmidt Hilkka Soininen Timothy A Thornton Giuseppe Tosto Christophe Tzourio Sven J van der Lee Cornelia M van Duijn Badri Vardarajan Weixin Wang Ellen Wijsman Richard K Wilson Daniela Witten Kim C Worley Xiaoling Zhang Celine Bellenguez Jean-Charles Lambert Mitja I Kurki Aarno Palotie Mark Daly Eric Boerwinkle Kathryn L Lunetta Anita L Destefano Josée Dupuis Eden R Martin Gerard D Schellenberg Sudha Seshadri Adam C Naj Myriam Fornage Lindsay A Farrer

Mol Psychiatry 2018 Aug 14. Epub 2018 Aug 14.

Departments of Biostatistics, Boston University School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41380-018-0112-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375806PMC
August 2018

Network Reconstruction From High-Dimensional Ordinary Differential Equations.

J Am Stat Assoc 2017 7;112(520):1697-1707. Epub 2017 Aug 7.

Departments of Biostatistics and Statistics, University of Washington, WA.

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http://dx.doi.org/10.1080/01621459.2016.1229197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880569PMC
August 2017

Nearly assumptionless screening for the mutually-exciting multivariate Hawkes process.

Electron J Stat 2017 11;11(1):1207-1234. Epub 2017 Apr 11.

Department of Biostatistics and Statistics, University of Washington, Seattle, WA 98195.

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http://dx.doi.org/10.1214/17-EJS1251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570442PMC
April 2017

Simultaneous detection and estimation of trait associations with genomic phenotypes.

Biostatistics 2017 01 5;18(1):147-164. Epub 2016 Aug 5.

Department of Statistics, University of Washington, Seattle, WA, 98195, USA and Department of Biostatistics, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1093/biostatistics/kxw033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082590PMC
January 2017

Replicates in high dimensions, with applications to latent variable graphical models.

Biometrika 2016 12 8;103(4):761-777. Epub 2016 Dec 8.

Department of Operations Research and Financial Engineering, Princeton University, Princeton, New Jersey 08544, U.S.A.,

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http://dx.doi.org/10.1093/biomet/asw050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5520622PMC
December 2016

Fused Lasso Additive Model.

J Comput Graph Stat 2016 10;25(4):1005-1025. Epub 2016 Nov 10.

Department of Biostatistics, University of Washington, Seattle WA 98195.

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http://dx.doi.org/10.1080/10618600.2015.1073155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321231PMC
November 2016

Hypothesis testing for differentially correlated features.

Biostatistics 2016 10 4;17(4):677-91. Epub 2016 Apr 4.

Department of Biostatistics, University of Washington, Seattle, Washington, USA and Veterans Affairs Seattle Medical Center, Seattle, Washington, USA

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http://dx.doi.org/10.1093/biostatistics/kxw013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031944PMC
October 2016

Convex Regression with Interpretable Sharp Partitions.

J Mach Learn Res 2016 Jun;17

Departments of Biostatistics and Statistics, University of Washington, Seattle, WA 98195.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5021451PMC
June 2016

Statistical properties of convex clustering.

Electron J Stat 2015;9(2):2324-2347. Epub 2015 Oct 14.

Departments of Statistics and Biostatistics, University of Washington, Seattle, WA 98195, U.S.A.,

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http://dx.doi.org/10.1214/15-EJS1074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014420PMC
October 2015

Convex Modeling of Interactions with Strong Heredity.

J Comput Graph Stat 2016 12;25(4):981-1004. Epub 2015 Aug 12.

Department of Biostatistics, University of Washington.

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http://dx.doi.org/10.1080/10618600.2015.1067217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353363PMC
August 2015

The cluster graphical lasso for improved estimation of Gaussian graphical models.

Comput Stat Data Anal 2015 May;85:23-36

Department of Biostatistics, University of Washington, Seattle, WA 98195-7232, USA.

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http://dx.doi.org/10.1016/j.csda.2014.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307846PMC
May 2015

Selection and estimation for mixed graphical models.

Biometrika 2015 Mar 24;102(1):47-64. Epub 2014 Dec 24.

Department of Biostatistics, University of Washington, Box 357232, Seattle, Washington 98195, U.S.A.

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http://dx.doi.org/10.1093/biomet/asu051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018402PMC
March 2015

Pathway Graphical Lasso.

