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index medicus (16) 16
animals (13) 13
evolution (11) 11
developmental biology (8) 8
vertebrates (8) 8
amphioxus (6) 6
genome (6) 6
lancelets - genetics (6) 6
zebrafish (6) 6
gene expression regulation, developmental (5) 5
phylogeny (5) 5
signal transduction (5) 5
article (4) 4
beta-catenin (4) 4
branchiostoma (4) 4
embryo, nonmammalian - metabolism (4) 4
embryos (4) 4
expression (4) 4
gene (4) 4
gene expression (4) 4
genomes (4) 4
humans (4) 4
lancelets - embryology (4) 4
life sciences (4) 4
multidisciplinary sciences (4) 4
transcription factors (4) 4
biology (3) 3
cell biology (3) 3
conservation (3) 3
developmental expression (3) 3
embryonic structures (3) 3
evolution, molecular (3) 3
evolutionary biology (3) 3
eyes (3) 3
female (3) 3
gene regulation (3) 3
gene regulatory networks (3) 3
genes (3) 3
genetic aspects (3) 3
genetics (3) 3
genetics & heredity (3) 3
homeodomain proteins - genetics (3) 3
male (3) 3
molecular genetics (3) 3
mouse (3) 3
multigene family (3) 3
oryzias - embryology (3) 3
photoreceptors (3) 3
research article (3) 3
sense organs (3) 3
amphioxus genome (2) 2
analysis (2) 2
animal structures (2) 2
asymmetron-lucayanum (2) 2
axial patterning (2) 2
binding sites (2) 2
biological evolution (2) 2
body patterning - genetics (2) 2
body-plan (2) 2
bone morphogenetic protein-4 (2) 2
bone morphogenetic proteins (2) 2
branchiostoma-lanceolatum (2) 2
cephalochordata - genetics (2) 2
chordata - genetics (2) 2
chordates (2) 2
conserved sequence - genetics (2) 2
development biology (2) 2
dna binding proteins (2) 2
embryo (2) 2
embryo, nonmammalian - embryology (2) 2
embryology (2) 2
embryology and organogenesis (2) 2
eye - growth & development (2) 2
eye diseases (2) 2
gene-expression (2) 2
genetic structures (2) 2
genetic transcription (2) 2
genomics - methods (2) 2
homeodomain proteins - metabolism (2) 2
immunohistochemistry (2) 2
innovations (2) 2
lancelets - metabolism (2) 2
lens, crystalline - metabolism (2) 2
molecular sequence data (2) 2
neural crest (2) 2
neurons (2) 2
neurosciences (2) 2
opsin (2) 2
opsins - genetics (2) 2
organizer (2) 2
oryzias - genetics (2) 2
photoreceptor cells - metabolism (2) 2
proteins (2) 2
rhodopsin (2) 2
schizophrenia (2) 2
signaling pathway (2) 2
spantenriss (2) 2
transcription factors - genetics (2) 2
transcriptional regulation (2) 2
xenopus mesoderm (2) 2
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1. Full Text Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution
by Liegertová, Michaela and Pergner, Jiří and Kozmiková, Iryna and Fabian, Peter and Pombinho, Antonio R and Strnad, Hynek and Pačes, Jan and Vlček, Čestmír and Bartůněk, Petr and Kozmik, Zbyněk
Scientific Reports, ISSN 2045-2322, 07/2015, Volume 5, Issue 1, p. 11885
Animals sense light primarily by an opsin-based photopigment present in a photoreceptor cell. Cnidaria are arguably the most basal phylum containing a... 
