zebrafish

Organism: 70 papers with a page, 37 of them with their authors' code.

Friday, 18 September 2026 (1 paper)

[1] Code ↔ Paper doi:10.7554/elife.100880 [paper, repository]

An applicable and efficient retrograde monosynaptic circuit mapping tool for larval zebrafish.

Journal: eLife

Authors' code: navis-org/navis (GPL-3.0), soaringdu/Proj-RVCT (no license)

Status: code verified, 305 files readable, 1 match

Wednesday, 16 September 2026 (1 paper)

[2] Code ↔ Paper doi:10.1038/s42003-026-10957-8 [paper, repository]

Brain defence by the extracellular matrix protein Cochlin.

Journal: Communications biology

Authors' code: animesh/scripts (GPL-2.0), Raghumoy/Cochlin_manuscript (no license)

Status: code verified, 1,156 files readable, 9 matches

Tuesday, 8 September 2026 (1 paper)

[3] Code ↔ Paper doi:10.1093/braincomms/fcag323 [paper, repository]

Induced epileptic seizures in larval zebrafish reveal a synaptic modulation associated with the post-ictal state.

Journal: Brain communications

Authors' code: OSF sd5jy (no license)

Status: code verified, 24 files readable, 5 matches

Thursday, 3 September 2026 (2 papers)

[4] doi:10.1016/j.isci.2026.117343 [paper, data]

Zebrafish larvae reveal early neuropathology and host responses to nervous necrosis virus.

Journal: iScience

Status: data only, 2 datasets cited

[5] Code ↔ Paper doi:10.7554/elife.109104 [paper, repository]

Complementary vertebrate <i>Wac</i> models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome.

Journal: eLife

Authors' code: nordneurogenomicslab/publications (no license)

Status: code verified, 14 files readable, 3 matches

Tuesday, 1 September 2026 (1 paper)

[6] doi:10.1096/fj.202504890rr [paper, data]

Purinergic Receptor P2Y2 Regulates Neurogenesis and Functional Recovery Following Spinal Cord Injury in Zebrafish.

Journal: FASEB journal : official publication of the Federation of American Societies for Experimental Biology

Status: data only, 1 dataset cited

Thursday, 27 August 2026 (1 paper)

[7] Code ↔ Paper doi:10.1038/s41467-026-76242-8 [paper, repository]

Whole-brain, all-optical interrogation of neuronal dynamics underlying gut and vascular interoception in zebrafish.

Journal: Nature communications

Authors' code: benJames1212/gutBrainPipeline (MIT), mikarubi/voluseg (MIT), ades91/imdecorr (GPL-3.0), JaneliaSciComp/bigstream (BSD-3-Clause)

Status: code verified, 134 files readable, 5 matches

Monday, 24 August 2026 (1 paper)

[8] doi:10.1007/s12035-026-06127-w [paper, data]

Disrupting fzd9b in Zebrafish Recapitulates Stress- and Anxiety-Like Behaviours Relevant to Williams Syndrome.

Journal: Molecular neurobiology

Status: data only, 1 dataset cited

Tuesday, 18 August 2026 (1 paper)

[9] Code ↔ Paper doi:10.1016/j.isci.2026.117136 [paper, repository]

Complex pectoral-fin-driven locomotion underlies refined visuomotor behavior in the cichlid <i>Astatotilapia burtoni</i>.

Journal: iScience

Authors' code: Zenodo 21463359 (MIT), ncguilbeault/cichlid_omr_analysis (MIT)

Status: code verified, 66 files readable, 3 matches

Friday, 14 August 2026 (3 papers)

[10] Code ↔ Paper doi:10.1038/s41592-026-03179-7 [paper, repository]

Voltage imaging of neurons distributed across entire brains of larval zebrafish.

Journal: Nature methods

Authors' code: Zenodo 14920628 (CC-BY-4.0)

Status: code verified, 4 files readable, 1 match

[11] Code ↔ Paper doi:10.1016/j.isci.2026.117212 [paper, repository]

Critical neuronal avalanches arise from excitation-inhibition balanced spontaneous activity.

