PhD Project in carbohydrate and supramolecular chemsitry

The department of chemistry invites applicants for a PhD fellowship in supramolecular protecting groups for carbohydrate synthesis. The project is part of the research project European Network on the Supramolecular Chemistry of Carbohydrates (ENSCC) - a Marie Skłodowska-Curie European Doctorate Network (DN)funded by the European Commission (Grant agreement no: 101119492).

Start date is expected to be 1 September 2024 or as soon as possible thereafter.

The project In this project, we will use macrocycles, provided by members of the ENSCC network, for selective temporary protection of hydroxy groups on various carbohydrates. The substrates will be common carbohydrates with a minimum of protective groups. The temporally non-covalent “protection/activation” by the interaction with the macrocycle will allow for selective chemical derivatization of specific hydroxy groups, giving site-selective modifications. This could, as examples, be the installment of protective groups like esters, glycosylations or oxidation reactions. Initial studies will be performed using already available macrocycles, but in time, new types of macrocycles will be developed based on the results obtained. Some initial screening of host-guest interactions will be performed at UCPH and followed up by members of the ENSCC network.

Who are we looking for? We are looking for candidates within the field(s) of organic synthesis, with a background in carbohydrate and/or supramolecular chemistry. Experience with both synthesis and analytical chemistry is a plus. Good spoken and written English are also required.

Specifically, the candidate will work on:

• Synthesis of partly protected carbohydrates, that will be used as model compounds to study recognition and selective functionalization using supramolecular hosts provided by the ENSCC network.
• Synthesize new supramolecular molecules to interact with specific carbohydrates.
• Study the interactions and reaction outcomes by NMR spectroscopy as the main technique.
• Collaborate with researchers in the ENSCC network and participate actively in events.

Our group and research- and what do we offer? The group is a part of the section of organic chemistry, Department of Chemistry, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

We offer an international, creative and stimulating workinging enviroment. The principal supervisor will be Associate Professor Christian Marcus Pedersen.

The PhD programme

Qualifications needed for the regular programme To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. organic chemistry. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programmes

• Complete and pass the MSc education in accordance with the curriculum of the MSc programme
• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Professional qualifications relevant to the PhD project
• Relevant publications
• Relevant work experience
• Other relevant professional activities
• Curious mind-set with a strong interest in carbohydrate and supramolecular chemistry.
• Good language skills

Application and Assessment Procedure

 Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page)
2. Your motivation for applying for the specific PhD project
3. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
4. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
5. Publication list (if possible)
6. Reference letters (if available)

Application deadline The deadline for applications is 15 April 2024, 23:59 GMT +2.

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 deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

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

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position. 

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.

Job Description:  

Applications are invited for the Post of Junior Research Fellow (JRF) for the DST-SERB Funded Project (SRG/2023/000283) in the Department of Physics, School of Advance Sciences (SAS), at Vellore Institute of Technology (VIT), Vellore (dated 26-02-2024)

Title of the Project:

“Development of Chiroptical Semiconductor Nanocrystals for Photonic Applications”

Qualification:

M. Sc. (2 years) / Integrated M.Sc. (5 years) degree in Physics, Chemistry or Material sciences or in a related science or engineering fields.

Describe if any

Candidates having hands on experimental experiences in the field of nanomaterials designing, photonics and semiconductor optics will be given preference with valid GATE score.

Stipend:

Rs. 31,000/- per month fellowship + 8% HRA, will be given as per Institute norms.

Sponsoring Agency:

DST-SERB

Duration:

24 Months

Principal Investigator:

Dr. Amrita Dey Assistant Professor, Department of Physics School of Advance Sciences, Vellore Institute of Technology (VIT) Vellore - 632 014, Tamil Nadu.

 Send your detailed resume along with two letters of recommendations and latest passport size photo etc. on or before (28/03/2024) through online http://careers.vit.ac.in. The candidates can reach out to the principal investigator at amritadey@vit.ac.in for more details.

No TA and DA will be paid for appearing the interview. Shortlisted candidates will be called for an online interview later which will be intimated by email. The selected candidate will be expected to join immediately.

Department:

JRF Recruitment

Skills Required:

Candidates having hands on experimental experiences in the field of nanomaterials designing, photonics and semiconductor optics will be given preference with valid GATE score.

