PhD Fellowships in Palaeoproteomics

University of Copenhagen Globe Institute and Novo Nordisk Foundation Center for Protein Research

Four PhD fellowships in Palaeoproteomics at the Globe Institute and the Novo Nordisk Foundation Center for Protein Research

We are recruiting candidates for four PhD positions, three at the Globe Institute and one at Novo Nordisk Foundation Center for Protein Research, in palaeoproteomics for human evolution, starting 1 August 2020 or as soon as possible thereafter.

The fellowships are part of the European Training Network “PUSHH: Palaeoproteomics to Unleash Studies on Human History”, funded by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant Agreement No. 861389.

About PUSHH

The PUSHH ETN builds on the recent exciting advances in palaeoproteomics, i.e. mass spectrometry-based ancient protein sequencing. PUSHH will develop new proteomic methods, optimised for ancient protein analysis, that will be applied to address outstanding evolutionary questions in human and hominoid evolution. Currently, there are very few specialists that have been trained to analyse ancient proteins, but the growing demand for information provided by palaeoproteomics will require highly qualified profiles with backgrounds in analytical chemistry, bioinformatics, palaeoanthropology and palaeontology. PUSHH will fill this advanced training gap by providing international, and intersectoral doctoral (PhD) training, for 14 Early Stage Researchers (ESRs) in seven different EU countries. PUSHH will guide the ESRs to develop the advanced interdisciplinary competence they need to achieve seamless integration of palaeoproteomics with the established research approaches currently used in palaeoanthropology and archaeology. Read more about the network at www.pushh-etn.eu.

Job description

Your key tasks as a PhD student at SUND are:

  • Carry through an independent research project under supervision
  • Complete PhD courses or other equivalent education corresponding to approx. 30 ECTS points
  • Participate in active research environments including a stay at another research team
  • Obtain experience with teaching, or other types of dissemination related to your PhD project
  • Teach and disseminate your knowledge
  • Write a PhD thesis on the grounds of your project

As an ESR within the PUSHH network you are also expected to:

  • Actively attend all the mandatory network wide PUSHH activities, which will take place in multiple locations in and outside Europe
  • Travel for a mandatory secondment period (research stay) at another institution within the PUSHH consortium.
  • Actively take part in the research projects involving multiple institutions and ESRs within the PUSHH network
  • Deliver scientific articles and/or book chapters in collaboration with other PUSHH ESRs and supervisors
  • Communicate your scientific activity to a broad audience, for example through outreach activities, public lectures, podcasts, and social media
  • Comply with the highest standards of research integrity, as set out in the European Code of Conduct for Research Integrity.

Eligibility criteria

To be eligible for a PhD position in PUSHH on 1 August 2020 you must:

  • have not resided or carried out your main activity (work, studies, etc.) in Denmark for more than 12 months since 1 August 2017. Compulsory national service, short stays such as holidays, and time spent as part of a procedure for obtaining refugee status under the Geneva Convention are not taken into account.
  • be in the first four years (full-time equivalent research experience) of your research career and have not been awarded a doctoral degree. Full-time equivalent research experience is measured from the date when you obtained the first degree entitling you to embark on a doctorate (either in the country in which the degree was obtained or in the country in which you are recruited), even if a doctorate was never started or envisaged.

Key criteria for the assessment of applicants

  • The grade point average achieved
  • Professional qualifications relevant to the PhD project
  • Previous publications
  • Relevant work experience
  • Other professional activities
  • Curious mind-set with a strong interest in human evolution, proteomics, ancient biomolecules and bioinformatics
  • Demonstrated proficiency in both written and spoken English

Detailed information about each fellowship

Fellowship 1 (ESR6) Molecular-Based Phylogeny of Paranthropus robustus

Our group and research

The successful applicant will be part of the Cappellini Palaeoproteomics Group. The Cappellini Group is a major international player in using palaeoproteomics to retrieve deep-time genetic information, usually older than 1 million years, and reconstruct the phylogeny of extinct animal species, in particular hominids , by sequencing protein remains from fossils. In the last few years, the research activity pursued in the Cappellini Group significantly contributed to expand the application of proteomics, an approach initially developed for conventional biomedical applications, to ancient protein traces retrieved from paleontological, paleoanthropological and cultural heritage materials. The Cappellini Group is part of the Section for Evolutionary Genomics at the Globe Institute. With its 11 research groups, EvoGenomics investigates broad reaching questions of cross-disciplinary interest, including the correlation between phylogeny, chemical biology/biological interactions and natural products. Since 2009, the Cappellini Group has established a solid collaboration with the Mass Spectrometry for Quantitative Proteomics group lead by Prof. Jesper V. Olsen at NovoNordisk Foundation Center for Protein Research (CPR) at the Faculty of Health Sciences, University of Copenhagen, placing University of Copenhagen at the forefront of ancient proteomics investigation.

