Scientists are interested in how gene expression levels may vary under different treatments. They want to know which genes are expressed differently under treatment conditions and control conditions....
BIOINFORMATICS APPLICATIONS NOTE (2009)
Gene Expression, Ryo Yoshida, Tomoyuki Higuchi, Seiya Imoto, Satoru Miyano
Vol. 22 no. 12 2006, pages 1538–1539 doi:10.1093/bioinformatics/btl129 ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles
BIOINFORMATICS ORIGINAL PAPER (2009)
Gene Expression, Peng Qiu, Z. Jane Wang
Vol. 22 no. 8 2006, pages 959–966 doi:10.1093/bioinformatics/btl017 Polynomial model approach for resynchronization analysis of cell-cycle gene expression data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Shuangge Ma, Jian Huang
Regularized ROC method for disease classification and biomarker selection with microarray data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Karen Willbr, Francois Radvanyi, Jean-pierre Nadal, Jean-paul Thiery
Identifying genes from up–down properties of microarray expression series Vol. 21 no. 20 2005, pages 3859–3864 doi:10.1093/bioinformatics/bti549
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Joe Faith, Robert Mintram, Maia Angelova
Vol. 22 no. 21 2006, pages 2667–2673 doi:10.1093/bioinformatics/btl463 Targeted projection pursuit for visualizing gene expression data classifications
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Earl F. Glynn, Jie Chen, Arcady R. Mushegian
Vol. 22 no. 3 2006, pages 310–316 doi:10.1093/bioinformatics/bti789 Detecting periodic patterns in unevenly spaced gene expression time series using Lomb–Scargle periodograms
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, C. Prieto, M. J. Rivas, J. M. Sánchez, J. López-fidalgo, J. De, ...
Vol. 22 no. 9 2006, pages 1103–1110 doi:10.1093/bioinformatics/btl053 Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes
Gene Expression, Zuoshuang Xiang, Zhaohui S. Qin, Yongqun He
CRCView: a web server for analyzing and visualizing microarray gene expression data using model-based clustering
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Thomas Grotkjær, Ole Winther, Birgitte Regenberg, Jens Nielsen, Lars Kai Hansen
Robust multi-scale clustering of large DNA microarray datasets with the consensus algorithm Vol. 22 no. 1 2006, pages 58–67 doi:10.1093/bioinformatics/bti746
Identifying the biologically relevant gene categories based on gene expression and biological data: an example on prostate cancer
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Tsun-po Yang, Ting-yu Chang, Chi-hung Lin, Ming-ta Hsu, Hsei-wei Wang, ...
Vol. 22 no. 21 2006, pages 2697–2698 doi:10.1093/bioinformatics/btl457 ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Anbupalam Thalamuthu, Indranil Mukhopadhyay, Xiaojing Zheng, George C. Tseng
doi:10.1093/bioinformatics/btl406 Evaluation and comparison of gene clustering methods in microarray analysis
Gene Expression, Daniel M. Kemp, N. R. Nirmala, Joseph D. Szustakowski
Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yulan Liang, Bamidele Tayo, Xueya Cai, Arpad Kelemen
Differential and trajectory methods for time course gene expression data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Chad A. Davis, Fabian Gerick, Volker Hintermair, Caroline C. Friedel, Katrin Fundel, ...
Reliable gene signatures for microarray classification: assessment of stability and performance Vol. 22 no. 19 2006, pages 2356–2363 doi:10.1093/bioinformatics/btl400
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Gaëlle Lel, Pierre Vincens, Anne Badel-chagnon, Stéphane Vialette, Claude Jacq, ...
Vol. 22 no. 11 2006, pages 1359–1366 doi:10.1093/bioinformatics/btl087 Comparing gene expression networks in a multi-dimensional space to extract similarities and differences between organisms
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jiang Du, Joel S. Rozowsky, Jan O. Korbel, Zhengdong D. Zhang, Thomas E. Royce, ...
doi:10.1093/bioinformatics/btl515 A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Rajarajeswari Balasubramaniyan, Eyke Hüllermeier, Nils Weskamp, Jörg Kämper
Clustering of gene expression data using a local shape-based similarity measure
modified organisms (GMOs) (2008)
Gene Expression, Håvard Nesvold, Anja Bråthen Kristoffersen, Arne Holst-jensen, Knut G. Berdal
doi:10.1093/bioinformatics/bti248 Design of a DNA chip for detection of unknown genetically
BIOINFORMATICS ORIGINAL PAPER (2008)
Relational patterns of gene expression via non-metric multidimensional scaling analysis
in Recombinant Inbred Strains A Relational Model System to Explore Neurobehavioral (2008)
Giorgio A. Ascoli, Erik De Schutter, David N. Kennedy, Gene Expression, Elissa J. Chesler, Jintao Wang, ...
