Job Description Ref No 002450 Job Title

Research Assistant/Associate (Bioinformatician in chromatin epigenetics)

School / RI / College Reporting To

College of Medical, Veterinary and Life Sciences  Institute of Cancer Sciences Dr Adam West, Epigenetics Unit   Dr. David Vetrie, Epigenetics Unit

Job Purpose  You will be responsible for providing key bioinformatics support and research activities to the  West and Vetrie research groups, the aims of which are to address fundamental questions about  the chromosomal domain organisation of human cells and the regulatory processes that control  the expression of genes during mammalian haematopoietic development.    Further details of the work in our groups can be found at  www.gla.ac.uk/researchinstitutes/cancersciences/research/epigenetics     Relevant publications:  1: Hassan‐Zadeh V, Chilaka S, Cadoret JC, Ma MK, Boggetto N, West AG and Prioleau MN. USF  binding sequences from the HS4 insulator element impose early replication timing on a vertebrate  replicator. PLoS Biol. 2012, 10:e1001277.  2. Ma MK, Heath C, Hair A and West AG. Histone crosstalk directed by H2B ubiquitination is required  for chromatin boundary integrity. PLoS Genet. 2011 7:e1002175.  3: Dhami P et al. Complex exon‐intron marking by histone modifications is not determined solely by  nucleosome distribution. PLoS One. 2010, 5:e12339.  4: Dhami P et al. Genomic approaches uncover increasing complexities in the regulatory landscape at  the human SCL (TAL1) locus. PLoS One. 2010, 5:e9059.  5: Dickson J, Gowher H, Strogantsev R, Gaszner M, Hair A, Felsenfeld G and West AG. VEZF1  elements mediate protection from DNA methylation. PLoS Genet. 2010, 6:e1000804.  6: Bruce AW et al. Functional diversity for REST (NRSF) is defined by in vivo binding affinity  hierarchies at the DNA sequence level. Genome Res. 2009, 19:994‐1005.  7: ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the  human genome by the ENCODE pilot project. Nature. 2007 447(7146):799‐816.  8: Koch CM et al. The landscape of histone modifications across 1% of the human genome in five  human cell lines. Genome Res. 2007, 17:691‐707.

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Main Duties and Responsibilities Plan and implement, with limited supervision, all aspects of the design, implementation and  management of data and analytical pipelines to facilitate the research goals of the research  group. To perform statistical analyses, data mining and integrate biological data from various sources  with their associated genomic DNA sequence features. Data sources will include the analysis of  gene perturbation experiments assayed using expression microarrays, ChIP‐seq and RNA‐seq in  human and mouse systems. To develop and maintain collaborative interactions with other internal and external informatics  and experimental research groups. Research and maintain knowledge of current, new or alternative computer technologies/tools  which may be applicable to handling/analysing data from the relevant research projects. This  will include making these informatics tools available to the members of the team and provide  support and training for those tools. To contribute intellectually to the ongoing development within the team of innovative strategies  for i) defining chromosomal domain alterations during development or following gene  perturbation experiments and ii) exploring the relationships between chromatin states and the  progression of chronic myeloid leukaemia. To represent the group at internal/external meetings and conferences by giving talks and/or  presenting posters with scientific data. To contribute to the writing of papers for publication in peer‐reviewed journals. Development of ad hoc scripts for specific short‐term data handling needs, with an emphasis on  rapid implementation.  In addition for appointment at Grade 7:  To take the lead on writing papers for publication in peer‐reviewed journals and deciding on  appropriate journals with PI.  To take the lead in the drafting of grant applications.  Identify potential sources of funding and secure funding, as appropriate. 

