1. Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP. NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization. Nucleic Acids Res. 2022 Jul 12; Available from: http://dx.doi.org/10.1093/nar/gkac600 PMID: 35819192
  2. Gadkari M, Sun J, Carcamo A, Alessi H, Hu Z, Fraser ID, Pegoraro G, Franco LM. High-throughput imaging of mRNA at the single-cell level in human primary immune cells. RNA. 2022 Jun 28; Available from: http://dx.doi.org/10.1261/rna.079239.122 PMID: 35764396
  3. Finn EH, Misteli T. Nuclear position modulates long-range chromatin interactions. bioRxiv. 2022. p. 2022.05.31.494201. Available from: https://www.biorxiv.org/content/10.1101/2022.05.31.494201v1
  4. Schibler A, Jevtic P, Pegoraro G, Levy DL, Misteli T. Identification of epigenetic modulators as determinants of nuclear size and shape. bioRxiv. 2022. p. 2022.05.28.493845. Available from: https://www.biorxiv.org/content/10.1101/2022.05.28.493845v1
  5. Vidak S, Serebryannyy LA, Pegoraro G, Misteli T. Activation of endoplasmic reticulum stress via clustering of the inner nuclear membrane protein SUN2. bioRxiv. 2022. p. 2021.09.14.460295. Available from: https://www.biorxiv.org/content/10.1101/2021.09.14.460295v2
  6. Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell. 2022 Apr 27;mbcE21110593. PMID: 35476603
  7. Gallant K, Bektas A, Kaileh M, Lustig A, Ferrucci L, Pegoraro G, Misteli T. HiIDDD: a high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells. Sci Rep. 2022 Apr 15;12(1):1–13. PMID: 35428779
  8. Fons NR, Kines RC, Thompson CD, Day PM, Lowy DR, Schiller JT. Chondroitin Sulfate Proteoglycans Are De Facto Cellular Receptors for Human Papillomavirus 16 under High Serum Conditions. J Virol. 2022 Apr 13;96(7):e0185721. PMCID: PMC9006963
  9. Shilo A, Pegoraro G, Misteli T. HiFENS: High-throughput FISH detection of endogenous pre-mRNA splicing isoforms. bioRxiv. 2022. p. 2022.04.10.487792. Available from: https://www.biorxiv.org/content/10.1101/2022.04.10.487792v1
  10. Rinaldi L, Fettweis G, Kim S, Garcia DA, Fujiwara S, Johnson TA, Tettey TT, Ozbun L, Pegoraro G, Puglia M, Blagoev B, Upadhyaya A, Stavreva DA, Hager GL. The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation. Sci Adv. 2022 Apr;8(13):eabj8360. PMID: 35353576
  11. Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR. MYC amplifies gene expression through global changes in transcription factor dynamics. Cell Rep. 2022 Jan 25;38(4):110292. PMCID: PMC8849550
  12. Finn E, Misteli T, Pegoraro G. High-Throughput DNA FISH (hiFISH). In: Sexton T, editor. Spatial Genome Organization: Methods and Protocols. New York, NY: Springer US; 2022. p. 245–274.
  13. Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S. The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner. Sci Adv. 2021 Oct;7(40):eabg8306. PMID: 34597136
  14. Olbrich T, Vega-Sendino M, Tillo D, Wu W, Zolnerowich N, Pavani R, Tran AD, Domingo CN, Franco M, Markiewicz-Potoczny M, Pegoraro G, FitzGerald PC, Kruhlak MJ, Lazzerini-Denchi E, Nora EP, Nussenzweig A, Ruiz S. CTCF is a barrier for 2C-like reprogramming. Nat Commun. 2021 Aug 11;12(1):4856. PMCID: PMC8358036
  15. Stavreva DA, Collins M, McGowan A, Varticovski L, Raziuddin R, Brody DO, Zhao J, Lee J, Kuehn R, Dehareng E, Mazza N, Pegoraro G, Hager GL. Mapping multiple endocrine disrupting activities in Virginia rivers using effect-based assays. Sci Total Environ. 2021 Jun 15;773:145602. PMCID: PMC8026610
  16. Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR. Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell. 2021 May 27;184(11):2878–2895.e20. PMCID: PMC8183334
