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Items: 1 to 50 of 295

1.

Chromatin conformation remains stable upon extensive transcriptional changes driven by heat shock.

Ray J, Munn PR, Vihervaara A, Lewis JJ, Ozer A, Danko CG, Lis JT.

Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19431-19439. doi: 10.1073/pnas.1901244116. Epub 2019 Sep 10.

PMID:
31506350
2.

NSAID associated bilateral renal infarctions: a case report.

Jeon Y, Lis JB, Chang WG.

Int J Nephrol Renovasc Dis. 2019 Aug 1;12:177-181. doi: 10.2147/IJNRD.S212010. eCollection 2019.

3.

A 50 year history of technologies that drove discovery in eukaryotic transcription regulation.

Lis JT.

Nat Struct Mol Biol. 2019 Sep;26(9):777-782. doi: 10.1038/s41594-019-0288-9. Epub 2019 Aug 22. Review.

PMID:
31439942
4.

Nascent RNA analyses: tracking transcription and its regulation.

Wissink EM, Vihervaara A, Tippens ND, Lis JT.

Nat Rev Genet. 2019 Aug 9. doi: 10.1038/s41576-019-0159-6. [Epub ahead of print] Review.

PMID:
31399713
5.

Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features.

Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis JT, Heard E, Schulz EG, Marsico A.

Genome Res. 2019 Jul;29(7):1087-1099. doi: 10.1101/gr.245027.118. Epub 2019 Jun 7.

6.

Electronic transport in planar atomic-scale structures measured by two-probe scanning tunneling spectroscopy.

Kolmer M, Brandimarte P, Lis J, Zuzak R, Godlewski S, Kawai H, Garcia-Lekue A, Lorente N, Frederiksen T, Joachim C, Sanchez-Portal D, Szymonski M.

Nat Commun. 2019 Apr 5;10(1):1573. doi: 10.1038/s41467-019-09315-6.

7.
9.

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells.

Zhang Z, Chng KR, Lingadahalli S, Chen Z, Liu MH, Do HH, Cai S, Rinaldi N, Poh HM, Li G, Sung YY, Heng CL, Core LJ, Tan SK, Ruan X, Lis JT, Kellis M, Ruan Y, Sung WK, Cheung E.

Genome Res. 2019 Feb;29(2):223-235. doi: 10.1101/gr.230243.117. Epub 2019 Jan 3.

10.

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers.

Tome JM, Tippens ND, Lis JT.

Nat Genet. 2018 Nov;50(11):1533-1541. doi: 10.1038/s41588-018-0234-5. Epub 2018 Oct 22.

11.

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme.

Chu T, Rice EJ, Booth GT, Salamanca HH, Wang Z, Core LJ, Longo SL, Corona RJ, Chin LS, Lis JT, Kwak H, Danko CG.

Nat Genet. 2018 Nov;50(11):1553-1564. doi: 10.1038/s41588-018-0244-3. Epub 2018 Oct 22.

12.

A Cdk9-PP1 switch regulates the elongation-termination transition of RNA polymerase II.

Parua PK, Booth GT, Sansó M, Benjamin B, Tanny JC, Lis JT, Fisher RP.

Nature. 2018 Jun;558(7710):460-464. doi: 10.1038/s41586-018-0214-z. Epub 2018 Jun 13.

13.

Molecular mechanisms driving transcriptional stress responses.

Vihervaara A, Duarte FM, Lis JT.

Nat Rev Genet. 2018 Jun;19(6):385-397. doi: 10.1038/s41576-018-0001-6. Review.

14.

Clinical and economic impact of a one-year treatment with omalizumab in patients with severe allergic asthma within a drug programme in Poland.

Jahnz-Różyk K, Lis J, Warchoł M, Kucharczyk A.

BMC Pulm Med. 2018 Mar 16;18(1):48. doi: 10.1186/s12890-018-0610-z.

15.

Enhancer transcription: what, where, when, and why?

Tippens ND, Vihervaara A, Lis JT.

Genes Dev. 2018 Jan 1;32(1):1-3. doi: 10.1101/gad.311605.118. Review.

16.

Cdk9 regulates a promoter-proximal checkpoint to modulate RNA polymerase II elongation rate in fission yeast.

Booth GT, Parua PK, Sansó M, Fisher RP, Lis JT.

Nat Commun. 2018 Feb 7;9(1):543. doi: 10.1038/s41467-018-03006-4.

17.

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells.

Danko CG, Choate LA, Marks BA, Rice EJ, Wang Z, Chu T, Martins AL, Dukler N, Coonrod SA, Tait Wojno ED, Lis JT, Kraus WL, Siepel A.

