Terry Speed

Q: What Schools Are Affiliated With Terry Speed

Terry Speed is affiliated with the following schools: University of California, Berkeley, University of Melbourne, Monash University

Terry Speed's AcademicInfluence.com Rankings

Terry Speed

Mathematics

#2103

World Rank

#3298

Historical Rank

Statistics

#137

World Rank

#179

Historical Rank

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Mathematics

Why Is Terry Speed Influential?

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According to Wikipedia, Terence Paul "Terry" Speed , FAA FRS is an Australian statistician. A senior principal research scientist at the Walter and Eliza Hall Institute of Medical Research, he is known for his contributions to the analysis of variance and bioinformatics, and in particular to the analysis of microarray data.

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Terry Speed's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Exploration, normalization, and summaries of high density oligonucleotide array probe level data. (2003) (10847)
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias (2003) (8295)
Integrated Genomic Analyses of Ovarian Carcinoma (2011) (6411)
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. (2010) (5816)
Comprehensive genomic characterization defines human glioblastoma genes and core pathways (2008) (5775)
Summaries of Affymetrix GeneChip probe level data. (2003) (5248)
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. (2002) (3709)
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. (2006) (3085)
Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data (2002) (2855)
Normalization of cDNA microarray data. (2003) (2160)
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data (2005) (1891)
International network of cancer genome projects (2010) (1839)
STATISTICAL METHODS FOR IDENTIFYING DIFFERENTIALLY EXPRESSED GENES IN REPLICATED cDNA MICROARRAY EXPERIMENTS (2002) (1611)
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. (2004) (1319)
Normalization of RNA-seq data using factor analysis of control genes or samples (2014) (1303)
Design issues for cDNA microarray experiments (2002) (862)
Biological sequence analysis (2003) (850)
Summarizing and correcting the GC content bias in high-throughput sequencing (2012) (772)
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007) (715)
Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis (2018) (569)
Comparison of Methods for Image Analysis on cDNA Microarray Data (2002) (552)
Statistical issues in cDNA microarray data analysis. (2003) (517)
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008) (500)
Normalization for cDNA microarry data (2001) (448)
Subtype and pathway specific responses to anticancer compounds in breast cancer (2011) (439)
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions (2002) (433)
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites (2006) (409)
Using control genes to correct for unwanted variation in microarray data. (2012) (401)
A genotype calling algorithm for affymetrix SNP arrays (2006) (379)
Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA , IDH 1 , EGFR , and NF 1 Citation Verhaak (2010) (362)
PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor–positive breast cancer (2010) (340)
A benchmark for Affymetrix GeneChip expression measures (2004) (329)
Expression profiling in primates reveals a rapid evolution of human transcription factors (2006) (322)
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 (2013) (309)
Functional Genomic Analysis of Oligodendrocyte Differentiation (2006) (302)
Alveolar lining layer is thin and continuous: low-temperature scanning electron microscopy of rat lung. (1995) (292)
Sir2 Paralogues Cooperate to Regulate Virulence Genes and Antigenic Variation in Plasmodium falciparum (2009) (277)
Microarray expression profiling identifies genes with altered expression in HDL-deficient mice. (2000) (273)
A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression (2014) (252)
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. (2006) (250)
Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. (2003) (248)
Identification and Stoichiometry of Glycosylphosphatidylinositol-anchored Membrane Proteins of the Human Malaria Parasite Plasmodium falciparum*S (2006) (241)
Analysis of CDNA Microarray Images (2001) (240)
Network inference using informative priors (2008) (236)
A multivariate empirical Bayes statistic for replicated microarray time course data (2006) (232)
Resampling-based multiple testing for microarray data analysis (2003) (219)
Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex (2006) (213)
Analysis of the platypus genome suggests a transposon origin for mammalian imprinting (2009) (199)
Evolution of the relaxin-like peptide family (2005) (198)
Spotted long oligonucleotide arrays for human gene expression analysis. (2003) (192)
GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly (2017) (190)
