OPPORTUNITIES FOR EARLY-STAGE RESEARCHERS

Applications are invited for a number of highly motivated Early Stage Researcher (ESR) positions as part of the new H2020, EU-funded, Marie Skłodowska-Curie Innovative Training Network programme "Chromatin3D: Chromatin Dynamics in Development and Disease".
The Chromatin3D ITN (www.Chromatin3D.eu) brings together leading academic and industry groups to train a new generation of researchers. We are now looking for 15 highly motivated Early Stage Researchers (ESRs), researchers with a BSc or MSc degree within the first four years (full-time equivalent) of their research career. We offer a comprehensive, interactive and international training programme covering innovative and state-of-the-art approaches to current chromatin research. Training will be staged according to the 5 ‘i’ principle: individualized, intersectoral, international, interdisciplinary and innovation-oriented. The programme will combine research-specific skills, complementary skills and soft skills, and will involve both the academic and industry sectors aimed to prepare all researchers optimally for their future careers.

 

Eligibility criteria

According to the requirements of the prestigious Marie Skłodowska Curie Training Programme, Early Stage Researcher (ESR) positions allow the researcher to work towards a PhD, for a duration of 36 months. ESRs of any nationality should be within four years of the diploma granting them access to doctorate studies at the time of recruitment, and must not have resided or have carried out their main activity (work, study, etc.) for more than 12 months in the last 3 years in the country of the host institute of interest. Applicants should have an excellent proficiency in written and spoken English. Marie Skłodowska Curie fellows receive a competitive salary, which is adjusted for their host country. A mobility allowance and a family allowance (where applicable) are part of the employment package.

 

How to apply

Applications should be submitted to the email addresses provided for each position in the individual vacancy. Each applicant may apply separately for more than one position. Applications should consist of an up-to-date CV as well as a cover letter including the applicants’ motives to apply and the contact details of at least two referees. All requested information should be submitted as a compiled single .pdf document with a size less than 2Mb. Only complete applications will be considered.

 

Open positions (click on each position for details)

 

OPPORTUNITIES FOR EARLY-STAGE RESEARCHERS

Applications are invited for a number of highly motivated Early Stage Researcher (ESR) positions as part of the new H2020, EU-funded, Marie Skłodowska-Curie Innovative Training Network programme "Chromatin3D: Chromatin Dynamics in Development and Disease".
The Chromatin3D ITN (www.Chromatin3D.eu) brings together leading academic and industry groups to train a new generation of researchers. We are now looking for 15 highly motivated Early Stage Researchers (ESRs), researchers with a BSc or MSc degree within the first four years (full-time equivalent) of their research career. We offer a comprehensive, interactive and international training programme covering innovative and state-of-the-art approaches to current chromatin research. Training will be staged according to the 5 ‘i’ principle: individualized, intersectoral, international, interdisciplinary and innovation-oriented. The programme will combine research-specific skills, complementary skills and soft skills, and will involve both the academic and industry sectors aimed to prepare all researchers optimally for their future careers.

 

Eligibility criteria

According to the requirements of the prestigious Marie Skłodowska Curie Training Programme, Early Stage Researcher (ESR) positions allow the researcher to work towards a PhD, for a duration of 36 months. ESRs of any nationality should be within four years of the diploma granting them access to doctorate studies at the time of recruitment, and must not have resided or have carried out their main activity (work, study, etc.) for more than 12 months in the last 3 years in the country of the host institute of interest. Applicants should have an excellent proficiency in written and spoken English. Marie Skłodowska Curie fellows receive a competitive salary, which is adjusted for their host country. A mobility allowance and a family allowance (where applicable) are part of the employment package.

 

How to apply

Applications should be submitted to the email addresses provided for each position in the individual vacancy. Each applicant may apply separately for more than one position. Applications should consist of an up-to-date CV as well as a cover letter including the applicants’ motives to apply and the contact details of at least two referees. All requested information should be submitted as a compiled single .pdf document with a size less than 2Mb. Only complete applications will be considered.