Copyright ©Humana Press Inc.
Gene Expression, Attila Gyenesei, Ulrich Wagner, Simon Barkow-oesterreicher, Etzard Stolte, Ralph Schlapbach
Mining co-regulated gene profiles for the detection of functional associations in gene expression data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jangsun Baek, Young Sook Son, Geoffrey J. Mclachlan
doi:10.1093/bioinformatics/btl630 Segmentation and intensity estimation of microarray images using a gamma-t mixture model
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Fangxin Hong, Rainer Breitling, Connor W. Mcentee, Ben S. Wittner, Jennifer L. Nemhauser, ...
Vol. 22 no. 22 2006, pages 2825–2827 doi:10.1093/bioinformatics/btl476 RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Amela Prelić, Stefan Bleuler, Philip Zimmermann, Anja Wille, Peter Bühlmann, ...
Vol. 22 no. 9 2006, pages 1122–1129 doi:10.1093/bioinformatics/btl060 A systematic comparison and evaluation of biclustering methods for gene expression data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Curtis Huttenhower, Matt Hibbs, Chad Myers, Olga G. Troyanskaya
Vol. 22 no. 23 2006, pages 2890–2897 doi:10.1093/bioinformatics/btl492 A scalable method for integration and functional analysis of multiple microarray datasets
Original Article A Guide to Building Image-Centric Databases (2008)
Giorgio A. Ascoli, Erik De Schutter, David N. Kennedy, Gene Expression, William Bug, Jonathan Nissanov
Copyright ©Humana Press Inc.
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Anshuman Gupta, Costas D. Maranas, Réka Albert
Vol. 22 no. 2 2006, pages 209–214 doi:10.1093/bioinformatics/bti780 Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites
Gene Expression, Wotao Yin, Terrence Chen, Xiang Sean Zhou, Amit Chakraborty
doi:10.1093/bioinformatics/bti341 Background correction for cDNA microarray images using the
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Huiqing Liu, Jinyan Li, Limsoon Wong
doi:10.1093/bioinformatics/bti544 Use of extreme patient samples for outcome prediction from gene expression data
A knowledge-driven approach to cluster validity assessment (2008)
Gene Expression, Nadia Bolshakova, Francisco Azuaje, Pádraig Cunningham
doi:10.1093/bioinformatics/bti317
Gene Expression, Jelle J. Goeman, Peter Bühlmann
Analyzing gene expression data in terms of gene sets: methodological issues
Gene Expression, Hyunsoo Kim, Haesun Park
Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm322 (2008)
Gene Expression, Claudio Lottaz, Joern Toedling, Rainer Spang
Annotation-based distance measures for patient subgroup discovery in clinical microarray studies
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yudi Pawitan, Stefano Calza, Er Ploner
Estimation of false discovery proportion under general dependence
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yong Wang, Trupti Joshi, Xiang-sun Zhang, Dong Xu, Luonan Chen
Inferring gene regulatory networks from multiple microarray datasets Vol. 22 no. 19 2006, pages 2413–2420 doi:10.1093/bioinformatics/btl396
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Theodora Manoli, Norbert Gretz, Hermann-josef Gröne, Marc Kenzelmann, Benedikt Brors
doi:10.1093/bioinformatics/btl424 Group testing for pathway analysis improves comparability of different microarray datasets
A new summarization method for affymetrix probe level data (2008)
Gene Expression, Djork-arné Clevert, Klaus Obermayer
doi:10.1093/bioinformatics/btl033
Bias in the estimation of false discovery rate in microarray studies (2008)
Gene Expression, Yudi Pawitan, Stefan Michiels, Er Ploner
doi:10.1093/bioinformatics/bti626
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Antti Lehmussola, Pekka Ruusuvuori, Olli Yli-harja
Evaluating the performance of microarray segmentation algorithms Vol. 22 no. 23 2006, pages 2910–2917 doi:10.1093/bioinformatics/btl502
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Desheng Huang, Wei Pan
Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data Vol. 22 no. 10 2006, pages 1259–1268 doi:10.1093/bioinformatics/btl065
Gene Expression, Antonis Daskalakis, Dionisis Cavouras, Panagiotis Bougioukos, Spiros Kostopoulos, Dimitris Glotsos, ...