Gene set enrichment analysis made simple (2009) (185)
Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity (2010) (184)
Signatures of tumour immunity distinguish Asian and non-Asian gastric adenocarcinomas (2014) (181)
Mitochondrial-related gene expression changes are sensitive to agonal-pH state: implications for brain disorders (2006) (174)
Estimation and assessment of raw copy numbers at the single locus level (2008) (173)
A Subset of Plasmodium falciparum SERA Genes Are Expressed and Appear to Play an Important Role in the Erythrocytic Cycle* (2002) (171)
Statistics for Experimenters: Design, Innovation, and Discovery (2006) (171)
Regulation of apicomplexan actin-based motility (2006) (168)
Genome-Wide Analysis of Glucocorticoid Receptor Binding Regions in Adipocytes Reveal Gene Network Involved in Triglyceride Homeostasis (2010) (163)
Normalizing and integrating metabolomics data. (2012) (160)
Modeling interference in genetic recombination. (1995) (157)
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6 (2009) (156)
Invariants of Some Probability Models Used in Phylogenetic Inference (1993) (152)
Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. (2007) (147)
Reticulocyte and Erythrocyte Binding-Like Proteins Function Cooperatively in Invasion of Human Erythrocytes by Malaria Parasites (2010) (143)
Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation. (2014) (140)
Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians (2008) (138)
Experimental design and low-level analysis of microarray data. (2004) (138)
A molecular threshold for effector CD8+ T cell differentiation controlled by transcription factors Blimp-1 and T-bet (2016) (138)
A score test for the linkage analysis of qualitative and quantitative traits based on identity by descent data from sib-pairs. (2000) (137)
A Correlation for the 21st Century (2011) (136)
Identification of Proteins from Plasmodium falciparum That Are Homologous to Reticulocyte Binding Proteins inPlasmodium vivax (2001) (135)
Quality Assessment for Short Oligonucleotide Microarray Data (2007) (134)
Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling (2012) (134)
The Comparative Roles of Suppressor of Cytokine Signaling-1 and -3 in the Inhibition and Desensitization of Cytokine Signaling* (2006) (130)
Integrative analysis of RUNX1 downstream pathways and target genes (2008) (129)
FIRMA: a method for detection of alternative splicing from exon array data (2008) (129)
Statistical methods for handling unwanted variation in metabolomics data. (2015) (126)
Quality Assessment of Affymetrix GeneChip Data (2005) (125)
Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer (2010) (125)
Copy Number Variation in Patients with Disorders of Sex Development Due to 46,XY Gonadal Dysgenesis (2011) (125)
Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells (2017) (122)
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development (2013) (120)
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. (2010) (117)
Distinct Epigenetic Signatures Delineate Transcriptional Programs during Virus-Specific CD8 T Cell Differentiation (2014) (116)
Colon cancer prognosis prediction by gene expression profiling (2005) (115)
A statistical framework for analyzing deep mutational scanning data (2016) (113)
Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis (2010) (113)
Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children (2012) (111)
Finding short DNA motifs using permuted markov models (2004) (111)
Estrogen Receptor β Binds to and Regulates Three Distinct Classes of Target Genes* (2010) (110)
Statistical analysis of crossover interference using the chi-square model. (1995) (109)
Statistical modeling of sequencing errors in SAGE libraries. (2004) (109)
scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets (2019) (105)
Regulation of specific target genes and biological responses by estrogen receptor subtype agonists. (2010) (105)
The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program “CASCADE” (2016) (104)
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line (2012) (103)
Enzymic, Phylogenetic, and Structural Characterization of the Unusual Papain-like Protease Domain of Plasmodium falciparum SERA5* (2003) (101)
Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. (2007) (101)
A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography. (2004) (100)
A New Rodent Model to Assess Blood Stage Immunity to the Plasmodium falciparum Antigen Merozoite Surface Protein 119 Reveals a Protective Role for Invasion Inhibitory Antibodies (2003) (96)
Molecular Analysis of Gene Expression in the Developing Pontocerebellar Projection System (2002) (95)
[That BLUP is a Good Thing: The Estimation of Random Effects]: Comment (1991) (94)
A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. (2012) (94)
Genetic dissection of the human leukocyte antigen region by use of haplotypes of Tasmanians with multiple sclerosis. (2002) (93)
