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Direct Visualization of Single Nuclear Pore Complex Proteins Using Genetically-Encoded Probes for DNA-PAINT.

Schlichthaerle T, Strauss MT, Schueder F, Auer A, Nijmeijer B, Kueblbeck M, Jimenez Sabinina V, Thevathasan JV, Ries J, Ellenberg J, Jungmann R.

Angew Chem Int Ed Engl. 2019 Sep 9;58(37):13004-13008. doi: 10.1002/anie.201905685. Epub 2019 Aug 21.


Proceedings of the University of Pennsylvania 11th annual conference on statistical issues in clinical trials: Estimands, missing data and sensitivity analysis.

Ellenberg SS, Ellenberg JH.

Clin Trials. 2019 Aug;16(4):337-338. doi: 10.1177/1740774519853569. Epub 2019 Jun 27. No abstract available.


Determining cellular CTCF and cohesin abundances to constrain 3D genome models.

Cattoglio C, Pustova I, Walther N, Ho JJ, Hantsche-Grininger M, Inouye CJ, Hossain MJ, Dailey GM, Ellenberg J, Darzacq X, Tjian R, Hansen AS.

Elife. 2019 Jun 17;8. pii: e40164. doi: 10.7554/eLife.40164.


Absolute quantification of cohesin, CTCF and their regulators in human cells.

Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM.

Elife. 2019 Jun 17;8. pii: e46269. doi: 10.7554/eLife.46269.


Mysteries in embryonic development: How can errors arise so frequently at the beginning of mammalian life?

Schneider I, Ellenberg J.

PLoS Biol. 2019 Mar 6;17(3):e3000173. doi: 10.1371/journal.pbio.3000173. eCollection 2019 Mar.


Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.

Pękowska A, Klaus B, Xiang W, Severino J, Daigle N, Klein FA, Oleś M, Casellas R, Ellenberg J, Steinmetz LM, Bertone P, Huber W.

Cell Syst. 2018 Nov 28;7(5):482-495.e10. doi: 10.1016/j.cels.2018.09.003. Epub 2018 Nov 7.


A call for public archives for biological image data.

Ellenberg J, Swedlow JR, Barlow M, Cook CE, Sarkans U, Patwardhan A, Brazma A, Birney E.

Nat Methods. 2018 Nov;15(11):849-854. doi: 10.1038/s41592-018-0195-8. No abstract available.


Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells.

Popovic D, Koch B, Kueblbeck M, Ellenberg J, Pelkmans L.

Cell Syst. 2018 Oct 24;7(4):398-411.e6. doi: 10.1016/j.cels.2018.09.001. Epub 2018 Oct 17.


Experimental and computational framework for a dynamic protein atlas of human cell division.

Cai Y, Hossain MJ, Hériché JK, Politi AZ, Walther N, Koch B, Wachsmuth M, Nijmeijer B, Kueblbeck M, Martinic-Kavur M, Ladurner R, Alexander S, Peters JM, Ellenberg J.

Nature. 2018 Sep;561(7723):411-415. doi: 10.1038/s41586-018-0518-z. Epub 2018 Sep 10.


Correction: Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.

Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J.

J Cell Biol. 2018 Sep 3;217(9):3315-3316. doi: 10.1083/JCB.20170907408082018c. Epub 2018 Aug 22. No abstract available.


Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging.

Strauss S, Nickels PC, Strauss MT, Jimenez Sabinina V, Ellenberg J, Carter JD, Gupta S, Janjic N, Jungmann R.

Nat Methods. 2018 Sep;15(9):685-688. doi: 10.1038/s41592-018-0105-0. Epub 2018 Aug 20.


Dual-spindle formation in zygotes keeps parental genomes apart in early mammalian embryos.

Reichmann J, Nijmeijer B, Hossain MJ, Eguren M, Schneider I, Politi AZ, Roberti MJ, Hufnagel L, Hiiragi T, Ellenberg J.

Science. 2018 Jul 13;361(6398):189-193. doi: 10.1126/science.aar7462.


Quantitative live and super-resolution microscopy of mitotic chromosomes.

Walther N, Ellenberg J.

Methods Cell Biol. 2018;145:65-90. doi: 10.1016/bs.mcb.2018.03.014. Epub 2018 Apr 24. No abstract available.


Live imaging of cell division in preimplantation mouse embryos using inverted light-sheet microscopy.