 

Open positions (click on each position for details)

ESR1: “Epigenome stratification during Drosophila embryogenesis” (Germany)

Location

Germany Adolf-Butenandt Institute,
Ludwig-Maximilians-Universität München,
Germany

 

The Project

We are interested in how functional chromatin structures assemble during Drosophila embryogenesis. Projects are available in two different areas. First, we are interested in the contributions and functional cooperation of nucleosome remodeling complexes to chromatin organization. As an example, we will monitor the effect of the nucleosome remodelling machineries CHRAC/ACF, RSF and the 'Domino complexes' on H2A.V metabolism during development and in response to DNA damage. These experiments aim at describing the dynamic environment of chromatin that allows regulatory complexes to form. Second, as an example of a regulatory complex that requires access to chromatin, we will test hypotheses for the targeting of the Dosage Compensation Complex (DCC) to X-chromosomal High Affinity Site DNA.

We will make extensive use of an in vitro system derived from preblastoderm Drosophila embryos, which allows reconstituting chromatin on recombinant DNA. Recombinant forms of all proteins of interest will be expressed via baculovirus vectors and chromatin will be reconstituted on paramagnetic beads from defined components for structural studies, or using the embryo extracts for discovery. Chromosomal interactions will be monitored by ChIP-chip and ChIP-seq strategies. Transgenic flies expressing tagged versions of the target proteins will be generated by recombineering a range of tags into fosmid clones encoding the proteins of interest, followed by site-specific integration of these fosmids via the phiC31 system into fly genomes. This strategy will allow visualisation of the candidate proteins expressed form their native genomic environment and rapid affinity-purification of complexes they reside in.

 

Who we are

The student will complete their PhD with Professor Peter Becker at the Ludwig-Maximilians-Universität in Munich, Germany

 

Who we look for

A highly motivated student with a background in biochemistry, molecular cell biology or other relevant field, with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Diploma or Master’s degree in Biology or Biochemistry. Extensive practical experience through lab rotations and internships are of advantage.

 

How to apply

Applications should be submitted to Prof. Peter B. Becker (pbecker[AT]med.uni-muenchen.de) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until [30.05.2015].

 

ESR2: “The functional role of XPC in cancer and development” (Greece)

Location

Greece Institute of Molecular Biology & Biotechnology,
Foundation for Research and Technology Hellas,
Heraklion, Crete, Greece

 

The Project

The objective of research is to characterize XPC-associated protein (sub)complexes and genomic targets in development and disease. We will focus on the isolation and characterization of XPC-bound protein (sub) complexes, the identification of associated genomic targets and their role during development and disease in mice, as well as upon DNA damage. In order to achieve our aims, an in vivo biotinylation tagging methodology for the efficient direct purification of XPC protein partners will be used. More specifically, XPC will be tagged by fusing the 14aa biotinylation tag to XPC protein and expressing the biotinylation tag-fused XPC protein in established cell lines expressing the BirA biotin ligase knocked-in the Rosa26 locus. BirA specifically recognizes and biotinylates the short tag, creating a very high affinity “handle” for isolating tagged factors by binding to streptavidin. We will generate biotin-tagged XPC knock-in mice in the BirA genetic background by fusing the 14aa biotinylation tag to the endogenous C terminus of XPC. This will be used to specifically tag XPC for mass spectrometry and massive parallel sequencing (MPS) approaches in tissue protein extracts derived from bio-XPC knock-in mice.

 

Who we are

The student will complete their PhD with Professor George Garinis who is affiliated with the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology and the Department of Biology of the University of Crete in Heraklion, Crete, Greece.

