PubRank

Terence P Speed

Author PubWeight™ 480.13‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003 100.88
2 Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003 52.74
3 Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res 2002 40.03
4 Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010 39.09
5 GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics 2004 30.14
6 International network of cancer genome projects. Nature 2010 20.35
7 A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 2005 10.43
8 Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007 7.91
9 Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 2008 6.30
10 A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004 5.99
11 Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 2006 5.20
12 Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 2012 4.94
13 Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A 2011 4.55
14 Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature 2006 4.26
15 Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol 2006 3.45
16 Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res 2003 2.95
17 A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 2009 2.90
18 PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc Natl Acad Sci U S A 2010 2.79
19 Using control genes to correct for unwanted variation in microarray data. Biostatistics 2011 2.70
20 Functional genomic analysis of oligodendrocyte differentiation. J Neurosci 2006 2.64
21 Consolidation of the cancer genome into domains of repressive chromatin by long-range epigenetic silencing (LRES) reduces transcriptional plasticity. Nat Cell Biol 2010 2.38
22 Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal Chem 2003 2.28
23 Statistical modeling of sequencing errors in SAGE libraries. Bioinformatics 2004 2.25
24 Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011 2.18
25 Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol 2006 2.17
26 Integrative analysis of RUNX1 downstream pathways and target genes. BMC Genomics 2008 2.14
27 Network inference using informative priors. Proc Natl Acad Sci U S A 2008 1.96
28 Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malaria parasite Plasmodium falciparum. Mol Cell Proteomics 2006 1.86
29 Gene set enrichment analysis made simple. Stat Methods Med Res 2009 1.79
30 Regulation of apicomplexan actin-based motility. Nat Rev Microbiol 2006 1.78
31 Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias, and copy number variation. Genome Res 2010 1.77
32 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. PLoS Genet 2013 1.73
33 Sir2 paralogues cooperate to regulate virulence genes and antigenic variation in Plasmodium falciparum. PLoS Biol 2009 1.72
34 A subset of Plasmodium falciparum SERA genes are expressed and appear to play an important role in the erythrocytic cycle. J Biol Chem 2002 1.71
35 TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics 2010 1.70
36 A Tetrahymena Piwi bound to mature tRNA 3' fragments activates the exonuclease Xrn2 for RNA processing in the nucleus. Mol Cell 2012 1.65
37 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. J Exp Med 2003 1.61
38 Identification of candidate growth promoting genes in ovarian cancer through integrated copy number and expression analysis. PLoS One 2010 1.60
39 A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods. Bioinformatics 2009 1.53
40 A comparison of Affymetrix gene expression arrays. BMC Bioinformatics 2007 1.53
41 Reticulocyte and erythrocyte binding-like proteins function cooperatively in invasion of human erythrocytes by malaria parasites. Infect Immun 2010 1.52
42 The comparative roles of suppressor of cytokine signaling-1 and -3 in the inhibition and desensitization of cytokine signaling. J Biol Chem 2006 1.45
43 High-quality DNA sequence capture of 524 disease candidate genes. Proc Natl Acad Sci U S A 2011 1.41
44 Molecular analysis of gene expression in the developing pontocerebellar projection system. Neuron 2002 1.37
45 Protocol matters: which methylome are you actually studying? Epigenomics 2010 1.37
46 Genome-wide analysis of glucocorticoid receptor binding regions in adipocytes reveal gene network involved in triglyceride homeostasis. PLoS One 2010 1.36
47 SNPs on chips: the hidden genetic code in expression arrays. Biol Psychiatry 2006 1.36
48 Comparing somatic mutation-callers: beyond Venn diagrams. BMC Bioinformatics 2013 1.35
49 Force of infection is key to understanding the epidemiology of Plasmodium falciparum malaria in Papua New Guinean children. Proc Natl Acad Sci U S A 2012 1.33
50 Global analyses of mRNA translational control during early Drosophila embryogenesis. Genome Biol 2007 1.30
