Towards a gene regulatory network shaping the fins of the Princess cichlid

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TRANSFAC(R): transcriptional regulation, from patterns to profiles

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Gene Regulatory Networks and the Evolution of Animal Body Plans

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The genomic substrate for adaptive radiation in African cichlid fish

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A gene regulatory network orchestrates neural crest formation

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The evolution of Fox genes and their role in development and disease

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The evolution of hierarchical gene regulatory networks

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Macrophages modulate adult zebrafish tail fin regeneration

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Live imaging reveals differing roles of macrophages and neutrophils during zebrafish tail fin regeneration

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Fox's in development and disease

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Induced Hypothermia Does Not Harm Hemodynamics after Polytrauma: A Porcine Model

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Regenerative Growth in Drosophila Imaginal Discs Is Regulated by Wingless and Myc

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THE CELL CYCLE AND MYC INTERSECT WITH MECHANISMS FOR PLURIPOTENCY AND REPROGRAMMING

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Reiterated Wnt signaling during zebrafish neural crest development

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The art of fin regeneration in zebrafish

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The Protooncogene c-Myc Is an Essential Regulator of Neural Crest Formation in Xenopus

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Digits and fin rays share common developmental histories

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Transient inflammatory response mediated by interleukin-1β is required for proper regeneration in zebrafish fin fold

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Matrix metalloproteinase 9 modulates collagen matrices and wound repair

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Signaling networks organizing regenerative growth of the zebrafish fin

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Foxc1 reinforces quiescence in self-renewing hair follicle stem cells

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Proteomic analysis of blastema formation in regenerating axolotl limbs

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Expression of stem cell pluripotency factors during regeneration in newts

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Limited dedifferentiation provides replacement tissue during zebrafish fin regeneration

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Sequential and Opposing Activities of Wnt and BMP Coordinate Zebrafish Bone Regeneration

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Egr1 mediates p53-independent c-Myc–induced apoptosis via a noncanonical ARF-dependent transcriptional mechanism

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The conserved role of Krox-20 in directing Hox gene expression during vertebrate hindbrain segmentation.

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Mutations in connexin43 (GJA1) perturb bone growth in zebrafish fins

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From pioneer to repressor: Bimodal foxd3 activity dynamically remodels neural crest regulatory landscape <i>in vivo</i>

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Overexpression of the transcriptional repressor FoxD3 prevents neural crest formation in Xenopus embryos

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Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

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From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo

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Epidermal Growth Factor Receptor (EGFR) Signaling Promotes Proliferation and Survival in Osteoprogenitors by Increasing Early Growth Response 2 (EGR2) Expression

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Transcriptional Profiling of Caudal Fin Regeneration in Zebrafish

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Gene expression and functional analysis of zebrafish larval fin fold regeneration

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Cellular and molecular processes of regeneration, with special emphasis on fish fins

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Tfap2a and Foxd3 regulate early steps in the development of the neural crest progenitor population

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Regulatory gene networks that shape the development of adaptive phenotypic plasticity in a cichlid fish

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Regeneration and reprogramming compared

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Conserved mechanisms regulate outgrowth in zebrafish fins

Iovine, M. K. (2007) · Nature Chemical Biology · doi:10.1038/nchembio.2007.36 · Cited by 92 · see citing works

COXPRESdb: a database to compare gene coexpression in seven model animals

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Forkhead box transcription factors in embryonic heart development and congenital heart disease

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Early gene expression during natural spinal cord regeneration in the salamander Ambystoma mexicanum

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Comparative Expression Profiling Reveals an Essential Role for Raldh2 in Epimorphic Regeneration

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Identification of IRF-8 and IRF-1 target genes in activated macrophages

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Connexin43 regulates joint location in zebrafish fins

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Regenerative Growth Is Impacted by TCDD: Gene Expression Analysis Reveals Extracellular Matrix Modulation

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The origin of the bifurcated axial skeletal system in the twin-tail goldfish

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Tetrapod limb and sarcopterygian fin regeneration share a core genetic programme

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Innate Immunity to Intraphagosomal Pathogens Is Mediated by Interferon Regulatory Factor 8 (IRF-8) That Stimulates the Expression of Macrophage-specific Nramp1 through Antagonizing Repression by c-Myc

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Transcriptional dynamics of a conserved gene expression network associated with craniofacial divergence in Arctic charr

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Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation

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The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

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Inhibition of Kinesin‐5, a Microtubule‐Based Motor Protein, As a Strategy for Enhancing Regeneration of Adult Axons

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Intracellular Cleavage of the Cx43 C‐Terminal Domain by Matrix‐Metalloproteases: A Novel Contributor to Inflammation?