 

Who we look for

A highly motivated student with a background in Biology or other relevant field. Excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Bachelor’s or MSc degree. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. George Garinis (Garinis[AT]imbb.forth.gr) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR3: “Role of SATB1 in gene networks that define CD4+ cell plasticity” (Greece)

Location

Greece Institute of Molecular Biology & Biotechnology,
Foundation for Research and Technology Hellas,
Heraklion, Crete, Greece

 

The Project

The objective of research is the study the SATB1-mediated interactome of mouse CD4+ T cells based upon cytokine and transcription factor gene networks in development and disease. Adaptive immune responses rely upon the differentiation of naïve CD4+ cells into different T helper cell lineages. The different CD4+ T cell fates are determined via complex and cross-interactive networks consisted by cytokines and transcription factors. The co-expression of the latter affects the functional capabilities and the flexibility of the different CD4+ T cell subsets. Moreover, the three dimensional organization of the eukaryotic genome and the interplay of specific protein factors in regulating long range interactions between diverse regulatory elements is becoming appreciated as a possible epigenetic mechanism of cell memory and cell lineage specification. The apparent question is how the protein partners regulate the shaping of the genome.

We will focus on the identification of the SATB1 protein interactors in naïve CD4+ T cells and differentiated T helper cell lineages by performing co-immunoprecipitation experiments utilizing a SATB1 antibody to identify the protein candidates by mass spectrometry. ChIP-sequencing experiments performed using SATB1 specific antibodies and selected protein interactors with chromatin prepared from non-differentiated and differentiated CD4+ cells, will unravel the associated genomic targets.

 

Who we are

The student will complete their PhD with Professor Charalampos Spilianakis who is an affiliated professor with the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology and the Department of Biology of the University of Crete in Heraklion, Crete, Greece.

 

Who we look for

A highly motivated student with a background in molecular biology, biochemistry and/or immunology or other relevant field with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Diploma or Master’s degree in Biology or Biochemistry. Experience in biocomputing analysis will be positively considered. Extensive practical experience through lab rotations and internships are of advantage. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Charalampos Spilianakis (spiliana[AT]imbb.forth.gr) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR4: “Defining the SATB1-dependent three dimensional chromatin structure in CD4+ cells” (Greece)

Location

Greece Institute of Molecular Biology & Biotechnology,
Foundation for Research and Technology Hellas,
Heraklion, Crete, Greece

 

The Project

The objective of research is the study the SATB1-mediated interactome of mouse CD4+ T cells based upon cytokine and transcription factor gene networks in development and disease. Adaptive immune responses rely upon the differentiation of naïve CD4+ cells into different T helper cell lineages. The different CD4+ T cell fates are determined via complex and cross-interactive networks consisted by cytokines and transcription factors. The co-expression of the latter affects the functional capabilities and the flexibility of the different CD4+ T cell subsets. Moreover, the three dimensional organization of the eukaryotic genome and the interplay of specific protein factors in regulating long range interactions between diverse regulatory elements is becoming appreciated as a possible epigenetic mechanism of cell memory and cell lineage specification. The apparent question is how the protein partners regulate the shaping of the genome.

ESR4 will perform and analyse genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET) in order to map the long-range chromatin interactions mediated by SATB1 in CD4+ T cells before and after differentiation.

 

Who we are

The student will complete their PhD with Professor Charalampos Spilianakis who is an affiliated professor with the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology and the Department of Biology of the University of Crete in Heraklion, Crete, Greece.

 

Who we look for

A highly motivated student with a background in molecular biology, biochemistry and/or immunology or other relevant field with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Diploma or Master’s degree in Biology or Biochemistry. Experience in biocomputing analysis will be positively considered. Extensive practical experience through lab rotations and internships are of advantage. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Charalampos Spilianakis (spiliana[AT]imbb.forth.gr) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR5: “The role of FOG-1 in mediating chromatin looping” (Greece)

Location

Greece Institute of Molecular Biology & Biotechnology,
Foundation for Research and Technology Hellas,
Heraklion, Crete, Greece

 

The Project

The objective of research is to investigate the molecular basis for Friend of GATA 1 (FOG-1)-mediated chromatin loop organization in red blood cells by: (1) characterizing the FOG-1 protein complexes, (2) identifying the genome wide chromatin profile of FOG-1 in erythroid cells and (3) uncovering the three-dimensional chromatin mediated by FOG-1.