Position of post-doc in the SONATA project entitled "Structure-function studies of human PNPase" financed by the National Science Centre, Poland, is open for application. This is an opportunity to learn the breakthrough technique of cryoelectron microscopy which is revolutionizing structural biology. The project aims to investigate mitochondrial RNA metabolism with potential implications for example in CRISPR gene therapy. Project leader: dr Katarzyna Bandyra.

We are looking for motivated candidates:

• with a PhD degree in biology, chemistry or related sciences obtained not earlier than in 2017, awarded by another institution than University of Warsaw, unless the candidate have completed a continuous and documented at least 10 months long post- doctoral fellowship in another institution than University of Warsaw and in another country than the one in which they have completed a PhD course. This period may be extended by: 1) a time of long-term (in excess of 90 days) documented sick leaves or rehabilitation leaves granted on account of being unfit to work (during the 7 years long period counted from the day of obtaining PhD certificate); 2) the number of months of a child care leave granted pursuant to the Labour Code; 3) in case of women, by 18 months for every child born or adopted, whichever manner of accounting for career breaks is preferable (both before and during the 7 year long period counted from the day of obtaining PhD certificate).
• good spoken and written English
• good knowledge and experience with basic molecular biology techniques
• experience with manipulation of human cell culture (the project includes investigation of protein-protein and protein-RNA interactions in human mitochondria)
• experience with super resolution microscopy would be an advantage
• ability to work in the team
• work commitment and good organisation skills

We offer: a temporary contract with the University of Warsaw (full time position/employment contract from 1/05/2026 for the period of 24 months). We are young, dynamically developing team  specialising in structural studies of proteins and protein-RNA complexes. We are interested in protein function, biochemistry, engineering and mitochondrial RNA metabolism. More information about our group can be found on our website: https://gorna.uw.edu.pl/en.

Required documents:

• Curriculum Vitae (CV),
• Motivation letter
• 2 Letters of recommendation (preferably) or 2 referee contact details
• Copy of the PhD diploma or a certificate of doctoral defense date
• declaration of reading and acceptance of the rules for conducting competitions at the University of Warsaw (a template available at: http://www.chem.uw.edu.pl/oferty-pracy/,)
• information on the processing of personal data (the template available at: http://www.chem.uw.edu.pl/oferty-pracy/ ),

Please submit the documents no later than 18/04/2024 to: recruit.bandyra@gmail.com (PDF is the preferred format). E-mail entitled: “Sonata postdoc”

Applications are invited for the following Post in the Technological University Dublin:

Post: Post-Doctoral Researcher - AICRI project - School of Physics, Clinical & Optometric Sciences (Fixed-term specified purpose for up to 5 years, with initial funding available for 2 years) (Reference 137a/2023)

Location:  The successful candidate will initially be based in TU Dublin, Camden Row but may be reassigned at the discretion of TU Dublin.

Hours of Work: A 37 hour working week is in operation.

Salary: The successful candidate will be appointed at point (01) of the Post-Doctoral researcher Salary Scale i.e. € 45,322 gross per annum. Remuneration may be adjusted from time to time in line with Government pay policy. Incremental credit may apply in line with University policy.

Closing Date: The closing date for applications is 5:00pm (Irish Time) on Friday 19^th April 2024. Late applications will not be accepted.

It is anticipated that interviews for this post will take place in week beginning 20^th May 2024. 

The interview assessment will be 30 minutes in length and will include a presentation of 10 minutes duration.  The topic of this presentation will be as follows:

“The candidate’s previous research experience and why they are a good fit for the current position”.

Application Details/Procedures:

For further information and to make an online application for the above post please visit website:  http://www.tudublin.ie/vacancies

www.tudublin.ie/vacancies  

Technological University Dublin is an equal opportunities employer

Knowledge and Experience

• A PhD or equivalent in Physical or Life Sciences (Essential)
• Evidence of a research profile and publication record within the subject area (Essential)
• Knowledge and experience of Raman and Infrared spectroscopic techniques including surface enhanced Raman spectroscopy (SERS) and surface enhanced infrared absorption (SEIRA) (Essential)
• Knowledge and experience of multivariate statistical analysis techniques (Essential)
• Experience of handling and working with patient samples (Desirable)

Skills, talents & abilities

• Commitment to high quality research (Essential)
• Effective written and verbal communication skills with ability to present complex information effectively to a range of audiences  
• Good organisational skills
• Ability to work collaboratively and as part of a team

Further information for Post-doctoral Researcher

In the case of a 1st Post-doctoral Fellowship where the applicant may not have graduated yet, the successful applicant must, at the time of appointment, provide a letter from the appropriate graduate studies office confirming that the student has completed the programme including all the examination requirements and is just awaiting the formal graduation ceremony and the likely date on which that will take place.

