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Bioinformatician looking for interesting work in Vaud

I am currently available for work
Serial No: 7136

List top 5 skills: c/c++, Perl, python, sap/abap
Short Bio:

Graduate from Imperial College, London. Doctorate in Computational Biology from London University. Computational biologist/ bioinformaticist for the Human Genome Project, Sanger Centre in Cambridge, where I was the data manager for the largest genetic research project in osteo-arthritis. I was also a co-developer for the European Molecular Biology Open Source Software (EMBOSS) group.

I am named as co-author in several publications in Nature, Science and Plos. Now living in Switzerland and l

Current location: 

Vaud, Switzerland - View on map

Nationality: 

English French Dual National

Preferred Sector of Employment: 

Pharmaceutical and Science, IT and Technology

Spoken languages: 

english, french

Locations I am interested in working:

switzerland

List of countries I have a visa to work in:

switzerland, United Kingdom



IT SKILLS SUMMARY

SAP, ABAP, C/C++, PERL, Windows, Linux, MacOSX, Unix, EMBOSS, SQL, CORBA, Globus

EMPLOYMENT HISTORY

2011 – Present Yireh GmbH

Yireh GmbH is a small SAP technical consultancy and software development house. Their key product, developed with Xiting AG, is the Automatic Role Builder as used by SAP and mentioned in OSS Note 1682316

I have been involved in several SAP projects, part-time from 2011, full time from 2013.

• Tools to assist 3rd party produces of SAP software development – comparing different releases of products from transports and version management, enabling better control of new releases of products to customers.

• Large scale Time zone analysis. A multinational client realised, that due to its international nature, many administrative tasks (such as procurement of stock, shipping and delivery dates, bookings, billing and payments) were being performed across multiple time zones. What was not necessarily known was whether any individuals performing these tasks, were working in their local date and time zone, or were working according to system time. This could potentially cause timing errors, in areas such as expected dates of delivery, or credit control.

My task was to go through the SAP system and analyse the impact of local time zones. This involved a systematic assessment of the system’s code and report :

◦ wherever user entry of dates and times were involved, and in each case if there was a conversion from local time to system time in the routine.

◦ Where there was no conversion, to assess the importance of each routine and decide if it was a potential problem.

◦ To prioritise the potential problem routines so that they could be addressed.

During the course of this project, I developed tools to automate much of the analysis work.

• “Last use” analysis. An “aged program” report, showing the number of programs not used since one, two, etc. months ago, according to the data held in transaction ST03.

• Analysis of the code dump SNAP table format for conversion to an XML file format.

• Algorithm for condensing specific internal tables. For this project, object pairs which have identical fields but with one field value different can be merged together.

With large internal tables containing many objects, there are many ways in which different object pairs can be defined and merged. Some of these merge patterns are more efficient than others, resulting in more compact tables. The algorithm imports an internal table, finds the most efficient object merge pattern for the data in the table, and then condenses and exports the table . This is a key part of the Automatic Role Builder

2011 – 2013 Line Manager, Inventec Performance Chemicals SA

• The team I ran was responsible for the refurbishment and cleaning of electronics and high performance and precision engineering components.

• The process included the use of a number of specially formulated organic compounds which were used as degreasing and dewatering agents. These organic compounds were volatile and could pose unique risks to the body. My scientific expertise was required to quickly identify and propose improvements and additions to the standard health and safety measures in the work place. These proposals were accepted by the upper management and adopted.

• Within six months of taking on the task as the team manager, I expanded the team and almost doubled turnover.

• The work required flexibility in order to adapt to different projects and sudden demand changes.

• I was responsible for:

◦ Coordinating the team, and workflow

◦ Ensuring quality control stayed at the high standard expected by Swiss engineering firms.

◦ Planning for the client’s demands.

◦ Streamlining the stock control and programming the stock control software.

◦ Maintaining supplies.

◦ Coordinating the deliveries

2009 – 2010 Statistical Genetics Programmer/Data Manager, The Wellcome Trust Sanger Institute,Hinxton,Cambridge

• I was responsible for maintaining the data for the arcOGEN project (Arthritis Research Campaign Osteoarthritis GENetics study). This is a large scale genome wide association investigation into the causes of osteoarthritis.

• My duties involved developing bespoke pipelines for data manipulation, statistical analyses and meta analyses for large genetic data sets.

• I investigated current relevant software applications and their integration into the study. Where there were no suitable tools present, I was responsible for developing them (mainly in perl).

• This involved working closely with all team members to provide them solutions and support for a very wide range of problems, applications and diverse programming languages.

