22/01/2018
Marie Skłodowska-Curie Actions

Marie Skłodowska Curie Actions ITN Early Stage Researcher: “Comparative Genomics of Non-Model Invertebrates” (IGNITE)

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  • ORGANISATION NAME
    Innovative Training Network IGNITE (H2020-MSCA-ITN-764840)
  • ORGANISATION COUNTRY
    Germany
  • DEADLINE DATE
    28/02/2018
  • RESEARCH FIELD
    Natural sciences

15 PhD positions available in the

 

Marie Skłodowska-Curie Actions (MSCA) Innovative Training Network (ITN)

“Comparative Genomics of Non-Model Invertebrates” (IGNITE)

(www.itn-ignite.eu).

 

15 PhD/Early Stage Researcher (ESR) positions are available in the Pan-European MSCA-ITN IGNITE Network of institutions and companies for a maximum duration of 36 months.

All positions are open from 1st July 2018 or as soon as possible thereafter.

The deadline for applications is 28th February 2018.

 

Invertebrates, i.e., animals without a backbone, represent 95% of animal diversity on earth but are a surprisingly underexplored reservoir of genetic resources. The content and architecture of their genomes remains poorly characterised, but such knowledge is needed to fully appreciate their evolutionary, ecological and socio­-economic importance, as well as to leverage the benefits they can provide to human well-being, for example as a source for novel drugs and biomimetic materials. Europe is home to world-leading expertise in invertebrate genomics and IGNITE will gather together this European excellence to train a new generation of scientists skilled in all aspects of invertebrate genomics. We will considerably enhance our knowledge and understanding of animal genome knowledge by generating and analysing novel data from undersampled invertebrate lineages and by developing innovative new tools for high-quality genome assembly and analysis. The well-trained genome scientists emerging from IGNITE will be in great demand in universities, research institutions, as well as in software, biomedical, agrofood and pharmaceutical companies. Through their excellent interdisciplinary and intersectoral training spanning from biology and geobiology to bioinformatics and computer science, our graduates will be in a prime position to take up leadership roles in both academia and industry in order to drive the complex changes needed to advance sustainability of our knowledge-based society and economy.

 

General requirements for all ESR positions

At the time of commencement, it is required that the candidates have not been awarded a doctorate degree and are within the first 4 years (full-time equivalent) of their research careers (see here: https://ec.europa.eu/research/participants/portal/desktop/en/support/faqs/faq-161.html). Furthermore, the candidates must not have resided or carried out their main activity (work, studies, etc.) in the enrollment country for more than 12 months in the 3 years immediately prior to their recruitment. Short stays, such as holidays, are not taken into account. Candidates are required to spend part of their project period at other institutions in the IGNITE consortium during secondments, as described in each individual projects.

 

The IGNITE consortium acknowledges that genomics is still a largely male-dominated field and aims to change this situation. Females are therefore strongly encouraged to apply.

 

Application for individual positions are through a central application tool available here: https://portal.graduatecenter-lmu.de/ocgc/ignite.

For a detailed description of the individual projects please see http://www.itn-ignite.eu/projects/

Please note that for projects 4, 6, and 12 you have to also apply at the host institution (information is given with the project descriptions).

 

The following ESR/PhD projects are available:

 

Project 1

Phylogenomics of non-bilaterian animals.

Supervisor: Gert Wörheide (LMU Munich), Co-supervisor Davide Pisani (University of Bristol)

Objectives: The phylogenetic relationships among non-bilaterian animals are still not unequivocally accepted but their robust resolution is necessary to understand early animal evolution and the emergence of key bilaterian traits, such as nervous systems, muscles, and guts. However, more non-bilaterian taxon sampling, especially from undersampled lineages within Porifera and Placozoa, as well as new primary sequence-independent phylogenetic markers, such as “rare genomic changes” (RGCs), are necessary to test the many controversially discussed hypotheses. O1: sequence two de novo genomes from undersampled lineages (for example Calcarea/Calcinea and Hexactinellida) of sponges as well as from a strain of the enigmatic phylum Placozoa, for which only one genome is published; O2: increase non-bilaterian gene and taxon sampling for phylogenomic analyses by supplementing publically available genomes with these novel genomes as well as our already in-house sequenced genomes of the marine demosponge Tethya wilhelma, and the two freshwater demosponges Spongilla lacustris and Ephydatia muelleri; O3: search for novel sequence-independent markers of phylogenetic value (RGCs) in novel and existing genomes to contribute corroborative evidence to test the plethora of controversial hypotheses about non-bilaterian relationships published in recent years; O4: conduct molecular clock analyses to better constrain the deep-time diversification of non-bilaterian in the Precambrian.

