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Items: 1 to 50 of 84

1.

In Vivo Chemical Probing for G-Quadruplex Formation.

Kouzine F, Wojtowicz D, Yamane A, Casellas R, Przytycka TM, Levens DL.

Methods Mol Biol. 2019;2035:369-382. doi: 10.1007/978-1-4939-9666-7_23.

PMID:
31444763
2.

A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers.

El Khattabi L, Zhao H, Kalchschmidt J, Young N, Jung S, Van Blerkom P, Kieffer-Kwon P, Kieffer-Kwon KR, Park S, Wang X, Krebs J, Tripathi S, Sakabe N, Sobreira DR, Huang SC, Rao SSP, Pruett N, Chauss D, Sadler E, Lopez A, Nóbrega MA, Aiden EL, Asturias FJ, Casellas R.

Cell. 2019 Aug 22;178(5):1145-1158.e20. doi: 10.1016/j.cell.2019.07.011. Epub 2019 Aug 8.

PMID:
31402173
3.

The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1.

Petermann F, Pękowska A, Johnson CA, Jankovic D, Shih HY, Jiang K, Hudson WH, Brooks SR, Sun HW, Villarino AV, Yao C, Singleton K, Akondy RS, Kanno Y, Sher A, Casellas R, Ahmed R, O'Shea JJ.

Mol Cell. 2019 Sep 19;75(6):1229-1242.e5. doi: 10.1016/j.molcel.2019.06.025. Epub 2019 Jul 31.

PMID:
31377117
4.

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.

5.

Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition.

Shastri N, Tsai YC, Hile S, Jordan D, Powell B, Chen J, Maloney D, Dose M, Lo Y, Anastassiadis T, Rivera O, Kim T, Shah S, Borole P, Asija K, Wang X, Smith KD, Finn D, Schug J, Casellas R, Yatsunyk LA, Eckert KA, Brown EJ.

Mol Cell. 2018 Oct 18;72(2):222-238.e11. doi: 10.1016/j.molcel.2018.08.047. Epub 2018 Oct 4.

6.

The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination.

Delgado-Benito V, Rosen DB, Wang Q, Gazumyan A, Pai JA, Oliveira TY, Sundaravinayagam D, Zhang W, Andreani M, Keller L, Kieffer-Kwon KR, Pękowska A, Jung S, Driesner M, Subbotin RI, Casellas R, Chait BT, Nussenzweig MC, Di Virgilio M.

Mol Cell. 2018 Nov 15;72(4):636-649.e8. doi: 10.1016/j.molcel.2018.08.042. Epub 2018 Oct 4.

7.

The Energetics and Physiological Impact of Cohesin Extrusion.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R.

Cell. 2018 Sep 20;175(1):292-294. doi: 10.1016/j.cell.2018.09.002. No abstract available.

8.

The Energetics and Physiological Impact of Cohesin Extrusion.

Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R.

Cell. 2018 May 17;173(5):1165-1178.e20. doi: 10.1016/j.cell.2018.03.072. Epub 2018 Apr 26. Erratum in: Cell. 2018 Sep 20;175(1):292-294.

9.

Epigenetic silencing of miR-125b is required for normal B-cell development.

Li G, So AY, Sookram R, Wong S, Wang JK, Ouyang Y, He P, Su Y, Casellas R, Baltimore D.

Blood. 2018 Apr 26;131(17):1920-1930. doi: 10.1182/blood-2018-01-824540. Epub 2018 Mar 19.

10.

The Reign of Antibodies: A Celebration of and Tribute to Michael Potter and His Homogeneous Immunoglobulin Workshops.

Gearhart PJ, Mock BA, Casellas R, Cancro MP.

J Immunol. 2018 Jan 1;200(1):23-26. doi: 10.4049/jimmunol.1701516. No abstract available.

11.

Cohesin Loss Eliminates All Loop Domains.

Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL.

Cell. 2017 Oct 5;171(2):305-320.e24. doi: 10.1016/j.cell.2017.09.026.

12.

Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation.

Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Tomassoni Ardori F, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R.

