메뉴 건너뛰기




Volumn 37, Issue 5, 2019, Pages 547-554

A comparison of single-cell trajectory inference methods

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; CYTOLOGY; LARGE DATASET; TOPOLOGY;

EID: 85063785657     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/s41587-019-0071-9     Document Type: Article
Times cited : (991)

References (55)
  • 1
    • 85017360311 scopus 로고    scopus 로고
    • Scaling single-cell genomics from phenomenology to mechanism
    • Tanay, A. & Regev, A. Scaling single-cell genomics from phenomenology to mechanism. Nature 541, 21350 (2017).
    • (2017) Nature , vol.541 , pp. 21350
    • Tanay, A.1    Regev, A.2
  • 2
    • 84922629832 scopus 로고    scopus 로고
    • Quantitative single-cell approaches to stem cell research
    • COI: 1:CAS:528:DC%2BC2cXhvVCktbjP, PID: 25517464
    • Etzrodt, M., Endele, M. & Schroeder, T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell 15, 546–558 (2014).
    • (2014) Cell Stem Cell , vol.15 , pp. 546-558
    • Etzrodt, M.1    Endele, M.2    Schroeder, T.3
  • 3
    • 84942940566 scopus 로고    scopus 로고
    • Defining cell types and states with single-cell genomics
    • COI: 1:CAS:528:DC%2BC2MXhs1Oitb%2FK, PID: 26430159
    • Trapnell, C. Defining cell types and states with single-cell genomics. Genome Res. 25, 1491–1498 (2015).
    • (2015) Genome Res. , vol.25 , pp. 1491-1498
    • Trapnell, C.1
  • 4
    • 84991571425 scopus 로고    scopus 로고
    • Computational methods for trajectory inference from single-cell transcriptomics
    • COI: 1:CAS:528:DC%2BC28Xhs1yrsLfK, PID: 27682842
    • Cannoodt, R., Saelens, W. & Saeys, Y. Computational methods for trajectory inference from single-cell transcriptomics. Eur. J. Immunol. 46, 2496–2506 (2016).
    • (2016) Eur. J. Immunol. , vol.46 , pp. 2496-2506
    • Cannoodt, R.1    Saelens, W.2    Saeys, Y.3
  • 5
    • 85045320368 scopus 로고    scopus 로고
    • Manifold learning-based methods for analyzing single-cell RNA-sequencing data
    • Moon, K. R. et al. Manifold learning-based methods for analyzing single-cell RNA-sequencing data.Curr. Opin. Syst. Biol. 7, 36–46 (2018).
    • (2018) Curr. Opin. Syst. Biol. , vol.7 , pp. 36-46
    • Moon, K.R.1
  • 6
    • 85021092677 scopus 로고    scopus 로고
    • Reconstructing cell cycle pseudo time-series via single-cell transcriptome data
    • PID: 28630425
    • Liu, Z. et al. Reconstructing cell cycle pseudo time-series via single-cell transcriptome data. Nat. Commun. 8, 22 (2017).
    • (2017) Nat. Commun. , vol.8
    • Liu, Z.1
  • 7
    • 85063153038 scopus 로고    scopus 로고
    • PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells
    • PID: 30890159
    • Wolf, F. A. et al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019).
    • (2019) Genome Biol. , vol.20 , pp. 59
    • Wolf, F.A.1
  • 8
    • 84931394611 scopus 로고    scopus 로고
    • Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow
    • COI: 1:CAS:528:DC%2BC2MXhtFSktLjN, PID: 26054720
    • Schlitzer, A. et al. Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat. Immunol. 16, 718–728 (2015).
    • (2015) Nat. Immunol. , vol.16 , pp. 718-728
    • Schlitzer, A.1
  • 9
    • 85015695567 scopus 로고    scopus 로고
    • Human haematopoietic stem cell lineage commitment is a continuous process
    • COI: 1:CAS:528:DC%2BC2sXltVWnsr0%3D, PID: 28319093
    • Velten, L. et al. Human haematopoietic stem cell lineage commitment is a continuous process. Nat. Cell Biol. 19, 271–281 (2017).
    • (2017) Nat. Cell Biol. , vol.19 , pp. 271-281
    • Velten, L.1
  • 10
    • 85027934223 scopus 로고    scopus 로고
    • Mapping the human DC lineage through the integration of high-dimensional techniques
    • PID: 28473638
    • See, P. et al. Mapping the human DC lineage through the integration of high-dimensional techniques. Science 356, eaag3009 (2017).