Role Overview

A postdoctoral researcher position is available with the Radiation and Environmental Science Centre (RESC) as part of the All Island Cancer Research Institute AICRIstart programme, (https://www.aicri.org/aicristart) funded by the Higher Education Authority North South Research Programme.  This project involves collaboration with Trinity College Dublin, Queen’s University Belfast and University of Galway in the area of liquid biopsies and will embed into the All-Ireland Cancer Liquid Biopsies Consortium (CLuB, https://clubcancerresearch.com/) which aims to overcome the limitations of tissue biopsies by offering minimally invasive alternatives focussing on circulating tumour-derived material.

This postdoctoral project aims to develop new methodologies based on vibrational spectroscopy (Raman and FTIR spectroscopy) and machine learning for liquid biopsy samples (CTCs, ctDNA and EVs) for cancer diagnosis, prognosis and prediction of treatment outcome.

The candidate will work in an interdisciplinary team of physical and life scientists and will also be required to liaise with collaborators at Trinity College Dublin, Queen’s University Belfast and University of Galway.

Applicants should have attained their PhD with background knowledge and experience in vibrational spectroscopy and multivariate analysis.

Applications are welcome from candidates who have previously taken a break from research, eg. For caring responsibilities or because of not being able to engage in research etc.

The work on this Research Programme is carried out by Postdoctoral Research Fellows and Senior Postdoctoral Research Fellows and is quasi-autonomous research activity. The mentoring Principal Investigator (PI) will advise the appointee on the conduct of their research which itself will be part of a research programme that the PI is responsible for. The intention is that during the employment of the appointee, they will avail of learning opportunities provided by TU Dublin and/or external agencies related to their particular research programme or research practice in general.  At the completion of the Senior/Postdoctoral Research Fellowship period, the appointee will be expected to leave the University and continue their academic formation and development in a different research environment. At the completion of the mentored training period, the appointee should be in a position to take up employment as a fully autonomous researcher with another employer.

Fellowship on chemical characterization of sewage sludge and conversion into biofuels.

JOB DESCRIPTION The Mathematical Institute of Leiden University invites applicants for a two-year postdoctoral fellowship with Dalia Terhesiu in ergodic theory/probability theory, on the topic Stochastic properties for group extensions of dynamical systems. You will be joining an active and growing group, situated within an even larger research group in Leiden specialising in ergodic theory and probability theory. The position comes with some light teaching duties.

This project seeks to investigate structural, spectral and geometric properties of a certain graph classes, like Neumaier graphs, Deza graphs or more generally, edge-regular graphs. In this project we will tackle this goal by using spectral methods and combining them with tools from other fields like combinatorial optimization and finite geometry. The successful candidate for this PhD position will work under the supervision of Bart de Bruyn and Aida Abiad in the a dynamic group in geometry and discrete mathematics (https://geometry.ugent.be/) of the Department of Mathematics: Algebra and Geometry at Ghent University. Your responsibilities include to perform scientific research on the topic of the above-mentioned project and to publish your results at international conferences and in international journals. For a small percentage of your time, you will be asked to assist with educational tasks at Ghent University (course support).

Post-doctoral position available to study the role of the Nav1.8 sodium channel in arrhythmic diseases at the Federal University of São Paulo's Medical School (EPM-UNIFESP) in Brazil. Knowledge of cellular biophysics is required, with an emphasis on the patch-clamp technique. Known-how in genetic manipulation of induced pluripotent stem cells is a plus. To demonstrate your interest, please send an email to jbpesquero@gmail.com with a motivation letter and updated CV (lattes for Brazilians). The interviews (which will be online) will take place at an opportune time and candidates will be notified via email. The position is open to candidates of any nationality. The selected candidate will receive a FAPESP Post-Doctoral Scholarship in the amount of R$ 9,047.40 per month and a Technical Reserve equivalent to 10% of the annual value of the scholarship to cover unforeseen expenses directly related to the research activity. Candidates living outside São Paulo will receive an additional 1-month stipend to cover moving expenses. More information about the fellowship is at: fapesp.br/oportunidades/6880.

