Featured Publications
Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data
Venkat A, Bhaskar D, Krishnaswamy S. Multiscale geometric and topological analyses for characterizing and predicting immune responses from single cell data. Trends In Immunology 2023, 44: 551-563. PMID: 37301677, DOI: 10.1016/j.it.2023.05.003.Peer-Reviewed Original ResearchCell cycle controls long-range calcium signaling in the regenerating epidermis
Moore J, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V. Cell cycle controls long-range calcium signaling in the regenerating epidermis. Journal Of Cell Biology 2023, 222: e202302095. PMID: 37102999, PMCID: PMC10140546, DOI: 10.1083/jcb.202302095.Peer-Reviewed Original ResearchCurrent trends in artificial intelligence in reproductive endocrinology
Bhaskar D, Chang TA, Wang S. Current trends in artificial intelligence in reproductive endocrinology. Current Opinion In Obstetrics & Gynecology 2022, 34: 159-163. PMID: 35895955, DOI: 10.1097/gco.0000000000000796.Peer-Reviewed Original ResearchTopological data analysis of collective and individual epithelial cells using persistent homology of loops
Bhaskar D, Zhang W, Wong I. Topological data analysis of collective and individual epithelial cells using persistent homology of loops. Soft Matter 2021, 17: 4653-4664. PMID: 33949592, PMCID: PMC8276269, DOI: 10.1039/d1sm00072a.Peer-Reviewed Original ResearchAnalyzing collective motion with machine learning and topology
Bhaskar D, Manhart A, Milzman J, Nardini JT, Storey KM, Topaz CM, Ziegelmeier L. Analyzing collective motion with machine learning and topology. Chaos An Interdisciplinary Journal Of Nonlinear Science 2019, 29: 123125. PMID: 31893635, PMCID: PMC7027427, DOI: 10.1063/1.5125493.Peer-Reviewed Original ResearchSupervised machine learning methodsMachine learning methodsTopological data analysisCollective motionMachine learningLearning methodsOrder parameterSimulation dataTopological approachPersistent homologyTraditional order parametersPrior knowledgeMachineCollective behaviorModel parametersData analysisLarge librariesNumerical simulationsTopologyMultiple scalesMotionTime seriesLearningDifferent typesParametersMolecular Graph Generation via Geometric Scattering
Bhaskar D, Grady J, Castro E, Perlmutter M, Krishnaswamy S. Molecular Graph Generation via Geometric Scattering. 2022, 00: 1-6. DOI: 10.1109/mlsp55214.2022.9943379.Peer-Reviewed Original ResearchMotility-limited aggregation of mammary epithelial cells into fractal-like clusters
Leggett SE, Neronha ZJ, Bhaskar D, Sim JY, Perdikari TM, Wong IY. Motility-limited aggregation of mammary epithelial cells into fractal-like clusters. Proceedings Of The National Academy Of Sciences Of The United States Of America 2019, 116: 17298-17306. PMID: 31413194, PMCID: PMC6717304, DOI: 10.1073/pnas.1905958116.Peer-Reviewed Original ResearchCoupling mechanical tension and GTPase signaling to generate cell and tissue dynamics
Zmurchok C, Bhaskar D, Edelstein-Keshet L. Coupling mechanical tension and GTPase signaling to generate cell and tissue dynamics. Physical Biology 2018, 15: 046004. PMID: 29473547, DOI: 10.1088/1478-3975/aab1c0.Peer-Reviewed Original ResearchSwarming Migration of Co-attracting Mesenchymal Cells into Fractal-Like Epithelial Clusters
Leggett S, Neronha Z, Bhaskar D, Perdikari T, Wong I. Swarming Migration of Co-attracting Mesenchymal Cells into Fractal-Like Epithelial Clusters. Biophysical Journal 2018, 114: 513a-514a. DOI: 10.1016/j.bpj.2017.11.2806.Peer-Reviewed Original ResearchPolarization and migration in the zebrafish posterior lateral line system
Knutsdottir H, Zmurchok C, Bhaskar D, Palsson E, Nogare D, Chitnis A, Edelstein-Keshet L. Polarization and migration in the zebrafish posterior lateral line system. PLOS Computational Biology 2017, 13: e1005451. PMID: 28369079, PMCID: PMC5393887, DOI: 10.1371/journal.pcbi.1005451.Peer-Reviewed Original ResearchConceptsPosterior lateral line primordiumZebrafish posterior lateral line systemCell-cell adhesionLateral line primordiumCollective cell migrationPosterior lateral line systemCell-based simulationsMutant phenotypeZebrafish embryosCell divisionFGF ligandsLateral line systemCell migrationTrailing cellsSensory structuresObserved motilityChemotaxisCellsImportant roleCXCL12aPrimordiaAdhesionEmbryosMigrationPhenotypeThe need for speed: Migratory cells in tight spaces boost their molecular clock
Bhaskar D, Hruska AM, Wong IY. The need for speed: Migratory cells in tight spaces boost their molecular clock. Cell Systems 2022, 13: 509-511. PMID: 35863324, PMCID: PMC10071288, DOI: 10.1016/j.cels.2022.06.002.Peer-Reviewed Original ResearchBreast Cancer Cells Transition from Mesenchymal to Amoeboid Migration in Tunable Three-Dimensional Silk–Collagen Hydrogels
