Jacob Musser
Assistant Professor in Molecular, Cellular and Developmental BiologyCards
About
Research
Publications
2025
The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution
Sebé-Pedrós A, Tanay A, Lawniczak M, Arendt D, Aerts S, Archibald J, Arnone M, Blaxter M, Cleves P, Coelho S, Dias M, Dunn C, Elek A, Frazer J, Gabaldón T, Gillis J, Grau-Bové X, Guigó R, Hobert O, Huerta-Cepas J, Irimia M, Klein A, Lewin H, Lowe C, Marlow H, Musser J, Nagy L, Najle S, Pachter L, Paez S, Papatheodorou I, Passalacqua M, Rajewsky N, Rhee S, Richards T, Sauka-Spengler T, Saunders L, Seuntjens E, Solana J, Song Y, Technau U, Wang B. The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution. Nature 2025, 645: 877-885. PMID: 40993253, DOI: 10.1038/s41586-025-09312-4.Peer-Reviewed Original ResearchConceptsTree of lifeEukaryotic treeGenome sequenceEukaryotic tree of lifeCell atlasMolecular characterizationHigh-quality genomesCell type-specific molecular profilingGene regulatory programsInter-organismal interactionsSingle-cell technologiesMolecular characterization of cellsDiversity of lifeGenomeCell diversityMolecular atlasRegulatory programsCell typesDifferentiation trajectoriesBiodiversityCellular levelCharacterization of cellsDiversityCellular resolutionSequenceComparative Analysis of Convergent Jellyfish Eyes Reveals Extensive Differences in Expression of Vision‐Related Genes
Picciani N, Berger C, Nielsen S, Musser J, Oel A, Stoilova M, Arendt D, Garm A, Oakley T. Comparative Analysis of Convergent Jellyfish Eyes Reveals Extensive Differences in Expression of Vision‐Related Genes. Ecology And Evolution 2025, 15: e71784. PMID: 40661905, PMCID: PMC12259307, DOI: 10.1002/ece3.71784.Peer-Reviewed Original ResearchLineage-specific patternsVision-related genesGene expressionLineage-specific patterns of gene expressionRepeatability of evolutionPatterns of gene expressionGene tree analysisGene reuseCnidarian speciesOpsin paralogsDeep homologyLineage-specificPhototransduction componentsGenesHomologySpeciesLineagesTraitsExpressionTree analysisOpsinComparative analysisOrthologsMedusozoaParalogs
2024
Tripartite origin of the chordate brain
Musser J. Tripartite origin of the chordate brain. Nature Ecology & Evolution 2024, 8: 1782-1783. PMID: 39164590, DOI: 10.1038/s41559-024-02528-z.Peer-Reviewed Original ResearchAuthor Correction: Cross-phyla protein annotation by structural prediction and alignment
Ruperti F, Papadopoulos N, Musser J, Mirdita M, Steinegger M, Arendt D. Author Correction: Cross-phyla protein annotation by structural prediction and alignment. Genome Biology 2024, 25: 50. PMID: 38374049, PMCID: PMC10875831, DOI: 10.1186/s13059-024-03196-9.Peer-Reviewed Original ResearchMolecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response
Ruperti F, Becher I, Stokkermans A, Wang L, Marschlich N, Potel C, Maus E, Stein F, Drotleff B, Schippers K, Nickel M, Prevedel R, Musser J, Savitski M, Arendt D. Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response. Current Biology 2024, 34: 361-375.e9. PMID: 38181793, DOI: 10.1016/j.cub.2023.12.021.Peer-Reviewed Original ResearchConceptsActomyosin stress fibersMolecular profilingCanal systemThermal proteome profilingExcurrent canal systemSecretion of proteinasesEpithelial cell junctionsSessile animalsQuantitative phosphoproteomicsStress fibersFunctional proteomicsVascular endothelial cellsComplex canal systemsUntargeted metabolomicsReactive oxygen speciesFilter feedingMolecular physiologyCell junctionsProteomic profilingCanal closureCanal cellsCellular relaxationParacrine signalingCell typesEndothelial cells
2023
Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories
