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Items: 1 to 50 of 141

1.

Versatile transcription control based on reversible dCas9 binding.

Widom JR, Rai V, Rohlman CE, Walter NG.

RNA. 2019 Jul 18. pii: rna.071613.119. doi: 10.1261/rna.071613.119. [Epub ahead of print]

2.

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.

Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL 3rd, Artsimovitch I, Walter NG.

Mol Cell. 2018 Nov 1;72(3):541-552.e6. doi: 10.1016/j.molcel.2018.08.046.

PMID:
30388413
3.

Temperature-dependent conformations of exciton-coupled Cy3 dimers in double-stranded DNA.

Kringle L, Sawaya NPD, Widom J, Adams C, Raymer MG, Aspuru-Guzik A, Marcus AH.

J Chem Phys. 2018 Feb 28;148(8):085101. doi: 10.1063/1.5020084.

4.

Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.

Ray S, Widom JR, Walter NG.

Chem Rev. 2018 Apr 25;118(8):4120-4155. doi: 10.1021/acs.chemrev.7b00519. Epub 2018 Jan 24. Review.

5.

Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.

Daher M, Widom JR, Tay W, Walter NG.

J Mol Biol. 2018 Feb 16;430(4):509-523. doi: 10.1016/j.jmb.2017.10.030. Epub 2017 Nov 8.

6.

Stability and Conformation of a Chemoreceptor HAMP Domain Chimera Correlates with Signaling Properties.

Sukomon N, Widom J, Borbat PP, Freed JH, Crane BR.

Biophys J. 2017 Apr 11;112(7):1383-1395. doi: 10.1016/j.bpj.2017.02.037.

7.

Towards Globally Optimal Crowdsourcing Quality Management: The Uniform Worker Setting.

Das Sarma A, Parameswaran A, Widom J.

Proc ACM SIGMOD Int Conf Manag Data. 2016 Jun-Jul;2016:47-62. doi: 10.1145/2882903.2882953.

8.

Bacterial Energy Sensor Aer Modulates the Activity of the Chemotaxis Kinase CheA Based on the Redox State of the Flavin Cofactor.

Samanta D, Widom J, Borbat PP, Freed JH, Crane BR.

J Biol Chem. 2016 Dec 9;291(50):25809-25814. Epub 2016 Nov 1.

9.

Structure of the frequency-interacting RNA helicase: a protein interaction hub for the circadian clock.

Conrad KS, Hurley JM, Widom J, Ringelberg CS, Loros JJ, Dunlap JC, Crane BR.

EMBO J. 2016 Aug 1;35(15):1707-19. doi: 10.15252/embj.201694327. Epub 2016 Jun 23.

10.

Surpassing Humans and Computers with JellyBean: Crowd-Vision-Hybrid Counting Algorithms.

Sarma AD, Jain A, Nandi A, Parameswaran A, Widom J.

Proc AAAI Conf Hum Comput Crowdsourc. 2015 Nov;2015:178-187.

11.

Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines.

Kahlscheuer ML, Widom J, Walter NG.

Methods Enzymol. 2015;558:539-570. doi: 10.1016/bs.mie.2015.01.009. Epub 2015 Mar 3.

12.

Electric Dipole Transition Moments and Solvent-Dependent Interactions of Fluorescent Boron-Nitrogen Substituted Indole Derivatives.

Saif M, Widom JR, Xu S, Abbey ER, Liu SY, Marcus AH.

J Phys Chem B. 2015 Jun 25;119(25):7985-93. doi: 10.1021/acs.jpcb.5b03485. Epub 2015 Jun 3.

13.

Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.

Sebeson A, Xi L, Zhang Q, Sigmund A, Wang JP, Widom J, Wang X.

PLoS One. 2015 May 18;10(5):e0127214. doi: 10.1371/journal.pone.0127214. eCollection 2015.

14.

Design and mechanism of tetrahydrothiophene-based ╬│-aminobutyric acid aminotransferase inactivators.

Le HV, Hawker DD, Wu R, Doud E, Widom J, Sanishvili R, Liu D, Kelleher NL, Silverman RB.

J Am Chem Soc. 2015 Apr 8;137(13):4525-33. doi: 10.1021/jacs.5b01155. Epub 2015 Mar 30.

15.

In vitro selection of DNAs with an increased propensity to form small circles.

Rosanio G, Widom J, Uhlenbeck OC.

Biopolymers. 2015 Jun;103(6):303-20. doi: 10.1002/bip.22608.

PMID:
25620396
16.

Meeting report: SMART timing--principles of single molecule techniques course at the University of Michigan 2014.

Bartke RM, Cameron EL, Cristie-David AS, Custer TC, Denies MS, Daher M, Dhakal S, Ghosh S, Heinicke LA, Hoff JD, Hou Q, Kahlscheuer ML, Karslake J, Krieger AG, Li J, Li X, Lund PE, Vo NN, Park J, Pitchiaya S, Rai V, Smith DJ, Suddala KC, Wang J, Widom JR, Walter NG.

Biopolymers. 2015 May;103(5):296-302. doi: 10.1002/bip.22603.

