C. elegans

Organism: 34 papers with a page, 22 of them with their authors' code.

Tuesday, 15 September 2026 (1 paper)

[1] Code ↔ Paper doi:10.1371/journal.pcbi.1014152 [paper, repository]

Synchronization properties in C. elegans: Relating behavioral circuits to structural and functional neuronal connectivity.

Journal: PLoS computational biology

Authors' code: gourab-sar/C-elegans-synchronization (no license)

Status: code verified, 24 files readable, 7 matches

Tuesday, 1 September 2026 (1 paper)

[2] Code ↔ Paper doi:10.1098/rstb.2024.0461 [paper, repository]

Shallow recurrent decoders for neural and behavioural dynamics.

Journal: Philosophical transactions of the Royal Society of London. Series B, Biological sciences

Authors' code: amysrude/neuralSHRED (no license), meganebers/mobileSHRED (no license)

Status: code verified, 27 files readable, 5 matches

Tuesday, 25 August 2026 (1 paper)

[3] Code ↔ Paper doi:10.1016/j.isci.2026.117309 [paper, repository]

Intracellular regulation of a serotonin-gated ion channel links receptor trafficking to memory.

Journal: iScience

Authors' code: slowkow/ggrepel (GPL-3.0)

Status: code verified, 37 files readable

Tuesday, 11 August 2026 (1 paper)

[4] Code ↔ Paper doi:10.1038/s41467-026-76320-x [paper, repository]

Intrinsic and non-cell-autonomous roles for the neurodevelopmental syndrome-linked transcription factor UNC-3/EBF.

Journal: Nature communications

Authors' code: KratsiosLab (no license), Zenodo 21345127 (CC-BY-4.0), kratsioslab/smith_etal_2026 (no license)

Status: code verified

Saturday, 1 August 2026 (1 paper)

[5] doi:10.1002/alz.71680 [paper, data]

A combined artificial intelligence-wet lab approach identifies a pivotal role of the NAD<sup>+</sup>-mitophagy axis on aging and neurodegeneration.

Journal: Alzheimer's & dementia : the journal of the Alzheimer's Association

Status: data only, 1 dataset cited

Friday, 31 July 2026 (1 paper)

[6] doi:10.1126/sciadv.aec9329 [paper, data]

Cohesin and NuRD antagonistically drive alternative neuronal fates via PLZF transcription factors.

Journal: Science advances

Status: data only, 1 dataset cited

Thursday, 30 July 2026 (1 paper)

[7] doi:10.1523/eneuro.0430-25.2026 [paper, data]

Altered <i>glr-1</i> Expression after EtOH Withdrawal Is Linked to Associative Behavior Deficits in <i>C. elegans</i>.

Journal: eNeuro

Status: data only, 1 dataset cited

Saturday, 25 July 2026 (1 paper)

[8] Code ↔ Paper doi:10.1038/s41467-026-75352-7 [paper, repository]

Mechanosensory encoding of surface mechanics optimizes locomotion.

Journal: Nature communications

Authors' code: gitlab.icfo.net/nmsb/track-live-close-loop (no license), gitlab.icfo.net/nmsb/cal-free-m-worm (no license), gitlab.icfo.net/nmsb/traction-force-worm (no license), gitlab.icfo.net/nmsb/net-sim-worm (no license)

Status: code verified, 43 files readable, 9 matches

Thursday, 23 July 2026 (1 paper)

[9] Code ↔ Paper doi:10.1016/j.molcel.2026.07.006 [paper, repository]

DeorphaNN: Virtual screening of GPCR peptide agonists using AlphaFold-predicted active-state complexes and deep learning embeddings.

Journal: Molecular cell

Authors' code: Zebreu/DeorphaNN (MIT), Zenodo 20862123 (CC-BY-4.0), Zenodo 20865768 (MIT), Maryam-Haghani/NEFFy (GPL-3.0), facebookresearch/esm (MIT), ElofssonLab/FoldDock (Apache-2.0), huhlim/alphafold-multistate (no license), google-deepmind/alphafold (Apache-2.0)

Status: code verified, 569 files readable, 15 matches

Wednesday, 22 July 2026 (1 paper)

[10] Code ↔ Paper doi:10.1371/journal.pcbi.1013441 [paper, repository]

Large vision model framework for automated C. elegans analysis: From static morphometry to dynamic neural activity.