Project description

In Africa, the Plio-Pleistocene hominin fossil record is characterised by the presence of the genus Austrolopithecus, from which the genus Homo emerged. Robust members of Australopithecus, including both South African and East African specimens, have frequently been included into a separate genus, Paranthropus. The successful candidate for this position will extract ancient protein remains from Paranthropus dental enamel specimens from South Africa. The candidate will then reconstruct Paranthropus dental enamel protein sequences and will compare them to the homologous ones from modern and extinct hominin species to infer the Paranthropus robustus phylogenetic position in the hominin tree. Such an achievement will represent a breakthrough in biomolecular-based hominin phylogeny as both ancient DNA and ancient skeletal proteins are generally considered challenging to retrieve from the Early Pleistocene African hominin fossil record. Specimens will be made available, and data interpretation will be conducted in collaboration with Professor Rogers Ackermann (University of Cape Town, South Africa), an expert in the South African hominin fossil record. 

Specific requirements

Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project e.g. biochemistry, proteomics, molecular biology, evolutionary biology, biological anthropology, or similar discipline.

Other important criteria for the assessment of applicants are:

  • Demonstrated knowledge of protein biochemistry and/or ancient biomolecules degradation processes,
  • Demonstrated and extensive experience in designing, implementing, and optimizing analytical methods for: sample preparation, genomic and/or tandem mass spectrometry (MS)-based proteomics data generation, and data interpretation in high-throughput ancient DNA and/or ancient protein experimental workflows,
  • Experience in protein identification and/or amino acid/DNA sequence reconstruction from on MS/MS-based (palaeo)proteomics and/or (palaeo)genomic data,
  • Demonstrated experience in statistical validation of (palaeo)proteomics and/or (palaeo)genomic data and results,
  • Experience in processing and interpreting (palaeo)proteomics and/or (palaeo)genomic data for phylogenetic inference and/or population genomics reconstructions,
  • Ability to write, with a high level of independence, scientific manuscripts, reporting the original results generated, for publication in the most prestigious peer-reviewed journals. 
  • Ability to work both independently and as a team member in a highly interdisciplinary environment with colleagues with different scientific backgrounds

Desirable criteria for the assessment include: advanced experience in implementing, and optimizing palaeoproteomics methods; experience in  human and/or primate phylogenetic inference and/or population genomics; experience in molecular-based evolutionary biology and population; demonstrated experience in development and delivery of public outreach initiatives; and advanced computational skills for command line-based manipulation and statistical analysis of large genomic/proteomic datasets on large computational infrastructures.

Principal supervisor is Associate Professor Enrico Cappellini, Globe Institute, ecapellini@sund.ku.dk, +45 35321338.

Start:                  1 August 2020 or as soon as possible thereafter

Duration:           3 years (36 months) as a PhD student

Fellowship 2 (ESR3) Gigantopithecus and Asian Miocene primates using proteomics and 3D imagery

Our group and research

The successful candidate will be part of a multidisciplinary group composed of world top specialists in molecular biology, palaeoproteomics, palaeoanthropology, palaeontology and 3D imaging. The candidate will be based at either Geogenetics Center or at Cappellini Palaeoproteomics Group both based at the Globe Institute. Geogenetics is a Centre of excellence that studies ancient DNA, environmental DNA and human evolution to disease association. This highly multidisciplinary and international group, including specialists from China, Spain, France and Denmark, is interested in human and primates origins generally and in Southeast Asia. It has a long record of field work and lab work especially in China, Vietnam, Cambodia and Laos.

Project description

The successful candidate will study the characteristics and morphology of the teeth of Asian primates from the Miocene period including a molecular profiling. The selected candidate will study the relationships among them and other primates such as Sivapithecus and Gigantopithecus as well as other aspects, including sexual dimorphism, morphological characteristics and lineage specific evolutionary challenges. The candidate will be trained in 3D imagery and morphometric geometrics applied to teeth and in palaeoproteomics in order to recover molecular data from fossils dating mainly from the Miocene. The phylogenetic lineage of extinct fossils will be studied combining different methodological approaches, such as: 3D imagery, palaeoproteomics and population genomics.