NERVOUS-SYSTEM | EYES | MULTIPLE PHOTOSYSTEMS | GENE | MULTIDISCIPLINARY SCIENCES | LIGHT | RHODOPSIN | PROTEIN-COUPLED RECEPTORS | HYDRA CNIDARIA | JELLYFISH | VISUAL PIGMENT | Cubozoa - metabolism | Gene Expression | Multigene Family | Opsins - genetics | Signal Transduction | RNA, Messenger - genetics | Chromosome Mapping | Phylogeny | Biological Evolution | Cubozoa - genetics | Animals | Photoreceptor Cells - metabolism | Opsins - metabolism | Genome | Genomics - methods | Cyclic AMP - metabolism | GTP-Binding Proteins - metabolism | Phylogenetics | Photoreceptors | Evolution | Retina | Genomes
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2. Full Text The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6
by Antosova, Barbora and Smolikova, Jana and Klimova, Lucie and Lachova, Jitka and Bendova, Michaela and Kozmikova, Iryna and Machon, Ondrej and Kozmik, Zbynek
PLoS Genetics, ISSN 1553-7390, 12/2016, Volume 12, Issue 12, p. e1006441
Lens induction is a classical developmental model allowing investigation of cell specification, spatiotemporal control of gene expression, as well as how... 
NASAL DEVELOPMENT | ANIRIDIA | MORPHOGENESIS | HOMEOBOX-CONTAINING GENE | MOUSE | GENETICS & HEREDITY | DIFFERENTIATION | NEURAL CREST | EYE DEVELOPMENT | SURFACE ECTODERM | EXPRESSION | Eye - metabolism | Eye - pathology | PAX6 Transcription Factor - metabolism | Gene Regulatory Networks - genetics | Homeodomain Proteins - metabolism | Humans | Lens, Crystalline - growth & development | Eye - growth & development | Lens, Crystalline - metabolism | Ectoderm - growth & development | Neoplasm Proteins - metabolism | Lens, Crystalline - pathology | Homeodomain Proteins - genetics | PAX6 Transcription Factor - genetics | Zebrafish - genetics | Ectoderm - pathology | Animals | Gene Expression Regulation, Developmental | Enhancer Elements, Genetic - genetics | Mice | Myeloid Ecotropic Viral Integration Site 1 Protein | Neoplasm Proteins - genetics | Binding Sites | Transcription factors | Laboratories | Rodents | Genetics | Biology | Gene expression | Experiments
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3. Dorsal-ventral patterning in amphioxus: current understanding, unresolved issues, and future directions
by Kozmikova, Iryna and Yu, Jr-Kai
The International journal of developmental biology, 2017, Volume 61, Issue 10-11-12, p. 601
How the embryonic body axis is generated is a fundamental question in developmental biology. The molecular mechanisms involved in this process have been the... 
Lancelets - genetics | Animals | Lancelets - metabolism | Gene Expression Regulation, Developmental | Embryo, Nonmammalian - metabolism | Cytoskeleton - metabolism | Embryo, Nonmammalian - embryology | Lancelets - embryology | Signal Transduction - genetics | Body Patterning - genetics
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4. Full Text Using amphioxus as a basal chordate model to study BMP signaling pathway
by Yong, Luok Wen and Kozmikova, Iryna and Yu, Jr-Kai
Methods in Molecular Biology, ISSN 1064-3745, 2019, Volume 1891, pp. 91 - 114
The BMP signaling pathway has been shown to be involved in different aspects of embryonic development across diverse metazoan phyla. Comparative studies on the... 
Dorsomorphin | Amphioxus | Embryo | BMP | In situ hybridization | Immunostaining
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5. Full Text Amphioxus functional genomics and the origins of vertebrate gene regulation
by Marlétaz, Ferdinand and Firbas, Panos N and Maeso, Ignacio and Tena, Juan J and Bogdanovic, Ozren and Perry, Malcolm and Wyatt, Christopher D. R and de la Calle-Mustienes, Elisa and Bertrand, Stephanie and Burguera, Demian and Acemel, Rafael D and van Heeringen, Simon J and Naranjo, Silvia and Herrera-Ubeda, Carlos and Skvortsova, Ksenia and Jimenez-Gancedo, Sandra and Aldea, Daniel and Marquez, Yamile and Buono, Lorena and Kozmikova, Iryna and Permanyer, Jon and Louis, Alexandra and Albuixech-Crespo, Beatriz and Le Petillon, Yann and Leon, Anthony and Subirana, Lucie and Balwierz, Piotr J and Duckett, Paul Edward and Farahani, Ensieh and Aury, Jean-Marc and Mangenot, Sophie and Wincker, Patrick and Albalat, Ricard and Benito-Gutiérrez, Èlia and Cañestro, Cristian and Castro, Filipe and D’Aniello, Salvatore and Ferrier, David E. K and Huang, Shengfeng and Laudet, Vincent and Marais, Gabriel A. B and Pontarotti, Pierre and Schubert, Michael and Seitz, Hervé and Somorjai, Ildiko and Takahashi, Tokiharu and Mirabeau, Olivier and Xu, Anlong and Yu, Jr-Kai and Carninci, Piero and Martinez-Morales, Juan Ramon and Crollius, Hugues Roest and Kozmik, Zbynek and Weirauch, Matthew T and Garcia-Fernàndez, Jordi and Lister, Ryan and Lenhard, Boris and Holland, Peter W. H and Escriva, Hector and Gómez-Skarmeta, Jose Luis and Irimia, Manuel
Nature, ISSN 0028-0836, 12/2018, Volume 564, Issue 7734, pp. 64 - 70
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that have been sculpted by two whole-genome... 