Improving gene quantification by adjustable spot-image restoration
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal
Vol. 22 no. 10 2006, pages 1251–1258 doi:10.1093/bioinformatics/btl068 A calibration method for estimating absolute expression levels from microarray data
TileMap: create chromosomal map of tiling array hybridizations (2008)
Gene Expression, Hongkai Ji, Wing Hung Wong
doi:10.1093/bioinformatics/bti593
Documentation dataSets Documentation> Tutorials> Functional annotation Publications About (2008)
Analysis Suite V, Gene Expression
experiments
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Antonio Reverter, Aaron Ingham, Sigrid A. Lehnert, Siok-hwee Tan, Yonghong Wang, ...
doi:10.1093/bioinformatics/btl392 Simultaneous identification of differential gene expression and connectivity in inflammation, adipogenesis and cancer
Clusterv: a tool for assessing the reliability of clusters (2008)
Gene Expression, Giorgio Valentini
discovered in DNA microarray data
Gene Expression, S Erban Nacu, Rebecca Critchley-thorne, Peter Lee, Susan Holmes
We address the problem of using expression data and prior biological knowledge to identify differentially expressed pathways or groups of genes. Following an idea of Ideker et al. (2002), we...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Lei Zhou, David M. Rocke
doi:10.1093/bioinformatics/bti665
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Claudio Lottaz, Xinan Yang, Stefanie Scheid, Rainer Spang
OrderedList—a bioconductor package for detecting similarity in ordered gene lists
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jinwook Seo, Heather Gordish-dressman, Eric P. Hoffman
doi:10.1093/bioinformatics/btk052 An interactive power analysis tool for microarray hypothesis testing and generation
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Matthias Scholz, Fatma Kaplan, Charles L. Guy, Joachim Kopka, Joachim Selbig
doi:10.1093/bioinformatics/bti634
Gene Expression, Wolfram Stacklies, Henning Redestig, Matthias Scholz, Dirk Walther, Joachim Selbig
pcaMethods—a bioconductor package providing PCA methods for incomplete data
Gene Expression, Irit Fishel, Alon Kaufman
Motivation: With the increasing availability of cancer microarray data sets there is a growing need for integrative computational methods that evaluate multiple independent microarray data sets...
Maximum significance clustering of oligonucleotide microarrays (2008)
Gene Expression, Dick De Ridder
doi:10.1093/bioinformatics/bti788
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, De-shuang Huang, Chun-hou Zheng
doi:10.1093/bioinformatics/btl190 Independent component analysis-based penalized discriminant method for tumor classification using gene expression data
Multidimensional local false discovery rate for microarray studies (2008)
Gene Expression, Er Ploner, Stefano Calza, Arief Gusnanto, Yudi Pawitan
doi:10.1093/bioinformatics/btk013
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yuting Yang, Levent Engin, Eve Syrkin Wurtele, Carolina Cruz-neira, Julie A. Dickerson
Integration of metabolic networks and gene expression in virtual reality Vol. 21 no. 18 2005, pages 3645–3650 doi:10.1093/bioinformatics/bti581
Collateral missing value imputation: a new robust missing value (2008)
Gene Expression, Muhammad Shoaib, B. Sehgal, Iqbal Gondal, Laurence S. Dooley
doi:10.1093/bioinformatics/bti345
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Daniel S. Yuan, Rafael A. Irizarry
Vol. 22 no. 24 2006, pages 3054–3060 doi:10.1093/bioinformatics/btl542 High-resolution spatial normalization for microarrays containing embedded technical replicates
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Xiaohui Chen, Ming Chen, Kaida Ning
Vol. 22 no. 23 2006, pages 2952–2954 doi:10.1093/bioinformatics/btl491 BNArray: an R package for constructing gene regulatory networks from microarray data by using Bayesian network
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, S. E. Ahnert, K. Willbr
Unbiased pattern detection in microarray data series
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Natasa Rajicic, Dianne M. Finkelstein, David A. Schoenfeld
doi:10.1093/bioinformatics/btl450
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yudi Pawitan, Stefan Michiels, Serge Koscielny, Arief Gusnanto, Alexander Ploner
doi:10.1093/bioinformatics/bti448 False discovery rate, sensitivity and sample size for microarray studies
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Max Bylesjö, Andreas Sjödin, Daniel Eriksson, Henrik Antti, Thomas Moritz, ...
