Single Cell Omics Data Analysis ------------------------------- (x in front of a number means the paper has been chosen.) (Some review papers are listed at the end.) 1: Rahmani E, Schweiger R, Shenhav L, Wingert T, Hofer I, Gabel E, Eskin E, Halperin E. BayesCCE: a Bayesian framework for estimating cell-type composition from DNA methylation without the need for methylation reference. Genome Biol. 2018 Sep 21;19(1):141. doi: 10.1186/s13059-018-1513-2. PubMed PMID: 30241486; PubMed Central PMCID: PMC6151042. 2: Arzalluz-Luque ??, Conesa A. Single-cell RNAseq for the study of isoforms-how is that possible? Genome Biol. 2018 Aug 10;19(1):110. doi: 10.1186/s13059-018-1496-z. Review. PubMed PMID: 30097058; PubMed Central PMCID: PMC6085759. 3: Wan Y, Larson DR. Splicing heterogeneity: separating signal from noise. Genome Biol. 2018 Jul 9;19(1):86. doi: 10.1186/s13059-018-1467-4. PubMed PMID: 29986741; PubMed Central PMCID: PMC6036703. 4: Morgan MD, Marioni JC. CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness. Genome Biol. 2018 Jun 26;19(1):81. doi: 10.1186/s13059-018-1461-x. PubMed PMID: 29945659; PubMed Central PMCID: PMC6020341. x5: Chuai G, Ma H, Yan J, Chen M, Hong N, Xue D, Zhou C, Zhu C, Chen K, Duan B, Gu F, Qu S, Huang D, Wei J, Liu Q. DeepCRISPR: optimized CRISPR guide RNA design by deep learning. Genome Biol. 2018 Jun 26;19(1):80. doi: 10.1186/s13059-018-1459-4. PubMed PMID: 29945655; PubMed Central PMCID: PMC6020378. 6: Petukhov V, Guo J, Baryawno N, Severe N, Scadden DT, Samsonova MG, Kharchenko PV. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome Biol. 2018 Jun 19;19(1):78. doi: 10.1186/s13059-018-1449-6. PubMed PMID: 29921301; PubMed Central PMCID: PMC6010209. x7: Chen W, Li Y, Easton J, Finkelstein D, Wu G, Chen X. UMI-count modeling and differential expression analysis for single-cell RNA sequencing. Genome Biol. 2018 May 31;19(1):70. doi: 10.1186/s13059-018-1438-9. PubMed PMID: 29855333; PubMed Central PMCID: PMC5984373. 8: Anvar SY, Allard G, Tseng E, Sheynkman GM, de Klerk E, Vermaat M, Yin RH, Johansson HE, Ariyurek Y, den Dunnen JT, Turner SW, 't Hoen PAC. Full-length mRNA sequencing uncovers a widespread coupling between transcription initiation and mRNA processing. Genome Biol. 2018 Mar 29;19(1):46. doi: 10.1186/s13059-018-1418-0. PubMed PMID: 29598823; PubMed Central PMCID: PMC5877393. 9: Sasagawa Y, Danno H, Takada H, Ebisawa M, Tanaka K, Hayashi T, Kurisaki A, Nikaido I. Quartz-Seq2: a high-throughput single-cell RNA-sequencing method that effectively uses limited sequence reads. Genome Biol. 2018 Mar 9;19(1):29. doi: 10.1186/s13059-018-1407-3. PubMed PMID: 29523163; PubMed Central PMCID: PMC5845169. 10: Van den Berge K, Perraudeau F, Soneson C, Love MI, Risso D, Vert JP, Robinson MD, Dudoit S, Clement L. Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications. Genome Biol. 2018 Feb 26;19(1):24. doi: 10.1186/s13059-018-1406-4. PubMed PMID: 29478411. 11: Wolf FA, Angerer P, Theis FJ. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 2018 Feb 6;19(1):15. doi: 10.1186/s13059-017-1382-0. PubMed PMID: 29409532; PubMed Central PMCID: PMC5802054. 