Post-Doctoral Researcher or Senior Post-Doctoral Researcher – Computational Biologist/Bioinformatician – Gut Inflammation Research APC 3/ Spoke 7
Description of project and role: We are seeking a highly motivated and experienced computational biologist/bioinformatician to join the APC’s BioIT core technology platform and Gut Inflammation Research Spoke to drive the discovery and validation of novel therapeutic targets in Inflammatory Bowel Disease (IBD) for the development of innovative medicines. The overall goal of our group is to identify and validate several new therapeutic targets for patients with IBD. Using functional genomics approaches, we will discover and map the cellular secretome-receptome inflammatory network in IBD and identify mediators and their specific receptor-mediated signalling pathways that drive inflammation in this disease. The successful applicant will analyse and integrate next generation sequencing (NGS) datasets (RNA-seq, ChIP-seq, DNA-seq) with the goal of identifying and validating new therapeutic targets for patients with IBD, including those patients that do not respond satisfactorily to current therapeutic approaches such as anti-TNF biologics. The successful candidate will apply their extensive experience in the collection, mining, integration and visualization of multiple -omics data sets, including genomics (Immunochip), transcriptomics (ChIPseq, RNAseq, Nanaostring), proteomics, RNAi screen data, flow data and clinical metadata to advance our biologic understanding of the secretome-receptome signalling networks driving inflammation and immunopathology in IBD. In this position, the individual is expected to make major scientific contributions to the research goals and milestones of the Gut Inflammation Spoke. The position will also provide the opportunity to develop leadership skills by providing guidance and mentorship to an active post-graduate community. The appointee will work as part of a larger well-established bioinformatics team in the APC’s BioIT core technology platform and will have the opportunity to collaborate with other bioinformaticians and research groups working on gut microbiome analysis in different projects. As a member of the BioIT core platform the successful candidate will have the opportunity to develop new analytical approaches and will receive specialist training as required. The successful candidate must be capable of working independently, of developing and applying computational solutions to biological questions, and of mentoring graduate students.
Required Qualifications/Experience: PhD (computer science, bioinformatics or biostatistics) and possessing significant experience with analysis of high-throughput datasets and integrative analysis of diverse omics datasets from different platforms. Must also have proven ability to conduct independent research to a very high level.
Preferred Qualifications/Experience:
Background and working knowledge in algorithms, scientific computing, machine learning or statistics.
Track record of independent critical thinking and scientific achievement evidenced by excellent publication record.
Significant experience with analysis of NGS datasets (RNA-seq, ChIP-seq, DNA-seq).
Experience with R/bioconductor, C/C++, Java, Perl, python, PLINK and the Unix (Linux) environment.
Experience in Gene Set Enrichment Analysis (GSEA) and data visualization approaches desirable.
The candidate should be knowledgeable, highly motivated, creative, and collaborative.
Excellent verbal and written communication skills.
Ability to work effectively in a highly collaborative research environment is required.
Background to Research Environment: The APC Microbiome Institute was formed in 2003 with funding from Science Foundation Ireland and over the last decade the APC has established itself as one of the leading global centres in gut microbiota and gut inflammation research. The APC Microbiome Institute has made several landmark discoveries and has published over 1300 research articles in peer-reviewed journals, generating many journal covers and associated editorials. The scientific organisation of the APC Microbiome Institute consists of several integrated research themes or ‘Spokes’ which are supported by multiple shared core technology platforms. The APC Microbiome Institute has significant strengths in microbiology, mucosal immunology, Inflammatory Bowel Disease (IBD) research, bioinformatics, pre-clinical and translational IBD research and is comprised of several multi-disciplinary teams investigating how the gut microbiome interacts with host systems to regulate human health and disease. The APC Microbiome Institute boosts a growing bioinformatics community, which has contributed to its success.
To Apply for position: Please submit a 1 page cover letter quoting the UNIQUE ID 7b, your C.V and the contacts of at least two referees to Grainne Heelan, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland. [email protected], on or before the closing date 31st January 2016.