The project “CoP4Justice: co-planning for climate justice” opens a call for post-doctoral fellowships. The fellow will be expected to develop multi-criteria analyses; a participatory system of synthetic indicators; and propose a participatory methodology for vulnerability analysis and risk assessment for climate justice. Requirements: - PhD in Human Sciences (geography, political science); Applied Social Sciences (Administration, Public Administration, Urban Planning, Economics); Engineering or related areas; - Advanced level of English; - Academic publications in the last five years, especially in peer-reviewed journals; - Full dedication to research; - Ability to communicate and disseminate science; - Knowledge/experience: Multicriteria Analysis (MCDA); mathematical modeling; preparation of indicators; - In-person work at the host institution (EACH-USP), with fieldwork in São Vicente, São Paulo state, Brazil. Post-Doctoral fellowship granted by the São Paulo Research Foundation (FAPESP) in the amount of R$ 9,047.40 monthly and a research contingency fund, equivalent to 10% of the annual value of the fellowship which should be spent on items directly related to the research activity (more details at https://fapesp.br/en/postdoc) Send an e-mail to Sylmara Dias (sgdias@usp.br) indicating “COP4Justice – PD Scholarship” in the subject line with the following documents attached: I. Work proposal - max. 6 pages II. 2 letters of recommendation III. Curriculum Vitae or Lattes Timetable: - Closing date for applications: April 19, 2024 (applications open to candidates of any nationality) - Announcement of results 1st phase: April 26, 2024 - Interviews: April 30, 2024 - Final result: May 06, 2024 More information about the fellowship is at: fapesp.br/oportunidades/6877.

Job no: 0061988 Location: Parkville Role type: Full-time; Fixed-Term (3-years) Faculty: Arts School: Social and Political Studies Salary: Level A - $101,460 – 108,906 p.a. plus 17% super

• Fantastic opportunity to develop your research profile, with guidance and mentoring from senior academic staff!
• $10,000 per annum in funding available to support research expenses
• Salary packaging, subsidised health and wellbeing services, fitness and cultural clubs, Myki discounts, and a 25% discount on graduate courses to our staff and their immediate families

About the Role

The Thomas and Margaret Ruth McArthur Fellowship Fund offers a prestigious Postdoctoral Fellowship opportunity within the Faculty of Arts at the University of Melbourne, targeting scholars specialising in Anthropology with a keen interest in the Asia-Pacific region.

As a Postdoctoral Fellow based in the esteemed School of Social and Political Sciences, you will benefit from unparalleled mentorship from senior academics, access to cutting-edge facilities, and the chance to refine your interdisciplinary research skills.

This fellowship not only empowers you to advance your research profile but also encourages active contributions to the School and Faculty's research initiatives. You will play a role in shaping the academic discourse in your field and furthering the Faculty's research agenda, further supported by research funds to cover appropriate research expenses up to the value of $10,000 per annum.

Per the terms of the bequest funding this fellowship, preference is given to candidates who identify as female. 

Responsibilities include:

• Undertake high quality research on their designated research project;
• Prepare reports and papers based on research findings for presentation at conferences and seminars;
• Publish research findings in accordance with the minimum expectations of the Faculty of Arts;
• Prepare and submit applications for external research grants where appropriate;
• Undertake limited administrative functions primarily connected with the Fellow’s research project;
• Undertake other limited duties as negotiated with the Head of School or Dean of the Faculty (such as research supervision, or occasional guest lecturing) that contribute to the incumbent’s professional development, and to the research and learning environment of the School of Social and Political Sciences.

Who We Are Looking For 

Our ideal candidate will have a PhD qualification in Anthropology and a proven ability to conduct independent research in the Asia-Pacific region. They will also demonstrate a strong publication record in reputable journals or publishing houses, along with excellent communication and interpersonal skills, essential for effective teamwork.

You will also have:

• PhD qualification in the field of Anthropology;
• Demonstrated ability to engage in independent scholarship and research in the Asia-Pacific;
• Demonstrated publication record in Anthropology in refereed journals and/or publishing houses, relative to opportunity, previous career path and level of appointment;
• Excellent communication (both written and verbal) and interpersonal skills and the ability to work effectively as part of a team.

For further information regarding responsibilities and requirements, please refer to the attached PD.

This position requires the incumbent to hold a current and valid Working with Children Check to ensure the University provides a safe environment for everyone. 

Please note: To be considered for this role you must have current valid work rights for Australia. Visa sponsorship is unavailable. 

