Tim Massingham
Overview
Explore the profile of Tim Massingham including associated specialties, affiliations and a list of published articles.
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19
Citations
4008
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Recent Articles
1.
Klopfstein S, Massingham T, Goldman N
Syst Biol
. 2017 Jun;
66(5):769-785.
PMID: 28595363
The accumulation of genome-scale molecular data sets for nonmodel taxa brings us ever closer to resolving the tree of life of all living organisms. However, despite the depth of data...
2.
Sipos B, Massingham T, Stutz A, Goldman N
PLoS One
. 2012 Aug;
7(8):e43359.
PMID: 22912860
The rise of Next Generation Sequencing (NGS) technologies has transformed de novo genome sequencing into an accessible research tool, but obtaining high quality eukaryotic genome assemblies remains a challenge, mostly...
3.
Massingham T, Goldman N
BMC Bioinformatics
. 2012 Jun;
13:145.
PMID: 22726842
Background: The Exact Call Chemistry for the SOLiD Next-Generation Sequencing platform augments the two-base-encoding chemistry with an additional round of ligation, using an alternative set of probes, that allows some...
4.
Massingham T, Goldman N
Genome Biol
. 2012 Mar;
13(2):R13.
PMID: 22377270
The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of...
5.
San Mauro D, Gower D, Cotton J, Zardoya R, Wilkinson M, Massingham T
Syst Biol
. 2012 Feb;
61(4):661-74.
PMID: 22328568
Taxon and character sampling are central to phylogenetic experimental design; yet, we lack general rules. Goldman introduced a method to construct efficient sampling designs in phylogenetics, based on the calculation...
6.
Lindblad-Toh K, Garber M, Zuk O, Lin M, Parker B, Washietl S, et al.
Nature
. 2011 Oct;
478(7370):476-82.
PMID: 21993624
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at...
7.
Sipos B, Massingham T, Jordan G, Goldman N
BMC Bioinformatics
. 2011 Apr;
12:104.
PMID: 21504561
Background: The Monte Carlo simulation of sequence evolution is routinely used to assess the performance of phylogenetic inference methods and sequence alignment algorithms. Progress in the field of molecular evolution...
8.
San Mauro D, Gower D, Massingham T, Wilkinson M, Zardoya R, Cotton J
Syst Biol
. 2010 Jun;
58(4):425-38.
PMID: 20525595
In molecular phylogenetic studies, a major aspect of experimental design concerns the choice of markers and taxa. Although previous studies have investigated the phylogenetic performance of different genes and the...
9.
Flicek P, Aken B, Ballester B, Beal K, Bragin E, Brent S, et al.
Nucleic Acids Res
. 2009 Nov;
38(Database issue):D557-62.
PMID: 19906699
Ensembl (http://www.ensembl.org) integrates genomic information for a comprehensive set of chordate genomes with a particular focus on resources for human, mouse, rat, zebrafish and other high-value sequenced genomes. We provide...
10.
Chor B, Horn D, Goldman N, Levy Y, Massingham T
Genome Biol
. 2009 Oct;
10(10):R108.
PMID: 19814784
Background: The empirical frequencies of DNA k-mers in whole genome sequences provide an interesting perspective on genomic complexity, and the availability of large segments of genomic sequence from many organisms...