Loi, Sherene, Sotiriou, Christos, Haibe-Kains, Benjamin, Lallemand, Francoise, Conus, Nelly M, Piccart, Martine J, ...
Abstract Background Within estrogen receptor-positive breast cancer (ER+ BC), the expression levels of proliferation-related genes can define two clinically distinct molecular subtypes. When treated...
Differential splicing using whole-transcript microarrays (2009)
Robinson, Mark D, Speed, Terence P
Abstract Background The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative...
GENE SET ENRICHMENT ANALYSIS MADE SIMPLE (2009)
Irizarry, Rafael A., Wang, Chi, Zhou, Yun, Speed, Terence P.
Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to...
GENE SET ENRICHMENT ANALYSIS MADE SIMPLE (2009)
Irizarry, Rafael A., Wang, Chi, Zhou, Yun, Speed, Terence P.
Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to...
GENE SET ENRICHMENT ANALYSIS MADE SIMPLE (2009)
Irizarry, Rafael A., Wang, Chi, Zhou, Yun, Speed, Terence P.
Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to...
GENE SET ENRICHMENT ANALYSIS MADE SIMPLE (2009)
Irizarry, Rafael A., Wang, Chi, Zhou, Yun, Speed, Terence P.
Among the many applications of microarray technology, one of the most popular is the identification of genes that are differentially expressed in two conditions. A common statistical approach is to...
Christopher J. Tonkin, Céline K. Carret, Manoj T. Duraisingh, Till S. Voss, Stuart A. Ralph, Mirja Hommel, ...
Cytoadherance of Plasmodium falciparum-infected erythrocytes in the brain, organs and peripheral microvasculature is linked to morbidity and mortality associated with severe malaria. Parasite-derived...
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting (2009)
Pask, Andrew J, Papenfuss, Anthony T, Ager, Eleanor I, McColl, Kaighin A, Speed, Terence P, Renfree, Marilyn B
Abstract Background Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in...
Bengtsson, Henrik, Ray, Amrita, Spellman, Paul, Speed, Terence P.
Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more...
Bengtsson, Henrik, Wirapati, Pratyaksha, Speed, Terence P.
Motivation: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also...
Sparse combinatorial inference with an application in cancer biology (2009)
Mukherjee, Sach, Pelech, Steven, Neve, Richard M., Kuo, Wen-Lin, Ziyad, Safiyyah, Spellman, Paul T., ...
Motivation: Combinatorial effects, in which several variables jointly influence an output or response, play an important role in biological systems. In many settings, Boolean functions provide a...
Integrative analysis of RUNX1 downstream pathways and target genes (2008)
Michaud, Joëlle, Simpson, Ken M, Escher, Robert, Buchet-Poyau, Karine, Beissbarth, Tim, Carmichael, Catherine, ...
Abstract Background The RUNX1 transcription factor gene is frequently mutated in sporadic myeloid and lymphoid leukemia through translocation, point mutation or amplification. It is also responsible...
Li, Xiao-Yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A., Iyer, Venky N., ...
Nusrat Rabbee, Terence P. Speed
Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the...
Transcription factor binding site prediction with multivariate gene expression data (2008)
Zhang, Nancy R., Wildermuth, Mary C., Speed, Terence P.
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between...
Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A. Pollard, Venky N. Iyer, ...
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to...
Analysis of gene expression during neurite outgrowth and regeneration (2007)
Szpara, Moriah L, Vranizan, Karen, Tai, Yu, Goodman, Corey S, Speed, Terence P, Ngai, John
Abstract Background The ability of a neuron to regenerate functional connections after injury is influenced by both its intrinsic state and also by extrinsic cues in its surroundings. Investigations...
Address for correspondence: (2007)
Jane Fridlyand, Terence P. Speed, Sandrine Dudoit, Sandrine Dudoit
* These authors contributed equally to this work.
Michael J. Buckley, Sandrine Dudoit, Terence P. Speed, Yee Hwa Yang, Yee Hwa Yang
Comparison of methods for image analysis on cDNA
Address for correspondence: (2007)
Rine Dudoit, Terence P. Speed, Yongchao Ge, Yongchao Ge
The burgeoning field of genomics has revived interest in multiple testing procedures by raising new methodological and computational challenges. For example, microarray experiments generate large...