Your New Team - The School of Social and Political Sciences

The appointee will join the School of Social and Political Sciences, which is at the forefront of teaching and research in the social sciences in Australia and internationally. The School’s aim is to redefine the world and change what matters, and our work is underpinned by the values of intellectual freedom, integrity, diversity, environmental sustainability and social justice.  We value collegiality and active citizenship and are committed to contributing strongly to public and institutional life, and to providing an engaged and distinctive social science and arts education for our students.

About the University of Melbourne 

We take pride in our people, who all contribute to our mission to benefit society through the transformative impact of education and research. Discover more via our website and stay connected with our stories and people on LinkedIn.

We offer the opportunity to be part of a vibrant community and enjoy a range of benefits, check out our benefits page!

Be Yourself! 

The University of Melbourne values the unique backgrounds, experiences and contributions that each person brings to our community and welcomes and celebrates diversity.  Candidates of all backgrounds are encouraged to apply. Our aim is to create a workforce that reflects the Diversity and Inclusion of the community in which we live.

If you require any reasonable adjustments with the recruitment process, please contact the email address listed at the bottom of the page.

Aboriginal and Torres Strait Islander Applicants  

We aspire to be the University of choice for Indigenous Australians, with unprecedented investment to attract, nurture, and retain Aboriginal and Torres Strait Islander students and staff. We are proud of our 2023-2027 Indigenous Strategy. Tangible support through a range of programs and initiatives will ensure that you personally succeed and flourish while at the University of Melbourne.

Join Us! 

If you feel this role is right for you, please apply with the following documents:

• Resume
• Cover Letter outlining your interest and experience
• The responses against the Selection Criteria^ (found in the Position Description)

^For information to help you with compiling short statements to answer the selection criteria and competencies, please go to http://about.unimelb.edu.au/careers/selection-criteria

If you have any questions regarding the recruitment process, please feel free to contact Ana Gencic via email at Faculties-TA@unimelb.edu.au, ensuring that you include the Position Number and the Job Title as the subject. Please do not share your application to this email address.

If you have any particular questions regarding the job please follow the details listed on the Position Description.

Applications close: 21 APRIL 2024 11:55 PM Australian Eastern Standard Time (AEST) 

Position Description: 0061988_McArthur Fellowship PD

Position Description

Applications close: 21 Apr 2024 11:55 PM AUS Eastern Standard Time

"FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods" MSCA-DN-JD Doctoral Network. The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims to develop doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities, and social sciences. Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterised. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable. Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: the University of Bologna (UNIBO), Italy and the University of Szeged (USZ), Hungary. Objectives: We are looking for one Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (Physics, Computer science, Mathematics, Statistics, Engineering or related fields) interested in learning and developing AI-assisted tools for information extraction from domain-specific scientific texts (journals, books, etc.) related to novel food engineering, microbial catalogues, fermentation, and other relevant processes. The information acquired and related semantic analysis will be utilised to build knowledge graphs and more general ontologies. The candidate will learn AI algorithms mainly related to Natural Language Processing and information embedding (eg word2vec, Transformer Networks, G-retriever) and connection of topics and keywords (e.g. through Network Diffusion processes), and within the context of FAIRomics will apply for specific case studies:

• Development of AI-assisted tools to enhance the yield of the research team in literature search and processing.
• Automatic and semi-automatic information extraction from domain-specific scientific texts (journals, books, etc.) related to novel food engineering, fermentation, and other relevant processes.
• Demonstrate the efficacy of the developed system, focusing on a carefully selected pool of previously collected articles and books. The information acquired and semantic analysis will be utilised to build knowledge graphs and more general ontologies, which will be used to enhance the method's performance and expand the knowledge base of domain-specific databases such as microbe collection catalogues.

Expected results: Expected is a prototype AI tool that can process a pool of documents by automatically analysing their text and retrieving topic-specific information in terms of key concepts and named elements and finding the connection among them. This supports the building of a knowledge graph and/or, more generally, an ontology according to the domain defined by the documents. The extracted information can be used, on the one hand, to find related documents or identify parts of documents for a set of user-specified concepts. On the other hand, extracted and processed information in terms of a knowledge graph can be used to incorporate new data into existing knowledge bases and data catalogues. Possibly, the developed tools will also be applied in other related contexts, e.g. social networks. Location and planned secondments: The first secondment will occur at the Department of Software Engineering, University of Szeged HU (Prof. Laszlo Vidacs), Month 14 (18 months), to develop automatic and semi-automatic information extraction and processing to build knowledge graphs and ontologies. The second secondment will occur at the Department of Computer Science, University Paderborn DE (Prof. Axel-Cyrille Ngonga Ngomo), Month 28 (2 months), to learn about state-of-the-art knowledge-driven data science methods. Enrolment in Doctoral degree: 1st-degree awarding organisation: Alma Mater Studiorum – University of Bologna, Bologna IT, https://www.unibo.it/en/homepage 2nd-degree awarding organisation: University of Szeged, Szeged HU, https://u-szeged.hu/english