Vol. 22 no. 20 2006, pages 2554–2555 doi:10.1093/bioinformatics/btl434 MASQOT-GUI: spot quality assessment for the two-channel microarray platform
BIOINFORMATICS APPLICATIONS NOTE (2008)
Gene Expression, Ignacio Medina, David Montaner, Joaquín Tárraga, Joaquín Dopazo
Prophet, a web-based tool for class prediction using microarray data Vol. 23 no. 3 2007, pages 390–391 doi:10.1093/bioinformatics/btl602
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Cathal Seoighe, Victoria Nembaware, Konrad Scheffler
Vol. 22 no. 24 2006, pages 3032–3039 doi:10.1093/bioinformatics/btl521 Maximum likelihood inference of imprinting and allele-specific expression from EST data
Difference Gel Electrophoresis (2008)
Aik Choon Tan, Director Icm Ccbm, Prof Donald Geman, Prof Daniel Naiman, Lei Xu, ...
15 10 5 0 7.5 5
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jun Liu, Jaaved Mohammed, James Carter, Sanjay Ranka, Tamer Kahveci, ...
doi:10.1093/bioinformatics/btl185
Avoiding model selection bias in small-sample genomic datasets (2008)
Gene Expression, Daniel Berrar, Ian Bradbury, Werner Dubitzky
doi:10.1093/bioinformatics/btl066
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yifan Huang, Haiyan Xu, Violeta Calian, Jason C. Hsu
To permute or not to permute
segmentation of microarray images (2008)
Gene Expression, Qunhua Li, Chris Fraley, Roger E. Bumgarner, Ka Yee Yeung, Adrian E. Raftery
Motivation: Inner holes, artifacts and blank spots are common in microarray images, but current image analysis methods do not pay them enough attention. We propose a new robust model-based method for...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Francesca Martella
doi:10.1093/bioinformatics/bti779
Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Huai Li, Yu Sun, Ming Zhan
The discovery of transcriptional modules by a two-stage matrix decomposition approach
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Yang Xie, Wei Pan, Arkady B. Khodursky
doi:10.1093/bioinformatics/bti685 A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Golan Yona, William Dirks, Shafquat Rahman, David M. Lin
Effective similarity measures for expression profiles
Domain-enhanced analysis of microarray data using GO (2008)
Gene Expression, Jiajun Liu, J. Alan Menius
annotations
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Shu-dong Zhang, Timothy W. Gant
doi:10.1093/bioinformatics/bti717 Effect of pooling samples on the efficiency of comparative studies using microarrays
Gene Expression, Sijian Wang, Ji Zhu
Improved centroids estimation for the nearest shrunken centroid classifier
Integrative Array Analyzer: a software package for analysis (2008)
Gene Expression, Fei Pan, Kiran Kamath, Kangyu Zhang, Sudip Pulapura, Avinash Achar, ...