Piovani L, Leite D, Yañez Guerra L, Simpson F, Musser J, Salvador-Martínez I, Marlétaz F, Jékely G, Telford M. Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories. Science Advances 2023, 9: eadg6034. PMID: 37531419, PMCID: PMC10396302, DOI: 10.1126/sciadv.adg6034.Peer-Reviewed Original ResearchConceptsMarine larvaeClade-specific innovationsAncestor of animalsApical organComplex evolutionary historyPelagic larval stageGland cellsOrigin of larvaeGene ageSingle-cell atlasCiliary band cellsAnimal phylaEvolutionary historySelection pressureTrochophore larvaeShell gland cellsCell typesOyster larvaeLarval stageGenesLarvaeCellsLophotrochozoansPhylumSpiraliaCross-phyla protein annotation by structural prediction and alignment
Ruperti F, Papadopoulos N, Musser J, Mirdita M, Steinegger M, Arendt D. Cross-phyla protein annotation by structural prediction and alignment. Genome Biology 2023, 24: 113. PMID: 37173746, PMCID: PMC10176882, DOI: 10.1186/s13059-023-02942-9.Peer-Reviewed Original ResearchConceptsSequence-based predictionProtein annotationFunctional annotationFunctional annotation of proteinsSponge cell typesAnnotation of proteinsNon-model organismsNon-model speciesSequence-based methodsStructural similarityFunction of proteinsGene orthologsEvolutionary distanceProtein sequencesHomologous proteinsSponge epitheliaStructure predictionModel organismsProtein structureOmics datasetsHistory of animalsRedox metabolismProtein identityConclusionsOur workCell wall
2022
Crustacean leg regeneration restores complex microanatomy and cell diversity
Almazán A, Çevrim Ç, Musser J, Averof M, Paris M. Crustacean leg regeneration restores complex microanatomy and cell diversity. Science Advances 2022, 8: eabn9823. PMID: 36001670, PMCID: PMC9401613, DOI: 10.1126/sciadv.abn9823.Peer-Reviewed Original ResearchSingle-nuclei sequencingExternal sensory organsLeg regenerationGene expression dynamicsCell-type compositionCell molecular profilesExpression dynamicsTranscriptional profilesRegenerating legsCell diversitySensory organsComplex organismsMolecular profilingComplementary approachesCellular compositionCellsGenesOrganizationSequenceCrustaceansMicroanatomyDiversityComplex microanatomySpatial distribution
2021
Single cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome
Paganos P, Voronov D, Musser J, Arendt D, Arnone M. Single cell RNA sequencing of the Strongylocentrotus purpuratus larva reveals the blueprint of major cell types and nervous system of a non-chordate deuterostome. ELife 2021, 10: e70416. PMID: 34821556, PMCID: PMC8683087, DOI: 10.7554/elife.70416.Peer-Reviewed Original ResearchConceptsCell typesRNA sequencingSea urchinsAncestral cell typesGene regulatory networksEarly pluteus larvaeSingle-cell RNA sequencingSingle cell RNA sequencingSea urchin developmentNon-chordate deuterostomesCell RNA sequencingRegulatory networksNeuronal cell typesScRNA-seqMolecular fingerprintsEndocrine pancreatic cellsKnockdown experimentsNon-feedingDevelopmental lineageDevelopmental transitionsNeuronal identityPluteus larvaePDX-1Feeding larvaeVertebratesProfiling cellular diversity in sponges informs animal cell type and nervous system evolution
Musser J, Schippers K, Nickel M, Mizzon G, Kohn A, Pape C, Ronchi P, Papadopoulos N, Tarashansky A, Hammel J, Wolf F, Liang C, Hernández-Plaza A, Cantalapiedra C, Achim K, Schieber N, Pan L, Ruperti F, Francis W, Vargas S, Kling S, Renkert M, Polikarpov M, Bourenkov G, Feuda R, Gaspar I, Burkhardt P, Wang B, Bork P, Beck M, Schneider T, Kreshuk A, Wörheide G, Huerta-Cepas J, Schwab Y, Moroz L, Arendt D. Profiling cellular diversity in sponges informs animal cell type and nervous system evolution. Science 2021, 374: 717-723. PMID: 34735222, PMCID: PMC9233960, DOI: 10.1126/science.abj2949.Peer-Reviewed Original ResearchConceptsEvolutionary originCell typesMetazoan cell typesSingle-cell RNA sequencingAnimal cell typesNervous system evolutionSecretory vesiclesRNA sequencingCellular diversityAmoeboid phagocytesCellular projectionsChoanocytesReceptor proteinConservation moduleSpongeNervous systemCellsPinacocytesPostsynapseProteinAnimalsSequenceVesiclesCiliaDiversity