Supervisors team

The lead supervisor is D. Remondini, full professor at the Department of Physics and Astronomy at Alma Mater Studorium – Bologna University. He works in the application of mathematical models in Biology, such as Network Theory for the study of Complex Systems, and the development of innovative algorithms for the analysis of high dimensional biological, biomedical and virological data (multiple omics, NGSeq, Neuroimaging, text data) with Machine Learning and AI techniques. He actually leads a group with 4 PhD students (1 ITN PhD student) 3 PostDoc Students, and 3 Research Assistants, with >50 Undergraduate and Master Thesis students in Physics. The Co-supervisor is E. Giampieri (Assistant Professor), with expertise in scientific computing, data management analysis and modelling, and supervisor of >20 Undergraduate and Master Thesis students in Physics. The Hungarian team is composed of Vidács László and Balázs Nagy, professors in artificial intelligence, natural language processing, and software engineering.

Host institutions description:

The project will occur at the Laboratory of Applied Physics and Systems Biophysics, Department of Physics and Astronomy (DIFA) of the Alma Mater Studiorum - University of Bologna, Italy. DIFA is one Department of the Science School and one of the most scientifically productive Physics Departments in Italy. DIFA has a large computing facility, available to the Biophysics group (14-core HPC, 2 GPU server with >1TB RAM and 2 nVidia A100, mirrored storage server with >100 Tb storage), and to the whole Department (OPH HPC facility, >200 cores). Prof. Daniel Remondini is the director of the lab, with specific expertise in biomedical data analysis (Machine Learning, Deep Learning), complex network theory and its applications to BioMedicine. Dr Enrico Giampieri has specific expertise in scientific computing, including networks, stochastic processes and statistics in High-Performance Computing environments. All the lab members are involved in several national and EU projects (Precision Medicine, Epidemiology, Public Health, Food Production). The University of Szeged(USZ) is recognised as a top research institution in Hungary, boasting a diverse student body of over 21,000, including more than 4,000 international students from 115 countries. Led by László Vidács, the Applied Artificial Intelligence Research Group is dedicated to advancing cutting-edge AI research. We specialise in diverse AI applications, from natural language understanding to image processing. Our tailored machine learning and deep learning solutions address real-world challenges in many domains, including medical imaging diagnostics, forensic text analysis, and program source code processing.