Journal: iScience

Authors' code: adrianponce/ExcInh_Neuronal_Avalanches (no license)

Status: code verified, 8 files readable, 8 matches

[12] doi:10.1016/j.isci.2026.117207 [paper]

Physical activity stimulates neurogenesis via sensory neuron activity in postembryonic zebrafish.

Journal: iScience

Status: code on request

Friday, 7 August 2026 (3 papers)

[13] Code ↔ Paper doi:10.1016/j.neuron.2026.07.016 [paper, repository]

Inferring brain-wide interactions using data-constrained recurrent neural network models.

Journal: Neuron

Authors' code: HarveyLab/Acquisition2P_class (MIT), OSF u3kcp (no license), rajanlab/CURBD (GPL-3.0)

Status: code verified, 165 files readable, 8 matches

[14] Code ↔ Paper doi:10.1016/j.xpro.2026.104766 [paper, repository]

Protocol for live-imaging of blood flow and vascular permeability in zebrafish larvae.

Journal: STAR protocols

Authors' code: Zenodo 14770236 (CC0-1.0), preethirajamannar/zebrafish-pituitary-blood-flow (CC0-1.0)

Status: code verified, 4 files readable

[15] Code ↔ Paper doi:10.1038/s41467-026-76267-z [paper, repository]

Modulation of habenula axon terminals supports action-outcome associations in larval zebrafish.

Journal: Nature communications

Authors' code: portugueslab/brunoise (GPL-3.0), portugueslab/Paoli_et_al_2025 (no license)

Status: code verified, 32 files readable, 1 match

Monday, 27 July 2026 (1 paper)

[16] doi:10.1371/journal.pone.0316959 [paper, data]

In vivo changes in zebrafish anesthetic sensitivity in response to the loss of kif5Aa are associated with the alteration of mitochondrial motility.

Journal: PloS one

Status: data only, 1 dataset cited

Friday, 24 July 2026 (1 paper)

[17] Code ↔ Paper doi:10.1242/dmm.052747 [paper, repository]

Cell death analysis of inducible, titratable neurodegenerative disease models in zebrafish and human stem cell-derived retinal organoids.

Journal: Disease models & mechanisms

Authors' code: mummlab/Cell-Death-in-NTR2.0-mediated-RGC-Ablation (no license)

Status: code verified, 6 files readable, 3 matches

Monday, 20 July 2026 (1 paper)

[18] Code ↔ Paper doi:10.7554/elife.110370 [paper, repository]

Serotonergic modulation of motor subspace dynamics drives a sleep-independent quiescent state.

Journal: eLife

Authors' code: wenquan/BayesianHMDS (MIT), kexin2016/zebrafish-quiescent-state (MIT)

Status: code verified, 61 files readable, 15 matches

Thursday, 16 July 2026 (2 papers)

[19] Code ↔ Paper doi:10.1038/s41467-026-75490-y [paper, repository]

Topographically organized dorsal raphe activity modulates forebrain sensory-motor representations and contributes to defensive behaviors.

Journal: Nature communications

Authors' code: yaksilab/drn_paper (no license), Zenodo 19452784 (CC-BY-4.0)

Status: code verified, 1,690 files readable

[20] doi:10.1080/19490976.2026.2694805 [paper, data]

Enteric-colonized <i>Cronobacter</i> spp. can disrupt the central nervous system without translocation across the host barriers.

Journal: Gut microbes

Status: data only, 1 dataset cited

Wednesday, 15 July 2026 (1 paper)

[21] doi:10.3390/biomedicines14071585 [paper, data]

Live Visualization of Endoplasmic Reticulum Redox Potential in Zebrafish Embryos Reveals Region-Specific Heterogeneity.

Journal: Biomedicines

Status: data only, 4 datasets cited

Tuesday, 14 July 2026 (1 paper)

[22] doi:10.1172/jci.insight.200106 [paper, data]

HDAC6 inhibition alleviates mitochondrial trafficking in models of Charcot-Marie-Tooth disease type 2A.