Nat Ecol Evol. 2018 Mar;2(3):537-548. doi: 10.1038/s41559-017-0447-5. Epub 2018 Jan 29.

18.

Corrigendum: The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Dec 14;552(7684):278. doi: 10.1038/nature24667. Epub 2017 Nov 22.

PMID:
29168505
19.

CBP Regulates Recruitment and Release of Promoter-Proximal RNA Polymerase II.

Boija A, Mahat DB, Zare A, Holmqvist PH, Philip P, Meyers DJ, Cole PA, Lis JT, Stenberg P, Mannervik M.

Mol Cell. 2017 Nov 2;68(3):491-503.e5. doi: 10.1016/j.molcel.2017.09.031. Epub 2017 Oct 19.

20.

Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol.

Dukler N, Booth GT, Huang YF, Tippens N, Waters CT, Danko CG, Lis JT, Siepel A.

Genome Res. 2017 Nov;27(11):1816-1829. doi: 10.1101/gr.222935.117. Epub 2017 Oct 12.

21.

The 4D nucleome project.

Dekker J, Belmont AS, Guttman M, Leshyk VO, Lis JT, Lomvardas S, Mirny LA, O'Shea CC, Park PJ, Ren B, Politz JCR, Shendure J, Zhong S; 4D Nucleome Network.

Nature. 2017 Sep 13;549(7671):219-226. doi: 10.1038/nature23884. Erratum in: Nature. 2017 Nov 22;:.

22.

A Molecular Method to Detect Wound Cells in Bloodstains Resultant of Sharp Force Injuries for Crime Scene Reconstruction.

Johnson DJ, Raymond DE, Chen C, Quon M, Lis J, Choi MR, Lopez C, Han A, de Leon RD, Bir C.

J Forensic Sci. 2018 May;63(3):842-848. doi: 10.1111/1556-4029.13623. Epub 2017 Aug 23.

PMID:
28834611
23.

Transcriptional response to stress is pre-wired by promoter and enhancer architecture.

Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L.

Nat Commun. 2017 Aug 15;8(1):255. doi: 10.1038/s41467-017-00151-0.

24.

Use of conditioned media is critical for studies of regulation in response to rapid heat shock.

Mahat DB, Lis JT.

Cell Stress Chaperones. 2017 Jan;22(1):155-162. doi: 10.1007/s12192-016-0737-x. Epub 2016 Nov 3.

25.

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB.

Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131. doi: 10.1038/nsmb.3316. Epub 2016 Oct 31.

27.

High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML.

Zhao Y, Liu Q, Acharya P, Stengel KR, Sheng Q, Zhou X, Kwak H, Fischer MA, Bradner JE, Strickland SA, Mohan SR, Savona MR, Venters BJ, Zhou MM, Lis JT, Hiebert SW.

Cell Rep. 2016 Aug 16;16(7):2003-16. doi: 10.1016/j.celrep.2016.07.032. Epub 2016 Aug 4.

28.

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation.

Duarte FM, Fuda NJ, Mahat DB, Core LJ, Guertin MJ, Lis JT.

Genes Dev. 2016 Aug 1;30(15):1731-46. doi: 10.1101/gad.284430.116. Epub 2016 Aug 4.

29.

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq).

Mahat DB, Kwak H, Booth GT, Jonkers IH, Danko CG, Patel RK, Waters CT, Munson K, Core LJ, Lis JT.

Nat Protoc. 2016 Aug;11(8):1455-76. doi: 10.1038/nprot.2016.086. Epub 2016 Jul 21.

30.

Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device.

Reinholt SJ, Ozer A, Lis JT, Craighead HG.

Sci Rep. 2016 Jul 19;6:29771. doi: 10.1038/srep29771.

31.
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33.
35.

Corrigendum: Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast.

Booth GT, Wang IX, Cheung VG, Lis JT.

Genome Res. 2016 Jul;26(7):1010-1. doi: 10.1101/gr.210161.116. No abstract available.

36.

Divergence of a conserved elongation factor and transcription regulation in budding and fission yeast.

Booth GT, Wang IX, Cheung VG, Lis JT.

Genome Res. 2016 Jun;26(6):799-811. doi: 10.1101/gr.204578.116. Epub 2016 May 12. Erratum in: Genome Res. 2016 Jul;26(7):1010-1.

37.

Mammalian Heat Shock Response and Mechanisms Underlying Its Genome-wide Transcriptional Regulation.

Mahat DB, Salamanca HH, Duarte FM, Danko CG, Lis JT.