    • (2017) Science , vol.356 , pp. eaag3009
    • See, P.1
  • 11
    • 85032583384 scopus 로고    scopus 로고
    • SCENIC: Single-cell regulatory network inference and clustering
    • COI: 1:CAS:528:DC%2BC2sXhs1aitL7P, PID: 28991892
    • Aibar, S. et al. SCENIC: Single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 1083-1086
    • Aibar, S.1
  • 12
    • 85040459896 scopus 로고    scopus 로고
    • Science forum: the human cell atlas
    • PID: 29206104
    • Regev, A. et al. Science forum: the human cell atlas. eLife 6, e27041 (2017).
    • (2017) eLife , vol.6
    • Regev, A.1
  • 13
    • 85042366842 scopus 로고    scopus 로고
    • Mapping the mouse cell atlas by microwell-seq
    • COI: 1:CAS:528:DC%2BC1cXjt12ltr4%3D, PID: 29474909
    • Han, X. et al. Mapping the mouse cell atlas by microwell-seq. Cell 172, 1091–1107.e17 (2018).
    • (2018) Cell , vol.172 , pp. 1091-1107.e17
    • Han, X.1
  • 14
    • 85055080981 scopus 로고    scopus 로고
    • Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris
    • Schaum, N. et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372 (2018).
    • (2018) Nature , vol.562 , pp. 367-372
    • Schaum, N.1
  • 15
    • 85041430720 scopus 로고    scopus 로고
    • Single cells make big data: new challenges and opportunities in transcriptomics
    • Angerer, P. et al. Single cells make big data: new challenges and opportunities in transcriptomics. Curr. Opin. Syst. Biol. 4, 85–91 (2017).
    • (2017) Curr. Opin. Syst. Biol. , vol.4 , pp. 85-91
    • Angerer, P.1
  • 16
  • 18
    • 85049372156 scopus 로고    scopus 로고
    • Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database
    • &
    • Zappia, L., Phipson, B. & Oshlack, A. Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database. PLoS Comput. Biol. 14, e1006245 (2018)
    • (2018) PLoS Comput. Biol. , vol.14
    • Zappia, L.1    Phipson, B.2    Oshlack, A.3
  • 19
    • 84899574465 scopus 로고    scopus 로고
    • Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development
    • COI: 1:CAS:528:DC%2BC2cXntFGgsr8%3D, PID: 24766814
    • Bendall, S. C. et al. Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development. Cell 157, 714–725 (2014).
    • (2014) Cell , vol.157 , pp. 714-725
    • Bendall, S.C.1
  • 20
    • 84941010341 scopus 로고    scopus 로고
    • Single-cell RNA-seq with waterfall reveals molecular cascades underlying adult neurogenesis
    • COI: 1:CAS:528:DC%2BC2MXhtlOmtbjP, PID: 26299571
    • Shin, J. et al. Single-cell RNA-seq with waterfall reveals molecular cascades underlying adult neurogenesis. Cell Stem Cell 17, 360–372 (2015).
    • (2015) Cell Stem Cell , vol.17 , pp. 360-372
    • Shin, J.1
  • 22
    • 84984643819 scopus 로고    scopus 로고
    • Diffusion pseudotime robustly reconstructs lineage branching
    • COI: 1:CAS:528:DC%2BC28XhsVWrs7zI, PID: 27571553
    • Haghverdi, L., Büttner, M., Wolf, F. A., Buettner, F. & Theis, F. J. Diffusion pseudotime robustly reconstructs lineage branching. Nat. Methods 13, 845–848 (2016).
    • (2016) Nat. Methods , vol.13 , pp. 845-848
    • Haghverdi, L.1    Büttner, M.2    Wolf, F.A.3    Buettner, F.4    Theis, F.J.5
  • 23
    • 84974587998 scopus 로고    scopus 로고
    • Wishbone identifies bifurcating developmental trajectories from single-cell data
    • COI: 1:CAS:528:DC%2BC28XmvFOqsrs%3D, PID: 27136076
    • Setty, M. et al. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nat. Biotechnol. 34, 637–645 (2016).
