[SocBiN] PhD student positions in zebrafish genome annotation, gene regulation and data integration

[Carsten Daub]

Dear colleagues,

I am looking for two excellent PhD student candidates for our open calls, see below. 

Candidates must not have resided or carried out their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately prior to the recruitment, and have no more than 4 years of research experience since the degree that would qualify for admission onto the PhD programme, e.g. Masters degree.

The application deadline is May 18, 2015. 

Cheers,
Carsten 
---
Carsten O. Daub, PhD
Associate Professor, Group Leader 
Department of Biosciences and Nutrition & Science for Life Laboratory 
Karolinska Institutet
Stockholm, Sweden
http://ki.se/bionut/daub/

Phone +46 (0) 8-524-81224
Mobile: +46 (0) 72-250-6890





Position I: 

PhD student position in data integration and visualization for zebrafish genome annotation (Bioinformatics) in Stockholm, Sweden

http://www.nature.com/naturejobs/science/jobs/520467-phd-student-position-in-data-integration-and-visualization-for-zebrafish-genome-annotation-bioinformatics

Duties
The consortium will produce a variety of complementary genome-wide data including ChIP-Seq, CAGE, miniCAGE, and RNA-Seq. The PhD student will first develop data structures that are the basis for sharing heterogeneous data across the consortium as well as for data dissemination with the publication. The student will consolidate consortium data and develop annotation strategies together with the consortium members. Importantly, the student will creatively develop and implement data visualization methods for the consortium data including primary data and analysis results. The student will also be involved in data analysis of consortium data related to specific biological questions.

Qualifications
The PhD program at Karolinska Institutet corresponds to 4 years full time studies. We are seeking a highly motivated and talented PhD student who creatively plans, thoroughly executes and interprets data structures, annotation and visualization of heterogeneous high-throughput sequencing data. As successful candidate you have a masters degree in Bioinformatics, computer science, computational biology or a related field. Systematic thinking and excellent programming skills are essential. Experience with analysis of high-throughput data and experience with sequencing data is a strong plus. Excellent communication skills, a proactive and constructive personality as well as fluent English speaking and writing abilities are expected.




Position II: 

PhD student position in zebrafish genome annotation and gene regulation (Bioinformatics) in Stockholm, Sweden 

http://www.nature.com/naturejobs/science/jobs/520465-doctoral-phd-student-position-in-zebrafish-genome-annotation-and-gene-regulation-bioinformatics

Duties
The PhD student will focus on developing methods to bring together zebrafish annotation developed in the consortium with mammalian annotation and large-scale data (for exampled from ENCODE and FANTOMprojects) in order to generate a unified understanding of vertebrate genomic elements and to establish/strengthen zebrafish as a model organism for human functional genomics. This includes applying and developing computational methods to find key regulatory events driving for example specific developmental stages or lineage speciation events. Importantly, the student will also evaluate how and to what extend these functionally relevant regulatory features in zebrafish correspond to gene regulatory events in human development or disease.

Qualifications
The PhD program at Karolinska Institutet corresponds to 4 years full time studies. We are seeking a highly motivated and talented PhD student who creatively plans, thoroughly executes and interprets cross-species comparisons of functional genomic elements, functional annotation and gene-regulatory events and networks. As successful candidate you have a masters degree in Bioinformatics, computational biology or a related field. Creative and systematic thinking together with an interest in biological questions are essential. Experience with analysis of high-throughput data and experience with sequencing data is a strong plus. Excellent communication skills, a proactive and constructive personality as well as fluent English speaking and writing abilities are expected.