17.

Coherent two-dimensional photocurrent spectroscopy in a PbS quantum dot photocell.

Karki KJ, Widom JR, Seibt J, Moody I, Lonergan MC, Pullerits T, Marcus AH.

Nat Commun. 2014 Dec 18;5:5869. doi: 10.1038/ncomms6869.

PMID:
25519819
18.

Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.

Widom JR, Dhakal S, Heinicke LA, Walter NG.

Arch Toxicol. 2014 Nov;88(11):1965-85. doi: 10.1007/s00204-014-1357-9. Epub 2014 Sep 12. Review.

19.

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity.

Small EC, Xi L, Wang JP, Widom J, Licht JD.

Proc Natl Acad Sci U S A. 2014 Jun 17;111(24):E2462-71. doi: 10.1073/pnas.1400517111. Epub 2014 Jun 2.

20.

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo.

Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG.

Elife. 2014 Apr 15;3:e01861. doi: 10.7554/eLife.01861.

21.

A locally convoluted cluster model for nucleosome positioning signals in chemical map.

Xi L, Brogaard K, Zhang Q, Lindsay B, Widom J, Wang JP.

J Am Stat Assoc. 2014 Jan 1;109(505):48-62.

22.

High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster.

Freaney JE, Zhang Q, Yigit E, Kim R, Widom J, Wang JP, Horvath CM.

J Interferon Cytokine Res. 2014 Sep;34(9):676-85. doi: 10.1089/jir.2013.0118. Epub 2014 Mar 27.

23.

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning.

Moyle-Heyrman G, Zaichuk T, Xi L, Zhang Q, Uhlenbeck OC, Holmgren R, Widom J, Wang JP.

Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20158-63. doi: 10.1073/pnas.1315809110. Epub 2013 Nov 25.

24.

Solution conformation of 2-aminopurine (2-AP) dinucleotide determined by ultraviolet 2D fluorescence spectroscopy (UV-2D FS).

Widom JR, Johnson NP, von Hippel PH, Marcus AH.

New J Phys. 2013 Feb 1;15. doi: 10.1088/1367-2630/15/2/025028.

25.

Entangled photon-pair two-dimensional fluorescence spectroscopy (EPP-2DFS).

Raymer MG, Marcus AH, Widom JR, Vitullo DL.

J Phys Chem B. 2013 Dec 12;117(49):15559-75. doi: 10.1021/jp405829n. Epub 2013 Oct 14.

PMID:
24047447
26.

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs.

Nalabothula N, Xi L, Bhattacharyya S, Widom J, Wang JP, Reeve JN, Santangelo TJ, Fondufe-Mittendorf YN.

BMC Genomics. 2013 Jun 10;14:391. doi: 10.1186/1471-2164-14-391.

27.

A physical sciences network characterization of non-tumorigenic and metastatic cells.

Physical Sciences - Oncology Centers Network, Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH.

Sci Rep. 2013;3:1449. doi: 10.1038/srep01449.

28.

Updated structure of Drosophila cryptochrome.

Levy C, Zoltowski BD, Jones AR, Vaidya AT, Top D, Widom J, Young MW, Scrutton NS, Crane BR, Leys D.

Nature. 2013 Mar 21;495(7441):E3-4. doi: 10.1038/nature11995. No abstract available.

29.

Temperature-dependent conformations of a membrane supported zinc porphyrin tweezer by 2D fluorescence spectroscopy.

Widom JR, Lee W, Perdomo-Ortiz A, Rappoport D, Molinski TF, Aspuru-Guzik A, Marcus AH.

J Phys Chem A. 2013 Jul 25;117(29):6171-84. doi: 10.1021/jp400394z. Epub 2013 Mar 29.

30.

High-resolution nucleosome mapping of targeted regions using BAC-based enrichment.

Yigit E, Zhang Q, Xi L, Grilley D, Widom J, Wang JP, Rao A, Pipkin ME.

Nucleic Acids Res. 2013 Apr;41(7):e87. doi: 10.1093/nar/gkt081. Epub 2013 Feb 14.

31.

Nucleosome mapping across the CFTR locus identifies novel regulatory factors.

Yigit E, Bischof JM, Zhang Z, Ott CJ, Kerschner JL, Leir SH, Buitrago-Delgado E, Zhang Q, Wang JP, Widom J, Harris A.

Nucleic Acids Res. 2013 Mar 1;41(5):2857-68. doi: 10.1093/nar/gks1462. Epub 2013 Jan 15.

32.

Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling.

Airola MV, Huh D, Sukomon N, Widom J, Sircar R, Borbat PP, Freed JH, Watts KJ, Crane BR.

J Mol Biol. 2013 Mar 11;425(5):886-901. doi: 10.1016/j.jmb.2012.12.011. Epub 2012 Dec 26.

33.

Electronic transition moments of 6-methyl isoxanthopterin--a fluorescent analogue of the nucleic acid base guanine.

Widom JR, Rappoport D, Perdomo-Ortiz A, Thomsen H, Johnson NP, von Hippel PH, Aspuru-Guzik A, Marcus AH.

