POSTDOC IN 3D GENOMICS MODELLING – BIENKO GROUP

APPLICATION CLOSING DATE.
April 19th, Human Technopole (HT) is an interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health.
HT is composed of five Centers.
Neurogenomics, Computational Biology, Structural Biology, Genomics, and Health Data Science.
The Centers work together to enable interdisciplinary research and to create an open, collaborative environment that will help promote life science research both nationally and internationally.
About the lab.
The Bienko Group at HT (https://humantechnopole.
t/en/research-groups/bienko-group/) focuses on understanding the fundamental principles that regulate how chromatin is spatially organized in the nucleus of mammalian cells.
The Bienko Group also studies how the three-dimensional (3D) genome structure is affected by linear genome rearrangements, such as those commonly encountered in cancer.
The Bienko Group is now inviting outstanding candidates with a background in computational sciences/bioengineering/physics/mathematics to apply for a position as Computational Postdoc to develop innovative approaches for modelling the 3D genome structure in normal and cancer cells.
The candidates shall have a keen interest in applying quantitative approaches originally developed in hardcore sciences to biological problems, and a strong affinity for interdisciplinary research.
The Bienko Group is a culturally and gender diverse interdisciplinary team, where scientists from different academic backgrounds encompassing medicine, biology, biotechnology, and biophysics work synergistically to tackle challenging questions in the field of 3D genome biology and cancer genomics.
See previous work on the research topics of this call.
Here’s a list of sequencing methods that we have developed over the years.
scCircle-seq.
https://doi.
rg//rs.
.
s-/v1 scCUTseq.
https://doi.
rg/ GPSeq.
https://www.
ature.
om/articles/s-y BLISS.
https://www.
ature.
om/articles/s CUTseq.
https://www.
ature.
om/articles/s And here you can find some of the open-source software developed in our lab.
https://github.
om/BiCroLab https://github.
om/elgw/chromflock https://github.
om/elgw/deconwolf-gui Key tasks and responsibilities.
The successful candidate will apply advanced and out-of-the-box quantitative approaches to model how the genome is folded in 3D in the nucleus of different cell types/species, to assess the 3D genome dynamics during cell differentiation or pharmacologic/genetic perturbations, and to investigate how rearrangements of the linear genome sequence rewire the 3D genome structure, with a focus on cancer genomes.
The successful candidate will have access to a large volume of sequencing data that are being generated in the Bienko Lab by applying cutting-edge sequencing technologies to a variety of in vitro cell model systems (cell lines, organoids) as well as patient-derived samples.
Sequencing assays routinely deployed in the Bienko Lab include.
(i) whole-genome sequencing (WGS, both short- and long-read); (ii) Hi-C (both bulk and single-cell) to map DNA-DNA interactions at genome scale; (iii) GPSeq, a method previously developed in the Bienko to probe the radial arrangement of DNA in the cell nucleus (see https://www.
ature.
om/articles/s-y); (iv) various RNA-seq approaches (including scRNA-seq) to profile gene expression; (v) CUT&RUN to map DNA-protein interactions; (vi) BLISS, another method previously developed in the Bienko Lab, which maps DNA breaks genome wide (see https://www.
ature.
om/articles/s).
Specific tasks include.
Propose and implement innovative computational approaches for high-dimensional sequencing data integration and visualization (e.
., approaches to integrate the information provided by the sequencing methods listed above).
Develop advanced computational approaches for integrating single-cell Hi-C data with high-throughput DNA fluorescence in situ hybridization (FISH, a microscopy method for measuring the 3D cartesian position of any given DNA sequence in the cell nucleus) data obtained from the same cell.
Work closely with the experimentalists in the group to build/refine 3D genome models and guide new experiments based on model predictions, in an iterative fashion.
Study basic properties of the linear genome sequence and how they affect 3D genome structure across species.
Contribute to writing manuscripts describing the computational tools and analyses performed by the candidate, taking full responsibility for the content of the computational methods section, making source data available for other to reproduce all the analyses/plots, and making all related code available through a curated GitHub repository.
Essential requirements On the closing date for online applications, the candidate must fulfil all the following conditions.
Ph.
.
degree in Physics/Biophysics/Mathematics/Computer science/Computational biology.
Fluency in at least one of the following programming languages.
Bash; C++; Python; R; MATLAB.
Fluency in oral and written English.
Preferred requirements Candidates with background in polymer physics or who have previously worked with Hi-C or equivalent method data and/or on 3D genome modelling (as documented in a published paper or M.
c./Ph.
.
thesis) will be prioritized.
Organizational and social skills Problem-solving and forward-looking personality, i.
., they are motivated to solve challenging problems even if this requires extensive troubleshooting and often revising the original plan.
Strong collaborative attitude and ability to work with people from very different academic background, i.
., they are willing to communicate with people without a strong math/physics background and, in turn, are open to learn about biology from experimentalists with biological/medical background.
Application Instructions To apply, please send the following.
An updated CV.
A 1-page motivation letter in English relating your track record to the specifics of the call.
Names and contacts of 2 referees.
Why Human Technopole.
HT seeks scientific excellence, we recruit the best scientific talents through international, open calls.
Our working environment is international, friendly, and inclusive.
Our scientists work together across disciplines on research topics of biomedical relevance, leveraging synergies between their diverse skillsets and methodological approaches.
We believe that highly diverse teams yield the best and most innovative results.
We engage in outward-facing scientific activities aimed at benefiting the national and international research community.
Training is also at the heart of our activity, with initiatives and opportunities for our staff, including scientific courses, conferences, and workshops.
Main benefits Welfare plans.
Canteen service.
Work-life balance provisions.
Italian language training for foreigners.
Parental leave up to 1 year and other support for new parents.
Counseling.
Flexible working hours.
Remote working policy.
Support for relocation.
Researchers coming to Italy for the first time, or returning after residing abroad, benefit from very attractive income tax benefits.
Special consideration will be given to candidates who are part of the protected categories list, according to L.
.
Number of positions offered.
1 Contract offered.
CCNL Chimico Farmaceutico, Fixed-term 4 years – employee level.
Salary up to 40K.
The position is based in Milan.
Tagged as.
Life Sciences