Inner cell allocation in the mouse morula: the role of oriented division during fourth cleavage. (1990) (87)
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development (2011) (86)
Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib (2012) (85)
Id2-Mediated Inhibition of E2A Represses Memory CD8+ T Cell Differentiation (2013) (85)
Global analyses of mRNA translational control during early Drosophila embryogenesis (2007) (85)
Factors associated with human immunodeficiency virus seroconversion in homosexual men in three San Francisco cohort studies, 1984-1989. (1993) (85)
Correcting gene expression data when neither the unwanted variation nor the factor of interest are observed (2012) (85)
Over- and Underrepresentation of Short DNA Words in Herpesvirus Genomes (1996) (84)
NORMALIZATION , BASELINE CORRECTION AND ALIGNMENT OF HIGH-THROUGHPUT MASS SPECTROMETRY DATA (2004) (84)
Argon laser photocoagulation-induced modification of gene expression in the retina. (2003) (83)
Evidence for a Common Role for the Serine-Type Plasmodium falciparum Serine Repeat Antigen Proteases: Implications for Vaccine and Drug Design (2007) (78)
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets (2015) (78)
On genetic map functions. (1996) (75)
A comparison of Affymetrix gene expression arrays (2007) (75)
A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments (2007) (75)
Drug and Cell Type-Specific Regulation of Genes with Different Classes of Estrogen Receptor β-Selective Agonists (2009) (74)
A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters (2012) (74)
Using long-read sequencing to detect imprinted DNA methylation (2018) (74)
Evidence for a novel glaucoma locus at chromosome 3p21-22 (2005) (72)
A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis (2013) (72)
Design and analysis of comparative microarray experiments (2003) (72)
Comparing somatic mutation-callers: beyond Venn diagrams (2013) (70)
Evolution and comparative analysis of the MHC Class III inflammatory region (2006) (69)
Removing unwanted variation in a differential methylation analysis of Illumina HumanMethylation450 array data (2015) (67)
Temporal Global Expression Data Reveal Known and Novel Salicylate-Impacted Processes and Regulators Mediating Powdery Mildew Growth and Reproduction on Arabidopsis1[W][OA] (2009) (66)
An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss (2008) (66)
Statistical analysis of chromatid interference. (1995) (66)
A High Force of Plasmodium vivax Blood-Stage Infection Drives the Rapid Acquisition of Immunity in Papua New Guinean Children (2013) (66)
Incorporating prior information into the analysis of contingency tables. (1988) (64)
Expression profiling of a hemopoietic cell survival transcriptome implicates osteopontin as a functional prognostic factor in AML. (2009) (64)
Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer (2009) (64)
High-quality DNA sequence capture of 524 disease candidate genes (2011) (62)
TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays (2010) (61)
RLE plots: Visualizing unwanted variation in high dimensional data (2017) (60)
SNP mapping and candidate gene sequencing in the class I region of the HLA complex: searching for multiple sclerosis susceptibility genes in Tasmanians. (2007) (60)
Genes for Glycosylphosphatidylinositol Toxin Biosynthesis in Plasmodium falciparum (2002) (57)
Reproductive failure and the major histocompatibility complex. (1995) (57)
Parametric deconvolution of positive spike trains (2000) (56)
G protein-linked signaling pathways in bipolar and major depressive disorders (2013) (55)
Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (2021) (55)
A new normalization for Nanostring nCounter gene expression data (2019) (55)
Discovery and molecular characterization of a Bcl-2–regulated cell death pathway in schistosomes (2011) (55)
The effects of genotyping errors and interference on estimation of genetic distance. (1997) (54)
Phat--a gene finding program for Plasmodium falciparum. (2001) (53)
Dating Rare Mutations from Small Samples with Dense Marker Data (2014) (53)
On Gene Ranking Using Replicated Microarray Time Course Data (2009) (52)
SOME STEP-DOWN PROCEDURES CONTROLLING THE FALSE DISCOVERY RATE UNDER DEPENDENCE. (2008) (52)
A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics (2005) (52)
Microarrays (2009) (51)
The wound repair response controls outcome to cutaneous leishmaniasis (2005) (50)
Silencing of Odorant Receptor Genes by G Protein βγ Signaling Ensures the Expression of One Odorant Receptor per Olfactory Sensory Neuron (2014) (50)
Analysis of gene expression in the developing mouse retina (2003) (49)
Subcompartmentalisation of Proteins in the Rhoptries Correlates with Ordered Events of Erythrocyte Invasion by the Blood Stage Malaria Parasite (2012) (48)
Strategies to enable large-scale proteomics for reproducible research (2020) (48)