A comparison of Affymetrix gene expression arrays (2007)
Robinson, Mark D, Speed, Terence P
Abstract Background Affymetrix GeneChips™ are an important tool in many facets of biological research. Recently, notable design changes to the chips have been made. In this study, we use publicly...
Robinson, Mark D, De Souza, David P, Keen, Woon, Saunders, Eleanor C, McConville, Malcolm J, Speed, Terence P, ...
Abstract Background Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are...
Quality assessment for short oligonucleotide microarray data (2007)
Brettschneider, Julia, Collin, Francois, Bolstad, Benjamin M., Speed, Terence P.
Quality of microarray gene expression data has emerged as a new research topic. As in other areas, microarray quality is assessed by comparing suitable numerical summaries across microarrays, so that...
Belov, Katherine, Sanderson, Claire E., Deakin, Janine E., Wong, Emily S.W., Assange, Daniel, McColl, Kaighin A., ...
The availability of the first marsupial genome sequence has allowed us to characterize the immunome of the gray short-tailed opossum (Monodelphis domestica). Here we report the identification of key...
Global analyses of mRNA translational control during early Drosophilaembryogenesis (2007)
Qin, Xiaoli, Ahn, Soyeon, Speed, Terence P, Rubin, Gerald M
Abstract Background In many animals, the first few hours of life proceed with little or no transcription, and developmental regulation at these early stages is dependent on maternal cytoplasm rather...
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data (2007)
Carvalho, Benilton, Bengtsson, Henrik, Speed, Terence P., Irizarry, Rafael A.
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists, and clinicians. These data...
A multivariate empirical Bayes statistic for replicated microarray time course data (2007)
Tai, Yu Chuan, Speed, Terence P.
In this paper we derive one- and two-sample multivariate empirical Bayes statistics (the $\mathit{MB}$-statistics) to rank genes in order of interest from longitudinal replicated developmental...
Special and Limiting Cases for Longitudinal Posterior Odds (2007)
Yu Chuan Tai, Terence P. Speed
This section derives the posterior odds under some constraints on the prior distributions of the µd, µ and Σ. 1. ν → ∞. The posterior odds do not involve W anymore, and become O = p 1 − p...
On the gene ranking of replicated microarray time course data (2007)
Yu Chuan Tai, Terence P. Speed
Consider the gene ranking problem of replicated microarray time course experiments where there are multiple biological conditions, and genes of interest are those whose temporal profiles are...
Sparse, noisy Boolean functions (2007)
Sach Mukherjee, Terence P. Speed
This paper addresses the question of making inferences regarding Boolean functions under conditions of (i) noise, or stochastic variation in observed data, and (ii) sparsity, by which we mean that...
Markov chain Monte Carlo for Structural Inference with Prior Information (2007)
Sach Mukherjee, Terence P. Speed
This paper addresses the question of making inferences regarding features of conditional independence graphs in settings characterized by the availability of rich prior information regarding such...
BMC Bioinformatics BioMed Central Methodology article (2007)
Mark D Robinson, Woon Wai Keen, Eleanor C Saunders, Malcolm J Mcconville, Terence P Speed, ...
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments
Research article A comparison of Affymetrix gene expression arrays (2007)
Mark D Robinson, Terence P Speed, Mark D Robinson, Terence P Speed
This is an Open Access article distributed under the terms of the Creative Commons Attribution License
Disclosure Statement: The authors have nothing to declare. (2007)
Nitzan Levy, Xiaoyue Zhao, Hui Tang, Robert B. Jaffe, Terence P. Speed, Dale C
mobility shift assay; LBD, ligand binding domain; NKG2E, killer cell lectin-like receptor; Q-RT-PCR, quantitative real-time polymerase chain reaction; SDS, sodium dodecyl sulfate; siRNA, small...
McCoubrie, Joanne E., Miller, Susanne K., Sargeant, Tobias, Good, Robert T., Hodder, Anthony N., Speed, Terence P., ...
Serine repeat antigens (SERAs) are a family of secreted "cysteine-like" proteases of Plasmodium parasites. Several SERAs possess an atypical active-site serine residue in place of the...
McCoubrie, Joanne E., Miller, Susanne K., Sargeant, Tobias, Good, Robert T., Hodder, Anthony N., Speed, Terence P., ...
Serine repeat antigens (SERAs) are a family of secreted “cysteine-like” proteases of Plasmodium parasites. Several SERAs possess an atypical active-site serine residue in place of the...