TRANSGENESIS | EVOLUTION | CONSERVATION | ZEBRAFISH | CHROMATIN | MULTIDISCIPLINARY SCIENCES | BRANCHIOSTOMA-LANCEOLATUM | LANDSCAPES | PLURIPOTENCY | SEQ | DNA DEMETHYLATION | Vertebrates | Genetic aspects | Nucleotide sequencing | Genetic regulation | Observations | Methods | DNA sequencing | Chromatin | Gene regulation | Genomics | Innovations | Conservation | Genomes | Datasets | Consortia | Specialization | Developmental stages | Reproduction (copying) | DNA methylation | Evolution | Bioinformatics | Deoxyribonucleic acid--DNA | Nucleotide sequence | Gene families | Zebrafish | Gene expression | Embryos | Investigations | Enhancers | Morphology | Nematodes | Methylation | Molecular evolution | Functional genomics | Epigenomics | Life Sciences | Human health and pathology | Infectious diseases | chordate evolution | whole genome duplication | transcriptomics | DDC model | hourglass model | regulatory genomics
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6. Full Text vox homeobox gene: a novel regulator of midbrain-hindbrain boundary development in medaka fish?
by Fabian, Peter and Pantzartzi, Chrysoula N and Kozmikova, Iryna and Kozmik, Zbynek
Development Genes and Evolution, ISSN 0949-944X, 3/2016, Volume 226, Issue 2, pp. 99 - 107
The midbrain-hindbrain boundary (MHB) is one of the key organizing centers of the vertebrate central nervous system (CNS). Its patterning is governed by a... 
Life Sciences | Biochemistry, general | Neurosciences | Midbrain-hindbrain boundary | medaka | Gene regulatory network | Developmental Biology | fgf8 | vox | Cell Biology | Animal Genetics and Genomics | Heat shock element | FOREBRAIN | DEVELOPMENTAL BIOLOGY | SPECIFICATION | DEVELOPING BRAIN | CELL BIOLOGY | EVOLUTIONARY BIOLOGY | INTERACT | DOWNSTREAM | ZEBRAFISH GBX1 | EXPRESSION | ORGANIZER | POSTERIORIZATION | Mesencephalon - metabolism | Homeodomain Proteins - metabolism | Embryo, Nonmammalian - metabolism | Fish Proteins - metabolism | Gene Regulatory Networks | Homeodomain Proteins - genetics | Fish Proteins - genetics | Animals | Mesencephalon - embryology | Rhombencephalon - metabolism | Oryzias - genetics | Oryzias - embryology | Rhombencephalon - embryology | Brain | Anopheles | Molecular genetics | Analysis | Genes | Fibroblast growth factors | Genetic transcription | DNA binding proteins
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7. Full Text Assembly of the Cnidarian Camera-Type Eye from Vertebrate-Like Components
by Zbynek Kozmik and Jana Ruzickova and Kristyna Jonasova and Yoshifumi Matsumoto and Pavel Vopalensky and Iryna Kozmikova and Hynek Strnad and Shoji Kawamura and Joram Piatigorsky and Vaclav Paces and Cestmir Vlcek
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 7/2008, Volume 105, Issue 26, pp. 8989 - 8993
Animal eyes are morphologically diverse. Their assembly, however, always relies on the same basic principle, i.e., photoreceptors located in the vicinity of... 