To characterize the FOG-1 protein complexes we will generate mouse erythroleukemia (MEL) cell clones expressing biotin tagged forms for each of the three FOG-1 isoforms. BirA-mediated biotinylation tagging is an efficient approach for the rapid purification of protein complexes. Nuclear extracts will be bound to streptavidin beads and processed for protein identification by mass spectrometry. We will also use the MEL clones expressing biotin tagged FOG-1 isoforms to carry out streptavidin-ChIP coupled to massive parallel sequencing (ChIP-seq) in order to identify the genome wide chromatin occupancy profiles for FOG-1. Occupancy profiles will be compared to GATA-1 profiles previously published to identify common and unique gene targets. Validation of selected gene targets will be done by ChIP-qPCR.

 

Who we are

The student will complete their PhD with Dr. John Strouboulis who recently joined the Institute of Molecular Biology and Biotechnology of the Foundation for Research and Technology in Heraklion, Crete, Greece.

 

Who we look for

A highly motivated student with a Masters degree in molecular biology, biochemistry or other relevant field and experience in cell culture and standard molecular biology methods. Excellent analytical, communication and interpersonal skills are required. A team player. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Dr. John Strouboulis (john_strouboulis[AT]imbb.forth.gr) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until April 30, 2015.

 

ESR6: “The role of chromatin regulators in Myc-induced lymphomagenesis” (Italy)

Location

Italy Center for Genomic Science,
Fondazione Istituto Italiano di Tecnologia,
Milan, Italy

 

The Project

The objective of research is to determine which among the known chromatin-modifying enzymes and associated proteins are critical for the progression and maintenance of Myc-induced lymphomas.

In the host lab, ChIP-seq is used to map key histone modifications in B cells of Eµ-myc transgenic mice in order to determine which chromatin alterations are associated with the progression of Myc-induced lymphoma in this model. We will complement this epigenomic analysis with functional screens in which we will specifically target chromatin-modifying enzymes in the same model. Eµ-myc mice have been used in the host lab to develop the aforementioned shRNA screens. We will perform screens with homemade retroviral shRNA-coding libraries. The libraries will encode pools of shRNAs that target the mRNAs encoding all known chromatin-modifying enzymes and associated subunits in multi-protein complexes. We will use these libraries to transduce either hematopoietic precursors prepared from Eµ-myc transgenic mice, or lymphomas obtained from the same mouse strain. Genomic shRNA profiles during tumor progression will be determined by next-generation sequencing, leading to the identification of positively and negatively selected shRNAs. We will thus proceed with validation and characterization at the single-gene level. Of particular interest will be methyltransferases and acetyltransferases that catalyse the histone marks that are currently being mapped by ChIP-seq along the genomes of precursor and cancer cells.

This position is subject to the selection process of the European School of Molecular Medicine, SEMM.

APPLICATIONS SHOULD BE MADE ONLY AND EXCLUSIVELY THROUGH SEMM, AT THE FOLLOWING WEB SITE:

Semm - How to apply.

THE APPLICATION PROCESS WILL OPEN IN EARLY JULY AND CLOSE AT THE END OF AUGUST.

 

Who we are

The student will complete their PhD with Professor Bruno Amati at the Center for Genomic Science of the Fondazione Istituto Italiano di Tecnologia in Milan, Italy.

 

Who we look for

A highly motivated student with a Masters degree in molecular biology, biochemistry or other relevant field and experience in cell culture and standard molecular biology methods. Excellent analytical, communication and interpersonal skills are required. A team player. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Bruno Amati (Bruno.Amati[AT]iit.it) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR7: “Mechanisms of long-range gene regulation by chromatin topology” (UK)

Location

United Kingdom MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine,
University of Edinburgh,
Edinburgh, UK

 

The Project

The objective of research is (1) to determine how cis-acting sequences, thousand to millions of base pairs away from target genes, regulate the spatial and temporal control of gene expression in development, (2) to relate these levels of gene regulation to chromatin folding and to genome topology, and (3) to determine how genetic variation in such regulatory elements contributes to common human disease and quantitative traits.