  17. Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T. Self-assembly of multi-component mitochondrial nucleoids via phase separation. EMBO J. 2021 Mar 15;40(6):e107165. PMCID: PMC7957436
  18. Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell. 2021 Feb 3; Available from: http://dx.doi.org/10.1016/j.molcel.2021.01.013 PMID: 33561389
  19. Zaki G, Gudla PR, Lee K, Kim J, Ozbun L, Shachar S, Gadkari M, Sun J, Fraser IDC, Franco LM, Misteli T, Pegoraro G. A Deep Learning Pipeline for Nucleus Segmentation. Cytometry A. 2020 Dec;97(12):1248–1264. PMID: 33141508
  20. Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P. Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability. Mol Cell. 2020 Sep 3;79(5):836–845.e7. PMCID: PMC7483679
  21. Vayttaden SJ, Smelkinson M, Ernst O, Carlson RJ, Sun J, Bradfield C, Dorrington MG, Liang J, Bouladoux N, Gottschalk RA, Oh KS, Pegoraro G, Ganesan S, De Nardo D, Latz E, Belkaid Y, Varma RR, Fraser IDC. IRAK1-mediated coincidence detection of microbial signals licenses inflammasome activation. bioRxiv. 2019. p. 2019.12.26.888776. Available from: https://www.biorxiv.org/content/10.1101/2019.12.26.888776v1
  22. Liskovykh M, Goncharov NV, Petrov N, Aksenova V, Pegoraro G, Ozbun LL, Reinhold WC, Varma S, Dasso M, Kumeiko V, Masumoto H, Earnshaw WC, Larionov V, Kouprina N. A novel assay to screen siRNA libraries identifies protein kinases required for chromosome transmission. Genome Res. 2019 Oct;29(10):1719–1732. PMCID: PMC6771407
  23. Stavreva DA, Garcia DA, Fettweis G, Gudla PR, Zaki GF, Soni V, McGowan A, Williams G, Huynh A, Palangat M, Schiltz RL, Johnson TA, Presman DM, Ferguson ML, Pegoraro G, Upadhyaya A, Hager GL. Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility. Mol Cell. 2019 Sep 19;75(6):1161–1177.e11. PMCID: PMC6754282
  24. Jevtic P, Schibler AC, Wesley CC, Pegoraro G, Misteli T, Levy DL. The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity. EMBO Rep. 2019 Jun;20(6). Available from: http://dx.doi.org/10.15252/embr.201847283 PMCID: PMC6549122
  25. Serebryannyy LA, Misteli T. HiPLA: High-throughput imaging proximity ligation assay. Methods. 2019 Mar 15;157:80–87. PMCID: PMC6401276
  26. Serebryannyy LA, Ball DA, Karpova TS, Misteli T. Single molecule analysis of lamin dynamics. Methods. 2019 Mar 15;157:56–65. PMCID: PMC6387858
  27. Finn EH, Pegoraro G, Brandão HB, Valton AL, Oomen ME, Dekker J, Mirny L, Misteli T. Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization. Cell. 2019 Mar 7;176(6):1502–1515.e10. PMCID: PMC6408223
  28. Adriaens C, Serebryannyy LA, Feric M, Schibler A, Meaburn KJ, Kubben N, Trzaskoma P, Shachar S, Vidak S, Finn EH, Sood V, Pegoraro G, Misteli T. Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol. 2018 Dec;150(6):579–592. PMCID: PMC6290477
  29. Shen Y, Kubben N, Candia J, Morozov AV, Misteli T, Losert W. RefCell: multi-dimensional analysis of image-based high-throughput screens based on “typical cells.” BMC Bioinformatics. 2018 Nov 16;19(1):427. PMCID: PMC6240236
  30. Jowhar Z, Shachar S, Gudla PR, Wangsa D, Torres E, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. Effects of human sex chromosome dosage on spatial chromosome organization. Mol Biol Cell. Am Soc Cell Biol; 2018 Oct 1;29(20):2458–2469. PMCID: PMC6233059
  31. Jowhar Z, Gudla PR, Shachar S, Wangsa D, Russ JL, Pegoraro G, Ried T, Raznahan A, Misteli T. HiCTMap: Detection and analysis of chromosome territory structure and position by high-throughput imaging. Methods. 2018 Jun 1;142:30–38. PMCID: PMC5993577
