{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,6]],"date-time":"2025-05-06T21:15:11Z","timestamp":1746566111048,"version":"3.37.3"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2017,9,14]],"date-time":"2017-09-14T00:00:00Z","timestamp":1505347200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["157154"],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,15]]},"abstract":"Abstract<\/jats:title>Motivation<\/jats:title>Single cell transcriptional profiling opens up a new avenue in studying the functional role of cell-to-cell variability in physiological processes. The analysis of single cell expression profiles creates new challenges due to the distributive nature of the data and the stochastic dynamics of gene transcription process. The reconstruction of gene regulatory networks (GRNs) using single cell transcriptional profiles is particularly challenging, especially when directed gene-gene relationships are desired.<\/jats:p><\/jats:sec>Results<\/jats:title>We developed SINCERITIES (SINgle CEll Regularized Inference using TIme-stamped Expression profileS) for the inference of GRNs from single cell transcriptional profiles. We focused on time-stamped cross-sectional expression data, commonly generated from transcriptional profiling of single cells collected at multiple time points after cell stimulation. SINCERITIES recovers directed regulatory relationships among genes by employing regularized linear regression (ridge regression), using temporal changes in the distributions of gene expressions. Meanwhile, the modes of the gene regulations (activation and repression) come from partial correlation analyses between pairs of genes. We demonstrated the efficacy of SINCERITIES in inferring GRNs using in silico time-stamped single cell expression data and single cell transcriptional profiles of THP-1 monocytic human leukemia cells. The case studies showed that SINCERITIES could provide accurate GRN predictions, significantly better than other GRN inference algorithms such as TSNI, GENIE3 and JUMP3. Moreover, SINCERITIES has a low computational complexity and is amenable to problems of extremely large dimensionality. Finally, an application of SINCERITIES to single cell expression data of T2EC chicken erythrocytes pointed to BATF as a candidate novel regulator of erythroid development.<\/jats:p><\/jats:sec>Availability and implementation<\/jats:title>MATLAB and R version of SINCERITIES are freely available from the following websites: http:\/\/www.cabsel.ethz.ch\/tools\/sincerities.html and https:\/\/github.com\/CABSEL\/SINCERITIES. The single cell THP-1 and T2EC transcriptional profiles are available from the original publications (Kouno et al., 2013; Richard et al., 2016). The in silico single cell data are available on SINCERITIES websites.<\/jats:p><\/jats:sec>Supplementary information<\/jats:title>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx575","type":"journal-article","created":{"date-parts":[[2017,9,13]],"date-time":"2017-09-13T19:13:03Z","timestamp":1505329983000},"page":"258-266","source":"Crossref","is-referenced-by-count":176,"title":["SINCERITIES: inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles"],"prefix":"10.1093","volume":"34","author":[{"given":"Nan","family":"Papili Gao","sequence":"first","affiliation":[{"name":"Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}]},{"given":"S M Minhaz","family":"Ud-Dean","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA"}]},{"given":"Olivier","family":"Gandrillon","sequence":"additional","affiliation":[{"name":"Laboratory of Biology and Modelling of the Cell, Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR, INSERM Lyon, France"},{"name":"Inria Team Dracula, Inria Center Grenoble Rh\u00f4ne-Alpes, Rh\u00f4ne-Alpes, France"}]},{"given":"Rudiyanto","family":"Gunawan","sequence":"additional","affiliation":[{"name":"Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland"},{"name":"Swiss Institute of Bioinformatics, Lausanne, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2017,9,14]]},"reference":[{"key":"2023012712240510800_btx575-B1","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1016\/j.cell.2010.04.033","article-title":"Cellular Heterogeneity: Do Differences Make a Difference?","volume":"141","author":"Altschuler","year":"2010","journal-title":"Cell"},{"key":"2023012712240510800_btx575-B2","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1038\/nbt.2594","article-title":"viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia","volume":"31","author":"Amir","year":"2013","journal-title":"Nat. Biotechnol"},{"key":"2023012712240510800_btx575-B3","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1214\/aoms\/1177704477","article-title":"On the distribution of the Two-Sample Cramer-von Mises criterion","volume":"33","author":"Anderson","year":"1962","journal-title":"Ann. Math. Stat"},{"key":"2023012712240510800_btx575-B4","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1214\/aoms\/1177729437","article-title":"Asymptotic