Reichmann J, Eguren M, Lin Y, Schneider I, Ellenberg J.

Methods Cell Biol. 2018;145:279-292. doi: 10.1016/bs.mcb.2018.03.030. Epub 2018 Apr 26.


Proceedings of the University of Pennsylvania 10th annual conference on statistical issues in clinical trials: Current issues regarding Data and Safety Monitoring Committees in clinical trials.

Ellenberg SS, Ellenberg JH.

Clin Trials. 2018 Aug;15(4):319-320. doi: 10.1177/1740774518781817. Epub 2018 Jun 22. No abstract available.


The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.

Ivanov MP, Ladurner R, Poser I, Beveridge R, Rampler E, Hudecz O, Novatchkova M, Hériché JK, Wutz G, van der Lelij P, Kreidl E, Hutchins JR, Axelsson-Ekker H, Ellenberg J, Hyman AA, Mechtler K, Peters JM.

EMBO J. 2018 Aug 1;37(15). pii: e97150. doi: 10.15252/embj.201797150. Epub 2018 Jun 21.


Quantitative mapping of fluorescently tagged cellular proteins using FCS-calibrated four-dimensional imaging.

Politi AZ, Cai Y, Walther N, Hossain MJ, Koch B, Wachsmuth M, Ellenberg J.

Nat Protoc. 2018 Jun;13(6):1445-1464. doi: 10.1038/nprot.2018.040. Epub 2018 May 24.


Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing.

Koch B, Nijmeijer B, Kueblbeck M, Cai Y, Walther N, Ellenberg J.

Nat Protoc. 2018 Jun;13(6):1465-1487. doi: 10.1038/nprot.2018.042. Epub 2018 May 24.


A quantitative map of human Condensins provides new insights into mitotic chromosome architecture.

Walther N, Hossain MJ, Politi AZ, Koch B, Kueblbeck M, Ødegård-Fougner Ø, Lampe M, Ellenberg J.

J Cell Biol. 2018 Jul 2;217(7):2309-2328. doi: 10.1083/jcb.201801048. Epub 2018 Apr 9.


Real-time 3D single-molecule localization using experimental point spread functions.

Li Y, Mund M, Hoess P, Deschamps J, Matti U, Nijmeijer B, Sabinina VJ, Ellenberg J, Schoen I, Ries J.

Nat Methods. 2018 May;15(5):367-369. doi: 10.1038/nmeth.4661. Epub 2018 Apr 9.


Correlative live and super-resolution imaging reveals the dynamic structure of replication domains.

Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J.

J Cell Biol. 2018 Jun 4;217(6):1973-1984. doi: 10.1083/jcb.201709074. Epub 2018 Mar 23. Erratum in: J Cell Biol. 2018 Sep 3;217(9):3315-3316.


ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.

Barton C, Morganella S, Ødegård-Fougner Ø, Alexander S, Ries J, Fitzgerald T, Ellenberg J, Birney E.

PLoS Comput Biol. 2018 Mar 9;14(3):e1006002. doi: 10.1371/journal.pcbi.1006002. eCollection 2018 Mar.


Author Correction: Sister chromatid resolution is an intrinsic part of chromosome organization in prophase.

Nagasaka K, Hossain MJ, Roberti MJ, Ellenberg J, Hirota T.

Nat Cell Biol. 2018 Apr;20(4):503. doi: 10.1038/s41556-018-0044-0.


Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings.

Otsuka S, Steyer AM, Schorb M, Hériché JK, Hossain MJ, Sethi S, Kueblbeck M, Schwab Y, Beck M, Ellenberg J.

Nat Struct Mol Biol. 2018 Jan;25(1):21-28. doi: 10.1038/s41594-017-0001-9. Epub 2017 Nov 27.


Topologically associating domains and chromatin loops depend on cohesin and are regulated by CTCF, WAPL, and PDS5 proteins.

Wutz G, Várnai C, Nagasaka K, Cisneros DA, Stocsits RR, Tang W, Schoenfelder S, Jessberger G, Muhar M, Hossain MJ, Walther N, Koch B, Kueblbeck M, Ellenberg J, Zuber J, Fraser P, Peters JM.

EMBO J. 2017 Dec 15;36(24):3573-3599. doi: 10.15252/embj.201798004. Epub 2017 Dec 7.