    • (2016) Nat. Biotechnol. , vol.34 , pp. 637-645
    • Setty, M.1
  • 24
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 2859 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 2859
    • Trapnell, C.1
  • 25
    • 84975764298 scopus 로고    scopus 로고
    • SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation
    • PID: 27277014
    • Matsumoto, H. & Kiryu, H. SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation. BMC Bioinformatics 17, 232 (2016).
    • (2016) BMC Bioinformatics , vol.17
    • Matsumoto, H.1    Kiryu, H.2
  • 26
    • 85031017685 scopus 로고    scopus 로고
    • Reversed graph embedding resolves complex single-cell trajectories
    • COI: 1:CAS:528:DC%2BC2sXhtlKjtbbK, PID: 28825705
    • Qiu, X. et al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 979-982
    • Qiu, X.1
  • 27
    • 85048725973 scopus 로고    scopus 로고
    • Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
    • PID: 29914354
    • Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
    • (2018) BMC Genomics , vol.19
    • Street, K.1
  • 28
    • 84982806105 scopus 로고    scopus 로고
    • TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
    • PID: 27179027
    • Ji, Z. & Ji, H. TSCAN: pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis. Nucleic Acids Res. 44, e117–e117 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , pp. e117
    • Ji, Z.1    Ji, H.2
  • 29
    • 84969505817 scopus 로고    scopus 로고
    • SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
    • PID: 27215581
    • Welch, J. D., Hartemink, A. J. & Prins, J. F. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome. Biol. 17, 106 (2016).
    • (2016) Genome. Biol. , vol.17
    • Welch, J.D.1    Hartemink, A.J.2    Prins, J.F.3
  • 30
    • 84987652887 scopus 로고    scopus 로고
    • CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
    • PID: 27620863
    • duVerle, D. A., Yotsukura, S., Nomura, S., Aburatani, H. & Tsuda, K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics 17, 363 (2016).
    • (2016) BMC Bioinformatics , vol.17
    • duVerle, D.A.1    Yotsukura, S.2    Nomura, S.3    Aburatani, H.4    Tsuda, K.5
  • 32
    • 85040750667 scopus 로고    scopus 로고
    • Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria
    • PID: 28345074
    • Lönnberg, T. et al. Single-cell RNA-seq and computational analysis using temporal mixture modeling resolves TH1/TFH fate bifurcation in malaria. Sci. Immunol. 2, eaal2192 (2017).
    • (2017) Sci. Immunol. , vol.2 , pp. eaal2192
    • Lönnberg, T.1
  • 33
    • 85039160886 scopus 로고    scopus 로고
    • Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers
    • PID: 28503665
    • Campbell, K. R. & Yau, C. Probabilistic modeling of bifurcations in single-cell gene expression data using a Bayesian mixture of factor analyzers. Wellcome Open Res. 2, 19 (2017).
    • (2017) Wellcome Open Res. , vol.2 , pp. 19
    • Campbell, K.R.1    Yau, C.2
  • 35
    • 79961200389 scopus 로고    scopus 로고
    • GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods
    • COI: 1:CAS:528:DC%2BC3MXhtVSiurjO
    • Schaffter, T., Marbach, D. & Floreano, D. GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods. Bioinformatics 27, 2263–2270 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2263-2270
    • Schaffter, T.1    Marbach, D.2    Floreano, D.3
  • 36
    • 85029212828 scopus 로고    scopus 로고
    • Splatter: simulation of single-cell RNA sequencing data
    • PID: 28899397
    • Zappia, L., Phipson, B. & Oshlack, A. Splatter: simulation of single-cell RNA sequencing data. Genome. Biol. 18, 174 (2017).
    • (2017) Genome. Biol. , vol.18
    • Zappia, L.1    Phipson, B.2    Oshlack, A.3
  • 37
    • 85044252958 scopus 로고    scopus 로고
    • Exponential scaling of single-cell RNA-seq in the past decade
    • COI: 1:CAS:528:DC%2BC1cXjs1agu74%3D, PID: 29494575
    • Svensson, V., Vento-Tormo, R. & Teichmann, S. A. Exponential scaling of single-cell RNA-seq in the past decade. Nat. Protoc. 13, 599–604 (2018).
    • (2018) Nat. Protoc. , vol.13 , pp. 599-604
    • Svensson, V.1    Vento-Tormo, R.2    Teichmann, S.A.3
  • 39
    • 84894277295 scopus 로고    scopus 로고
    • Shape constrained additive models
    • Pya, N. & Wood, S. N. Shape constrained additive models. Stat. Comput. 25, 543–559 (2015).
