Bioinformatician, Bienko Group

Bioinformatician, Bienko Group

HT - Human Technopole

Milan, Italy

Job description

APPLICATION CLOSING DATE: February 18^th, 2024

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.it/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 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.

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.org/10.21203/rs.3.rs-2617401/v1;
scCUTseq:https://doi.org/10.1101/2023.11.07.566123;
GPSeq:https://www.nature.com/articles/s41587-020-0519-y;
BLISS:https://www.nature.com/articles/s41596-020-0397-2;
CUTseq:https://www.nature.com/articles/s41467-019-12570-2.

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 https://www.nature.com/articles/s41587-020-0519-y); (iv) full-length RNA-seq; (v) CUT&Tag; (vi) BLISS, another method previously developed in the Bienko Lab, which maps DNA double-strand breaks (DSBs) genome wide (see https://www.nature.com/articles/s41596-020-0397-2).

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);
• 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 and participate in writing manuscripts describing the results of the analyses performed by the candidate.

Job requirements

Essential requirements:

On the closing date for online applications, the candidate must fulfil all the following conditions:

• M.Sc. or Ph.D. degree (obtained within the call closure) in Quantitative Biology, Biotechnology, Bioengineering, Genomic Sciences, or equivalent. Candidates with M.Sc. or Ph.D. degree in Mathematics or Physics and a genuine interest in learning biology and working on challenging biological problems are also welcome to apply;
• Fluency in at least one of the following programming languages: Phyton; R; Bash; MATLAB;
• Problem-solving and forward-looking personality;
• Strong collaborative attitude;
• Willingness to work alongside experimentalists who do not necessarily have a strong background in bioinformatics and statistics, providing an explanation of the computational methods used and analytical results obtained that can be understood by them;
• Fluency in oral and written English.

Preferential requirements:

• Candidates who have previously worked on the analysis of data produced with one or more of the following methods (as documented in a published paper or M.Sc./Ph.D. thesis) will be given high priority: Hi-C (and derivatives); ChIP-seq; CUT&Run/CUT&Tag; ATAC-seq; (sc)RNA-seq; WGS/WES.

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.

Special consideration will be given to candidates who are part of the protected categories list, according to L. 68/99.

Number of positions offered: 1
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