  32. Baranes-Bachar K, Levy-Barda A, Oehler J, Reid DA, Soria-Bretones I, Voss TC, Chung D, Park Y, Liu C, Yoon JB, Li W, Dellaire G, Misteli T, Huertas P, Rothenberg E, Ramadan K, Ziv Y, Shiloh Y. The Ubiquitin E3/E4 Ligase UBE4A Adjusts Protein Ubiquitylation and Accumulation at Sites of DNA Damage, Facilitating Double-Strand Break Repair. Mol Cell. 2018 Mar 1;69(5):866–878.e7. PMCID: PMC6265044
  33. Gudla PR, Nakayama K, Pegoraro G, Misteli T. SpotLearn: Convolutional Neural Network for Detection of Fluorescence In Situ Hybridization (FISH) Signals in High-Throughput Imaging Approaches. Cold Spring Harb Symp Quant Biol. 2017 Nov 28;82:57–70. PMCID: PMC6350914
  34. Pegoraro G, Misteli T. High-Throughput Imaging for the Discovery of Cellular Mechanisms of Disease. Trends Genet. 2017 Sep;33(9):604–615. PMCID: PMC5562530
  35. Zane L, Chapus F, Pegoraro G, Misteli T. HiHiMap: single-cell quantitation of histones and histone posttranslational modifications across the cell cycle by high-throughput imaging. Mol Biol Cell. 2017 Aug 15;28(17):2290–2302. PMCID: PMC5555657
  36. Liu J, Kruswick A, Dang H, Tran AD, Kwon SM, Wang XW, Oberdoerffer P. Ubiquitin-specific protease 21 stabilizes BRCA2 to control DNA repair and tumor growth. Nat Commun. 2017 Jul 26;8(1):137. PMCID: PMC5526993
  37. Finn EH, Pegoraro G, Shachar S, Misteli T. Comparative analysis of 2D and 3D distance measurements to study spatial genome organization. Methods. 2017 Jul 1;123:47–55. PMCID: PMC5522766
  38. Sawyer IA, Hager GL, Dundr M. Specific genomic cues regulate Cajal body assembly. RNA Biol. 2017 Jun 3;14(6):791–803. PMCID: PMC5519236
  39. Veschi V, Liu Z, Voss TC, Ozbun L, Gryder B, Yan C, Hu Y, Ma A, Jin J, Mazur SJ, Lam N, Souza BK, Giannini G, Hager GL, Arrowsmith CH, Khan J, Appella E, Thiele CJ. Epigenetic siRNA and Chemical Screens Identify SETD8 Inhibition as a Therapeutic Strategy for p53 Activation in High-Risk Neuroblastoma. Cancer Cell. 2017 Jan 9;31(1):50–63. PMCID: PMC5233415
  40. Stavreva DA, Varticovski L, Levkova L, George AA, Davis L, Pegoraro G, Blazer V, Iwanowicz L, Hager GL. Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants. Toxicology. 2016 Aug 10;368-369:69–79. PMCID: PMC5069182
  41. Kubben N, Zhang W, Wang L, Voss TC, Yang J, Qu J, Liu GH, Misteli T. Repression of the Antioxidant NRF2 Pathway in Premature Aging. Cell. 2016 Jun 2;165(6):1361–1374. PMCID: PMC4893198
  42. Wang Q, Sawyer IA, Sung MH, Sturgill D, Shevtsov SP, Pegoraro G, Hakim O, Baek S, Hager GL, Dundr M. Cajal bodies are linked to genome conformation. Nat Commun. 2016 Mar 21;7:10966. PMCID: PMC4802181
  43. Day CR, Chen H, Coulon A, Meier JL, Larson DR. High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics. Methods. 2016 Mar 1;96:59–68. PMCID: PMC4766052
  44. Kubben N, Brimacombe KR, Donegan M, Li Z, Misteli T. A high-content imaging-based screening pipeline for the systematic identification of anti-progeroid compounds. Methods. 2016 Mar 1;96:46–58. PMID: 26341717
  45. Pegoraro G, Misteli T. High-throughput Imaging as a versatile and unbiased discovery tool. Methods. 2016 Mar 1;96:1–2. PMCID: PMC6342277
  46. Ji X, Dadon DB, Powell BE, Fan ZP, Borges-Rivera D, Shachar S, Weintraub AS, Hnisz D, Pegoraro G, Lee TI, Misteli T, Jaenisch R, Young RA. 3D Chromosome Regulatory Landscape of Human Pluripotent Cells. Cell Stem Cell. 2016 Feb 4;18(2):262–275. PMCID: PMC4848748
  47. Shachar S, Pegoraro G, Misteli T. HIPMap: A High-Throughput Imaging Method for Mapping Spatial Gene Positions. Cold Spring Harb Symp Quant Biol. Cold Spring Harbor Laboratory Press; 2015 Oct 15;80:73–81. PMCID: PMC6317989
  48. Shachar S, Voss TC, Pegoraro G, Sciascia N, Misteli T. Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping. Cell. 2015 Aug 13;162(4):911–923. PMCID: PMC4538709