Mol Cell. 2017 Aug 17;67(4):566-578.e10. doi: 10.1016/j.molcel.2017.07.013. Epub 2017 Aug 10.

13.

Genome Organization Drives Chromosome Fragility.

Canela A, Maman Y, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Aiden EL, Casellas R, Nussenzweig A.

Cell. 2017 Jul 27;170(3):507-521.e18. doi: 10.1016/j.cell.2017.06.034. Epub 2017 Jul 20.

14.

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.

Kouzine F, Wojtowicz D, Baranello L, Yamane A, Nelson S, Resch W, Kieffer-Kwon KR, Benham CJ, Casellas R, Przytycka TM, Levens D.

Cell Syst. 2017 Mar 22;4(3):344-356.e7. doi: 10.1016/j.cels.2017.01.013. Epub 2017 Feb 22.

15.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, Zou J, Sartorelli V.

Cell Rep. 2017 Jan 3;18(1):297. doi: 10.1016/j.celrep.2016.12.036. No abstract available.

16.

Fas/CD95 prevents autoimmunity independently of lipid raft localization and efficient apoptosis induction.

Cruz AC, Ramaswamy M, Ouyang C, Klebanoff CA, Sengupta P, Yamamoto TN, Meylan F, Thomas SK, Richoz N, Eil R, Price S, Casellas R, Rao VK, Lippincott-Schwartz J, Restifo NP, Siegel RM.

Nat Commun. 2016 Dec 23;7:13895. doi: 10.1038/ncomms13895.

17.

The cell cycle restricts activation-induced cytidine deaminase activity to early G1.

Wang Q, Kieffer-Kwon KR, Oliveira TY, Mayer CT, Yao K, Pai J, Cao Z, Dose M, Casellas R, Jankovic M, Nussenzweig MC, Robbiani DF.

J Exp Med. 2017 Jan;214(1):49-58. doi: 10.1084/jem.20161649. Epub 2016 Dec 20.

18.

Roles of H3K27me2 and H3K27me3 Examined during Fate Specification of Embryonic Stem Cells.

Juan AH, Wang S, Ko KD, Zare H, Tsai PF, Feng X, Vivanco KO, Ascoli AM, Gutierrez-Cruz G, Krebs J, Sidoli S, Knight AL, Pedersen RA, Garcia BA, Casellas R, Zou J, Sartorelli V.

Cell Rep. 2016 Oct 25;17(5):1369-1382. doi: 10.1016/j.celrep.2016.09.087. Erratum in: Cell Rep. 2017 Jan 3;18(1):297.

19.

HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells.

Zhang S, Zhu I, Deng T, Furusawa T, Rochman M, Vacchio MS, Bosselut R, Yamane A, Casellas R, Landsman D, Bustin M.

Nucleic Acids Res. 2016 Sep 6;44(15):7144-58. doi: 10.1093/nar/gkw323. Epub 2016 Apr 25.

20.

Mutations, kataegis and translocations in B cells: understanding AID promiscuous activity.

Casellas R, Basu U, Yewdell WT, Chaudhuri J, Robbiani DF, Di Noia JM.

Nat Rev Immunol. 2016 Mar;16(3):164-76. doi: 10.1038/nri.2016.2. Epub 2016 Feb 22. Review.

21.

Somatic Rearrangement in B Cells: It's (Mostly) Nuclear Physics.

Aiden EL, Casellas R.

Cell. 2015 Aug 13;162(4):708-11. doi: 10.1016/j.cell.2015.07.034. Review.

22.

RAG Represents a Widespread Threat to the Lymphocyte Genome.

Teng G, Maman Y, Resch W, Kim M, Yamane A, Qian J, Kieffer-Kwon KR, Mandal M, Ji Y, Meffre E, Clark MR, Cowell LG, Casellas R, Schatz DG.

Cell. 2015 Aug 13;162(4):751-65. doi: 10.1016/j.cell.2015.07.009. Epub 2015 Jul 30.

23.

Mechanisms of clonal evolution in childhood acute lymphoblastic leukemia.