51 A dynamic programming approach for the alignment of signal peaks in multiple gas chromatography-mass spectrometry experiments. BMC Bioinformatics 2007 1.29
52 Evidence for a common role for the serine-type Plasmodium falciparum serine repeat antigen proteases: implications for vaccine and drug design. Infect Immun 2007 1.23
53 On gene ranking using replicated microarray time course data. Biometrics 2008 1.21
54 Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. Genome Res 2007 1.21
55 Estrogen receptor beta binds to and regulates three distinct classes of target genes. J Biol Chem 2010 1.21
56 Genetic dissection of the human leukocyte antigen region by use of haplotypes of Tasmanians with multiple sclerosis. Am J Hum Genet 2002 1.21
57 A component of the mir-17-92 polycistronic oncomir promotes oncogene-dependent apoptosis. Elife 2013 1.20
58 Evolution of the relaxin-like peptide family. BMC Evol Biol 2005 1.20
59 Bayesian inference of signaling network topology in a cancer cell line. Bioinformatics 2012 1.17
60 Enzymic, phylogenetic, and structural characterization of the unusual papain-like protease domain of Plasmodium falciparum SERA5. J Biol Chem 2003 1.17
61 Identifying nineteenth century genealogical links from genotypes. Hum Genet 2005 1.17
62 Finding short DNA motifs using permuted Markov models. J Comput Biol 2005 1.13
63 Genome-wide analysis of glucocorticoid receptor-binding sites in myotubes identifies gene networks modulating insulin signaling. Proc Natl Acad Sci U S A 2012 1.12
64 Regulation of specific target genes and biological responses by estrogen receptor subtype agonists. Curr Opin Pharmacol 2010 1.12
65 Copy-number-aware differential analysis of quantitative DNA sequencing data. Genome Res 2012 1.12
66 Multiple testing and its applications to microarrays. Stat Methods Med Res 2009 1.10
67 Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer. BMC Med Genomics 2009 1.09
68 Analysis of gene expression in the developing mouse retina. Proc Natl Acad Sci U S A 2003 1.09
69 Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes. Proc Natl Acad Sci U S A 2011 1.09
70 Normalizing and integrating metabolomics data. Anal Chem 2012 1.08
71 Unifying gene expression measures from multiple platforms using factor analysis. PLoS One 2011 1.06
72 Evidence for a novel glaucoma locus at chromosome 3p21-22. Hum Genet 2005 1.06
73 The wound repair response controls outcome to cutaneous leishmaniasis. Proc Natl Acad Sci U S A 2005 1.06
74 A high force of plasmodium vivax blood-stage infection drives the rapid acquisition of immunity in papua new guinean children. PLoS Negl Trop Dis 2013 1.04
75 Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing. Nucleic Acids Res 2010 1.03
76 An integrated genetic and functional analysis of the role of type II transmembrane serine proteases (TMPRSSs) in hearing loss. Hum Mutat 2008 1.02
77 Differential splicing using whole-transcript microarrays. BMC Bioinformatics 2009 1.02
78 Mind the gap: analysis of marker-assisted breeding strategies for inbred mouse strains. Mamm Genome 2006 1.02
79 Spatial patterns of gene expression in the olfactory bulb. Proc Natl Acad Sci U S A 2004 1.01
80 Conserved role of unc-79 in ethanol responses in lightweight mutant mice. PLoS Genet 2010 1.00
81 Analysis of gene expression during neurite outgrowth and regeneration. BMC Neurosci 2007 1.00
82 A proteome strategy for fractionating proteins and peptides using continuous free-flow electrophoresis coupled off-line to reversed-phase high-performance liquid chromatography. Anal Chem 2004 1.00
83 Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol 2009 1.00
84 Drug and cell type-specific regulation of genes with different classes of estrogen receptor beta-selective agonists. PLoS One 2009 0.99
85 Expression profiling of a hemopoietic cell survival transcriptome implicates osteopontin as a functional prognostic factor in AML. Blood 2009 0.97
86 Differential regulation of native estrogen receptor-regulatory elements by estradiol, tamoxifen, and raloxifene. Mol Endocrinol 2007 0.97
87 Id2-mediated inhibition of E2A represses memory CD8+ T cell differentiation. J Immunol 2013 0.96
88 Multiple transcription factor elements collaborate with estrogen receptor alpha to activate an inducible estrogen response element in the NKG2E gene. Endocrinology 2007 0.96
89 Argon laser photocoagulation-induced modification of gene expression in the retina. Invest Ophthalmol Vis Sci 2003 0.95
90 Cisplatin-induced primordial follicle oocyte killing and loss of fertility are not prevented by imatinib. Nat Med 2012 0.95