Proc Conf AAAI Artif Intell 2015 Jan;2015:2617-2623

University of Washington, Seattle, WA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4497513PMC
January 2015

Learning Graphical Models With Hubs.

J Mach Learn Res 2014 Oct;15:3297-3331

Department of Biostatistics, University of Washington, Seattle, WA 98195.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302963PMC
October 2014

Inferring clonal composition from multiple sections of a breast cancer.

PLoS Comput Biol 2014 Jul 10;10(7):e1003703. Epub 2014 Jul 10.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America; Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091710PMC
July 2014

A general framework for estimating the relative pathogenicity of human genetic variants.

Nat Genet 2014 Mar 2;46(3):310-5. Epub 2014 Feb 2.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/ng.2892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3992975PMC
March 2014

The joint graphical lasso for inverse covariance estimation across multiple classes.

J R Stat Soc Series B Stat Methodol 2014 Mar;76(2):373-397

Department of Biostatistics, University of Washington, USA.

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http://doi.wiley.com/10.1111/rssb.12033
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http://dx.doi.org/10.1111/rssb.12033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4012833PMC
March 2014

Graph Estimation with Joint Additive Models.

Biometrika 2014 Mar;101(1):85-101

Department of Biostatistics, University of Washington, Seattle, Washington, 98195-7232, U.S.A.

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https://academic.oup.com/biomet/article-lookup/doi/10.1093/b
Publisher Site
http://dx.doi.org/10.1093/biomet/ast053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4084701PMC
March 2014

Node-Based Learning of Multiple Gaussian Graphical Models.

J Mach Learn Res 2014 Jan;15(1):445-488

Departments of Computer Science and Engineering, Genome Sciences, University of Washington, Seattle WA, 98195.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193819PMC
January 2014

Sparse Biclustering of Transposable Data.

J Comput Graph Stat 2014 ;23(4):985-1008

Department of Biostatistics, University of Washington, 1705 NE Pacific Street, Box 357232, F-649 Health Sciences Building, Seattle, WA 98195-7232.

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http://dx.doi.org/10.1080/10618600.2013.852554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4212513PMC
January 2014

Is GATA3 expression maintained in regional metastases?: a study of paired primary and metastatic urothelial carcinomas.

Am J Surg Pathol 2013 Dec;37(12):1876-81

*Department of Pathology, University of Chicago, Chicago, IL Departments of †Biostatistics ‡Pathology, University of Washington, Seattle, WA.

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http://dx.doi.org/10.1097/PAS.0b013e31829e2525DOI Listing
December 2013

Scientific research in the age of omics: the good, the bad, and the sloppy.

J Am Med Inform Assoc 2013 Jan 4;20(1):125-7. Epub 2012 Oct 4.

Department of Biostatistics, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1136/amiajnl-2012-000972DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3555320PMC
January 2013

Penalized unsupervised learning with outliers.

Authors:
Daniela M Witten

Stat Interface 2013 ;6(2):211-221

Box 357232, Department of Biostatistics, University of Washington, Seattle WA 98195-7232.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716393PMC
January 2013

Molecular signatures from omics data: from chaos to consensus.

Biotechnol J 2012 Aug 23;7(8):946-57. Epub 2012 Apr 23.

Institute for Systems Biology, Seattle, WA, USA.

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http://doi.wiley.com/10.1002/biot.201100305
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http://dx.doi.org/10.1002/biot.201100305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3418428PMC
August 2012

Normalization, testing, and false discovery rate estimation for RNA-sequencing data.

Biostatistics 2012 Jul 14;13(3):523-38. Epub 2011 Oct 14.

Department of Statistics, Stanford University, Stanford, CA 94305, USA.

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https://academic.oup.com/biostatistics/article-lookup/doi/10
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http://dx.doi.org/10.1093/biostatistics/kxr031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3372940PMC
July 2012

The Stanford Integrated Psychosocial Assessment for Transplantation (SIPAT): a new tool for the psychosocial evaluation of pre-transplant candidates.

Psychosomatics 2012 Mar-Apr;53(2):123-32

Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1016/j.psym.2011.12.012DOI Listing
July 2012

The benefits of implant removal from the foot and ankle.

J Bone Joint Surg Am 2012 Jul;94(14):1316-20

Stanford University, Redwood City, California 94063, USA.

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http://dx.doi.org/10.2106/JBJS.J.01756DOI Listing
July 2012

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements.