Journal: PLoS computational biology

Authors' code: lillyguisnet/TWARDISv0.1 (MIT), huggingface.co/lillyguisnet/celegans-classifier-vit-h-14-finetuned (no license)

Status: code verified, 19 files readable, 13 matches

Friday, 17 July 2026 (1 paper)

[11] Code ↔ Paper doi:10.1371/journal.pcbi.1014489 [paper, repository]

PumpKin: A machine-learning pipeline for automatically tracking localized kinematics in freely moving C. elegans.

Journal: PLoS computational biology

Authors' code: lu-lab/PumpKin (MIT)

Status: code verified, 16 files readable, 7 matches

Monday, 13 July 2026 (1 paper)

[12] Code ↔ Paper doi:10.1242/jcs.264565 [paper, repository]

A conserved Arf-GEF modulates axonal integrity through RAB-35 by altering neuron-epidermal attachment.

Journal: Journal of cell science

Authors' code: Zenodo 6031709 (other-open), igorbonap/signal-probability-along-line (GPL-3.0)

Status: code verified, 16 files readable

Monday, 6 July 2026 (2 papers)

[13] Code ↔ Paper doi:10.1016/j.cub.2026.06.016 [paper, repository]

Neuronal RNAi and oxygen-sensing circuit shape germline resilience to heat stress.

Journal: Current biology : CB

Authors' code: GuyTeichman/RNAlysis (MIT), wormtracker/zentracker (no license)

Status: code verified, 139 files readable, 4 matches

[14] doi:10.3390/biom16070992 [paper, data]

Molecular Networks and Key Regulators Underlying Resilience of the Human Brain to Aging and Dementia.

Journal: Biomolecules

Status: data only, 1 dataset cited

Monday, 29 June 2026 (1 paper)

[15] Code ↔ Paper doi:10.1371/journal.pgen.1012196 [paper, repository]

Microtubule stiffening by the doublecortin-domain protein ZYG-8 contributes to mitotic spindle orientation during zygote division in Caenorhabditis elegans.

Journal: PLoS genetics

Authors' code: Zenodo 14246919 (cecill-2.1)

Status: code verified, 514 files readable, 3 matches

Saturday, 27 June 2026 (1 paper)

[16] doi:10.1038/s44318-026-00841-w [paper]

NDR kinase SAX-1 controls dendrite branch-specific elimination during neuronal remodeling in C. elegans.

Journal: The EMBO journal

Status: data only

Thursday, 25 June 2026 (1 paper)

[17] Code ↔ Paper doi:10.7554/elife.108675 [paper, repository]

SynaptoTagMe, a toolkit for in vivo mapping and modulating neurotransmission at single-cell resolution.

Journal: eLife

Authors' code: colonramoslab/Cuentas-Condori-et-al.-2025-Toolkit- (MIT)

Status: code verified, 3 files readable

Friday, 29 May 2026 (1 paper)

[18] 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 (1 paper)

[19] doi:10.1186/s12915-026-02641-4 [paper, data]

Signed motif analysis of the Caenorhabditis elegans neuronal network reveals positive feedforward and negative feedback loops.

Journal: BMC biology

Status: data only, 11 datasets cited

Thursday, 21 May 2026 (1 paper)

[20] doi:10.1038/s41598-026-54384-5 [paper, data]

Optimization of connectome weights for a neural network model generating both forward and backward locomotion in C. elegans.

Journal: Scientific reports

Status: data only, 1 dataset cited

Tuesday, 19 May 2026 (2 papers)

[21] Code ↔ Paper doi:10.1038/s41467-026-72710-3 [paper, repository]

A modular multi-color fluorescence microscope for simultaneous tracking of cellular activity and behavior.

Journal: Nature communications

Authors' code: scholz-lab.github.io/glowtracker (no license), scholz-lab/Macroscope-Paper (no license), scholz-lab/GlowTracker (GPL-3.0)

Status: code verified, 47 files readable, 6 matches

[22] Code ↔ Paper doi:10.1038/s41467-026-72709-w [paper, repository]

An epifluorescence microscope design for naturalistic behavior and cellular activity in freely moving Caenorhabditis elegans.

Journal: Nature communications

Authors' code: Zenodo 19477903 (CC-BY-4.0), Hendricks-Worm-Lab/WormsPy_paper_analysis (no license), sebzdead.github.io/wormspy (no license), Zenodo 19477899 (CC-BY-4.0), Zenodo 19477902 (CC-BY-4.0), hendricks-worm-lab/gcamp_analysis (no license)

Status: code verified, 63 files readable, 2 matches

Wednesday, 13 May 2026 (1 paper)

[23] Code ↔ Paper doi:10.1038/s41586-026-10501-y [paper, repository]

Long-term editing of brain circuits using an engineered electrical synapse.

