Speed, Terence P.

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

Verhaak, R. G. W., Hoadley, K. A., Purdom, E., Wang, V., Qi, Y., Wilkerson, M. D., Miller, C. R., Ding, L., Golub, T., Mesirov, J. P., et al. (2010) · Cancer Cell

Glioma Diagnosis and TreatmentCancer Genomics and Diagnostics

Cited by 7,575

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

Risso, D., Ngai, J., Speed, T. P., & Dudoit, S. (2014) · Nature Biotechnology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 2,052

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

Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab), Savas, P., Virassamy, B., Ye, C., Salim, A., Mintoff, C. P., Caramia, F., Salgado, R., Byrne, D. J., Teo, Z. L., et al. (2018) · Nature Medicine

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

Cited by 992

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

Benjamini, Y., & Speed, T. P. (2012) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 913

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

Broad Institute Genome Sequencing Platform, Mikkelsen, T. S., Broad Institute Whole Genome Assembly Team, Wakefield, M. J., Aken, B., Amemiya, C. T., Chang, J. L., Duke, S., Garber, M., Gentles, A. J., et al. (2007) · Nature

Chromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Cited by 711

Using control genes to correct for unwanted variation in microarray data

Gagnon-Bartsch, J. A., & Speed, T. P. (2012) · Biostatistics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 442

Functional Genomic Analysis of Oligodendrocyte Differentiation

Dugas, J. C., Tai, Y. C., Speed, T. P., Ngai, J., & Barres, B. A. (2006) · The Journal of Neuroscience

Neurogenesis and neuroplasticity mechanismsMultiple Sclerosis Research Studies

Cited by 324

A statistical framework for analyzing deep mutational scanning data

Rubin, A. F., Gelman, H., Lucas, N., Bajjalieh, S. M., Papenfuss, A. T., Speed, T. P., & Fowler, D. M. (2017) · Genome Biology

CRISPR and Genetic EngineeringGenomics and Rare Diseases

Cited by 262

The Comparative Roles of Suppressor of Cytokine Signaling-1 and -3 in the Inhibition and Desensitization of Cytokine Signaling

Wormald, S., Zhang, J.-G., Krebs, D. L., Mielke, L. A., Silver, J., Alexander, W. S., Speed, T. P., Nicola, N. A., & Hilton, D. J. (2006) · Journal of Biological Chemistry

Cytokine Signaling Pathways and InteractionsProtein Tyrosine Phosphatases

Cited by 123

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

Belov, K., Sanderson, C. E., Deakin, J. E., Wong, E. S. W., Assange, D., McColl, K. A., Gout, A., de Bono, B., Barrow, A. D., Speed, T. P., et al. (2007) · Genome Research

Immune Response and InflammationGenomics and Phylogenetic Studies

Cited by 116

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

Peixoto, L., Risso, D., Poplawski, S. G., Wimmer, M. E., Speed, T. P., Wood, M. A., & Abel, T. (2015) · Nucleic Acids Research

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 105

Identification of cancer sex-disparity in the functional integrity of p53 and its X chromosome network

Haupt, S., Caramia, F., Herschtal, A., Soussi, T., Lozano, G., Chen, H., Liang, H., Speed, T. P., & Haupt, Y. (2019) · Nature Communications

Cancer-related Molecular PathwaysCancer Genomics and Diagnostics

Cited by 94

Global analyses of mRNA translational control during early Drosophila embryogenesis

Qin, X., Ahn, S., Speed, T. P., & Rubin, G. M. (2007) · Genome Biology

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 86

Evaluating stably expressed genes in single cells

Lin, Y., Ghazanfar, S., Strbenac, D., Wang, A., Patrick, E., Lin, D. M., Speed, T., Yang, J. Y. H., & Yang, P. (2019) · GigaScience

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 84

Removing unwanted variation with CytofRUV to integrate multiple CyTOF datasets

Trussart, M., Teh, C. E., Tan, T., Leong, L., Gray, D. H., & Speed, T. P. (2020) · eLife

Single-cell and spatial transcriptomicsAdvanced Proteomics Techniques and Applications

Cited by 51

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

Rubio, J. P., Tubridy, N., Bahlo, M., Stankovich, J., Burfoot, R., Butzkueven, H., Chapman, C., Johnson, L., Marriott, M., Mraz, G., et al. (2004) · Human Genetics

Multiple Sclerosis Research StudiesGenetic Associations and Epidemiology

Cited by 43