COS cells | Vertebrates | Eyes | Opsins | Retinal pigments | Jellyfishes | Antibodies | Photoreceptors | Evolution | Melanin | Opsin | Gene | Cnidaria | Photoreceptor | FINE-STRUCTURE | gene | MULTIDISCIPLINARY SCIENCES | opsin | photoreceptor | TRIPEDALIA-CYSTOPHORA | MITF | evolution | BOX JELLYFISH | DROSOPHILA | cnidaria | EYELESS GENE | CUBOMEDUSAN | NEURAL CREST | TRANSCRIPTIONAL REGULATION | Crystallins - metabolism | Cercopithecus aethiops | Molecular Sequence Data | Melanins - metabolism | Photoreceptor Cells, Invertebrate - ultrastructure | Rod Opsins - metabolism | Cilia - ultrastructure | Cubozoa - growth & development | Photoreceptor Cells, Invertebrate - cytology | Microphthalmia-Associated Transcription Factor - metabolism | Eye - ultrastructure | Gene Expression Regulation | Eye - cytology | Eye - growth & development | Lens, Crystalline - metabolism | Pigmentation | Sequence Homology, Nucleic Acid | Vertebrates - growth & development | Cilia - metabolism | Vision, Ocular - genetics | Animals | Models, Biological | Photoreceptor Cells, Invertebrate - metabolism | COS Cells | Microphthalmia-Associated Transcription Factor - genetics | RNA, Messenger | Eye | Coelenterata | Physiological aspects | Genetic aspects | Research | Properties | Natural history | Biological Sciences
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8. Full Text A conserved regulatory program initiates lateral plate mesoderm emergence across chordates
by Prummel, KD and Hess, C and Nieuwenhuize, S and Parker, HJ and Rogers, KW and Kozmikova, I and Racioppi, C and Brombacher, EC and Czarkwiani, A and Knapp, D and Burger, S and Chiayacci, E and Shah, G and Burger, A and Huisken, J and Yun, MH and Christiaen, L and Kozmik, Z and Muller, P and Bronner, M and Krumlauf, R and Mosimann, C
NATURE COMMUNICATIONS, ISSN 2041-1723, 08/2019, Volume 10, Issue 1, pp. 3857 - 15
Cardiovascular lineages develop together with kidney, smooth muscle, and limb connective tissue progenitors from the lateral plate mesoderm (LPM). How the LPM... 
TRANSCRIPTION FACTORS | STEM-CELLS | ZEBRAFISH | EVOLUTION | MULTIDISCIPLINARY SCIENCES | IN-VIVO | MOUSE | AMPHIOXUS | ENDODERM SPECIFICATION | HOMEOBOX PROTEIN | HOMEODOMAIN PROTEIN | Smad protein | Transcription factors | Gastrulation | Poultry | Muscles | Mesoderm | Smooth muscle | Zebrafish | Embryos | Connective tissues | Vertebrates | Emergence | Mesendoderm
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9. Full Text Conservation and diversification of an ancestral chordate gene regulatory network for dorsoventral patterning
by Kozmikova, Iryna and Smolikova, Jana and Vlcek, Cestmir and Kozmik, Zbynek
PLoS ONE, ISSN 1932-6203, 2011, Volume 6, Issue 2, p. e14650
Formation of a dorsoventral axis is a key event in the early development of most animal embryos. It is well established that bone morphogenetic proteins (Bmps)... 