Swaminathan S, Klemm L, Park E, Papaemmanuil E, Ford A, Kweon SM, Trageser D, Hasselfeld B, Henke N, Mooster J, Geng H, Schwarz K, Kogan SC, Casellas R, Schatz DG, Lieber MR, Greaves MF, Müschen M.

Nat Immunol. 2015 Jul;16(7):766-774. doi: 10.1038/ni.3160. Epub 2015 May 18.

24.

MicroRNA-146a regulates ICOS-ICOSL signalling to limit accumulation of T follicular helper cells and germinal centres.

Pratama A, Srivastava M, Williams NJ, Papa I, Lee SK, Dinh XT, Hutloff A, Jordan MA, Zhao JL, Casellas R, Athanasopoulos V, Vinuesa CG.

Nat Commun. 2015 Mar 6;6:6436. doi: 10.1038/ncomms7436.

25.

Epigenetic targeting of activation-induced cytidine deaminase.

Wang Q, Oliveira T, Jankovic M, Silva IT, Hakim O, Yao K, Gazumyan A, Mayer CT, Pavri R, Casellas R, Nussenzweig MC, Robbiani DF.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18667-72. doi: 10.1073/pnas.1420575111. Epub 2014 Dec 15.

26.

B cell super-enhancers and regulatory clusters recruit AID tumorigenic activity.

Qian J, Wang Q, Dose M, Pruett N, Kieffer-Kwon KR, Resch W, Liang G, Tang Z, Mathé E, Benner C, Dubois W, Nelson S, Vian L, Oliveira TY, Jankovic M, Hakim O, Gazumyan A, Pavri R, Awasthi P, Song B, Liu G, Chen L, Zhu S, Feigenbaum L, Staudt L, Murre C, Ruan Y, Robbiani DF, Pan-Hammarström Q, Nussenzweig MC, Casellas R.

Cell. 2014 Dec 18;159(7):1524-37. doi: 10.1016/j.cell.2014.11.013. Epub 2014 Dec 4.

27.

Convergent transcription at intragenic super-enhancers targets AID-initiated genomic instability.

Meng FL, Du Z, Federation A, Hu J, Wang Q, Kieffer-Kwon KR, Meyers RM, Amor C, Wasserman CR, Neuberg D, Casellas R, Nussenzweig MC, Bradner JE, Liu XS, Alt FW.

Cell. 2014 Dec 18;159(7):1538-48. doi: 10.1016/j.cell.2014.11.014. Epub 2014 Dec 4.

28.

A mouse model of HIES reveals pro- and anti-inflammatory functions of STAT3.

Steward-Tharp SM, Laurence A, Kanno Y, Kotlyar A, Villarino AV, Sciume G, Kuchen S, Resch W, Wohlfert EA, Jiang K, Hirahara K, Vahedi G, Sun HW, Feigenbaum L, Milner JD, Holland SM, Casellas R, Powrie F, O'Shea JJ.

Blood. 2014 May 8;123(19):2978-87. doi: 10.1182/blood-2013-09-523167. Epub 2014 Mar 14.

29.

Design and performance evaluation of an OpenFlow-based control plane for software-defined elastic optical networks with direct-detection optical OFDM (DDO-OFDM) transmission.

Liu L, Peng WR, Casellas R, Tsuritani T, Morita I, Martínez R, Muñoz R, Yoo SJ.

Opt Express. 2014 Jan 13;22(1):30-40. doi: 10.1364/OE.22.000030.

PMID:
24514962
30.

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.

Kieffer-Kwon KR, Tang Z, Mathe E, Qian J, Sung MH, Li G, Resch W, Baek S, Pruett N, Grøntved L, Vian L, Nelson S, Zare H, Hakim O, Reyon D, Yamane A, Nakahashi H, Kovalchuk AL, Zou J, Joung JK, Sartorelli V, Wei CL, Ruan X, Hager GL, Ruan Y, Casellas R.

Cell. 2013 Dec 19;155(7):1507-20. doi: 10.1016/j.cell.2013.11.039.