theory of certain \u2018Goodness of Fit\u2019 criteria based on stochastic processes","volume":"23","author":"Anderson","year":"1952","journal-title":"Ann. Math. Stat"},{"key":"2023012712240510800_btx575-B5","doi-asserted-by":"crossref","first-page":"63.","DOI":"10.1186\/s13059-016-0927-y","article-title":"Design and computational analysis of single-cell RNA-sequencing experiments","volume":"17","author":"Bacher","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B6","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B7","doi-asserted-by":"crossref","first-page":"552","DOI":"10.1038\/nrg3244","article-title":"Studying and modelling dynamic biological processes using time-series gene expression data","volume":"13","author":"Bar-Joseph","year":"2012","journal-title":"Nat. Rev. Genet"},{"key":"2023012712240510800_btx575-B8","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.cell.2014.04.005","article-title":"Single-cell trajectory detection uncovers progression and regulatory coordination in human B cell development","volume":"157","author":"Bendall","year":"2014","journal-title":"Cell"},{"key":"2023012712240510800_btx575-B9","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nbt.3102","article-title":"Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells","volume":"33","author":"Buettner","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023012712240510800_btx575-B10","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1093\/bioinformatics\/btu134","article-title":"Probabilistic PCA of censored data: accounting for uncertainties in the visualization of high-throughput single-cell qPCR data","volume":"30","author":"Buettner","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B11","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1038\/nature06965","article-title":"Transcriptome-wide noise controls lineage choice in mammalian progenitor cells","volume":"453","author":"Chang","year":"2008","journal-title":"Nature"},{"key":"2023012712240510800_btx575-B12","doi-asserted-by":"crossref","first-page":"128.","DOI":"10.1186\/1471-2105-14-128","article-title":"Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023012712240510800_btx575-B13","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1093\/bioinformatics\/btu777","article-title":"Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development","volume":"31","author":"Chen","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B14","doi-asserted-by":"crossref","first-page":"173.","DOI":"10.1186\/s13059-016-1033-x","article-title":"Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm","volume":"17","author":"Chu","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B15","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.acha.2006.04.006","article-title":"Diffusion maps","volume":"21","author":"Coifman","year":"2006","journal-title":"Appl. Comput. Harmon. Anal"},{"key":"2023012712240510800_btx575-B16","doi-asserted-by":"crossref","first-page":"2.","DOI":"10.1186\/1752-0509-4-2","article-title":"On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter","volume":"4","author":"Coulon","year":"2010","journal-title":"BMC Syst. Biol"},{"key":"2023012712240510800_btx575-B17","doi-asserted-by":"crossref","first-page":"9205","DOI":"10.1038\/sj.onc.1207049","article-title":"The MEK-1\/ERKs signalling pathway is differentially involved in the self-renewal of early and late avian erythroid progenitor cells","volume":"22","author":"Dazy","year":"2003","journal-title":"Oncogene"},{"key":"2023012712240510800_btx575-B18","doi-asserted-by":"crossref","first-page":"e1001618","DOI":"10.1371\/journal.pbio.1001618","article-title":"Stochastic cytokine expression induces mixed T helper cell States","volume":"11","author":"Fang","year":"2013","journal-title":"PLoS Biol"},{"key":"2023012712240510800_btx575-B19","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1093\/mnras\/225.1.155","article-title":"A multidimensional version of the Kolmogorov\u2013Smirnov test","volume":"225","author":"Fasano","year":"1987","journal-title":"Mon. Not. R. Astron. Soc"},{"key":"2023012712240510800_btx575-B20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"Friedman","year":"2010","journal-title":"J. Stat. Softw"},{"key":"2023012712240510800_btx575-B21","doi-asserted-by":"crossref","first-page":"2764","DOI":"10.1093\/emboj\/18.10.2764","article-title":"TGF-beta cooperates with TGF-alpha to induce the self-renewal of normal erythrocytic progenitors: evidence for an autocrine mechanism","volume":"18","author":"Gandrillon","year":"1999","journal-title":"EMBO J"},{"key":"2023012712240510800_btx575-B22","doi-asserted-by":"crossref","first-page":"424","DOI":"10.2307\/1912791","article-title":"Investigating Causal Relations by Econometric Models and Cross-spectral