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2021
Bass AJ, Storey JD. The optimal discovery procedure for significance analysis of general gene expression studies. Bioinformatics. 2021 ;37(3):367-374.
2020
Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, et al. RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. N Engl J Med. 2020 ;383(3):218-228.
2019
Gaska JM, Parsons L, Balev M, Cirincione A, Wang W, Schwartz RE, et al. Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. Life Sci Alliance. 2019 ;2(5).
Chan MM, Smith ZD, Grosswendt S, Kretzmer H, Norman TM, Adamson B, et al. Molecular recording of mammalian embryogenesis. Nature. 2019 ;570(7759):77-82.
2018
Kaletsky R, Yao V, Williams A, Runnels AM, Tadych A, Zhou S, et al. Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression. PLoS Genet. 2018 ;14(8):e1007559.
2017
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.
2016
Crocker A, Guan X-J, Murphy CT, 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.
Adamson B, Norman TM, Jost M, Cho MY, Nuñez JK, Chen Y, et al.. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016 ;167(7):1867-1882.e21.
Dixit A, Parnas O, Li B, Chen J, Fulco CP, Jerby-Arnon L, et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016 ;167(7):1853-1866.e17.
Charruau P, Johnston RA, Stahler DR, Lea A, Snyder-Mackler N, Smith DW, et al. Pervasive Effects of Aging on Gene Expression in Wild Wolves. Mol Biol Evol. 2016 ;33(8):1967-78.
2015
Papenfort K, Förstner KU, Cong J-P, Sharma CM, Bassler BL. 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.
Robinson JL, Brynildsen MP. 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.
Robinson DG, Wang JY, Storey JD. A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays. Nucleic Acids Res. 2015 ;43(20):e131.
2014
Rogers RL, Shao L, Sanjak JS, Andolfatto P, Thornton KR. Revised annotations, sex-biased expression, and lineage-specific genes in the Drosophila melanogaster group. G3 (Bethesda). 2014 ;4(12):2345-51.
Robinson DG, Storey JD. subSeq: determining appropriate sequencing depth through efficient read subsampling. Bioinformatics. 2014 ;30(23):3424-6.