"FAIRification des données multiOmics pour relier des bases de données et créer des graphes de connaissances pour les aliments fermentés" Réseau doctoral MSCA-DN-JD. L'initiative FAIROmics, un programme de recherche interdisciplinaire, rassemblera des universités, des centres de recherche et des entreprises privées pour permettre la FAIRification de l'interopérabilité des données et des bases de données omiques et développer des graphiques de connaissances pour une prise de décision basée sur les données afin de concevoir rationnellement des communautés microbiennes pour conférer les caractéristiques souhaitables aux plantes. à base d'aliments fermentés dans le contexte de la science ouverte et de sa réglementation. Le programme de formation FAIROmics vise à développer les compétences des doctorants à l'interface entre l'intelligence artificielle, les sciences de la vie, les sciences humaines et sociales.      Les alternatives végétales aux produits laitiers et à la viande ont gagné en popularité ces dernières années pour diverses raisons, notamment la durabilité et les bienfaits pour la santé, ainsi que les tendances de style de vie et les restrictions alimentaires. Cependant, les produits alimentaires à base de plantes peuvent être déséquilibrés sur le plan nutritionnel et leurs profils aromatiques peuvent limiter leur acceptation par les consommateurs. Les micro-organismes sont utilisés dans la fabrication de produits alimentaires depuis des millénaires. Cependant, la diversité des communautés microbiennes à l’origine des fermentations végétales, ainsi que leurs principales caractéristiques génétiques et phénotypiques ainsi que les synergies potentielles entre les membres de la communauté, restent mal caractérisées. De nombreuses données existent, mais elles sont réparties dans différentes littératures (scientifiques et grises) ou, dans le meilleur des cas, dans différentes bases de données. Cependant, elles ne sont pas toujours réutilisables car difficiles à trouver et à accéder et parce que les bases de données ne sont pas systématiquement interopérables. A noter que ce poste de doctorat donnera lieu à l'obtention d'un double diplôme après la réalisation d'un séjour dans chacun de ces organismes : L'Université de Paris-Saclay (UPSaclay), France et l' Université de Szeged (USZ), Hongrie. Objectifs: Nous recherchons un doctorant (DC) pour rejoindre notre projet sur plusieurs sites dans l'UE avec un master dans une discipline pertinente (Master en ingénierie, physique, biologie des systèmes, mathématiques appliquées, biotechnologie) intéressé par la modélisation, l'analyse et contrôle des systèmes biologiques dans le cadre des fermentations microbiennes. Le projet de thèse vise à développer des méthodes d'extraction d'informations (IE) pour produire automatiquement un graphe de connaissances sur la biologie microbienne impliquée dans la transformation ou la conservation des aliments à base de plantes. Le graphe de connaissances formalisera les molécules produites et dégradées par les micro-organismes lors du processus de fermentation. Les méthodes IE impliqueront la reconnaissance d'entités nommées, la normalisation d'entités par rapport aux références sémantiques et l'extraction de relations. Ils s'appuieront sur les approches d'apprentissage profond les plus récentes qui entraînent des modèles de langage en utilisant peu ou pas d'exemples de formation par transfert d'apprentissage ou en exploitant des informations structurées existantes, c'est-à-dire des bases de connaissances et des ontologies pour l'apprentissage à distance ou faible en incluant des informations pertinentes en fonction des besoins du Cas d'utilisation dédiés à FAIROmics (par exemple NCBI Taxonomy pour les taxons, FoodEX2 pour les aliments, ChEBI pour les molécules, KEGG pour les voies). Les corpus annotés existants serviront de point de départ à la formation (ex : CHEMDNER, Pathway Curation, Bacteria Biotope). Le projet s'appuiera sur les outils et ressources existants sur la biologie microbienne développés par les partenaires de MaIAGE (ex : application Omnicrobe*, ontologie Ontobiotope*, workflow d'extraction). Résultats attendus: Le doctorant concevra et évaluera des méthodes originales basées sur l'apprentissage automatique pour extraire des informations sur le métabolisme de la fermentation végétale à partir d'un texte. Les modèles et logiciels seront accessibles à la communauté scientifique sous une licence open source. Les connaissances extraites alimenteront un graphique de connaissances accessible au public sur les propriétés microbiennes. Les résultats seront publiés dans les principaux sites de PNL et dans les revues bioinformatiques pertinentes. Localisation et détachements prévus : Le doctorant sera principalement localisé sur le site INRAE ​​de Jouy-en-Josas pendant 24 mois et à l'Université de Szeged pour un détachement de 12 mois . Inscription au doctorat : Organisme délivrant le 1er diplôme : Université Paris-Saclay, https://www.universite-paris-saclay.fr/ Organisme délivrant le 2ème diplôme : Université de Szeged, https://u-szeged.hu/english

Équipe de superviseurs

Equipe française : Deux équipes MaIAGE seront impliquées dans l'encadrement de la thèse : l'équipe Bibliome* et l'équipe StatInfOmics* :

• Robert Bossy (Bibliome) : Traitement du langage naturel et application à la microbiologie, génie logiciel.
• Claire Nédellec (Bibliome) : Traitement du langage naturel et application à la microbiologie, représentation des connaissances et ontologie.
• Hélène Chiapello (StatInfOmics) : Bioinformatique microbienne, données omiques.
• Sandra Dérozier (StatInfOmics) : Bioinformatique microbienne, génie logiciel.

Equipe hongroise :

• Vidács Lázló : Intelligence artificielle, traitement du langage naturel, génie logiciel.
• Balázs Nagy : Intelligence artificielle, traitement du langage naturel, génie logiciel.