Methods","volume":"37","author":"Granger","year":"1969","journal-title":"Econometrica"},{"key":"2023012712240510800_btx575-B23","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.cell.2011.07.026","article-title":"Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells","volume":"146","author":"Gupta","year":"2011","journal-title":"Cell"},{"key":"2023012712240510800_btx575-B24","doi-asserted-by":"crossref","first-page":"2989","DOI":"10.1093\/bioinformatics\/btv325","article-title":"Diffusion maps for high-dimensional single-cell analysis of differentiation data","volume":"31","author":"Haghverdi","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B25","doi-asserted-by":"crossref","first-page":"525","DOI":"10.1137\/S0036144500378302","article-title":"An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations","volume":"43","author":"Higham","year":"2001","journal-title":"SIAM Rev"},{"key":"2023012712240510800_btx575-B26","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/nature18320","article-title":"Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios","volume":"535","author":"Hoppe","year":"2016","journal-title":"Nature"},{"key":"2023012712240510800_btx575-B27","doi-asserted-by":"crossref","first-page":"E4797","DOI":"10.1073\/pnas.1407388111","article-title":"Time-variant clustering model for understanding cell fate decisions","volume":"111","author":"Huang","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712240510800_btx575-B28","doi-asserted-by":"crossref","first-page":"e12776.","DOI":"10.1371\/journal.pone.0012776","article-title":"Inferring regulatory networks from expression data using tree-based methods","volume":"5","author":"Huynh-Thu","year":"2010","journal-title":"PLoS One"},{"key":"2023012712240510800_btx575-B29","doi-asserted-by":"crossref","first-page":"1614","DOI":"10.1093\/bioinformatics\/btu863","article-title":"Combining tree-based and dynamical systems for the inference of gene regulatory networks","volume":"31","author":"Huynh-Thu","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B30","doi-asserted-by":"crossref","first-page":"e117","DOI":"10.1093\/nar\/gkw430","article-title":"TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis","volume":"44","author":"Ji","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712240510800_btx575-B31","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/S0167-7152(97)00020-5","article-title":"A multivariate Kolmogorov\u2013Smirnov test of goodness of fit","volume":"35","author":"Justel","year":"1997","journal-title":"Stat. Probab. Lett"},{"key":"2023012712240510800_btx575-B32","doi-asserted-by":"crossref","first-page":"W96","DOI":"10.1093\/nar\/gkq418","article-title":"ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems","volume":"38","author":"Kaimal","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023012712240510800_btx575-B33","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/s13059-015-0692-3","article-title":"Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells","volume":"16","author":"Kim","year":"2015","journal-title":"Genome Biol"},{"year":"1995","author":"Kohavi","key":"2023012712240510800_btx575-B34"},{"key":"2023012712240510800_btx575-B35","doi-asserted-by":"crossref","first-page":"R118.","DOI":"10.1186\/gb-2013-14-10-r118","article-title":"Temporal dynamics and transcriptional control using single-cell gene expression analysis","volume":"14","author":"Kouno","year":"2013","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B36","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature13920","article-title":"Deconstructing transcriptional heterogeneity in pluripotent stem cells","volume":"516","author":"Kumar","year":"2014","journal-title":"Nature"},{"key":"2023012712240510800_btx575-B37","first-page":"364","article-title":"Network of mutually repressive metastasis regulators can promote cell heterogeneity and metastatic transitions","volume":"111","author":"Lee","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712240510800_btx575-B38","doi-asserted-by":"crossref","first-page":"355.","DOI":"10.1186\/s12859-016-1235-y","article-title":"BTR: training asynchronous Boolean models using single-cell expression data","volume":"17","author":"Lim","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"2023012712240510800_btx575-B39","doi-asserted-by":"crossref","first-page":"182","DOI":"10.12688\/f1000research.7223.1","article-title":"Single-cell transcriptome sequencing: recent advances and remaining challenges","volume":"5","author":"Liu","year":"2016","journal-title":"F1000Research"},{"key":"2023012712240510800_btx575-B41","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1089\/cmb.2008.09TT","article-title":"Generating realistic in silico gene networks for performance assessment of reverse engineering methods","volume":"16","author":"Marbach","year":"2009","journal-title":"J. Comput. Biol"},{"key":"2023012712240510800_btx575-B42","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/nmeth.2016","article-title":"Wisdom of crowds for robust gene network