Knowledge, Qualifications, Skills and Experience Knowledge/Qualifications Essential: A1. BSc in scientific discipline  A2. Knowledge of relevant resources for data‐mining for genome‐scale analyses  A3. Theoretical knowledge of basic principles of mammalian gene regulation  A4. Theoretical knowledge of expression and CHIP‐chip microarray analysis  A5. Knowledge of biological analysis pipelines For appointment at Grade 7:  A6. PhD in biological or bioinformatics/computational science. Skills Essential: C1. Extensive programming and scripting skills in appropriate languages, including Perl and Python  C2. Ability to work independently and as part of a team  C3. Capable of day‐to‐day direction of tasked projects  C4. Problem solving skills  C5. Efficient time management  C6. Excellent communication skills to present complex data in simple terms  C7. Keen eye for detail  C8. Data mining of microarray data using a variety of commercial/academic tools  C9. Capable of generating new ideas for data analysis  C10. Capable of identifying recurring DNA sequence motifs associated with biological data  C11. Facility with Ensembl API Experience Essential: E1. Minimum of 1‐2 years research experience   E2. Experience of developing software systems, with emphasis on text processing/report generation  E3. Experience of working with relational databases  E4. Experience using annotation/data analysis tools/genome browsers  E5. Experience in high‐throughput genomics research  E6. Experience of constructing biological data analysis pipelines  E7. Experience of preparing manuscripts for publication  E8. Experience in supervising other team members on bioinformatics projects  E9. Experience of mathematical programming in numerical Python  In addition for appointment at grade 7:  E10. 5 years research experience with 1‐2 years postdoctoral experience. Dimensions Length of contract  Four years from 1st August 2012 GU staff training and research support  Provide bioinformatics training to research scientists and postgraduate students (maximum of one at any time)  Ad hoc expert/professional advice to scientists in the Epigenetics Unit, and potentially other GU departments (typically 15 peers) Research  Plan and carry out ongoing research projects with Dr West’s and/or Dr Vetrie’s direction.  The recording and storing of data for the above projects  Publication of research papers from own data analysis and tool development Representation of Glasgow University Representing Glasgow University and promoting GU research at national and international scientific meetings

Job Features Planning and Organising Plan and implement a data analysis pipeline and relational database to support the work of several  projects over varying timescales which complement the research programme of the group. This will  involve planning and supervising his/her own work as well as liaising closely with members of the  team (post‐doctoral scientists, PhD students, group leader). Regular meetings with the group leader  are structured to help define longer term goals of the projects within the framework of the research  aims of the group.  Decision Making Responsible for making day‐to‐day and short‐term decisions with regards to the execution and  delivery of computational work. These include the ordering of equipment and consumables for the  work, evaluation and implementation of suitable softwares and algorithms and choosing suitable  peer‐review journals and conferences for presentation of the work in order to maximise  international exposure and enhance the reputation of the research group. Decisions regarding long‐ term goals and directions of the projects will be made in consultation with the research group leader  at regular (3‐monthly) meetings. Internal/External Relationships Establishing and maintaining collaborations; train/advise in specific computational methods and  softwares with both internal and external scientists and visiting workers.  Develop, foster and establish internal collaborations with senior and junior staff of the Institute and  attend internal interest group meetings.  Present/exchange data in the form of talks and/or posters in meetings (with collaborators), and at  conferences to the larger scientific community.  Day‐to‐day co‐ordination and supervision of work, presentation and discussion at group meetings  with other members of the research team.  Problem Solving To solve problems, together with experimental scientists, related to the interpretation of  computational results based on data generated within the group. In some instances, problem‐solving  will extend to the computational results of internal/external collaborators.  Other Salary will be on the University’s Research and Teaching Grade 6 (26,004 – £29,249) or Grade 7  (£31,948 – £35,938) per annum depending on experience.     The funding for this post is available immediately and is for 3 years in the first instance.    New entrants to the University will be required to serve a probationary period of 6 months.    The successful applicant will be eligible to join the Universities' Superannuation Scheme. Further  information regarding the scheme is available from the Superannuation Officer, who is also prepared  to advise on questions relating to the transfer of Superannuation benefits.    All research and related activities, including grants, donations, clinical trials, contract research,  consultancy and commercialisation are required to be managed through the University’s relevant  processes (e.g. contractual and financial), in accordance with the University Court’s policies.  Applications must be made online at www.glasgow.ac.uk/jobs.    Closing date: 20 August 2012.

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Dr Adam West Dr David Vetrie

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binding sequences from the HS4 insulator element impose early replication timing on a vertebrate replicator. PLoS Biol. 2012, 10:e1001277. 2. Ma MK, Heath C, ...

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