Terence Speed

A new normalization for Nanostring nCounter gene expression data

Ramyar Molania, Johann A Gagnon-Bartsch, Alexander Dobrovic, Terence P Speed

Journal article  |  2019  |  Nucleic Acids Research

The Nanostring nCounter gene expression assay uses molecular barcodes and single molecule imaging to detect and count hundreds of ..

scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Yingxin Lin, Shila Ghazanfar, Kevin YX Wang, Johann A Gagnon-Bartsch, Kitty K Lo, Xianbin Su, Ze-Guang Han, John T Ormerod, Terence P Speed, Pengyi Yang, Jean Yee Hwa Yang

Journal article  |  2019  |  Proceedings of the National Academy of Sciences

Using long-read sequencing to detect imprinted DNA methylation

Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence P Speed, Marnie E Blewitt, Matthew E Ritchie

Journal article  |  2019  |  Nucleic Acids Research

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, Terence P Speed, Susan J Clark

Journal article  |  2019  |  Bioinformatics

Maps of variability in cell lineage trees

Damien Hicks, Terence Speed, Mohammed Yassin, Sarah Russell

Journal article  |  2019  |  PLoS Computational Biology

New approaches to lineage tracking allow the study of cell differentiation over many generations of cells during development in mu..

Maps of variability in cell lineage trees

Damien G Hicks, Terence P Speed, Mohammed Yassin, Sarah M Russell

Journal article  |  2019  |  PLOS Computational Biology

Characterization of high TIL breast cancers reveals a prognostic and functionally distinct tissue-resident memory subpopulation

P Savas, B Virassamy, C Ye, A Salim, CP Mintoff, F Caramia, R Salgado, ZL Teo, S Dushyanthen, A Byrne, SJ Luen, SB Fox, TP Speed, LK Mackay, PJ Neeson, S Loi

Conference Proceedings  |  2019  |  Poster Discussion Abstracts

Dysregulated IL-1-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine

Man Lyang Kim, William J Martin, Gabriela Minigo, Joanne L Keeble, Alexandra L Garnham, Guido Pacini, Gordon K Smyth, Terence P Speed, Jonathan Carapetis, Ian P Wicks

Journal article  |  2018  |  Circulation

Using long-read sequencing to detect imprinted DNA methylation

Scott Gigante, Quentin Gouil, Alexis Lucattini, Andrew Keniry, Tamara Beck, Matthew Tinning, Lavinia Gordon, Chris Woodruff, Terence Speed, Marnie Blewitt, Matthew Ritchie

Journal article  |  2018

Systematic variation in the methylation of cytosines at CpG sites plays a critical role in early development of humans and other m..

The healthy ageing gene expression signature for Alzheimer's disease diagnosis: a random sampling perspective

Laurent Jacob, Terence P Speed

Journal article  |  2018  |  Genome Biology

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

Peter Savas, Balaji Virassamy, Chengzhong Ye, Agus Salim, Christopher P Mintoff, Franco Caramia, Roberto Salgado, David J Byrne, Zhi L Teo, Sathana Dushyanthen, Ann Byrne, Lironne Wein, Stephen J Luen, Catherine Poliness, Sophie S Nightingale, Anita S Skandarajah, David E Gyorki, Chantel M Thornton, Paul A Beavis, Stephen B Fox, et al.

Journal article  |  2018  |  Nature Medicine

A statistical framework for analyzing deep mutational scanning data (vol 18, 150, 2017)

Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler

Journal article  |  2018  |  Genome Biology

RLE plots: Visualizing unwanted variation in high dimensional data

Luke C Gandolfo, Terence P Speed

Journal article  |  2018  |  PLOS ONE

Joint Modeling of Mixed Plasmodium Species Infections Using a Bivariate Poisson Lognormal Model

Kathryn L Colborn, Ivo Mueller, Terence P Speed

Journal article  |  2018  |  The American Journal of Tropical Medicine and Hygiene

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel L Cameron, Jan Schroder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence P Speed, Anthony T Papenfuss

Journal article  |  2017  |  Genome Research

A statistical framework for analyzing deep mutational scanning data

Alan F Rubin, Hannah Gelman, Nathan Lucas, Sandra M Bajjalieh, Anthony T Papenfuss, Terence P Speed, Douglas M Fowler

Journal article  |  2017  |  Genome Biology

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

Daniel Cameron, Jan Schroeder, Jocelyn Sietsma Penington, Hongdo Do, Ramyar Molania, Alexander Dobrovic, Terence Speed, Anthony Papenfuss

Journal article  |  2017

ABSTRACT The identification of genomic rearrangements, particularly in cancers, with high sensitivity and specificity using massiv..

Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells

Yong Jin Choi, Chao-Po Lin, Davide Risso, Sean Chen, Thomas Aquinas Kim, Meng How Tan, Jin Billy Li, Yalei Wu, Caifu Chen, Zhenyu Xuan, Todd Macfarlan, Weiqun Peng, KC Kent Lloyd, Sang Yong Kim, Terence P Speed, Lin He

Journal article  |  2017  |  Science

The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE"

Peter Savas, Zhi Ling Teo, Christophe Lefevre, Christoffer Flensburg, Franco Caramia, Kathryn Alsop, Mariam Mansour, Prudence A Francis, Heather A Thorne, Maria Joao Silva, Nnennaya Kanu, Michelle Dietzen, Andrew Rowan, Maik Kschischo, Stephen Fox, David D Bowtell, Sarah-Jane Dawson, Terence P Speed, Charles Swanton, Sherene Loi

Journal article  |  2016  |  PLOS Medicine

Contextual fear conditioning induces differential alternative splicing

Shane G Poplawski, Lucia Peixoto, Giulia S Porcari, Mathieu E Wimmer, Anna G McNally, Keiko Mizuno, K Peter Giese, Snehajyoti Chatterjee, John N Koberstein, Davide Risso, Terence P Speed, Ted Abel

Journal article  |  2016  |  Neurobiology of Learning and Memory

Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex

Jason R Gerstner, John N Koberstein, Adam J Watson, Nikolai Zapero, Davide Risso, Terence P Speed, Marcos G Frank, Lucia Peixoto

Journal article  |  2016  |  BMC Genomics

A molecular threshold for effector CD8( ) T cell differentiation controlled by transcription factors Blimp-1 and T-bet

Annie Xin, Frederick Masson, Yang Liao, Simon Preston, Tianxia Guan, Renee Gloury, Moshe Olshansky, Jian-Xin Lin, Peng Li, Terence P Speed, Gordon K Smyth, Matthias Ernst, Warren J Leonard, Marc Pellegrini, Susan M Kaech, Stephen L Nutt, Wei Shi, Gabrielle T Belz, Axel Kallies

Journal article  |  2016  |  Nature Immunology

MicroRNAs in CD4( ) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes

Yuxia Zhang, Zhi-Ping Feng, Gaetano Naselli, Fiona Bell, James Wettenhall, Priscilla Auyeung, Justine A Ellis, Anne-Louise Ponsonby, Terence P Speed, Mark MW Chong, Leonard C Harrison

Journal article  |  2016  |  Journal of Autoimmunity

Combining single and paired end RNA-seq data for differential expression analyses

ZP Feng, F Collin, TP Speed

Conference Proceedings  |  2016  |  Abel Symposia

Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed

Laurent Jacob, Johann A Gagnon-Bartsch, Terence P Speed

Journal article  |  2016  |  Biostatistics

Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas

Suling J Lin, Johann A Gagnon-Bartsch, Iain Beehuat Tan, Sophie Earle, Louise Ruff, Katherine Pettinger, Bauke Ylstra, Nicole van Grieken, Sun Young Rha, Hyun Cheol Chung, Ju-Seog Lee, Jae Ho Cheong, Sung Hoon Noh, Toru Aoyama, Yohei Miyagi, Akira Tsuburaya, Takaki Yoshikawa, Jaffer A Ajani, Alex Boussioutas, Khay Guan Yeoh, et al.

Journal article  |  2015  |  Gut

Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

Katie T Huang, Thomas Mikeska, Jason Li, Elena A Takano, Ewan KA Millar, Peter H Graham, Samantha E Boyle, Ian G Campbell, Terence P Speed, Alexander Dobrovic, Stephen B Fox

Journal article  |  2015  |  BMC Cancer

Systematic noise degrades gene co-expression signals but can be corrected

Saskia Freytag, Johann Gagnon-Bartsch, Terence P Speed, Melanie Bahlo

Journal article  |  2015  |  BMC Bioinformatics

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

Lucia Peixoto, Davide Risso, Shane G Poplawski, Mathieu E Wimmer, Terence P Speed, Marcelo A Wood, Ted Abel

Journal article  |  2015  |  Nucleic Acids Research

Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data

Jovana Maksimovic, Johann A Gagnon-Bartsch, Terence P Speed, Alicia Oshlack

Journal article  |  2015  |  Nucleic Acids Research

Statistical Methods for Handling Unwanted Variation in Metabolomics Data

Alysha M De Livera, Marko Sysi-Aho, Laurent Jacob, Johann A Gagnon-Bartsch, Sandra Castillo, Julie A Simpson, Terence P Speed

Journal article  |  2015  |  Analytical Chemistry

Distinct Epigenetic Signatures Delineate Transcriptional Programs during Virus-Specific CD8( ) T Cell Differentiation