Systematic noise degrades gene co-expression signals but can be corrected (2015) (47)
Analysis of gene expression during neurite outgrowth and regeneration (2007) (46)
Deriving statistical models for predicting peptide tandem MS product ion intensities. (2003) (46)
scClassify: sample size estimation and multiscale classification of cells using single and multiple reference (2020) (46)
Neuron-Specific mRNA Complexity Responses during Hippocampal Apoptosis after Traumatic Brain Injury (2004) (45)
Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network (2019) (44)
Differential regulation of native estrogen receptor-regulatory elements by estradiol, tamoxifen, and raloxifene. (2008) (44)
Protocol matters: which methylome are you actually studying? (2010) (43)
Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis (2004) (42)
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods (2009) (42)
Chromosomes X, 9, and the H2 locus interact epistatically to control Leishmania major infection (1999) (42)
Mitochondrial related gene expression changes are sensitive to agonal-pH state (2006) (42)
Tests of random mating for a highly polymorphic locus: application to HLA data. (1995) (41)
Conserved Role of unc-79 in Ethanol Responses in Lightweight Mutant Mice (2010) (40)
The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees. (2004) (39)
Evaluating stably expressed genes in single cells (2018) (39)
Coevolution of the Relaxin‐Like Peptides and Their Receptors (2005) (39)
The N‐terminal domains of SOCS proteins: A conserved region in the disordered N‐termini of SOCS4 and 5 (2012) (39)
Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements (2009) (37)
Mind the gap: analysis of marker-assisted breeding strategies for inbred mouse strains (2006) (36)
Rooting a phylogenetic tree with nonreversible substitution models (2005) (36)
Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans (2020) (36)
Colon tumour secretopeptidome: insights into endogenous proteolytic cleavage events in the colon tumour microenvironment. (2013) (35)
A review of methods for identifying QTLs in experimental crosses (1999) (34)
Genetic mapping and DNA sequencing (1996) (33)
Statistical analysis of metabolomics data. (2013) (33)
Accurate RNA Sequencing From Formalin-Fixed Cancer Tissue to Represent High-Quality Transcriptome From Frozen Tissue (2018) (33)
Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in Eμ-v-abl transgenic mice (2002) (33)
SNPs on Chips: The Hidden Genetic Code in Expression Arrays (2007) (32)
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data (2017) (32)
Long‐term effect of therapeutic laser photocoagulation on gene expression in the eye (2006) (31)
An algorithm for haplotype analysis (1997) (31)
MicroRNAs in CD4(+) T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes. (2016) (30)
Evolution of the Relaxin‐Like Peptide Family: From Neuropeptide to Reproduction (2005) (30)
Multiple transcription factor elements collaborate with estrogen receptor alpha to activate an inducible estrogen response element in the NKG2E gene. (2007) (30)
An estimate of the crosstalk matrix in four‐dye fluorescence‐based DNA sequencing (1999) (30)
Incorporating crossover interference into pedigree analysis using the chi 2 model. (1996) (29)
Multiple testing and its applications to microarrays (2009) (28)
Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex (2016) (27)
The microarray: potential applications for ophthalmic research. (2002) (27)
Robustness of the no-interference model for ordering genetic markers. (1992) (27)
Improving linkage analysis in outcrossed forest trees – an example from Acacia mangium (2002) (27)
Atypical regions in large genomic DNA sequences. (1994) (26)
Statistical analysis of half-tetrads. (1998) (26)
Spatial patterns of gene expression in the olfactory bulb. (2004) (26)
Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing (2010) (26)
Testing for segregation distortion in the HLA complex. (1994) (25)
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development (2021) (25)
Copy-number-aware differential analysis of quantitative DNA sequencing data (2012) (25)
Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time‐lapse microscopy (2013) (25)
A score test for linkage using identity by descent data from sibships (1999) (25)
A systematic approach for comprehensive T-cell epitope discovery using peptide libraries (2005) (24)
Tissue-Specific Regulation of Genes by Estrogen Receptors (2012) (24)
Contextual fear conditioning induces differential alternative splicing (2016) (24)
Restricted Maximum Likelihood (REML) (2006) (24)
Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery (2014) (24)
Sparse combinatorial inference with an application in cancer biology (2009) (24)
Dysregulated IL-1&bgr;-GM-CSF Axis in Acute Rheumatic Fever That Is Limited by Hydroxychloroquine (2018) (23)
Unliganded estrogen receptor-β regulation of genes is inhibited by tamoxifen (2010) (23)