of cross-platform and cross-species microarray data
Gene Expression, Alan R. Dabney
nearest centroids
Gene Expression, Hanchuan Peng
Automatic recognition and annotation of gene expression patterns of fly embryos
BIOINFORMATICSAPPLICATIONS NOTE (2008)
Gene Expression, Richard E. Kennedy, Robnet T. Kerns, Xiangrong Kong, Kellie J. Archer, Michael F. Miles
SScore: an R package for detecting differential gene expression without gene expression summaries
Gene Expression, Diego Diez, Rebeca Alvarez, Ana Dopazo
expression bioarrays
BIOINFORMATICS ORIGINAL PAPER (2008)
doi:10.1093/bioinformatics/bti824 Survival prediction of diffuse large-B-cell lymphoma based on both clinical and gene expression information
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Jianhua Ruan, Weixiong Zhang
Vol. 22 no. 3 2006, pages 332–340 doi:10.1093/bioinformatics/bti792 A bi-dimensional regression tree approach to the modeling of gene expression regulation
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Ritesh Agrawal, Gary D. Stormo
doi:10.1093/bioinformatics/btl076 Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans
RSIR: regularized sliced inverse regression for motif discovery (2008)
Gene Expression, Wenxuan Zhong, Peng Zeng, Ping Ma, Jun S. Liu, Yu Zhu
doi:10.1093/bioinformatics/bti680
Gene Expression, Jianping Hua, Zixiang Xiong, James Lowey, Edward Suh, Edward R. Dougherty
doi:10.1093/bioinformatics/bti171 Optimal number of features as a function of sample size for
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Ranadip Pal, Aniruddha Datta, Albert J. Fornace, Michael L. Bittner, Edward R. Dougherty
Vol. 21 no. 8 2005, pages 1542–1549 doi:10.1093/bioinformatics/bti214 Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS
Bioinformatics Original Paper (2008)
Vol No Pages, Gene Expression, Chao Sima, Ulisses Braga-neto, Edward R. Dougherty
Motivation: Ranking feature sets is a key issue for classification, for instance, phenotype classification based on gene expression. Since ranking is often based on error estimation, and error...
Gene Expression, Roy Varshavsky, Assaf Gottlieb, David Horn, Michal Linial
meeting the challenges of biological data
Gene Expression, Istvan Bogdan, Daniel Coca, Jenny Rivers, Robert J Beynon, Golan Yona
Hardware acceleration of processing of mass spectrometric data for proteomics
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Andrea Malossini, Enrico Blanzieri, Raymond T. Ng
doi:10.1093/bioinformatics/btl346 Detecting potential labeling errors in microarrays by data perturbation
Gene Expression, Xiaowen Liu, Lusheng Wang
Computing the maximum similarity bi-clusters of gene
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Wolfgang Huber, Joern Toedling, Lars M. Steinmetz
Transcript mapping with high-density oligonucleotide tiling arrays Vol. 22 no. 16 2006, pages 1963–1970 doi:10.1093/bioinformatics/btl289
Kalman filtering for disease-state estimation from microarray data (2006)
Gene Expression, János Z. Kelemen, Attila Kertész-farkas, András Kocsor, László G. Puskás
doi:10.1093/bioinformatics/btl545
composite GO annotation (2006)
Gene Expression, Dougu Nam, Sang-bae Kim, Seon-kyu Kim, Sungjin Yang, Seon-young Kim
doi:10.1093/bioinformatics/btl378 ADGO: analysis of differentially expressed gene sets using
Gene Expression, Gavin C. Cawley
doi:10.1093/bioinformatics/btl386
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Dong Wang, Yingli Lv, Zheng Guo, Xia Li, Yanhui Li, ...
doi:10.1093/bioinformatics/btl339 Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, A. Callegaro, D. Basso, S. Bicciato
A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions Vol. 22 no. 21 2006, pages 2658–2666 doi:10.1093/bioinformatics/btl455
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Nitai D. Mukhopadhyay, Snigdhansu Chatterjee
Causality and pathway search in microarray time series experiment
BIOINFORMATICS APPLICATIONS NOTE (2006)
doi:10.1093/bioinformatics/btl564 AGScan: a pluggable microarray image quantification software based on the ImageJ library
BIOINFORMATICS ORIGINAL PAPER (2006)
Gene Expression, Jun Liu, Sanjay Ranka, Tamer Kahveci
doi:10.1093/bioinformatics/btl624
Interpretation of ANOVA models for microarray data using PCA (2006)
Gene Expression, R. Wehrens, S. Bauerschmidt, E. Piek, ...