Journal: JCI insight

Status: data only, 1 dataset cited

Monday, 13 July 2026 (1 paper)

[23] doi:10.1016/j.isci.2026.116707 [paper]

Ptprz1b phosphatase binds Prickle2 to promote its membrane localization.

Journal: iScience

Status: code on request

Thursday, 9 July 2026 (1 paper)

[24] doi:10.1161/circresaha.126.328910 [paper, data]

AMPKγ2 Regulates Cardiac Hypertrophy and Arrhythmias via Interacting With Myosin.

Journal: Circulation research

Status: code on request, 1 dataset cited

Wednesday, 8 July 2026 (1 paper)

[25] doi:10.1038/s41467-026-75307-y [paper]

Dynamic interactions between epithelial skin cells and a sensory cavity sculpt the growing olfactory orifice.

Journal: Nature communications

Status: code on request

Tuesday, 7 July 2026 (1 paper)

[26] doi:10.1016/j.isci.2026.116562 [paper]

Adenylyl cyclase 9: Fundamental change of regulation in vertebrates and gene sub-functionalization after teleost-specific whole-genome duplication.

Journal: iScience

Status: code on request

Wednesday, 1 July 2026 (2 papers)

[27] doi:10.1111/jne.70230 [paper, data]

Single-nuclei RNA sequencing reveals heterogeneity within developing GnRH3 neurons in zebrafish.

Journal: Journal of neuroendocrinology

Status: data only, 1 dataset cited

[28] doi:10.1016/j.stemcr.2026.102966 [paper]

Optimized chemogenetic ablation and regeneration of enteric nervous system neurons in zebrafish.

Journal: Stem cell reports

Status: code on request

Thursday, 25 June 2026 (1 paper)

[29] Code ↔ Paper doi:10.1016/j.stemcr.2026.102977 [paper, repository]

Integrative analysis of drug-gene signatures in human pluripotent stem cells reveals prazosin as a novel SQSTM1 regulator for ALS therapeutics.

Journal: Stem cell reports

Authors' code: maximilianh/crisporWebsite (other), usadellab/trimmomatic (GPL-3.0)

Status: code verified, 1,012 files readable, 2 matches

Thursday, 18 June 2026 (1 paper)

[30] Code ↔ Paper doi:10.1038/s41467-026-74434-w [paper, repository]

The alx gene family confers segmental identity to frontonasal cranial neural crest cells.

Journal: Nature communications

Authors' code: AbiRMM/alx3-alx4-scRNA-seq-Analysis (no license)

Status: code verified, 2 files readable, 3 matches

Tuesday, 16 June 2026 (1 paper)

[31] doi:10.1038/s41598-026-58107-8 [paper, data]

Three-dimensional voltage imaging in live larval zebrafish brains using fully genetically encoded voltage indicator.

Journal: Scientific reports

Status: data only, 1 dataset cited

Thursday, 11 June 2026 (1 paper)

[32] Code ↔ Paper doi:10.1016/j.isci.2026.116206 [paper, repository]

Gut distension evokes rapid neural dynamics in vagal and hindbrain populations of larval zebrafish.

Journal: iScience

Authors' code: gitlab.oit.duke.edu/ean26/arinel-et-al_2026 (no license), naumann-lab/caimageanalysis (no license), Naumann-Lab/alignment (MIT), Zenodo 20127931 (CC-BY-4.0), Zenodo 20128341 (MIT), arthur-pe/slicetca (MIT)

Status: code verified, 86 files readable, 19 matches

Friday, 5 June 2026 (1 paper)

[33] doi:10.1016/j.isci.2026.116190 [paper]

Behavioral algorithms of ontogenetic switching in larval and juvenile zebrafish phototaxis.

Journal: iScience

Status: code on request

Tuesday, 2 June 2026 (1 paper)

[34] Code ↔ Paper doi:10.1021/ehp.6c00394 [paper, repository]

Multibehavioral Phenotyping in Early-Life-Stage Zebrafish for Identifying Disruptors of Nonassociative Learning.