Khoo AS, Valentin TM, Leggett SE, Bhaskar D, Bye EM, Benmelech S, Ip BC, Wong IY. Breast Cancer Cells Transition from Mesenchymal to Amoeboid Migration in Tunable Three-Dimensional Silk–Collagen Hydrogels. ACS Biomaterials Science & Engineering 2019, 5: 4341-4354. PMID: 31517039, PMCID: PMC6739834, DOI: 10.1021/acsbiomaterials.9b00519.Peer-Reviewed Original ResearchCell-matrix adhesionStrong cell-matrix adhesionMesenchymal morphologyCancer cell transitionCancer cellsCollagen I concentrationAmoeboid morphologyMetastatic breast cancer cellsCancer cell migrationCytoskeletal functionECM protein concentrationMigration phenotypeAmoeboid migrationCell transitionMesenchymal migrationBiochemical cuesBreast cancer cellsCell migrationExtracellular matrixRounded morphologyBiphasic dependencePlate formatCollagen ICellsBiomaterial platform3D printed self-adhesive PEGDA–PAA hydrogels as modular components for soft actuators and microfluidics
Valentin T, DuBois E, Machnicki C, Bhaskar D, Cui F, Wong I. 3D printed self-adhesive PEGDA–PAA hydrogels as modular components for soft actuators and microfluidics. Polymer Chemistry 2019, 10: 2015-2028. DOI: 10.1039/c9py00211a.Peer-Reviewed Original ResearchHydrogel building blocksSoft machinesAnionic polymer chainsBuilding blocksCation concentrationMicrofluidic deviceHigh molecular weightHigher cation concentrationsPoor interfacial adhesionPolymer chainsResponsive hydrogelsIonic crosslinkingTrivalent cationsHydrogel surfaceMolecular weightInterfacial adhesionSerpentine micromixerSoft actuatorsHydrogel partComposite hydrogelsMechanical connectorsHydrogelsHydrogel blocksDevice geometryMicrofluidic device geometryTopological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion
Bhaskar D, Zhang W, Volkening A, Sandstede B, Wong I. Topological data analysis of spatial patterning in heterogeneous cell populations: clustering and sorting with varying cell-cell adhesion. Npj Systems Biology And Applications 2023, 9: 43. PMID: 37709793, PMCID: PMC10502054, DOI: 10.1038/s41540-023-00302-8.Peer-Reviewed Original ResearchConceptsTopological data analysisPersistence imagesClassification accuracyHigh classification accuracyMachine learningRobust classificationDimensionality reductionUnsupervised classificationHierarchical architectureData analysisArchitectureHierarchical clusteringImagesTopological featuresClassificationDifferent topological featuresAutoencoderAccuracyClusteringLearningSimulationsInformationRecent developmentsA Flow Artist for High-Dimensional Cellular Data
MacDonald K, Bhaskar D, Thampakkul G, Nguyen N, Zhang J, Perlmutter M, Adelstein I, Krishnaswamy S. A Flow Artist for High-Dimensional Cellular Data. 2023, 00: 1-6. DOI: 10.1109/mlsp55844.2023.10285942.Peer-Reviewed Original ResearchTransformer-based protein generation with regularized latent space optimization
Castro E, Godavarthi A, Rubinfien J, Givechian K, Bhaskar D, Krishnaswamy S. Transformer-based protein generation with regularized latent space optimization. Nature Machine Intelligence 2022, 4: 840-851. DOI: 10.1038/s42256-022-00532-1.Peer-Reviewed Original Research
2024
Dissecting glial scar formation by spatial point pattern and topological data analysis
Manrique-Castano D, Bhaskar D, ElAli A. Dissecting glial scar formation by spatial point pattern and topological data analysis. Scientific Reports 2024, 14: 19035. PMID: 39152163, PMCID: PMC11329771, DOI: 10.1038/s41598-024-69426-z.Peer-Reviewed Original ResearchLearnable Filters for Geometric Scattering Modules
Tong A, Wenkel F, Bhaskar D, Macdonald K, Grady J, Perlmutter M, Krishnaswamy S, Wolf G. Learnable Filters for Geometric Scattering Modules. IEEE Transactions On Signal Processing 2024, 72: 2939-2952. DOI: 10.1109/tsp.2024.3378001.Peer-Reviewed Original ResearchGraph neural networksGraph classification benchmarksEncode graph structureData exploration tasksGeometric scattering transformGraph wavelet filtersClassification benchmarksLearned representationsLearnable filtersLearning parametersGraph structureNeural networkExploration tasksWavelet filtersBand-pass featureBiochemical domainNetworkAdaptive tuningWaveletGraphPredictive performanceScattering modulationScattering transformMathematical propertiesFilterCorrection: Cell cycle controls long-range calcium signaling in the regenerating epidermis
Moore J, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V. Correction: Cell cycle controls long-range calcium signaling in the regenerating epidermis. Journal Of Cell Biology 2024, 223: e20230209503052024c. PMID: 38477880, PMCID: PMC10938063, DOI: 10.1083/jcb.20230209503052024c.Peer-Reviewed Original Research
2023
Wire Before You Walk
Asmara T, Bhaskar D, Adelstein I, Krishnaswamy S, Perlmutter M. Wire Before You Walk. 2023, 00: 714-716. DOI: 10.1109/ieeeconf59524.2023.10477089.Peer-Reviewed Original Research