Nucleic Acids Res 2012 May 20;40(9):3849-55. Epub 2012 Jan 20.

Department of Biostatistics, University of Washington, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/nar/gks012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3351188PMC
May 2012

Structured Learning of Gaussian Graphical Models.

Adv Neural Inf Process Syst 2012 ;2012:629-637

Electrical Engineering, Univ. of Washington.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211023PMC
January 2012

Penalized classification using Fisher's linear discriminant.

J R Stat Soc Series B Stat Methodol 2011 Nov;73(5):753-772

Department of Biostatistics, University of Washington, USA.

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http://dx.doi.org/10.1111/j.1467-9868.2011.00783.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272679PMC
November 2011

The prognostic value of tumor-associated macrophages in leiomyosarcoma: a single institution study.

Am J Clin Oncol 2011 Feb;34(1):82-6

Division of Oncology, Department of Medicine, Stanford University Medical Center, Stanford, CA, 94305, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4816680PMC
http://dx.doi.org/10.1097/coc.0b013e3181d26d5eDOI Listing
February 2011

MicroRNA expression profiles associated with mutational status and survival in malignant melanoma.

J Invest Dermatol 2010 Aug 1;130(8):2062-70. Epub 2010 Apr 1.

Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1038/jid.2010.63DOI Listing
August 2010

Survival analysis with high-dimensional covariates.

Stat Methods Med Res 2010 Feb 4;19(1):29-51. Epub 2009 Aug 4.

Department of Statistics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1177/0962280209105024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4806549PMC
February 2010

Breast Angiosarcoma: Case Series and Expression of Vascular Endothelial Growth Factor.

Case Rep Oncol 2009 Dec 11;2(3):242-250. Epub 2009 Dec 11.

Department of Internal Medicine, Stanford University Medical Center, Stanford, Calif., USA.

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http://dx.doi.org/10.1159/000264637DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914389PMC
December 2009

Extensions of sparse canonical correlation analysis with applications to genomic data.

Stat Appl Genet Mol Biol 2009 9;8:Article28. Epub 2009 Jun 9.

Stanford University, USA.

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http://dx.doi.org/10.2202/1544-6115.1470DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861323PMC
September 2009

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis.

Biostatistics 2009 Jul 17;10(3):515-34. Epub 2009 Apr 17.

Department of Statistics, Stanford University, Stanford, CA 94305, USA.

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http://dx.doi.org/10.1093/biostatistics/kxp008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2697346PMC
July 2009

Hierarchical maintenance of MLL myeloid leukemia stem cells employs a transcriptional program shared with embryonic rather than adult stem cells.

Cell Stem Cell 2009 Feb;4(2):129-40

Department of Pathology, Stanford University, Stanford, CA 94305, USA; Cancer Research UK Leukaemia Biology Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, UK.

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http://linkinghub.elsevier.com/retrieve/pii/S193459090800617
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http://dx.doi.org/10.1016/j.stem.2008.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2670853PMC
February 2009

Covariance-regularized regression and classification for high-dimensional problems.

J R Stat Soc Series B Stat Methodol 2009 Feb;71(3):615-636

Department of Statistics, Stanford University, 390 Serra Mall, Stanford CA 94305, USA. E-mail:

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http://dx.doi.org/10.1111/j.1467-9868.2009.00699.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806603PMC
February 2009

Postoperative pain following foot and ankle surgery: a prospective study.

Foot Ankle Int 2008 Nov;29(11):1063-8

Stanford University Medical Center, Department of Orthopaedic Surgery, 300 Pasteur Drive, Room R111, MC 5343, Stanford, CA 94305-5343, USA.

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http://journals.sagepub.com/doi/10.3113/FAI.2008.1063
Publisher Site
http://dx.doi.org/10.3113/FAI.2008.1063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743476PMC
November 2008

A recoding method to improve the humoral immune response to an HIV DNA vaccine.

PLoS One 2008 Sep 15;3(9):e3214. Epub 2008 Sep 15.

Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003214PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2529374PMC
September 2008

TESTING SIGNIFICANCE OF FEATURES BY LASSOED PRINCIPAL COMPONENTS.

Ann Appl Stat 2008 Sep;2(3):986-1012

Department of Statistics Stanford University 390 Serra Mall Stanford, California 94305 USA E-mail:

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http://dx.doi.org/10.1214/08-AOAS182SUPPDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743444PMC
September 2008