Description des institutions d'accueil

INRAE ​​est le premier institut de recherche agronomique d'Europe et le deuxième centre mondial des sciences agricoles. Ses scientifiques travaillent à la recherche de solutions aux grands défis de société. RU1404 MaIAGE rassemble des mathématiciens, informaticiens, bioinformaticiens et biologistes pour aborder des problématiques issues de la biologie, de l'agronomie et de l'écologie. Nos recherches portent sur des processus à différents niveaux, allant des niveaux moléculaires, cellulaires ou multicellulaires aux organismes, populations et écosystèmes entiers. L' Université de Szeged (USZ) est reconnue comme l'une des principales institutions de recherche de Hongrie, avec un corps étudiant diversifié de plus de 21 000 étudiants, dont plus de 4 000 étudiants internationaux provenant de 115 pays. Dirigé par László Vidács, le groupe de recherche sur l’intelligence artificielle appliquée se consacre à l’avancement de la recherche de pointe sur l’IA. Nous sommes spécialisés dans diverses applications d’IA, de la compréhension du langage naturel au traitement d’images. Nos solutions personnalisées d'apprentissage automatique et d'apprentissage profond répondent aux défis du monde réel dans de nombreux domaines, notamment le diagnostic d'imagerie médicale, l'analyse de textes médico-légaux et le traitement du code source des programmes.

"FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods" MSCA-DN-JD Doctoral Network.

The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims to develop doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities, and social sciences.

Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterised. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: The CSIC - Insititute for Integrative Systems Biology (I²SysBio), Spain and the University of Paris-Saclay (UPSaclay), France.

We are looking for one Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (Master’s degree in engineering, physics, systems biology, applied mathematics, biotechnology) interested in Modeling, analysis and control of biological systems in the context of microbial fermentations.

Objectives:

Elucidating key genes, enzymes and proteins responsible for differential metabolic and cellular responses using model-based analysis techniques:

• Identifying the key regulators and most suitable variables for control of the fermentation/ripening process.
• Conceptualisation and formulation of the control problems to be addressed in order to drive the microorganism population to a desired state in order to meet the a priori desired product-specific control and optimisation objectives (including the control of key metabolic shifts) in the presence of uncertainty and molecular noise.
• Developing methods and software tools for the control and optimisation of gene regulation and metabolism of microorganism populations during the fermentation/ripening process.

Expected results:

• List of the identified key regulators and variables for control of the microorganism population.
• Definition of the control problems to be addressed in order to drive the microorganism population to a desired state.
• Methods and tools for model-based feedback control of the microbial population under molecular noise.

Location and planned secondment:

The PhD student will mainly be located at the  CSIC - Insititute for Integrative Systems Biology (I²SysBio) site in Valencia for 20 months. A secondment at the UMRSayFood - INRAE/AgroParisTech is also planned for a duration of 16 months.

Enrolment in Doctoral degree:

1st-degree awarding organisation: Universitat Politècnica de València https://www.upv.es/index-en.html 2nd-degree awarding organisation: Université Paris-Saclay https://www.universite-paris-saclay.fr/en

Supervisors team

The supervisor team is composed of Irene Otero-Muras (I2SysBio), Cristian Trelea and Emmanuel Bernuau (AgroParisTech). The PhD candidate will benefit from the research experience in dynamic modelling and automatic control in CSIC-I2SysBio and APT. Both partners develop complementary tools for model analysis, parameter identification, and multi-objective dynamic optimisation and have extensive experience with theory and applications of automatic control to biological processes. Specifically, at CSIC-I2SysBio, the DC will benefit from the expertise in advanced mathematical analysis and control of biomolecular systems (including regulation, signalling and metabolism), whereas at APT, the DC will develop theoretical and computational tools for dynamic system control during fermentation/ripening processes.

Host institutions description

Institute for Integrative Systems Biology: The Spanish National Research Council (CSIC-Agencia Estatal Consejo Superior de Investigaciones Científicas) https://www.csic.es/en/csic is an autonomous, multi-disciplinary public research body affiliated to the Spanish Ministry of Science and Innovation. The CSIC has its own legal structure and is represented throughout the Spanish territory with a total of 105 centres/institutes. CSIC is the first Spanish organisation in the Framework Program of the European Union by number of projects and economic return. The I²SysBio https://www.uv.es/i2sysbio is a joint research institute involving Universitat de València (UV) and CSIC. I²SysBio Scientific Programs focus on research into the structure, function, dynamics, evolution, and manipulation of complex biological systems.

AgroParisTech is a school of engineering in the field of life sciences https://www.agroparistech.fr/en, part of the Paris-Saclay University. The DC will be hosted at the Paris-Saclay Food and Bioproduct Engineering Research Unit (SayFood). This lab’s research interests are physical, biochemical and microbiological processes that govern the food and non-food transformations of bioproducts. SayFood is a joint research unit between AgroParisTech and INRAE national research institute on agriculture, food and environment https://www.inrae.fr/en.