PhD Student position in bioinformatics or functional
PhD student position available in the laboratory headed by Prof. Jussi Taipale and Dr. Norman Zielke at the Finnish Center of Excellence in Tumor Genetics Research (CoETG) at the University of Helsinki.
Our laboratory employs diverse systems-biology approaches to understand how tissue-specific transcription factors collaborate with oncogenic signals to drive cell proliferation. Current lines of work include computational and experimental identification of TF binding sites, and combination of the generated datasets for identification of regulatory elements that control cell growth during normal development or in cancer. The identified regulatory elements are validated using CRISPR/CAS9-mediated genome editing in cultured cells and model organisms.
Selected publications from Taipale lab:
K. Palin et al., Contribution of allelic imbalance to colorectal cancer. Nat. Commun. 9, 3664 (2018).
F. Zhu et al., The interaction landscape between transcription factors and the nucleosome. Nature (2018).
B. Wei et al., A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility. Nat. Biotechnol. (2018).
Y. Yin et al., Impact of cytosine methylation on DNA binding specificities of human transcription factors. Science. 356 (2017).
K. Dave et al., Mice deficient of Myc super-enhancer region reveal differential control mechanism between normal and pathological growth. Elife. 6 (2017),
K. Sur et al., Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors. Science. 338, 1360–1363 (2012).
N. Zielke et al., Control of Drosophila endocycles by E2F and CRL4. Nature. 480, 123–127 (2011).
A successful candidate has, or is close to obtaining a MSc or in either molecular biology, genetics, biotechnology or computer science or mathematics and most importantly, strong enthusiasm to solve complex biological problems, such
as those presented in molecular oncology.
Desired skills in Bioinformatics
The candidate should have solid programming skills (e.g. R, C, Python), knowledge of mathematical network modelling approaches, and ability to work independently in a multi-disciplinary team (i.e. ability to work and communicate with biologists is essential).
Desired skills in Functional Genomics
Experience in at least one of the listed areas is required: CRISPR/CAS9-mediated genome editing, mammalian cell culture with detailed knowledge on lentiviral transfection, Drosophila genetics, ChIP-Seq and related methods, preparation of libraries for next-generation sequencing approaches, data analysis.
Applications containing CV and two letters of reference should be submitted through the University webpage. The deadline for applications is 31th March 2019. For further information contact: firstname.lastname@example.org
The designated starting date would preferably be between June and October 2019, but can be negotiated under special circumstances. The initial contract of employment will be 2 years and includes a trial period of six months. Salary will be based on the Universities salary scheme for teaching and research personnel composed of both task specific and personal
performance components that will be evaluated during the first year, with typical starting levels of 2/5 (approx. 2400 EUR).
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