inference","volume":"9","author":"Marbach","year":"2012","journal-title":"Nat. Methods"},{"key":"2023012712240510800_btx575-B43","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1073\/pnas.1408993111","article-title":"Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape","volume":"111","author":"Marco","year":"2014","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023012712240510800_btx575-B44","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/01621459.1951.10500769","article-title":"The Kolmogorov\u2013Smirnov Test for Goodness of Fit","volume":"46","author":"Massey","year":"1951","journal-title":"J. Am. Stat. Assoc"},{"key":"2023012712240510800_btx575-B45","first-page":"76","article-title":"SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation","volume":"43","author":"Matsumoto","year":"2017","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B46","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nbt.3154","article-title":"Decoding the regulatory network of early blood development from single-cell gene expression measurements","volume":"33","author":"Moignard","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023012712240510800_btx575-B47","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1038\/nrg.2016.98","article-title":"Transition states and cell fate decisions in epigenetic landscapes","volume":"17","author":"Moris","year":"2016","journal-title":"Nat. Rev. Genet"},{"key":"2023012712240510800_btx575-B48","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/nri3470","article-title":"Specificity through cooperation: BATF\u2013IRF interactions control immune-regulatory networks","volume":"13","author":"Murphy","year":"2013","journal-title":"Nat. Rev. Immunol"},{"key":"2023012712240510800_btx575-B49","doi-asserted-by":"crossref","first-page":"i89","DOI":"10.1093\/bioinformatics\/btv257","article-title":"Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data","volume":"31","author":"Ocone","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B50","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.ifacol.2016.12.117","article-title":"Gene regulatory network inference using time-stamped cross-sectional single cell expression data","volume":"49","author":"Papili Gao","year":"2016","journal-title":"IFAC-PapersOnLine"},{"key":"2023012712240510800_btx575-B52","doi-asserted-by":"crossref","first-page":"iii","DOI":"10.1038\/nmeth.f.259","article-title":"Fluidigm Dynamic Arrays provide a platform for single-cell gene expression analysis","volume":"6","author":"Pieprzyk","year":"2009","journal-title":"Nat. Methods"},{"key":"2023012712240510800_btx575-B53","doi-asserted-by":"crossref","first-page":"241.","DOI":"10.1186\/s13059-015-0805-z","article-title":"ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis","volume":"16","author":"Pierson","year":"2015","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B54","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1016\/j.celrep.2015.05.016","article-title":"Single-cell network analysis identifies DDIT3 as a nodal lineage regulator in hematopoiesis","volume":"11","author":"Pina","year":"2015","journal-title":"Cell Rep"},{"key":"2023012712240510800_btx575-B55","doi-asserted-by":"crossref","first-page":"e12912.","DOI":"10.1371\/journal.pone.0012912","article-title":"From knockouts to networks: establishing direct cause-effect relationships through graph analysis","volume":"5","author":"Pinna","year":"2010","journal-title":"PLoS One"},{"key":"2023012712240510800_btx575-B56","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/nbt.2967","article-title":"Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex","volume":"32","author":"Pollen","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023012712240510800_btx575-B58","doi-asserted-by":"crossref","first-page":"e1002585.","DOI":"10.1371\/journal.pbio.1002585","article-title":"Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process","volume":"14","author":"Richard","year":"2016","journal-title":"PLOS Biol"},{"year":"2017","author":"Rosenberg","key":"2023012712240510800_btx575-B59"},{"key":"2023012712240510800_btx575-B60","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1038\/nature08243","article-title":"Developmental and species-divergent globin switching are driven by BCL11A","volume":"460","author":"Sankaran","year":"2009","journal-title":"Nature"},{"key":"2023012712240510800_btx575-B61","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.1093\/bioinformatics\/btr373","article-title":"GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods","volume":"27","author":"Schaffter","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B62","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/nature13437","article-title":"Single-cell RNA-seq reveals dynamic paracrine control of cellular variation","volume":"510","author":"Shalek","year":"2014","journal-title":"Nature"},{"key":"2023012712240510800_btx575-B63","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1111\/j.2517-6161.1951.tb00088.x","article-title":"The Interpretation of Interaction in Contingency Tables","volume":"13","author":"Simpson","year":"1951","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023012712240510800_btx575-B64","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/nrg3833","article-title":"Computational