Secondments: Jean-François Flot (Brussels), Davide Pisani (Bristol), Lyubomir Penev (Pensoft Publishers, Sofia)

 

Project 2

Comparative genomics of sponge holobionts.

Supervisor: Gert Wörheide (LMU Munich), Co-supervisor Agostinho Antunes (CIIMAR Porto)

Objectives: A holobiont is a metaorganism that consists of a host and its associated symbionts, frequently microbes - humans are a good example with their gut microbes. It is increasingly appreciated that the interaction between the different players shape the development, function and adaptation of the holobiont, but the exact modes and pathways of interaction remain frequently poorly understood. Sponges (Porifera) are another example of a holobiont system with a long evolutionary history, likely more that 550 million years. In addition, sponges are among the most potent marine producers of bioactive compounds but the interplay between host and symbionts in producing these pharmaceutically valuable molecules is not fully understood yet. We are successfully culturing the emerging demosponge model Tethya wilhelma (a low microbial abundance [LMA] sponge) since many years in our lab and have sequenced its nuclear genome as well as the genomes of its two core bacterial symbionts. O1: sequence novel sponge holobiont genomes from two Tethya sister species (T. minuta, T. actinia); O2: comparatively analyse patterns, pathways, and processes of sponge-microbe (holobiont) interaction and metabolic links in these sister-species using single-cell sequencing; O3: investigate common or divergent genomic signatures of secondary metabolite pathways in these sister-species and reconstruct their evolution.

Secondments: Detlev Arendt (EMBL Heidelberg), Agostinho Antunes (CIIMAR Porto), Lyubomir Penev (Pensoft Publishers, Sofia)

 

Project 3

Genome-wide assessment of the genetic basis of invertebrate adaptation.

Supervisor: Agostinho Antunes (CIIMAR Porto), Co-supervisor Grace McCormack (NUIG Galway)

Objectives: Major adaptive phenotypic changes in invertebrates, including the development of specialized functionalities for sensorial perception and predation/defense (e.g. natural venoms), occurred through the evolution of various gene products over the last 500 Ma. Understanding genomic processes responsible for their diversification provides fundamental insight about species evolution, ecological fitness, and diseases. Such naturally engineered genomic novelties also holds large potential for biotechnological applications of environmental and human health benefit, such as drug discovery or compounds to repel animal disease vectors. O1: characterize the diversification of multigene families involved in invertebrate adaptation in available sequenced genomes (e.g. sensory and venom genes primarily in mollusks and cnidarians, but also considering examples from other groups) complemented with deep-sequencing transcriptomics and bioinformatic analyses); O2: use proteomic analyses and cutting-edge computational methods to test the role of mutation and positive selection in enzymatic (e.g. complex ligand-receptor) and protein-protein interactions, followed by further validation with experimental functional assays; O3: translate the genomic/proteomic findings into a possible wide range of applications (e.g. gene-replacement therapies, new drugs and antidotes design, biological repellents, etc).

Secondments: Aude Violette (Alphabiotoxine, Belgium), Grace McCormack (NUIG Galway), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich).

 

Project 4

Comparative single-cell transcriptomics in sponges and placozoans.