12: Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq. Genome Biol. 2017 Nov 7;18(1):212. doi: 10.1186/s13059-017-1334-8. PubMed PMID: 29115968; PubMed Central PMCID: PMC5674756. 13: Zafar H, Tzen A, Navin N, Chen K, Nakhleh L. SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models. Genome Biol. 2017 Sep 19;18(1):178. doi: 10.1186/s13059-017-1311-2. PubMed PMID: 28927434; PubMed Central PMCID: PMC5606061. 14: Zappia L, Phipson B, Oshlack A. Splatter: simulation of single-cell RNA sequencing data. Genome Biol. 2017 Sep 12;18(1):174. doi: 10.1186/s13059-017-1305-0. PubMed PMID: 28899397; PubMed Central PMCID: PMC5596896. 15: G??mez-Schiavon M, Chen LF, West AE, Buchler NE. BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells. Genome Biol. 2017 Sep 4;18(1):164. doi: 10.1186/s13059-017-1297-9. PubMed PMID: 28870226; PubMed Central PMCID: PMC5582403. 16: Welch JD, Hartemink AJ, Prins JF. MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. Genome Biol. 2017 Jul 24;18(1):138. doi: 10.1186/s13059-017-1269-0. PubMed PMID: 28738873; PubMed Central PMCID: PMC5525279. 17: Ponnaluri VKC, Zhang G, Est??ve PO, Spracklin G, Sian S, Xu SY, Benoukraf T, Pradhan S. NicE-seq: high resolution open chromatin profiling. Genome Biol. 2017 Jun 28;18(1):122. doi: 10.1186/s13059-017-1247-6. PubMed PMID: 28655330; PubMed Central PMCID: PMC5488340. 18: Huang Y, Sanguinetti G. BRIE: transcriptome-wide splicing quantification in single cells. Genome Biol. 2017 Jun 27;18(1):123. doi: 10.1186/s13059-017-1248-5. PubMed PMID: 28655331; PubMed Central PMCID: PMC5488362. 19: Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 May 8;18(1):84. doi: 10.1186/s13059-017-1218-y. Review. PubMed PMID: 28482897; PubMed Central PMCID: PMC5421338. 20: Jiang Y, Zhang NR, Li M. SCALE: modeling allele-specific gene expression by single-cell RNA sequencing. Genome Biol. 2017 Apr 26;18(1):74. doi: 10.1186/s13059-017-1200-8. PubMed PMID: 28446220; PubMed Central PMCID: PMC5407026. x21: Angermueller C, Lee HJ, Reik W, Stegle O. DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning. Genome Biol. 2017 Apr 11;18(1):67. doi: 10.1186/s13059-017-1189-z. Erratum in: Genome Biol. 2017 May 12;18(1):90. PubMed PMID: 28395661; PubMed Central PMCID: PMC5387360. x22: Lin P, Troup M, Ho JW. CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data. Genome Biol. 2017 Mar 28;18(1):59. doi: 10.1186/s13059-017-1188-0. PubMed PMID: 28351406; PubMed Central PMCID: PMC5371246. 23: Salehi S, Steif A, Roth A, Aparicio S, Bouchard-C??t?? A, Shah SP. ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data. Genome Biol. 2017 Mar 1;18(1):44. doi: 10.1186/s13059-017-1169-3. PubMed PMID: 28249593; PubMed Central PMCID: PMC5333399. 24: de Santiago I, Liu W, Yuan K, O'Reilly M, Chilamakuri CS, Ponder BA, Meyer KB, Markowetz F. BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes. Genome Biol. 2017 Feb 24;18(1):39. doi: 10.1186/s13059-017-1165-7. PubMed PMID: 28235418; PubMed Central PMCID: PMC5326502. 25: Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY. Single-cell epigenomic variability reveals functional cancer heterogeneity. Genome Biol. 2017 Jan 24;18(1):15. doi: 10.1186/s13059-016-1133-7. PubMed PMID: 28118844; PubMed Central PMCID: PMC5259890. 