Evolution and comparative analysis of the MHC Class III inflammatory region (2006)
Deakin, Janine E, Papenfuss, Anthony T, Belov, Katherine, Cross, Joseph GR, Coggill, Penny, Palmer, Sophie, ...
Abstract Background The Major Histocompatibility Complex (MHC) is essential for immune function. Historically, it has been subdivided into three regions (Class I, II, and III), but a cluster of...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity (2006)
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Abstract Background Signal transducer and activator of transcription (STAT) proteins are key regulators of gene expression in response to the interferon (IFN) family of anti-viral and anti-microbial...
A multivariate empirical Bayes statistic for replicated microarray time course data (2006)
Tai, Yu Chuan, Speed, Terence P.
In this paper we derive one- and two-sample multivariate empirical Bayes statistics (the MB-statistics) to rank genes in order of interest from longitudinal replicated developmental microarray time...
EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA (2006)
Carvalho, Benilton, Speed, Terence P., Irizarry, Rafael A
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data...
EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA (2006)
Carvalho, Benilton, Speed, Terence P., Irizarry, Rafael A
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data...
EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA (2006)
Carvalho, Benilton, Speed, Terence P., Irizarry, Rafael A
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data...
EXPLORATION, NORMALIZATION, AND GENOTYPE CALLS OF HIGH DENSITY OLIGONUCLEOTIDE SNP ARRAY DATA (2006)
Carvalho, Benilton, Speed, Terence P., Irizarry, Rafael A
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data...
Katherine Belov, Janine E. Deakin, Anthony T. Papenfuss, Michelle L. Baker, Sandra D. Melman, Hannah V. Siddle, ...
Opossum genomic sequence data permit researchers to fill gaps in our knowledge of how the Major Histocompatibility Complex evolved within the mammalian lineage.
Katherine Belov, Janine E. Deakin, Anthony T. Papenfuss, Michelle L. Baker, Sandra D. Melman, Hannah V. Siddle, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum) sequence to construct the...
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites (2006)
Sargeant, Tobias J, Marti, Matthias, Caler, Elisabet, Carlton, Jane M, Simpson, Ken, Speed, Terence P, ...
Abstract Background The apicomplexan parasite Plasmodium falciparum causes the most severe form of malaria in humans. After invasion into erythrocytes, asexual parasite stages drastically alter their...
Benilton Carvalho, Henrik Bengtsson, Terence P. Speed, Rafael A. Irizarry
In most microarray technologies, a number of critical steps are required to convert raw intensity mea-surements into the data relied upon by data analysts, biologists and clinicians. These data...
A genotype calling algorithm for Affymetrix SNP arrays (2006)
Nusrat Rabbee, Terence P. Speed
∗ To whom correspondence should be addressed Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling...
A genotype calling algorithm for Affymetrix SNP arrays (2006)
Nusrat Rabbee, Terence P. Speed
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
Exploration, Normalization, and Genotype Calls of High Density Oligonucleotide SNP Array Data (2006)
Carvalho, Benilton, Bengtsson, Henrik, Speed, Terence P., Irizarry, Rafael A.
In most microarray technologies, a number of critical steps are required to convert raw intensity measurements into the data relied upon by data analysts, biologists and clinicians. These data...
Incorporating interference into linkage analysis for experimental crosses (2006)
Armstrong, Nicola J., McPeek, Mary Sara, Speed, Terence P.
The phenomenon of interference in genetic recombination is well-known and studied in a wide variety of organisms. Multilocus linkage analysis, which makes use of recombination patterns among all...
A genotype calling algorithm for affymetrix SNP arrays (2006)
Rabbee, Nusrat, Speed, Terence P.
Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the...
Evolution of the relaxin-like peptide family (2005)
Wilkinson, Tracey N, Speed, Terence P, Tregear, Geoffrey W, Bathgate, Ross AD
Abstract Background The relaxin-like peptide family belongs in the insulin superfamily and consists of 7 peptides of high structural but low sequence similarity; relaxin-1, 2 and 3, and the...
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries (2005)
Beißbarth, Tim, Tye-Din, Jason A., Smyth, Gordon K., Speed, Terence P., Anderson, Robert P.
Motivation: T-cell response to peptides bound on MHC Class I or Class II molecules is essential for immune recognition of pathogens. T-cells are activated by specific peptide epitopes that are...
