Comparative genomics of non-model invertebrates

Resultado final

Popularization events and activities

Popularization events and activities documented

IGNITE logo, flyers, website

IGNITE logo, flyers, website established and available.

First scientific publications drafted

First scientific publications drafted and prepared for submission.

Phylogenies

Phylogenies published

Genome evolution reconstruction

Genome evolution reconstruction completed

Scientific publications published

Main scientific publications published

Lists of developmental, cell & tissue genes

Lists of developmental cell tissue genes published

Timetrees

Timetrees published

Lists of holobiont & bioproduct genes

Lists of holobiont bioproduct genes published

International Scientific Conference and its report

International Scientific Conference conducted and its report published.

Publicaciones

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

Autores: Sergio Vargas; Gert Wörheide; Nicola Conci; Martin Lehmann
Publicado en: Genome Biology and Evolution, Edición 12/9, 2020, Página(s) 1623–1635, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1101/2019.12.30.891028

Eukaryogenesis and oxygen in Earth history

Autores: Mills DB, Boyle RA, Daines SJ, Sperling EA, Pisani D, Donoghue PCJ & Lenton TM
Publicado en: Nature Ecology and Evolution, 2022, ISSN 2397-334X
Editor: Springer Nature
DOI: 10.1038/s41559-022-01733-y

Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Autores: Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E, Arora R, Cariou M, Cruaud C, Gaudray FR, Gilbert C, Guiglielmoni N, Hespeels B, Kozlowski DKL, Labadie K, Limasset A, Llirós M, Marbouty M, Terwagne M, Virgo J, Cordaux R, Danchin EGJ, Hallet B, Koszul R, Lenormand T, Flot J-F, Van Doninck K
Publicado en: Science Advances, 2021, ISSN 2375-2548
Editor: American Association for the Advancement of Science
DOI: 10.1126/sciadv.abg4216

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

Autores: 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
Publicado en: Genome Biology, Edición 21/1, 2020, Página(s) 148, ISSN 1474-760X
Editor: BioMed Central
DOI: 10.1186/s13059-020-02041-z

Integrated phylogenomic and fossil evidence of stick and leaf insects (Phasmatodea) reveal a Permian–Triassic coorigination with insectivores

Autores: Tihelka E, Chenyang C, Giacomelli M, Pisani D, Donoghue PCJ
Publicado en: R Soc. Open Sciences, 2020, ISSN 2054-5703
Editor: Royal Society
DOI: 10.1098/rsos.201689

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

Autores: 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
Publicado en: The ISME Journal, Edición 13/12, 2019, Página(s) 2938-2953, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-019-0482-0

Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Autores: Benoit Morel, Pierre Barbera, Lucas Czech, Ben Bettisworth, Lukas Hübner, Sarah Lutteropp, Dora Serdari, Evangelia-Georgia Kostaki, Ioannis Mamais, Alexey M Kozlov, Pavlos Pavlidis, Dimitrios Paraskevis, Alexandros Stamatakis
Publicado en: Molecular Biology and Evolution, 2020, ISSN 1537-1719
Editor: Society for Molecular Biology and Evolution
DOI: 10.1093/molbev/msaa314

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

Autores: Nicola Conci, Gert Wörheide, Sergio Vargas
Publicado en: Genome Biology and Evolution, Edición 11/11, 2019, Página(s) 3068-3081, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evz199

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

Autores: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Publicado en: Nature Communications, Edición 10/1, 2019, Página(s) 4534, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-12259-6

Computer vision for pattern detection in chromosome contact maps

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, Página(s) 5795, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-19562-7

Comparative genomics and the nature of placozoan species

Autores: 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
Publicado en: PLOS Biology, Edición 16/7, 2018, Página(s) e2005359, ISSN 1545-7885
Editor: Public Library of Science
DOI: 10.1371/journal.pbio.2005359

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

Autores: Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
Publicado en: Nature Communications, Edición 10/1, 2019, Página(s) 2295, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-019-10244-7

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

Autores: 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
Publicado en: Genome Biology and Evolution, Edición 11/8, 2019, Página(s) 2055-2070, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evz097

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

Autores: Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
Publicado en: Publications, Edición 7/2, 2019, Página(s) 38, ISSN 2304-6775
Editor: MDPI
DOI: 10.3390/publications7020038

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

Autores: Paschalis Natsidis, Philipp H. Schiffer, Irepan Salvador-Martínez, Maximilian J. Telford
Publicado en: Scientific Reports, Edición 9/1, 2019, Página(s) 19477, ISSN 2045-2322
Editor: Nature Publishing Group
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

Autores: Özgül Doğan, Michael Schrödl, Zeyuan Chen
Publicado en: PeerJ, Edición 8, 2020, Página(s) e8603, ISSN 2167-8359
Editor: PeerJ
DOI: 10.7717/peerj.8603

Overcoming uncollapsed haplotypes in long-read assemblies of non-model organisms

Autores: Guiglielmoni N, Houtain A, Derzelle A, Van Doninck K, Flot J-F
Publicado en: BMC Bioinformatics, 2021, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.1186/s12859‐021‐04118‐3

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

Autores: Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
Publicado en: Biodiversity Information Science and Standards, Edición 4, 2020, Página(s) e59041, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.4.59041

The Ediacaran origin of Ecdysozoa: integrating fossil and phylogenomic data.