26: Chen L, Jin P, Qin ZS. DIVAN: accurate identification of non-coding disease-specific risk variants using multi-omics profiles. Genome Biol. 2016 Dec 6;17(1):252. PubMed PMID: 27923386; PubMed Central PMCID: PMC5139035. 27: Nelms BD, Waldron L, Barrera LA, Weflen AW, Goettel JA, Guo G, Montgomery RK, Neutra MR, Breault DT, Snapper SB, Orkin SH, Bulyk ML, Huttenhower C, Lencer WI. CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types. Genome Biol. 2016 Sep 29;17(1):201. PubMed PMID: 27687735; PubMed Central PMCID: PMC5043525. 28: Jiang L, Chen H, Pinello L, Yuan GC. GiniClust: detecting rare cell types from single-cell gene expression data with Gini index. Genome Biol. 2016 Jul 1;17(1):144. doi: 10.1186/s13059-016-1010-4. PubMed PMID: 27368803; PubMed Central PMCID: PMC4930624. 29: Davis A, Navin NE. Computing tumor trees from single cells. Genome Biol. 2016 May 26;17(1):113. doi: 10.1186/s13059-016-0987-z. PubMed PMID: 27230879; PubMed Central PMCID: PMC4881295. 30: Ntranos V, Kamath GM, Zhang JM, Pachter L, Tse DN. Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. Genome Biol. 2016 May 26;17(1):112. doi: 10.1186/s13059-016-0970-8. PubMed PMID: 27230763; PubMed Central PMCID: PMC4881296. 31: Welch JD, Hartemink AJ, Prins JF. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biol. 2016 May 23;17(1):106. doi: 10.1186/s13059-016-0975-3. PubMed PMID: 27215581; PubMed Central PMCID: PMC4877799. 32: Crow M, Paul A, Ballouz S, Huang ZJ, Gillis J. Exploiting single-cell expression to characterize co-expression replicability. Genome Biol. 2016 May 6;17:101. doi: 10.1186/s13059-016-0964-6. PubMed PMID: 27165153; PubMed Central PMCID: PMC4862082. 33: Hu Y, Huang K, An Q, Du G, Hu G, Xue J, Zhu X, Wang CY, Xue Z, Fan G. Simultaneous profiling of transcriptome and DNA methylome from a single cell. Genome Biol. 2016 May 5;17:88. doi: 10.1186/s13059-016-0950-z. PubMed PMID: 27150361; PubMed Central PMCID: PMC4858893. 34: Jahn K, Kuipers J, Beerenwinkel N. Tree inference for single-cell data. Genome Biol. 2016 May 5;17:86. doi: 10.1186/s13059-016-0936-x. PubMed PMID: 27149953; PubMed Central PMCID: PMC4858868. 35: Hashimshony T, Senderovich N, Avital G, Klochendler A, de Leeuw Y, Anavy L, Gennert D, Li S, Livak KJ, Rozenblatt-Rosen O, Dor Y, Regev A, Yanai I. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome Biol. 2016 Apr 28;17:77. doi: 10.1186/s13059-016-0938-8. PubMed PMID: 27121950; PubMed Central PMCID: PMC4848782. 36: Clark SJ, Lee HJ, Smallwood SA, Kelsey G, Reik W. Single-cell epigenomics: powerful new methods for understanding gene regulation and cell identity. Genome Biol. 2016 Apr 18;17:72. doi: 10.1186/s13059-016-0944-x. Review. PubMed PMID: 27091476; PubMed Central PMCID: PMC4834828. 37: Vallejos CA, Richardson S, Marioni JC. Beyond comparisons of means: understanding changes in gene expression at the single-cell level. Genome Biol. 2016 Apr 15;17:70. doi: 10.1186/s13059-016-0930-3. PubMed PMID: 27083558; PubMed Central PMCID: PMC4832562. 38: Ross EM, Markowetz F. OncoNEM: inferring tumor evolution from single-cell sequencing data. Genome Biol. 2016 Apr 15;17:69. doi: 10.1186/s13059-016-0929-9. PubMed PMID: 27083415; PubMed Central PMCID: PMC4832472. 