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Transcriptome

  • 1.
    Hansen J, Sealfon R, Menon R, Eadon M, Lake B, Steck B, Anjani K, Parikh S, Sigdel T, Zhang G, Velickovic D, Barwinska D, Alexandrov T, Dobi D, Rashmi P, Otto E, Rivera M, Rose M, Anderton C, Shapiro J, Pamreddy A, Winfree S, Xiong Y, He Y, de Boer I, Hodgin J, Barisoni L, Naik A, Sharma K, Sarwal M, Zhang K, Himmelfarb J, Rovin B, El-Achkar T, Laszik Z, He J, Dagher P, Valerius T, Jain S, Satlin L, Troyanskaya O, Kretzler M, Iyengar R, Azeloglu E, Kidney Precision Medicine Project. A reference tissue atlas for the human kidney. Sci Adv. 2022;8(23):eabn4965. PMCID: PMC9176741
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    Chen X, Du Y, Broussard G, Kislin M, Yuede C, Zhang S, Dietmann S, Gabel H, Zhao G, Wang S, Zhang X, Bonni A. Transcriptomic mapping uncovers Purkinje neuron plasticity driving learning. Nature. 2022;605(7911):722–727. PMCID: PMC9887520
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    Zhang Z, Zamojski M, Smith G, Willis T, Yianni V, Mendelev N, Pincas H, Seenarine N, Amper M, Vasoya M, Cheng W, Zaslavsky E, Nair V, Turgeon J, Bernard D, Troyanskaya O, Andoniadou C, Sealfon S, Ruf-Zamojski F. Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms. Cell Rep. 2022;38(10):110467. PMCID: PMC8957708
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    Kleiner R. Interrogating the transcriptome with metabolically incorporated ribonucleosides. Mol Omics. 2021;17(6):833–841. PMCID: PMC8648987
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  • 1.
    Lindström N, Sealfon R, Chen X, Parvez R, Ransick A, Brandine G, Guo J, Hill B, Tran T, Kim A, Zhou J, Tadych A, Watters A, Wong A, Lovero E, Grubbs B, Thornton M, McMahon J, Smith A, Ruffins S, Armit C, Troyanskaya O, McMahon A. Spatial transcriptional mapping of the human nephrogenic program. Dev Cell. 2021;56(16):2381–2398.e6. PMCID: PMC8396064
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    Quinn J, Jones M, Okimoto R, Nanjo S, Chan M, Yosef N, Bivona T, Weissman J. Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts. Science. 2021;371(6532). PMCID: PMC7983364
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  • 1.
    Ruf-Zamojski F, Zhang Z, Zamojski M, Smith G, Mendelev N, Liu H, Nudelman G, Moriwaki M, Pincas H, Castanon R, Nair V, Seenarine N, Amper M, Zhou X, Ongaro L, Toufaily C, Schang G, Nery J, Bartlett A, Aldridge A, Jain N, Childs G, Troyanskaya O, Ecker J, Turgeon J, Welt C, Bernard D, Sealfon S. Single nucleus multi-omics regulatory landscape of the murine pituitary. Nat Commun. 2021;12(1):2677. PMCID: PMC8113460
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  • 1.
    Goodwin K, Nelson C. Uncovering cellular networks in branching morphogenesis using single-cell transcriptomics. Curr Top Dev Biol. 2021;143:239–280. PMID: 33820623
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  • 1.
    Ledo J, Zhang R, Mesin L, Mourão-Sá D, Azevedo E, Troyanskaya O, Bustos V, Greengard P. Lack of a site-specific phosphorylation of Presenilin 1 disrupts microglial gene networks and progenitors during development. PLoS One. 2020;15(8):e0237773. PMCID: PMC7444478
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  • 1.
    Cao W, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low T, Siddiqui N, Cheng M, Angers S, Smibert C, Wühr M, Wahle E, Lipshitz H. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep. 2020;31(12):107783. PMCID: PMC7372737
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  • 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
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  • 1.
    Replogle J, Norman T, Xu A, Hussmann J, Chen J, Cogan Z, Meer E, Terry J, Riordan D, Srinivas N, Fiddes I, Arthur J, Alvarado L, Pfeiffer K, Mikkelsen T, Weissman J, Adamson B. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol. 2020;38(8):954–961. PMCID: PMC7416462
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  • 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
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  • 1.
    Preston C, Storm E, Burdine R, Bradley T, Uttecht A, Faustino R. Nucleoporin insufficiency disrupts a pluripotent regulatory circuit in a pro-arrhythmogenic stem cell line. Sci Rep. 2019;9(1):12691. PMCID: PMC6722237
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  • 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
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  • 1.
    Sanfilippo J, Lorestani A, Koch M, Bratton B, Siryaporn A, Stone H, Gitai Z. Microfluidic-based transcriptomics reveal force-independent bacterial rheosensing. Nat Microbiol. 2019;4(8):1274–1281. PMCID: PMC6656604
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  • 1.
    Federspiel J, Greco T, Lum K, Cristea I. Hdac4 Interactions in Huntington’s Disease Viewed Through the Prism of Multiomics. Mol Cell Proteomics. 2019;18(8 suppl 1):S92-S113. PMCID: PMC6692770
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  • 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
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  • 1.
    Harder J, Menon R, Otto E, Zhou J, Eddy S, Wys N, O’Connor C, Luo J, Nair V, Cebrian C, Spence J, Bitzer M, Troyanskaya O, Hodgin J, Wiggins R, Freedman B, Kretzler M, European Renal cDNA Bank (ERCB), Nephrotic Syndrome Study Network (NEPTUNE). Organoid single cell profiling identifies a transcriptional signature of glomerular disease. JCI Insight. 2019;4(1). PMCID: PMC6485369
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  • 1.
    Douam F, Ziegler C, Hrebikova G, Fant B, Leach R, Parsons L, Wang W, Gaska J, Winer B, Heller B, Shalek A, Ploss A. Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. Nat Commun. 2018;9(1):5031. PMCID: PMC6262001
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  • 1.
    vonHoldt B, Ji S, Aardema M, Stahler D, Udell M, Sinsheimer J. Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. Genome Biol Evol. 2018;10(6):1546–1553. PMCID: PMC6007319
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  • 1.
    Templeman N, Luo S, Kaletsky R, Shi C, Ashraf J, Keyes W, Murphy C. Insulin Signaling Regulates Oocyte Quality Maintenance with Age via Cathepsin B Activity. Curr Biol. 2018;28(5):753–760.e4. PMCID: PMC5893159
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  • 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
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  • 1.
    Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang C, Qian J, Lie N, Lanzillotta C, Rabinowitz J, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol. 2018;471:22–32. PMCID: PMC5702591
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  • 1.
    Tate A, Andolfatto P, Demuth J, Graham A. The within-host dynamics of infection in trans-generationally primed flour beetles. Mol Ecol. 2017;26(14):3794–3807. PMCID: PMC5653231
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  • 1.
    Gorenshteyn D, Zaslavsky E, Fribourg M, Park C, Wong A, Tadych A, Hartmann B, Albrecht R, García-Sastre A, Kleinstein S, Troyanskaya O, Sealfon S. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity. 2015;43(3):605–14. PMCID: PMC4753773
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  • 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.
    Kaletsky R, Lakhina V, Arey R, Williams A, Landis J, Ashraf J, Murphy C. The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators. Nature. 2016;529(7584):92–6. PMCID: PMC4708089
    Reference Link

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