Terence P. Speed

42 papers B 5Journal 36Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
The current landscape and emerging challenges of benchmarking single-cell methods.
Briefings Bioinform.
Yue Cao, Lijia Yu, Marni Torkel, Sanghyun Kim, Yingxin Lin, Pengyi Yang, Terence P. Speed, Shila Ghazanfar, Jean Yee Hwa Yang
2022 J jnl
Spectral PCA for MANOVA and data over binary trees.
J. Multivar. Anal.
Terence P. Speed, Damien G. Hicks
2020 J jnl
Finding a suitable library size to call variants in RNA-Seq.
BMC Bioinform.
Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
2019 J jnl
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data.
Bioinform.
Chengzhong Ye, Terence P. Speed, Agus Salim
2019 J jnl
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements.
Bioinform.
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, Terence P. Speed, Susan J. Clark
2019 J jnl
Maps of variability in cell lineage trees.
PLoS Comput. Biol.
Damien G. Hicks, Terence P. Speed, Mohammed Yassin, Sarah M. Russell
2015 J jnl
Systematic noise degrades gene co-expression signals but can be corrected.
BMC Bioinform.
Saskia Freytag, Johann Gagnon-Bartsch, Terence P. Speed, Melanie Bahlo
2014 J jnl
Combining calls from multiple somatic mutation-callers.
BMC Bioinform.
Su Yeon Kim, Laurent Jacob, Terence P. Speed
2013 J jnl
Comparing somatic mutation-callers: Beyond Venn diagrams.
BMC Bioinform.
Su Yeon Kim, Terence P. Speed
2012 J jnl
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line.
Bioinform.
Steven M. Hill, Yiling Lu, Jennifer Molina, Laura Heiser, Paul T. Spellman, Terence P. Speed, Joe W. Gray, Gordon B. Mills, Sach Mukherjee
2012 J jnl
SRMA: an R package for resequencing array data analysis.
Bioinform.
Nianxiang Zhang, Yan Xu, Martin O'Hely, Terence P. Speed, Curt Scharfe, Wenyi Wang
2011 J jnl
An integrative bioinformatic predictor of protein sub-cellular localisation in malaria.
BMC Bioinform.
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
2011 J jnl
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.
Nucleic Acids Res.
Wenyi Wang, Peidong Shen, Sreedevi Thiyagarajan, Shengrong Lin, Curtis J. Palm, Rita Horvath, Thomas Klopstock, David Cutler, Lynn Pique, Iris Schrijver, Ronald W. Davis, Michael Mindrinos, Terence P. Speed, Curt Scharfe
2010 J jnl
Methods for Allocating Ambiguous Short-reads.
Commun. Inf. Syst.
Doron Lipson, Terence P. Speed, Margaret Taub
2010 J jnl
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays.
BMC Bioinform.
Henrik Bengtsson, Pierre Neuvial, Terence P. Speed
2009 J jnl
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.
Bioinform.
Henrik Bengtsson, Pratyaksha Wirapati, Terence P. Speed
2009 J jnl
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods.
Bioinform.
Henrik Bengtsson, Amrita Ray, Paul T. Spellman, Terence P. Speed
2009 J jnl
Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments.
J. Comput. Biol.
Yunxia Sui, Xiaoyue Zhao, Terence P. Speed, Zhijin Wu
2009 J jnl
Differential splicing using whole-transcript microarrays.
BMC Bioinform.
Mark D. Robinson, Terence P. Speed
2009 J jnl
Sparse combinatorial inference with an application in cancer biology.
Bioinform.
Sach Mukherjee, Steven Pelech, Richard M. Neve, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed
2008 J jnl
Estimation and assessment of raw copy numbers at the single locus level.
Bioinform.
Henrik Bengtsson, Rafael A. Irizarry, Benilton S. Carvalho, Terence P. Speed
2008 J jnl
FIRMA: a method for detection of alternative splicing from exon array data.
Bioinform.
E. Purdom, Ken M. Simpson, Mark D. Robinson, J. G. Conboy, A. V. Lapuk, Terence P. Speed
2008 J jnl
Quality Assessment for Short Oligonucleotide Microarray Data.
Technometrics
Julia Brettschneider, François Collin, Benjamin M. Bolstad, Terence P. Speed
2008 J jnl
Rejoinder.
Technometrics
Julia Brettschneider, François Collin, Benjamin M. Bolstad, Terence P. Speed
2007 J jnl
A comparison of Affymetrix gene expression arrays.
BMC Bioinform.
Mark D. Robinson, Terence P. Speed
2007 J jnl
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments.
BMC Bioinform.
Mark D. Robinson, David P. De Souza, Woon Wai Keen, Eleanor C. Saunders, Malcolm J. McConville, Terence P. Speed, Vladimir A. Likic
2007 B ed.
Research in Computational Molecular Biology, 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings
RECOMB
Terence P. Speed, Haiyan Huang
2006 J jnl
A genotype calling algorithm for affymetrix SNP arrays.
Bioinform.
Nusrat Rabbee, Terence P. Speed
2005 — conf
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries.
ISMB (Supplement of Bioinformatics)
Tim Beißbarth, Jason A. Tye-Din, Gordon K. Smyth, Terence P. Speed, Robert P. Anderson
2005 J jnl
Finding Short DNA Motifs Using Permuted Markov Models.
J. Comput. Biol.
Xiaoyue Zhao, Haiyan Huang, Terence P. Speed
2004 J jnl
A benchmark for Affymetrix GeneChip expression measures.
Bioinform.
Leslie Cope, Rafael A. Irizarry, Harris A. Jaffee, Zhijin Wu, Terence P. Speed
2004 B conf
Finding short DNA motifs using permuted markov models.
RECOMB
Xiaoyue Zhao, Haiyan Huang, Terence P. Speed
2003 J jnl
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bioinform.
Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, Terence P. Speed
2003 B conf
Low-level analyses of microarray data.
RECOMB
Terence P. Speed
2003 J jnl
Machine learning in low-level microarray analysis.
SIGKDD Explor.
Benjamin I. P. Rubinstein, Jon D. McAuliffe, Simon Cawley, Marimuthu Palaniswami, Kotagiri Ramamohanarao, Terence P. Speed
2002 J jnl
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
Bioinform.
Mauro Delorenzi, Terence P. Speed
2001 J jnl
Analysis of CDNA Microarray Images.
Briefings Bioinform.
Yee Hwa Yang, Michael J. Buckley, Terence P. Speed
2000 J jnl
DNA Sequencing with Transposons.
J. Comput. Biol.
Simon Cawley, Terence P. Speed
1997 J jnl
An Algorithm for Haplotype Analysis.
J. Comput. Biol.
Shili Lin, Terence P. Speed
1997 B conf
An algorithm for haplotype analysis.
RECOMB
Shili Lin, Terence P. Speed
1997 B conf
Variations on a theme of Lander and Waterman (abstract).
RECOMB
Terence P. Speed
1996 J jnl
Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes.
J. Comput. Biol.
Ming-Ying Leung, G. M. Marsh, Terence P. Speed