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Junior Researcher(m/f)_BIOPOLIS2024-59_BIOPOLIS - Teaming Job description: Position: Junior Researcher Reference: BIOPOLIS 2024-59 Main research field: Biological Sciences Sub research field: Evolutionary Genomics 1. Associação BIOPOLIS opens an international call for PhD holder Researchers, under a non-fixed work contract with an expected duration of 6 months. This announcement is for one Junior Researcher position ( Reference BIOPOLIS 2024-59) to conduct scientific research activities within the Project " Using the Ancestral Recombination Graph to understand the Evolution of structural variants and their role in ecological speciation ” funded by "BIOPOLIS • Teaming to Upgrade Excellence in Environmental Biology, Ecosystem Research, and AgroBiodiversity” (Grant agreement 857251). The research will focus on the scientific area of Biological Sciences/Evolutionary Genomics, with the goal of inferring the evolutionary history of chromosomal inversions in Littorina marine snails and their role in adaptation and speciation. The project is coordinated by Rui Faria from BIOPOLIS-CIBIO in collaboration with Pierre-Alexandre-Gagnaire from ISEM, University of Montpellier (Principal Investigators) and involves a strong bioinformatics component to analyse population genomics data. The work plan includes the following tasks: 1) detection of chromosomal rearrangements in different species of Littorina marine snails using multiple sources of data; 3) production an analysis of phased sequence data for Littorina saxatilis using haplotagging; 4) inference of the evolutionary history of inversions, including the amount of gene flux between arrangements using Ancestral Recombination Graphs; 5) organization of workshops; and 6) implementation of pipelines for analysis of haplotagging data. 2. Applicable Legislation Decree-Law no. 57/2016 of August 29th, amended by Law 57/2017 and Regulatory Decree No. 11- A / 2017 which approved the doctorate hiring regime destined to stimulate scientific and technological employment for all knowledge areas (RJEC); Portuguese Labour Code, approved by Law 7/2009 of February 12, in its actual form. 3. Pursuant to article 13 of RJEC, the tender selection panel is formed by: Rui Faria (Associate Investigator and Group Leader at BIOPOLIS/CIBIO-InBIO; President of the Jury), Miguel Carneiro (Principal Investigator at BIOPOLIS/CIBIO-InBIO), and Pierre-Alexandre Gagnaire (Researcher at University of Montpellier, vowel). 4. The workplace shall be at Associação BIOPOLIS/ CIBIO – Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, Rua Padre Armando Quintas, N7, 4485-661 Vairão, PORTUGAL, and may involve travel in Portugal and abroad in service or representation of contract entity. 5. Monthly remuneration to be paid is that set by subheading a) nr.1 article 15 of RJEC and article nr 2 of the Regulatory Decree nr. 11-A/2017 , corresponding to level 33 of the Tabela Remuneratória Única, approved by Order no. 1553-C/2008 of December 31st, i.e. 2.294,95 Euros. 6. Application can be submitted by any national, foreign and stateless candidate(s) holding a doctorate degree in Biology and related areas, and a scientific and professional background that aligns with the specific activities described below (item 7). In case the doctorate degree was awarded by a foreign higher education institution, it must comply with the provisions of Decree-Law no. 66/2018 of 16 October , and all formalities established therein must be complied with at the signature of work contract. 7. The tender admission general requirements are those defined in the previous point 6, and additional specific requirements are: Experience in detecting inversions using population genomics data, as well as long-read sequencing, and Hi-C data as well as using synteny comparison tools. Experience in bioinformatics and analysis of large population genomics datasets Experience in the study of Littorina marine snails; Experience in the construction of pipelines for analysis of NGS data; Experience in scripting in R, Python, Bash, and similar languages; Interest and experience in the study of adaptation and speciation Experience in participation in marine evolution projecta and student supervision 8. Pursuant to article 5 of RJEC, the selection is to be made based on the evaluation of the scientific and curricular career of the candidate. 9. Scientific and curricular career evaluation focuses on relevance, quality and up-to-datedness: a) of scientific, technological, cultural or artistic production in the last five years, considered most relevant by the candidate; b) of research activities, fundamental or applied science, developed in the last five years, considered of higher impact by the candidate; c) of knowledge extension and dissemination activities developed in the last five years specifically related to the promotion of culture and scientific practices, as deemed most relevant by the candidate. d) of activities of science management, technology and innovation programs, as well as experience in observing and monitoring the scientific and technological system or higher education, in Portugal or abroad. 