Brendan E Russ, Moshe Olshanksy, Heather S Smallwood, Jasmine Li, Alice E Denton, Julia E Prier, Angus T Stock, Hayley A Croom, Jolie G Cullen, Michelle LT Nguyen, Stephanie Rowe, Matthew R Olson, David B Finkelstein, Anne Kelso, Paul G Thomas, Terry P Speed, Sudha Rao, Stephen J Turner

Journal article  |  2014  |  Immunity

Normalization of RNA-seq data using factor analysis of control genes or samples

Davide Risso, John Ngai, Terence P Speed, Sandrine Dudoit

Journal article  |  2014  |  Nature Biotechnology

Dating Rare Mutations from Small Samples with Dense Marker Data

Luke C Gandolfo, Melanie Bahlo, Terence P Speed

Journal article  |  2014  |  Genetics

Combining calls from multiple somatic mutation-callers

Su Yeon Kim, Laurent Jacob, Terence P Speed

Journal article  |  2014  |  BMC Bioinformatics

A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression

Nobuhiro Okada, Chao-Po Lin, Marcelo C Ribeiro, Anne Biton, Gregory Lai, Xingyue He, Pengcheng Bu, Hannes Vogel, David M Jablons, Andreas C Keller, J Erby Wilkinson, Biao He, Terry P Speed, Lin He

Journal article  |  2014  |  Genes & Development

Silencing of Odorant Receptor Genes by G Protein beta gamma Signaling Ensures the Expression of One Odorant Receptor per Olfactory Sensory Neuron

Todd Ferreira, Sarah R Wilson, Yoon Gi Choi, Davide Risso, Sandrine Dudoit, Terence P Speed, John Ngai

Journal article  |  2014  |  Neuron

Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery

Dineika Chandrananda, Natalie P Thorne, Devika Ganesamoorthy, Damien L Bruno, Yuval Benjamini, Terence P Speed, Howard R Slater, Melanie Bahlo

Journal article  |  2014  |  PLoS One

Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data

Ingrid M Loennstedt, Franco Caramia, Jason Li, Debora Fumagalli, Roberto Salgado, Andrew Rowan, Max Salm, Nnennaya Kanu, Peter Savas, Stuart Horswell, Stephan Gade, Sibylle Loibl, Patrick Neven, Christos Sotiriou, Charles Swanton, Sherene Loi, Terence P Speed

Journal article  |  2014  |  Genome Biol

G protein-linked signaling pathways in bipolar and major depressive disorders

H Tomita, ME Ziegler, HB Kim, SJ Evans, PV Choudary, JZ Li, F Meng, M Dai, RM Myers, CR Neal, TP Speed, JD Barchas, AF Schatzberg, SJ Watson, H Akil, EG Jones, WE Bunney, MP Vawter

Journal article  |  2013  |  Frontiers in Genetics

A brief history of the statistics department of the University of California at Berkeley

T Speed, J Pitman, J Rice

Book Chapter  |  2013

Colon tumour secretopeptidome: Insights into endogenous proteolytic cleavage events in the colon tumour microenvironment

David W Greening, Eugene A Kapp, Hong Ji, Terry P Speed, Richard J Simpson

Journal article  |  2013  |  Biochimica et Biophysica Acta-Proteins and Proteomics

A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis

Virginie Olive, Erich Sabio, Margaux J Bennett, Caitlin S De Jong, Anne Biton, James C McGann, Samantha K Greaney, Nicole M Sodir, Alicia Y Zhou, Asha Balakrishnan, Mona Foth, Micah A Luftig, Andrei Goga, Terence P Speed, Zhenyu Xuan, Gerard I Evan, Ying Wan, Alex C Minella, Lin He

Journal article  |  2013  |  eLife

Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients

DM Ross, M O'Hely, PA Bartley, P Dang, J Score, JM Goyne, M Sobrinho-Simoes, NCP Cross, JV Melo, TP Speed, TP Hughes, AA Morley

Journal article  |  2013  |  Leukemia

A High Force of Plasmodium vivax Blood-Stage Infection Drives the Rapid Acquisition of Immunity in Papua New Guinean Children

Cristian Koepfli, Kathryn L Colborn, Benson Kiniboro, Enmoore Lin, Terence P Speed, Peter M Siba, Ingrid Felger, Ivo Mueller

Journal article  |  2013  |  PLoS Neglected Tropical Diseases

Comparing somatic mutation-callers: beyond Venn diagrams

Su Yeon Kim, Terence P Speed

Journal article  |  2013  |  BMC Bioinformatics

Id2-Mediated Inhibition of E2A Represses Memory CD8( ) T Cell Differentiation

Frederick Masson, Martina Minnich, Moshe Olshansky, Ivan Bilic, Adele M Mount, Axel Kallies, Terence P Speed, Meinrad Busslinger, Stephen L Nutt, Gabrielle T Belz

Journal article  |  2013  |  Journal of Immunology

Effect of vascular endothelial growth factor upregulation on retinal gene expression in the Kimba mouse

Nicolette Binz, Ireni S Ali Rahman, Holly R Chinnery, Richard McKeone, Ken M Simpson, Terence P Speed, Chooi-May Lai, P Elizabeth Rakoczy

Journal article  |  2013  |  Clinical & Experimental Ophthalmology

Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts

E Purdom, C Restall, RA Busuttil, H Schluter, A Boussioutas, EW Thompson, RL Anderson, TP Speed, I Haviv

Journal article  |  2013  |  Genetics Research

Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time-lapse microscopy

Kim Pham, Raz Shimoni, Mandy J Ludford-Menting, Cameron J Nowell, Pavel Lobachevsky, Ze'ev Bomzon, Min Gu, Terence P Speed, C Jane McGlade, Sarah M Russell

Journal article  |  2013  |  Immunology and Cell Biology

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis

Yu Zhang, Oleg Mayba, Anne Pfeiffer, Hui Shi, James M Tepperman, Terence P Speed, Peter H Quail

Journal article  |  2013  |  PLoS Genetics

Statistical Analysis of Metabolomics Data

Alysha M De Livera, Moshe Olshansky, Terence P Speed

Journal article  |  2013  |  Methods in Molecular Biology

Copy-number-aware differential analysis of quantitative DNA sequencing data

Mark D Robinson, Dario Strbenac, Clare Stirzaker, Aaron L Statham, Jenny Song, Terence P Speed, Susan J Clark

Journal article  |  2012  |  Genome Research

Copy-number-aware differential analysis of quantitative DNA sequencing data.

MD Robinson, D Strbenac, C Stirzaker, AL Statham, J Song, TP Speed, SJ Clark

Journal article  |  2012  |  Genome research

A Tetrahymena Piwi Bound to Mature tRNA 3 ' Fragments Activates the Exonuclease Xrn2 for RNA Processing in the Nucleus

Mary T Couvillion, Gergana Bounova, Elizabeth Purdom, Terence P Speed, Kathleen Collins

Journal article  |  2012  |  Molecular Cell

Bayesian Inference of Signaling Network Topology in a Cancer Cell Line

Steven M Hill, Yiling Lu, Jennifer Molina, Laura M Heiser, Paul T Spellman, Terence P Speed, Joe W Gray, Gordon B Mills, Sach Mukherjee

Journal article  |  2012  |  Bioinformatics

Subcompartmentalisation of Proteins in the Rhoptries Correlates with Ordered Events of Erythrocyte Invasion by the Blood Stage Malaria Parasite

Elizabeth S Zuccala, Alexander M Gout, Chaitali Dekiwadia, Danushka S Marapana, Fiona Angrisano, Lynne Turnbull, David T Riglar, Kelly L Rogers, Cynthia B Whitchurch, Stuart A Ralph, Terence P Speed, Jake Baum

Journal article  |  2012  |  PLoS One

Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib

Jeffrey B Kerr, Karla J Hutt, Michele Cook, Terence P Speed, Andreas Strasser, Jock K Findlay, Clare L Scott

Journal article  |  2012  |  Nature Medicine

SRMA: an R package for resequencing array data analysis

Nianxiang Zhang, Yan Xu, Martin O'Hely, Terence P Speed, Curt Scharfe, Wenyi Wang

Journal article  |  2012  |  Bioinformatics

Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling

Taiyi Kuo, Michelle J Lew, Oleg Mayba, Charles A Harris, Terence P Speed, Jen-Chywan Wang

Journal article  |  2012  |  Proceedings of the National Academy of Sciences

Using control genes to correct for unwanted variation in microarray data

Johann A Gagnon-Bartsch, Terence P Speed

Journal article  |  2012  |  Biostatistics

Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children

Ivo Mueller, Sonja Schoepflin, Thomas A Smith, Kathryn L Benton, Michael T Bretscher, Enmoore Lin, Benson Kiniboro, Peter A Zimmerman, Terence P Speed, Peter Siba, Ingrid Felger

Journal article  |  2012  |  Proceedings of the National Academy of Sciences

A DNA resequencing array for genes involved in Parkinson's disease

EJ Wilkins, JP Rubio, KE Kotschet, TF Cowie, WC Boon, M O'Hely, R Burfoot, W Wang, CM Sue, TP Speed, J Stankovitch, MK Horne

Journal article  |  2012  |  Parkinsonism and Related Disorders

Summarizing and correcting the GC content bias in high-throughput sequencing

Yuval Benjamini, Terence P Speed

Journal article  |  2012  |  Nucleic Acids Research

The N-terminal domains of SOCS proteins: A conserved region in the disordered N-termini of SOCS4 and 5

Zhi-Ping Feng, Indu R Chandrashekaran, Andrew Low, Terence P Speed, Sandra E Nicholson, Raymond S Norton

Journal article  |  2012  |  Proteins - Structure, Function, and Bioinformatics

Subtype and pathway specific responses to anticancer compounds in breast cancer

Laura M Heiser, Anguraj Sadanandam, Wen-Lin Kuo, Stephen C Benz, Theodore C Goldstein, Sam Ng, William J Gibb, Nicholas J Wang, Safiyyah Ziyad, Frances Tong, Nora Bayani, Zhi Hu, Jessica I Billig, Andrea Dueregger, Sophia Lewis, Lakshmi Jakkula, James E Korkola, Steffen Durinck, Francois Pepin, Yinghui Guan, et al.

