William Langdon 2014 Abstracts (except Genetic Programming)

Discussion of the state of the art in and future research on Software Testing during NII Shonan Meeting Computational Intelligence for Software Engineering, Seminar 053, 20-23 October 2014. The discussions between software engineers and experts in artificial intelligence were mainly lead by Andreas Zeller and Jens Krinke

Mycoplasma Contamination in The 1000 Genomes Project

Press Release

Sources

Genes Jump Silicon Barrier

ABSTRACT

In silco Biology is increasingly important and is often based on public data. While the problem of contamination is well recognised in microbiology labs the corresponding problem of database corruption has received less attention [1 More Mouldy Data In Silico Infection of the Human Genome].

Mapping 50 billion next generation DNA sequences from The Thousand Genome Project against published genomes reveals many that match one or more Mycoplasma but are not included in the reference human genome GRCh37.p5. Many of these are of low quality but NCBI BLAST searches confirm some high quality, high entropy sequences match Mycoplasma but no human sequences.

Molecular Biology, Microbiology, genetics, metagenomic, Data mining, Next-generation DNA sequencing, Data cleansing, High Throughput, Solexa, 454, SOLiD.

Schematic showing major data flows in Mycoplasma analysis of The Thousand Genome Project (top color). A random sample of next generation scan are copied across the Internet to the computer at UCL (black). Bowtie [1] is used to extract individual and paired-end DNA measurements which match one or more of the published Mycoplasma genomes. Bowtie is used a second time to exclude DNA measurements which match the reference human genome, leaving 75879 Mycoplasma DNA measurements from 2055 scans of the 4058 downloaded.

Cites include

Endosymbiotic origin and differential loss of eukaryotic genes, Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Filipa L. Sousa, Peter J. Lockhart, David Bryant, Einat Hazkani-Covo, James O. McInerney, Giddy Landan & William F. Martin, Nature 524, 427-432 doi:10.1038/nature14963 PMID: 26287458

Using populations of human and microbial genomes for organism detection in metagenomes, Sasha K. Ames, Shea N. Gardner, Jose Manuel Marti, Tom R. Slezak, Maya B. Gokhale, Jonathan E. Allen, Genome Res. 2015 July; 25(7): 1056-1067. doi: 10.1101/gr.184879.114 PMCID: PMC4484388

Large-scale contamination of microbial isolate genomes by Illumina PhiX control. Supratim Mukherjee, Marcel Huntemann, Natalia Ivanova, Nikos C Kyrpides and Amrita Pati, Standards in Genomic Sciences 2015, 10:18 PMCID: PMC4511556

A Novel Method for Detecting Contaminated Sample Based on Illumina Sequencing Data. International Journal of Bioscience, Biochemistry and Bioinformatics, 4(2) 2014, Zheng Huang and Qibin Li and Wei Jin and Qijun Liao and Xiao Sun http://www.ijbbb.org/papers/322-E0014.pdf

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive, Anthony O. Olarerin-George, John B. Hogenesch Nucleic Acids Res. 2015 March 11; 43(5): 2535-2542. doi: 10.1093/nar/gkv136 PMCID: PMC4357728

Here, there, and everywhere: From PCRs to next-generation sequencing technologies and sequence databases, DNA contaminants creep in from the most unlikely places, Karl Gruber, EMBO Rep. 2015 August; 16(8): 898-901 PMID: 26150097

W B Langdon Non-GP 2014 Abstracts

Computational Intelligence and Testing