Journal: Environmental health perspectives

Authors' code: figshare 26819914 (CC-BY-4.0)

Status: code verified

Monday, 1 June 2026 (4 papers)

[35] doi:10.1093/jmcb/mjaf052 [paper, data]

NOC4L coordinates neuronal and pharyngeal arch development by regulating ribosome biogenesis.

Journal: Journal of molecular cell biology

Status: data only, 1 dataset cited

[36] doi:10.1002/glia.70158 [paper]

A Dynamic Change of Microglial States Occurs During the Transition From Photoreceptor Degeneration to Regeneration in Zebrafish pde6c Mutants.

Journal: Glia

Status: data only

[37] Code ↔ Paper doi:10.1101/gr.280817.125 [paper, repository]

RECOMBINE identifies recurrent composite markers of cell types and states.

Journal: Genome research

Authors' code: korkutlab/recombine (Apache-2.0)

Status: code verified, 22 files readable, 17 matches

[38] doi:10.1371/journal.pgen.1012171 [paper, data]

Canalization of neural dynamics by δ-protocadherins in the developing zebrafish optic tectum.

Journal: PLoS genetics

Status: data only, 1 dataset cited

Friday, 29 May 2026 (2 papers)

[39] Code ↔ Paper doi:10.1126/sciadv.aeb5860 [paper, repository]

The cerebellum implements structured representation of valence to support adaptive behavior control.

Journal: Science advances

Authors' code: Zenodo 18317482 (CC-BY-4.0)

Status: code verified

[40] Code ↔ Paper doi:10.1016/j.crmeth.2026.101471 [paper, repository]

Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging.

Journal: Cell reports methods

Authors' code: Fakorede-Olumayowa/Temporal_Domain_Multiplexing (no license), Fakorede-Olumayowa/BAMM (no license), Zenodo 19615672 (bsd-2-clause-netbsd), Zenodo 19616489 (CC-BY-4.0), gitlab.wllsb.edu.cn/blank22/kiryl-piatkevich (no license)

Status: code verified, 8 files readable, 1 match

Friday, 22 May 2026 (2 papers)

[41] Code ↔ Paper doi:10.1038/s41467-026-73325-4 [paper, repository]

A scalable Tn5-based method for genome-wide DNA methylation profiling in development and disease.

Journal: Nature communications

Authors' code: EpiGN-EPFL/CmeCUT-Tag (no license), Zenodo 19555724 (CC-BY-4.0)

Status: code verified, 38 files readable, 18 matches

[42] Code ↔ Paper doi:10.1016/j.isci.2026.116095 [paper, repository]

The tectal melanocortin system modulates energy-dependent visual avoidance behavior in zebrafish.

Journal: iScience

Authors' code: Zenodo 20015261 (CC-BY-4.0)

Status: code verified, 1 file readable

Wednesday, 20 May 2026 (3 papers)

[43] doi:10.7554/elife.105935 [paper, data]

Uncovering the electrical synapse proteome in retinal neurons via in vivo proximity labeling.

Journal: eLife

Status: data only, 1 dataset cited

[44] Code ↔ Paper doi:10.1016/j.xpro.2026.104591 [paper, repository]

Protocol for using the multi-cellular analysis toolbox in ImageJ for single-cell calcium imaging analysis.

Journal: STAR protocols

Authors' code: Zenodo 17610801 (MIT)

Status: code verified, 21 files readable, 1 match

[45] Code ↔ Paper doi:10.1038/s41467-026-73389-2 [paper, repository]

Physics-informed multi-encoder adaptive optics enables rapid aberration correction for intravital microscopy of deep complex tissue.

Journal: Nature communications

Authors' code: Zenodo 17118222 (CC-BY-4.0), lukachan41/MeNet-AO (MIT), Zenodo 19315205 (MIT)

Status: code verified, 52 files readable, 4 matches

Tuesday, 19 May 2026 (2 papers)

[46] Code ↔ Paper doi:10.1038/s41586-026-10658-6 [paper, repository]

An AI system to help scientists write expert-level empirical software.

