COLOMARK Network

We are seeking 9 highly motivated fellows to pursue a career in science, obtain a PhD abroad and work in one of the three-year research projects we are offering under the Doctoral Network Marie Skłodowska-Curie Action ColoMARK. 

The ColoMARK network integrates 17 teams with multidisciplinary expertise (omics, epidemiology, microbiome, circulating tumour DNA, bioinformatics, statistics & machine learning, assay development, circulating RNAs, circulating tumour cells, tumour profiling, clinics) aiming at the identification and development of novel colorectal cancer (CRC) biomarkers via state-of-the-art liquid biopsy approaches. ColoMARK will provide cross- and interdisciplinary innovative training with special emphasis on transversal competences to 10 doctoral candidates (DCs). They will constitute a next generation of effective, multi-skilled and https://www.idisantiago.es/empleo/proactive future professionals that comply with the tenets of the Principles for Innovative Doctoral Training, and that achieve enhanced intersectoral employability.

Eligibility criteria for all DC positions under MSCA

• The applicants MUST not have resided or carried out their main activity (work, studies, etc.) in the country of the recruiting beneficiary for more than 12 months in the 36 months immediately before the recruitment date (unless as part of a compulsory national service or a procedure for obtaining refugee status under the Geneva Convention).
• Applicants MUST NOT be in possession of a PhD.
•  Additional eligibility criteria may be described for each position in the descriptions below. For more information on the open positions, please contact the partners directly depending on the research interest.

Working conditions

DCs will receive a fully funded working contract for three years including health insurance and social benefits. Salaries will comply with MSCA and local institution regulations. This quantity describes the living allowance for the DCs, including all costs related to the contract, including social security and insurance, where appropriate. A flat rate Mobility allowance will also be included in the contract. Additional allowances (family, long-term and special needs) will be added if applicable.

Description of DC projects and postions

DC1. Study of ctDNA biomarkers in the context of bowel cancer screening programmes

DC1 will evaluate the different ctDNA available technologies (NGS-based, ddPCR-based) and identify that with the highest sensitivity/specificity for early stages (pre-malignant polyps and localised tumours). Then, for each of the 150 patients, he/she will obtain the genomic profiles of: a) somatic mutation of the primary growth (including hotspot driver mutations; and b) the circulatory somatic mutation profile. The ctDNA predictivity will also be compared and/or used in conjunction with the a priori genetic polygenic risk score obtained from the genotyping of the 200+ SNPs that influence CRC risk. Models will be created to conjugate the fixed predisposition component together with epidemiological risk factors and dynamic ctDNA values to identify patients that should undergo colonoscopy

Recruiting centre: Fundación Instituto de Investigación Sanitaria de Santiago (FIDIS), Santiago de Compostela (Spain).

Academic qualications requested:  BSc in biomedical sciences* (or similar, depending on country) + MSc in bioinformatics OR  BSc in computer science* + MSc in genomics*.

*similar (in content) degrees may be considered (depending on description), as the titles may vary depending on country of origin

Skills requested:

• Proven bioinformatic understanding of NGS data analysis, particularly DNA variant calling.
• Working abilities on Linux environment and programming skills on R, bash or python.

Skills valued:

• Previous experience with ctDNA data analysis.
• Lab experience working with ctDNA Knowledge/work on cancer genetics/genomics.
• Previous experience with prediction models, including polygenic risk scores.
• Previous experience on biomarker development

Application procedure: Applicants should follow the application procedure and submit the files as a single pdf here: FIDIS Job Opportunities (position 001/2023).

DC2. A multi-omics and pathway centric investigation of the relationship between lifestyle factors & CRC risk

DC2 will develop and apply supervised and unsupervised machine learning methods for the construction of omics and multi-omics signatures associated with CRC risk. Multi-omics signatures of CRC risk derived in different subgroups of individuals characterised by specific lifestyle patterns will lead to the identification of candidate metabolites and genes that might underpin the impact of lifestyle on colorectal cancer development. The corresponding biological pathways will be explored making use of state-of-the art bioinformatics network-based tools to combine our results with prior knowledge from the literature and biochemical databases.

Recruiting centre: International Agency for Research on Cancer (IARC), Lyon (France).

Academic qualifications requested: An MSc with appropriate training in statistics, biostatistics, machine learning, or related fields.

Skills requested: Strong background in R and/or Python.

Skills valued: Experience with cancer epidemiology, with the analysis and/or pre-processing of omics data.

Application procedure: Applicants should follow the application procedure and send the files to nmb@iarc.fr and indicate “Application for ColoMARK PhD position” in the subject line.

DC3. Exploring the role of the microbiome, gut barrier dysfunction, host genetics, and metabolic interactions in the development of colorectal cancer

DC3 will involve laboratory assays such as ELISA assays, qPCR, and metagenomic sequencing, but there will be a major focus on biostatistical and bioinformatic approaches. Together, this will help shed light on the involvement of microbial translocation and microbially derived metabolic perturbations on adenoma progression and CRC development.