Nucleic Acids Res. 2013 Jan;41(2):995-1004. doi: 10.1093/nar/gks1148. Epub 2012 Nov 26.

34.

Controls of nucleosome positioning in the human genome.

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK.

PLoS Genet. 2012;8(11):e1003036. doi: 10.1371/journal.pgen.1003036. Epub 2012 Nov 15.

35.

Compressed Sensing for Multidimensional Spectroscopy Experiments.

Sanders JN, Saikin SK, Mostame S, Andrade X, Widom JR, Marcus AH, Aspuru-Guzik A.

J Phys Chem Lett. 2012 Sep 20;3(18):2697-702. doi: 10.1021/jz300988p. Epub 2012 Sep 11.

PMID:
26295894
36.

A chemical approach to mapping nucleosomes at base pair resolution in yeast.

Brogaard KR, Xi L, Wang JP, Widom J.

Methods Enzymol. 2012;513:315-34. doi: 10.1016/B978-0-12-391938-0.00014-8.

37.

Conformation and electronic population transfer in membrane-supported self-assembled porphyrin dimers by 2D fluorescence spectroscopy.

Perdomo-Ortiz A, Widom JR, Lott GA, Aspuru-Guzik A, Marcus AH.

J Phys Chem B. 2012 Sep 6;116(35):10757-70. doi: 10.1021/jp305916x. Epub 2012 Aug 28.

PMID:
22882118
38.

A map of nucleosome positions in yeast at base-pair resolution.

Brogaard K, Xi L, Wang JP, Widom J.

Nature. 2012 Jun 28;486(7404):496-501. doi: 10.1038/nature11142.

39.

Structure-based identification of new high-affinity nucleosome binding sequences.

Battistini F, Hunter CA, Moore IK, Widom J.

J Mol Biol. 2012 Jun 29;420(1-2):8-16. doi: 10.1016/j.jmb.2012.03.026. Epub 2012 Apr 1.

PMID:
22472421
40.

Two-step mechanism for modifier of transcription 1 (Mot1) enzyme-catalyzed displacement of TATA-binding protein (TBP) from DNA.

Moyle-Heyrman G, Viswanathan R, Widom J, Auble DT.

J Biol Chem. 2012 Mar 16;287(12):9002-12. doi: 10.1074/jbc.M111.333484. Epub 2012 Feb 1.

41.

Structure of full-length Drosophila cryptochrome.

Zoltowski BD, Vaidya AT, Top D, Widom J, Young MW, Crane BR.

Nature. 2011 Nov 13;480(7377):396-9. doi: 10.1038/nature10618. Erratum in: Nature. 2013 Apr 11;496(7444):252.

42.

Conformation of self-assembled porphyrin dimers in liposome vesicles by phase-modulation 2D fluorescence spectroscopy.

Lott GA, Perdomo-Ortiz A, Utterback JK, Widom JR, Aspuru-Guzik A, Marcus AH.

Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16521-6. doi: 10.1073/pnas.1017308108. Epub 2011 Sep 22.

43.

What does physics have to do with cancer?

Michor F, Liphardt J, Ferrari M, Widom J.

Nat Rev Cancer. 2011 Aug 18;11(9):657-70. doi: 10.1038/nrc3092. Review.

44.

Structural constraints in collaborative competition of transcription factors against the nucleosome.

Moyle-Heyrman G, Tims HS, Widom J.

J Mol Biol. 2011 Sep 30;412(4):634-46. doi: 10.1016/j.jmb.2011.07.032. Epub 2011 Jul 29.

45.

Dynamics of nucleosome invasion by DNA binding proteins.

Tims HS, Gurunathan K, Levitus M, Widom J.

J Mol Biol. 2011 Aug 12;411(2):430-48. doi: 10.1016/j.jmb.2011.05.044. Epub 2011 Jun 6.

46.

Modeling DNA-bending in the nucleosome: role of AA periodicity.

Prytkova TR, Zhu X, Widom J, Schatz GC.

J Phys Chem B. 2011 Jul 7;115(26):8638-44. doi: 10.1021/jp203564q. Epub 2011 Jun 16.

47.

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology.

Kaplan N, Hughes TR, Lieb JD, Widom J, Segal E.

Genome Biol. 2010;11(11):140. doi: 10.1186/gb-2010-11-11-140. Epub 2010 Nov 30.

48.

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy.

Lidor Nili E, Field Y, Lubling Y, Widom J, Oren M, Segal E.

Genome Res. 2010 Oct;20(10):1361-8. doi: 10.1101/gr.103945.109. Epub 2010 Aug 17.

49.

Nucleosome sequence preferences influence in vivo nucleosome organization.

Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E.

Nat Struct Mol Biol. 2010 Aug;17(8):918-20. doi: 10.1038/nsmb0810-918. No abstract available.

50.

Predicting nucleosome positioning using a duration Hidden Markov Model.

Xi L, Fondufe-Mittendorf Y, Xia L, Flatow J, Widom J, Wang JP.

BMC Bioinformatics. 2010 Jun 24;11:346. doi: 10.1186/1471-2105-11-346.

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