Unifying Gene Expression Measures from Multiple Platforms Using Factor Analysis (2011) (23)
What is a genetic map function (1996) (22)
Proximal genomic localization of STAT1 binding and regulated transcriptional activity (2006) (21)
Discussion on the meeting on ‘Statistical modelling and analysis of genetic data’ (2002) (21)
Distribution of genomic breakpoints in chronic myeloid leukemia: analysis of 308 patients (2013) (20)
Identifying nineteenth century genealogical links from genotypes (2005) (20)
Statistical Issues in Constructing High Resolution Physical Maps (1994) (20)
Differential splicing using whole-transcript microarrays (2009) (19)
Combining calls from multiple somatic mutation-callers (2014) (19)
The Poisson-skip model of crossing-over (1997) (19)
Machine learning in low-level microarray analysis (2003) (19)
Analysis of extended HLA haplotypes in multiple sclerosis and narcolepsy families confirms a predisposing effect for the class I region in Tasmanian MS patients (2007) (18)
TRANSCRIPTION FACTOR BINDING SITE PREDICTION WITH MULTIVARIATE GENE EXPRESSION DATA (2008) (18)
Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells (2022) (18)
A genetic screen for behavioral mutations that perturb dopaminergic homeostasis in mice (2005) (18)
Time for DNA disclosure. (2009) (17)
Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets (2020) (17)
Statistical Analysis of Microarray Time Course Data (2005) (17)
Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells (2020) (17)
Serum microRNA is a biomarker for post-operative monitoring in glioma (2020) (17)
Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes (2010) (17)
On the utility of data from the International HapMap Project for Australian association studies (2006) (17)
The Role of Spike-In Standards in the Normalization of RNA-seq (2014) (16)
Estimating the fraction of invariable codons with a capture-recapture method (1992) (16)
The Role of Spike-In Standards in the Normalization of RNA-seq (2014) (16)
Mapping of the Plasmodium chabaudi Resistance Locus char2 (2006) (16)
The Role of Spike-In Standards in the Normalization of RNA-seq (2014) (16)
Microarray analysis of two interacting treatments: a linear model and trends in expression over time (2005) (16)
Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data (2014) (15)
Direct versus indirect designs for cDNA microarray experiments (2002) (15)
Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis (2018) (14)
A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. (2010) (14)
Deconvolution of Sparse Positive Spikes (2004) (14)
Housekeeping genes, revisited at the single-cell level (2017) (14)
Estimation and correction for GC-content bias in high throughput sequencing (2011) (14)
Estrogenic Plant Extracts Reverse Weight Gain and Fat Accumulation without Causing Mammary Gland or Uterine Proliferation (2011) (14)
Microarray Expression Profiling Identifies Genes with Altered Expression in HDL-Deficient Mice (2000) (14)
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression (2022) (13)
SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data (2002) (13)
Modeling DNA Base Substitution in Large Genomic Regions from Two Organisms (2003) (13)
Triangle Constraints for Sib-Pair Identity by Descent Probabilities under a General Multilocus Model for Disease Susceptibility (1998) (13)
Estimation of antigen-responsive T cell frequencies in PBMC from human subjects. (1996) (13)
Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data (2006) (12)
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 (2015) (12)
Relative efficiencies of chi 2 models of recombination for exclusion mapping and gene ordering. (1995) (12)
Statistical analysis of ordered tetrads. (1998) (11)
Maps of variability in cell lineage trees (2018) (11)
scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication (2018) (11)
scClassify: hierarchical classification of cells (2019) (11)
CHAPTER 2 Design and Analysis of Comparative Microarray Experiments (2002) (11)
Power and robustness of a score test for linkage analysis of quantitative traits using identity by descent data on sib pairs (2001) (11)
A DNA resequencing array for genes involved in Parkinson's disease. (2012) (10)
Statistical Analysis of Single Nucleotide Polymorphism Microarrays in Cancer Studies (2011) (10)
Introduction to Fisher (1926) The Arrangement of Field Experiments (1992) (10)
Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments (2009) (10)
Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis (2018) (10)
A study of isolation procedures for multiple infections of Salmonella and Arizona in a wild marsupial, the quokka (Setonix brachyurus). (1982) (9)
Id 2-Mediated Inhibition of E 2 A Represses Memory CD 8 + T Cell Differentiation (2013) (9)
The Ratio of Exhausted to Resident Infiltrating Lymphocytes Is Prognostic for Colorectal Cancer Patient Outcome (2020) (9)
The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective (2016) (9)
