Supported by CCR Office of Science and Technology Resources (OSTR)

Publications and Preprints

Project Development
Image Analysis


Native FISH: A low- and high-throughput assay to analyze the alternative lengthening of telomere (ALT) pathway

Azeroglu B, Ozbun L, Pegoraro G, Lazzerini Denchi E.  Methods in Cell Biology. Academic Press; 2022.

Science Direct Link

HiFENS: high-throughput FISH detection of endogenous pre-mRNA splicing isoforms

Shilo A, Pegoraro G, Misteli T.  Nucleic Acids Res [Internet]. 2022 Oct 16; PMID: 36243969

PubMed Link

Nuclear position modulates long-range chromatin interactions

Finn EH, Misteli T  PLoS Genet. 2022 Oct;18(10): e1010451. PMCID: PMC9581366

PubMed Link

High-throughput imaging of mRNA at the single-cell level in human primary immune cells

Gadkari M, Sun J, Carcamo A, Alessi H, Hu Z, Fraser IDC, Pegoraro G, Franco LM

RNA. 2022 Sep;28(9):1263–1278. PMCID: PMC9380748
PubMed Link

NURF301 contributes to gypsy chromatin insulator-mediated nuclear organization

Chen S, Rosin LF, Pegoraro G, Moshkovich N, Murphy PJ, Yu G, Lei EP Nucleic Acids Res. 2022 Aug 12;50(14):7906–7924. PMCID: PMC9371915

PubMed Link

Large-scale mapping of positional changes of hypoxia-responsive genes upon activation

Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T Mol Biol Cell. 2022 Jul 1;33(8):ar72. PMCID: PMC9635277

PubMed Link

Identification of epigenetic modulators as determinants of nuclear size and shape

Schibler A, Jevtic P, Pegoraro G, Levy DL, Misteli T [Internet]. bioRxiv. 2022 [cited 2022 Dec 21]. p. 2022.05.28.493845. Available from:

Direct Link

Activation of endoplasmic reticulum stress via clustering of the inner nuclear membrane protein SUN2

Vidak S, Serebryannyy LA, Pegoraro G, Misteli T bioRxiv. 2022 [cited 2022 Dec 21]. p. 2021.09.14.460295. Available from:

Direct Link

HiIDDD: a high-throughput imaging pipeline for the quantitative detection of DNA damage in primary human immune cells

Gallant K, Bektas A, Kaileh M, Lustig A, Ferrucci L, Pegoraro G, Misteli T Sci Rep. Nature Publishing Group; 2022 Apr 15;12(1):6335. PMCID: PMC9022135

PubMed Link

Chondroitin Sulfate Proteoglycans Are De Facto Cellular Receptors for Human Papillomavirus 16 under High Serum Conditions

Fons NR, Kines RC, Thompson CD, Day PM, Lowy DR, Schiller JT J Virol. 2022 Apr 13;96(7): e0185721. PMCID: PMC9006963

PubMed Link

The glucocorticoid receptor associates with the cohesin loader NIPBL to promote long-range gene regulation

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 Sci Adv. 2022 Apr;8(13): eabj8360. PMCID: PMC8967222


MYC amplifies gene expression through global changes in transcription factor dynamics

Patange S, Ball DA, Wan Y, Karpova TS, Girvan M, Levens D, Larson DR Cell Rep. 2022 Jan 25;38(4):110292. PMCID: PMC8849550

PubMed Link

High-Throughput DNA FISH (hiFISH)

Finn E, Misteli T, Pegoraro G In: Sexton T, editor. Spatial Genome Organization: Methods and Protocols. New York, NY: Springer US; 2022. p. 245–274.

PubMed Link


The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner

Vega-Sendino M, Olbrich T, Tillo D, Tran AD, Domingo CN, Franco M, FitzGerald PC, Kruhlak MJ, Ruiz S Sci Adv. 2021 Oct;7(40): eabg8306. PMID: 34597136

PubMed Link

CTCF is a barrier for 2C-like reprogramming

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 Nat Commun. Nature Publishing Group; 2021 Aug 11;12(1):4856. PMCID: PMC8358036

PubMed Link

Mapping multiple endocrine disrupting activities in Virginia rivers using effect-based assays

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 Sci Total Environ. 2021 Jun 15; 773:145602. PMCID: PMC8026610

PubMed Link

Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection

Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR Cell. 2021 May 27;184(11):2878–2895.e20. PMCID: PMC8183334

PubMed Link

An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors

Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL Mol Cell. 2021 Apr 1;81(7):1484–1498.e6. PMCID: PMC9258326

PubMed Link

Self-assembly of multi-component mitochondrial nucleoids via phase separation

Feric M, Demarest TG, Tian J, Croteau DL, Bohr VA, Misteli T EMBO J. 2021 Mar 15;40(6): e107165. PMCID: PMC7957436

PubMed Link


A Deep Learning Pipeline for Nucleus Segmentation

Zaki G, Gudla PR, Lee K, Kim J, Ozbun L, Shachar S, Gadkari M, Sun J, Fraser IDC, Franco LM, Misteli T, Pegoraro G Cytometry A. 2020 Dec;97(12):1248–1264. PMCID: PMC8914348

PubMed Link

Epigenetic Regulation of DNA Repair Pathway Choice by MacroH2A1 Splice Variants Ensures Genome Stability

Sebastian R, Hosogane EK, Sun EG, Tran AD, Reinhold WC, Burkett S, Sturgill DM, Gudla PR, Pommier Y, Aladjem MI, Oberdoerffer P Mol Cell. 2020 Sep 3;79(5):836–845.e7. PMCID: PMC7483679

PubMed Link