Mol Cell. 2016 Apr 7;62(1):63-78. doi: 10.1016/j.molcel.2016.02.025. Epub 2016 Mar 24.

38.

Human Gene Promoters Are Intrinsically Bidirectional.

Andersson R, Chen Y, Core L, Lis JT, Sandelin A, Jensen TH.

Mol Cell. 2015 Nov 5;60(3):346-7. doi: 10.1016/j.molcel.2015.10.015. No abstract available.

39.

Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality.

Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA.

Cell Rep. 2015 Oct 13;13(2):337-49. doi: 10.1016/j.celrep.2015.08.075. Epub 2015 Sep 24.

40.

Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling.

Ozer A, Tome JM, Friedman RC, Gheba D, Schroth GP, Lis JT.

Nat Protoc. 2015 Aug;10(8):1212-33. doi: 10.1038/nprot.2015.074. Epub 2015 Jul 16.

41.

Pembrolizumab versus investigator-choice chemotherapy for ipilimumab-refractory melanoma (KEYNOTE-002): a randomised, controlled, phase 2 trial.

Ribas A, Puzanov I, Dummer R, Schadendorf D, Hamid O, Robert C, Hodi FS, Schachter J, Pavlick AC, Lewis KD, Cranmer LD, Blank CU, O'Day SJ, Ascierto PA, Salama AK, Margolin KA, Loquai C, Eigentler TK, Gangadhar TC, Carlino MS, Agarwala SS, Moschos SJ, Sosman JA, Goldinger SM, Shapira-Frommer R, Gonzalez R, Kirkwood JM, Wolchok JD, Eggermont A, Li XN, Zhou W, Zernhelt AM, Lis J, Ebbinghaus S, Kang SP, Daud A.

Lancet Oncol. 2015 Aug;16(8):908-18. doi: 10.1016/S1470-2045(15)00083-2. Epub 2015 Jun 23.

PMID:
26115796
42.

GAGA factor maintains nucleosome-free regions and has a role in RNA polymerase II recruitment to promoters.

Fuda NJ, Guertin MJ, Sharma S, Danko CG, Martins AL, Siepel A, Lis JT.

PLoS Genet. 2015 Mar 27;11(3):e1005108. doi: 10.1371/journal.pgen.1005108. eCollection 2015 Mar.

43.

Identification of active transcriptional regulatory elements from GRO-seq data.

Danko CG, Hyland SL, Core LJ, Martins AL, Waters CT, Lee HW, Cheung VG, Kraus WL, Lis JT, Siepel A.

Nat Methods. 2015 May;12(5):433-8. doi: 10.1038/nmeth.3329. Epub 2015 Mar 23.

44.

Getting up to speed with transcription elongation by RNA polymerase II.

Jonkers I, Lis JT.

Nat Rev Mol Cell Biol. 2015 Mar;16(3):167-77. doi: 10.1038/nrm3953. Epub 2015 Feb 18. Review.

45.

[Uroplakins as markers of diseases of the urinary system].

Lis J, Kątnik-Prastowska I, Tupikowski K, Matejuk A.

Postepy Hig Med Dosw (Online). 2015 Jan 21;69:98-113. Review. Polish.

PMID:
25614678
46.

Systematic review and meta-analysis of randomized clinical trials comparing efficacy and safety outcomes of insulin glargine with NPH insulin, premixed insulin preparations or with insulin detemir in type 2 diabetes mellitus.

Rys P, Wojciechowski P, Rogoz-Sitek A, Niesyczyński G, Lis J, Syta A, Malecki MT.

Acta Diabetol. 2015 Aug;52(4):649-62. doi: 10.1007/s00592-014-0698-4. Epub 2015 Jan 14. Review.

47.
48.

Towards resolving a problem of the identity of the Aethus species (Hemiptera: Heteroptera: Cydnidae) occurring in Cambodia.

Lis JA, Lis B, Ziaja DJ, Nakatani Y.

Zootaxa. 2014 Dec 16;3895(3):446-50. doi: 10.11646/zootaxa.3895.3.9.

PMID:
25543581
49.

Application of denaturing gradient gel electrophoresis (DGGE) for assessing fecal pollution sources at a recreational beach.

Esseili MA, Kassem II, Lis J, Sigler V.

J Water Health. 2014 Dec;12(4):846-57. doi: 10.2166/wh.2014.034.

PMID:
25473994
50.

Glycosylation of uroplakins. Implications for bladder physiopathology.

Kątnik-Prastowska I, Lis J, Matejuk A.

Glycoconj J. 2014 Dec;31(9):623-36. doi: 10.1007/s10719-014-9564-4. Epub 2014 Nov 15. Review.

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