Effect of vascular endothelial growth factor upregulation on retinal gene expression in the Kimba mouse (2012) (9)
Power calculations for selective genotyping in QTL mapping in backcross mice. (2004) (9)
Evaluation of cross-platform and interlaboratory concordance via consensus modelling of genomic measurements (2018) (8)
PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in breast cancer (2010) (8)
Relative efficiencies of the Chi‐square recombination models for gene mapping with human pedigree data (1999) (7)
Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial (2020) (7)
A hierarchical approach to removal of unwanted variation for large-scale metabolomics data (2020) (7)
Stochastic modeling of the crossover process during meiosis (1998) (6)
A Bayesian analysis for mapping from radiation hybrid data. (1992) (6)
Measures of Block Design Efficiency Recovering Interblock Information (1983) (6)
A derivation of all linear invariants for a nonbalanced transversion model (1992) (6)
Proceedings of the 11th annual international conference on Research in computational molecular biology (2007) (6)
Deconvolution of Sparse Positive Spikes: Is It Ill-Posed? (2000) (6)
Quality Assessment for Short Oligonucleotide Microarray Data. Rejoinder. (2008) (6)
Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE" (2017) (6)
Differing total mRNA expression shapes the molecular and clinical phenotype of cancer (2020) (6)
An integrative bioinformatic predictor of protein sub-cellular localisation in malaria (2011) (6)
On the gene ranking of replicated microarray time course data (2007) (5)
Invariant moments and cumulants (1990) (5)
Removing unwanted variation from large-scale RNA sequencing data with PRPS (2022) (5)
STATISTICS AND GENE EXPRESSION ANALYSIS (5)
A Characterization of Crossover Models That Possess Map Functions (1993) (5)
Correction: Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm (2008) (4)
Statistical Issues Arising in the Analysis of DNA-DNA Hybridization Data (1996) (4)
Predicting progress in directed mapping projects. (1994) (4)
RUV-III-NB: normalization of single cell RNA-seq data (2021) (4)
Intestinal transport of monosaccharide after biliary diversion in the rat. (1978) (4)
Selected Works of Terry Speed (2012) (4)
Power of a score test for quantitative trait linkage analysis of relative pairs (2000) (4)
Correction to: A statistical framework for analyzing deep mutational scanning data (2018) (4)
Statistical Inference in Cell Lineage Trees (2018) (3)
Uses of statistical parsimony in HIV analyses (1999) (3)
A Holm-type procedure controlling the false discovery rate (2007) (3)
Incorporating interference into linkage analysis for experimental crosses. (2005) (3)
Markov chain Monte Carlo for Structural Inference with Prior Information (2007) (3)
The power of two‐locus affected sib‐pair linkage analysis to detect interacting disease loci (2008) (3)
Comparing somatic mutation-callers (2013) (3)
What can bioinformatics do for parasitology research? (1998) (3)
Interview of Albert Tucker (1975) (3)
Determining epithelial contribution to in vivo mesenchymal tumour expression signature using species-specific microarray profiling analysis of xenografts. (2013) (3)
Strain-level sample characterisation using long reads and MAPQ scores (2020) (3)
Ferrous-glutathione coupling mediates ferroptosis and frailty in Caenorhabditis elegans (2019) (3)
Finding a suitable library size to call variants in RNA-Seq (2019) (3)
Identifying differentially expressed genes in cDNA microarray experiments authors. (2001) (3)
Early immune pressure imposed by tissue resident memory T cells sculpts tumour evolution in non-small cell lung cancer (2021) (2)
A species-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for preimplantation development (2021) (2)
The unreasonable effectiveness of statistics in genome science (2010) (2)
Incorporating Previous Results Into the Analysis of General Balanced Designed Experiments (1987) (2)
MSCypher: an integrated database searching and machine learning workflow for multiplexed proteomics (2018) (2)
Physics Meets Mineralogy: Statistical Analysis of Phase-Boundary Observations (2000) (2)
Reconstructing an Ancestral MammalianImmune Supercomplex from a Marsupial MajorHistocompatibility Complex (2006) (2)
Lack of correlation of neoantigens arising from tumor somatic mutations with tumor infiltrating lymphocytes (TILs) or survival in HER2-positive breast cancer (HER2+ BC). (2015) (2)
A new normalization for the Nanostring nCounter gene expression assay (2018) (2)
In-house training of the nanonet local basecaller: opportunities and challenges (2017) (2)
A comparison of match-only algorithms for the analysis of Plasmodium falciparum oligonucleotide arrays. (2005) (2)
The limits of random fingerprinting. (1997) (2)
Erratum: Gene set enrichment analysis made simple (Statistical Methods in Medical Research (2009) 18:6 (565-575)) (2011) (2)
