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Gene Expression Profiling

  • 1.
    Li S, Nofal M, Parsons L, Rabinowitz J, Gitai Z. Monitoring mammalian mitochondrial translation with MitoRiboSeq. Nat Protoc. 2021;16(6):2802–2825. PMCID: PMC8610098
    Reference Link
  • 1.
    Posfai E, Schell J, Janiszewski A, Rovic I, Murray A, Bradshaw B, Yamakawa T, Pardon T, Bakkali M, Talon I, De Geest N, Kumar P, To S, Petropoulos S, Jurisicova A, Pasque V, Lanner F, Rossant J. Evaluating totipotency using criteria of increasing stringency. Nat Cell Biol. 2021;23(1):49–60. PMCID: 2846056
    Reference Link
  • 1.
    Menon R, Otto E, Sealfon R, Nair V, Wong A, Theesfeld C, Chen X, Wang Y, Boppana A, Luo J, Yang Y, Kasson P, Schaub J, Berthier C, Eddy S, Lienczewski C, Godfrey B, Dagenais S, Sohaney R, Hartman J, Fermin D, Subramanian L, Looker H, Harder J, Mariani L, Hodgin J, Sexton J, Wobus C, Naik A, Nelson R, Troyanskaya O, Kretzler M. SARS-CoV-2 receptor networks in diabetic and COVID-19-associated kidney disease. Kidney Int. 2020;98(6):1502–1518. PMCID: PMC7543950
    Reference Link
  • 1.
    Roussarie J-P, Yao V, Rodriguez-Rodriguez P, Oughtred R, Rust J, Plautz Z, Kasturia S, Albornoz C, Wang W, Schmidt E, Dannenfelser R, Tadych A, Brichta L, Barnea-Cramer A, Heintz N, Hof P, Heiman M, Dolinski K, Flajolet M, Troyanskaya O, Greengard P. Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis. Neuron. 2020;107(5):821–835.e12. PMCID: PMC7580783
    Reference Link
  • 1.
    Kaletsky R, Murphy C. Transcriptional Profiling of C. elegans Adult Cells and Tissues with Age. Methods Mol Biol. 2020;2144:177–186. PMID: 32410035
    Reference Link
  • 1.
    Menon R, Otto E, Hoover P, Eddy S, Mariani L, Godfrey B, Berthier C, Eichinger F, Subramanian L, Harder J, Ju W, Nair V, Larkina M, Naik A, Luo J, Jain S, Sealfon R, Troyanskaya O, Hacohen N, Hodgin J, Kretzler M, Kpmp K, Nephrotic Syndrome Study Network (NEPTUNE). Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker. JCI Insight. 2020;5(6). PMCID: PMC7213795
    Reference Link
  • 1.
    Przytycki P, Singh M. Differential Allele-Specific Expression Uncovers Breast Cancer Genes Dysregulated by Cis Noncoding Mutations. Cell Syst. 2020;10(2):193–203.e4. PMCID: PMC7457951
    Reference Link
  • 1.
    Arey R, Kaletsky R, Murphy C. Nervous system-wide profiling of presynaptic mRNAs reveals regulators of associative memory. Sci Rep. 2019;9(1):20314. PMCID: PMC6937282
    Reference Link
  • 1.
    Nechay M, Kleiner R. High-throughput approaches to profile RNA-protein interactions. Curr Opin Chem Biol. 2020;54:37–44. PMCID: PMC7131871
    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.
    Zhou J, Schor I, Yao V, Theesfeld C, Marco-Ferreres R, Tadych A, Furlong E, Troyanskaya O. Accurate genome-wide predictions of spatio-temporal gene expression during embryonic development. PLoS Genet. 2019;15(9):e1008382. PMCID: PMC6779412
    Reference Link
  • 1.
    Chen X, Robinson D, Storey J. The functional false discovery rate with applications to genomics. Biostatistics. 2021;22(1):68–81. PMCID: PMC7846131
    Reference Link
  • 1.
    Lee Y-S, Krishnan A, Oughtred R, Rust J, Chang C, Ryu J, Kristensen V, Dolinski K, Theesfeld C, Troyanskaya O. A Computational Framework for Genome-wide Characterization of the Human Disease Landscape. Cell Syst. 2019;8(2):152–162.e6. PMCID: PMC7374759
    Reference Link
  • 1.
