Tim Massingham, Ph.D. - Publications

University of Oxford, Oxford, United Kingdom 

22/22 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Klopfstein S, Massingham T, Goldman N. More on the Best Evolutionary Rate for Phylogenetic Analysis. Systematic Biology. PMID 28595363 DOI: 10.1093/Sysbio/Syx051  1
2012 Sipos B, Massingham T, Stütz AM, Goldman N. An improved protocol for sequencing of repetitive genomic regions and structural variations using mutagenesis and next generation sequencing. Plos One. 7: e43359. PMID 22912860 DOI: 10.1371/Journal.Pone.0043359  1
2012 Massingham T, Goldman N. Error-correcting properties of the SOLiD Exact Call Chemistry. Bmc Bioinformatics. 13: 145. PMID 22726842 DOI: 10.1186/1471-2105-13-145  1
2012 Massingham T, Goldman N. All Your Base: a fast and accurate probabilistic approach to base calling. Genome Biology. 13: R13. PMID 22377270 DOI: 10.1186/Gb-2012-13-2-R13  1
2012 San Mauro D, Gower DJ, Cotton JA, Zardoya R, Wilkinson M, Massingham T. Experimental design in phylogenetics: testing predictions from expected information. Systematic Biology. 61: 661-74. PMID 22328568 DOI: 10.1093/Sysbio/Sys028  1
2011 Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, ... ... Massingham T, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/Nature10530  1
2011 Sipos B, Massingham T, Jordan GE, Goldman N. PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. Bmc Bioinformatics. 12: 104. PMID 21504561 DOI: 10.1186/1471-2105-12-104  1
2010 Flicek P, Aken BL, Ballester B, Beal K, Bragin E, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Fernandez-Banet J, Gordon L, Gräf S, Haider S, ... ... Massingham T, et al. Ensembl's 10th year. Nucleic Acids Research. 38: D557-62. PMID 19906699 DOI: 10.1093/Nar/Gkp972  1
2009 San Mauro D, Gower DJ, Massingham T, Wilkinson M, Zardoya R, Cotton JA. Experimental design in caecilian systematics: phylogenetic information of mitochondrial genomes and nuclear rag1. Systematic Biology. 58: 425-38. PMID 20525595 DOI: 10.1093/Sysbio/Syp043  1
2009 Chor B, Horn D, Goldman N, Levy Y, Massingham T. Genomic DNA k-mer spectra: models and modalities. Genome Biology. 10: R108. PMID 19814784 DOI: 10.1186/Gb-2009-10-10-R108  1
2008 Taylor MS, Massingham T, Hayashizaki Y, Carninci P, Goldman N, Semple CA. Rapidly evolving human promoter regions. Nature Genetics. 40: 1262-3; author reply. PMID 18957975 DOI: 10.1038/Ng1108-1262  1
2008 Massingham T. Detecting the presence and location of selection in proteins. Methods in Molecular Biology (Clifton, N.J.). 452: 311-329. PMID 18566771 DOI: 10.1007/978-1-60327-159-2_15  1
2008 Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A. Determination and validation of principal gene products. Bioinformatics (Oxford, England). 24: 11-7. PMID 18006548 DOI: 10.1093/Bioinformatics/Btm547  1
2007 Massingham T, Goldman N. Statistics of the log-det estimator. Molecular Biology and Evolution. 24: 2277-85. PMID 17703055 DOI: 10.1093/Molbev/Msm160  1
2007 Geuten K, Massingham T, Darius P, Smets E, Goldman N. Experimental design criteria in phylogenetics: where to add taxa. Systematic Biology. 56: 609-22. PMID 17654365 DOI: 10.1080/10635150701499563  1
2007 Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, ... ... Massingham T, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816. PMID 17571346 DOI: 10.1038/Nature05874  0.96
2007 Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M, Taylor J, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, ... ... Massingham T, et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Research. 17: 760-74. PMID 17567995 DOI: 10.1101/Gr.6034307  1
2006 Freilich S, Massingham T, Blanc E, Goldovsky L, Thornton JM. Relating tissue specialization to the differentiation of expression of singleton and duplicate mouse proteins. Genome Biology. 7: R89. PMID 17029626 DOI: 10.1186/Gb-2006-7-10-R89  1
2005 Freilich S, Massingham T, Bhattacharyya S, Ponsting H, Lyons PA, Freeman TC, Thornton JM. Relationship between the tissue-specificity of mouse gene expression and the evolutionary origin and function of the proteins. Genome Biology. 6: R56. PMID 15998445 DOI: 10.1186/Gb-2005-6-7-R56  1
2005 Massingham T, Goldman N. Detecting amino acid sites under positive selection and purifying selection. Genetics. 169: 1753-62. PMID 15654091 DOI: 10.1534/Genetics.104.032144  1
2001 Massingham T, Davies LJ, Liò P. Analysing gene function after duplication Bioessays. 23: 873-876. PMID 11598954 DOI: 10.1002/bies.1128  1
2000 Massingham T, Goldman N. EDIBLE: experimental design and information calculations in phylogenetics. Bioinformatics (Oxford, England). 16: 294-5. PMID 10869025 DOI: 10.1093/Bioinformatics/16.3.294  1
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