Comparative Single-Cell Transcriptomics Reveals Novel Genes Involved in Bivalve Embryonic Shell Formation and Questions Ontogenetic Homology of Molluscan Shell Types

Single-Cell RNA Sequencing Atlas From a Bivalve Larva Enhances Classical Cell Lineage Studies

(2022) David A. Salamanca-Díaz et al.   Frontiers in Ecology and Evolution

Non-collinear Hox gene expression in bivalves and the evolution of morphological novelties in mollusks

(2021) David A. Salamanca-Díaz et al.   Scientific Reports

Rooting the Animal Tree of Life

(2021) Yuanning Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Hydrophilic Shell Matrix Proteins of Nautilus pompilius and the Identification of a Core Set of Conchiferan Domains

(2021) Davin H. E. Setiamarga et al.   Genes

Identification of three cell populations from the shell gland of a bivalve mollusc

(2020) Gang Liu et al.   DEVELOPMENT GENES AND EVOLUTION

Gene gain and loss across the metazoan tree of life

(2020) Rosa Fernández et al.   Nature Ecology & Evolution

Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics

(2020) Melody S. Clark et al.   BIOLOGICAL REVIEWS

Mollusc shellomes: Past, present and future

(2020) Frédéric Marin   JOURNAL OF STRUCTURAL BIOLOGY

Ancestral Role of Ecdysis-Related Neuropeptides in Animal Life Cycle Transitions

(2020) Elisabeth Zieger et al.   CURRENT BIOLOGY

Phylogenetic comparisons reveal mosaic histories of larval and adult shell matrix protein deployment in pteriomorph bivalves

(2020) Ran Zhao et al.   Scientific Reports

Resolving the relationships of clams and cockles: dense transcriptome sampling drastically improves the bivalve tree of life

(2019) Sarah Lemer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The quagga mussel genome and the evolution of freshwater tolerance

(2019) Andrew D Calcino et al.   DNA RESEARCH

Dorsoventral decoupling of Hox gene expression underpins the diversification of molluscs

(2019) Pin Huan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The evolution of molluscs

(2018) Andreas Wanninger et al.   BIOLOGICAL REVIEWS

Dual gene repertoires for larval and adult shells reveal molecules essential for molluscan shell formation

(2018) Ran Zhao et al.   MOLECULAR BIOLOGY AND EVOLUTION

Staggered Hox expression is more widespread among molluscs than previously appreciated

(2018) Tim Wollesen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Co-option and de novo gene evolution underlie molluscan shell diversity

(2017) Felipe Aguilera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Origin and the Early Evolution of the Phylum Mollusca

(2017) P. Yu. Parkhaev   PALEONTOLOGICAL JOURNAL

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization

(2016) Kevin M. Kocot et al.   Frontiers in Zoology

The mid-developmental transition and the evolution of animal body plans

(2016) Michal Levin et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The Shell of the Invasive Bivalve Species Dreissena polymorpha: Biochemical, Elemental and Textural Investigations

(2016) Françoise Immel et al.   PLoS One

Unexpected co-linearity of Hox gene expression in an aculiferan mollusk

(2015) M. Fritsch et al.   BMC EVOLUTIONARY BIOLOGY

Combined metabolome and proteome analysis of the mantle tissue from Pacific oyster Crassostrea gigas exposed to elevated pCO2

(2015) Lei Wei et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas

(2014) Emma Timmins-Schiffman et al.   BMC GENOMICS

Metazoan calcium carbonate biomineralizations: macroevolutionary trends – challenges for the coming decade

(2014) Frédéric Marin et al.   BULLETIN DE LA SOCIETE GEOLOGIQUE DE FRANCE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The origins of molluscs

(2014) Jakob Vinther   PALAEONTOLOGY

The Lottia gigantea shell matrix proteome: re-analysis including MaxQuant iBAQ quantitation and phosphoproteome analysis

(2014) Karlheinz Mann et al.   Proteome Science

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Different secretory repertoires control the biomineralization processes of prism and nacre deposition of the pearl oyster shell

(2012) B. Marie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Novel Proteins from the Calcifying Shell Matrix of the Pacific Oyster Crassostrea gigas

(2011) Benjamin Marie et al.   MARINE BIOTECHNOLOGY

Proteomic Identification of Novel Proteins from the Calcifying Shell Matrix of the Manila Clam Venerupis Philippinarum

(2011) Benjamin Marie et al.   MARINE BIOTECHNOLOGY

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell

(2010) Benjamin Marie et al.   Proteome Science

Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix

(2010) Karlheinz Mann et al.   Proteome Science

Molluscan shell evolution with review of shell calcification hypothesis

(2009) Takeshi Furuhashi et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Involvement of Hox genes in shell morphogenesis in the encapsulated development of a top shell gastropod (Gibbula varia L.)

(2009) Leyli Samadi et al.   DEVELOPMENT GENES AND EVOLUTION

A novel role for dpp in the shaping of bivalve shells revealed in a conserved molluscan developmental program

(2009) Koryu Kin et al.   DEVELOPMENTAL BIOLOGY

Parallel Evolution of Nacre Building Gene Sets in Molluscs

(2009) Daniel J. Jackson et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expression patterns of engrailed and dpp in the gastropod Lymnaea stagnalis

(2008) Minoru Iijima et al.   DEVELOPMENT GENES AND EVOLUTION

The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes

(2008) Karlheinz Mann et al.   Proteome Science

Early Development of the Japanese Spiny Oyster (Saccostrea kegaki): Characterization of Some Genetic Markers

(2008) Shota Kakoi et al.   ZOOLOGICAL SCIENCE