31.

The origin of B cell recurrent chromosomal translocations: proximity versus DNA damage.

Casellas R, Resch W, Hakim O, Nussenzweig MC.

Mol Cell. 2013 Aug 8;51(3):275-6. doi: 10.1016/j.molcel.2013.07.020. No abstract available.

32.

Fate mapping for activation-induced cytidine deaminase (AID) marks non-lymphoid cells during mouse development.

Rommel PC, Bosque D, Gitlin AD, Croft GF, Heintz N, Casellas R, Nussenzweig MC, Kriaucionis S, Robbiani DF.

PLoS One. 2013 Jul 8;8(7):e69208. doi: 10.1371/journal.pone.0069208. Print 2013.

33.

B cell-specific deficiencies in mTOR limit humoral immune responses.

Zhang S, Pruitt M, Tran D, Du Bois W, Zhang K, Patel R, Hoover S, Simpson RM, Simmons J, Gary J, Snapper CM, Casellas R, Mock BA.

J Immunol. 2013 Aug 15;191(4):1692-703. doi: 10.4049/jimmunol.1201767. Epub 2013 Jul 15.

34.

Partition of Myc into immobile vs. mobile complexes within nuclei.

Rosales T, Nie Z, Kapoor V, Casellas R Jr, Knutson JR, Levens D.

Sci Rep. 2013;3:1953. doi: 10.1038/srep01953.

35.

A genome-wide map of CTCF multivalency redefines the CTCF code.

Nakahashi H, Kieffer Kwon KR, Resch W, Vian L, Dose M, Stavreva D, Hakim O, Pruett N, Nelson S, Yamane A, Qian J, Dubois W, Welsh S, Phair RD, Pugh BF, Lobanenkov V, Hager GL, Casellas R.

Cell Rep. 2013 May 30;3(5):1678-1689. doi: 10.1016/j.celrep.2013.04.024. Epub 2013 May 23.

36.

Global regulation of promoter melting in naive lymphocytes.

Kouzine F, Wojtowicz D, Yamane A, Resch W, Kieffer-Kwon KR, Bandle R, Nelson S, Nakahashi H, Awasthi P, Feigenbaum L, Menoni H, Hoeijmakers J, Vermeulen W, Ge H, Przytycka TM, Levens D, Casellas R.

Cell. 2013 May 23;153(5):988-99. doi: 10.1016/j.cell.2013.04.033.

37.

Experimental demonstration of an OpenFlow based software-defined optical network employing packet, fixed and flexible DWDM grid technologies on an international multi-domain testbed.

Channegowda M, Nejabati R, Rashidi Fard M, Peng S, Amaya N, Zervas G, Simeonidou D, Vilalta R, Casellas R, Martínez R, Muñoz R, Liu L, Tsuritani T, Morita I, Autenrieth A, Elbers JP, Kostecki P, Kaczmarek P.

Opt Express. 2013 Mar 11;21(5):5487-98. doi: 10.1364/OE.21.005487.

PMID:
23482120
38.

Experimental assessment of dynamic integrated restoration in GMPLS multi-layer (MPLS-TP/WSON) networks.

Martínez R, Casellas R, Muñoz R.

Opt Express. 2013 Mar 11;21(5):5481-6. doi: 10.1364/OE.21.005481.

PMID:
23482119
39.

OpenSlice: an OpenFlow-based control plane for spectrum sliced elastic optical path networks.

Liu L, Muñoz R, Casellas R, Tsuritani T, Martínez R, Morita I.

Opt Express. 2013 Feb 25;21(4):4194-204. doi: 10.1364/OE.21.004194.

PMID:
23481953
40.

Experimental demonstration of an OpenFlow/PCE integrated control plane for IP over translucent WSON with the assistance of a per-request-based dynamic topology server.

Liu L, Casellas R, Tsuritani T, Morita I, Martínez R, Muñoz R.

Opt Express. 2013 Feb 25;21(4):4183-93. doi: 10.1364/OE.21.004183.

PMID:
23481952
41.