Journal article  |  2012  |  Proceedings of the National Academy of Sciences

A correlation for the 21st century (Science (2011) (1502))

T Speed

Journal article  |  2012  |  Science

Parametric deconvolution of positive spike trains

L Li, TP Speed

Book Chapter  |  2012

Questions, answers and statistics:

T Speed

Book Chapter  |  2012

Incorporating interference into linkage analysis for experimental crosses

NJ Armstrong, MS Mcpeek, TP Speed

Book Chapter  |  2012

Biological sequence analysis

TP Speed

Book Chapter  |  2012

Density estimation by stochastic complexity

J Rissanen, TP Speed, B Yu

Book Chapter  |  2012

A note on random times

JW Pitman, TP Speed

Book Chapter  |  2012

Cumulants and partition lattices

TP Speed

Book Chapter  |  2012

A factorisation theorem for adequate statistics

TP Speed

Book Chapter  |  2012

Invariants of some probability models used in phylogenetic inference

SN Evans, TP Speed

Book Chapter  |  2012

On genetic map functions

H Zhao, TP Speed

Book Chapter  |  2012

Generalized wreath products of permutation groups

RA Bailey, CE Praeger, CA Rowley, TP Speed

Book Chapter  |  2012

Additive and multiplicative models and interactions

JN Darroch, TP Speed

Book Chapter  |  2012

On the order of prime ideals

TP Speed

Book Chapter  |  2012

Comment

T Speed

Book Chapter  |  2012

Tissue-Specific Regulation of Genes by Estrogen Receptors

Dale C Leitman, Sreenivasan Paruthiyil, Chaoshen Yuan, Candice B Herber, Moshe Olshansky, Mary Tagliaferri, Isaac Cohen, Terence P Speed

Journal article  |  2012  |  Seminars in Reproductive Medicine

Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation

YH Yang, S Dudoit, P Luu, DM Lin, V Peng, J Ngai, TP Speed

Book Chapter  |  2012

Mathematics. A correlation for the 21st century.

Terry Speed

Journal article  |  2011  |  Science

Estrogenic Plant Extracts Reverse Weight Gain and Fat Accumulation without Causing Mammary Gland or Uterine Proliferation

Elise F Saunier, Omar I Vivar, Andrea Rubenstein, Xiaoyue Zhao, Moshe Olshansky, Scott Baggett, Richard E Staub, Mary Tagliaferri, Isaac Cohen, Terence P Speed, John D Baxter, Dale C Leitman

Journal article  |  2011  |  PLoS ONE

Erratum: Gene set enrichment analysis made simple (Statistical Methods in Medical Research (2009) 18:6 (565-575))

RA Irizarry, C Wang, Y Zhou, TP Speed

Journal article  |  2011  |  Statistical Methods in Medical Research

Integrated genomic analyses of ovarian carcinoma

D Bell, A Berchuck, M Birrer, J Chien, DW Cramer, F Dao, R Dhir, P DiSaia, H Gabra, P Glenn, AK Godwin, J Gross, L Hartmann, M Huang, DG Huntsman, M Iacocca, M Imielinski, S Kalloger, BY Karlan, DA Levine, et al.

Journal article  |  2011  |  Nature

Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes

Erinna F Lee, Oliver B Clarke, Marco Evangelista, Zhiping Feng, Terence P Speed, Elissaveta B Tchoubrieva, Andreas Strasser, Bernd H Kalinna, Peter M Colman, W Douglas Fairlie

Journal article  |  2011  |  Proceedings of the National Academy of Sciences of the United States of America

High-quality DNA sequence capture of 524 disease candidate genes

Peidong Shen, Wenyi Wang, Sujatha Krishnakumar, Curtis Palm, Aung-Kyaw Chi, Gregory M Enns, Ronald W Davis, Terence P Speed, Michael N Mindrinos, Curt Scharfe

Journal article  |  2011  |  Proceedings of the National Academy of Sciences

Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis

Xin Victoria Wang, Roel GW Verhaak, Elizabeth Purdom, Paul T Spellman, Terence P Speed

Journal article  |  2011  |  PLoS ONE

Copy Number Variation in Patients with Disorders of Sex Development Due to 46,XY Gonadal Dysgenesis

Stefan White, Thomas Ohnesorg, Amanda Notini, Kelly Roeszler, Jacqueline Hewitt, Hinda Daggag, Craig Smith, Erin Turbitt, Sonja Gustin, Jocelyn van den Bergen, Denise Miles, Patrick Western, Valerie Arboleda, Valerie Schumacher, Lavinia Gordon, Katrina Bell, Henrik Bengtsson, Terry Speed, John Hutson, Garry Warne, et al.

Journal article  |  2011  |  PLoS One

Reticulocyte and Erythrocyte Binding-Like Proteins Function Cooperatively in Invasion of Human Erythrocytes by Malaria Parasites

Sash Lopaticki, Alexander G Maier, Jennifer Thompson, Danny W Wilson, Wai-Hong Tham, Tony Triglia, Alex Gout, Terence P Speed, James G Beeson, Julie Healer, Alan F Cowman

Journal article  |  2011  |  Infection and Immunity

Too much or too little scepticism?

T Speed

Journal article  |  2011  |  Significance

Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development

Marilyn B Renfree, Anthony T Papenfuss, Janine E Deakin, James Lindsay, Thomas Heider, Katherine Belov, Willem Rens, Paul D Waters, Elizabeth A Pharo, Geoff Shaw, Emily Swwong, Christophe M Lefevre, Kevin R Nicholas, Yoko Kuroki, Matthew J Wakefield, Kyall R Zenger, Chenwei Wang, Malcolm Ferguson-Smith, Frank W Nicholas, Danielle Hickford, et al.

Journal article  |  2011  |  Genome Biology

A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments

MD Robinson, DP De Souza, WW Keen, EC Saunders, MJ McConville, TP Speed, VA Likić

Book Chapter  |  2011

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation (vol 20, pg 1719, 2010)

Mark D Robinson, Clare Stirzaker, Aaron L Statham, Marcel W Coolen, Jenny Z Song, Shalima S Nair, Dario Strbenac, Terence P Speed, Susan J Clark

Journal article  |  2011  |  Genome Research

Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing

Wenyi Wang, Peidong Shen, Sreedevi Thiyagarajan, Shengrong Lin, Curtis Palm, Rita Horvath, Thomas Klopstock, David Cutler, Lynn Pique, Iris Schrijver, Ronald W Davis, Michael Mindrinos, Terence P Speed, Curt Scharfe

Journal article  |  2011  |  Nucleic Acids Research

Genome-Wide Analysis of Glucocorticoid Receptor Binding Regions in Adipocytes Reveal Gene Network Involved in Triglyceride Homeostasis

Chi-Yi Yu, Oleg Mayba, Joyce V Lee, Joanna Tran, Charlie Harris, Terence P Speed, Jen-Chywan Wang

Journal article  |  2010  |  PLoS ONE

A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility

Iris KL Tan, Leanne Mackin, Nancy Wang, Anthony T Papenfuss, Colleen M Elso, Michelle P Ashton, Fiona Quirk, Belinda Phipson, Melanie Bahlo, Terence P Speed, Gordon K Smyth, Grant Morahan, Thomas C Brodnicki

Journal article  |  2010  |  Genome Research

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

Mark D Robinson, Clare Stirzaker, Aaron L Statham, Marcel W Coolen, Jenny Z Song, Shalima S Nair, Dario Strbenac, Terence P Speed, Susan J Clark

Journal article  |  2010  |  Genome Research

Regulation of specific target genes and biological responses by estrogen receptor subtype agonists

Dale C Leitman, Sreenivasan Paruthiyil, Omar I Vivar, Elise F Saunier, Candice B Herber, Isaac Cohen, Mary Tagliaferri, Terence P Speed

Journal article  |  2010  |  Current Opinion in Pharmacology

The unreasonable effectiveness of statistics in genome science

T Speed

Journal article  |  2010  |  Significance

Protocol matters: which methylome are you actually studying?

