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Comparative genomics of non-model invertebrates

Deliverables

First scientific publications drafted

First scientific publications drafted and prepared for submission.

International Scientific Conference and its report

International Scientific Conference conducted and its report published.

IGNITE logo, flyers, website

IGNITE logo, flyers, website established and available.

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Publications

Comparative proteomics of octocoral and scleractinian skeletomes and the evolution of coral calcification

Author(s): Sergio Vargas; Gert Wörheide; Nicola Conci; Martin Lehmann
Published in: Genome Biology and Evolution, Issue 12/9, 2020, Page(s) 1623–1635, ISSN 1759-6653
DOI: 10.1101/2019.12.30.891028

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Author(s): Lyam Baudry, Nadège Guiglielmoni, Hervé Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelho, Romain Koszul
Published in: Genome Biology, Issue 21/1, 2020, Page(s) 148, ISSN 1474-760X
DOI: 10.1186/s13059-020-02041-z

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Author(s): J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds, Elizabeth C. Shaver, Andrew A. Shantz, Esther C. Peters, Michael Eitel, Gert Wörheide, Koty H. Sharp, Deron E. Burkepile, Brian R. Silliman, Rebecca L. Vega Thurber
Published in: The ISME Journal, Issue 13/12, 2019, Page(s) 2938-2953, ISSN 1751-7362
DOI: 10.1038/s41396-019-0482-0

New Non-Bilaterian Transcriptomes Provide Novel Insights into the Evolution of Coral Skeletomes

Author(s): Nicola Conci, Gert Wörheide, Sergio Vargas
Published in: Genome Biology and Evolution, Issue 11/11, 2019, Page(s) 3068-3081, ISSN 1759-6653
DOI: 10.1093/gbe/evz199

Author Correction: Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Author(s): Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Published in: Nature Communications, Issue 10/1, 2019, Page(s) 4534, ISSN 2041-1723
DOI: 10.1038/s41467-019-12259-6

Computer vision for pattern detection in chromosome contact maps

Author(s): Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Rémi Montagne, Nadège Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Méot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
Published in: Nature Communications, Issue 11/1, 2020, Page(s) 5795, ISSN 2041-1723
DOI: 10.1038/s41467-020-19562-7

Comparative genomics and the nature of placozoan species

Author(s): Michael Eitel, Warren R. Francis, Frédérique Varoqueaux, Jean Daraspe, Hans-Jürgen Osigus, Stefan Krebs, Sergio Vargas, Helmut Blum, Gray A. Williams, Bernd Schierwater, Gert Wörheide
Published in: PLOS Biology, Issue 16/7, 2018, Page(s) e2005359, ISSN 1545-7885
DOI: 10.1371/journal.pbio.2005359

Increasing species sampling in chelicerate genomic-scale datasets provides support for monophyly of Acari and Arachnida

Author(s): Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Published in: Nature Communications, Issue 10/1, 2019, Page(s) 2295, ISSN 2041-1723
DOI: 10.1038/s41467-019-10244-7

Pancrustacean Evolution Illuminated by Taxon-Rich Genomic-Scale Data Sets with an Expanded Remipede Sampling

Author(s): Jesus Lozano-Fernandez, Mattia Giacomelli, James F Fleming, Albert Chen, Jakob Vinther, Philip Francis Thomsen, Henrik Glenner, Ferran Palero, David A Legg, Thomas M Iliffe, Davide Pisani, Jørgen Olesen
Published in: Genome Biology and Evolution, Issue 11/8, 2019, Page(s) 2055-2070, ISSN 1759-6653
DOI: 10.1093/gbe/evz097

OpenBiodiv: A Knowledge Graph for Literature-Extracted Linked Open Data in Biodiversity Science

Author(s): Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
Published in: Publications, Issue 7/2, 2019, Page(s) 38, ISSN 2304-6775
DOI: 10.3390/publications7020038

Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers

Author(s): Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Published in: Scientific Reports, Issue 9/1, 2019, Page(s) 19477, ISSN 2045-2322
DOI: 10.1038/s41598-019-55573-1

The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora

Author(s): Özgül Doğan, Michael Schrödl, Zeyuan Chen
Published in: PeerJ, Issue 8, 2020, Page(s) e8603, ISSN 2167-8359
DOI: 10.7717/peerj.8603

Streamlined Conversion of Omics Metadata into Manuscript Facilitates Publishing and Reuse of Omics Data