Incorporating interference into linkage analysis for experimental crosses (2005)
Armstrong, Nicola J., McPeek, Mary Sara, Speed, Terence P.
The phenomenon of interference in genetic recombination is well known and studied in a wide variety of organisms. Multilocus linkage analysis, which makes use of recombination patterns among all...
A genotype calling algorithm for Affymetrix SNP arrays (2005)
Rabbee, Nusrat, Speed, Terence P.
Motivation: A classification algorithm, based on a multi-chip, multi-SNP approach is proposed for Affymetrix SNP arrays. Current procedures for calling genotypes on SNP arrays process all the...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
GOstat: find statistically overrepresented Gene Ontologies within a group of genes (2004)
Beißbarth, Tim, Speed, Terence P.
Summary: Modern experimental techniques, as for example DNA microarrays, as a result usually produce a long list of genes, which are potentially interesting in the analyzed process. In order to gain...
Statistical modeling of sequencing errors in SAGE libraries (2004)
Beißbarth, Tim, Hyde, Lavinia, Smyth, Gordon K., Job, Chris, Boon, Wee-Ming, Tan, Seong-Seng, ...
Motivation: Sequencing errors may bias the gene expression measurements made by Serial Analysis of Gene Expression (SAGE). They may introduce non-existent tags at low abundance and decrease the real...
A benchmark for Affymetrix GeneChip expression measures (2004)
Cope, Leslie M., Irizarry, Rafael A., Jaffee, Harris A., Wu, Zhijin, Speed, Terence P.
Motivation: The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create...
Bourgon, Richard, Delorenzi, Mauro, Sargeant, Tobias, Hodder, Anthony N., Crabb, Brendan S., Speed, Terence P.
Plasmodium falciparum is the parasite responsible for the most acute form of malaria in humans. Recently, the serine repeat antigen (SERA) in P. falciparum has attracted attention as a potential...
Machine learning in low-level microarray analysis (2003)
Jon Mcauliffe, Simon Cawley, Marimuthu Palaniswami, Kotagiri Ramamohanarao, Terence P. Speed
Machine learning and data mining have found a multitude of successful applications in microarray analysis, with gene clustering and classification of tissue samples being widely cited examples....
Exploration, Normalization, and Summaries of High Density (2003)
Oligonucleotide Array Probe, Rafael A. Irizarry, Bridget Hobbs, Francois Collin, Kristen J. Antonellis, ...
In this paper we report exploratory analyses of high-density oligonucleotide array data from the Affymetrix system with the objective of improving upon currently used measures of gene expression.
Resampling-based Multiple Testing for Microarray Data Analysis (2003)
E Investigación Operativa, Yongchao Ge, Sandrine Dudoit, Terence P. Speed, Yongchao Ge, Sandrine Dudoit, ...
The burgeoning field of genomics has revived interest in multiple testing procedures by raising new methodological and computational challenges. For example, microarray experiments generate large...
Summaries of Affymetrix GeneChip probe level data (2003)
Irizarry, Rafael A., Bolstad, Benjamin M., Collin, Francois, Cope, Leslie M., Hobbs, Bridget, Speed, Terence P.
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are...
Irizarry, Rafael A., Hobbs, Bridget, Collin, Francois, Beazer-Barclay, Yasmin D., Antonellis, Kristen J., Scherf, Uwe, ...
In this paper we report exploratory analyses of high‐density oligonucleotide array data from the Affymetrix GeneChip® system with the objective of improving upon currently used measures of...
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis (2003)
Barczak, Andrea, Rodriguez, Madeleine Willkom, Hanspers, Kristina, Koth, Laura L., Tai, Yu Chuan, Bolstad, Benjamin M., ...
DNA microarrays produced by deposition (or `spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted...
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis (2003)
Barczak, Andrea, Rodriguez, Madeleine Willkom, Hanspers, Kristina, Koth, Laura L., Tai, Yu Chuan, Bolstad, Benjamin M., ...
DNA microarrays produced by deposition (or `spotting') of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted...
Predicting Progress in Shotgun Sequencing with Paired Ends (2002)
Yeh, Ru-Fang, Speed, Terence P, Waterman, Michael S, Li, Xiaoman
Paired-end shotgun sequencing has become widely used for large-scale sequencing projects in recent years, including whole genome shot-gun sequencing and map-based BAC clone sequencing. Under this...
