1.Zhou J, Troyanskaya O. An analytical framework for interpretable and generalizable single-cell data analysis. Nat Methods. 2021;18(11):1317–1321. PMCID: PMC8959118 Reference Link
1.Lee E, Kang Y. Lineage tracing reveals metastatic dynamics. Cancer Cell. 2021;39(8):1050–1052. PMID: 34171265 Reference Link
1.Bass A, Storey J. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. 2021;37(3):367–374. PMCID: PMC8058779 Reference Link
1.Orange D, Yao V, Sawicka K, Fak J, Frank M, Parveen S, Blachere N, Hale C, Zhang F, Raychaudhuri S, Troyanskaya O, Darnell R. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. N Engl J Med. 2020;383(3):218–228. PMCID: PMC7546156 Reference Link
1.Gaska J, Parsons L, Balev M, Cirincione A, Wang W, Schwartz R, Ploss A. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance. 2019;2(5). PMCID: PMC6814850 Reference Link
1.Chan M, Smith Z, Grosswendt S, Kretzmer H, Norman T, Adamson B, Jost M, Quinn J, Yang D, Jones M, Khodaverdian A, Yosef N, Meissner A, Weissman J. Molecular recording of mammalian embryogenesis. Nature. 2019;570(7759):77–82. PMCID: PMC7229772 Reference Link
1.Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A iv. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167(7):1853–1866.e17. PMCID: PMC5181115 Reference Link
1.Adamson B, Norman T, Jost M, Cho M, Nuñez J, Chen Y, Villalta J, Gilbert L, Horlbeck M, Hein M, Pak R, Gray A, Gross C, Dixit A, Parnas O, Regev A iv, Weissman J. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016;167(7):1867–1882.e21. PMCID: PMC5315571 Reference Link
1.Kaletsky R, Yao V, Williams A, Runnels A, Tadych A, Zhou S, Troyanskaya O, Murphy C. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet. 2018;14(8):e1007559. PMCID: PMC6105014 Reference Link
1.Charruau P, Johnston R, Stahler D, Lea A, Snyder-Mackler N, Smith D, vonHoldt B, Cole S, Tung J, Wayne R. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016;33(8):1967–78. PMCID: PMC5854094 Reference Link
1.Pritykin Y, Brito T, Schüpbach T, Singh M, Pane A. Integrative analysis unveils new functions for the Cutoff protein in noncoding RNA biogenesis and gene regulation. RNA. 2017;23(7):1097–1109. PMCID: PMC5473144 Reference Link
1.Robinson J, Brynildsen M. An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli. Metab Eng. 2015;31:22–34. PMID: 26112956 Reference Link
1.Crocker A, Guan X-J, Murphy C, Murthy M. Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression. Cell Rep. 2016;15(7):1580–1596. PMCID: PMC5047377 Reference Link
1.Robinson D, Storey J. subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics. 2014;30(23):3424–6. PMCID: PMC4296149 Reference Link
1.Robinson D, Wang J, Storey J. A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays. Nucleic Acids Res. 2015;43(20):e131. PMCID: PMC4787771 Reference Link
1.Rogers R, Shao L, Sanjak J, Andolfatto P, Thornton K. Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3 (Bethesda). 2014;4(12):2345–51. PMCID: PMC4267930 Reference Link
1.Papenfort K, Förstner K, Cong J-P, Sharma C, Bassler B. Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Proc Natl Acad Sci U S A. 2015;112(7):E766–75. PMCID: PMC4343088 Reference Link