10. The five-year period mentioned above can be extended by the panel, if requested by the candidate, whenever the suspension of scientific activities is reasoned by socially protected grounds like paternity leave, long-term serious illness, and other legal situations of unavailability to work. 11. Evaluation criteria are the following: The evaluation of the CV of the candidates, in particular the scientific merit and research experience will take into consideration the elements presented for the last five years of activity falling within the scope of the specific areas of the tender (see Point 1) and will be performed according to the following criteria: 11.1 Integrated assessment of the curriculum trajectory of the candidate, based on an overview of their scientific merits, namely: I. overall scientific coherence of the CV, including participating in research projects and supervision – 15% II. diversity and quality of scientific indicators, including relevant published peer-reviewed articles in the specific areas of the announcement (see point 1) • 10% 11.2 Relevant experience, proved in CV, in: I. Detection of chromosomal inversions, namely using population genomics data, long read sequences and Hi-C, as well as genome synteny analyses - 20% II. Analyses of whole genome sequencing data from multiple populations and species; including demographic modelling – 20% iii. Study of hybrid zones of Littorina snails- 20% iv. Using tools for Ancestral Recombination Graphs- based inference and development of bioinformatics pipelines - 15% 12. In the case of admitted candidates whose evaluation does not differ more than 10% from that obtained by the best positioned candidate, the jury will interview these candidates. This will be aimed at obtaining clarifications about the curricular elements and additional information, as well as to evaluate the attitude profile and motivation of the candidate. The final score of each jury member is obtained by the following assessment: 90% scientific and curricular career evaluation and 10% interview. 13. The candidates’ final classification system shall be given based on a scale 0 to 100. 14. The panel shall deliberate by means of roll-call vote justified under adopted and disclosed selection criteria, with no abstentions allowed. 15. Minutes of panel meetings shall be executed and include a summary of all occurrences of said meeting, as well as of all votes casted by the members and respective reasoning. 16. After selection criteria application, the panel shall prepare a sorted list of approved candidates and respective classification. 17. The panel’s final decision shall be validated by the leader of the institution, who is also in charge of deciding about the hiring. 18. Application formalization: 18.1. The applications are formalized at the electronic address https://www.cibio.up.pt/en/jobs/ with following documents in a digital form, in PDF format: i) Curriculum vitae ii) Motivation Letter iii) Qualifications Certificate (or declaration(s) of honour including the date of the PhD viva, stating that the candidate will provide the certificates before the contract starts) iv) Other relevant documentation 18.2. The application period is from 18 th of December 2024 until the 03 of January 2025. Expected starting date: 1 st of February 2025 19. All candidates who formalize their applications in an improper way or fail to prove the requirements imposed by this tender are excluded from admission. In case of doubt, the panel is entitled to request any candidate to present further documentation supporting their statements. 20. False statements provided by the candidates shall be punished by law. 21. The list of both admitted and excluded candidates and final classification list shall be notified by email. 22. After notification, all candidates have 10 working days to respond. Panel’s final decisions are pronounced within a period of 90 working days, from response period deadline. 23. This tender is exclusively destined to fill this specify position and can be terminated at any time until approval of final candidate list, expiring with the respective occupation of said position. 24. Non-discrimination and equal access policy: Associação BIOPOLIS actively promotes a non-discrimination and equal access policy, wherefore no candidate can be privileged, benefited, impaired or deprived of any rights whatsoever, or be exempt of any duties based on their ancestry, age, sex, sexual preference, marital status, family and economic conditions, instruction, origin or social conditions, genetic heritage, reduced work capacity, disability, chronic illness, nationality, ethnic origin or race, origin territory, language, religion, political or ideological convictions and union membership. 25. The panel has approved this announcement in meeting held on 17/12/2024 26. To comply with Law no. 4/2019, of 10 January, candidates must declare on the application form, under a statement of honour, their degree of disability, the type of disability and the means of communication/expression to be used in the selection process. --------------------------------------------------------------------------------------------------------PT----------------------------------------------------------------------------------------------------------------------------------- Posição: Investigador Júnior Referência: BIOPOLIS 2024-5 9 Área científica: Ciências Biológicas Sub área científica: Genómica Evolutiva 1. A Associação BIOPOLIS abre concurso de seleção internacional de doutorados para o exercício de atividades de investigação, em regime de contrato de trabalho a termo incerto, ao abrigo do Código do Trabalho, com uma duração prevista de 6 meses. O presente aviso destina-se a um lugar de Investigador Júnior (Referência BIOPOLIS 2024-59 ), para o exercício de atividades de investigação científica no âmbito do projeto "Using the Ancestral Recombination Graph to understand the Evolution of structural variants and their role in ecological speciation” financiado pelo "BIOPOLIS - Teaming to Upgrade Excellence in Environmental Biology, Ecosystem Research, and AgroBiodiversity” (Grant agreement 857251). A investigação incidirá na área científica das Ciências Biológicas/Genómica Evolutiva, com o objectivo de inferir a história evolutiva das inversões cromossómicas em caracóis marinhos do género Littorina e o seu papel na adaptação e especiação. O projeto é coordenado por Rui Faria do BIOPOLIS-CIBIO em colaboração com Pierre-Alexandre-Gagnaire do ISEM, Universidade de Montpellier (Investigadores Principais) e envolve uma forte componente de bioinformática para analisar dados genómicos populacionais. O plano de trabalhos inclui as seguintes tarefas: 1) detecção de rearranjos cromossómicos em diferentes espécies de ca