Job Description:
Responsibilities include taking raw and/or normalized deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) seq or array data from large cooperative group studies, examine for sample outliers (R2 values) and then analyze using gene set enrichment analysis (GSEA), independent practice associate (IPA), and any other platform that is relevant. Once the data has been generated from a combination of several of these methods, key gene signatures or driver hubs have been obtained based upon fold change or Z' values, you will be provided with the resources for biological confirmation of each of these signatures/ drivers to ensure that the signatures are of value. Address the technical performance of the various experiments (especially for array data) by comparing raw, quantile, cubic spline, and rank invariant for each of the experiments that have been run, and also compare the control samples of human brain and liver, as well as formalin fixed paraffin embedded (FFPE) sample controls inter and intra experiment. For the RNA Seq data, you will be responsible to assist with splice variant analysis and single nucleotide polymorphisms (SNP)/ copy number variation (CNV) analysis. This information will then need to be analyzed alongside the DNA seq, to determine if there are genomic drivers leading to altered expression or splicing of the RNA level. Requires a high degree of independence and will be responsible for assembling a data base of all known cancer drugs in terms of established or potential genomic biomarkers; this data base will need to be used in order to match targeted therapies with the gene signatures/ drivers in order to incorporate into the formal feedback in forward genomic protocols (i.e. for the sequencing tumor board). This will entail close communication with and travel to the Scripps La Jolla bioinformatics team. Data analysis plans will need to be established for each project, project tracking, standard uploading routines and reporting formats, weekly calls, abstract and manuscript generation. QUALIFICATIONS: MD PhD is required. Individual with at least 6 years experience in bioinformatics and at least 2 of those years in a managerial/leadership position. Demonstrated experience in next generation sequence analysis. Assembly and bioinformatics analysis of complex data-sets. Experience with electronic medical record (EMR) APIs and interfaces and movement of data out of and into EMRs. Experience programing in Python, Perl, R, and Java desirable. Experience with the integration and management of multiple data sources, workflows and enabling integrated management of and reporting on those data and processes through graphical user interfaces desirable. Preference will be given to individuals with expertise in genetic/epigenetic analyses and medical and/or research informatics experience. Essential to the applicants successful fulfillment of this role is a documented track record of academic and technical productivity with a demonstrated proficiency in budgeting and managing people.
Additional Info:
[Click Here to Access the Original Job Post]
Responsibilities include taking raw and/or normalized deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) seq or array data from large cooperative group studies, examine for sample outliers (R2 values) and then analyze using gene set enrichment analysis (GSEA), independent practice associate (IPA), and any other platform that is relevant. Once the data has been generated from a combination of several of these methods, key gene signatures or driver hubs have been obtained based upon fold change or Z' values, you will be provided with the resources for biological confirmation of each of these signatures/ drivers to ensure that the signatures are of value. Address the technical performance of the various experiments (especially for array data) by comparing raw, quantile, cubic spline, and rank invariant for each of the experiments that have been run, and also compare the control samples of human brain and liver, as well as formalin fixed paraffin embedded (FFPE) sample controls inter and intra experiment. For the RNA Seq data, you will be responsible to assist with splice variant analysis and single nucleotide polymorphisms (SNP)/ copy number variation (CNV) analysis. This information will then need to be analyzed alongside the DNA seq, to determine if there are genomic drivers leading to altered expression or splicing of the RNA level. Requires a high degree of independence and will be responsible for assembling a data base of all known cancer drugs in terms of established or potential genomic biomarkers; this data base will need to be used in order to match targeted therapies with the gene signatures/ drivers in order to incorporate into the formal feedback in forward genomic protocols (i.e. for the sequencing tumor board). This will entail close communication with and travel to the Scripps La Jolla bioinformatics team. Data analysis plans will need to be established for each project, project tracking, standard uploading routines and reporting formats, weekly calls, abstract and manuscript generation. QUALIFICATIONS: MD PhD is required. Individual with at least 6 years experience in bioinformatics and at least 2 of those years in a managerial/leadership position. Demonstrated experience in next generation sequence analysis. Assembly and bioinformatics analysis of complex data-sets. Experience with electronic medical record (EMR) APIs and interfaces and movement of data out of and into EMRs. Experience programing in Python, Perl, R, and Java desirable. Experience with the integration and management of multiple data sources, workflows and enabling integrated management of and reporting on those data and processes through graphical user interfaces desirable. Preference will be given to individuals with expertise in genetic/epigenetic analyses and medical and/or research informatics experience. Essential to the applicants successful fulfillment of this role is a documented track record of academic and technical productivity with a demonstrated proficiency in budgeting and managing people.
Requeriments :
Skills :
- DNA sequencing
- Genetics
- Next Generation Sequencing
- Programing in Python
- Programming in Java
- Programming in PERL
- Programming in R
- RNA-seq
Areas :
Additional Info:
[Click Here to Access the Original Job Post]