Literature DB >> 22926914

Classification of patients from time-course gene expression.

Yuping Zhang1, Robert Tibshirani, Ronald Davis.   

Abstract

Classifying patients into different risk groups based on their genomic measurements can help clinicians design appropriate clinical treatment plans. To produce such a classification, gene expression data were collected on a cohort of burn patients, who were monitored across multiple time points. This led us to develop a new classification method using time-course gene expressions. Our results showed that making good use of time-course information of gene expression improved the performance of classification compared with using gene expression from individual time points only. Our method is implemented into an R-package: time-course prediction analysis using microarray.

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Year:  2012        PMID: 22926914      PMCID: PMC3520502          DOI: 10.1093/biostatistics/kxs027

Source DB:  PubMed          Journal:  Biostatistics        ISSN: 1465-4644            Impact factor:   5.899


  9 in total

1.  Significance analysis of microarrays applied to the ionizing radiation response.

Authors:  V G Tusher; R Tibshirani; G Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-17       Impact factor: 11.205

2.  Significance analysis of time course microarray experiments.

Authors:  John D Storey; Wenzhong Xiao; Jeffrey T Leek; Ronald G Tompkins; Ronald W Davis
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-02       Impact factor: 11.205

3.  Analysis of factorial time-course microarrays with application to a clinical study of burn injury.

Authors:  Baiyu Zhou; Weihong Xu; David Herndon; Ronald Tompkins; Ronald Davis; Wenzhong Xiao; Wing Hung Wong; Mehmet Toner; H Shaw Warren; David A Schoenfeld; Laurence Rahme; Grace P McDonald-Smith; Douglas Hayden; Philip Mason; Shawn Fagan; Yong-Ming Yu; J Perren Cobb; Daniel G Remick; John A Mannick; James A Lederer; Richard L Gamelli; Geoffrey M Silver; Michael A West; Michael B Shapiro; Richard Smith; David G Camp; Weijun Qian; John Storey; Michael Mindrinos; Rob Tibshirani; Stephen Lowry; Steven Calvano; Irshad Chaudry; Michael A West; Mitchell Cohen; Ernest E Moore; Jeffrey Johnson; Lyle L Moldawer; Henry V Baker; Philip A Efron; Ulysses G J Balis; Timothy R Billiar; Juan B Ochoa; Jason L Sperry; Carol L Miller-Graziano; Asit K De; Paul E Bankey; Celeste C Finnerty; Marc G Jeschke; Joseph P Minei; Brett D Arnoldo; John L Hunt; Jureta Horton; J Perren Cobb; Bernard Brownstein; Bradley Freeman; Ronald V Maier; Avery B Nathens; Joseph Cuschieri; Nicole Gibran; Matthew Klein; Grant O'Keefe
Journal:  Proc Natl Acad Sci U S A       Date:  2010-05-17       Impact factor: 11.205

4.  Predicting patient survival from longitudinal gene expression.

Authors:  Yuping Zhang; Robert J Tibshirani; Ronald W Davis
Journal:  Stat Appl Genet Mol Biol       Date:  2010-11-22

5.  Diagnosis of multiple cancer types by shrunken centroids of gene expression.

Authors:  Robert Tibshirani; Trevor Hastie; Balasubramanian Narasimhan; Gilbert Chu
Journal:  Proc Natl Acad Sci U S A       Date:  2002-05-14       Impact factor: 11.205

6.  Regularization Paths for Generalized Linear Models via Coordinate Descent.

Authors:  Jerome Friedman; Trevor Hastie; Rob Tibshirani
Journal:  J Stat Softw       Date:  2010       Impact factor: 6.440

7.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection.

Authors:  C Li; W H Wong
Journal:  Proc Natl Acad Sci U S A       Date:  2001-01-02       Impact factor: 11.205

8.  Transcription-based prediction of response to IFNbeta using supervised computational methods.

Authors:  Sergio E Baranzini; Parvin Mousavi; Jordi Rio; Stacy J Caillier; Althea Stillman; Pablo Villoslada; Matthew M Wyatt; Manuel Comabella; Larry D Greller; Roland Somogyi; Xavier Montalban; Jorge R Oksenberg
Journal:  PLoS Biol       Date:  2004-12-28       Impact factor: 8.029

9.  Partial mixture model for tight clustering of gene expression time-course.

Authors:  Yinyin Yuan; Chang-Tsun Li; Roland Wilson
Journal:  BMC Bioinformatics       Date:  2008-06-18       Impact factor: 3.169

  9 in total
  6 in total

1.  Regularization method for predicting an ordinal response using longitudinal high-dimensional genomic data.

Authors:  Jiayi Hou; Kellie J Archer
Journal:  Stat Appl Genet Mol Biol       Date:  2015-02

2.  Meta-analysis of peptides to detect protein significance.

Authors:  Yuping Zhang; Zhengqing Ouyang; Wei-Jun Qian; Richard D Smith; Wing Hung Wong; Ronald W Davis
Journal:  Stat Interface       Date:  2020-07-31       Impact factor: 0.582

3.  Early epitope-specific IgE antibodies are predictive of childhood peanut allergy.

Authors:  Maria Suprun; Scott H Sicherer; Robert A Wood; Stacie M Jones; Donald Y M Leung; Alice K Henning; Peter Dawson; A Wesley Burks; Robert Lindblad; Robert Getts; Mayte Suárez-Fariñas; Hugh A Sampson
Journal:  J Allergy Clin Immunol       Date:  2020-08-11       Impact factor: 10.793

4.  Discriminating sample groups with multi-way data.

Authors:  Tianmeng Lyu; Eric F Lock; Lynn E Eberly
Journal:  Biostatistics       Date:  2017-07-01       Impact factor: 5.899

5.  Transcriptome modulation by hydrocortisone in severe burn shock: ancillary analysis of a prospective randomized trial.

Authors:  Jonathan Plassais; Fabienne Venet; Marie-Angélique Cazalis; Diane Le Quang; Alexandre Pachot; Guillaume Monneret; Sylvie Tissot; Julien Textoris
Journal:  Crit Care       Date:  2017-06-16       Impact factor: 9.097

Review 6.  Computational dynamic approaches for temporal omics data with applications to systems medicine.

Authors:  Yulan Liang; Arpad Kelemen
Journal:  BioData Min       Date:  2017-06-17       Impact factor: 2.522

  6 in total

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