Mark D Robinson, Aaron L Statham, Terence P Speed, Susan J Clark

Journal article  |  2010  |  Epigenomics

Conserved Role of unc-79 in Ethanol Responses in Lightweight Mutant Mice

David J Speca, Daisuke Chihara, Amir M Ashique, M Scott Bowers, Jonathan T Pierce-Shimomura, Jungsoo Lee, Nusrat Rabbee, Terence P Speed, Rodrigo J Gularte, James Chitwood, Juan F Medrano, Mark Liao, James M Sonner, Edmond I Eger, Andrew S Peterson, Steven L McIntire

Journal article  |  2010  |  PLoS Genetics

Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes

Catherine L Carmichael, Ella J Wilkins, Henrik Bengtsson, Marshall S Horwitz, Terence P Speed, Paul C Vincent, Graham Young, Christopher N Hahn, Robert Escher, Hamish S Scott

Journal article  |  2010  |  British Journal of Haematology

Model Averaging for Biological Networks with Prior Information

S Mukherjee, TP Speed, SM Hill

Book Chapter  |  2010

Estrogen Receptor beta Binds to and Regulates Three Distinct Classes of Target Genes

Omar I Vivar, Xiaoyue Zhao, Elise F Saunier, Chandi Griffin, Oleg S Mayba, Mary Tagliaferri, Isaac Cohen, Terence P Speed, Dale C Leitman

Journal article  |  2010  |  Journal of Biological Chemistry

Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer

Anna Lapuk, Henry Marr, Lakshmi Jakkula, Helder Pedro, Sanchita Bhattacharya, Elizabeth Purdom, Zhi Hu, Ken Simpson, Lior Pachter, Steffen Durinck, Nicholas Wang, Bahram Parvin, Gerald Fontenay, Terence Speed, James Garbe, Martha Stampfer, Hovig Bayandorian, Shannon Dorton, Tyson A Clark, Anthony Schweitzer, et al.

Journal article  |  2010  |  Molecular Cancer Research

PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer

Sherene Loi, Benjamin Haibe-Kains, Samira Majjaj, Francoise Lallemand, Virginie Durbecq, Denis Larsimont, Ana M Gonzalez-Angulo, Lajos Pusztai, W Fraser Symmans, Alberto Bardelli, Paul Ellis, Andrew NJ Tutt, Cheryl E Gillett, Bryan T Hennessy, Gordon B Mills, Wayne A Phillips, Martine J Piccart, Terence P Speed, Grant A McArthur, Christos Sotiriou

Journal article  |  2010  |  Proceedings of the National Academy of Sciences of the United States of America

TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays

Henrik Bengtsson, Pierre Neuvial, Terence P Speed

Journal article  |  2010  |  BMC Bioinformatics

International network of cancer genome projects

Thomas J Hudson, Warwick Anderson, Axel Aretz, Anna D Barker, Cindy Bell, Rosa R Bernabe, MK Bhan, Fabien Calvo, Iiro Eerola, Daniela S Gerhard, Alan Guttmacher, Mark Guyer, Fiona M Hemsley, Jennifer L Jennings, David Kerr, Peter Klatt, Patrik Kolar, Jun Kusuda, David P Lane, Frank Laplace, et al.

Journal article  |  2010  |  Nature

Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis

Manasa Ramakrishna, Louise H Williams, Samantha E Boyle, Jennifer L Bearfoot, Anita Sridhar, Terence P Speed, Kylie L Gorringe, Ian G Campbell

Journal article  |  2010  |  PLoS One

Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network.

Elizabeth J Atkinson, Shannon K McDonnell, John S Witte, Dana C Crawford, Yiping Fan, Brooke Fridley, Dalin Li, Lang Li, Andrei Rodin, Wolfgang Sadee, Terry Speed, Scott T Weiss, Jun Yang, Laura Yerges, Daniel J Schaid

Conference Proceedings  |  2010  |  Pharmacogenomics

The Pharmacogenomics Research Network holds a statistical analysis workshop every other year to share novel statistical methods an..

Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity

Marcel W Coolen, Clare Stirzaker, Jenny Z Song, Aaron L Statham, Zena Kassir, Carlos S Moreno, Andrew N Young, Vijay Varma, Terence P Speed, Mark Cowley, Paul Lacaze, Warren Kaplan, Mark D Robinson, Susan J Clark

Journal article  |  2010  |  Nature Cell Biology

Unliganded estrogen receptor-beta regulation of genes is inhibited by tamoxifen

Nitzan Levy, Sreenivasan Paruthiyil, Xiaoyue Zhao, Omar I Vivar, Elise F Saunier, Chandi Griffin, Mary Tagliaferri, Isaac Cohen, Terence P Speed, Dale C Leitman

Journal article  |  2010  |  Molecular and Cellular Endocrinology

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

Roel GW Verhaak, Katherine A Hoadley, Elizabeth Purdom, Victoria Wang, Yuan Qi, Matthew D Wilkerson, C Ryan Miller, Li Ding, Todd Golub, Jill P Mesirov, Gabriele Alexe, Michael Lawrence, Michael O'Kelly, Pablo Tamayo, Barbara A Weir, Stacey Gabriel, Wendy Winckler, Supriya Gupta, Lakshmi Jakkula, Heidi S Feiler, et al.

Journal article  |  2010  |  Cancer Cell

Time for DNA Disclosure

DE Krane, V Bahn, D Balding, B Barlow, H Cash, BL Desportes, P D'Eustachio, K Devlin, TE Doom, I Dror, S Ford, C Funk, J Gilder, G Hampikian, K Inman, A Jamieson, PE Kent, R Koppl, I Kornfield, S Krimsky, et al.

Report  |  2009  |  Science

Gene set enrichment analysis made simple

Rafael A Irizarry, Chi Wang, Yun Zhou, Terence P Speed

Journal article  |  2009  |  Statistical Methods in Medical Research

Microarrays

Terry Speed, Hongyu Zhao

Journal article  |  2009  |  Statistical Methods in Medical Research

Multiple testing and its applications to microarrays

Yongchao Ge, Stuart C Sealfon, Terence P Speed

Journal article  |  2009  |  Statistical Methods in Medical Research

Expression profiling of a hemopoietic cell survival transcriptome implicates osteopontin as a functional prognostic factor in AML

Jason A Powell, Daniel Thomas, Emma F Barry, Chung H Kok, Barbara J McClure, Anna Tsykin, L Bik To, Anna Brown, Ian D Lewis, Kirsten Herbert, Gregory J Goodall, Terence P Speed, Norio Asou, Bindya Jacob, Motomi Osato, David N Haylock, Susan K Nilsson, Richard J D'Andrea, Angel F Lopez, Mark A Guthridge

Journal article  |  2009  |  Blood

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

Journal article  |  2009  |  Bioinformatics

Drug and Cell Type-Specific Regulation of Genes with Different Classes of Estrogen Receptor beta-Selective Agonists

Sreenivasan Paruthiyil, Aleksandra Cvoro, Xiaoyue Zhao, Zhijin Wu, Yunxia Sui, Richard E Staub, Scott Baggett, Candice B Herber, Chandi Griffin, Mary Tagliaferri, Heather A Harris, Isaac Cohen, Leonard F Bjeldanes, Terence P Speed, Fred Schaufele, Dale C Leitman

Journal article  |  2009  |  PLoS ONE

Differential splicing using whole-transcript microarrays

Mark D Robinson, Terence P Speed

Journal article  |  2009  |  BMC Bioinformatics

Sir2 Paralogues Cooperate to Regulate Virulence Genes and Antigenic Variation in Plasmodium falciparum

Christopher J Tonkin, Celine K Carret, Manoj T Duraisingh, Till S Voss, Stuart A Ralph, Mirja Hommel, Michael F Duffy, Liliana Mancio da Silva, Artur Scherf, Alasdair Ivens, Terence P Speed, James G Beeson, Alan F Cowman

Journal article  |  2009  |  PLoS Biology

A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods

Henrik Bengtsson, Amrita Ray, Paul Spellman, Terence P Speed

Journal article  |  2009  |  Bioinformatics

On Gene Ranking Using Replicated Microarray Time Course Data

Yu Chuan Tai, Terence P Speed

Conference Proceedings  |  2009  |  Biometrics

Temporal Global Expression Data Reveal Known and Novel Salicylate-Impacted Processes and Regulators Mediating Powdery Mildew Growth and Reproduction on Arabidopsis

Divya Chandran, Yu Chuan Tai, Gregory Hather, Julia Dewdney, Carine Denoux, Diane G Burgess, Frederick M Ausubel, Terence P Speed, Mary C Wildermuth

Journal article  |  2009  |  Plant Physiology

Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements

Lonnele J Ball, Nitzan Levy, Xiaoyue Zhao, Chandi Griffin, Mary Tagliaferri, Isaac Cohen, William A Ricke, Terence P Speed, Gary L Firestone, Dale C Leitman

Journal article  |  2009  |  Molecular and Cellular Endocrinology

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

Journal article  |  2009  |  Bioinformatics

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

Andrew J Pask, Anthony T Papenfuss, Eleanor I Ager, Kaighin A Mccoll, Terence P Speed, Marilyn B Renfree

Journal article  |  2009  |  Genome Biology

Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments

Yunxia Sui, Xiaoyue Zhao, Terence P Speed, Zhijin Wu

Journal article  |  2009  |  Journal of Computational Biology

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

L Chin, M Meyerson, K Aldape, D Bigner, T Mikkelsen, S VandenBerg, A Kahn, R Penny, ML Ferguson, DS Gerhard, G Getz, C Brennan, BS Taylor, W Winckler, P Park, M Ladanyi, KA Hoadley, RGW Verhaak, DN Hayes, Paul T Spellman, et al.