Dynamic virtual GMPLS-controlled WSON using a Resource Broker with a VNT Manager on the ADRENALINE testbed.

Vilalta R, Muñoz R, Casellas R, Martinez R.

Opt Express. 2012 Dec 31;20(28):29149-54. doi: 10.1364/OE.20.029149.

PMID:
23388740
42.

Inter-layer traffic engineering with hierarchical-PCE in MPLS-TP over wavelength switched optical networks.

Casellas R, Martinez R, Muñoz R, Liu L, Tsuritani T, Morita I.

Opt Express. 2012 Dec 31;20(28):29137-42. doi: 10.1364/OE.20.029137.

PMID:
23388738
43.

Identification of early replicating fragile sites that contribute to genome instability.

Barlow JH, Faryabi RB, Callén E, Wong N, Malhowski A, Chen HT, Gutierrez-Cruz G, Sun HW, McKinnon P, Wright G, Casellas R, Robbiani DF, Staudt L, Fernandez-Capetillo O, Nussenzweig A.

Cell. 2013 Jan 31;152(3):620-32. doi: 10.1016/j.cell.2013.01.006. Epub 2013 Jan 24. Review.

44.

Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching.

Di Virgilio M, Callen E, Yamane A, Zhang W, Jankovic M, Gitlin AD, Feldhahn N, Resch W, Oliveira TY, Chait BT, Nussenzweig A, Casellas R, Robbiani DF, Nussenzweig MC.

Science. 2013 Feb 8;339(6120):711-5. doi: 10.1126/science.1230624. Epub 2013 Jan 10.

45.

RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle.

Yamane A, Robbiani DF, Resch W, Bothmer A, Nakahashi H, Oliveira T, Rommel PC, Brown EJ, Nussenzweig A, Nussenzweig MC, Casellas R.

Cell Rep. 2013 Jan 31;3(1):138-47. doi: 10.1016/j.celrep.2012.12.006. Epub 2013 Jan 3.

46.

53BP1 alters the landscape of DNA rearrangements and suppresses AID-induced B cell lymphoma.

Jankovic M, Feldhahn N, Oliveira TY, Silva IT, Kieffer-Kwon KR, Yamane A, Resch W, Klein I, Robbiani DF, Casellas R, Nussenzweig MC.

Mol Cell. 2013 Feb 21;49(4):623-31. doi: 10.1016/j.molcel.2012.11.029. Epub 2013 Jan 3.

47.

Experimental evaluation of efficient routing and distributed spectrum allocation algorithms for GMPLS elastic networks.

Muñoz R, Casellas R, Martínez R, Liu L, Tsuritani T, Morita I.

Opt Express. 2012 Dec 17;20(27):28532-7. doi: 10.1364/OE.20.028532.

PMID:
23263090
48.

Mechanism of DNA resection during intrachromosomal recombination and immunoglobulin class switching.

Bothmer A, Rommel PC, Gazumyan A, Polato F, Reczek CR, Muellenbeck MF, Schaetzlein S, Edelmann W, Chen PL, Brosh RM Jr, Casellas R, Ludwig T, Baer R, Nussenzweig A, Nussenzweig MC, Robbiani DF.

J Exp Med. 2013 Jan 14;210(1):115-23. doi: 10.1084/jem.20121975. Epub 2012 Dec 17.

49.

c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells.

Nie Z, Hu G, Wei G, Cui K, Yamane A, Resch W, Wang R, Green DR, Tessarollo L, Casellas R, Zhao K, Levens D.

Cell. 2012 Sep 28;151(1):68-79. doi: 10.1016/j.cell.2012.08.033.

50.

Oncogenic Myc translocations are independent of chromosomal location and orientation of the immunoglobulin heavy chain locus.

Spehalski E, Kovalchuk AL, Collins JT, Liang G, Dubois W, Morse HC 3rd, Ferguson DO, Casellas R, Dunnick WA.

Proc Natl Acad Sci U S A. 2012 Aug 21;109(34):13728-32. doi: 10.1073/pnas.1202882109. Epub 2012 Aug 6.

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