CytofRUV: Removing unwanted variation to integrate multiple CyTOF datasets (2020) (2)
Corrigendum to 'MicroRNAs in CD4+ T cell subsets are markers of disease risk and T cell dysfunction in individuals at risk for type 1 diabetes' [J. Autoimmun. 68C (2016) 52-61]. (2016) (2)
Improved Normalization of Nanostring nCounter Gene Expression Data (2018) (2)
Power gain: how normalization affects reproducibility and biological insight of RNA-seq studies in neuroscience (2015) (1)
Learning and Inference in Computational Systems Biology. Computational Molecular Biology. Edited by Neil D. Lawrence, Mark Girolami, Magnus Rattray, and Guido Sanguinetti. Cambridge (Massachusetts): MIT Press. $40.00. viii + 362 p.; ill.; index. ISBN: 978-0-262-01386-4. 2010. (2012) (1)
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 (2015) (1)
Investigating tamoxifen resistance in the luminal B estrogen receptor positive breast cancer subtype: Tailoring treatment in hormone responsive breast cancer (2007) (1)
Long–term modulation of gene expression in the mouse eye following laser photocoagulation (2004) (1)
The healthy ageing gene expression signature for Alzheimer’s disease diagnosis: a random sampling perspective (2018) (1)
Removal of unwanted variation reveals novel patterns of gene expression linked to sleep homeostasis in murine cortex (2016) (1)
On a Markov model for chromatid interference (1999) (1)
Combining calls from multiple somatic mutation-callers (2014) (1)
Systematic noise degrades gene co-expression signals but can be corrected (2015) (1)
DNA Sequencing with Transposons (2000) (1)
hRUV: Hierarchical approach to removal of unwanted variation for large- 1 scale metabolomics data 2 (2021) (1)
Multiple sclerosis: a haplotype association study. (2005) (1)
Analysis of ChIP-Seq Data (2007) (1)
Genetic Map Functions (2014) (1)
The current state of multiple sclerosis genetic research. (2000) (1)
Restricted Maximum Likelihood: Overview (2014) (1)
SRMA: an R package for resequencing array data analysis (2012) (1)
Molecular Evolution , Substitution Models , and Phylogenies (1)
Correction to: Serum microRNA is a biomarker for post-operative monitoring in glioma (2020) (1)
Comparing somatic mutation-callers: beyond Venn diagrams (2013) (1)
Predicting Progress in Shotgun Sequencing with Paired Ends (2002) (1)
Joint Modeling of Mixed Plasmodium Species Infections Using a Bivariate Poisson Lognormal Model. (2018) (1)
A Brief History of the Statistics Department of the University of California at Berkeley (2012) (1)
Rejoinder (2008) (1)
Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data (2014) (1)
Finding a suitable library size to call variants in RNA-Seq (2020) (1)
On a shared allele test of random mating (1995) (1)
Trilobites and us (2014) (1)
Microarray Analysis of Retinal Laser Photocoagulation (2002) (0)
Congenic mouse strains identify a novel gene for which allelic variation affects susceptibility to type 1 diabetes (47.9) (2011) (0)
Tumor cell total mRNA expression shapes the molecular and clinical phenotype of cancer (2021) (0)
Abstract PD5-03: Characterization of high TIL breast cancers reveals a prognostic and functionally distinct tissue-resident memory subpopulation (2019) (0)
Annotation of the Opossum Major Histocompatibility Complex and Analysis of Conserved Non-coding Regions (2005) (0)
Intratumoral CD8+ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer. (2023) (0)
Finding optimal coverage (2016) (0)
Last Words on Anova (2012) (0)
Remove unwanted variation retrieves unknown experimental designs (2023) (0)
RUV retrieves unknown experimental designs (2023) (0)
Removing unwanted variation from large-scale cancer RNA-sequencing data (2021) (0)
Removing Unwanted Variation for classification and clustering (2015) (0)
Recovering DNA Sequences from Electrophoresis Data (1996) (0)
Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial (2020) (0)
Advances in Statistical Bioinformatics: DNA Variant Calling in Targeted Sequencing Data (2013) (0)
Expression Profiling of a Hemopoietic Cell Survival Transcriptome Identifies a Functional Prognostic Gene Signature in Normal Karyotype AML. (2009) (0)
To be published in Technometrics ( with Discussion ) (2008) (0)
Identification of a New Angiogenesis Associated Gene in the Retina (2007) (0)
Statistical Analysis of Replicated Microarray Time Series Data (2004) (0)
Re-analysis of publicly available datasets (2015) (0)
Copy-number-aware differential analysis of (2012) (0)
A statistical framework for analyzing deep mutational scanning data (2017) (0)
Correction: Identification of Candidate Growth Promoting Genes in Ovarian Cancer through Integrated Copy Number and Expression Analysis (2011) (0)
Supplementary materials: Molecular analysis of positional identity in the developing mouse retina (2002) (0)
Group symmetries in the lineage trees of single cells (2018) (0)
IDENTIFICATION OF GENES REGULATED BY ACCELERATED DEBRIS ACCUMULATION IN THE RETINAL PIGMENT EPITHELIAL CELLS OF THE MCD1 TRANSGENIC MOUSE (2004) (0)