Journal article  |  2008  |  Nature

Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians

JP Rubio, J Stankovich, J Field, N Tubridy, M Marriott, C Chapman, M Bahlo, D Perera, LJ Johnson, BD Tait, MD Varney, TP Speed, BV Taylor, SJ Foote, H Butzkueven, TJ Kilpatrick

Journal article  |  2008  |  Genes and Immunity

Network inference using informative priors

Sach Mukherjee, Terence P Speed

Journal article  |  2008  |  Proceedings of the National Academy of Sciences

Journal of Computational Biology: Preface

T Speed

Conference Proceedings  |  2008  |  Journal of Computational Biology

Preface

Terry Speed

Book  |  2008  |  Journal of Computational Biology

FIRMA: a method for detection of alternative splicing from exon array data

E Purdom, KM Simpson, MD Robinson, JG Conboy, AV Lapuk, TP Speed

Journal article  |  2008  |  Bioinformatics

Quality Assessment for Short Oligonucleotide Microarray Data

Julia Brettschneider, Francois Collin, Benjamin M Bolstad, Terence P Speed

Journal article  |  2008  |  Technometrics

Quality Assessment for Short Oligonucleotide Microarray Data Rejoinder

Julia Brettschneider, Francois Collin, Benjamin M Bolstad, Terence P Speed

Journal article  |  2008  |  Technometrics

Integrative analysis of RUNX1 downstream pathways and target genes

Joelle Michaud, Ken M Simpson, Robert Escher, Karine Buchet-Poyau, Tim Beissbarth, Catherine Carmichael, Matthew E Ritchie, Frederic Schuetz, Ping Cannon, Marjorie Liu, Xiaofeng Shen, Yoshiaki Ito, Wendy H Raskind, Marshall S Horwitz, Motomi Osato, David R Turner, Terence P Speed, Maria Kavallaris, Gordon K Smyth, Hamish S Scott

Journal article  |  2008  |  BMC Genomics

Variants of ST8SIA1 Are Associated with Risk of Developing Multiple Sclerosis

Seema Husain, Cagri Yildirim-Toruner, Justin P Rubio, Judith Field, Marvin Schwalb, Stuart Cook, Marcella Devoto, Emilia Vitale

Journal article  |  2008  |  PLoS One

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm (vol 6, pg e27, 2008)

Xiao-yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, et al.

Journal article  |  2008  |  PLoS Biology

Some step-down procedures controlling the false discovery rate under dependence

Yon-Chao Ge, Stuart C Sealfon, Terence P Speed

Journal article  |  2008  |  Statistica Sinica

Chromosome Maps

TP Speed, H Zhao

Book Chapter  |  2008

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission

Ariel T Arthur, Patricia J Armati, Chris Bye, Robert NS Heard, Graeme J Stewart, John D Pollard, David R Booth

Journal article  |  2008  |  BMC Medical Genetics

Estimation and assessment of raw copy numbers at the single locus level

H Bengtsson, R Irizarry, B Carvalho, TP Speed

Journal article  |  2008  |  Bioinformatics

TRANSCRIPTION FACTOR BINDING SITE PREDICTION WITH MULTIVARIATE GENE EXPRESSION DATA

Nancy R Zhang, Mary C Wildermuth, Terence P Speed

Journal article  |  2008  |  The Annals of Applied Statistics

Differential regulation of native estrogen receptor-regulatory elements by estradiol, tamoxifen, and raloxifene

Nitzan Levy, Dierdre Tatomer, Candice B Herber, Xiaoyue Zhao, Hui Tang, Toby Sargeant, Lonnele J Ball, Jonathan Summers, Terence P Speed, Dale C Leitman

Journal article  |  2008  |  Molecular Endocrinology

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

Xiao-Yong Li, Stewart MacArthur, Richard Bourgon, David Nix, Daniel A Pollard, Venky N Iyer, Aaron Hechmer, Lisa Simirenko, Mark Stapleton, Cris L Luengo Hendriks, Hou Cheng Chu, Nobuo Ogawa, William Inwood, Victor Sementchenko, Amy Beaton, Richard Weiszmann, Susan E Celniker, David W Knowles, Tom Gingeras, Terence P Speed, et al.

Journal article  |  2008  |  PLoS Biology

An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss

Michel Guipponi, Min-Yen Toh, Justin Tan, Daeho Park, Kelly Hanson, Ester Ballana, David Kwong, Ping ZF Cannon, Qingyu Wu, Alex Gout, Mauro Delorenzi, Terence P Speed, Richard JH Smith, Henrik H Dahl, Michael Petersen, Rohan D Teasdale, Xavier Estivill, Woo Jin Park, Hamish S Scott

Journal article  |  2008  |  Human Mutation

SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians

RK Burfoot, CJ Jensen, J Field, J Stankovich, MD Varney, LJ Johnson, H Butzkueven, D Booth, M Bahlo, BD Tait, BV Taylor, TP Speed, R Heard, GJ Stewart, SJ Foote, TJ Kilpatrick, JP Rubio

Journal article  |  2008  |  Tissue Antigens

The power of two-locus affected sib-pair linkage analysis to detect interacting disease loci

Ingileif B Hallgrimsdottir, Terence P Speed

Journal article  |  2008  |  Genetic Epidemiology

Comprehensive survey of gain and loss in Plasmodium falciparum clinical isolates.

CK Carret, H Bengtsson, T Speed, C Newbold, AC Ivens

Conference Proceedings  |  2008  |  INTERNATIONAL JOURNAL FOR PARASITOLOGY

A Holm-type procedure controlling the false discovery rate

Yongchao Ge, Stuart C Sealfon, Chi-Hong Tseng, Terence P Speed

Journal article  |  2007  |  Statistics & Probability Letters

Evidence for a common role for the serine-type Plasmodium falciparum serine repeat antigen proteases: Implications for vaccine and drug design

Joanne E McCoubrie, Susanne K Miller, Tobias Sargeant, Robert T Good, Anthony N Hodder, Terence P Speed, Tania F de Koning-Ward, Brendan S Crabb

Journal article  |  2007  |  Infection and Immunity

Analysis of gene expression during neurite outgrowth and regeneration

Moriah L Szpara, Karen Vranizan, Yu Chuan Tai, Corey S Goodman, Terence P Speed, John Ngai

Journal article  |  2007  |  BMC Neuroscience

Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb-MuvB/dREAM complex in proliferating cells

Daphne Georlette, Soyeon Ahn, David M MacAlpine, Evelyn Cheung, Peter W Lewis, Eileen L Beall, Stephen P Bell, Terry Speed, J Robert Manak, Michael R Botchan

Journal article  |  2007  |  Genes & Development

A comparison of Affymetrix gene expression arrays

Mark D Robinson, Terence P Speed

Journal article  |  2007  |  BMC Bioinformatics

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

Journal article  |  2007  |  BMC Bioinformatics

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface

T Speed

Conference Proceedings  |  2007  |  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system

Katherine Belov, Claire E Sanderson, Janine E Deakin, Emily SW Wong, Daniel Assange, Kaighin A McColl, Alex Gout, Bernard de Bono, Alexander D Barrow, Terence P Speed, John Trowsdale, Anthony T Papenfuss

Journal article  |  2007  |  Genome Research

Multiple transcription factor elements collaborate with estrogen receptor alpha to activate an inducible estrogen response element in the NKG2E gene

Nitzan Levy, Xiaoyue Zhao, Hui Tang, Robert B Jaffe, Terence P Speed, Dale C Leitman

Journal article  |  2007  |  Endocrinology

Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences

Tarjei S Mikkelsen, Matthew J Wakefield, Bronwen Aken, Chris T Amemiya, Jean L Chang, Shannon Duke, Manuel Garber, Andrew J Gentles, Leo Goodstadt, Andreas Heger, Jerzy Jurka, Michael Kamal, Evan Mauceli, Stephen MJ Searle, Ted Sharpe, Michelle L Baker, Mark A Batzer, Panayiotis V Benos, Katherine Belov, Michele Clamp, et al.

Journal article  |  2007  |  Nature

Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data

Benilton Carvalho, Henrik Bengtsson, Terence P Speed, Rafael A Irizarry

Journal article  |  2007  |  Biostatistics

Analysis of extended HLA haplotypes in multiple sclerosis and narcolepsy families confirms a predisposing effect for the class I region in Tasmanian MS patients

Justin P Rubio, Melanie Bahlo, Jim Stankovich, Rachel K Burfoot, Laura J Johnson, Stewart Huxtable, Helmut Butzkueven, Ling Lin, Bruce V Taylor, Terence P Speed, Trevor J Kilpatrick, Emmanuel Mignot, Simon J Foote

Journal article  |  2007  |  Immunogenetics

SNPs on chips: The hidden genetic code in expression arrays

Elzbieta Sliwerska, Fan Meng, Terence P Speed, Edward G Jones, William E Bunney, Huda Akil, Stanley J Watson, Margit Burmeister

Journal article  |  2007  |  Biological Psychiatry

Global analyses of mRNA translational control during early Drosophila embryogenesis

Xiaoli Qin, Soyeon Ahn, Terence P Speed, Gerald M Rubin

Journal article  |  2007  |  Genome Biology

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

Richard M Neve, Koei Chin, Jane Fridlyand, Jennifer Yeh, Frederick L Baehner, Tea Fevr, Laura Clark, Nora Bayani, Jean-Philippe Coppe, Frances Tong, Terry Speed, Paul T Spellman, Sandy DeVries, Anna Lapuk, Nick J Wang, Wen-Lin Kuo, Jackie L Stilwell, Daniel Pinkel, Donna G Albertson, Frederic M Waldman, et al.