Mechanisms of nuclear pore complex assembly - two different ways of building one molecular machine.

Otsuka S, Ellenberg J.

FEBS Lett. 2018 Feb;592(4):475-488. doi: 10.1002/1873-3468.12905. Epub 2017 Nov 22. Review.


Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement.

Germier T, Kocanova S, Walther N, Bancaud A, Shaban HA, Sellou H, Politi AZ, Ellenberg J, Gallardo F, Bystricky K.

Biophys J. 2017 Oct 3;113(7):1383-1394. doi: 10.1016/j.bpj.2017.08.014.


Proceedings of the University of Pennsylvania ninth annual conference on statistical issues in clinical trials: Where are we with adaptive clinical trial designs?

Ellenberg SS, Ellenberg JH.

Clin Trials. 2017 Oct;14(5):415-416. doi: 10.1177/1740774517723606. Epub 2017 Aug 4. No abstract available.


Profiling DNA damage response following mitotic perturbations.

S Pedersen R, Karemore G, Gudjonsson T, Rask MB, Neumann B, Hériché JK, Pepperkok R, Ellenberg J, Gerlich DW, Lukas J, Lukas C.

Nat Commun. 2016 Dec 15;7:13887. doi: 10.1038/ncomms13887.


Proceedings of the University of Pennsylvania eighth annual conference on statistical issues in clinical trials: Statistical issues in pragmatic clinical trials.

Ellenberg SS, Ellenberg JH.

Clin Trials. 2016 Oct;13(5):469-70. doi: 10.1177/1740774516655347. No abstract available.


Nuclear pore assembly proceeds by an inside-out extrusion of the nuclear envelope.

Otsuka S, Bui KH, Schorb M, Hossain MJ, Politi AZ, Koch B, Eltsov M, Beck M, Ellenberg J.

Elife. 2016 Sep 15;5. pii: e19071. doi: 10.7554/eLife.19071.


A proposal for validation of antibodies.

Uhlen M, Bandrowski A, Carr S, Edwards A, Ellenberg J, Lundberg E, Rimm DL, Rodriguez H, Hiltke T, Snyder M, Yamamoto T.

Nat Methods. 2016 Oct;13(10):823-7. doi: 10.1038/nmeth.3995. Epub 2016 Sep 5. No abstract available.


Ki-67 acts as a biological surfactant to disperse mitotic chromosomes.

Cuylen S, Blaukopf C, Politi AZ, Müller-Reichert T, Neumann B, Poser I, Ellenberg J, Hyman AA, Gerlich DW.

Nature. 2016 Jul 14;535(7611):308-12. doi: 10.1038/nature18610. Epub 2016 Jun 29.


The cellular microscopy phenotype ontology.

Jupp S, Malone J, Burdett T, Heriche JK, Williams E, Ellenberg J, Parkinson H, Rustici G.

J Biomed Semantics. 2016 May 18;7:28. doi: 10.1186/s13326-016-0074-0. eCollection 2016.


A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay.

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin AC.

Nat Protoc. 2016 Jun;11(6):1021-38. doi: 10.1038/nprot.2016.059. Epub 2016 May 5.


Sister chromatid resolution is an intrinsic part of chromosome organization in prophase.

Nagasaka K, Hossain MJ, Roberti MJ, Ellenberg J, Hirota T.

Nat Cell Biol. 2016 Jun;18(6):692-9. doi: 10.1038/ncb3353. Epub 2016 May 2. Erratum in: Nat Cell Biol. 2018 Feb 12;:.


Low Vision Rehabilitation for Adult African Americans in Two Settings.

Draper EM, Feng R, Appel SD, Graboyes M, Engle E, Ciner EB, Ellenberg JH, Stambolian D.

Optom Vis Sci. 2016 Jul;93(7):673-82. doi: 10.1097/OPX.0000000000000870.


ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores.

Isokane M, Walter T, Mahen R, Nijmeijer B, Hériché JK, Miura K, Maffini S, Ivanov MP, Kitajima TS, Peters JM, Ellenberg J.

J Cell Biol. 2016 Mar 14;212(6):647-59. doi: 10.1083/jcb.201408089. Epub 2016 Mar 7.


Inverted light-sheet microscope for imaging mouse pre-implantation development.

Strnad P, Gunther S, Reichmann J, Krzic U, Balazs B, de Medeiros G, Norlin N, Hiiragi T, Hufnagel L, Ellenberg J.