Journal: Nature

Authors' code: carlson-lab/FETCH (no license), carlson-lab/VMD-and-NAMD-Connexin-Protein-Simulation-Protocol (CC-BY-4.0), carlson-lab/OptoLinCx (no license)

Status: code verified, 74 files readable, 13 matches

Tuesday, 5 May 2026 (1 paper)

[24] doi:10.1038/s42003-026-10188-x [paper, data]

FLP-15 functions through the GPCR NPR-3 to regulate local and global search behaviours in Caenorhabditis elegans.

Journal: Communications biology

Status: data only, 1 dataset cited

Friday, 1 May 2026 (1 paper)

[25] Code ↔ Paper doi:10.1093/nar/gkag451 [paper, repository]

An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.

Journal: Nucleic acids research

Authors' code: Zenodo 15757714 (Apache-2.0)

Status: code verified, 4 files readable, 1 match

Monday, 27 April 2026 (3 papers)

[26] doi:10.7554/elife.106496 [paper, data]

AFD thermosensory neurons mediate tactile-dependent locomotion modulation in <i>C. elegans</i>.

Journal: eLife

Status: data only, 1 dataset cited

[27] doi:10.1038/s41419-026-08791-1 [paper, data]

The PM20D1-OLE pathway induces microglia rewiring to ameliorate Alzheimer disease.

Journal: Cell death & disease

Status: code on request, 1 dataset cited

[28] doi:10.1186/s12929-026-01246-x [paper, data]

Phosphatidylinositol transfer protein-1 integrates insulin/IGF-1 and TOR signaling to negatively regulate lifespan and healthspan in Caenorhabditis elegans.

Journal: Journal of biomedical science

Status: data only, 5 datasets cited

Friday, 24 April 2026 (1 paper)

[29] Code ↔ Paper doi:10.7554/elife.101936 [paper, repository]

The olfactory receptor SNIF-1 mediates foraging for leucine-enriched diets in <i>C. elegans</i>.

Journal: eLife

Authors' code: supp:PMC13108967/elife-101936-code1.zip (no license)

Status: code verified, 1 file readable

Monday, 20 April 2026 (1 paper)

[30] Code ↔ Paper doi:10.7554/elife.102309 [paper, repository]

Dimorphic neural network architecture prioritizes sexual-related behaviors in male <i>Caenorhabditis elegans</i>.

Journal: eLife

Authors' code: supp:PMC13095209/elife-102309-code1.zip (no license)

Status: code verified, 1 file readable

Thursday, 16 April 2026 (1 paper)

[31] doi:10.1016/j.cub.2026.03.053 [paper]

External mechanical force drives axonal cytoskeletal rearrangements.

Journal: Current biology : CB

Status: code on request

Wednesday, 15 April 2026 (1 paper)

[32] Code ↔ Paper doi:10.1126/sciadv.adv8387 [paper, repository]

<i>C. elegans</i> somatostatin/allatostatin C signaling regulates sleep, metabolism, survival, and memory via a sleep-active neuron.

Journal: Science advances

Authors' code: datadryad.org/share/ouen3lvphpyfsny9mpc3f1g9gsnbemn0fpmk0reg06y (no license)

Status: code verified

Friday, 10 April 2026 (1 paper)

[33] Code ↔ Paper doi:10.1038/s41593-026-02257-5 [paper, repository]

Neural sequences underlying directed turning in Caenorhabditis elegans.

Journal: Nature neuroscience

Authors' code: flavell-lab/SAAV_Decoding (GPL-3.0), flavell-lab/preprocess_videos (GPL-3.0), flavell-lab/head_detector_unet2d (GPL-3.0), Zenodo 12611760 (MIT)

Status: code verified, 43 files readable, 5 matches

Wednesday, 1 April 2026 (1 paper)

[34] Code ↔ Paper doi:10.1038/s41586-026-10348-3 [paper, repository]

An enteric neuron ionotropic receptor regulates salt stress resistance.

Journal: Nature

Authors' code: venkatachalamlab/Yeon-2025-pumping-analysis (MIT), Zenodo 13748735 (CC-BY-4.0)

Status: code verified, 208 files readable