Using fluorescence in situ hybridization (FISH), including novel FISH methodology developed by the host lab, together with the 5C chromosome conformation capture technique, we will learn to integrate different approaches to unravel the chromatin architecture at developmentally regulated gene loci controlled by large complex regulatory landscapes. We will use a similar methodology to compare the chromatin topologies at a regulatory region of the genome where human isolated population genetics have identified two major haplotypes with strong effects on the thickness of the human cornea region – a risk factor for glaucoma. Putative mechanisms will be tested by the ectopic recruitment of specific proteins to these regions via TALEN proteins.

 

Who we are

The student will complete their PhD with Professor Wendy Bickmore at the MRC Human Genetics Unit MRC IGMM, University of Edinburgh Western General Hospital in United Kingdom.

 

Who we look for

A highly motivated student with a background in molecular biology, cell biology, genetics or other relevant fields. Requires enthusiasm for scientific enquiry, excellent analytical, communication and interpersonal skills. The applicant should hold an undergraduate degree in a relevant biological science. Experience in molecular biology methods including; cloning, cell transfection is desirable.

Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Wendy Bickmore (wendy.bickmore[AT]igmm.ed.ac.uk) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until [13.03.2015].

 

ESR8: “microRNA profiles in tumors associated with epigenetic defects” (Spain)

Location

Spain Cancer Epigenetic and Biology Program,
Fundació Institut d'Investigació Biomèdica de Bellvitge,
Barcelona, Spain

 

The Project

The objective of research is to investigate the role of specific miRNAs (and their regulation) in tumors of the nervous system and how this regulatory mechanism connects with histone modifications and CpG methylation alterations during tumorigenesis

A double approach will be applied: first, we will evaluate the changes in miRNAs expression in samples associated with NSD1 defects and their association with specific molecular pathways; and second, will assess whether differential miRNA expression can be achieved due to CpG methylation. We will use tumor cell lines with expression or silencing of NSD1 as experimental models, together with Sotos patients that will be employed as in vivo controls of NSD1 abrogation.

 

Who we are

The student will complete their PhD with Dr Manel Esteller at Fundació Institut d'Investigació Biomèdica de Bellvitge in Barcelona, Spain.

 

Who we look for

A highly motivated student with a background in molecular biology, cell biology, genetics or other relevant fields with excellent analytical, communication and interpersonal skills. The applicant should hold an undergraduate or MSc degree in a relevant biological science.

Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Dr Manel Esteller (mesteller[AT]idibell.cat) and Dr Helena Lopez (hdiaz[AT]idibell.cat) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR9: “Hierarchy of chromatin fibre interactions in development and disease” (Sweden)

Location

Sweden Microbiology, Tumor & Cell Biology,
Karolinska Institutet,
Stockholm, Sweden

 

The Project

The objective of research is to determine the organization of chromatin conformations and how these functionally relate to developmental processes as well as disease progression.

We will apply newly developed techniques to map chromatin conformations and their hierarchy in human cells with a special emphasis on the identification of epigenetic modifiers acting in 3D. One technique, termed “ChrISP” for chromatin in situ proximity, detects higher order chromatin conformations with a resolution beyond the light microscope (<170Å) in single cells. This technique will also be used to identify protein complexes that underlie the molecular ties between chromatin fibres. We will employ a second technique, termed “nodewalk” which can simultaneously score for genomewide interaction patterns of multiple baits. The nodewalk technique will above all analyse cancer stem cells showing perturbed epigenome in collaborative efforts. Thus, regions shown to be epigenetically perturbed in cancer patients will be used as baits to determine perturbances in chromatin network organizations both in single cells (ChrISP) and in large cell populations (nodewalk) from the same set of patients with matching normal controls. In addition, we will attempt to experimentally mutate key regulatory regions forming the so-called Achilles’ heel identified in such screens with the ambition to mimic epigenetic ramifications resulting from loss of chromatin networks.