Description of project and role: We are seeking a highly motivated and experienced computational biologist/bioinformatician to join the APC’s BioIT core technology platform and Gut Inflammation Research Spoke to drive the discovery and validation of novel therapeutic targets in Inflammatory Bowel Disease (IBD) for the development of innovative medicines. The overall goal of our group is to identify and validate several new therapeutic targets for patients with IBD. Using functional genomics approaches, we will discover and map the cellular secretome-receptome inflammatory network in IBD and identify mediators and their specific receptor-mediated signalling pathways that drive inflammation in this disease. The successful applicant will analyse and integrate next generation sequencing (NGS) datasets (RNA-seq, ChIP-seq, DNA-seq) with the goal of identifying and validating new therapeutic targets for patients with IBD, including those patients that do not respond satisfactorily to current therapeutic approaches such as anti-TNF biologics. The successful candidate will apply their extensive experience in the collection, mining, integration and visualization of multiple -omics data sets, including genomics (Immunochip), transcriptomics (ChIPseq, RNAseq, Nanaostring), proteomics, RNAi screen data, flow data and clinical metadata to advance our biologic understanding of the secretome-receptome signalling networks driving inflammation and immunopathology in IBD. In this position, the individual is expected to make major scientific contributions to the research goals and milestones of the Gut Inflammation Spoke. The position will also provide the opportunity to develop leadership skills by providing guidance and mentorship to an active post-graduate community. The appointee will work as part of a larger well-established bioinformatics team in the APC’s BioIT core technology platform and will have the opportunity to collaborate with other bioinformaticians and research groups working on gut microbiome analysis in different projects. As a member of the BioIT core platform the successful candidate will have the opportunity to develop new analytical approaches and will receive specialist training as required. The successful candidate must be capable of working independently, of developing and applying computational solutions to biological questions, and of mentoring graduate students.
Required Qualifications/Experience: PhD (computer science, bioinformatics or biostatistics) and possessing significant experience with analysis of high-throughput datasets and integrative analysis of diverse omics datasets from different platforms. Must also have proven ability to conduct independent research to a very high level.
Preferred Qualifications/Experience:
Background and working knowledge in algorithms, scientific computing, machine learning or statistics.
Track record of independent critical thinking and scientific achievement evidenced by excellent publication record.
Significant experience with analysis of NGS datasets (RNA-seq, ChIP-seq, DNA-seq).
Experience with R/bioconductor, C/C++, Java, Perl, python, PLINK and the Unix (Linux) environment.
Experience in Gene Set Enrichment Analysis (GSEA) and data visualization approaches desirable.
The candidate should be knowledgeable, highly motivated, creative, and collaborative.
Excellent verbal and written communication skills.
Ability to work effectively in a highly collaborative research environment is required.
Background to Research Environment: The APC Microbiome Institute was formed in 2003 with funding from Science Foundation Ireland and over the last decade the APC has established itself as one of the leading global centres in gut microbiota and gut inflammation research. The APC Microbiome Institute has made several landmark discoveries and has published over 1300 research articles in peer-reviewed journals, generating many journal covers and associated editorials. The scientific organisation of the APC Microbiome Institute consists of several integrated research themes or ‘Spokes’ which are supported by multiple shared core technology platforms. The APC Microbiome Institute has significant strengths in microbiology, mucosal immunology, Inflammatory Bowel Disease (IBD) research, bioinformatics, pre-clinical and translational IBD research and is comprised of several multi-disciplinary teams investigating how the gut microbiome interacts with host systems to regulate human health and disease. The APC Microbiome Institute boosts a growing bioinformatics community, which has contributed to its success.
To Apply for position: Please submit a 1 page cover letter quoting the UNIQUE ID 7b, your C.V and the contacts of at least two referees to Grainne Heelan, Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland. [email protected], on or before the closing date 31st January 2016.