Recruiting centre: University College Dublin (UCD), Dublin (Ireland).

Academic qualifications requested:

• Applicants must have, or expect to have, reached a minimum of an upper second-class (2.1) degree or your institute’s equivalent in a relevant honours Bachelor’s + a Master’s degree.
• Relevant degree studies include Statistics, Bioinformatics, Mathematics, Computer Science, Microbiology, Biology, Genetics, Nutrition, Biochemistry, Biotechnology, Biomedical Science, Immunology, Public Health, Epidemiology.
• Excellent written and oral communication skills and a high level of competence in the English language are essential (see http://www.ucd.ie/registry/admissions/elr.html).

Skills requested:

• The successful candidate should have interests in both laboratory experiments and biostatistical and bioinformatic techniques, and microbial, nutrition, and genetics/genomics research in cancer.
• Preferred fields of study and training include Biostatistics, Bioinformatics, Epidemiology, Microbiology, Nutrition, and Genetics.
• A knowledge and / or enthusiasm for bioinformatic and statistical analysis of molecular data (such as ELISA protein concentrations, blood serotyping, genetic variation analyses, next generation metagenomic sequencing, and metabolomics) is essential.
• The candidate must either have experience of, or be willing to learn the biostatistical and bioinformatic methodologies for the analyses required in this project.
• A commitment to research integrity is essential.

Skills valued:

• Experience in basic biostatistical analysis methodologies is highly valued.
• Good verbal communication & writing skills are essential.
• Highly desirable skills include working abilities on database management and conducting data analysis using statistical software, e.g., R, SPSS, STATA, SAS, MATLAB, and/or experience of Linux and programming skills on R, bash or python.
• Experience with several techniques including ELISA, qPCR, and DNA sequencing.
• Experience in metagenomic and/or genomic sequence analysis.
• Experience in Metabolomics and/or Mass spectrometry.
• Experience with cell free DNA laboratory experiments.
• Knowledge/work on cancer epidemiology (or relevant aspects of microbiome, nutrients, metabolites or genetics/genomics).
• Previous experience on biomarker development.
• Experience in reviewing scientific literature.
• Excellent organisational skills.

Application procedure: Applicants should follow the application procedure and submit the files via email to david.hughes@ucd.ie as a single pdf document.

DC5. Retention of subtyping from tissues to liquid biopsies

DC5 will largely focus on the bioinformatic characterization of the primary/metastatic CMS, originating from tissue biopsy NGS data, and correlate this with matched liquid biopsy NGS data. In addition, the candidate will be heavily involved in collaborative projects that ultimately aim to push consortium-wide data integration.

Recruiting centre: GenomeScan B.V., (GenomeScan), Leiden (the Netherlands).

Academic qualifications requested:MSc in Bioinformatics/System Biology, or Biomedical sciences/Molecular Biology (or similar, depending on the country).

Skills requested: Proven understanding of Bioinformatic/System Biology approaches. Proficiency in R and/or Python programming. Knowledge on cancer genetics/genomics.

Skills valued: Previous experience with NGS data analysis. Previous experience on biomarker development.

Application procedure: Candidates are invited to submit all application documents in English to Manager Human Resources Mrs. Vivienne Heemskerk (hr@genomescan.nl).

DC6. Development of dynamic chemistry labelling assays to quantify circulating small non-coding RNAs directly from body fluids for the early detection of Colorectal Cancer

The PhD candidate will perform the design and solid-phase synthesis of functionalized PNA oligomers (DESTINA probes) as well as novel tagged SMARTBases.

Recruiting centre: DESTINA Genomica SL (DESTINA), Granada (Spain).

Academic qualifications requested: MSc in Chemistry, Biochemistry or Pharmaceutical Chemistry and Technology (or similar, depending on the country).

Skills requested: Comprehensive organic and solid-phase synthesis and coupling reactions. Knowledge on molecular biology techniques (qPCR, NGS, Microarrays). Basic knowledge on RNA biology especially on sncRNAs and interest in liquid biopsy. English language proficiency is required.

Skills valued: Organic chemistry laboratory experiments. Previous experience with design and synthesis of small molecules, peptides and/or ideally peptide nucleic acids (PNAs). Knowledge/work with RNA analysis, molecular biology techniques and nucleic acid testing (NAT).

Application procedure: The application must be submitted to spain@destinagenomics.com. For further info on the position, please contact Dr. Salvatore Pernagallo (salvatore@destinagenomics.com).

DC7. Circulating non-coding RNAs as a source of biomarkers for colorectal cancer prognosis and monitoring

The main aim of this project is to identify and validate novel 

sncRNA-based CRC biomarkers with prognostic value via liquid biopsy approaches by comparing different state-of-the-art technologies.

