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2021
Posfai E, Schell JPaul, Janiszewski A, Rovic I, Murray A, Bradshaw B, et al. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021 ;23(1):49-60.
Chen X, Robinson DG, Storey JD. The functional false discovery rate with applications to genomics. Biostatistics. 2021 ;22(1):68-81.
Li SHsin-Jung, Nofal M, Parsons LR, Rabinowitz JD, Gitai Z. Monitoring mammalian mitochondrial translation with MitoRiboSeq. Nat Protoc. 2021 ;16(6):2802-2825.
2020
Przytycki PF, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst. 2020 ;10(2):193-203.e4.
Nechay M, Kleiner RE. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020 ;54:37-44.
Menon R, Otto EA, Sealfon R, Nair V, Wong AK, Theesfeld CL, et al. SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease. Kidney Int. 2020 ;98(6):1502-1518.
Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, et al. Selective Neuronal Vulnerability in Alzheimer's Disease: A Network-Based Analysis. Neuron. 2020 ;107(5):821-835.e12.
Menon R, Otto EA, Hoover P, Eddy S, Mariani L, Godfrey B, et al. Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight. 2020 ;5(6).
Kaletsky R, Murphy CT. Transcriptional Profiling of C. elegans Adult Cells and Tissues with Age. Methods Mol Biol. 2020 ;2144:177-186.
2019
Zhou J, Schor IE, Yao V, Theesfeld CL, Marco-Ferreres R, Tadych A, et al. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019 ;15(9):e1008382.
Lee Y-S, Krishnan A, Oughtred R, Rust J, Chang CS, Ryu J, et al. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019 ;8(2):152-162.e6.
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).
Arey RN, Kaletsky R, Murphy CT. Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory. Sci Rep. 2019 ;9(1):20314.
2018
Painter HJ, Chung NChristophe, Sebastian A, Albert I, Storey JD, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun. 2018 ;9(1):2656.
Fröhlich KS, Förstner KU, Gitai Z. Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res. 2018 ;46(20):10969-10982.
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
Pomeranz LE, Ekstrand MI, Latcha KN, Smith GA, Enquist LW, Friedman JM. Gene Expression Profiling with Cre-Conditional Pseudorabies Virus Reveals a Subset of Midbrain Neurons That Participate in Reward Circuitry. J Neurosci. 2017 ;37(15):4128-4144.
Celià-Terrassa T, Liu DD, Choudhury A, Hang X, Wei Y, Zamalloa J, et al.. Normal and cancerous mammary stem cells evade interferon-induced constraint through the miR-199a-LCOR axis. Nat Cell Biol. 2017 ;19(6):711-723.
Son HG, Seo M, Ham S, Hwang W, Lee D, An SWoo A, et al. RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans. Nat Commun. 2017 ;8:14749.
Wilson MZ, Ravindran PT, Lim WA, Toettcher JE. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017 ;67(5):757-769.e5.
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.
Henry TC, Brynildsen MP. Development of Persister-FACSeq: a method to massively parallelize quantification of persister physiology and its heterogeneity. Sci Rep. 2016 ;6:25100.
Matthews BJ, McBride CS, DeGennaro M, Despo O, Vosshall LB. The neurotranscriptome of the Aedes aegypti mosquito. BMC Genomics. 2016 ;17:32.
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.