Journal article  |  2006  |  Cancer Cell

Evolution and comparative analysis of the MHC Class III inflammatory region

Janine E Deakin, Anthony T Papenfuss, Katherine Belov, Joseph GR Cross, Penny Coggill, Sophie Palmer, Sarah Sims, Terence P Speed, Stephan Beck, Jennifer A Marshall Graves

Journal article  |  2006  |  BMC Genomics

Functional genomic analysis of oligodendrocyte differentiation

Jason C Dugas, Yu Chuan Tai, Terence P Speed, John Ngai, Ben A Barres

Journal article  |  2006  |  Journal of Neuroscience

Proximal genomic localization of STATI binding and regulated transcriptional activity

Samuel Wormald, Douglas J Hilton, Gordon K Smyth, Terence P Speed

Journal article  |  2006  |  BMC Genomics

Mapping of the Plasmodium chabaudi resistance locus char2

Enmoore Lin, Tony Pappenfuss, Rachel B Tan, Danielle Senyschyn, Melanie Bahlo, Terence P Speed, Simon J Foote

Journal article  |  2006  |  Infection and Immunity

A multivariate empirical Bayes statistic for replicated microarray time course data

Yu Chuan Tai, Terence P Speed

Journal article  |  2006  |  The Annals of Statistics

Regulation of apicomplexan actin-based motility

Jake Baum, Anthony T Papenfuss, Buzz Baum, Terence P Speed, Alan F Cowman

Journal article  |  2006  |  Nature Reviews Microbiology

Incorporating interference into linkage analysis for experimental crosses

NJ Armstrong, MS McPeek, TP Speed

Journal article  |  2006  |  Biostatistics

Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders.

MP Vawter, H Tomita, F Meng, B Bolstad, J Li, S Evans, P Choudary, M Atz, L Shao, C Neal, DM Walsh, M Burmeister, T Speed, R Myers, EG Jones, SJ Watson, H Akil, WE Bunney

Journal article  |  2006  |  Molecular Psychiatry

Mitochondrial defects in gene expression have been implicated in the pathophysiology of bipolar disorder and schizophrenia. We hav..

Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders

MP Vawter, H Tomita, F Meng, B Bolstad, J Li, S Evans, P Choudary, M Atz, L Shao, C Neal, DM Walsh, M Burmeister, T Speed, R Myers, EG Jones, SJ Watson, H Akil, WE Bunney

Journal article  |  2006  |  Molecular Psychiatry

Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malaria parasite Plasmodium falciparum

Paul R Gilson, Thomas Nebl, Damjan Vukcevic, Robert L Moritz, Tobias Sargeant, Terence P Speed, Louis Schofield, Brendan S Crabb

Journal article  |  2006  |  Molecular & Cellular Proteomics

The comparative roles of suppressor of cytokine signaling-1 and-3 in the inhibition and desensitization of cytokine signaling

S Wormald, JG Zhang, DL Krebes, LA Mielke, J Silver, WS Alexander, TP Speed, NA Nicola, DJ Hilton

Journal article  |  2006  |  Journal of Biological Chemistry

Mind the gap: analysis of marker-assisted breeding strategies for inbred mouse strains

NJ Armstrong, TC Brodnicki, TP Speed

Journal article  |  2006  |  Mammalian Genome

Expression profiling in primates reveals a rapid evolution of human transcription factors

Y Gilad, A Oshlack, GK Smyth, TP Speed, KP White

Journal article  |  2006  |  Nature

Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex

K Belov, JE Deakin, AT Papenfuss, ML Baker, SD Melman, HV Siddle, N Gouin, DL Goode, TJ Sargeant, MD Robinson, MJ Wakefield, S Mahony, JGR Cross, PV Benos, PB Samollow, TP Speed, JAM Graves, RD Miller

Journal article  |  2006  |  PLoS Biology

Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data

M Bahlo, J Stankovich, TP Speed, JP Rubio, RK Burfoot, SJ Foote

Journal article  |  2006  |  Human Genetics

On the utility of data from the International HapMap Project for Australian association studies

J Stankovich, CJ Cox, RB Tan, DS Montgomery, SJ Huxtable, JP Rubio, MG Ehm, L Johnson, H Butzkueven, TJ Kilpatrick, TP Speed, AD Roses, M Bahlo, SJ Foote

Journal article  |  2006  |  Human Genetics

A genetic screen for behavioral mutations that perturb dopaminergic homeostasis in mice

DJ Speca, N Rabbee, D Chihara, TP Speed, AS Peterson

Journal article  |  2006  |  Genes, Brain and Behavior

Long-term effect of therapeutic laser photocoagulation on gene expression in the eye

Nicolette Binz, Caroline E Graham, Ken Simpson, Yvonne KY Lai, Wei-Yong Shen, Chooi-May Lai, Terence P Speed, P Elizabeth Rakoczy

Journal article  |  2006  |  The FASEB Journal

Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites

TJ Sargeant, M Marti, E Caler, JM Carlton, K Simpson, TP Speed, AF Cowman

Journal article  |  2006  |  Genome Biology

A genotype calling algorithm for affymetrix SNP arrays

N Rabbee, TP Speed

Journal article  |  2006  |  Bioinformatics

A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics

VA Likic, PR Gooley, TP Speed, EE Strehler

Journal article  |  2005  |  Protein Science

Annotation of the opossum major histocompatibility complex and analysis of conserved non-coding regions

AT Papenfuss, K Belov, JE Deakin, TP Speed, JAM Graves, RD Miller

Conference Proceedings  |  2005  |  TISSUE ANTIGENS

Haplotype mapping in the HLA complex implicates variation in the MOG gene in susceptibility to multiple sclerosis

JP Rubio, RK Burfoot, LJ Johnson, J Stankovich, C Jensen, R Meyhandan, M Bahlo, H Butzkueven, N Tubridy, M Marriott, C Chapman, B Taylor, D Booth, R Heard, GJ Stewart, TP Speed, TJ Kilpatrick, SJ Foote

Conference Proceedings  |  2005  |  TISSUE ANTIGENS

The wound repair response controls outcome to cutaneous leishmaniasis

A Sakthianandeswaren, CM Elso, K Simpson, JM Curtis, B Kumar, TP Speed, E Handman, SJ Foote

Journal article  |  2005  |  Proceedings of the National Academy of Sciences of the United States of America

Gene expression and genotyping studies implicate the interleukin 7 receptor in the pathogenesis of primary progressive multiple sclerosis

DR Booth, AT Arthur, SM Teutsch, C Bye, J Rubio, PJ Armati, JD Pollard, RNS Heard, GJ Stewart

Journal article  |  2005  |  Journal of Molecular Medicine

Colon cancer prognosis prediction by gene expression profiling

A Barrier, A Lemoine, PY Boelle, C Tse, D Brault, F Chiappini, J Breittschneider, F Lacaine, S Houry, M Huguier, MJ Van der Laan, T Speed, B Debuire, A Flahault, S Dudoit

Journal article  |  2005  |  Oncogene

SNPs on chips: A word of caution on the hidden genetic code in expression arrays

M Burmeister, F Meng, E Sliwerska, TP Speed, EG Jones, WE Bunney, H Akil, SJ Watson

Conference Proceedings  |  2005  |  AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Identifying nineteenth century genealogical links from genotypes

J Stankovich, M Bahlo, JP Rubio, CR Wilkinson, R Thomson, A Banks, M Ring, SJ Foote, TP Speed

Journal article  |  2005  |  Human Genetics

Finding short DNA motifs using permuted Markov models

XY Zhao, HY Huang, TP Speed

Conference Proceedings  |  2005  |  Journal of Computational Biology

Evidence for a novel glaucoma locus at chromosome 3p21-22

PN Baird, SJ Foote, DA Mackey, J Craig, TP Speed, A Bureau

Journal article  |  2005  |  Human Genetics

A systematic approach for comprehensive T-cell epitope discovery using peptide libraries

T Beissbarth, JA Tye-Din, GK Smyth, TP Speed, RP Anderson

Journal article  |  2005  |  Bioinformatics

A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays

KM Simpson, J Baum, RT Good, EA Winzeler, AF Cowman, TP Speed

Journal article  |  2005  |  International Journal for Parasitology

Evolution of the relaxin-like peptide family

TN Wilkinson, TP Speed, GW Tregear, RA Bathgate

Journal article  |  2005  |  BMC Evolutionary Biology

Rooting a phylogenetic tree with nonreversible substitution models

VB Yap, T Speed

Journal article  |  2005  |  BMC Evolutionary Biology

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

MH Dai, PL Wang, AD Boyd, G Kostov, B Athey, EG Jones, WE Bunney, RM Myers, TP Speed, H Akil, SJ Watson, F Meng

Journal article  |  2005  |  Nucleic Acids Research

NUSE and RLE: Quality assessment of oligonucleotide microarray data to quantify systemic variation.