DNA-BINDING | SIGNALING PATHWAY | BIOLOGY | AMPHIOXUS | BONE MORPHOGENETIC PROTEIN-4 | BETA-CATENIN | HOMEOBOX GENE | XENOPUS MESODERM | TRANSCRIPTIONAL REPRESSOR | EMBRYOS | NEGATIVE REGULATOR | Chordata - genetics | Conserved Sequence - genetics | Humans | Molecular Sequence Data | Phylogeny | Gene Regulatory Networks | Zebrafish - embryology | Genetic Variation - physiology | Goosecoid Protein - genetics | Gene Expression Regulation, Developmental | Base Sequence | Oryzias - genetics | Xenopus laevis - genetics | Amino Acid Sequence | Xenopus laevis - embryology | Cells, Cultured | Homeodomain Proteins - genetics | Zebrafish - genetics | Sequence Homology, Amino Acid | Animals | 5' Untranslated Regions | Embryo, Nonmammalian | Genetic Variation - genetics | Body Patterning - genetics | Oryzias - embryology | Evolution, Molecular | Genes | Genetic research | Bone morphogenetic proteins | Genetic aspects | Genetic transcription | DNA binding proteins | Cells | Transcription factors | Wnt protein | Innovations | Conservation | Zebrafish | Genomes | Biology | Chordin | Gene expression | Embryos | Promoters | Complexity | Homeobox | Proteins | Vertebrates | Gene silencing | Signal transduction | Signaling | Reporter gene | Evolutionary conservation | Cell lines | Binding sites
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10. Full Text Essential role of Bmp signaling and its positive feedback loop in the early cell fate evolution of chordates
by Kozmikova, Iryna and Candiani, Simona and Fabian, Peter and Gurska, Daniela and Kozmik, Zbynek
Developmental Biology, ISSN 0012-1606, 10/2013, Volume 382, Issue 2, pp. 538 - 554
In chordates, early separation of cell fate domains occurs prior to the final specification of ectoderm to neural and non-neural as well as mesoderm to dorsal... 
Evolution | Axial patterning | Chordates | Cell fate | Bmp signaling | VENTRALIZING FACTOR | DEVELOPMENTAL BIOLOGY | AMPHIOXUS GENOME | XENOPUS MESODERM | ANEMONE NEMATOSTELLA-VECTENSIS | VERTEBRATE NEURAL CREST | SEA-ANEMONE | BONE MORPHOGENETIC PROTEIN-4 | ZEBRAFISH GASTRULA | TRANSCRIPTIONAL REGULATION | GENE REGULATORY NETWORKS | Neural Crest - cytology | Lancelets - metabolism | Signal Transduction | Embryo, Nonmammalian - metabolism | RNA, Messenger - metabolism | Neural Crest - metabolism | Oryzias - metabolism | Bone Morphogenetic Proteins - metabolism | Feedback, Physiological | Animals | Body Patterning | Lancelets - embryology | Oryzias - embryology | Bone morphogenetic proteins | Molecular genetics | RNA | Analysis
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11. Full Text Novel polyclonal antibodies as a useful tool for expression studies in amphioxus embryos
by Bozzo, Matteo and Pergner, Jiri and Kozmik, Zbynek and Kozmikova, Iryna
International Journal of Developmental Biology, ISSN 0214-6282, 2017, Volume 61, Issue 10-12, pp. 793 - 800
Cephalochordates, commonly called amphioxus or lancelets, are widely regarded as a useful proxy for the chordate ancestor. In recent decades, expression... 
Amphioxus | Branchiostoma | Antibody | Expression pattern | expression pattern | antibody | DEVELOPMENTAL BIOLOGY | BETA-CATENIN | GENOME | amphioxus | ASYMMETRON-LUCAYANUM | EVOLUTION | LIM-HOMEOBOX GENE | VERTEBRATES | BRANCHIOSTOMA-LANCEOLATUM | LANCELET | DEVELOPMENTAL EXPRESSION | INSIGHTS
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12. Full Text Pax2/5/8 and Pax6 alternative splicing events in basal chordates and vertebrates: A focus on paired box domain
by Fabian, Peter and Kozmikova, Iryna and Kozmik, Zbynek and Pantzartzi, Chrysoula N
Frontiers in Genetics, ISSN 1664-8021, 2015, Volume 6, p. 228
Paired box transcription factors play important role in development and tissue morphogenesis. The number of Pax homologs varies among species studied so far,... 
Paired domain | Alternative splicing | Pax6 | Splice variants | Pax258
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13. Full Text Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates
by Kozmikova, Iryna and Kozmik, Zbynek
Marine Genomics, ISSN 1874-7787, 12/2015, Volume 24, pp. 159 - 166
Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the... 