Recruiting centre: Fundació Clinic per a la Recerca Biomèdica (FCRB)/IDIBAPS, Barcelona (Spain).

Academic qualifications requested: BSc + MSc in biomedical sciences* (or similar in content, depending on country of origin).

Skills requested: Previous molecular biology lab experience. Proficient in microsoft office and statistical analysis applied to biomedical sciences (including logistic regression and survival analysis). Ability to work with high level of autonomy. English writing and oral communication skills. Teamwork ability. Previous working mobility experience.

Skills valued: Previous lab experience with clinical samples and use of databases. Previous experience in RNA extraction, RT-qPCR and/or microRNA analysis. Knowledge on cancer biology. Knowledge on non-coding RNA molecular biology. Knowledge in bioinformatic analysis. Previous experience on biomarker development. Previous experience in delivering public presentations. Responsibility, having initiative and creativity will also be considered .

Application procedure: Applicants should follow the application procedure and submit the files in English in a single .pdf document to mgirone@recerca.clinic.cat AND fcrbrrhh@recerca.clinic.cat indicating “Application for DC7COLOMARK” in the e-mail subject line.

DC8. Diagnostic Leukapheresis and intraoperative samples to enhance CTC detection in early CRC

With this project we aim specifically: 1) To test the value of Diagnostic Leukapheresis (DLA) and intraoperative samples (from the tumour-draining vein and central venous line) in localised CRC for CTC-detection and identification of patients at risk for metastatic disease. 2) To check the utility of DLA and intraoperatively collected CTCs for clinically relevant diagnostic tests (KRAS mutation testing, EGFR expression etc.). 3) To take advantage of the increased CTC yields in DLA products and intraoperative blood samples for comprehensive molecular analysis to dissect the biology of the potential precursor cells of metastatic relapse. 4) To test the value of DLA and intraoperative blood samples for detection of other circulating biomarkers (ctDNA, ctmiRNAs, microbiome and metabolomics). 5) Explore correlation between circulating tumour biomarkers (CTCs, ctDNA) and the integrity status of the gut-blood barrier.

Recruitment centre :Heinrich-Heine University Medical Center, Düsseldorf (UDUS); Düsseldorf (Germany).

Academic qualifications requested: BSc + MSc in Biomedical sciences/Molecular Biology/Biotechnology* (or similar, depending on country).

Skills requested:Basic knowledge on (cancer) genomics.Basic knowledge on molecular biology techniques.

Skills valued: Experience with molecular biology techniques (e.g. NGS Library Preparation). Experience with Linux environment and programming skills (e.g. on R, python, bash).Experience on analysis of NGS data. Experience in technologies for CTC enrichment or molecular analysis. Experience with cell culture/biology techniques (e.g. flow cytometry, fluorescence microscopy).

Application procedure: Applicants should submit the application documents via email to: rui.neves@med.uni-duesseldorf.de.

DC9. Prognostic value of TP53 in exosomes from liquid biopsy studies

DC9 will study TP53 in ctDNA and exosomes in relation to prognosis in CRC, with a focus on TP53β. A variety of techniques will be used, including RNA and protein expression analysis and NGS based ctDNA detection techniques. The most optimal exosome detection methods will be compared and investigated for our studies.

Recruiting centre: Leiden University Medical Center (LUMC), Leiden (Netherlands).

Academic qualifications requested: MSc in Biomedical sciences or Molecular Biology (or similar, depending on country).

Skills requested:Knowledge on (cancer) genetics/genomics. Knowledge on molecular biology techniques. Lab experience working with DNA or RNA.

Application procedure: Applicants should  submit the application documents via email to: t.van_wezel@lumc.n.

DC10. Single-cell RNA sequencing of circulating tumour cells (CTCs) in CRC patients to identify novel biomarkers of disease monitoring and progression

The main aim of this project is to utilise circulating tumour cells (CTCs) and their transcriptomic landscape over the course of the disease and treatment to identify novel biomarkers that can help us guide therapeutic strategies.

Recruiting centre: Fundación Instituto de Investigación Sanitaria de Santiago (FIDIS), Santiago de Compostela (Spain).

Academic qualifications requested: BSc in biomedical sciences* (or similar, depending on country) + MSc on bioinformatics OR BSc in computer science* + MSc in genomics*.

*similar (in content) degrees may be considered (depending on description), as the titles may vary depending on country of origin.

Skills requested: Proven bioinformatic understanding of NGS data analysis, particularly transcriptomics. Working abilities on Linux environment and programming skills on R, bash or python.

Skills valued: Previous experience with RNAseq data analysis. Lab experience working with CTCs. Knowledge/work on cancer genetics/genomics. Previous experience with prediction models, including predictors. Previous experience on biomarker development.

Application procedure: Applicants should follow the application procedure and submit the files as a single pdf here: FIDIS Job Opportunities (position 002/2023).