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ADP-ribosylation Levels and Patterns Correlate with Gene Expression and Clinical Outcomes in Ovarian Cancers.

Conrad LB, Lin KY, Nandu T, Gibson BA, Lea JS, Kraus WL.

Mol Cancer Ther. 2019 Oct 8. pii: molcanther.0569.2019. doi: 10.1158/1535-7163.MCT-19-0569. [Epub ahead of print]


Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells.

Murakami S, Li R, Nagari A, Chae M, Camacho CV, Kraus WL.

Mol Cancer Res. 2019 Dec;17(12):2356-2368. doi: 10.1158/1541-7786.MCR-19-0393. Epub 2019 Sep 24.


Genome-wide Analysis and Functional Prediction of the Estrogen-Regulated Transcriptional Response in the Mouse Uterus.

Vasquez YM, Nandu TS, Kelleher AM, Ramos EI, Gadad SS, Kraus WL.

Biol Reprod. 2019 Sep 12. pii: ioz183. doi: 10.1093/biolre/ioz183. [Epub ahead of print]


Activation of PARP-1 by snoRNAs Controls Ribosome Biogenesis and Cell Growth via the RNA Helicase DDX21.

Kim DS, Camacho CV, Nagari A, Malladi VS, Challa S, Kraus WL.

Mol Cell. 2019 Sep 19;75(6):1270-1285.e14. doi: 10.1016/j.molcel.2019.06.020. Epub 2019 Jul 24.


Identifying Genomic Sites of ADP-Ribosylation Mediated by Specific Nuclear PARP Enzymes Using Click-ChIP.

Rogge RA, Gibson BA, Kraus WL.

Methods Mol Biol. 2018;1813:371-387. doi: 10.1007/978-1-4939-8588-3_25.


Generating Protein-Linked and Protein-Free Mono-, Oligo-, and Poly(ADP-Ribose) In Vitro.

Lin KY, Huang D, Kraus WL.

Methods Mol Biol. 2018;1813:91-108. doi: 10.1007/978-1-4939-8588-3_7. Erratum in: Methods Mol Biol. 2018;1813:C3.


Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis.

Ryu KW, Nandu T, Kim J, Challa S, DeBerardinis RJ, Kraus WL.

Science. 2018 May 11;360(6389). pii: eaan5780. doi: 10.1126/science.aan5780.


Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes.

Xi Y, Shi J, Li W, Tanaka K, Allton KL, Richardson D, Li J, Franco HL, Nagari A, Malladi VS, Coletta LD, Simper MS, Keyomarsi K, Shen J, Bedford MT, Shi X, Barton MC, Kraus WL, Li W, Dent SYR.

BMC Genomics. 2018 Feb 20;19(1):150. doi: 10.1186/s12864-018-4533-0.


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.


Transcriptome signature identifies distinct cervical pathways induced in lipopolysaccharide-mediated preterm birth.

Willcockson AR, Nandu T, Liu CL, Nallasamy S, Kraus WL, Mahendroo M.

Biol Reprod. 2018 Mar 1;98(3):408-421. doi: 10.1093/biolre/iox180.


Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.

Franco HL, Nagari A, Malladi VS, Li W, Xi Y, Richardson D, Allton KL, Tanaka K, Li J, Murakami S, Keyomarsi K, Bedford MT, Shi X, Li W, Barton MC, Dent SYR, Kraus WL.

Genome Res. 2018 Feb;28(2):159-170. doi: 10.1101/gr.226019.117. Epub 2017 Dec 22.


Generation and Characterization of Recombinant Antibody-like ADP-Ribose Binding Proteins.

Gibson BA, Conrad LB, Huang D, Kraus WL.

Biochemistry. 2017 Dec 5;56(48):6305-6316. doi: 10.1021/acs.biochem.7b00670. Epub 2017 Nov 22.


Dynamic assembly and activation of estrogen receptor α enhancers through coregulator switching.

Murakami S, Nagari A, Kraus WL.

Genes Dev. 2017 Aug 1;31(15):1535-1548. doi: 10.1101/gad.302182.117. Epub 2017 Sep 8.


PARP Inhibitors for Cancer Therapy.

Lin KY, Kraus WL.

Cell. 2017 Apr 6;169(2):183. doi: 10.1016/j.cell.2017.03.034.


Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci.

Liu Z, Kraus WL.

Mol Cell. 2017 Feb 16;65(4):589-603.e9. doi: 10.1016/j.molcel.2017.01.017.


PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes.

Gupte R, Liu Z, Kraus WL.

Genes Dev. 2017 Jan 15;31(2):101-126. doi: 10.1101/gad.291518.116. Review.


PARP-1 Controls the Adipogenic Transcriptional Program by PARylating C/EBPβ and Modulating Its Transcriptional Activity.

Luo X, Ryu KW, Kim DS, Nandu T, Medina CJ, Gupte R, Gibson BA, Soccio RE, Yu Y, Gupta RK, Kraus WL.

Mol Cell. 2017 Jan 19;65(2):260-271. doi: 10.1016/j.molcel.2016.11.015.


Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.

Nagari A, Murakami S, Malladi VS, Kraus WL.

Methods Mol Biol. 2017;1468:121-38. doi: 10.1007/978-1-4939-4035-6_10.


miR-200 Regulates Endometrial Development During Early Pregnancy.

Jimenez PT, Mainigi MA, Word RA, Kraus WL, Mendelson CR.

Mol Endocrinol. 2016 Sep;30(9):977-87. doi: 10.1210/me.2016-1050. Epub 2016 Aug 17.


Who Put the "A" in ATP? Generation of ATP from ADP-Ribose in the Nucleus for Hormone-Dependent Gene Regulation.

Ryu KW, Kraus WL.

Mol Cell. 2016 Aug 4;63(3):349-51. doi: 10.1016/j.molcel.2016.07.018.


Editorial: Centennial Celebration - A Focus on Endocrine Disrupting Chemicals… One Hundred Years in the Making.

Kraus WL.

Mol Endocrinol. 2016 Aug;30(8):827-8. doi: 10.1210/me.2016-1097. No abstract available.


Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation.

Gibson BA, Zhang Y, Jiang H, Hussey KM, Shrimp JH, Lin H, Schwede F, Yu Y, Kraus WL.

Science. 2016 Jul 1;353(6294):45-50. doi: 10.1126/science.aaf7865. Epub 2016 Jun 2.


SMARCAD1 is an ATP-dependent stimulator of nucleosomal H2A acetylation via CBP, resulting in transcriptional regulation.

Doiguchi M, Nakagawa T, Imamura Y, Yoneda M, Higashi M, Kubota K, Yamashita S, Asahara H, Iida M, Fujii S, Ikura T, Liu Z, Nandu T, Kraus WL, Ueda H, Ito T.

Sci Rep. 2016 Feb 18;6:20179. doi: 10.1038/srep20179.


Editorial: Would You Like A Hypothesis With Those Data? Omics and the Age of Discovery Science.

Kraus WL.

Mol Endocrinol. 2015 Nov;29(11):1531-4. doi: 10.1210/me.2015-1253. No abstract available.


No driver behind the wheel? Targeting transcription in cancer.

Franco HL, Kraus WL.

Cell. 2015 Sep 24;163(1):28-30. doi: 10.1016/j.cell.2015.09.013.


Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways.

Liu X, Kraus WL, Bai X.

Trends Biochem Sci. 2015 Sep;40(9):516-25. doi: 10.1016/j.tibs.2015.07.003. Epub 2015 Aug 4. Review.


Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells.

Sun M, Gadad SS, Kim DS, Kraus WL.

Mol Cell. 2015 Aug 20;59(4):698-711. doi: 10.1016/j.molcel.2015.06.023. Epub 2015 Jul 30.


groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data.

Chae M, Danko CG, Kraus WL.

BMC Bioinformatics. 2015 Jul 16;16:222. doi: 10.1186/s12859-015-0656-3.


PARPs and ADP-Ribosylation: 50 Years … and Counting.

Kraus WL.

Mol Cell. 2015 Jun 18;58(6):902-10. doi: 10.1016/j.molcel.2015.06.006.


PARPs and ADP-Ribosylation Come Into Focus.

Kraus WL.

Mol Cell. 2015 Jun 18;58(6):901. doi: 10.1016/j.molcel.2015.06.014. No abstract available.


A PreSTIGEous use of LncRNAs to predict enhancers.

Murakami S, Gadad SS, Kraus WL.

Cell Cycle. 2015;14(11):1619-20. doi: 10.1080/15384101.2015.1032650. No abstract available.


Linking the aryl hydrocarbon receptor with altered DNA methylation patterns and developmentally induced aberrant antiviral CD8+ T cell responses.

Winans B, Nagari A, Chae M, Post CM, Ko CI, Puga A, Kraus WL, Lawrence BP.

