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    Opportunity: Bioinformatics research associate -- Metagenomic data scientist @ MCB UJ -- Kraków, Poland
    Submitted by Pawel Labaj; posted on Tuesday, November 23, 2021

    BACKGROUND

    Extended microbiome characterization by the exploitation of the microbial intra-community synergies – towards better understanding of the Exposome

    In recent years the more focus has been placed on human exposome and how it affects human health and well-being. Exposome understood as the set of human environmental exposures (complementing the genome) from conception onwards includes: a general external environment, a specific external environment, and internal environment factors. In all three categories, an alive part of the exposome are different microbiomes, e.g. urban microbiome, skin microbiome, gut microbiome.

    There are many efforts around the world to pursue the knowledge behind many different types of microbiomes and to extract the information directly from metagenomes. Projects such as MetaHIT, Human Microbiome Project or American Gut Project/Microsetta Initiative had led to the growth of information about plenty of gut connected diseases such as obesity, inflammatory bowel syndrome or ulcerative colitis. Similar insight has been gained by projects focused on skin microbiota (The Human Skin Microbiome Project), environmental microbiome (Earth Microbiome Project), urban and subway microbiomes (MetaSUB International Consortium metasub.org), and many more. However, only a few of them had also considered establishing interactions between microorganisms among themselves, with the environment, and with human beings as one of the main goals.

    Microbiomes are diverse, dynamic, and complex parts of exposomes that are crucial for determining health. The composition of these biomes by nature is strongly related to the ecological niche they occupy and thus synergies and anergies are here dominant factors. Thus, the goal of the project is to extend our knowledge about interactions within and between features that arise in three complementary views on the microbiome: view through the lenses of compositional/taxonomical profile (i.e., abundance of microbial species), view through the lenses of functionalities related to the phenomena under scrutiny and view using variables derived directly from the samples (i.e., sequences obtained from a sample). Where in the last view no prior knowledge of microbial genomes and sequences of functional proteins are used.

    In particular, we want to explore synergistic interactions between features and by this go beyond currently available approaches that are ill-fitted to analyse metagenomic data as they are not exploiting the existence of these relations.

    Specifically, we will investigate synergies in three exposome related use-cases:
    • Anomaly detection in microbiomes – identification of resistomes for AMR studies
    • Patient stratification – usage of microbiota profiles for establishing health status of the patient
    • Calculation of distances between microbiomes – prediction of the geographical origin of the sample
    The proposed type of analysis in the context of selected use-cases can lead to the discovery of new functionalities or new species that are relevant for the interesting phenomena.

    RESPONSIBILITIES

    Your work will be focused on bioinformatic analysis of available and newly acquired metagenomic microbiome data in defined use cases in order to exploit microbial intra-community synergies. You will be closely collaborating with our partners from University of Białystok responsible for development of MultiDimensional Feature Selection (MDFS) solution capable to identify microbial synergies. You will be also responsible for follow up machine learning based analysis and support in results contextualization. You are going to work closely with a PhD students and other Group members involved in this project.

    As the data are coming from various collaborations/consortia/projects you will be also involved in active collaboration with those, especially with MetaSUB International Consortium (metasub.org).

    The position will be funded by National Science Centre SONATA BIS 10 programme.

    REQUIREMENTS

    The successful candidate will:
    • Have PhD degree in computer science, biology, bioinformatics, automatic control, physics, mathematics or related disciplines
    • Have excellent written and oral communication skills in English
    • Have an expertise in at least one programming language (esp. Python)
    • Have an expertise in metagenomic data analysis, big data exploration, or in machine learning
    • Have an ability to collaborate
    • Enjoy interdisciplinary work
    • Understand the importance of communication and interactions with other members of the Group, collaborators and other members of the Centre

    COMPENSATION

    We offer:
    • Competitive salary commensurate with experience (according to National Science Centre regulations)
    • Opportunity to collaborate with world-class researchers from MCB and institutions such as Weill Cornell Medicine, ETH Zurich, University of Białystok, Acibadem University, East China Normal University
    • Scientific and professional mentorship
    • Position 100% focused on research and development (no compulsory teaching)
    • Opportunity to work on an ambitious and important scientific problem with interdisciplinary applications
    • Opportunity and support to participate scientific meetings across the globe
    • Flexible working time
    • Opportunity to work (partly) remotely

    HOW TO APPLY

    Please send an email to mcb[at]labaj.org (in email title please include "SONATA BIS Research Associate" and your first and last names) with documents as specified here: mcb.uj.edu.pl/docu[...]357a8

    DEADLINE

    17th December 2022

    ABOUT US

    The Group:
    We are a young bioinformatics group which research interests cover the methodological advances in data science and their application to topical biomedical challenges, with the focus on advancing transcriptomics and metagenomics on the road to precision medicine.

    In this manner we have played a lead role in the SEQC consortium co-ordinated by the U.S. Food and Drug Administration (FDA) for the benchmarking of largescale gene expression profiling technologies, including RNA-Seq. Currently, in the second phase of SEQC we are investigating the complementarity of targeted RNASeq and genome sequencing for refined cancer diagnosis. We are also active in the MetaSUB International Consortium where we do focus on establishing environmental metagenomics assays in healthcare as well as on enabling the use of environmental microbiome analysis for forensic purposes. We also extensively collaborate with local and international research groups and companies to grow and deliver cutting-edge, open and reproducible research which would serve the community.

    bioinf.mcb.uj.edu.pl/groups/pawelab
    scholar.google.com/cita[...]AAAAJ
    orcid.org/0000-0002-4994-0234

    Institution:
    Małopolska Centre for Biotechnology (MCB) is a flagship biotechnology institute of Southern Poland and one of the most promising biomedical institutes in Central/Eastern Europe. It is part of the Jagiellonian University, and its excellence is based on three main areas: computational biology, structural biology and plant biology. The first area, computational biology, has recently been undergoing rapid growth, with a recent start of several groups, including Microbial Genomics (Dr. Rafał Mostowy), Structural and Functional Genomics (Dr. Tomasz Kościółek), and Transcriptomics/Metagenomics (myself). The institute will also profit from the interactions with the nearby industry (Ardigen). Microbiome is a nascent field in Central/Eastern Europe and at the moment Kraków, especially MCB with 3 groups oriented around different facets of microbiome research, are rising as the leaders in this field.

    MCB offers an international and collaborative environment with access to state-ofthe-art infrastructure in both experimental and computational biology. MCB hosts many world-class research groups, including the Max Planck Research Group in Structural Biology (Glatt Lab), the Bionanoscience and Biochemistry Group (Heddle Lab), the Plant Molecular Biology Group (Yamada Lab) or the Virogenetics and Virology Group (Pyrć Lab).

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