Supervisor: Detlev Arendt (EMBL Heidelberg), Co-supervisor Gert Wörheide (LMU Munich)

Objectives: The nature of the last common ancestor of the Metazoa is largely unsolved, due to uncertainties in the branching pattern of non-bilaterian clades and, consequently, in the significance of the apparent morphological simplicity. For instance, our understanding and interpretation of the simple body plan of sponges and placozoa largely depends on their actual position in the animal tree of life. If they branched off early, they may be primarily simple; should they be closer related to cnidarians than for instance ctenophores, they probably underwent secondary simplification. One way to decide between these hypotheses is to examine their cell-type complexity. The PhD student of project 4 will closely interact with students of projects 1 & 2, who will generate novel genomes for species of three sponge classes, as well as on one placozoan species cultured at LMU Munich, by selecting those as experimental species. O1: establish cell dissociation protocols and single-cell sequencing protocols. For sponges, different life-cycle stages will be covered; O2: sequence cells with at least 1x coverage with regard to the total number of cells, to capture all cell types; O3: analyse single-cell transcriptomes with an established bioinformatics normalization pipeline for intra- and interspecific comparison.

Secondments: Grace McCormack (Galway), Gert Wörheide (Munich), Lyubomir Penev (Pensoft Publishers, Sofia).

Application note: For this project, you have to additionally apply at the EMBL International PhD programme.

 

Project 5

Using chromosome conformation capture to assemble genomes to perfection.

Supervisor: Jean-François Flot (University of Brussels), Co-supervisor Romain Koszul (Institut Pasteur, Paris)

Objectives: Despite a near-exponential increase in the number of eukaryotic genome projects over the last few year, the vast majority of them yield only "permanent drafts", i.e., genomes that remain heavily fragmented at the end of the project and are deposited as such in public databases. This is because the large and abundant repeats found in eukaryotic genomes make them extremely difficult to bring to the "golden standard" of one contig per chromosome. Bleeding-edge chromosome conformation capture (3C) approaches, however, appear as a promising path to overcome the repeat issue and could make "perfect" genome assemblies a routine outcome for eukaryotic genomes, thereby increasing the power of downstream analyses. O1: improve existing 3C procedures to make them more suited to non-model invertebrates; O2: improve existing computational pipeline to enable de novo assembly of 3C data from invertebrates with maximal accuracy and completeness; O3: apply these approaches to the genome of a chaetognath (a group whose genome has proved very challenging to assemble using conventional approaches) and shed light on its evolution by comparative genomics.

Secondments: Romain Koszul (Institut Pasteur, Paris), Eduardo Pareja (Granada), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich).

 

Project 6

Comparative and functional genomics of oogenesis and animal-vegetal axis specification of animals.

Supervisor: Andreas Hejnol (University of Bergen), Co-supervisor Davide Pisani (EMBL Heidelberg)

Objectives: The animal-vegetal axis of the fertilized egg is the first embryonic axis (primary axis) around which the major body axes (e.g., anterior-posterior, dorsal-ventral and left-right) are organized. The aims of the project is to understand primary axis formation in animals and to reconstruct the evolutionary history of the primary axis specification using comparative genomics and transcriptomics and functional validation of the finding in diverse undersampled ecdysozoan invertebrates (priapulids, marine nematodes and nematomorphs and spiralian outgroups (Nemertea, Gastrotricha)). O1: combine single cell transcriptomics, comparative genomics and organismal approaches to determine the genes involved in oogenesis across taxa to detect major evolutionary changes. Single cell and tissue transcriptomics of gonadal tissue and oocytes will deliver a list of new candidate genes; O2: test identified genes for their function by detection of mRNA during oogenesis and localization in the fertilized egg; O3: survey of publically available genomes and novel genomes sequenced in IGNITE to reconstruct the evolutionary history of target genes and provide insights into the variability of the essential process of axis determination in animals.

Secondments: Detlev Arendt (Heidelberg), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich), Eduardo Pareja (Granada)

Application note: For this project, you have to additionally apply at the job portal of the University of Bergen.

 

Project 7

Using an 'OMICS' approach to uncover novel biosynthetic pathways in sponges.