    • (2015) Stat. Comput. , vol.25 , pp. 543-559
    • Pya, N.1    Wood, S.N.2
  • 40
    • 85018304908 scopus 로고    scopus 로고
    • Ten simple rules for making research software more robust
    • &
    • Taschuk, M. & Wilson, G. Ten simple rules for making research software more robust. PLoS Comput. Biol. 13, e1005412 (2017).
    • (2017) PLoS Comput. Biol. , vol.13
    • Taschuk, M.1    Wilson, G.2
  • 42
    • 84893773697 scopus 로고    scopus 로고
    • Best practices for scientific computing
    • PID: 24415924
    • Wilson, G. et al. Best practices for scientific computing. PLoS Biol. 12, e1001745 (2014).
    • (2014) PLoS Biol. , vol.12
    • Wilson, G.1
  • 43
    • 85010840297 scopus 로고    scopus 로고
    • Top 10 metrics for life science software good practices
    • Artaza, H. et al. Top 10 metrics for life science software good practices. F1000Res. 5, 2000 (2016).
    • (2016) F1000Res. , vol.5 , pp. 2000
    • Artaza, H.1
  • 44
    • 85044288670 scopus 로고    scopus 로고
    • A comprehensive evaluation of module detection methods for gene expression data
    • PID: 29545622
    • Saelens, W., Cannoodt, R. & Saeys, Y. A comprehensive evaluation of module detection methods for gene expression data. Nat. Commun. 9, 1090 (2018).
    • (2018) Nat. Commun. , vol.9
    • Saelens, W.1    Cannoodt, R.2    Saeys, Y.3
  • 45
    • 85052109231 scopus 로고    scopus 로고
    • RNA velocity of single cells
    • PID: 30089906
    • Manno, G. L. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
    • (2018) Nature , vol.560 , pp. 494-498
    • Manno, G.L.1
  • 46
    • 80054088224 scopus 로고    scopus 로고
    • The self-assessment trap: Can we all be better than average?
    • PID: 21988833
    • Norel, R., Rice, J. J. & Stolovitzky, G. The self-assessment trap: Can we all be better than average? Mol. Syst. Biol. 7, 537 (2011).
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 537
    • Norel, R.1    Rice, J.J.2    Stolovitzky, G.3
  • 48
    • 84886017663 scopus 로고    scopus 로고
    • Temporal dynamics and transcriptional control using single-cell gene expression analysis
    • PID: 24156252
    • Kouno, T. et al. Temporal dynamics and transcriptional control using single-cell gene expression analysis. Genome. Biol. 14, R118 (2013).
    • (2013) Genome. Biol. , vol.14
    • Kouno, T.1
  • 50
    • 85065217201 scopus 로고    scopus 로고
    • PROSSTT: Probabilistic simulation of single-cell RNA-seq data for complex differentiation processes
    • Papadopoulos, N., Parra, R. G. & Soeding, J. PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinformatics, btz078 (2019).
    • (2019) Bioinformatics
    • Papadopoulos, N.1    Parra, R.G.2    Soeding, J.3
  • 51
    • 85010931059 scopus 로고    scopus 로고
    • A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
    • PID: 27909575
    • Lun, A. T., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 5, 2122 (2016).
    • (2016) F1000Res. , vol.5 , pp. 2122
    • Lun, A.T.1    McCarthy, D.J.2    Marioni, J.C.3
  • 53
    • 85016782791 scopus 로고    scopus 로고
    • Ranger: A fast implementation of random forests for high dimensional data in C++ and R
    • Wright, M. N. & Ziegler, A. Ranger: a fast implementation of random forests for high dimensional data in C++ and R. J. Stat. Softw. 77, 1-17 (2017).
    • (2017) J. Stat. Softw. , vol.77 , pp. 1-17
    • Wright, M.N.1    Ziegler, A.2
  • 54
    • 85017331188 scopus 로고    scopus 로고
    • Reproducibility of computational workflows is automated using continuous analysis
    • Beaulieu-Jones, B. K. & Greene, C. S. Reproducibility of computational workflows is automated using continuous analysis. Nat. Biotechnol. 35, 3780 (2017).
    • (2017) Nat. Biotechnol. , vol.35 , pp. 3780
    • Beaulieu-Jones, B.K.1    Greene, C.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.