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Cross talk between Wnt/β-catenin and Irf8 in leukemia progression and drug resistance

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Dermoskeleton morphogenesis in zebrafish fins

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Molecular mechanisms underlying the exceptional adaptations of batoid fins

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Nrp2 deficiency leads to trabecular bone loss and is accompanied by enhanced osteoclast and reduced osteoblast numbers

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Proteomics analysis of regenerating amphibian limbs: changes during the onset of regeneration

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Semaphorin 3d promotes cell proliferation and neural crest cell development downstream of TCF in the zebrafish hindbrain

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β-Catenin Signaling Drives Differentiation and Proinflammatory Function of IRF8-Dependent Dendritic Cells

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Semaphorin3d mediates Cx43-dependent phenotypes during fin regeneration

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Integration of zebrafish fin regeneration genes with expression data of human tumors in silico uncovers potential novel melanoma markers

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Loading-related Regulation of Transcription Factor EGR2/Krox-20 in Bone Cells Is ERK1/2 Protein-mediated and Prostaglandin, Wnt Signaling Pathway-, and Insulin-like Growth Factor-I Axis-dependent

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IL‐1β inhibits osteogenesis of human bone marrow‐derived mesenchymal stem cells by activating FoxD3/microRNA‐496 to repress wnt signaling

Huang, J., & Chen, L. (2017) · genesis · doi:10.1002/dvg.23040 · Cited by 34 · see citing works

Esco2 regulates cx43 expression during skeletal regeneration in the zebrafish fin

Banerji, R., Eble, D. M., Iovine, M. K., & Skibbens, R. V. (2015) · Developmental Dynamics · doi:10.1002/dvdy.24354 · Cited by 33 · see citing works

Early growth response 2 negatively modulates osteoclast differentiation through upregulation of Id helix–loop–helix proteins

Kim, H., Hong, J. M., Yoon, K., Kim, N., Cho, D., Choi, J., Lee, I. K., & Kim, S. (2012) · Bone · doi:10.1016/j.bone.2012.07.015 · Cited by 33 · see citing works

Identification of an evx1-Dependent Joint-Formation Pathway during FIN Regeneration

Ton, Q. V., & Iovine, M. K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081240 · Cited by 30 · see citing works

Differential expression of the aryl hydrocarbon receptor pathway associates with craniofacial polymorphism in sympatric Arctic charr

Ahi, E. P., Steinhäuser, S. S., Pálsson, A., Franzdóttir, S. R., Snorrason, S. S., Maier, V. H., & Jónsson, Z. O. (2015) · EvoDevo · doi:10.1186/s13227-015-0022-6 · Cited by 28 · see citing works

Cysteine‐ and glycine‐rich protein 1a is involved in spinal cord regeneration in adult zebrafish

Ma, L., Yu, Y., Guo, Y., Hart, R. P., & Schachner, M. (2012) · European Journal of Neuroscience · doi:10.1111/j.1460-9568.2011.07958.x · Cited by 28 · see citing works

Role of annexin gene and its regulation during zebrafish caudal fin regeneration

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Genetic and developmental basis for fin shape variation in African cichlid fishes

Navon, D., Olearczyk, N., & Albertson, R. C. (2016) · Molecular Ecology · doi:10.1111/mec.13905 · Cited by 26 · see citing works

Migration of mesenchymal cell fated to blastema is necessary for fish fin regeneration

Nakatani, Y., Nishidate, M., Fujita, M., Kawakami, A., & Kudō, A. (2007) · Development Growth & Differentiation · doi:10.1111/j.1440-169x.2007.00977.x · Cited by 24 · see citing works

A gene expression study of ornamental fin shape in Neolamprologus brichardi, an African cichlid species

Ahi, E. P., Richter, F., & Sefc, K. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-17778-0 · Cited by 22 · see citing works

Two Different Functions of Connexin43 Confer Two Different Bone Phenotypes in Zebrafish

Misu, A., Yamanaka, H., Aramaki, T., Kondo, S., Skerrett, I. M., Iovine, M. K., & Watanabe, M. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.720110 · Cited by 21 · see citing works