Journal: Nature

Authors' code: salesforceairesearch/gift-eval (Apache-2.0), google-research/era (Apache-2.0)

Status: code verified, 64 files readable, 11 matches

[47] doi:10.1038/s42003-026-10141-y [paper, data]

Directionally biased neuronal responses to pitch-axis vestibular stimulation in larval zebrafish compared to roll-axis responses.

Journal: Communications biology

Status: code on request, 1 dataset cited

Tuesday, 5 May 2026 (1 paper)

[48] Code ↔ Paper doi:10.1038/s41467-026-72222-0 [paper, repository]

Eye movement kinematics reveal novel circadian organization of sleep substates.

Journal: Nature communications

Authors' code: crheller/saccade-ms (no license)

Status: dead link

Monday, 4 May 2026 (1 paper)

[49] doi:10.1186/s12929-026-01249-8 [paper, data]

β-Sitosterol β-D-glucoside (BSSG) triggers intestinal inflammation in zebrafish and mouse models prior to neurodegeneration onset.

Journal: Journal of biomedical science

Status: data only, 2 datasets cited

Friday, 1 May 2026 (2 papers)

[50] doi:10.3390/molecules31091511 [paper, data]

5-(Benzofuran-2-yl)-3-(2-chloro-4-fluorobenzyl)-1,3,4-oxadiazol-2(3H)-one (GM-90663) Alleviates Dravet Syndrome via Inhibiting Monoamine Oxidase Activity.

Journal: Molecules (Basel, Switzerland)

Status: data only, 1 dataset cited

[51] doi:10.1111/dgd.70060 [paper, data]

Atypical Cadherin Fat2 is Involved in Axogenesis of Cerebellar Granule Cells in Zebrafish.

Journal: Development, growth & differentiation

Status: data only, 1 dataset cited

Friday, 24 April 2026 (3 papers)

[52] doi:10.7554/elife.108071 [paper, data]

The dual molecular identity of vestibular kinocilia bridges structural and functional traits of primary and motile cilia.

Journal: eLife

Status: data only, 1 dataset cited

[53] doi:10.1038/s41598-026-40684-3 [paper]

Escape behaviors are transiently modulated after acutely induced epileptic seizures in larval zebrafish.

Journal: Scientific reports

Status: code on request

[54] Code ↔ Paper doi:10.1038/s41593-026-02247-7 [paper, repository]

Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo.

Journal: Nature neuroscience

Authors' code: ehoffmanlab/Weinschutz-Mendes-et-al-2023-behavior (GPL-3.0), jrihel/sleep-analysis (CC0-1.0), Zenodo 7644898 (other-open), Zenodo 7644073 (other-open), synapse.org/synapse:syn72039767 (no license), cran.r-project.org/package=webgestaltr (no license), Zenodo 7644897 (other-open)

Status: code verified, 125 files readable, 2 matches

Friday, 17 April 2026 (4 papers)

[55] doi:10.26508/lsa.202503431 [paper, data]

miR-133a-3p and miR-338-3p shape neural crest derivatives in zebrafish.

Journal: Life science alliance

Status: data only, 1 dataset cited

[56] doi:10.1038/s41467-026-71640-4 [paper, data]

Neural temporal scaling accounts for robust hunting behavior across temperatures.

Journal: Nature communications

Status: data only, 1 dataset cited

[57] doi:10.1038/s41467-026-71371-6 [paper, data]

Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors.

Journal: Nature communications

Status: data only, 1 dataset cited

[58] doi:10.1038/s41420-026-03106-x [paper, data]

Mytho/Phaf1 is required to prevent DNA damage and tissue degeneration in Danio rerio.

Journal: Cell death discovery

Status: data only, 1 dataset cited

Wednesday, 15 April 2026 (1 paper)

[59] Code ↔ Paper doi:10.7554/elife.96980 [paper, repository]

Heterogeneity of Sonic Hedgehog response dynamics and fate specification in single neural progenitors.