    Fröhlich K, Förstner K, Gitai Z. Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Nucleic Acids Res. 2018;46(20):10969–10982. PMCID: PMC6237742
    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.
    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.
    Painter H, Chung N, Sebastian A, Albert I, Storey J, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun. 2018;9(1):2656. PMCID: PMC6037754
    Reference Link
  • 1.
    Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080
    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.
    Celià-Terrassa T, Liu D, Choudhury A, Hang X, Wei Y, Zamalloa J, Alfaro-Aco R, Chakrabarti R, Jiang Y-Z, Koh B, Smith H, DeCoste C, Li J-J, Shao Z-M, Kang Y. Normal and cancerous mammary stem cells evade interferon-induced constraint through the miR-199a-LCOR axis. Nat Cell Biol. 2017;19(6):711–723. PMCID: PMC5481166
    Reference Link
  • 1.
    Pomeranz L, Ekstrand M, Latcha K, Smith G, Enquist L, Friedman J. 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. PMCID: PMC5391685
    Reference Link
  • 1.
    Son H, Seo M, Ham S, Hwang W, Lee D, An S, Artan M, Seo K, Kaletsky R, Arey R, Ryu Y, Ha C, Kim Y, Murphy C, Roh T-Y, Nam H, Lee S-J. 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. PMCID: PMC5347137
    Reference Link
  • 1.
    Henry T, Brynildsen M. Development of Persister-FACSeq: a method to massively parallelize quantification of persister physiology and its heterogeneity. Sci Rep. 2016;6:25100. PMCID: PMC4855238
    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.
    Chung N, Storey J. Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics. 2015;31(4):545–54. PMCID: PMC4325543
    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.
    McBride C, Baier F, Omondi A, Spitzer S, Lutomiah J, Sang R, Ignell R, Vosshall L. Evolution of mosquito preference for humans linked to an odorant receptor. Nature. 2014;515(7526):222–7. PMCID: PMC4286346
    Reference Link
  • 1.
    Matthews B, McBride C, DeGennaro M, Despo O, Vosshall L. The neurotranscriptome of the Aedes aegypti mosquito. BMC Genomics. 2016;17:32. PMCID: PMC4704297
    Reference Link
  • 1.
    Digianantonio K, Hecht M. A protein constructed de novo enables cell growth by altering gene regulation. Proc Natl Acad Sci U S A. 2016;113(9):2400–5. PMCID: PMC4780649
    Reference Link
  • 1.
    Song R, Koyuncu O, Greco T, Diner B, Cristea I, Enquist L. Two Modes of the Axonal Interferon Response Limit Alphaherpesvirus Neuroinvasion. mBio. 2016;7(1):e02145–15. PMCID: PMC4742712
    Reference Link
  • 1.
    Wagner E, Stolfi A, Choi Y, Levine M. Islet is a key determinant of ascidian palp morphogenesis. Development. 2014;141(15):3084–92. PMCID: PMC4197658
    Reference Link
  • 1.
    Wang J, Kaletsky R, Silva M, Williams A, Haas L, Androwski R, Landis J, Patrick C, Rashid A, Santiago-Martinez D, Gravato-Nobre M, Hodgkin J, Hall D, Murphy C, Barr M. Cell-Specific Transcriptional Profiling of Ciliated Sensory Neurons Reveals Regulators of Behavior and Extracellular Vesicle Biogenesis. Curr Biol. 2015;25(24):3232–8. PMCID: PMC4698341
    Reference Link
  • 1.
    Douam F, Gaska J, Winer B, Ding Q, von Schaewen M, Ploss A. Genetic Dissection of the Host Tropism of Human-Tropic Pathogens. Annu Rev Genet. 2015;49:21–45. PMCID: PMC5075990
    Reference Link
  • 1.
    Rutherford S, van Kessel J, Shao Y, Bassler B. AphA and LuxR/HapR reciprocally control quorum sensing in vibrios. Genes Dev. 2011;25(4):397–408. PMCID: PMC3042162
    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

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