Supervisor: Grace McCormack (NUIG Galway), Co-supervisor Denis Tagu (INRA Rennes)

Objectives: Haplosclerid demosponges, one of the most diverse sponge groups, produce a range of bioactive compounds potentially useful for developing novel antimicrobial, antiviral & anticancer drugs, such as steroids, alkaloids, and especially a unique diversity of 3-alkylpyridine derivatives. The complexity of these compounds, likely of sponge origin, varies across species suggesting differences in as yet unknown biosynthesis pathways. We will extend the scarce genome and transcriptome data for haplosclerids to identify bioactive compound pathways in a broader variety of Haplosclerida, esp. for the 3-alkylpyridine derivatives. O1: Generate genomes from Haliclona oculata (type species of genus), H. simulans, and H. indistincta. These species have been selected because they are accessible, belong to different major haplosclerid groups (clades) and have previously been determined to produce specific (and different) bioactive compounds; O2: Generate additional transcriptomes from H. cinerea, H. viscosa, H. mucuosa, easily accessible around Ireland and the Mediterranean, for comparative purposes; O3: Combine comparative data-mining and metabolomics to identify genes involved in 3-alkylpyridine derivative production and understand their evolution; O4: Explore epigenetic factors that may influence compound production by experimental manipulation of sponges in research aquaria, followed by metabolomics and expression studies of targeted pathways; O5: Attempt production of one targeted natural product using recombinant gene expression.

Secondments: Dominique Lavenier (INRIA, Rennes), Denis Tagu (Rennes), Lyubomir Penev (Pensoft Publishers, Sofia).

 

Project 8

Ecdysozoa as a model system to test early animal evolution.

Supervisor: Davide Pisani (University of Bristol), Co-supervisor Max Telford (UCL, London)

Objectives: The "Cambrian explosion" (~ 520 millions of year ago, MA) is the fossil signature of the radiation of bilaterally symmetrical animals (from worms to chordates). The history of Bilateria before the “explosion” is poorly understood, and molecular clocks suggest they are significantly older than the Cambrian (~650 MA). The discrepancy between rocks and clocks is often explained by claiming that early animals were microscopic (i.e. meiofaunal). Ecdysozoa (e.g. priapulid worms and arthropods) dominated the Cambrian, but while extant ecdysozoans include both microscopic and macroscopic species, it is unclear whether Precambrian ecdysozoans are unknown because they were microscopic or because they did not exist yet. Here we will use genomic information to test whether Ecdysozoa had a hidden Precambrian history. O1: sequence de novo genomes from unsampled and poorly sampled ecdysozoan phyla (Loricifera, Kinorhyncha, Priapulida, Tardigrada and Nematomorpha); O2: generate a new phylogenomic dataset, including multiple microscopic and macroscopic species across all ecdysozoan phyla by combining own data with public data; O3: identify signatures of secondary miniaturisation (e.g. lineage specific losses of regulatory elements) through comparative genomics; O4: understand ecdysozoan miniaturisation and test whether the last common ecdysozoan ancestor was meiofaunal.

Secondments: Max Telford (London), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich), Lyubomir Penev (Pensoft Publishers, Sofia).

 

Project 9

Auto-tuned & flexible phylogenetic likelihood calculations.

Supervisor: Alexandros Stamatakis (HITS Heidelberg & Karlsruhe Institute of Techhnology), Co-supervisor Kristian Vlahovicek (University of Zagreb)

Objectives: There currently exists a plethora of computational tricks that allow for accelerating the phylogenetic likelihood function (e.g., site repeats, subtree equality vectors, terrace-aware algorithms) and simultaneously reducing its memory requirements. The phylogenetic likelihood function represents the main bottleneck for all large-scale phylogenomic inferences using statistical models of evolution. However, not all of these tricks work for every type of dataset or computing pattern (e.g., parameter estimation on a fixed tree versus tree searches) and most of them are not available in current production-level software. With respect to parallelization some require novel data distribution schemes to achieve high parallel efficiency. O1: implement a flexible low-level phylogenetic library that can automatically select the best likelihood implementation flavor for the data set and type of computation at hand, that is, an auto-tuned phylogenetic inference kernel. The kernel will use SSE3 and AVX vectors intrinsics and be optimized for cache efficiency; O2: design the code such that complex models and inference tools (e.g., mixture or heterotachous models) can be seamlessly implemented; O3: develop energy-efficient parallel tools and new data distribution (load balance) algorithms for maximum likelihood and Bayesian tree inferences as well as statistical post-analyses.

Secondments: Eduardo Pareja (Granada), Kristian Vlahovicek (Zagreb), Gert Wörheide (Munich).

 

Project 10

Genomics and resilience of Limacina pteropods.

