Comparative Genomics of Non-Model Invertebrates

Resources

Publications


Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition

Aabha Deshpande, Ramón E. Rivera-Vicéns, Narsinh L. Thakur, Gert Wörheide
YEAR: 2021
JOURNAL: bioRxiv

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

Claude Rispe, Fabrice Legeai, Paul D. Nabity, et al.
YEAR: 2020
PUBLISHER/PLACE: BioMed Central
JOURNAL: BMC Biology
VOLUME/ISSUE: 18/1
PAGES: 90

Computer vision for pattern detection in chromosome contact maps

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
YEAR: 2020
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 11/1
PAGES: 5795

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

Jeremy A. Miller, Yanell Braumuller, Puneet Kishor, David Peter Shorthouse, Mariya Dimitrova, Guido Sautter, Donat Agosti
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e37078

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

Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 10/1
PAGES: 2295

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

Jesus Lozano-Fernandez, Alastair R. Tanner, Mattia Giacomelli, Robert Carton, Jakob Vinther, Gregory D. Edgecombe, Davide Pisani
YEAR: 2019
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communications
VOLUME/ISSUE: 10/1
PAGES: 4534

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

Jesus Lozano-Fernandez, Mattia Giacomelli, James F. Fleming, Albert Chen, Jakob Vinther, Philip F. Thomsen, Henrik Glenner, Ferran Palero, David A. Legg, Thomas Iliffe, Davide Pisani, Jorgen Olsen
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Oxford University Press
JOURNAL: Genome Biology and Evolution
VOLUME/ISSUE: 11/8
PAGES: 2055–2070

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

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
YEAR: 2020
PUBLISHER/PLACE: BioMed Central
JOURNAL: Genome Biology
VOLUME/ISSUE: 21/1
PAGES: 148

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

Lyubomir Penev, Mariya Dimitrova, Viktor Senderov, Georgi Zhelezov, Teodor Georgiev, Pavel Stoev, Kiril Simov
YEAR: 2019
PUBLISHER/PLACE: MDPI
JOURNAL: Publications
VOLUME/ISSUE: 7(2)
PAGES: 38

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

Lyubomir Penev, Teodor Georgiev, Mariya Dimitrova, Yasen Mutafchiev, Pavel Stoev, Robert Mesibov
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35019

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

Lyubomir Penev, Teodor Georgiev, Viktor Senderov, Mariya Dimitrova, Pavel Stoev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35902

A streamlined workflow for conversion, peer review, and publication of genomics metadata as omics data papers

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent Smith, Lyubomir Penev
YEAR: 2021
JOURNAL: GigaScience
VOLUME/ISSUE: 10/5

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

Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Teodor Georgiev, Georgi Zhelezov, Seyhan Demirov, Vincent S. Smith, Lyubomir Penev
YEAR: 2020
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 4
PAGES: e59041

Infrastructure and Population of the OpenBiodiv Biodiversity Knowledge Graph

Mariya Dimitrova, Viktor E Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
YEAR: 2021
JOURNAL: Biodiversity Data Journal
VOLUME/ISSUE: 9: e67671

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

Mariya Dimitrova, Viktor Senderov, Kiril Simov, Teodor Georgiev, Lyubomir Penev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35773

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

Mariya Dimitrova, Viktor Senderov, Teodor Georgiev, Georgi Zhelezov, Lyubomir Penev
YEAR: 2019
PLACE: Bulgaria
PUBLISHER/PLACE: Pensoft Publishers
JOURNAL: Biodiversity Information Science and Standards
VOLUME/ISSUE: 3
PAGES: e35089

Comparative genomics and the nature of placozoan species

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
YEAR: 2018
PLACE: San Francisco
PUBLISHER/PLACE: Public Library of Science
JOURNAL: PLOS Biology
VOLUME/ISSUE: 16/7
PAGES: e2005359

"Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult "

Morel B, Barbera P, Czech L, Bettisworth B, Hübner L, Lutteropp S, Serdari D, Kostaki E-G, Mamais I, Kozlov AM, Pavlidis P, Paraskevis D, Stamatakis A
YEAR: 2020
PUBLISHER/PLACE: Oxford University Press
JOURNAL: Molecular Biology and Evolution
PAGES: msaa314

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

Nadège Guiglielmoni, Antoine Houtain, Alessandro Derzelle, Karine Van Doninck, Jean-François Flot
YEAR: 2021
PUBLISHER/PLACE: BioMed Central
JOURNAL: BMC Bioinformatics
VOLUME/ISSUE: 22
PAGES: 303

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

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
YEAR: 2020
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Nature Communication
VOLUME/ISSUE: 11/1
PAGES: 3676

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

Özgül Doğan, Michael Schrödl, Zeyuan Chen
YEAR: 2020
PUBLISHER/PLACE: PeerJ
JOURNAL: PeerJ
VOLUME/ISSUE: 8
PAGES: e8603

Lack of support for Deuterostomia prompts reinterpretation of the first Bilateria

Paschalia Kapli, Paschalis Natsidis, Daniel J. Leite, Maximilian Fursman, Nadia Jeffrie, Imran A. Rahman, Hervé Philippe, Richard R. Copley, and Maximilian J. Telford
YEAR: 2021
JOURNAL: Science Advances
VOLUME/ISSUE: 7/12

Systematic errors in orthology inference and their effects on evolutionary analyses

Paschalis Natsidis, Paschalia Kapli, Philipp H. Schiffer, Maximilian J. Telford
YEAR: 2021
PUBLISHER/PLACE: Cell Press
JOURNAL: iScience
VOLUME/ISSUE: 24/2
PAGES: 102110

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

Paschalis Natsidis, Philip H. Schiffer, Irepan Salvador-Martíne, Maximilian J. Telford
YEAR: 2019
PLACE: UK
PUBLISHER/PLACE: Nature Publishing Group
JOURNAL: Scientific Reports
VOLUME/ISSUE: 9/1
PAGES: 19477

Homologous chromosomes in asexual rotifer Adineta vaga suggest automixis

Paul Simion, Jitendra Narayan, Antoine Houtain, Alessandro Derzelle, Lyam Baudry, Emilien Nicolas, Marie Cariou, Nadège Guiglielmoni, Djampa KL Kozlowski, Florence Rodriguez Gaudray, Matthieu Terwagne, Julie Virgo, Benjamin Noel, Patrick Wincker, Etienne GJ Danchin, Martial Marbouty, Bernard Hallet, Romain Koszul, Antoine Limasset, Jean-François Flot, Karine Van Doninck
YEAR: 2020
JOURNAL: bioRxiv

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

R.E. Rivera-Vicéns, C.A. Garcia-Escudero, N. Conci, M. Eitel, G. Wörheide
YEAR: 2021
JOURNAL: bioRxiv

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

Roland Faure, ProfileNadège Guiglielmoni, ProfileJean-François Flot
YEAR: 2021
JOURNAL: bioRxiv