 

Who we are

The student will complete their PhD with Professor Rolf Ohlsson at the Department of Microbiology, Tumor & Cell Biology of the Karolinska Institutet in Stockholm, Sweden.

 

Who we look for

A highly motivated student with a background in molecular genetics, biochemistry, cell biology or any other relevant field. Excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Master’s degree in Genetics, Biochemistry or Molecular Biology/Genetics. Experience in analytical methods, such as chromatin immunoprecipitation, DNA/RNA FISH, confocal microscopy, transfection, culturing cells, is essential, while experience with MALDI-TOF MS, R language and a background in interdisciplinary research is advantageous. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Rolf Ohlsson (rolf.ohlsson[AT]ki.se) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR10: “Hierarchy of chromatin fibre interactions in disease” (Sweden)

Location

Sweden Microbiology, Tumor & Cell Biology,
Karolinska Institutet,
Stockholm, Sweden

 

The Project

The objective of research is to determine the organization of chromatin conformations and how these functionally relate to developmental processes as well as disease progression.

We will apply newly developed techniques to map chromatin conformations and their hierarchy in human cells with a special emphasis on the identification of epigenetic modifiers acting in 3D. One technique, termed “ChrISP” for chromatin in situ proximity, detects higher order chromatin conformations with a resolution beyond the light microscope (< 170Å) in single cells. This technique will also be used to identify protein complexes that underlie the molecular ties between chromatin fibres. We will employ a second technique, termed “nodewalk” which can simultaneously score for genomewide interaction patterns of multiple baits. The nodewalk technique will above all analyse cancer stem cells showing perturbed epigenome in collaborative efforts. Thus, regions shown to be epigenetically perturbed in cancer patients will be used as baits to determine perturbances in chromatin network organizations both in single cells (ChrISP) and in large cell populations (nodewalk) from the same set of patients with matching normal controls. In addition, we will attempt to experimentally mutate key regulatory regions forming the so-called Achilles’ heel identified in such screens with the ambition to mimic epigenetic ramifications resulting from loss of chromatin networks.

 

Who we are

The student will complete their PhD with Professor Rolf Ohlsson at the Department of Microbiology, Tumor & Cell Biology of the Karolinska Institutet in Stockholm, Sweden.

 

Who we look for

A highly motivated student with a background in molecular genetics, biochemistry, cell biology or any other relevant field. Excellent analytical, communication and interpersonal skills. A team player. The applicant should hold a Master’s degree in Genetics, Biochemistry or Molecular Biology/Genetics. Experience in analytical methods, such as chromatin immunoprecipitation, DNA/RNA FISH, confocal microscopy, transfection, culturing cells, is essential, while experience with MALDI-TOF MS, R language and a background in interdisciplinary research is advantageous. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Rolf Ohlsson (rolf.ohlsson[AT]ki.se) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR11: “From genotype to phenotype: The effect of genetic variation on chromatin organization” (Israel)

Location

Israel Computer Science & Applied Mathematics,
Weizmann Institute of Science,
Rehovot, Israel

 

The Project

The objective of research is to unravel the effect of genotype differences among human individuals on chromatin organization and gene expression.

We will adapt this technology to human cell lines, and apply it to systematically reveal rules of DNA-encoded gene regulation in human, including the effect on expression of: sequence-dependent mechanical properties of DNA; sequences that affect nucleosome positioning; and locations of factor binding sites relative to nucleosomes and to transcription start sites. Using the recently available genomes of many individuals, we will select ~100 regulatory regions that include proximal promoters, and for each such regulatory region, design sequences in the library that correspond to ~100 different variants from ~100 different individuals. This will provide a direct measure for the causal effect on expression of genetic differences in regulatory regions of human individuals. By accurately measuring the transcriptional effect of ~10,000 different regulatory sequences with carefully designed mutations to specific such regulatory building blocks, we will provide an unprecedented ~1000-fold increase over previous studies, and significantly advance our understanding of the regulatory code in human. We will use these data to devise quantitative models of transcriptional regulation based on the language of probabilistic graphical models.

