Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes. - Ming-Ying Leung; G. M. Marsh; Terence P. Speed (J. Comput. Biol., 1996)

Variations on a theme of Lander and Waterman (abstract). - Terence P. Speed (RECOMB, 1997)

An Algorithm for Haplotype Analysis. - Shili Lin; Terence P. Speed (J. Comput. Biol., 1997)

DNA Sequencing with Transposons. - Simon Cawley; Terence P. Speed (J. Comput. Biol., 2000)

Analysis of CDNA Microarray Images. - Yee Hwa Yang; Michael J. Buckley; Terence P. Speed (Briefings Bioinform., 2001)

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. - Mauro Delorenzi; Terence P. Speed (Bioinform., 2002)

Low-level analyses of microarray data. - Terence P. Speed (RECOMB, 2003)

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. - Benjamin M. Bolstad; Rafael A. Irizarry; Magnus Åstrand; Terence P. Speed (Bioinform., 2003)

Machine learning in low-level microarray analysis. - Benjamin I. P. Rubinstein; Jon D. McAuliffe; Simon Cawley; Marimuthu Palaniswami; Kotagiri Ramamohanarao; Terence P. Speed (SIGKDD Explor., 2003)

A benchmark for Affymetrix GeneChip expression measures. - Leslie Cope; Rafael A. Irizarry; Harris A. Jaffee; Zhijin Wu; Terence P. Speed (Bioinform., 2004)

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. - Tim Beißbarth; Jason A. Tye-Din; Gordon K. Smyth; Terence P. Speed; Robert P. Anderson (ISMB (Supplement of Bioinformatics), 2005)

Finding Short DNA Motifs Using Permuted Markov Models. - Xiaoyue Zhao; Haiyan Huang; Terence P. Speed (J. Comput. Biol., 2005)

A genotype calling algorithm for affymetrix SNP arrays. - Nusrat Rabbee; Terence P. Speed (Bioinform., 2006)

A comparison of Affymetrix gene expression arrays. - Mark D. Robinson; Terence P. Speed (BMC Bioinform., 2007)

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. - Mark D. Robinson; David P. De Souza; Woon Wai Keen; Eleanor C. Saunders; Malcolm J. McConville; Terence P. Speed; Vladimir A. Likic (BMC Bioinform., 2007)

Estimation and assessment of raw copy numbers at the single locus level. - Henrik Bengtsson; Rafael A. Irizarry; Benilton S. Carvalho; Terence P. Speed (Bioinform., 2008)

FIRMA: a method for detection of alternative splicing from exon array data. - E. Purdom; Ken M. Simpson; Mark D. Robinson; J. G. Conboy; A. V. Lapuk; Terence P. Speed (Bioinform., 2008)

Quality Assessment for Short Oligonucleotide Microarray Data. - Julia Brettschneider; François Collin; Benjamin M. Bolstad; Terence P. Speed (Technometrics, 2008)

Rejoinder. - Julia Brettschneider; François Collin; Benjamin M. Bolstad; Terence P. Speed (Technometrics, 2008)

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. - Henrik Bengtsson; Amrita Ray; Paul T. Spellman; Terence P. Speed (Bioinform., 2009)

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. - Henrik Bengtsson; Pratyaksha Wirapati; Terence P. Speed (Bioinform., 2009)

Sparse combinatorial inference with an application in cancer biology. - Sach Mukherjee; Steven Pelech; Richard M. Neve; Wen-Lin Kuo; Safiyyah Ziyad; Paul T. Spellman; Joe W. Gray; Terence P. Speed (Bioinform., 2009)

Differential splicing using whole-transcript microarrays. - Mark D. Robinson; Terence P. Speed (BMC Bioinform., 2009)

Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments. - Yunxia Sui; Xiaoyue Zhao; Terence P. Speed; Zhijin Wu (J. Comput. Biol., 2009)

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. - Henrik Bengtsson; Pierre Neuvial; Terence P. Speed (BMC Bioinform., 2010)

Methods for Allocating Ambiguous Short-reads. - Doron Lipson; Terence P. Speed; Margaret Taub (Commun. Inf. Syst., 2010)

An integrative bioinformatic predictor of protein sub-cellular localisation in malaria. - Ben J. Woodcroft; Robert Radloff; Lee M. Yeoh; Kristie-Lee Scanlon; Maria A. Doyle; Giel G. van Dooren; Geoffrey I. McFadden; Christopher J. Tonkin; Terence P. Speed; Stuart A. Ralph (BMC Bioinform., 2011)

Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. - Wenyi Wang 001; Peidong Shen; Sreedevi Thiyagarajan; Shengrong Lin; Curtis J. Palm; Rita Horvath; Thomas Klopstock; David Cutler; Lynn Pique; Iris Schrijver; Ronald W. Davis; Michael Mindrinos; et al. (Nucleic Acids Res., 2011)

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line. - Steven M. Hill; Yiling Lu; Jennifer Molina; Laura Heiser; Paul T. Spellman; Terence P. Speed; Joe W. Gray; Gordon B. Mills; Sach Mukherjee (Bioinform., 2012)

SRMA: an R package for resequencing array data analysis. - Nianxiang Zhang; Yan Xu; Martin O'Hely; Terence P. Speed; Curt Scharfe; Wenyi Wang 001 (Bioinform., 2012)

Comparing somatic mutation-callers: Beyond Venn diagrams. - Su Yeon Kim; Terence P. Speed (BMC Bioinform., 2013)

Combining calls from multiple somatic mutation-callers. - Su Yeon Kim; Laurent Jacob; Terence P. Speed (BMC Bioinform., 2014)

Systematic noise degrades gene co-expression signals but can be corrected. - Saskia Freytag; Johann Gagnon-Bartsch; Terence P. Speed; Melanie Bahlo (BMC Bioinform., 2015)

Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements. - Timothy J. Peters; Hugh J. French; Stephen T. Bradford; Ruth Pidsley; Clare Stirzaker; Hilal Varinli; Shalima Nair; Wenjia Qu; Jenny Song; Katherine A. Giles; Aaron L. Statham; Helen Speirs; et al. (Bioinform., 2019)

DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data. - Chengzhong Ye; Terence P. Speed; Agus Salim (Bioinform., 2019)

Maps of variability in cell lineage trees. - Damien G. Hicks; Terence P. Speed; Mohammed Yassin; Sarah M. Russell (PLoS Comput. Biol., 2019)

Finding a suitable library size to call variants in RNA-Seq. - Anna Quaglieri; Christoffer Flensburg; Terence P. Speed; Ian J. Majewski (BMC Bioinform., 2020)

Spectral PCA for MANOVA and data over binary trees. - Terence P. Speed; Damien G. Hicks (J. Multivar. Anal., 2022)