Approximate Ewens formulae for symmetric overdominance selection (2002)
Grote, Mark N., Speed, Terence P.
We derive a family of approximate sampling distributions for the symmetric overdominance model of population genetics. The distributions are selective versions of the Ewens Sampling Formula, which...
Rine Dudoit, Jane Fridly, Terence P. Speed
A reliable and precise classi � cation of tumors is essential for successful diagnosis and treatment of cancer. cDNA microarrays and highdensity oligonucleotide chips are novel biotechnologies...
Rine Dudoit, Yee Hwa Yang, Matthew J. Callow, Terence P. Speed
Abstract: DNA microarrays are a new and promising biotechnology whichallows the monitoring of expression levels in cells for thousands of genes simultaneously. The present paper describes statistical...
Sandrine Dudoit Yeehwayang, Rine Dudoit, Matthew J. Callow, Terence P. Speed, Sandrine Dudoit
Microarrays are part of a new class of biotechnologies which allow the monitoring of expression levels for thousands of genes simultaneously. This paper describes statistical methods for the...
Direct versus indirect designs for cDNA microarray experiments (2002)
Yee Hwa Yang, Terence P. Speed, Terence P. Speed
We calculate the variances of two classes of estimates of di#erential gene expression based on log ratios of fluorescence intensities from cDNA microarray experiments: direct estimates, using...
Yang, Yee Hwa, Dudoit, Sandrine, Luu, Percy, Lin, David M., Peng, Vivian, Ngai, John, ...
There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent...
Deconvolution of sparse positive spikes: is it ill-posed (2001)
Deconvolution is usually regarded as one of the so called ill-posed problems of applied mathematics if no constraints on the unknowns can be assumed. In this paper, we discuss the idea of...
Terence P. Speed, Yee Hwa Yang, Michael J. Buckley, Terence P. Speed
is a PhD student at the
Analysis of cDNA microarray images (2001)
Yang, Yee Hwa, Buckley, Michael J., Speed, Terence P.
Microarrays are part of a new class of biotechnologies that allow the monitoring of expression levels for thousands of genes simultaneously. Image analysis is an important aspect of microarray...
Parametric deconvolution of positive spike trains (2000)
This paper describes a parametric deconvolution method (PDPS) appropriate for a particular class of signals which we call spike-convolution models. These models arise when a sparse spike train...
Parametric Deconvolution of Positive Spike Trains (2000)
This paper describes a parametric deconvolution method(PDPS) appropriate for a particular class of signals which we call spike-convolution models. These models arise when a sparse spike train---Dirac...
Jane Fridlyand, Terence P. Speed, Sandrine Dudoit, Sandrine Dudoit
A reliable and precise classification of tumors is essential for successful treatment of cancer. cDNA microarrays and high-density oligonucleotide chips are novel biotechnologies which are being used...
Matthew J. Callow, Yee Hwa Yang, Terence P. Speed, Sandrine Dudoit, Sandrine Dudoit
Microarrays are part of a new class of biotechnologies which allow the monitoring of expression levels for thousands of genes simultaneously. This paper describes statistical methods for the...
Parametric Deconvolution of Positive Spike Trains (2000)
Lei Li Florida, Lei Li, Terence P. Speed
This paper describes a parametric deconvolution method(PDPS) appropriate for a particular class of signals which we call spike-convolution models. These models arise when a sparse spike train---Dirac...
A score test for linkage using identity by descent data from sibships (1999)
Dudoit, Sandrine, Speed, Terence P.
We consider score tests of the null hypothesis $H_0: \theta = 1/2$ against the alternative hypothesis $H_1: 0 \leq \theta < 1/2$, based upon counts multinomially distributed with parameters $n$ and...
The Poisson-skip model of crossing-over (1997)
Lange, Kenneth, Speed, Terence P., Zhao, Hongyu
The Poisson-skip model introduced in this paper generalizes the chi-square model of crossover interference. Both models are constructed from the random points of a Poisson process occurring along a...
Finding, Evaluating and Counting DNA Physical Maps (1993)
Lee Aaron Newberg, Terence P. Speed, Lee Aaron Newberg, Lee Aaron Newberg
Finding, Evaluating, and Counting DNA Physical Maps (1993)
Terence P. Speed, Lee Aaron Newberg, Lee Aaron Newberg, Lee Aaron Newberg
Finding, Evaluating, and Counting DNA Physical Maps by Lee Aaron Newberg Doctor of Philosophy in Computer Science University of California at Berkeley Professor Richard M. Karp, Chair The...
