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Charles Bradshaw

Charles Bradshaw PhD

Core Bioinformatics

Co-workers: George Allen

Plain English: Modern molecular biology has become heavily dependent on computers, both to analyse data, and to provide access to external data resources and the means to display them. The core bioinformatics group provides embedded expert support for research scientists to understand these resources better, and to help with the interpretation and use of information and tools. Based on the needs of the institute we work to improve tools and develop new computational methods to aid biological research.

The core bioinformatics group is embedded into the research of the institute. We provide computational support for any area of modern biology, from sequence similarity searches to analysing genome-wide screening and Next Generation Sequencing (NGS) data. As we are integrated in the institute we are able to provide the closest possible collaborations and develop new tools and techniques based on novel discoveries.

Current research focuses:
* Analysis of NGS data (DNA-Seq, RNA-Seq and ChIP-Seq)
* Efficient processing of large datasets on our in-house cluster
* Tools for Biologists to better understand their sequencing data
* Integration of data from Biological Resources
* de novo assembly from NGS data and its application to NGS analysis methods
* Extracting biological meaning from genome-wide experiments (screens, microarray, NGS)

Charles Bradshaw

Experience and skills:
* Analysis of ChIP-Seq data (peak calling and motif detection)
* Analysis of RNA-Seq data (expression profiling, detection of novel isoforms)
* Analysis of DNA-Seq data (detection of sequence variants including SNPs and SVs)
* Replication profiling from NGS data
* de novo transcriptome assembly from NGS data
* de novo genome assembly and comparative analysis from NGS data
* Quality Control of NGS data (detection of contaminants)
* Large scale RNAi screen mapping, annotation and analysis
* Design of shRNAs, siRNAs and esiRNAs
* Annotation of proteomics mass spectrometry data
* Sequence analysis through inter-species conservation
* Large scale BLAST searches, and subsequent analysis for the detection of orthologs, paralogs and homologs
* Large scale domain detection through both sequence conservation and structural conservation
* Functional analysis through distant homology and weak sequence similarity
* Multiple sequence alignments and phylogenetic analysis
* Providing bioinformatics software and tools to users through web interfaces or local installations

* HMMerThread Database of remotely conserved domains

Selected publications:

Koziol MJ, Bradshaw CR, Allen GE, Costa AS, Frezza C, Gurdon JB (2015) Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat Struct Mol Biol 23(1) 24-30

Tang WW, Dietmann S, Irie N, Leitch HG, Floros VI, Bradshaw CR, Hackett JA, Chinnery PF, Surani MA (2015) A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development. Cell 161(6):1454-67

Jullien J, Miyamoto K, Pasque V, Allen GE, Bradshaw CR, Garrett NJ, Halley-Stott RP, Kimura H, Ohsumi K, Gurdon JB (2014) Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming. Mol Cell 55(4), 524-35

Miyamoto K, Teperek M, Yusa K, Allen GE, Bradshaw CR, Gurdon JB (2013) Nuclear Wave1 is required for reprogramming transcription in oocytes and for normal development. Science 341(6149), 1002-5

Collart C, Allen GE, Bradshaw CR, Smith JC, Zegerman P (2013) Titration of four replication factors is essential for the Xenopus laevis midblastula transition. Science 341(6148), 893-6

Rodriguez R, Miller KM, Forment JV, Bradshaw CR, Nikan M, Britton S, Oelschlaegel T, Xhemalce B, Balasubramanian S, Jackson SP (2012) Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat Chem Biol Feb 5;8;(3):301-10

Winter JF, Höpfner S, Korn K, Farnung BO, Bradshaw CR, Marsico G, Volkmer M, Habermann B, Zerial M (2012) Caenorhabditis elegans screen reveals role of PAR-5 in RAB-11-recycling endosome positioning and apicobasal cell polarity. Nat Cell Biol 14(7), 666-676

Bradshaw CR, Surendranath V, Henschel R, Mueller M and Habermann HH (2011) HMMerThread: Detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition. PLoS ONE 6(3): e17568

Collinet C, Stöter M, Bradshaw CR, Samusik N, Rink JC, Kenski D, Habermann B, Buchholz F, Henschel R, Mueller MS, Nagel WE, Fava E, Kalaidzidis Y and Zerial M (2010) Systems survey of endocytosis by multiparametric image analysis. Nature 464(7286), 243-9