Sr. Bioinformatician​/Bioinformatician, Bienko Group, ERC Consolidator Grant; RADIALIS project

Position: Sr. Bioinformatician/Bioinformatician, Bienko Group, ERC Consolidator Grant (RADIALIS project)
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Final date to receive applications:
September 15th, 2025
Application Instructions

To apply , please forward a single document containing:
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.
The  Human Technopole Foundation  ( HT ) is an interdisciplinary research institute, created and supported by the Italian government, whose aim is to develop innovative strategies to promote human health and healthy aging through a multidisciplinary and integrated approach, combining genomics, computational biology, structural biology, neuroscience and health data science. HT scientists work together to enable interdisciplinary research and to create an open, collaborative environment to help promote life science research nationally and internationally.

In line with its mission to serve the research community at large, HT operates National Facilities, specifically aimed at making HT’s technologies, methods and tools available to the national scientific community.
About the lab:
The Bienko Group at HT ((Use the "Apply for this Job" box below).) focuses on understanding the fundamental principles that regulate how chromatin is spatially organized in the nucleus of mammalian cells. The group also studies how the three-dimensional (3D) genome structure is affected by complex genomic rearrangements, such as those commonly encountered in human cancers.
The group is now inviting outstanding candidates with expertise in NGS bioinformatics and a strong interest in 3D genome biology and cancer genomics, to apply for a position as a  Bioinformatician/Sr. Bioinformatician .
Key tasks and responsibilities:
The successful candidate will work in an international and interdisciplinary team, applying state-of-the-art computational tools to  investigate how complex genomic rearrangements rewire the 3D genome structure and, in turn, affect gene expression .
To this end, the successful candidate will analyse a large amount of sequencing datasets that are being generated in the Bienko Lab by applying a variety of omic assays to map the 3D genome, breakome, epigenome, and transcriptome of cells engineered in vitro to harbour chromosomal translocations and other genomic rearrangements, as well as of patient-derived tumor specimens.
NGS 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); (iii) GPSeq, a method previously developed in the Bienko to probe the radial arrangement of chromatin in the cell nucleus (see ); (iv) full-length RNA-seq; (v) CUT&RUN; (vi) BLISS, another method previously developed in the Bienko Lab, which maps DNA double-strand breaks (DSBs) genome wide (see ).
Specific tasks include:
Implement, maintain, and apply state-of-the-art pipelines and software for: (i) processing Hi-C, WGS (both short and long-read), RNA-seq, CUT&Tag, and BLISS data; (ii) calling somatic copy number alterations (SCNAs) and structural variants (SVs) by integrating WGS and Hi-C data; (iii) calling A/B compartments, TADs, and chromatin loops from Hi-C data; (iv) peak calling from CUT&Tag data; (v) gene expression quantification, transcript isoform mapping, gene set enrichment, etc;

(vi) multi-omic data integration, including comparison with publically available datasets (e.g., from ENCODE, TCGA, PCWGA).
Maintaining and updating the lab’s Git Hub repositories.
Use rigorous statistical methods to study the relationship between linear genome sequence, 3D genome structure, epigenome, and transcriptome.
Propose and implement innovative ways of analysing and/or visualizing the available rich datasets.
Curate the deposition of the datasets in public repositories, such as ENA or SRA.
Work closely with the experimentalists in the group who generate the data analysed, advising on experimental design, providing feedback on data quality, and offering internal workshops to explain the analytical tools used and the obtained results.
Producing plots for…