TARGETING CELL SURVIVAL PATHWAYS IN ACUTE MYELOID LEUKEMIA (2010) (0)
Combining Single and Paired End RNA-seq Data for Differential Expression Analyses (2016) (0)
Genetic mechanisms and heterogeneity in familial myeloid leukemia (2007) (0)
implicates osteopontin as a functional prognostic factor in AML Expression profiling of a hemopoietic cell survival transcriptome (2014) (0)
Author response: Changes in ferrous iron and glutathione promote ferroptosis and frailty in aging Caenorhabditis elegans (2020) (0)
Low-level analyses of microarray data. (2003) (0)
Model Averaging for Biological Networks with Prior Information (2010) (0)
Variations on a theme of Lander and Waterman (abstract) (1997) (0)
NB-RUV: Removing Unwanted Variation from single-cell RNA-seq data (2019) (0)
Sparse , noisy Boolean functions (2007) (0)
Deep Profiling of Chronic Lymphocytic Leukaemia (CLL) and Healthy Immune Cells By Mass Cytometry Resolves Impacts of Venetoclax Pressure (2021) (0)
Combining calls from multiple somatic (2014) (0)
Commentary on D. Basu’s Papers on Sufficiency and Related Topics (2011) (0)
Statistical and computational challenges in physical mapping (1994) (0)
Author response: Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets (2020) (0)
Invited: low-level analyses of microarray data (2003) (0)
Tissue Selective Estrogen Receptor-α Agonists for the Prevention of Obesity , Diabetes , and Metabolic Syndrome (2012) (0)
Comprehensive survey of gain and loss in Plasmodium falciparum clinical isolates. (2008) (0)
An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences (2022) (0)
Exploration and Analysis of DNA Microarray and Protein Array Data.Wiley Series in Probability and Statistics.ByDhammika Amaratungaand, Javier Cabrera.Hoboken (New Jersey): Wiley‐Interscience. $84.95. xiv + 246 p; ill.; author and subject indexes. ISBN: 0–471–27398–8. 2004. (2005) (0)
668 A toolkit for the quantitative analysis of the spatial distribution of cells of the tumor immune microenvironment (2020) (0)
Analysis of inter-laboratory metabolomics experiments (2011) (0)
Web-based Supplementary Materials for on the Gene Ranking of Replicated Microarray Time Course Data Special and Limiting Cases for Longitudinal Posterior Odds (2007) (0)
Incorporating tiling array expression data into a gene predictor (2008) (0)
Correction to: A statistical framework for analyzing deep mutational scanning data (2018) (0)
What Is Mentoring, and Why Is It a Good Thing? (2016) (0)
Model-based analysis of oligonucleotide arrays and issues in cDNA microarray analysis (2003) (0)
Too much or too little scepticism? (2011) (0)
Two current analysis challenges: Single Cell Omics and Nanopore Long-read Sequence Data (2017) (0)
Prediction of coiled-coil domains (0)
Good Gene Hunting (2010) (0)
BakBH3 in complex with sjA (2011) (0)
Genetic dissection of the HLA region using haplotypes of Tasmanians with multiple sclerosis (2002) (0)
PETER GAVIN HALL (2018) (0)
Preface (2008) (0)
Linkage Analysis, Multipoint† (2014) (0)
Microarray data analysis for beginners (2003) (0)
Director's Letter Mission and Goals Institute Partners Organizing Committee for Emphasis Year Scientific Advisory Committee 20042005 Local Scientific Advisory Committee Program Participa Tion Workshop 4: Emerging Genomic Technologies and Data Inte Gration Problems: February 2124, 2005 (0)
Research in Computational Molecular Biology, 11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007, Proceedings (2007) (0)
Discussions on “A Bayesian Approach to DNA Sequence Segmentation” (2004) (0)
Iterative Proportional Fitting (2005) (0)
Never ask for or give advice, make mistakes, accept mediocrity, enthuse (2014) (0)
Linkage Analysis, Multipoint (2005) (0)
T Cell Differentiation + Memory CD8 Id2-Mediated Inhibition of E2A Represses (2013) (0)
Publisher Correction: Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis (2018) (0)
Statistical Methods for Analyzing DNA-DNA Hybridization Data (2008) (0)
How to do Statistical Research (2013) (0)
Gene Expression Analysis (2005) (0)
Acollectionofbreastcancercelllinesforthestudyoffunctionally distinct cancer subtypes (2006) (0)
Freedom, Degrees of (2001) (0)
Clustering microarray data (2003) (0)
Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network. (2010) (0)
Abstract PD3-1: Evaluation and clinical impact of intra-tumor heterogeneity (ITH) in primary HER2-overexpressing breast cancers (HER2+BC) treated with adjuvant trastuzumab and chemotherapy (CT) (2015) (0)
Contextual Fear Conditioning Induces Differential Alternative Splicing Abbreviated Title : Alternative splicing after contextual learning (2016) (0)
Genomic characterisation of hormone receptor-positive breast cancer arising in very young women. (2023) (0)
Stem cell plasticity, acetylation of H3K14, and de novo gene activation rely on KAT7. (2023) (0)
Contributors and Participants (1982) (0)

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