 

Who we are

The student will complete their PhD with Professor Eran Segal at the Department of Computer Science & Applied Mathematics of the Weizmann Institute of Science in Rehovot, Israel.

 

Who we look for

A highly motivated student with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold an undergraduate or MSc degree in a relevant to the project science.

Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Eran Segal (eran.segal[AT]weizmann.ac.il) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR12: “Mass Spectrometry compatible chromatin extraction” (Belgium)

Location

Belgium DIAGENODE SA,
Liège, Belgium

 

The Project

The objective of research is to develop an optimized method for the isolation of chromatin from fixed cells compatible with mass-spectrometry analysis of protein complexes.

We will develop an approach for the comprehensive investigation of DNA-binding proteins with in vivo formaldehyde cross-linking. After the cross-linking reaction, cell nuclei will be isolated, and chromatin will be sheared and immunoprecipitated with specific antibodies for proteins with a great interest to the network’s partners. The DNA-protein complexes will be subsequently purified and the cross-linking will be reversed to release the DNA-binding proteins. DNA will be utilized for massive parallel sequencing and the purified DNA-binding proteins will be digested in solution using trypsin and will be interrogated by LC-MS/MS. By optimizing this method, we will be able to identify the protein partners that a specific protein is interacting with within a specific DNA region either co-ordinately or separately.

 

Who we are

The student will work with Renaud Schoemans at DIAGENODE SA in Liege, Belgium.

 

Who we look for

A highly motivated student with a background in Biology or other relevant field with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold an undergraduate or Master’s degree in Chemistry, Biochemistry or Molecular Biology. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Renaud Schoemans (renaud.schoemans[AT]diagenode.com) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR13: “Developing tools for clinical epigenetic studies” (Hungary)

Location

Hungary UD-GENOMED Medical Genomic Technologies,
Debrecen, Hungary

 

The Project

The objective of research is to develop clinically relevant and financially affordable diagnostic tools based on the already developed process controls for chromatin IP and miRNA studies.

UD-GenoMed developed a microparticle based ChIP process control that can be used to monitor the efficiency of a ChIP reaction or to compare the efficiency of different protocols. The technology is patented and based on this technology we will generate IP controls for marker transcription factors. In the first phase we will develop spike-in controls for the following of ubiquitously expressed transcription factors: RXR and CTCF. We will test these process controls in cell lines, frozen samples and real pathological samples. In the second phase, ER-receptor binding will be monitored from the MCF7 cell line and breast cancer samples. We will develop an ER-specific ChIP Spiking control. The results in ChIP and ChIP Seq will be compared and the feasibility of the development of a diagnostic application will be investigated.

 

Who we are

The student will complete their PhD with Dr. László Nagy at UD-GENOMED Medical Genomic Technologies in Debrecen, Hungary.

 

Who we look for

A highly motivated student with a background in Molecular Biology, Biochemistry, Cellular Biology or other relevant field with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold an undergraduate or Master’s degree in Chemistry, Biochemistry or Molecular Biology. Experience is also essential in biotechnology methods. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Gábor Zahuczky (zahu[AT]ud-genomed.hu) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR14: “(Pre-clinical) proteome analysis for the identification of disease-related biomarkers” (Germany)

Location

Germany Mosaiques Diagnostics GmbH,
Hannover, Germany

 

The Project

Our objective is to conduct a unique clinical proteome analysis, thus generating a highly information-rich dataset for a number of biological processes that go beyond gene expression. This approach will allow us to gain insight into fundamental questions related to disease-specific pathologies.

We will develop a set of novel CE-MS-based approaches to identify disease-related protein biomarkers in easily accessible biofluids i.e. urine, blood or cell cultures to test the efficiency of (pre-clinical) treatments in counteracting distinct disease-related pathologies. We will also develop novel bioinformatics applications and multiparametric statistical algorithms for processing the protein data and derive valid biomarkers for disease-related pathological situations.