39: Liu SJ, Nowakowski TJ, Pollen AA, Lui JH, Horlbeck MA, Attenello FJ, He D, Weissman JS, Kriegstein AR, Diaz AA, Lim DA. Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 2016 Apr 14;17:67. doi: 10.1186/s13059-016-0932-1. PubMed PMID: 27081004; PubMed Central PMCID: PMC4831157. 40: Ma Q, Chang HY. Single-cell profiling of lncRNAs in the developing human brain. Genome Biol. 2016 Apr 14;17:68. doi: 10.1186/s13059-016-0933-0. PubMed PMID: 27079200; PubMed Central PMCID: PMC4831122. 41: Bacher R, Kendziorski C. Design and computational analysis of single-cell RNA-sequencing experiments. Genome Biol. 2016 Apr 7;17:63. doi: 10.1186/s13059-016-0927-y. Review. PubMed PMID: 27052890; PubMed Central PMCID: PMC4823857. x42: Sekelja M, Paulsen J, Collas P. 4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation? Genome Biol. 2016 Apr 7;17:54. doi: 10.1186/s13059-016-0923-2. Review. PubMed PMID: 27052789; PubMed Central PMCID: PMC4823877. 43: Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Classification of low quality cells from single-cell RNA-seq data. Genome Biol. 2016 Feb 17;17:29. doi: 10.1186/s13059-016-0888-1. PubMed PMID: 26887813; PubMed Central PMCID: PMC4758103. 44: Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 2015 Dec 10;16:278. doi: 10.1186/s13059-015-0844-5. PubMed PMID: 26653891; PubMed Central PMCID: PMC4676162. 45: Pierson E, Yau C. ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 2015 Nov 2;16:241. doi: 10.1186/s13059-015-0805-z. PubMed PMID: 26527291; PubMed Central PMCID: PMC4630968. 46: Iacono G, Mereu E, Guillaumet-Adkins A, Corominas R, Cusc?? I, Rodr??guez-Esteban G, Gut M, P??rez-Jurado LA, Gut I, Heyn H. bigSCale: an analytical framework for big-scale single-cell data. Genome Res. 2018 Jun;28(6):878-890. doi: 10.1101/gr.230771.117. Epub 2018 May 3. PubMed PMID: 29724792; PubMed Central PMCID: PMC5991513. 48: Ding J, Aronow BJ, Kaminski N, Kitzmiller J, Whitsett JA, Bar-Joseph Z. Reconstructing differentiation networks and their regulation from time series single-cell expression data. Genome Res. 2018 Jan 9. doi: 10.1101/gr.225979.117. [Epub ahead of print] PubMed PMID: 29317474; PubMed Central PMCID: PMC5848617. 49: Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976. 50: Derr A, Yang C, Zilionis R, Sergushichev A, Blodgett DM, Redick S, Bortell R, Luban J, Harlan DM, Kadener S, Greiner DL, Klein A, Artyomov MN, Garber M. End Sequence Analysis Toolkit (ESAT) expands the extractable information from single-cell RNA-seq data. Genome Res. 2016 Oct;26(10):1397-1410. Epub 2016 Jul 28. PubMed PMID: 27470110; PubMed Central PMCID: PMC5052061. 51: Zhang XO, Dong R, Zhang Y, Zhang JL, Luo Z, Zhang J, Chen LL, Yang L. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Res. 2016 Sep;26(9):1277-87. doi: 10.1101/gr.202895.115. Epub 2016 Jun 30. PubMed PMID: 27365365; PubMed Central PMCID: PMC5052039. 52: Keren L, van Dijk D, Weingarten-Gabbay S, Davidi D, Jona G, Weinberger A, Milo R, Segal E. Noise in gene expression is coupled to growth rate. Genome Res. 2015 Dec;25(12):1893-902. doi: 10.1101/gr.191635.115. Epub 2015 Sep 9. PubMed PMID: 26355006; PubMed Central PMCID: PMC4665010. 