F Collin, AL Asare, SA Kolchinsky, TP Speed, VL Seyert-Margolis

Conference Proceedings  |  2005  |  CLINICAL IMMUNOLOGY

Evolution of the relaxin-like peptide family - From neuropeptide to reproduction

TN Wilkinson, TP Speed, GW Tregear, RAD Bathgate

Conference Proceedings  |  2005  |  Annals of The New York Academy of Sciences

Coevolution of the relaxin-like peptides and their receptors

TN Wilkinson, TP Speed, GW Tregear, RAD Bathgate

Conference Proceedings  |  2005  |  Annals of The New York Academy of Sciences

Multiple sclerosis: a haplotype association study.

Simon J Foote, Justin P Rubio, Melanie Bahlo, Trevor J Kilpatrick, Terence P Speed, Jim Stankovich, Rachel Burfoot, Helmut Butzkueven, Laura Johnson, Chris Wilkinson, Bruce Taylor, Michele Sale, Ingrid AF van der Mei, Joanne L Dickinson, Patricia Groom

Book Chapter  |  2005  |  Novartis Foundation symposium

Results are presented from a genomewide haplotype association study on multiple sclerosis (MS) cases from Tasmania, an island stat..

Deconvolution of sparse positive spikes

LM Li, TP Speed

Journal article  |  2004  |  Journal of Computational and Graphical Statistics

The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: The impact of GC content and reconciliation of gene and species trees

R Bourgon, M Delorenzi, T Sargeant, AN Hodder, BS Crabb, TP Speed

Journal article  |  2004  |  Mol. Biol. Evol.

Power calculations for selective genotyping in QTL mapping in backcross mice

N Rabbee, D Speca, NJ Armstrong, TP Speed

Journal article  |  2004  |  Genetical Research

Discussions on "A Bayesian approach to DNA sequence segmentation"

C Lawrence, I Auger, M Gupta, JS Liu, T Speed, JL Thorne

Journal article  |  2004  |  Biometrics

A Bayesian approach to DNA sequence segmentation - Discussion

T Speed

Journal article  |  2004  |  Biometrics

Spatial patterns of gene expression in the olfactory bulb

DM Lin, YH Yang, JA Scolnick, LJ Brunet, H Marsh, V Peng, Y Okazaki, Y Hayashizaki, TP Speed, J Ngai

Journal article  |  2004  |  Proceedings of the National Academy of Sciences

A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography

RL Moritz, H Ji, F Schutz, LM Connolly, EA Kapp, TP Speed, RJ Simpson

Journal article  |  2004  |  Analytical Chemistry

Statistical modeling of sequencing errors in SAGE libraries

Tim Beissbarth, Lavinia Hyde, Gordon K Smyth, Chris Job, Wee-Ming Boon, Seong-Seng Tan, Hamish S Scott, Terence P Speed

Journal article  |  2004  |  Bioinformatics

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

T Beissbarth, TP Speed

Journal article  |  2004  |  Bioinformatics

Finding short DNA motifs using permuted Markov models

X Zhao, H Huang, TP Speed

Conference Proceedings  |  2004  |  Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Evaluation of the measles clinical case definition

SS Hutchins, MJ Papania, R Amler, EF Maes, M Grabowsky, K Bromberg, V Glasglow, T Speed, WJ Bellini, WA Orenstein

Journal article  |  2004  |  The Journal of Infectious Diseases

Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis

JP Rubio, M Bahlo, N Tubridy, J Stankovich, R Burfoot, H Butzkueven, C Chapman, L Johnson, M Marriott, G Mraz, B Tait, C Wilkinson, B Taylor, TP Speed, SJ Foote, TJ Kilpatrick

Journal article  |  2004  |  Human Genetics

Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury

PG Marciano, J Brettschneider, E Manduchi, JE Davis, S Eastman, R Raghupathi, KE Saatman, TP Speed, CJ Stoeckert, JH Eberwine, TK McIntosh

Journal article  |  2004  |  Journal of Neuroscience

A benchmark for affymetrix GeneChip expression measures

LM Cope, RA Irizarry, HA Jaffee, ZJ Wu, TP Speed

Journal article  |  2004  |  Bioinformatics

Modeling DNA base substitution in large genomic regions from two organisms

VB Yap, TP Speed

Journal article  |  2004  |  Journal of Molecular Evolution

Experimental design and low-level analysis of microarray data

BM Bolstad, F Collin, KM Simpson, RA Irizarry, TP Speed

Book  |  2004  |  International Review of Neurobiology

Normalization of cDNA microarray data

GK Smyth, T Speed

Journal article  |  2003  |  Methods

Ancestral inference in population genetics models with selection - Discussion

M Bahlo, R Thomson, T Speed

Journal article  |  2003  |  AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS

Deriving statistical models for predicting peptide tandem MS product ion intensities

F Schutz, EA Kapp, RJ Simpson, TP Speed

Journal article  |  2003  |  Biochemical Society Transactions

Discussion

M Bahlo, R Thomson, T Speed

Journal article  |  2003  |  Australian and New Zealand Journal of Statistics

Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5

AN Hodder, DR Drew, VC Epa, M Delorenzi, R Bourgon, SK Miller, RL Moritz, DF Frecklington, RJ Simpson, TP Speed, RN Pike, BS Crabb

Journal article  |  2003  |  J. Biol. Chem.

Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation

EA Kapp, F Schutz, GE Reid, JS Eddes, RL Moritz, RAJ O'Hair, TP Speed, RJ Simpson

Journal article  |  2003  |  Analytical Chemistry

A new rodent model to assess blood stage immunity to the Plasmodium falciparum antigen merozoite surface protein 1(19) reveals a protective role for invasion inhibitory antibodies

TF de Koning-Ward, RA O'Donnell, DR Drew, R Thomson, TP Speed, BS Crabb

Journal article  |  2003  |  The Journal of Experimental Medicine

Spotted long oligonucleotide arrays for human gene expression analysis

A Barczak, MW Rodriguez, K Hanspers, LL Koth, YC Tai, BM Bolstad, TP Speed, DJ Erle

Journal article  |  2003  |  Genome Research

Resampling-based multiple testing for microarray data analysis

YC Ge, S Dudoit, TP Speed

Journal article  |  2003  |  Test

Analysis of gene expression in the developing mouse retina

E Diaz, YH Yang, T Ferreira, KC Loh, Y Okazaki, Y Hayashizaki, M Tessier-Lavigne, TP Speed, J Ngai

Journal article  |  2003  |  Proceedings of the National Academy of Sciences

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

RA Irizarry, B Hobbs, F Collin, YD Beazer-Barclay, KJ Antonellis, U Scherf, TP Speed

Journal article  |  2003  |  Biostatistics

Argon laser photocoagulation-induced modification of gene expression in the retina

AS Wilson, BG Hobbs, WY Shen, TP Speed, U Schmidt, CG Begley, PE Rakoczy

Journal article  |  2003  |  Investigative Opthalmology & Visual Science

Summaries of affymetrix GeneChip probe level data

RA Irizarry, BM Bolstad, F Collin, LM Cope, B Hobbs, TP Speed

Journal article  |  2003  |  Nucleic Acids Research

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

BM Bolstad, RA Irizarry, M Astrand, TP Speed

Journal article  |  2003  |  Bioinformatics

Low-level analyses of microarray data

T Speed

Conference Proceedings  |  2003  |  Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycle

SK Miller, RT Good, DR Drew, M Delorenzi, PR Sanders, AN Hodder, TP Speed, AF Cowman, TF de Koning-Ward, BS Crabb

Journal article  |  2002  |  Journal of Biological Chemistry

Improving linkage analysis in outcrossed forest trees - An example from Acacia mangium

PA Butcher, ER Williams, D Whitaker, S Ling, TP Speed, GF Moran

Journal article  |  2002  |  Theoretical and Applied Genetics

John W. Tukey's contributions to analysis of variance

TP Speed

Journal article  |  2002  |  The Annals of Statistics

Molecular analysis of gene expression in the developing pontocerebellar projection system

E Diaz, YC Ge, YH Yang, KC Loh, TA Serafini, Y Okazaki, Y Hayashizaki, TP Speed, J Ngai, P Scheiffele

Journal article  |  2002  |  Neuron

SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data

P Banerjee, M Bahlo, JR Schwartz, GG Loots, KA Houston, I Dubchak, TP Speed, EM Rubin

Journal article  |  2002  |  Mammalian Genome

Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E mu-v-abl transgenic mice

RCA Symons, MJ Daly, J Fridlyand, TP Speed, WD Cook, S Gerondakis, AW Harris, SJ Foote

Journal article  |  2002  |  Proceedings of the National Academy of Sciences

Design issues for cDNA microarray experiments

YH Yang, T Speed

Journal article  |  2002  |  Nature Reviews Genetics

Genes for glycosylphosphatidylinositol toxin biosynthesis in Plasmodium falciparum

M Delorenzi, A Sexton, H Shams-Eldin, RT Schwarz, T Speed, L Schofield

Journal article  |  2002  |  Infection and Immunity

The microarray: Potential applications for ophthalmic research

AS Wilson, BG Hobbs, TP Speed, PE Rakoczy

Journal article  |  2002  |  Molecular Vision

Genetic dissection of the human leukocyte antigen region by use of haplotypes of Tasmanians with multiple sclerosis

JP Rubio, M Bahlo, H Butzkueven, IAF van der Mei, MM Sale, JL Dickinson, P Groom, LJ Johnson, RD Simmons, B Tait, M Varney, B Taylor, T Dwyer, R Williamson, NM Gough, TJ Kilpatrick, TP Speed, SJ Foote