doi:10.1093/bioinformatics/btl572
BIOINFORMATICSAPPLICATIONS NOTE (2005)
Gene Expression, David Lowe, Ian T. Nabney, Vassilis Mersinias, Colin P. Smith
MILVA: An interactive tool for the exploration of multidimensional microarray data
Network constrained clustering for gene microarray data (2005)
Gene Expression, Dongxiao Zhu, Alfred O Hero, Hong Cheng, Ritu Khanna
doi:10.1093/bioinformatics/bti655
Availability: The Doelan application is distributed under the GNU (2005)
Gene Expression, Laurent Jourdren, Stéphane Le Crom
Doelan: a solution for quality control monitoring of microarray production
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Gunnar Wrobel, Frédéric Chalmel, Michael Primig
goCluster integrates statistical analysis and functional interpretation of microarray expression data
BIOINFORMATICS LETTER TO THE EDITOR (2005)
Gene Expression, Kevin K. Dobbin, Joanna H. Shih, Richard M. Simon
Vol. 21 no. 12 2005, pages 2803–2804 doi:10.1093/bioinformatics/bti428 Comment on ‘Evaluation of the gene-specific dye bias in cDNA microarray experiments’
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Steffen Durinck, Yves Moreau, Arek Kasprzyk, Sean Davis, Bart De Moor, ...
Vol. 21 no. 16 2005, pages 3439–3440 doi:10.1093/bioinformatics/bti525 BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
Automated Microarray Image Analysis Toolbox for MATLAB (2005)
Gene Expression, A M. White, Don S. Daly, Alan R. Willse, Miroslava Protic, Darrell P. Ch
Summary: The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source, microarray image analysis tool that allows the user to customize analyses of microarray image...
Gene Expression, Amira Djebbari, Svetlana Karamycheva, Eleanor Howe, John Quackenbush
Vol. 21 no. 15 2005, pages 3324–3326 doi:10.1093/bioinformatics/bti503 MeSHer: identifying biological concepts in microarray assays
BIOINFORMATICSAPPLICATIONS NOTE (2005)
Gene Expression, R. D. Drummond, A. Pinheiro, C. S. Rocha, M. Menossi
ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Wenjiang J. Fu, Raymond J. Carroll, Suojin Wang
Estimating misclassification error with small samples via bootstrap cross-validation
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Frank De Smet, Kathleen Marchal, ...
doi:10.1093/bioinformatics/bti495
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Aedín C. Culhane, Jean Thioulouse, Guy Perrière, Desmond G. Higgins
MADE4: an R package for multivariate analysis of gene expression data Vol. 21 no. 11 2005, pages 2789–2790 doi:10.1093/bioinformatics/bti394
Sample size for gene expression microarray experiments (2005)
Gene Expression, Chen-an Tsai, Sue-jane Wang, Dung-tsa Chen, James J. Chen
doi:10.1093/bioinformatics/bti162
Simpleaffy: a BioConductor package for Affymetrix quality control and data analysis (2005)
Gene Expression, Claire L. Wilson, Crispin J. Miller
Summary: Quality Control is a fundamental aspect of successful microarray data analysis. Simpleaffy is a BioConductor package that provides access to a variety of QC metrics for assessing the quality...
