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Articles published in
PLoS Comput Biol
    March 2021
  1. BROWN J, Barry C, Schmitz MT, Argus C, et al
    Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells.
    PLoS Comput Biol. 2021;17:e1008778.
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    February 2021
  2. JAEGER KH, Wall S, Tveito A
    Computational prediction of drug response in short QT syndrome type 1 based on measurements of compound effect in stem cell-derived cardiomyocytes.
    PLoS Comput Biol. 2021;17:e1008089.
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    January 2021
  3. MARTINEZ-GARCIA PM, Garcia-Torres M, Divina F, Terron-Bautista J, et al
    Genome-wide prediction of topoisomerase IIbeta binding by architectural factors and chromatin accessibility.
    PLoS Comput Biol. 2021;17:e1007814.
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  4. LOUIE W, Shen MW, Tahiry Z, Zhang S, et al
    Machine learning based CRISPR gRNA design for therapeutic exon skipping.
    PLoS Comput Biol. 2021;17:e1008605.
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  5. GIAMMONA J, Campas O
    Physical constraints on early blastomere packings.
    PLoS Comput Biol. 2021;17:e1007994.
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    December 2020
  6. CARCAMO-ORIVE I, Henrion MYR, Zhu K, Beckmann ND, et al
    Predictive network modeling in human induced pluripotent stem cells identifies key driver genes for insulin responsiveness.
    PLoS Comput Biol. 2020;16:e1008491.
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    October 2020
  7. LIU YYF, Lu Y, Oh S, Conduit GJ, et al
    Machine learning to predict mesenchymal stem cell efficacy for cartilage repair.
    PLoS Comput Biol. 2020;16:e1008275.
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    September 2020
  8. TRAN TN, Bader GD
    Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data.
    PLoS Comput Biol. 2020;16:e1008205.
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  9. RAPHEL F, De Korte T, Lombardi D, Braam S, et al
    A greedy classifier optimization strategy to assess ion channel blocking activity and pro-arrhythmia in hiPSC-cardiomyocytes.
    PLoS Comput Biol. 2020;16:e1008203.
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    August 2020
  10. KERNIK DC, Yang PC, Kurokawa J, Wu JC, et al
    A computational model of induced pluripotent stem-cell derived cardiomyocytes for high throughput risk stratification of KCNQ1 genetic variants.
    PLoS Comput Biol. 2020;16:e1008109.
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    July 2020
  11. ZHENG X, Huang Y, Zou X
    scPADGRN: A preconditioned ADMM approach for reconstructing dynamic gene regulatory network using single-cell RNA sequencing data.
    PLoS Comput Biol. 2020;16:e1007471.
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  12. WILSON JL, Lu D, Corr N, Fullerton A, et al
    An in vitro quantitative systems pharmacology approach for deconvolving mechanisms of drug-induced, multilineage cytopenias.
    PLoS Comput Biol. 2020;16:e1007620.
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    April 2020
  13. VASCONCELOS E SA J, Simao D, Terrasso AP, Silva MM, et al
    Unveiling dynamic metabolic signatures in human induced pluripotent and neural stem cells.
    PLoS Comput Biol. 2020;16:e1007780.
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  14. BUSTO-MONER L, Morival J, Ren H, Fahim A, et al
    Stochastic modeling reveals kinetic heterogeneity in post-replication DNA methylation.
    PLoS Comput Biol. 2020;16:e1007195.
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    January 2020
  15. TAYLOR-KING JP, Riseth AN, Macnair W, Claassen M, et al
    Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming.
    PLoS Comput Biol. 2020;16:e1007491.
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    December 2019
  16. ZHANG H, Shao X, Peng Y, Teng Y, et al
    A novel machine learning based approach for iPS progenitor cell identification.
    PLoS Comput Biol. 2019;15:e1007351.
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  17. BARRY C, Schmitz MT, Argus C, Bolin JM, et al
    Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics.
    PLoS Comput Biol. 2019;15:e1007543.
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    November 2019
  18. SHI J, Li T, Chen L, Aihara K, et al
    Quantifying pluripotency landscape of cell differentiation from scRNA-seq data by continuous birth-death process.
    PLoS Comput Biol. 2019;15:e1007488.
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  19. VIJAYABASKAR MS, Goode DK, Obier N, Lichtinger M, et al
    Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets.
    PLoS Comput Biol. 2019;15:e1007337.
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    July 2019
  20. ZHOU D, Luo Y, Dingli D, Traulsen A, et al
    The invasion of de-differentiating cancer cells into hierarchical tissues.
    PLoS Comput Biol. 2019;15:e1007167.
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    May 2019
  21. SHARMA AK, Sormanni P, Ahmed N, Ciryam P, et al
    A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.
    PLoS Comput Biol. 2019;15:e1007070.
