About
Liam Childs’ Homepage
Research Interests
Next-Generation sequencing analysis
Currently I’m working on the OncoPath project. Current goals include the annotation of sequence variants detected in colo-rectal cancer samples.
Genome Wide Association Studies
I’m interested in developing tools that help integrate and disseminate data produced by GWAS. Recently I developed and produced Matapax, an online pipeline to make GWAS available to all Arabidopsis researchers. I am currently working on making several improvement to Matapax to improve run-time, ease-of-use and hope to eventually develop a database to store results that Matapax produces. RNA regulation of gene expression
Investigating several ways in which RNA structure may regulate the transcription and translation of genes in general, including phenomenon such as riboswitches and structured UTR regions in prokaryotic and eukaryotic genomes.
Prediction of ncRNA genes
Investigated the use of graph properties based on RNA structure in the prediction of ncRNA genes and their functions. The investigations culminated in the implementation of a tool called GraPPLE that provides predictions on the functionality of RNA sequences such as whether the molecule is functional or not and if so, then a possible function that it could take. This prediction is accompanied with a confidence measure. Effect of Polymorphisms on RNA Structure and Genes
By using tiling arrays to study several different Arabidopsis thaliana accessions we are able to predict Single Feature Polymorphisms (SFPs). Upon mapping these SFPs to the Arabidopsis genome we can investigate the effects that they have on potentially regulatory RNA structure.
Academic History
2006 - 2009
PhD (Bioinformatics)
“Bioinformatics approach to analysing RNA mediated regulation of gene expression”
University of Potsdam ([[http://www.uni-potsdam.de/english/|English]],[[http://www.uni-potsdam.de/|Deutsch]])
Potsdam
Germany\
2000 - 2004
B.Sc. (Bioinformatics) Honours 1st class
Sydney University
Sydney
Australia
Employment History
2013 - present
Post Doctoral Fellow
Humboldt University
Berlin
Germany
2009 - 2013
Post Doctoral Fellow
Max-Planck Institute for Molecular Plant Physiology
Potsdam
Germany
2004 - 2006
Bioinformatics Data Analyst
CSIRO Plant Industry
Black Mountain
Australia
Tools and Skills
Programming
Languages: C, C++, C#, Java, Python, SQL, R, Silverlight, Javascript
Paradigms: Waterfall, Test Driven Development, Agile Programming
Web technologies: web2py, cgi, ajax, rest
Association Mapping
TASSEL, GAPIT, EMMA
Tiling Arrays
TAS General CEL file analysis using R (Bioconductor) and Python.
Contact
Address
Knowledge Management in Bioinformatics
Institute for Computer Science
Humboldt-Universitaet zu Berlin
Rudower Chaussee 25
12489 Berlin
liam (dot) childs (at) hu (minus) berlin (dot) de
Publications
Zhang J, Ruf S, Hasse C, Childs LH, Scharff LB and Bock R (2012) Identification of cis-elements conferring high levels of gene expression in non-green plastids,The Plant Journal.
Zuther E, Schulz E, Childs LH, Hincha DK (2012). Clinal variation in the nonacclimated and cold acclimated freezing tolerance of Arabidopsis thaliana accessions. Plant, cell & environment.
Childs LH, Lisec J, Walther D (2012). Matapax: An Online High-Throughput Genome-Wide Association Study Pipeline. Plant Phys. 158: 1-8. doi: 10.1104/pp.112.194027
Ryngajllo M, Childs LH, Lohse M, Giorgi FM, Lude A, Selbig J, Usadel B (2011) SLocX: Predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Frontiers in Plant Science
Childs LH, Scharff LB , Walther D, Bock R, (2011) Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites. PLoS Genet 7(6): e1002155. doi:10.1371/journal.pgen.1002155
Lohse M, Nunes-Nesi A, Krueger P, Nagel A, Hannemann J, Giorgi FM, Childs LH, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B (2010) Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiology
Childs LH, Witucka-Wall H, Günther T, Sulpice R, von Korff M, Stitt M, Walther D, Schmid KJ, and Altmann T (2010) Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11: 188
Childs LH, Nikoloski Z, May P, Walther D (2009) Identification and classification of ncRNA molecules using graph properties. Nucl. Acids Res. 37(9): e66. doi:10.1093/nar/gkp20
Software
GraPPLE (originally: The RNA sorting hat)