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Hao Helen Zhang, Jeongyoun Ahn, Xiaodong Lin, Cheolwoo Park
Gene selection using support vector machines with non-convex penalty Vol. 22 no. 1 2006, pages 88–95 doi:10.1093/bioinformatics/bti736
Gene Expression, Jonathon Blake, Christian Schwager, Misha Kapushesky, Alvis Brazma
ChroCoLoc: an application for calculating the probability of co-localization of microarray gene expression
BIOINFORMATICS ORIGINAL PAPER (2005)
Vol. 21 no. 23 2005, pages 4255–4262 doi:10.1093/bioinformatics/bti684 Noise and rank-dependent geometrical filter improves sensitivity of highly specific discovery by microarrays
ADAPT: a database of affymetrix probesets and transcripts (2005)
Gene Expression, Hui Sun Leong, Tim Yates, Claire Wilson, Crispin J. Miller
doi:10.1093/bioinformatics/bti359
Biomarker discovery in microarray gene expression data with Gaussian processes (2005)
Gene Expression, Wei Chu, Zoubin Ghahramani, Francesco Falciani, David L. Wild
doi:10.1093/bioinformatics/bti526
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, S. Peddada, S. Harris, J. Zajd, E. Harvey
ORIOGEN: order restricted inference for ordered gene expression data
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Jung Kyoon Choi, Ungsik Yu, Ook Joon Yoo, Sangsoo Kim
Differential coexpression analysis using microarray data and its application to human cancer Vol. 21 no. 24 2005, pages 4348–4355 doi:10.1093/bioinformatics/bti722
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Yuan Gao, George Church
Improving molecular cancer class discovery through sparse non-negative matrix factorization
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Susmita Datta, Somnath Datta
doi:10.1093/bioinformatics/bti301 Empirical Bayes screening of many p-values with applications to microarray studies
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Jiang Gui, Hongzhe Li
doi:10.1093/bioinformatics/bti422 Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data
BIOINFORMATICS APPLICATIONS NOTE (2005)
Gene Expression, Alexei A. Sharov, Dawood B. Dudekula
Vol. 21 no. 10 2005, pages 2548–2549 doi:10.1093/bioinformatics/bti343 A web-based tool for principal component and significance analysis of microarray data
clustering of microarray gene expression data (2005)
Motivation: Cluster analysis of gene expression profiles has been widely applied to clustering genes for gene function discovery. Many approaches have been proposed. The rationale is that the genes...
BIOINFORMATICS ORIGINAL PAPER (2005)
Gene Expression, Guido Sanguinetti, Marta Milo, Magnus Rattray, Neil D. Lawrence
Accounting for probe-level noise in principal component analysis of microarray data
Gene Expression, James M. Wettenhall, Ken M. Simpson, Keith Satterley, Gordon K. Smyth
single channel microarray data
BIOINFORMATICS ORIGINAL PAPER (2004)
Motivation: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being...
BIOINFORMATICS ORIGINAL PAPER (2004)
Gene Expression, Yuhang Wang, Fillia S. Makedon, James C. Ford, Justin Pearlman
doi:10.1093/bioinformatics/bti192 HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data
BIOINFORMATICS ORIGINAL PAPER (2004)
Gene Expression, Gersende Fort, Sophie Lambert-lacroix
Classification using partial least squares with penalized logistic regression
BIOINFORMATICS APPLICATIONS NOTE (2004)
Gene Expression, Ivan G. Costa, Er Schönhuth, Er Schliep
Vol. 21 no. 10 2005, pages 2544–2545 doi:10.1093/bioinformatics/bti311 The Graphical Query Language: a tool for analysis of gene expression time-courses
OLIN: optimized normalization, visualization and quality testing of (2004)
Gene Expression, Matthias E. Futschik, Toni Crompton
two-channel microarray data
BIOINFORMATICS ORIGINAL PAPER (2004)
Gene Expression, Er Statnikov, Constantin F. Aliferis, Ioannis Tsamardinos, Douglas Hardin, Shawn Levy
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
BIOINFORMATICS ORIGINAL PAPER (2004)
Gene Expression, F. R. Pinto, L. Ashley Cowart, Yusuf A. Hannun, B. Rohrer, J. S. Almeida
Local correlation of expression profiles with gene annotations—proof of concept for a general conciliatory method
Er Statnikov, Ioannis Tsamardinos, Yerbolat Dosbayev, Constantin F. Aliferis, Gene Expression
system for automated cancer diagnosis and biomarker discovery from microarray gene
Gene Expression, William T. Barry, Andrew B. Nobel, Fred A. Wright
Significance analysis of functional categories in gene expression studies: a structured permutation approach
ISSN 1539--2791 Volume 1 . Number 4 . 2003 (2003)
Editors Giorgio Ascoli, Giorgio A. Ascoli, Erik De Schutter, David N. Kennedy, Gene Expression, Glenn D. Rosen, ...
In recent years, there has been an explosion in the number of tools and techniques available to researchers interested in exploring the genetic basis of all aspects of central nervous system (CNS)...
Medmesh summarizer: text mining for gene clusters (2002)
P. Kankar, S. Adak, A. Sarkar, K. Murari, G. Sharma, Gene Expression
Gene Expression is the process by which a gene’s coded information is translated into the proteins present and operating in the cell. Changes in gene expression are associated with many important...