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    April 2019
  22. PARK DS, Akuffo AA, Muench DE, Grimes HL, et al
    Clonal hematopoiesis of indeterminate potential and its impact on patient trajectories after stem cell transplantation.
    PLoS Comput Biol. 2019;15:e1006913.
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    March 2019
  23. YE Y, Kang X, Bailey J, Li C, et al
    An enriched network motif family regulates multistep cell fate transitions with restricted reversibility.
    PLoS Comput Biol. 2019;15:e1006855.
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  24. KHEIFETZ Y, Scholz M
    Modeling individual time courses of thrombopoiesis during multi-cyclic chemotherapy.
    PLoS Comput Biol. 2019;15:e1006775.
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    January 2019
  25. OSTBLOM J, Nazareth EJP, Tewary M, Zandstra PW, et al
    Context-explorer: Analysis of spatially organized protein expression in high-throughput screens.
    PLoS Comput Biol. 2019;15:e1006384.
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    November 2018
  26. CROOK OM, Mulvey CM, Kirk PDW, Lilley KS, et al
    A Bayesian mixture modelling approach for spatial proteomics.
    PLoS Comput Biol. 2018;14:e1006516.
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    October 2018
  27. XU S, Kim S, Chen ISY, Chou T, et al
    Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.
    PLoS Comput Biol. 2018;14:e1006489.
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    September 2018
  28. BRACKSTON RD, Lakatos E, Stumpf MPH
    Transition state characteristics during cell differentiation.
    PLoS Comput Biol. 2018;14:e1006405.
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    August 2018
  29. TSE MJ, Chu BK, Gallivan CP, Read EL, et al
    Rare-event sampling of epigenetic landscapes and phenotype transitions.
    PLoS Comput Biol. 2018;14:e1006336.
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    June 2018
  30. MON PERE N, Lenaerts T, Pacheco JM, Dingli D, et al
    Evolutionary dynamics of paroxysmal nocturnal hemoglobinuria.
    PLoS Comput Biol. 2018;14:e1006133.
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    April 2018
  31. ZHANG H, Lee CAA, Li Z, Garbe JR, et al
    A multitask clustering approach for single-cell RNA-seq analysis in Recessive Dystrophic Epidermolysis Bullosa.
    PLoS Comput Biol. 2018;14:e1006053.
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  32. SCHOTT B, Traub M, Schlagenhauf C, Takamiya M, et al
    EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.
    PLoS Comput Biol. 2018;14:e1006128.
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    March 2018
  33. DUFOUR A, Gontran E, Deroulers C, Varlet P, et al
    Modeling the dynamics of oligodendrocyte precursor cells and the genesis of gliomas.
    PLoS Comput Biol. 2018;14:e1005977.
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  34. LUO Y, He J, Xu X, Sun MA, et al
    Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells.
    PLoS Comput Biol. 2018;14:e1006034.
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    February 2018
  35. DU H, Wang Y, Haensel D, Lee B, et al
    Multiscale modeling of layer formation in epidermis.
    PLoS Comput Biol. 2018;14:e1006006.
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  36. LIN YT, Hufton PG, Lee EJ, Potoyan DA, et al
    A stochastic and dynamical view of pluripotency in mouse embryonic stem cells.
    PLoS Comput Biol. 2018;14:e1006000.
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  37. ALVARADO C, Fider NA, Wearing HJ, Komarova NL, et al
    Optimizing homeostatic cell renewal in hierarchical tissues.
    PLoS Comput Biol. 2018;14:e1005967.
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  38. PALM MM, Elemans M, Beltman JB
    Heritable tumor cell division rate heterogeneity induces clonal dominance.
    PLoS Comput Biol. 2018;14:e1005954.
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    January 2018
  39. NAZARI F, Pearson AT, Nor JE, Jackson TL, et al
    A mathematical model for IL-6-mediated, stem cell driven tumor growth and targeted treatment.
    PLoS Comput Biol. 2018;14:e1005920.
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  40. KIMMEL JC, Chang AY, Brack AS, Marshall WF, et al
    Inferring cell state by quantitative motility analysis reveals a dynamic state system and broken detailed balance.
    PLoS Comput Biol. 2018;14:e1005927.
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  41. DI MININ G, Postlmayr A, Wutz A
    HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cells.
    PLoS Comput Biol. 2018;14:e1005950.
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    October 2017
  42. ASHCROFT P, Manz MG, Bonhoeffer S
    Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.
    PLoS Comput Biol. 2017;13:e1005803.
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  43. KAKUMANU A, Velasco S, Mazzoni E, Mahony S, et al
    Deconvolving sequence features that discriminate between overlapping regulatory annotations.
    PLoS Comput Biol. 2017;13:e1005795.
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    September 2017
  44. GREAVES RB, Dietmann S, Smith A, Stepney S, et al
    A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells.
    PLoS Comput Biol. 2017;13:e1005713.
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