  49. Burman B, Misteli T, Pegoraro G. Quantitative detection of rare interphase chromosome breaks and translocations by high-throughput imaging. Genome Biol. BioMed Central Ltd; 2015 Aug 3;16(1):146. PMCID: PMC4531802
  50. Burman B, Zhang ZZ, Pegoraro G, Lieb JD, Misteli T. Histone modifications predispose genome regions to breakage and translocation. Genes Dev. Cold Spring Harbor Lab; 2015 Jul 1;29(13):1393–1402. PMCID: PMC4511214
  51. Zong D, Callén E, Pegoraro G, Lukas C, Lukas J, Nussenzweig A. Ectopic expression of RNF168 and 53BP1 increases mutagenic but not physiological non-homologous end joining. Nucleic Acids Res. 2015 May 26;43(10):4950–4961. PMCID: PMC4446425
  52. Salton M, Kasprzak WK, Voss T, Shapiro BA, Poulikakos PI, Misteli T. Inhibition of vemurafenib-resistant melanoma by interference with pre-mRNA splicing. Nat Commun. 2015 May 14;6:7103. PMCID: PMC4435825
  53. Roukos V, Pegoraro G, Voss TC, Misteli T. Cell cycle staging of individual cells by fluorescence microscopy. Nat Protoc. 2015 Feb;10(2):334–348. PMCID: PMC6318798
  54. Salton M, Voss TC, Misteli T. Identification by high-throughput imaging of the histone methyltransferase EHMT2 as an epigenetic regulator of VEGFA alternative splicing. Nucleic Acids Res. 2014 Dec 16;42(22):13662–13673. PMCID: PMC4267647
  55. Stavreva D, Varticovski L, Hager G. Quantitative High Throughput Assay for Detection of Biologically Active Endocrine Disrupting Chemicals in Water. Aquananotechnology. CRC Press; 2014. p. 723–736.
  56. Dittmer TA, Sahni N, Kubben N, Hill DE, Vidal M, Burgess RC, Roukos V, Misteli T. Systematic identification of pathological lamin A interactors. Mol Biol Cell. 2014 May;25(9):1493–1510. PMCID: PMC4004598
  57. Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, Misteli T. Spatial dynamics of chromosome translocations in living cells. Science. American Association for the Advancement of Science; 2013 Aug 9;341(6146):660–664. PMID: 23929981
  58. Hakim O, Sung MH, Nakayamada S, Voss TC, Baek S, Hager GL. Spatial congregation of STAT binding directs selective nuclear architecture during T-cell functional differentiation. Genome Res. Cold Spring Harbor Lab; 2013 Mar;23(3):462–472. PMCID: PMC3589535
  59. Miranda TB, Voss TC, Hager GL. High-throughput fluorescence-based screen to identify factors involved in nuclear receptor recruitment to response elements. Methods Mol Biol. Totowa, NJ: Humana Press; 2013;1042(Chapter 1):3–12. PMID: 23979996
  60. Stavreva DA, George AA, Klausmeyer P, Varticovski L, Sack D, Voss TC, Schiltz RL, Blazer VS, Iwanowicz LR, Hager GL. Prevalent glucocorticoid and androgen activity in US water sources. Sci Rep. 2012 Dec 6;2:937. PMCID: PMC3515810
  61. Pegoraro G, Voss TC, Martin SE, Tuzmen P, Guha R, Misteli T. Identification of mammalian protein quality control factors by high-throughput cellular imaging. PLoS One. Public Library of Science; 2012 Feb 20;7(2):e31684. PMCID: PMC3282772
  62. Hakim O, Resch W, Yamane A, Klein I, Kieffer-Kwon KR, Jankovic M, Oliveira T, Bothmer A, Voss TC, Ansarah-Sobrinho C, Mathe E, Liang G, Cobell J, Nakahashi H, Robbiani DF, Nussenzweig A, Hager GL, Nussenzweig MC, Casellas R. DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes. Nature. 2012 Feb 7;484(7392):69–74. PMCID: PMC3459314
  63. Voss TC, Schiltz RL, Sung MH, Yen PM, Stamatoyannopoulos JA, Biddie SC, Johnson TA, Miranda TB, John S, Hager GL. Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism. Cell. 2011 Aug 19;146(4):544–554. PMCID: PMC3210475
Last updated by Pegoraro, Gianluca (NIH/NCI) [E] on Aug 30, 2022