Anterior-posterior gene expression differences in three Lake Malawi cichlid fishes with variation in body stripe orientation

Ahi, E. P., & Sefc, K. M. (2017) · PeerJ · doi:10.7717/peerj.4080 · Cited by 21 · see citing works

Transcriptomics of two evolutionary novelties: how to make a sperm‐transfer organ out of an anal fin and a sexually selected “sword” out of a caudal fin

Kang, J. H., Manousaki, T., Franchini, P., Kneitz, S., Schartl, M., & Meyer, A. (2015) · Ecology and Evolution · doi:10.1002/ece3.1390 · Cited by 11 · see citing works

Molecular Evolution of the Neural Crest Regulatory Network in Ray-Finned Fish

Kratochwil, C. F., Geißler, L., Irisarri, I., & Meyer, A. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv200 · Cited by 9 · see citing works

CardioTF, a database of deconstructing transcriptional circuits in the heart system

Zhen, Y. (2016) · PeerJ · doi:10.7717/peerj.2339 · Cited by 1 · see citing works

Molecular mechanisms underlying nuchal hump formation in dolphin cichlid, Cyrtocara moorii

Lecaudey, L. A., Sturmbauer, C., Singh, P., & Ahi, E. P. (2019) · Scientific Reports · doi:10.1038/s41598-019-56771-7 · Cited by 30 · see citing works

Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling

Ahi, E. P., Brunel, M., Tsakoumis, E., & Schmitz, M. (2019) · Scientific Reports · doi:10.1038/s41598-019-56779-z · Cited by 29 · see citing works

Gene co-expression network analysis reveals mechanisms underlying ozone-induced carbamazepine toxicity in zebrafish (Danio rerio) embryos

Pohl, J., Golovko, O., Carlsson, G., Örn, S., Schmitz, M., & Ahi, E. P. (2021) · Chemosphere · doi:10.1016/j.chemosphere.2021.130282 · Cited by 27 · see citing works

Divergence in larval jaw gene expression reflects differential trophic adaptation in haplochromine cichlids prior to foraging

Ahi, E. P., Singh, P., Duenser, A., Gessl, W., & Sturmbauer, C. (2019) · BMC Evolutionary Biology · doi:10.1186/s12862-019-1483-3 · Cited by 27 · see citing works

Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species

Ahi, E. P., Richter, F., Lecaudey, L. A., & Sefc, K. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-45599-w · Cited by 24 · see citing works

Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris

Lecaudey, L. A., Singh, P., Sturmbauer, C., Duenser, A., Gessl, W., & Ahi, E. P. (2021) · BMC Genomics · doi:10.1186/s12864-021-07775-z · Cited by 19 · see citing works

Conserved Molecular Players Involved in Human Nose Morphogenesis Underlie Evolution of the Exaggerated Snout Phenotype in Cichlids

Duenser, A., Singh, P., Lecaudey, L. A., Sturmbauer, C., Albertson, R. C., Gessl, W., & Ahi, E. P. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad045 · Cited by 17 · see citing works

Regulation of Skeletogenic Pathways by m6A RNA Modification: A Comprehensive Review

Ahi, E. P. (2025) · Calcified Tissue International · doi:10.1007/s00223-025-01367-9 · Cited by 14 · see citing works

Expression variations in ectodysplasin-A gene (eda) may contribute to morphological divergence of scales in haplochromine cichlids

Wagner, M., Bračun, S., Duenser, A., Sturmbauer, C., Gessl, W., & Ahi, E. P. (2022) · BMC Ecology and Evolution · doi:10.1186/s12862-022-01984-0 · Cited by 13 · see citing works

Seasonal and genetic effects on lipid profiles of juvenile Atlantic salmon

House, A. H., Debes, P. V., Holopainen, M., Käkelä, R., Donner, I., Frapin, M., Ahi, E. P., Kurko, J., Ruhanen, H., & Primmer, C. R. (2024) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2024.159565 · Cited by 13 · see citing works

A pituitary gene network linking vgll3 to regulators of sexual maturation in male Atlantic salmon

Ahi, E. P., Sinclair‐Waters, M., Donner, I., & Primmer, C. R. (2022) · Comparative Biochemistry and Physiology Part A Molecular & Integrative Physiology · doi:10.1016/j.cbpa.2022.111337 · Cited by 12 · see citing works

Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection

Rincón-Sandoval, M., De‐Kayne, R., Shank, S. D., Pirro, S., Ko’ou, A., Abueg, L. A. L., Tracey, A., Mountcastle, J., O’Toole, B., Balacco, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-54184-3 · Cited by 11 · see citing works

Hypothalamic expression analysis of m6A RNA methylation associated genes suggests a potential role of epitranscriptomics in sexual maturation of Atlantic salmon

Ahi, E. P., Frapin, M., Hukkanen, M., & Primmer, C. R. (2023) · Aquaculture · doi:10.1016/j.aquaculture.2023.740151 · Cited by 11 · see citing works

Transcriptome analyses of betta fish (Betta splendens) provide novel insights into fin regeneration and color-related genes

Zhang, Y., Mei, Y., Cao, A., Li, S., He, C., Song, L., Gao, J., Zhu, Y., & Cao, X. (2023) · Gene · doi:10.1016/j.gene.2023.147508 · Cited by 8 · see citing works

Appetite regulating genes may contribute to herbivory versus carnivory trophic divergence in haplochromine cichlids

Ahi, E. P., Duenser, A., Singh, P., Gessl, W., & Sturmbauer, C. (2020) · PeerJ · doi:10.7717/peerj.8375 · Cited by 7 · see citing works

Transcriptional study reveals a potential leptin-dependent gene regulatory network in zebrafish brain

Ahi, E. P., Tsakoumis, E., Brunel, M., & Schmitz, M. (2021) · Fish Physiology and Biochemistry · doi:10.1007/s10695-021-00967-0 · Cited by 6 · see citing works

Molecular basis of variations in facial soft tissues: insights from cichlid fishes

Ahi, E. P., Sturmbauer, C., Albertson, R. C., & Singh, P. (2025) · Developmental Biology · doi:10.1016/j.ydbio.2025.10.014 · Cited by 3 · see citing works

Gene expression patterns associated with caudal fin shape in the cichlid Lamprologus tigripictilis

Ahi, E. P., Richter, F. M., & Sefc, K. M. (2022) · Hydrobiologia · doi:10.1007/s10750-022-05068-4 · Cited by 3 · see citing works

Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

Duenser, A., Singh, P., Lecaudey, L. A., Sturmbauer, C., Albertson, C., Gessl, W., & Ahi, E. P. (2022) · bioRxiv · doi:10.1101/2022.01.13.476207 · Cited by 1 · see citing works

Ectodysplasin-A (EDA) Signaling Cross-Talk in Skeletogenesis

Ahi, E. P., Moustakas-Verho, J. E., & Singh, P. (2026) · Calcified Tissue International · doi:10.1007/s00223-026-01502-0 · Cited by 1 · see citing works

Preface: advances in cichlid research V: behavior, ecology, and evolutionary biology

Koblmüller, S., Albertson, R. C., Genner, M. J., Takahashi, T., & Sefc, K. M. (2023) · Hydrobiologia · doi:10.1007/s10750-023-05240-4 · Cited by 1 · see citing works

Post-transcriptional regulation of FGF signaling: insights from musculoskeletal system

Lecaudey, L. A., Ghasemishahrestani, Z., Saqagandomabadi, V., Wesche, J., & Ahi, E. P. (2026) · Journal of Molecular Biology · doi:10.1016/j.jmb.2026.170087

Gene expression patterns associated with caudal fin shape in the cichlid Lamprologus tigripictilis

Ahi, E. P., Richter, F. M., & Sefc, K. M. (2022) · Hydrobiologia · doi:10.1007/s10750-022-05068-4 · Cited by 3 · see citing works

A gene expression study of ornamental fin shape in Neolamprologus brichardi, an African cichlid species

Ahi, E. P., Richter, F., & Sefc, K. M. (2017) · Scientific Reports · doi:10.1038/s41598-017-17778-0 · Cited by 22 · see citing works

Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species

Ahi, E. P., Richter, F., Lecaudey, L. A., & Sefc, K. M. (2019) · Scientific Reports · doi:10.1038/s41598-019-45599-w · Cited by 24 · see citing works

Gene expression patterns associated with fin shape differ between two lamprologine cichlidsPreprint

Ahi, E. P., Richter, F. M., & Sefc, K. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.02.494591

Shh/Gremlin/Fgf regulatory network genes are expressed during both fin and urogenital development in paddlefish

(2021) · DigitalCommons - Kennesaw State University (Kennesaw State University)