ESR 14 will develop a set of novel CE-MS-based approaches to identify disease-related protein biomarkers in easily accessible biofluids i.e. urine, blood or cell cultures to test the efficiency of (pre-clinical) treatments in counteracting distinct disease-related pathologies. ESR14 will also develop novel bioinformatics applications and multiparametric statistical algorithms for processing the protein data and derive valid biomarkers for age-related pathological situations.

 

Who we are

The student will complete their PhD with Professor Harald Mischak at Mosaiques Diagnostics GmbH in Hanover, Germany.

 

Who we look for

A highly motivated student with a background in chemistry, molecular biology or other relevant field with excellent analytical, communication and interpersonal skills. A team player. The applicant should hold an undergraduate or Master’s degree in Chemistry, Biochemistry or Molecular Biology. Experience is also essential in biotechnology methods. The applicant should also have experience using analytical techniques including Spectroscopy and chromatography. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to Prof. Harald Mischak (mischak[AT]mosaiques-diagnostics.com) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.

 

ESR15: Cell-Based Models for Chromatin-Targeted Therapeutic Intervention (UK)

Location

United Kingdom AvantiCell Science Ltd.,
Ayr, Scotland, UK

 

The Project

The project shall develop novel in vitro models based on human cells with tissue- and disease-specific phenotypes, which allow evaluation of therapeutic intervention using chromatin-targeted strategies. The aim shall be to build analytical tools that enable study of partner-generated materials and which are suitable for subsequent post-project commercial exploitation.

ESR15 shall build novel human cell models suitable for the study of chromatin manipulation strategies developed within the Chromatin3D programme. The models shall be built around human primary cancer cells or cancer stem cells, and the principal target cancers shall be colon cancer and pancreatic cancer. ESR15 shall learn and apply methods for producing 3D micro-tissues in multiwell plates, and shall acquire skills in population-based analysis of these cultures by visual sectioning and the use of image deconvolution techniques. To promote testing of partner-generated materials, the appointee shall investigate novel methods for introduction of shRNAs into the cell models. The focus shall be on strategies using novel biodegradable transfection reagents or nanoparticle-mediated techniques, some drawing upon materials and protocols available to ACS through other strategic partnerships. Protocols and cellular responses demonstrated in Caucasian donor samples shall be compared with those observed with other donor genotypes, using ethnically-diverse tumor cells sourced from an ACS subsidiary company, which is in process of launching ethically-accredited human cell biobanking in partnership with a leading medical institution.

 

Who we are

The student will complete his/her PhD with Dr Colin Wilde at ACS - AvantiCell Science Ltd. ACS is a biotechnology Company specialising in cell biology and cell culture technology. The Company was founded in 2006, is profitable, and is presently located in Ayr, South Ayrshire, Scotland, UK.The Company’s business is founded on the principle that advances in cell culture technology enable the development of physiologically-relevant alternatives to animal testing in research and drug discovery.

 

Who we look for

A highly motivated student with a background in cell biology or a related field. She/he shall possess excellent analytical, communication and interpersonal skills, and be a team player. The applicant should hold a Bachelor’s or equivalent undergraduate degree and Master’s degree in Biochemistry, Cell Biology or Molecular Biology. Experience in mammalian cell culture is essential, and the applicant should also have knowledge of analytical techniques including flow-cytometric analysis, PCR-based gene expression and microscopy. Experience of project management processes and quality assurance systems will be advantageous. Candidates should also meet the eligibility criteria for the programme (see above).

 

How to apply

Applications should be submitted to the Office Manager, AvantiCell Science Ltd (admin[AT]avanticell.com) as well as the Chromatin3D project manager (manager[AT]chromatin3d.eu). Please indicate “Chromatin3D-ITN PhD application” in the subject line of your e-mail.

 

Deadline

This vacancy will be open for applications until 31st March 2015.