Yang, Yee Hwa, Dudoit, Sandrine, Luu, Percy, Lin, David M., Peng, Vivian, Ngai, John, ...
There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent...
Symons, R. C. Andrew, Daly, Mark J., Fridlyand, Jane, Speed, Terence P., Cook, Wendy D., Gerondakis, Steven, ...
There is a great difference in susceptibility to v-abl transgene-induced plasmacytoma between the BALB/cAn and the relatively resistant C57BL/6J mouse strains. We have used the Mapmaker/SURVIVOR...
Summaries of Affymetrix GeneChip probe level data
Irizarry, Rafael A., Bolstad, Benjamin M., Collin, Francois, Cope, Leslie M., Hobbs, Bridget, Speed, Terence P.
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are...
Analysis of gene expression in the developing mouse retina
Díaz, Elva, Yang, Yee Hwa, Ferreira, Todd, Loh, Kenneth C., Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
In the visual system, differential gene expression underlies development of the anterior–posterior and dorsal–ventral axes. Here we present the results of a microarray screen to identify genes...
Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice
Callow, Matthew J., Dudoit, Sandrine, Gong, Elaine L., Speed, Terence P., Rubin, Edward M.
Based on the assumption that severe alterations in the expression of genes known to be involved in high-density lipoprotein (HDL) metabolism may affect the expression of other genes, we screened an...
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
Barczak, Andrea, Rodriguez, Madeleine Willkom, Hanspers, Kristina, Koth, Laura L., Tai, Yu Chuan, Bolstad, Benjamin M., ...
DNA microarrays produced by deposition (or `spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted...
Spatial patterns of gene expression in the olfactory bulb
Lin, David M., Yang, Yee Hwa, Scolnick, Jonathan A., Brunet, Lisa J., Marsh, Heather, Peng, Vivian, ...
How olfactory sensory neurons converge on spatially invariant glomeruli in the olfactory bulb is largely unknown. In one model, olfactory sensory neurons interact with spatially restricted guidance...
Belov, Katherine, Deakin, Janine E, Papenfuss, Anthony T, Baker, Michelle L, Melman, Sandra D, Siddle, Hannah V, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the...
Evolution of the relaxin-like peptide family
Wilkinson, Tracey N, Speed, Terence P, Tregear, Geoffrey W, Bathgate, Ross AD
The wound repair response controls outcome to cutaneous leishmaniasis
Sakthianandeswaren, Anuratha, Elso, Colleen M., Simpson, Ken, Curtis, Joan M., Kumar, Beena, Speed, Terence P., ...
Chronic microbial infections are associated with fibrotic and inflammatory reactions known as granulomas showing similarities to wound-healing and tissue repair processes. We have previously mapped...
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites
Sargeant, Tobias J, Marti, Matthias, Caler, Elisabet, Carlton, Jane M, Simpson, Ken, Speed, Terence P, ...
A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Evolution and comparative analysis of the MHC Class III inflammatory region
Deakin, Janine E, Papenfuss, Anthony T, Belov, Katherine, Cross, Joseph GR, Coggill, Penny, Palmer, Sophie, ...
Yang, Yee Hwa, Dudoit, Sandrine, Luu, Percy, Lin, David M., Peng, Vivian, Ngai, John, ...
There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent...
Symons, R. C. Andrew, Daly, Mark J., Fridlyand, Jane, Speed, Terence P., Cook, Wendy D., Gerondakis, Steven, ...
There is a great difference in susceptibility to v-abl transgene-induced plasmacytoma between the BALB/cAn and the relatively resistant C57BL/6J mouse strains. We have used the Mapmaker/SURVIVOR...
Summaries of Affymetrix GeneChip probe level data
Irizarry, Rafael A., Bolstad, Benjamin M., Collin, Francois, Cope, Leslie M., Hobbs, Bridget, Speed, Terence P.
High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are...
Analysis of gene expression in the developing mouse retina
Díaz, Elva, Yang, Yee Hwa, Ferreira, Todd, Loh, Kenneth C., Okazaki, Yasushi, Hayashizaki, Yoshihide, ...
In the visual system, differential gene expression underlies development of the anterior–posterior and dorsal–ventral axes. Here we present the results of a microarray screen to identify genes...
Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice
Callow, Matthew J., Dudoit, Sandrine, Gong, Elaine L., Speed, Terence P., Rubin, Edward M.
Based on the assumption that severe alterations in the expression of genes known to be involved in high-density lipoprotein (HDL) metabolism may affect the expression of other genes, we screened an...
Spotted Long Oligonucleotide Arrays for Human Gene Expression Analysis
Barczak, Andrea, Rodriguez, Madeleine Willkom, Hanspers, Kristina, Koth, Laura L., Tai, Yu Chuan, Bolstad, Benjamin M., ...
DNA microarrays produced by deposition (or `spotting')of a single long oligonucleotide probe for each gene may be an attractive alternative to other types of arrays. We produced spotted...
Rubio, Justin P., Bahlo, Melanie, Butzkueven, Helmut, Van der Mei, Ingrid A. F., Sale, Michèle M., Dickinson, Joanne L., ...
Association of multiple sclerosis (MS) with the human leukocyte antigen (HLA) class II haplotype DRB1*1501-DQB1*0602 is the most consistently replicated finding of genetic studies of the disease....
Spatial patterns of gene expression in the olfactory bulb
Lin, David M., Yang, Yee Hwa, Scolnick, Jonathan A., Brunet, Lisa J., Marsh, Heather, Peng, Vivian, ...
How olfactory sensory neurons converge on spatially invariant glomeruli in the olfactory bulb is largely unknown. In one model, olfactory sensory neurons interact with spatially restricted guidance...
Evolution of the relaxin-like peptide family
Wilkinson, Tracey N, Speed, Terence P, Tregear, Geoffrey W, Bathgate, Ross AD
The wound repair response controls outcome to cutaneous leishmaniasis
Sakthianandeswaren, Anuratha, Elso, Colleen M., Simpson, Ken, Curtis, Joan M., Kumar, Beena, Speed, Terence P., ...
Chronic microbial infections are associated with fibrotic and inflammatory reactions known as granulomas showing similarities to wound-healing and tissue repair processes. We have previously mapped...
Belov, Katherine, Deakin, Janine E, Papenfuss, Anthony T, Baker, Michelle L, Melman, Sandra D, Siddle, Hannah V, ...
The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used theMonodelphis domestica (gray short-tailed opossum) sequence to construct the...
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites
Sargeant, Tobias J, Marti, Matthias, Caler, Elisabet, Carlton, Jane M, Simpson, Ken, Speed, Terence P, ...
A new software was used to predict exported proteins that are conserved between malaria parasites infecting rodents and those infecting humans, revealing a lineage-specific expansion of exported...
Proximal genomic localization of STAT1 binding and regulated transcriptional activity
Wormald, Samuel, Hilton, Douglas J, Smyth, Gordon K, Speed, Terence P
Evolution and comparative analysis of the MHC Class III inflammatory region
Deakin, Janine E, Papenfuss, Anthony T, Belov, Katherine, Cross, Joseph GR, Coggill, Penny, Palmer, Sophie, ...
Mapping of the Plasmodium chabaudi Resistance Locus char2†
Lin, Enmoore, Pappenfuss, Tony, Tan, Rachel B., Senyschyn, Danielle, Bahlo, Melanie, Speed, Terence P., ...
Animals congenic for the char2 host response locus to the murine malarial parasite Plasmodium chabaudi have been bred, and they demonstrated a phenotypic difference from the parental lines. These...
A model selection approach for the identification of quantitative trait loci in experimental crosses
Karl W. Broman, Terence P. Speed
We consider the problem of identifying the genetic loci (called quantitative trait loci (QTLs)) contributing to variation in a quantitative trait, with data on an experimental cross. A large number...
Global analyses of mRNA translational control during early Drosophila embryogenesis
Qin, Xiaoli, Ahn, Soyeon, Speed, Terence P, Rubin, Gerald M
The polysomal profiles of over 15,000 transcripts during the first ten hours after egg laying have been determined.
Belov, Katherine, Sanderson, Claire E., Deakin, Janine E., Wong, Emily S.W., Assange, Daniel, McColl, Kaighin A., ...
The availability of the first marsupial genome sequence has allowed us to characterize the immunome of the gray short-tailed opossum (Monodelphis domestica). Here we report the identification of key...