As part of the PhD training it will be possible to take courses in palaeontology, palaeoanthropology, bioinformatics and palaeoproteomics. The selected candidate will also have the opportunity to work with internationally renowned specialists in the field of paleontology, palaeoanthropology, palaeoproteomics, molecular biology, bioinformatics, including: T. Marques-Bonet, C. Zanolli, A-M. Bacon, Wang Wei, E. Cappellini, F. Welker, F. Racimo.

Specific requirements

Applicants must have an MSc degree or equivalent, with a background in one or more of the following areas: evolutionary biology, palaeontology, palaeoanthropology, morphometric geometrics, genomics, proteomics. Experience in genomics or proteomics is encouraged but not required for application.

Principal supervisor is Assist. Prof. Fabrice Demeter, Lundbeck GeoGenetics Centre, Globe Institute, f.demeter@sund.ku.dk, Direct Phone: +33620654274

Co-supervisor is Prof. Tomas Marques-Bonet, Institute of Evolutionary Biology, Barcelona.

Advisor is Dr Clément Zanolli, CNRS-University of Bordeaux

Start:                 1 August 2020 or as soon as possible thereafter

Duration:           3 years (36 months) as a PhD student

Fellowship 3 (ESR13) Reconstructing the population history of archaic hominins using ancient proteomes

Our group and research

The Racimo group focuses on using ancient and present-day genomes and proteomes to understand prehistoric patterns of population divergence, selection and admixture over time, and to develop new ways to jointly analyze evolutionary and functional genomic data. We are currently composed of 2 postdocs, 2 PhD students and several MSc students, and our research is at the interface of methods development and data analysis. The Racimo group is part of the Section for Geogenetics at the Globe Institute. For more information, see: https://sites.google.com/site/fernandoracimo/home

Project description

The successful candidate will have the opportunity to use paleoproteomics data to reconstruct ancient population histories and determine the relationships among different groups of hominins, whose genomes are currently unreachable due to their age. The candidate will combine ancient protein sequences with in silico translated protein sequences from archaic and modern hominins, and develop methods that can maximize the amount of information that can be extracted from these sequences. The candidate will use state-of-the-art techniques from population genetics, coalescent theory, phylogenetics and statistical inference, and apply the newly developed methods to different hominin datasets, so as to infer the deep population history of multiple hominin groups, including population split times and admixture events.

As part of the PhD training it will be possible to take courses in bioinformatics, computer science, statistical inference, machine learning, data science, population genetics, paleogenomics, paleoproteomics, and archaeological science, among others. The candidate will also have the opportunity to collaborate with international leaders in the fields of palaeoproteomics and paleogenomics including Enrico Cappellini, Frido Welker, Tomas Marques-Bonet, Kirsty Penkman and Jürgen Cox.

Specific requirements

Applicants must have an MSc degree or equivalent, with a background in one or more of the following areas: evolutionary biology, archaeology, population genetics, computational biology, bioinformatics, genomics, mathematics and/or statistics. Experience in proteomics is encouraged but not required for application.

Other important criteria for the assessment of applicants are:

  • Demonstrated working proficiency in one or more programming languages commonly used in data science (e.g. experience in Python, R, C/C++, Java or Julia) and have experience in the UNIX operating environment.

Principal supervisor is Assist. Prof. Fernando Racimo, Lundbeck GeoGenetics Centre, Globe Institute, fracimo@sund.ku.dk, Direct Phone: +45 22 96 36 96

Start:                  1 August 2020 or as soon as possible thereafter

Duration:           3 years (36 months) as a PhD student

Place of employment for fellowships 1-3

The place of employment is at the Globe Institute, part of the Faculty of Health and Medical Sciences at the University of Copenhagen. The Institute’s main purpose is to address basic scientific questions through interdisciplinary approaches. The institute operates at the intersection of natural and medical sciences and the humanities. The Globe Institute’s underlying philosophy is that resolution to complex problems stems from integration of multiple scientific approaches and interaction of diverse mindsets.

Fellowship 4 (ESR11) High-resolution mass spectrometry for palaeoproteomics

Our group and research

The “Mass Spectrometry for Quantitative Proteomics” group is headed by Prof. Dr. Jesper V. Olsen, who is also vice director of the Novo Nordisk Foundation Center for Protein Research (CPR) at the Faculty of Health Sciences, University of Copenhagen. The Olsen Group has 15 members and it is a highly interdisciplinary group consisting of international researchers with diverse competences in analytical chemistry, mass spectrometry, proteomics, molecular biology and bioinformatics. They are developing and applying mass spectrometry-based proteomics technologies to solve questions in biology and biomedicine as well as palaeoproteomics. We have for more than ten years been collaborating closely with the Cappellini Palaeoproteomics Group at the Globe Institute and we are now among the world-leading laboratories in mass spectrometry-based palaeoproteomics technology developments. We also work closely with the leading vendors in proteomics hardware and software developments. Over the years, we have used our palaeoproteomics technology developments to analyze ancient protein remains and address a number of interesting questions that cannot be answered by ancient DNA.