Supervisor: Michael Schrödl (Zoological State Collection Munich), Co-supervisor Andreas Hejnol (University of Bergen)

Objectives: Planktonic thecosome snails ("sea butterflies", Limacina spp.) are abundant and ecologically important in global oceans. Their thin aragonitic shells are highly sensitive to seawater acidification and they have become valuable model organisms for studying the effects of ocean acidification. However, Limacina species cannot be reliably identified using conventional approaches. In particular, the typically used and widespread model “species” Limacina helicina is likely a species complex, where cryptic species might have different ecological and physiological preferences and tolerances. Here we will use whole genome sequences to establish a solid taxonomic foundation of the Limacina helicina group and explore adaptations and resilience of its members. O1: estimate genome sizes of various Limacina species using fluorometry, sequence and assemble up to eight de novo genomes of different Limacina species; O2: align and compare these genomes to identify informative genes for species distinction and shell production (biomineralization); O3: delimit cryptic species; O4: search for genome regions under selection for insights into how genomic mechanisms responsible for the synthesis of mineralized skeletons are influenced by environmental changes and their resilience to change (or lack thereof).

Secondments: Grace McCormack (Galway), Dominique Lavenier (INRIA, Rennes), Andreas Hejnol (Bergen).

 

Project 11

Assembly and annotation of heterozygous insect genomes.

Supervisor: Denis Tagu (INRA Rennes), Co-supervisor Dominique Lavenier (INRIA, Rennes)

Objectives: Although there are countless initiatives such as i5K for sequencing insects, these efforts are hampered by their often complex, very large, and highly heterozygous genomes. New hybrid assembly strategies using both short (Illumina) and long reads (Oxford Nanopore/PacBio), as well as approaches based on chromosome conformation capture (3C) may be used to alleviate these problems. This project will aim to test new approaches for increasing the quality of the assembly of large and complex heterozygous genomes with the aim to infer different traits (host recognition, reproduction) involved in the adaptation of target insect species to their environment. O1: analyse raw sequencing data from a set of insects of agricultural interest, Acyrthosiphon pisum, Dysaphis plantagineae, Spodoptera littoralis and frugiperda, Melinaea marseus, Ixodes ricines; O2: test and optimize available assembling strategies and programs on these genomes and to assess the quality of the resulting assemblies; O3: test and optimize automatic annotation procedures using expression data (RNA-Seq), k-mer-based approaches (in collaboration with ESR14), dedicated databases (Uniprot), and specific databases (of closely related species); O4: provide a web interface for browsing, blasting, annotating genomes on the IGNITE GALAXY server hosted at Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich.

Secondments: Dominique Lavenier (INRIA, Rennes), Jean-François Flot (Brussels), Michael Schrödl (Munich).

 

Project 12

Comparative genomics and phylogenetics of the Deuterostomes.

Supervisor: Max Telford (UC London), Co-supervisor Davide Pisani (University of Bristol)

Objectives: The Deuterostomes are one of the two major branches of bilaterian animals and are of particular interest to humans as we are members of one its phyla - the Chordata. Clarifying the relationships between groups of deuterostomes will allow subsequent mapping of the evolutionary history of diverse genomic, developmental and morphological characters and is essential to understand the route from invertebrates to vertebrates. While the clade itself is very widely accepted, there is uncertainty over several important aspects of deuterostomes phylogeny including, surprisingly, a weak signal supporting their monophyly. To reconstruct the tree, genomes of some significant missing clades will be assembled and annotated allowing both tree reconstruction and subsequent mapping of genomic characters. O1: sequence, assemble and annotate genomes from important unsampled groups (the slow evolving acoelomorph Paratomella rubra and the pterobranch hemichordate Rhabdopleura); O2: test the phylogeny of the deuterostomes (including the disputed Xenacoelomorpha); O3: reconstruct a time tree of deuterostome evolution; O4: reconstruct the genome content of deuterostome ancestors; O5: link patterns of gene loss, gain, duplication and diversification in deuterostome genomes with morphological change.

Secondments: Eduardo Pareja (Granada), Alexandros Stamatakis (Heidelberg), Davide Pisani (Bristol).

Application note: For this project, you have to additionally apply at the job portal of the University College London.