Author(s): Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Published in: Biodiversity Information Science and Standards, Issue 4, 2020, Page(s) e59041, ISSN 2535-0897
DOI: 10.3897/biss.4.59041

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author(s): Claude Rispe, Fabrice Legeai, Paul D. Nabity, Rosa Fernández, Arinder K. Arora, Patrice Baa-Puyoulet, Celeste R. Banfill, Leticia Bao, Miquel Barberà, Maryem Bouallègue, Anthony Bretaudeau, Jennifer A. Brisson, Federica Calevro, Pierre Capy, Olivier Catrice, Thomas Chertemps, Carole Couture, Laurent Delière, Angela E. Douglas, Keith Dufault-Thompson, Paula Escuer, Honglin Feng, Astrid Forneck,
Published in: BMC Biology, Issue 18/1, 2020, Page(s) Article number: 90, ISSN 1741-7007
DOI: 10.1186/s12915-020-00820-5

Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Author(s): Nathan J. Kenny, Warren R. Francis, Ramón E. Rivera-Vicéns, Ksenia Juravel, Alex de Mendoza, Cristina Díez-Vives, Ryan Lister, Luis A. Bezares-Calderón, Lauren Grombacher, Maša Roller, Lael D. Barlow, Sara Camilli, Joseph F. Ryan, Gert Wörheide, April L. Hill, Ana Riesgo, Sally P. Leys
Published in: Nature Communications, Issue 11/1, 2020, Page(s) 3676, ISSN 2041-1723
DOI: 10.1038/s41467-020-17397-w

The role of homology and orthology in the phylogenomic analysis of metazoan gene content

Author(s): Davide Pisani; Gert Wörheide; Michael Eitel; Maja Adamska; Marcin Adamski; Warren R. Francis; Walker Pett
Published in: Molecular Biology and Evolution, Issue 36/4, 2019, Page(s) 643–649, ISSN 0737-4038
DOI: 10.1093/molbev/msz013

Anaerobic metabolism of Foraminifera thriving below the seafloor

Author(s): William D. Orsi, Raphaël Morard, Aurele Vuillemin, Michael Eitel, Gert Wörheide, Jana Milucka, Michal Kucera
Published in: The ISME Journal, Issue 14/10, 2020, Page(s) 2580-2594, ISSN 1751-7362
DOI: 10.1038/s41396-020-0708-1

Correction: Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

Author(s): J. Grace Klinges, Stephanie M. Rosales, Ryan McMinds, Elizabeth C. Shaver, Andrew A. Shantz, Esther C. Peters, Michael Eitel, Gert Wörheide, Koty H. Sharp, Deron E. Burkepile, Brian R. Silliman, Rebecca L. Vega Thurber
Published in: The ISME Journal, Issue 14/1, 2020, Page(s) 322-322, ISSN 1751-7362
DOI: 10.1038/s41396-019-0509-6

OpenBiodiv-O Ontology: Bridging the Gap Between Biodiversity Data and Biodiversity Publishing

Author(s): Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
Published in: Biodiversity Information Science and Standards, Issue 3, 2019, Page(s) e35773, ISSN 2535-0897
DOI: 10.3897/biss.3.35773

Data Auditing, Cleaning and Quality Assurance Workflows from the Experience of a Scholarly Publisher

Author(s): Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
Published in: Biodiversity Information Science and Standards, Issue 3, 2019, Page(s) e35019, ISSN 2535-0897
DOI: 10.3897/biss.3.35019

The Pensoft Data Publishing Workflow: The FAIRway from articles to Linked Open Data

Author(s): Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
Published in: Biodiversity Information Science and Standards, Issue 3, 2019, Page(s) e35902, ISSN 2535-0897
DOI: 10.3897/biss.3.35902

Mobilizing Data from Taxonomic Literature for an Iconic Species (Dinosauria, Theropoda, Tyrannosaurus rex)

Author(s): Jeremy Miller, Yanell Braumuller, Puneet Kishor, David Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
Published in: Biodiversity Information Science and Standards, Issue 3, 2019, Page(s) e37078, ISSN 2535-0897
DOI: 10.3897/biss.3.37078

OpenBiodiv: Linking Type Materials, Institutions, Locations and Taxonomic Names Extracted From Scholarly Literature

Author(s): Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
Published in: Biodiversity Information Science and Standards, Issue 3, 2019, Page(s) e35089, ISSN 2535-0897
DOI: 10.3897/biss.3.35089