• I extensively used open source genetics packages such as PLINK, and frequently wrote perl scripts to manipulate the input and output data and of such packages. I also wrote genome wide association pipelining scripts in perl to automate and control the use of packages such as PLINK, GWAMA and R. Simplifying the processes for meta-analyses, forest plotting, regional plotting and other data reporting.

2006 – 2009 Computational Biologist, The Wellcome Trust Sanger Institute,Hinxton,Cambridge

• My duties included developing applications in C to analyse the relationships between point mutations (SNPs), Copy number variations (CNVs), and gene expression within populations. All development had been from the ground up.

• This project was computationally highly intensive and required the handling of very large amounts of data, involving the use of large cluster computing.

• I worked closely with team members providing rapid design of perl based analysis tools and assistance with perl programming problems.

2001 – 2005 Post Doc Boinformatician, Human Genome Mapping Project Resource Centre, Human Genome Project Campus, Hinxton, Cambridgeshire

• I investigated the technologies of distributed programming to be used in conjunction with EMBOSS (European Molecular Biology Open Source Suite).

• To this end I developed a multi-threaded CORBA based EMBOSS application server using the C programming language and the EMBOSS libraries

• I examined the use of the Grid toolkit Globus 2.4, and developed a prototype EMBOSS application server using globus, EMBOSS and C.

• I was the site administrator for “The Bioinformatics Resource” website .This involved a major internal redevelopment of the original website, on-going maintenance, query processing and database management

1998 – 2001 PhD Student, Crystallography Department Birkbeck College, London

• I developed a prototype algorithm to predict MHCII/Peptide binding

• This used the standard molecular dynamic program (AMBER) to generate the databases.

• PERL scripts were extensively used to scan and analyse the databases

• I developed this system on RedHat Linux and had to modify the AMBER source code to make it compatible with Linux.

• I carried out all installations and modifications of the operating system and applications myself.

1995 – 1998 Research Assistant, Crystallography Department, Birkbeck College, London.

• I developed C++ class libraries on UNIX (Irix 5.2), as part of a London University based research team, for use with a wide range of biological applications

1994 – 1995 Analyst Programmer, Charing Cross Hospital, London.

• I developed applications in Excel VBA, to analyse data produced in scientific research.

• To this end, I built relational databases using FoxPro 2.5 and SQL.

• I also successfully implemented a project to build a database/C++ application for monitoring levels of radioactive materials in use in the department

1993 – 1994 Volunteer Work, Hungary

• I travelled around Hungary liaising with humanitarian groups and working with homeless people, Romanian gypsies, orphans and young offenders

1992 – 1993 Research Biochemist, Regional Endocrine Unit, Southampton General Hospital, Southampton

• I worked on protein/hapten conjugation reactions, which were used to produce antibodies for further immunoassay research.

• I also measured urine growth hormone levels for medical research

1991 – 1992 Research Assistant, Diagnostics Research Unit, Bournemouth

• I developed Fluoro-Immunoassay techniques for measuring urine hormone levels.

EDUCATION

1998 – 2001 Birkbeck College, London University

PhD – Bioinformatics

1993 – 1994 Birkbeck College, London University

MSc- Computer Modelling of Molecular and Biological Processes

1987 – 1991 Associate of The Royal College of Science (ARCS)

1987 – 1991 Imperial College, London University

BSc.- (Hons) Biology

PUBLICATIONS

2010 Bioinformatics: (2010) 26(19): 2474-2476 :online doi:10.1093/bioinformatics/btq452

Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies

2010 PLoS Genet 6(4): e1000895. doi:10.1371/journal.pgen.1000895

Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations

2009 Science DOI: 10.1126/science.1174148

Common Regulatory Variation Impacts Gene Expression in a Cell Type–Dependent Manner

2008 PLoS Genet. 2008 Oct;4(10):e1000244. Epub 2008 Oct 31.

Modifier effects between regulatory and protein-coding variation.

2007 Nat Genet. 2007 Sep 16; : 17873874

Population genomics of human gene expression.

2007 Genome Biol. 2007 Jun 19;8(6):R118

Fast-evolving noncoding sequences in the human genome.

2007 Science. 2007 Feb 9;315(5813):848-53.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

2004 PhD Thesis

MUNCH: – A Prototype Algorithm for Predicting Peptide Binding to Major Histocompatibility Complex Class II Proteins

2003 Molecular Medicine; 9(9-12): 220-5.

A Novel Predictive Technique for the MHC Class II Peptide-Binding Interaction

1995 Proceedings of the ACB National Meeting

Abstract: Reduced Urinary Sodium/Potassium Ratio in the Luteal Phase of Women with Pre-Menstrual Syndrome.