Nat Methods. 2016 Feb;13(2):139-42. doi: 10.1038/nmeth.3690. Epub 2015 Dec 14.


Warfarin Dosing Algorithms and the Need for Human Intervention.

Kasner SE, Wang L, French B, Messé SR, Ellenberg J, Kimmel SE; COAG Trial Steering Committee.

Am J Med. 2016 Apr;129(4):431-7. doi: 10.1016/j.amjmed.2015.11.012. Epub 2015 Nov 28.


A cell-based model system links chromothripsis with hyperploidy.

Mardin BR, Drainas AP, Waszak SM, Weischenfeldt J, Isokane M, Stütz AM, Raeder B, Efthymiopoulos T, Buccitelli C, Segura-Wang M, Northcott P, Pfister SM, Lichter P, Ellenberg J, Korbel JO.

Mol Syst Biol. 2015 Sep 28;11(9):828. doi: 10.15252/msb.20156505.


Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains.

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, van Noort V, Ellenberg J, Bork P, Gavin AC.

Cell Rep. 2015 Sep 1;12(9):1519-30. doi: 10.1016/j.celrep.2015.07.054. Epub 2015 Aug 20.


Proceedings of the University of Pennsylvania 7th annual conference on statistical issues in clinical trials: The use of biomarkers and surrogate endpoints in clinical trials.

Ellenberg SS, Ellenberg JH.

Clin Trials. 2015 Aug;12(4):297-8. doi: 10.1177/1740774515590088. No abstract available.


An actin-dependent spindle position checkpoint ensures the asymmetric division in mouse oocytes.

Metchat A, Eguren M, Hossain JM, Politi AZ, Huet S, Ellenberg J.

Nat Commun. 2015 Jul 15;6:7784. doi: 10.1038/ncomms8784. Retraction in: Nat Commun. 2015;6:8124.


Live imaging and modeling of inner nuclear membrane targeting reveals its molecular requirements in mammalian cells.

Boni A, Politi AZ, Strnad P, Xiang W, Hossain MJ, Ellenberg J.

J Cell Biol. 2015 Jun 8;209(5):705-20. doi: 10.1083/jcb.201409133.


The Impact of Inpatient Versus Outpatient Initiation on Early Warfarin Dosing.

Kasner SE, Wang L, French B, Messe SR, Horenstein R, Mohler ER 3rd, Muldowney JA 3rd, Ellenberg J, Kimmel SE.

Am J Cardiovasc Drugs. 2015 Aug;15(4):267-74. doi: 10.1007/s40256-015-0126-3.


Prematurity and respiratory outcomes program (PROP): study protocol of a prospective multicenter study of respiratory outcomes of preterm infants in the United States.

Pryhuber GS, Maitre NL, Ballard RA, Cifelli D, Davis SD, Ellenberg JH, Greenberg JM, Kemp J, Mariani TJ, Panitch H, Ren C, Shaw P, Taussig LM, Hamvas A; Prematurity and Respiratory Outcomes Program Investigators.

BMC Pediatr. 2015 Apr 10;15:37. doi: 10.1186/s12887-015-0346-3.


Respiratory consequences of prematurity: evolution of a diagnosis and development of a comprehensive approach.

Maitre NL, Ballard RA, Ellenberg JH, Davis SD, Greenberg JM, Hamvas A, Pryhuber GS; Prematurity and Respiratory Outcomes Program.

J Perinatol. 2015 May;35(5):313-321. doi: 10.1038/jp.2015.19. Epub 2015 Mar 26. Review.


High-throughput fluorescence correlation spectroscopy enables analysis of proteome dynamics in living cells.

Wachsmuth M, Conrad C, Bulkescher J, Koch B, Mahen R, Isokane M, Pepperkok R, Ellenberg J.

Nat Biotechnol. 2015 Apr;33(4):384-9. doi: 10.1038/nbt.3146. Epub 2015 Mar 16.


FUN-L: gene prioritization for RNAi screens.

Lees JG, Hériché JK, Morilla I, Fernández JM, Adler P, Krallinger M, Vilo J, Valencia A, Ellenberg J, Ranea JA, Orengo C.

Bioinformatics. 2015 Jun 15;31(12):2052-3. doi: 10.1093/bioinformatics/btv073. Epub 2015 Feb 8.


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