 

Project 13

Computational identification of major gene regulation modules in development and cell differentiation.

Supervisor: Kristian Vlahovicek (University of Zagreb), Co-supervisor Alexandros Stamatakis (HITS Heidelberg)

Objectives: Spatiotemporal data on gene expression and chromatin structure during the development and differentiation of different metazoan clades is important for detecting regulatory modules common for all multicellular organisms. It also has the potential to reveal clade-specific differences in these processes. This project will focus on genomic mechanisms for environmental adaptation to light and circadian rhythm. We will use two freshwater demosponges, Ephydatia muelleri and Eunapius subterraneus as models. Both are closely related and share their adaptation to freshwater, yet inhabit completely different ecosystems, above ground vs. subterranean, respectively. O1: collect novel NGS data on the developmental time course of these two species, specifically targeting small and noncoding RNA complement; O2: combine them with other data collected in IGNITE and compare with data we have already collected and analyzed in rodents; O3: identify putative common developmental and differentiation gene expression modules and (if they exist) basal metazoan specifics deviating from the common metazoan regulome; O4: corroborate this data with the computational search for transcription factor binding motifs in co-expressed loci in order to further describe the developmental and differentiation regulome.

Secondments: Michael Schrödl (Munich), Denis Tagu (Rennes), Andreas Hejnol (Bergen).

 

Project 14

Design and development of new kmer-based algorithms and application to sequence annotation, taxonomic assignment and transcriptome assembly.

Supervisor: Eduardo Pareja (Era7 Granada), Co-supervisor Jean-François Flot (University of Brussels)

Objectives: Kmer-based based algorithms are very promising approaches, faster and better performing for the analysis of massive data than classical bioinformatic methods. They are especially appropriate for integrative and comparative analyses since they can take advantage of new sequence indexing systems that are optimal for massive comparative analysis. We will design and implement new kmer-based algorithms and/ or will apply and test kmer-based algorithms designed and developed by the Era7 Bioinformatics research group. O1: develop and apply kmer-based algorithms to annotate the genomes assembled by other IGNITE participants (for example ESR11), and test new algorithms with publicly available annotated genomes and compare performance with the public annotation; O2: test new kmer-based algorithms for use in taxonomic assignment of sequences, which is of importance to detect, for example contamination by symbionts (useful for, e.g., ESR2 project) prior to the assembly of genomes; O3: test new kmer-based algorithms to improve transcriptome assembl; O4: implement kmer-based algorithms in cloud-based infrastructure at the Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich, or on AWS (Amazon Web Services), licensed under Open Source AGPLv3 license

Secondments: Jean-François Flot (Brussels), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich), Gert Wörheide (Munich).

 

Project 15

Semantic publication, dissemination, visualization and re-use of biodiversity-related genomic and metagenomic data.

Supervisor: Lyubomir Penev (Pensoft Publishers, Sofia), Co-supervisor Michael Schrödl (Zoological State Collection Munich)

Objectives: One of the increasingly worrying impediments in biodiversity sciences and genomics is the continuing use of non-machine-readable formats, for example PDF, HTML or even paper. To extract and reuse data from these formats a significant post-publication effort is needed. O1: integrate academic peer-review and publishing practices with the research process, so that to increase machine-readability, interoperability and reuse of the published content to the maximum extent possible; O2: deliver machine-readable content through XML and Application Programming Interface (API) to data aggregators and end users; O3: survey, develop and implement novel methods and workflows, including nano- and micro-publications, for genomic and metagenomic data publishing, visualisation, dissemination and reuse. A core part of the work for all three objectives will be the integration between leading genomic data management platforms (INSDC, BOLD, PlutoF, Galaxy, and others) with the ARPHA XML-based publishing platform for online collaborative peer-review and publication, through implementation of community-accepted standards for genomic / metagenomic data and metadata.

The applicants must have a basic knowledge and experience in informatics and software development and programming. Educational degrees in the above fields and especially in Linked Open Data, RDF and OWL will be considered as a major advantage.

Secondments: Agostinho Antunes (Porto), Michael Schrödl (Munich), Yu Wang (Leibniz-Supercomputing Centre of the Bavarian Academy of Science and Humanities, Munich).

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