Robinson, Mark D, De Souza, David P, Keen, Woon Wai, Saunders, Eleanor C, McConville, Malcolm J, Speed, Terence P, ...
Analysis of gene expression during neurite outgrowth and regeneration
Szpara, Moriah L, Vranizan, Karen, Tai, Yu Chuan, Goodman, Corey S, Speed, Terence P, Ngai, John
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Li, Xiao-yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A, Iyer, Venky N, ...
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to...
McCoubrie, Joanne E., Miller, Susanne K., Sargeant, Tobias, Good, Robert T., Hodder, Anthony N., Speed, Terence P., ...
Serine repeat antigens (SERAs) are a family of secreted “cysteine-like” proteases of Plasmodium parasites. Several SERAs possess an atypical active-site serine residue in place of the canonical...
Likić, Vladimir A., Gooley, Paul R., Speed, Terence P., Strehler, Emanuel E.
A sample of 35 independent molecular dynamics (MD) simulations of calmodulin (CaM) equilibrium dynamics was prepared from different but equally plausible initial conditions (20 simulations of the...
O'Donnell, Rebecca A., Drew, Damien R., Thomson, Russell, Speed, Terence P., Crabb, Brendan S.
Antibodies capable of inhibiting the invasion of Plasmodium merozoites into erythrocytes are present in individuals that are clinically immune to the malaria parasite. Those targeting the 19-kD...
Li, Xiao-yong, MacArthur, Stewart, Bourgon, Richard, Nix, David, Pollard, Daniel A, Iyer, Venky N, ...
Integrative analysis of RUNX1 downstream pathways and target genes
Michaud, Joëlle, Simpson, Ken M, Escher, Robert, Buchet-Poyau, Karine, Beissbarth, Tim, Carmichael, Catherine, ...
A Holm-type procedure controlling the false discovery rate
Ge, Yongchao, Sealfon, Stuart C., Tseng, Chi-Hong, Speed, Terence P.
Benjamini and Hochberg [1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Statist. Soc. Ser. B 57, 289-300] proposed a step-up procedure...
Levy, Nitzan, Tatomer, Dierdre, Herber, Candice B., Zhao, Xiaoyue, Tang, Hui, Sargeant, Toby, ...
Estrogen receptors (ERs) regulate gene transcription by interacting with regulatory elements. Most information regarding how ER activates genes has come from studies using a small set of target genes...
Network inference using informative priors
Mukherjee, Sach, Speed, Terence P.
Recent years have seen much interest in the study of systems characterized by multiple interacting components. A class of statistical models called graphical models, in which graphs are used to...
Tonkin, Christopher J, Carret, Céline K, Duraisingh, Manoj T, Voss, Till S, Ralph, Stuart A, Hommel, Mirja, ...
Cytoadherance of Plasmodium falciparum-infected erythrocytes in the brain, organs and peripheral microvasculature is linked to morbidity and mortality associated with severe malaria. Parasite-derived...
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting
Pask, Andrew J, Papenfuss, Anthony T, Ager, Eleanor I, McColl, Kaighin A, Speed, Terence P, Renfree, Marilyn B
Comparisons between the platypus and eutherian mammalian genomes provides new insights into how epigenetic imprinting may have evolved in mammalian genomes.
Chandran, Divya, Tai, Yu Chuan, Hather, Gregory, Dewdney, Julia, Denoux, Carine, Burgess, Diane G., ...
Salicylic acid (SA) is a critical mediator of plant innate immunity. It plays an important role in limiting the growth and reproduction of the virulent powdery mildew (PM) Golovinomyces orontii on...
Bengtsson, Henrik, Ray, Amrita, Spellman, Paul, Speed, Terence P.
Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a demand for increased precision and resolution of CN estimates. Recent studies have obtained CN estimates from more...
Loi, Sherene, Sotiriou, Christos, Haibe-Kains, Benjamin, Lallemand, Francoise, Conus, Nelly M, Piccart, Martine J, ...
Paruthiyil, Sreenivasan, Cvoro, Aleksandra, Zhao, Xiaoyue, Wu, Zhijin, Sui, Yunxia, Staub, Richard E., ...
Estrogens produce biological effects by interacting with two estrogen receptors, ERα and ERβ. Drugs that selectively target ERα or ERβ might be safer for conditions that have been traditionally...
Bengtsson, Henrik, Wirapati, Pratyaksha, Speed, Terence P.
Motivation: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also...