David Baulcombe's Group
Department of Plant Sciences
University of Cambridge
Cambridge, CB2 3EA
email: rvn21 [at] cam.ac.uk
Studying plant epigenetics using new and emerging tools from bioinformatics for sequence analysis.
My future plan is to gain experience in analysing all types of high-throughput sequencing libraries and develop skills to integrate related data from multiple experimental analysis to form networks in a systems biology framework.
- Bioinformatics software development of ADDAPTS, our inhouse data driven pipeline and web-based tracking system for automated analysis of raw sequence files from high throughput sequencing technologies to analysis, alignment and
Gbrowse visualisation. Majority of the data in our pipeline is from small RNA libraries from experiments studying epigenetics.
- Differential expression analysis of small RNA and contigs between C3 and C4 plants and between sections of leaves from a C4 plant. This project is in collaboration with Dr. Sylvain Aubry and Dr. Julian
- SNP calling analysis from genomics reads sequenced from Illumina sequencing technologies. This project was in collaboration with Professor John Gray, and we are in the process of preparing a manuscript.
MSc - Applied Bioinformatics (Distinction)
Award: Course Team Prize
Main Modules: Gene expression Informatics, Sequence Analysis, Metabolomics, Proteomics, Structural and Systems Biology.
Core Programming Languages: Perl (with MySQL, CGI and BioPerl), R and Java
Group Project: Development of a web-based networking application for researchers to search, manage, analyse, controllably share and collaboratively analyse large datasets.
Thesis Project: Supervisor: Dr. Lee Larcombe; Development of a NGS-phylogenetic web-based pipeline application for automated characterisation of metagenomic samples from raw 454 sequencing files.
BSc - Bioinformatics Specialization (2:1 equivalent)
University of Auckland, New Zealand.
Main subjects : Bioinformatics, Computational Biology, Biochemistry, Genetics, Proteins, Statistics using R, Statistical programming & modelling using SAS, Software Design & Construction, Algorithm & Data Structure, Mathematics using
Matlab, Internet Programming using php & JSP, Computer Graphics using C++.
- Perl programming using Perl 5, MVC- Catalyst, Mason, CGI, MySQL, PostgreSQL, SOAP, LWP, Eutilities, and BioPerl
- Linux Command Line
- Project revision control system (Subversion)
- R statistics environment (Bioconductor packages, multivariate data analysis)
- Other Statistical languages: MATLAB, SAS
- Some experience in Java, JSP, C++, UML design
- Sequence alignment, analysis and visualising tools (Bowtie, BWA, SSAHA2, PATMaN, SAMtools, IGV, Gbrowse)
- Machine learning techniques (ANN, HMM, SVM and Random Forests)
- Networks analysis, modelling & Reverse engineering (Cytoscape & MP System)
- SYBYL molecular modelling and in silica drug discovery. Gene Predictions.
- Proteomics data analysis techniques, algorithms & repositories (iTRAQ, Mascot, X!Tandem, OMSSA, PRIDE)
- Chromatography techniques (HPLC, mass spectroscopy)
- PCR (polymerase chain reaction), electrophoresis
- Extemporaneous pharmaceutical preparation procedures
- ISCB : International Society for Computational Biologists
- CNN : Cambridge Network Networks Society