Project description

This PhD project aims at developing and applying high-resolution orbitrap tandem mass spectrometry (MS/MS) based methods and associated computational proteomics strategies to maximise the extension and the reliability of amino acid sequences recovered from protein traces originating from fossils that are older than 1 million years. This is a major challenge as the proteins will be highly degraded and oxidative modifications abundant. The successful candidate will optimize different MS/MS acquisition strategies and make use of various front-end peptide separation technologies including offline high-pH reversed phase chromatography and high Field Asymmetric Ion Mobility Spectrometry (FAIMS). The candidate will work closely with ESR9 (at Devro plc) to optimize and adapt fast LC gradients using the EvoSEP One system in combination with data-independent acquisition (DIA) strategies on the benchtop hybrid Orbitrap platform. This rapid EvoSep-Orbitrap-DIA screening platform will also be implemented in collaboration with ESR7 (at Max Planck Institute for Evolutionary Anthropology) for analysis of thousands of bone chips from caves known to be occupied by anatomically modern humans, Neanderthals and Denisovans to identify hominin remains and further characterise them through deep palaeogenomic sequencing. The candidate will also work in close collaboration with ESR8 (at University of Bergen) on optimizing and improving the MS/MS capabilities of orbitrap tandem mass spectrometers for ancient protein sequencing to confidently identify protein binders present in liquefied ochre-rich mixtures from Blombos Cave, South Africa, dated to ~100 ka ago and considered among the first hallmarks of complex modern human cognition.

Specific requirements

Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project e.g. biotechnology, analytical chemistry, biochemistry or related fields of science.

Other important criteria for the assessment of applicants are:

  • Experience with script programming in the languages such as R or Python is a clear advantage.
  • Hands-on experience with high-resolution Orbitrap mass spectrometry (Q Exactive, Exploris 480 or Lumos instrumentation) is desirable.
  • Prior experience with liquid chromatography and tandem mass spectrometry for peptide analysis is a must.
  • Strong interest in analysis of protein post-translational modifications (PTMs).
  • Prior knowledge and experience with biostatistical analysis of large genomic/proteomic datasets on large computational infrastructures is a valued plus.

Principal supervisor is Professor Jesper V. Olsen, Novo Nordisk Foundation Center for Protein Research, jesper.olsen@cpr.ku.dk,  Direct Phone: +45 35 32 50 22

Start:                  1 August 2020 or as soon as possible thereafter

Duration:           3 years (36 months) as a PhD student


Place of employment for fellowship 4

The place of employment is at Novo Nordisk Foundation Center for Protein Research (CPR) and the successful applicants will mainly be based at the Proteomics Program at the Center, part of the Faculty of Health and Medical Sciences at University of Copenhagen, in Copenhagen city center. The research environment at CPR is vibrant, ambitious, and international, with approx. 200 employees covering 30 different nationalities. The Center comprises modern laboratories and state-of-the-art facilities within protein science. Seminars with high profiled international speakers and regular internal research seminars are organized at CPR .

Terms of employment for all four fellowships 

The employment as PhD fellow is full time and for 3 years.

It is conditioned upon the applicant’s successful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree. Salary, pension and terms of employment are in accordance with the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary begins around 27,593 DKK /approx. 3,695 EUR (April 2020-level) plus pension.

Questions

For specific information about each PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure

Your application must be submitted electronically by clicking ‘APPLY NOW’ below and select the fellowship, you would like to apply for. The application must include the following documents in PDF format: 

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Master of Science diploma and transcript of records. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor will do

4. Publication list (if possible)

Application deadline: 4 May 2020, 23:59 pm CET.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

The Faculty of Health and Medical Sciences comprises approximately 7500 students, 1500 PhD students and 3200 employees. The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community. The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position. 

APPLY NOW

Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

Contact

Jesper Velgaard Olsen
E-mail: jesper.olsen@cpr.ku.dk

Contact

Fernando Racimo
E-mail: fracimo@bio.ku.dk

Contact

Fabrice Demeter
E-mail: f.demeter@bio.ku.dk

Contact

Enrico Cappellini
E-mail: ecappellini@bio.ku.dk

Info

Application deadline: 04-05-2020
Employment start: 01-08-2020
Working hours: Full time
Department/Location: Globe Institute and Novo Nordisk Foundation Center for Protein Research