Journal: eLife

Authors' code: xionglab/NT_heterogeneity (CC-BY-4.0)

Status: code verified, 2 files readable

Thursday, 9 April 2026 (2 papers)

[60] doi:10.1038/s41467-026-71666-8 [paper, data]

Distinct distributed neural dynamics predict pallium-dependent social approach.

Journal: Nature communications

Status: data only, 1 dataset cited

[61] Code ↔ Paper doi:10.1038/s42003-026-09948-6 [paper, repository]

A scalable human-zebrafish xenotransplantation model reveals gastrosome-mediated processing of dying neurons by human microglia.

Journal: Communications biology

Authors' code: Zenodo 18997850 (GPL-3.0)

Status: code verified, 16 files readable, 2 matches

Wednesday, 8 April 2026 (1 paper)

[62] Code ↔ Paper doi:10.1371/journal.pone.0346255 [paper, repository]

Single-cell analysis of inhibitory efferent neurons of the zebrafish lateral line.

Journal: PloS one

Authors' code: Zenodo 1400710 (MIT), nf-core (no license), nf-core/rnaseq (MIT)

Status: code verified, 30 files readable, 1 match

Tuesday, 7 April 2026 (1 paper)

[63] doi:10.1038/s41684-026-01712-x [paper, data]

Ontogeny of zebrafish behaviors: comparative evaluation of locomotor, social and anxiety parameters in larval, juvenile and adult stages.

Journal: Lab animal

Status: data only, 1 dataset cited

Saturday, 4 April 2026 (1 paper)

[64] Code ↔ Paper doi:10.1038/s42003-026-09990-4 [paper, repository]

Head stabilization behavior and underlying circuit mechanisms in larval zebrafish.

Journal: Communications biology

Authors' code: Zenodo 18832196 (CC-BY-4.0)

Status: code verified

Thursday, 2 April 2026 (1 paper)

[65] Code ↔ Paper doi:10.1038/s41592-026-03057-2 [paper, repository]

CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.

Journal: Nature methods

Authors' code: aertslab/CREsted (other), aertslab/create_cisTarget_databases (no license), Zenodo 17791463 (CC-BY-4.0), aertslab/CREsted-paper (MIT), Zenodo 17791384 (CC-BY-4.0), Zenodo 17202107 (MIT), aertslab/tf-mindi (other)

Status: code verified, 258 files readable, 40 matches

Wednesday, 1 April 2026 (5 papers)

[66] doi:10.1093/toxsci/kfag022 [paper, data]

Integration of human microbiota (SIHUMIx) and zebrafish models reveals microbiome-mediated host responses to azoxystrobin.

Journal: Toxicological sciences : an official journal of the Society of Toxicology

Status: data only, 2 datasets cited

[67] Code ↔ Paper doi:10.1371/journal.pgen.1012090 [paper, repository]

Delta family protocadherins contribute to protoglomerular targeting of olfactory sensory neuron axons in the olfactory bulb.

Journal: PLoS genetics

Authors' code: DanielTBarnes/sc-RNAseq-of-Zebrafish-Olfactory-Sensory-Neurons (no license)

Status: code verified, 2 files readable, 4 matches

[68] Code ↔ Paper doi:10.1038/s41467-026-70989-w [paper, repository]

MIC-Drop-seq: scalable single-cell phenotyping of mutant vertebrate embryos.

Journal: Nature communications

Authors' code: clay-carey/MIC-Drop-seq (MIT), Zenodo 18615355 (MIT)

Status: code verified, 12 files readable, 20 matches

[69] Code ↔ Paper doi:10.1038/s41598-026-43301-5 [paper, repository]

Automated analysis of zebrafish vascular networks using the VISTA-Z pipeline.

Journal: Scientific reports

Authors' code: fishyvessels/VISTA-Z (MIT)

Status: code verified, 8 files readable, 6 matches

[70] Code ↔ Paper doi:10.1038/s41586-026-10312-1 [paper, repository]

Flexible ensheathment of axons enables myelination of complex CNS networks.

Journal: Nature

Authors' code: clcall/Call_ParanodalBridge_2022 (GPL-3.0)

Status: code verified, 56 files readable, 1 match