Transgenic animal | Vertebrates | Evolution | Chordates | Gene regulation | ZEBRAFISH | TBX5 | GENOME | HEDGEHOG | CONSERVATION | GENETICS & HEREDITY | FUNCTIONAL-ANALYSIS | DIVERGENCE | PROMOTER | DEVELOPMENTAL EXPRESSION | Biological Evolution | Lancelets - genetics | Animals | Lancelets - physiology | Vertebrates - genetics | Animals, Genetically Modified | Gene Expression Regulation - physiology | Vertebrates - metabolism
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14. Full Text Prolyl Isomerase Pin1 Regulates Axon Guidance by Stabilizing CRMP2A Selectively in Distal Axons
by Balastik, Martin and Zhou, Xiao Zhen and Alberich-Jorda, Meritxell and Weissova, Romana and Žiak, Jakub and Pazyra-Murphy, Maria F and Cosker, Katharina E and Machonova, Olga and Kozmikova, Iryna and Chen, Chun-Hau and Pastorino, Lucia and Asara, John M and Cole, Adam and Sutherland, Calum and Segal, Rosalind A and Lu, Kun Ping
Cell Reports, ISSN 2211-1247, 10/2015, Volume 13, Issue 4, pp. 812 - 828
Axon guidance relies on precise translation of extracellular signal gradients into local changes in cytoskeletal dynamics, but the molecular mechanisms... 
ZEBRAFISH | NEURITE OUTGROWTH | MECHANISM | RESPONSE MEDIATOR PROTEIN-2 | PHOSPHORYLATION | ALZHEIMERS-DISEASE | SEMAPHORIN | RHO-KINASE | NEURONS | GROWTH CONE | CELL BIOLOGY | Immunohistochemistry | Phosphorylation | Immunoprecipitation | Signal Transduction | Zebrafish Proteins - metabolism | Humans | Axons - metabolism | Male | Zebrafish | NIMA-Interacting Peptidylprolyl Isomerase | Nerve Tissue Proteins - genetics | Nerve Tissue Proteins - metabolism | Animals | Cell Line, Tumor | Female | Peptidylprolyl Isomerase - metabolism | Peptidylprolyl Isomerase - genetics | Zebrafish Proteins - genetics
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15. Full Text The opsin repertoire of the European lancelet: A window into light detection in a basal chordate
by Pantzartzi, Chrysoula N and Pergner, Jiri and Kozmikova, Iryna and Kozmik, Zbynek
International Journal of Developmental Biology, ISSN 0214-6282, 2017, Volume 61, Issue 10-12, pp. 763 - 772
Light detection in animals is predominantly based on the photopigment composed of a protein moiety, the opsin, and the chromophore retinal. Animal opsins... 
Amphioxus | Opsin | Branchiostoma | Expression | ATTACHMENT | expression | VERTEBRATE EYE | MELANOPSIN | opsin | DEVELOPMENTAL BIOLOGY | GENOME | PREDICTION | amphioxus | EVOLUTION | RHODOPSIN | WEB SERVER | PHOTORECEPTORS
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16. Full Text Dorsal-ventral patterning in amphioxus: Current understanding, unresolved issues, and future directions
by Kozmikova, Iryna and Sky Yu, Jr-Kai
International Journal of Developmental Biology, ISSN 0214-6282, 2017, Volume 61, Issue 10-12, pp. 601 - 610
How the embryonic body axis is generated is a fundamental question in developmental biology. The molecular mechanisms involved in this process have been the... 
Chordate | Evolution | Organizer | Signaling pathway | Dorsal-ventral patterning | BASAL CHORDATE AMPHIOXUS | BRANCHIOSTOMA-BELCHERI-TSINGTAUENSE | signaling pathway | NEURAL INDUCTION | DEVELOPMENTAL BIOLOGY | evolution | BETA-CATENIN | DORSOVENTRAL AXIS | chordate | dorsal-ventral patterning | WNT/BETA-CATENIN | organizer | GENE-EXPRESSION | XENOPUS EMBRYOS | SPEMANN ORGANIZER
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