Journal article  |  2002  |  American Journal of Human Genetics

Improving linkage analysis in outcrossed forest trees - an example from Acacia mangium

PA Butcher, ER Williams, D Whitaker, S Ling, TP Speed, GF Moran

Journal article  |  2002  |  Theoretical and Applied Genetics

Approximate Ewens formulae for symmetric overdominance selection

MN Grote, TP Speed

Journal article  |  2002  |  The Annals of Applied Probability

An HMM model for coiled-coil domains and a comparison with PSSM-based predictions

M Delorenzi, T Speed

Journal article  |  2002  |  Bioinformatics

Comparison of discrimination methods for the classification of tumors using gene expression data

S Dudoit, J Fridlyand, TP Speed

Journal article  |  2002  |  Journal of the American Statistical Association

Comparison of methods for image analysis on cDNA microarray data

YH Yang, MJ Buckley, S Dudoit, TP Speed

Journal article  |  2002  |  Journal of Computational and Graphical Statistics

Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation

YH Yang, S Dudoit, P Luu, DM Lin, V Peng, J Ngai, TP Speed

Journal article  |  2002  |  Nucleic Acids Research

Replicated microarray data

I Lonnstedt, T Speed

Journal article  |  2002  |  Statistica Sinica

Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments

S Dudoit, YH Yang, MJ Callow, TP Speed

Journal article  |  2002  |  Statistica Sinica

Discussion on the meeting on 'Statistical modelling and analysis of genetic data'

DJ Balding, AD Carothers, JL Marchini, LR Cardon, A Vetta, B Griffiths, BS Weir, WG Hill, D Goldstein, K Strimmer, S Myers, MA Beaumont, CA Glasbey, CD Mayer, S Richardson, C Marshall, R Durrett, R Nielsen, PM Visscher, SA Knott, et al.

Report  |  2002  |  Journal of the Royal Statistical Society Series B: Statistical Methodology

A model selection approach for the identification of quantitative trait loci in experimental crosses

KW Broman, TP Speed

Conference Proceedings  |  2002  |  Journal of the Royal Statistical Society: Series B (Statistical Methodology)

Analysis of cDNA microarray images.

YH Yang, MJ Buckley, TP Speed

Journal article  |  2001  |  Briefings in Bioinformatics

Microarrays are part of a new class of biotechnologies that allow the monitoring of expression levels for thousands of genes simul..

A complete set of constraints and parameterisation of two-locus affected sib-pair IBD probabilities.

O Bengtsson, TP Speed, S Dudoit

Conference Proceedings  |  2001  |  AMERICAN JOURNAL OF HUMAN GENETICS

Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs

DR Goldtstein, S Dudoit, TP Speed

Journal article  |  2001  |  Genetic Epidemiology

Identification of proteins from Plasmodium falciparum that are homologous to reticulocyte binding proteins in Plasmodium vivax

T Triglia, J Thompson, SR Caruana, M Delorenzi, T Speed, AF Cowman

Journal article  |  2001  |  Infection and Immunity

Normalization for cDNA microarray data

YH Yang, S Dudoit, P Luu, TP Speed

Conference Proceedings  |  2001  |  Microarrays: Optical Technologies and Informatics

Phat - a gene finding program for Plasmodium falciparum

S Cawley, A WIRTH, T Speed

Journal article  |  2001  |  Molecular and Biochemical Parasitology

Microarray expression profiling identifies genes with altered expression in HDL-deficient mice

MJ Callow, S Dudoit, EL Gong, TP Speed, EM Rubin

Journal article  |  2000  |  Genome Research

Parametric deconvolution of positive spike trains

L Li, TP Speed

Journal article  |  2000  |  The Annals of Statistics

The current state of multiple sclerosis genetic research.

JP Rubio, TP Speed, M Bahlo, TJ Kilpatrick, SJ Foote

Journal article  |  2000  |  Annals of the Academy of Medicine Singapore

INTRODUCTION: Multiple sclerosis (MS) is the most common genetic disease of the nervous system with onset usually in young adultho..

DNA sequencing with transposons

SE Cawley, TP Speed

Journal article  |  2000  |  Journal of Computational Biology

Power of a score test for quantitative trait linkage analysis of relative pairs

DR Goldstein, S Dudoit, TP Speed

Conference Proceedings  |  2000  |  Genetic Epidemiology

Robust transmission regression models for linkage and association.

DJ Schaid, CM Rowland

Conference Proceedings  |  2000  |  Genetic Epidemiology

We present a general regression model that accounts for both linkage and linkage disequilibrium (LD) when analyzing nuclear family..

Teaching statistics theory through applications

D Nolan, TP Speed

Journal article  |  1999  |  The American Statistician

Chromosomes X, 9, and the H2 locus interact epistatically to control Leishmania major infection

LJ Roberts, TM Baldwin, TP Speed, E Handman, SJ Foote

Journal article  |  1999  |  European Journal of Immunology

A score test for linkage using identity by descent data from sibships

S Dudoit, TP Speed

Journal article  |  1999  |  The Annals of Statistics

An estimate of the crosstalk matrix in four-dye fluorescence-based DNA sequencing

L Li, TP Speed

Journal article  |  1999  |  Electrophoresis

Teaching statistics theory through applications

D Nolan, TP Speed

Journal article  |  1999  |  The American Statistician

Relative efficiencies of the Chi-square recombination models for gene mapping with human pedigree data

S Lin, TP Speed

Journal article  |  1999  |  Annals of Human Genetics

Comment: Transferability of habitat suitability criteria

JG Williams, TP Speed, WF Forrest

Journal article  |  1999  |  North American Journal of Fisheries Management

Characterizing a joint probability distribution by conditionals (vol 55, pg 185, 1993)

A Gelman, TP Speed

Journal article  |  1999  |  Journal of the Royal Statistical Society: Series B (Statistical Methodology)

Statistical analysis of half-tetrads

HY Zhao, TP Speed

Journal article  |  1998  |  Genetics

What can bioinformatics do for parasitology research?

SJ Foote, T Speed, E Handman

Journal article  |  1998  |  Parasitology Today

Statistical analysis of ordered tetrads

HY Zhao, TP Speed

Journal article  |  1998  |  Genetics

A three-wavelength labeling approach for DNA sequencing using energy transfer primers and capillary electrophoresis

I Kheterpal, L Li, TP Speed, RA Mathies

Journal article  |  1998  |  Electrophoresis

Estimation of antigen-responsive T cell frequencies in PBMC from human subjects

K Broman, T Speed, M Tigges

Journal article  |  1998  |  STATISTICAL SCIENCE

Stochastic modeling of the crossover process during meiosis

HY Zhao, TP Speed

Journal article  |  1998  |  Communications in Statistics - Theory and Methods

An algorithm for haplotype analysis

SL Lin, TP Speed

Journal article  |  1997  |  Journal of Computational Biology

The effects of genotyping errors and interference on estimation of genetic distance

DR Goldstein, HY Zhao, TP Speed

Journal article  |  1997  |  Human Heredity

The limits of random fingerprinting

DO Nelson, TP Speed, B Yu

Journal article  |  1997  |  Genomics

Information and the clone mapping of chromosomes

B Yu, TP Speed

Journal article  |  1997  |  The Annals of Statistics

Algorithm for haplotype analysis

S Lin, TP Speed

Conference Proceedings  |  1997  |  Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB

The Poisson-skip model of crossing-over

K Lange, H Zhao, TP Speed

Journal article  |  1997  |  The Annals of Applied Probability

Variations on a theme of Lander and Waterman

T Speed

Conference Proceedings  |  1997  |  Proceedings of thr Annual International Conference on Computational Molecular Biology, RECOMB

Statistical issues arising in the analysis of DNA-DNA hybridization data

R Guerra, TP Speed

Journal article  |  1996  |  Systematic Biology

Estimation of antigen-responsive T cell frequencies in PBMC from human subjects

K Broman, T Speed, M Tigges

Journal article  |  1996  |  Journal of Immunological Methods

Incorporating crossover interference into pedigree analysis using the chi(2) model

SL Lin, TP Speed

Journal article  |  1996  |  Human Heredity

Over- and underrepresentation of short DNA words in herpesvirus genomes

MY Leung, GM Marsh, TP Speed

Journal article  |  1996  |  Journal of Computational Biology

Uncertainty and instream flow standards

DT Castleberry, JJ Cech, DC Erman, D Hankin, M Healey, GM Kondolf, M Mangel, M Mohr, PB Moyle, J Nielsen, TP Speed, JG Williams

Journal article  |  1996  |  Fisheries

A note on the combination of estimates of a recombination fraction

S Lin, TP Speed

Journal article  |  1996  |  Annals of Human Genetics

On genetic map functions

HY Zhao, TP Speed

Journal article  |  1996  |  Genetics

Statistical issues arising in the analysis of DNA-DNA hybridization data

R Guerra, TP Speed

Journal article  |  1996  |  Systematic Biology

ALVEOLAR LINING LAYER IS THIN AND CONTINUOUS - LOW-TEMPERATURE SCANNING ELECTRON-MICROSCOPY OF RAT LUNG

J BASTACKY, CYC LEE, J GOERKE, H KOUSHAFAR, D YAGER, L KENAGA, TP SPEED, Y CHEN, JA CLEMENTS

Journal article  |  1995  |  Journal of Applied Physiology