Autores: Howard RJ, Giacomelli M, Lozano-Fernandez J, Edgecombe GD, Fleming JF, Kristensen RM, Ma X, Olesen J, Sørensen MV, Thomsen PF, Wills MA, Donoghue PCJ, Pisani D
Publicado en: Journal of the Geological Society, 2022, ISSN 0016-7649
Editor: Geological Society Publishing House
DOI: 10.1144/jgs2021-107

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

Autores: 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,
Publicado en: BMC Biology, Edición 18/1, 2020, Página(s) Article number: 90, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-020-00820-5

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

Autores: 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
Publicado en: Nature Communications, Edición 11/1, 2020, Página(s) 3676, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-17397-w

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

Autores: Davide Pisani; Gert Wörheide; Michael Eitel; Maja Adamska; Marcin Adamski; Warren R. Francis; Walker Pett
Publicado en: Molecular Biology and Evolution, Edición 36/4, 2019, Página(s) 643–649, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msz013

Comparative analysis of the Mercenaria mercenaria genome provides insights into the diversity of transposable elements and immune molecules in bivalve mollusks

Autores: Farhat S, Bonnivard E, Pales Espinosa E, Tanguy A, Boutet I, Guiglielmoni N, Flot J-F, Allam B
Publicado en: BMC Genomics, 2022, ISSN 1471-2164
Editor: BioMed Central
DOI: 10.1186/s12864-021-08262-1

Integrated phylogenomicsand fossil data illuminatethe evolution of beetles

Autores: Cai C, Tihelka E, Giacomelli M, Lawrence JF, Ślipiński A, Kundrata R, Yamamoto S, Thayer MK, Newton AF, Leschen RAB, Gimmel ML, Lü L, Engel MS, Bouchard P, Huang D, Pisani D, Donoghue PCJ
Publicado en: R. Soc Open Sciences, 2022, ISSN 2054-5703
Editor: Royal Society
DOI: 10.1098/rsos.211771

Profiling cellular diversity in sponges informs animal cell type and nervous system evolution

Autores: Jacob M. Musser, Klaske J. Schippers, Michael Nickel, Giulia Mizzon, Andrea B. Kohn,Constantin Pape, Paolo Ronchi, Nikolaos Papadopoulos, Alexander J. Tarashansky,Jörg U. Hammel, Florian Wolf2, Cong Liang, Ana Hernández-Plaza, Carlos P. Cantalapiedra,Kaia Achim, Nicole L. Schieber6, Leslie Pan, Fabian Ruperti, Warren R. Francis, Sergio Vargas,Svenja Kling, Maike Renkert, Maxim Polikarpov, Gleb B
Publicado en: Science, 2021, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.1126/science.abj2949

Anaerobic metabolism of Foraminifera thriving below the seafloor

Autores: William D. Orsi, Raphaël Morard, Aurele Vuillemin, Michael Eitel, Gert Wörheide, Jana Milucka, Michal Kucera
Publicado en: The ISME Journal, Edición 14/10, 2020, Página(s) 2580-2594, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-020-0708-1

Root Digger: a root placement program for phylogenetic trees.

Autores: Ben Bettisworth; Alexandros Stamatakis; Alexandros Stamatakis
Publicado en: BMC Bioinformatics, 2021, ISSN 1471-2105
Editor: BioMed Central
DOI: 10.5445/ir/1000133165

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

Autores: 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
Publicado en: The ISME Journal, Edición 14/1, 2020, Página(s) 322-322, ISSN 1751-7362
Editor: Nature Publishing Group
DOI: 10.1038/s41396-019-0509-6

Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: steppingstones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

Autores: Darras H, Araujo N de S, Baudry L, Guiglielmoni N, Lorite P, Marbouty M, Rodriguez F, Arkhipova I, Koszul R, Flot J-F, Aron S
Publicado en: bioRxiv, 2022
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2022.01.07.475286

Empirical Analysis of Phylogenetic Quasi-Terraces

Autores: Paula Breitling, Ben Bettisworth, Lukasz Reszczynski, Olga Chernomor, Alexandros Stamatakis
Publicado en: bioRxiv, 2019
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/810309

GraphUnzip: unzipping assembly graphs with long reads and Hi-C

Autores: Faure R, Guiglielmoni N, Flot J-F
Publicado en: bioRxiv, 2021
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.01.29.428779

A deep dive into genome assemblies of non-vertebrate animals

Autores: Guiglielmoni N, Rivera-Vicéns R, Koszul R, Flot J-F
Publicado en: Preprints, 2021
Editor: Multidisciplinary Digital Publishing Institute
DOI: 10.20944/preprints202111.0170.v1

Phylourny: Predicting the Knock-out-phase of Tournaments via Phylogenetic Methods by example of the UEFA EURO 2020

Autores: Ben Bettisworth, Alexandros Stamatakis
Publicado en: bioRxiv, 2020
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.24.449715

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

Autores: Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
Publicado en: Biodiversity Information Science and Standards, Edición 3, 2019, Página(s) e35773, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.3.35773

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

Autores: Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
Publicado en: Biodiversity Information Science and Standards, Edición 3, 2019, Página(s) e35019, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.3.35019

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

Autores: Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
Publicado en: Biodiversity Information Science and Standards, Edición 3, 2019, Página(s) e35902, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.3.35902

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

Autores: Jeremy Miller, Yanell Braumuller, Puneet Kishor, David Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
Publicado en: Biodiversity Information Science and Standards, Edición 3, 2019, Página(s) e37078, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.3.37078

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

Autores: Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
Publicado en: Biodiversity Information Science and Standards, Edición 3, 2019, Página(s) e35089, ISSN 2535-0897
Editor: Pensoft Publishers
DOI: 10.3897/biss.3.35089

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