53: Nawy T. Tumor genetic analysis from single-cell RNA-seq data. Nat Methods. 2018 Aug;15(8):571. doi: 10.1038/s41592-018-0089-9. PubMed PMID: 30065381. 54: Lindeman I, Emerton G, Mamanova L, Snir O, Polanski K, Qiao SW, Sollid LM, Teichmann SA, Stubbington MJT. BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. Nat Methods. 2018 Aug;15(8):563-565. doi: 10.1038/s41592-018-0082-3. PubMed PMID: 30065371. 55: Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR. SAVER: gene expression recovery for single-cell RNA sequencing. Nat Methods. 2018 Jul;15(7):539-542. doi: 10.1038/s41592-018-0033-z. Epub 2018 Jun 25. PubMed PMID: 29941873; PubMed Central PMCID: PMC6030502. 56: Adiconis X, Haber AL, Simmons SK, Levy Moonshine A, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ. Comprehensive comparative analysis of 5'-end RNA-sequencing methods. Nat Methods. 2018 Jul;15(7):505-511. doi: 10.1038/s41592-018-0014-2. Epub 2018 Jun 4. PubMed PMID: 29867192; PubMed Central PMCID: PMC6075671. 57: Kiselev VY, Yiu A, Hemberg M. scmap: projection of single-cell RNA-seq data across data sets. Nat Methods. 2018 May;15(5):359-362. doi: 10.1038/nmeth.4644. Epub 2018 Apr 2. PubMed PMID: 29608555. x58: Edsg??rd D, Johnsson P, Sandberg R. Identification of spatial expression trends in single-cell gene expression data. Nat Methods. 2018 May;15(5):339-342. doi: 10.1038/nmeth.4634. Epub 2018 Mar 19. PubMed PMID: 29553578. 59: Alpert A, Moore LS, Dubovik T, Shen-Orr SS. Alignment of single-cell trajectories to compare cellular expression dynamics. Nat Methods. 2018 Apr;15(4):267-270. doi: 10.1038/nmeth.4628. Epub 2018 Mar 12. PubMed PMID: 29529018. 60: Soneson C, Robinson MD. Bias, robustness and scalability in single-cell differential expression analysis. Nat Methods. 2018 Apr;15(4):255-261. doi: 10.1038/nmeth.4612. Epub 2018 Feb 26. PubMed PMID: 29481549. 61: Aibar S, Gonz??lez-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, Rambow F, Marine JC, Geurts P, Aerts J, van den Oord J, Atak ZK, Wouters J, Aerts S. SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9. PubMed PMID: 28991892; PubMed Central PMCID: PMC5937676. 62: Woyke T, Doud DFR, Schulz F. The trajectory of microbial single-cell sequencing. Nat Methods. 2017 Oct 31;14(11):1045-1054. doi: 10.1038/nmeth.4469. Review. PubMed PMID: 29088131. 63: Schep AN, Wu B, Buenrostro JD, Greenleaf WJ. chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data. Nat Methods. 2017 Oct;14(10):975-978. doi: 10.1038/nmeth.4401. Epub 2017 Aug 21. PubMed PMID: 28825706; PubMed Central PMCID: PMC5623146. x64: Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C. Reversed graph embedding resolves complex single-cell trajectories. Nat Methods. 2017 Oct;14(10):979-982. doi: 10.1038/nmeth.4402. Epub 2017 Aug 21. PubMed PMID: 28825705; PubMed Central PMCID: PMC5764547. x65: Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC. Normalizing single-cell RNA sequencing data: challenges and opportunities. Nat Methods. 2017 Jun;14(6):565-571. doi: 10.1038/nmeth.4292. Epub 2017 May 15. PubMed PMID: 28504683; PubMed Central PMCID: PMC5549838. x66: Bacher R, Chu LF, Leng N, Gasch AP, Thomson JA, Stewart RM, Newton M, Kendziorski C. SCnorm: robust normalization of single-cell RNA-seq data. Nat Methods. 