91 Subcompartmentalisation of proteins in the rhoptries correlates with ordered events of erythrocyte invasion by the blood stage malaria parasite. PLoS One 2012 0.94
92 The serine repeat antigen (SERA) gene family phylogeny in Plasmodium: the impact of GC content and reconciliation of gene and species trees. Mol Biol Evol 2004 0.94
93 Multiple genetic loci modify susceptibility to plasmacytoma-related morbidity in E(mu)-v-abl transgenic mice. Proc Natl Acad Sci U S A 2002 0.93
94 Sparse combinatorial inference with an application in cancer biology. Bioinformatics 2008 0.93
95 Deciphering clonality in aneuploid breast tumors using SNP array and sequencing data. Genome Biol 2014 0.92
96 Modeling DNA base substitution in large genomic regions from two organisms. J Mol Evol 2004 0.91
97 Proximal genomic localization of STAT1 binding and regulated transcriptional activity. BMC Genomics 2006 0.90
98 Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis. Plant Physiol 2009 0.90
99 A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. PLoS One 2012 0.90
100 Extended haplotype analysis in the HLA complex reveals an increased frequency of the HFE-C282Y mutation in individuals with multiple sclerosis. Hum Genet 2004 0.89
101 Unliganded estrogen receptor-beta regulation of genes is inhibited by tamoxifen. Mol Cell Endocrinol 2009 0.89
102 Long-term effect of therapeutic laser photocoagulation on gene expression in the eye. FASEB J 2005 0.89
103 SOME STEP-DOWN PROCEDURES CONTROLLING THE FALSE DISCOVERY RATE UNDER DEPENDENCE. Stat Sin 2008 0.89
104 A recombination hotspot leads to sequence variability within a novel gene (AK005651) and contributes to type 1 diabetes susceptibility. Genome Res 2010 0.88
105 On the utility of data from the International HapMap Project for Australian association studies. Hum Genet 2006 0.88
106 Combining calls from multiple somatic mutation-callers. BMC Bioinformatics 2014 0.87
107 Evolution and comparative analysis of the MHC Class III inflammatory region. BMC Genomics 2006 0.87
108 Poor prognosis in familial acute myeloid leukaemia with combined biallelic CEBPA mutations and downstream events affecting the ATM, FLT3 and CDX2 genes. Br J Haematol 2010 0.87
109 Divergent lymphocyte signalling revealed by a powerful new tool for analysis of time-lapse microscopy. Immunol Cell Biol 2012 0.86
110 Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data. Hum Genet 2005 0.86
111 The N-terminal domains of SOCS proteins: a conserved region in the disordered N-termini of SOCS4 and 5. Proteins 2012 0.86
112 Mapping of the Plasmodium chabaudi resistance locus char2. Infect Immun 2006 0.86
113 Coevolution of the relaxin-like peptides and their receptors. Ann N Y Acad Sci 2005 0.83
114 A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics. Protein Sci 2005 0.82
115 Statistical analysis of metabolomics data. Methods Mol Biol 2013 0.82
116 Cell type- and estrogen receptor-subtype specific regulation of selective estrogen receptor modulator regulatory elements. Mol Cell Endocrinol 2008 0.82
117 Neuron-specific mRNA complexity responses during hippocampal apoptosis after traumatic brain injury. J Neurosci 2004 0.81
118 Power calculations for selective genotyping in QTL mapping in backcross mice. Genet Res 2004 0.81
119 Estrogenic plant extracts reverse weight gain and fat accumulation without causing mammary gland or uterine proliferation. PLoS One 2011 0.80
120 Tissue-specific regulation of genes by estrogen receptors. Semin Reprod Med 2012 0.80
121 The microarray: potential applications for ophthalmic research. Mol Vis 2002 0.80
122 SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. Mamm Genome 2002 0.79
123 Background adjustment for DNA microarrays using a database of microarray experiments. J Comput Biol 2009 0.79
124 Analysis of extended HLA haplotypes in multiple sclerosis and narcolepsy families confirms a predisposing effect for the class I region in Tasmanian MS patients. Immunogenetics 2007 0.78
125 Effect of vascular endothelial growth factor upregulation on retinal gene expression in the Kimba mouse. Clin Experiment Ophthalmol 2012 0.78
126 A systematic approach for comprehensive T-cell epitope discovery using peptide libraries. Bioinformatics 2005 0.77
127 The power of two-locus affected sib-pair linkage analysis to detect interacting disease loci. Genet Epidemiol 2008 0.76
128 SRMA: an R package for resequencing array data analysis. Bioinformatics 2012 0.75
129 Multiple sclerosis: a haplotype association study. Novartis Found Symp 2005 0.75
130 Incorporating interference into linkage analysis for experimental crosses. Biostatistics 2005 0.75
131 Correction: The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE". PLoS Med 2017 0.75