and analytical challenges in single-cell transcriptomics","volume":"16","author":"Stegle","year":"2015","journal-title":"Nat. Rev. Genet"},{"key":"2023012712240510800_btx575-B65","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1186\/1752-0509-5-177","article-title":"Inference of complex biological networks: distinguishability issues and optimization-based solutions","volume":"5","author":"Szederk\u00e9nyi","year":"2011","journal-title":"BMC Syst. Biol"},{"key":"2023012712240510800_btx575-B66","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/S0037-1963(00)90038-6","article-title":"Red blood cell surface adhesion molecules: their possible roles in normal human physiology and disease","volume":"37","author":"Telen","year":"2000","journal-title":"Semin. Hematol"},{"key":"2023012712240510800_btx575-B67","doi-asserted-by":"crossref","first-page":"e1003197.","DOI":"10.1371\/journal.pcbi.1003197","article-title":"Transcriptional regulation of lineage commitment\u2013a stochastic model of cell fate decisions","volume":"9","author":"Teles","year":"2013","journal-title":"PLoS Comput. Biol"},{"key":"2023012712240510800_btx575-B68","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression shrinkage and selection via the lasso","author":"Tibshirani","year":"1996","journal-title":"J R. Stat. Soc. B"},{"key":"2023012712240510800_btx575-B69","doi-asserted-by":"crossref","first-page":"R121.","DOI":"10.1186\/gb-2009-10-11-r121","article-title":"Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis","volume":"10","author":"Tomaru","year":"2009","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B70","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nbt.2859","article-title":"The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells","volume":"32","author":"Trapnell","year":"2014","journal-title":"Nat. Biotechnol"},{"key":"2023012712240510800_btx575-B71","doi-asserted-by":"crossref","first-page":"e103812.","DOI":"10.1371\/journal.pone.0103812","article-title":"Ensemble inference and inferability of gene regulatory networks","volume":"9","author":"Ud-Dean","year":"2014","journal-title":"PLoS One"},{"key":"2023012712240510800_btx575-B72","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1186\/s13059-016-0930-3","article-title":"Beyond comparisons of means: understanding changes in gene expression at the single-cell level","volume":"17","author":"Vallejos","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712240510800_btx575-B73","doi-asserted-by":"crossref","first-page":"8141","DOI":"10.1093\/nar\/gkq729","article-title":"Building promoter aware transcriptional regulatory networks using siRNA perturbation and deepCAGE","volume":"38","author":"Vitezic","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023012712240510800_btx575-B74","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1038\/nrg2509","article-title":"Stochastic modelling for quantitative description of heterogeneous biological systems","volume":"10","author":"Wilkinson","year":"2009","journal-title":"Nat. Rev. Genet"},{"key":"2023012712240510800_btx575-B75","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.csda.2016.07.014","article-title":"A fast algorithm for two-dimensional Kolmogorov\u2013Smirnov two sample tests","volume":"105","author":"Xiao","year":"2017","journal-title":"Comput. Stat. Data Anal"},{"key":"2023012712240510800_btx575-B76","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btv088","article-title":"Identification of cell types from single-cell transcriptomes using a novel clustering method","volume":"31","author":"Xu","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012712240510800_btx575-B77","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1016\/j.jmva.2009.09.017","article-title":"An unbiased Cp criterion for multivariate ridge regression","volume":"101","author":"Yanagihara","year":"2010","journal-title":"J. Multivar. Anal"},{"key":"2023012712240510800_btx575-B78","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","article-title":"Regularization and variable selection via the elastic net","volume":"67","author":"Zou","year":"2005","journal-title":"J. R. Stat. Soc. Ser. B"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/258\/48913242\/bioinformatics_34_2_258.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/2\/258\/48913242\/bioinformatics_34_2_258.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,26]],"date-time":"2024-06-26T22:56:39Z","timestamp":1719442599000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/2\/258\/4158033"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,14]]},"references-count":75,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2018,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx575","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/089110","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,1,15]]},"published":{"date-parts":[[2017,9,14]]}}}