2017 Jun;14(6):584-586. doi: 10.1038/nmeth.4263. Epub 2017 Apr 17. PubMed PMID: 28418000; PubMed Central PMCID: PMC5473255. 67: Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. SC3: consensus clustering of single-cell RNA-seq data. Nat Methods. 2017 May;14(5):483-486. doi: 10.1038/nmeth.4236. Epub 2017 Mar 27. PubMed PMID: 28346451; PubMed Central PMCID: PMC5410170. 68: Dong X, Zhang L, Milholland B, Lee M, Maslov AY, Wang T, Vijg J. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nat Methods. 2017 May;14(5):491-493. doi: 10.1038/nmeth.4227. Epub 2017 Mar 20. PubMed PMID: 28319112; PubMed Central PMCID: PMC5408311. 69: Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Power analysis of single-cell RNA-sequencing experiments. Nat Methods. 2017 Apr;14(4):381-387. doi: 10.1038/nmeth.4220. Epub 2017 Mar 6. PubMed PMID: 28263961; PubMed Central PMCID: PMC5376499. x70: Wang B, Zhu J, Pierson E, Ramazzotti D, Batzoglou S. Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nat Methods. 2017 Apr;14(4):414-416. doi: 10.1038/nmeth.4207. Epub 2017 Mar 6. PubMed PMID: 28263960. 71: Vitak SA, Torkenczy KA, Rosenkrantz JL, Fields AJ, Christiansen L, Wong MH, Carbone L, Steemers FJ, Adey A. Sequencing thousands of single-cell genomes with combinatorial indexing. Nat Methods. 2017 Mar;14(3):302-308. doi: 10.1038/nmeth.4154. Epub 2017 Jan 30. PubMed PMID: 28135258; PubMed Central PMCID: PMC5908213. 72: Qiu X, Hill A, Packer J, Lin D, Ma YA, Trapnell C. Single-cell mRNA quantification and differential analysis with Census. Nat Methods. 2017 Mar;14(3):309-315. doi: 10.1038/nmeth.4150. Epub 2017 Jan 23. PubMed PMID: 28114287; PubMed Central PMCID: PMC5330805. 73: Haghverdi L, B??ttner M, Wolf FA, Buettner F, Theis FJ. Diffusion pseudotime robustly reconstructs lineage branching. Nat Methods. 2016 Oct;13(10):845-8. doi: 10.1038/nmeth.3971. Epub 2016 Aug 29. PubMed PMID: 27571553. 74: Navin NE, Chen K. Genotyping tumor clones from single-cell data. Nat Methods. 2016 Jun 29;13(7):555-6. doi: 10.1038/nmeth.3903. PubMed PMID: 27355792. 75: Frei AP, Bava FA, Zunder ER, Hsieh EW, Chen SY, Nolan GP, Gherardini PF. Highly multiplexed simultaneous detection of RNAs and proteins in single cells. Nat Methods. 2016 Mar;13(3):269-75. doi: 10.1038/nmeth.3742. Epub 2016 Jan 25. PubMed PMID: 26808670; PubMed Central PMCID: PMC4767631. 76: Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV. Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat Methods. 2016 Mar;13(3):241-4. doi: 10.1038/nmeth.3734. Epub 2016 Jan 18. PubMed PMID: 26780092; PubMed Central PMCID: PMC4772672. 77: Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018 Jun;36(5):411-420. doi: 10.1038/nbt.4096. Epub 2018 Apr 2. PubMed PMID: 29608179. 78: Raj B, Wagner DE, McKenna A, Pandey S, Klein AM, Shendure J, Gagnon JA, Schier AF. Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol. 2018 Jun;36(5):442-450. doi: 10.1038/nbt.4103. Epub 2018 Mar 28. PubMed PMID: 29608178; PubMed Central PMCID: PMC5938111. 79: Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. 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