J Immunol. 2015 May 1;194(9):4446-57. doi: 10.4049/jimmunol.1402044. Epub 2015 Mar 25.


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.


TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome.

Franco HL, Nagari A, Kraus WL.

Mol Cell. 2015 Apr 2;58(1):21-34. doi: 10.1016/j.molcel.2015.02.001. Epub 2015 Mar 5.


New facets in the regulation of gene expression by ADP-ribosylation and poly(ADP-ribose) polymerases.

Ryu KW, Kim DS, Kraus WL.

Chem Rev. 2015 Mar 25;115(6):2453-81. doi: 10.1021/cr5004248. Epub 2015 Jan 9. Review. No abstract available.


From Discovery to Function: The Expanding Roles of Long Non-Coding RNAs in Physiology and Disease.

Sun M, Kraus WL.

Endocr Rev. 2015 Jan 7:er00009999. [Epub ahead of print]


From discovery to function: the expanding roles of long noncoding RNAs in physiology and disease.

Sun M, Kraus WL.

Endocr Rev. 2015 Feb;36(1):25-64. doi: 10.1210/er.2014-1034. Epub 2014 Nov 26. Review.


Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms.

Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA, Sullivan KD, Galbraith MD, Luo X, Kraus WL, Dowell RD, Espinosa JM.

Elife. 2014 May 27;3:e02200. doi: 10.7554/eLife.02200.


The histone variant MacroH2A1 regulates target gene expression in part by recruiting the transcriptional coregulator PELP1.

Hussey KM, Chen H, Yang C, Park E, Hah N, Erdjument-Bromage H, Tempst P, Gamble MJ, Kraus WL.

Mol Cell Biol. 2014 Jul;34(13):2437-49. doi: 10.1128/MCB.01315-13. Epub 2014 Apr 21.


Editorial: Do you see what I see? Quality, reliability, and reproducibility in biomedical research.

Kraus WL.

Mol Endocrinol. 2014 Mar;28(3):277-80. doi: 10.1210/me.2014-1036. No abstract available.


Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses.

Luo X, Chae M, Krishnakumar R, Danko CG, Kraus WL.

BMC Genomics. 2014 Feb 24;15:155. doi: 10.1186/1471-2164-15-155.


Mapping ERβ genomic binding sites reveals unique genomic features and identifies EBF1 as an ERβ interactor.

Le TP, Sun M, Luo X, Kraus WL, Greene GL.

PLoS One. 2013 Aug 8;8(8):e71355. doi: 10.1371/journal.pone.0071355. eCollection 2013.


Minireview: Long noncoding RNAs: new "links" between gene expression and cellular outcomes in endocrinology.

Sun M, Kraus WL.

Mol Endocrinol. 2013 Sep;27(9):1390-402. doi: 10.1210/me.2013-1113. Epub 2013 Jul 24. Review.


Hormone-regulated transcriptomes: lessons learned from estrogen signaling pathways in breast cancer cells.

Hah N, Kraus WL.

Mol Cell Endocrinol. 2014 Jan 25;382(1):652-664. doi: 10.1016/j.mce.2013.06.021. Epub 2013 Jun 28. Review.


Enhancer transcripts mark active estrogen receptor binding sites.

Hah N, Murakami S, Nagari A, Danko CG, Kraus WL.

Genome Res. 2013 Aug;23(8):1210-23. doi: 10.1101/gr.152306.112. Epub 2013 May 1.


Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells.

Danko CG, Hah N, Luo X, Martins AL, Core L, Lis JT, Siepel A, Kraus WL.

Mol Cell. 2013 Apr 25;50(2):212-22. doi: 10.1016/j.molcel.2013.02.015. Epub 2013 Mar 21. Erratum in: Mol Cell. 2013 Jun 6;50(5):778.


PARP-1 and gene regulation: progress and puzzles.

Kraus WL, Hottiger MO.

Mol Aspects Med. 2013 Dec;34(6):1109-23. doi: 10.1016/j.mam.2013.01.005. Epub 2013 Jan 26. Review.


New insights into the molecular and cellular functions of poly(ADP-ribose) and PARPs.

Gibson BA, Kraus WL.

Nat Rev Mol Cell Biol. 2012 Jun 20;13(7):411-24. doi: 10.1038/nrm3376. Review.


Estrogen regulates JNK1 genomic localization to control gene expression and cell growth in breast cancer cells.

Sun M, Isaacs GD, Hah N, Heldring N, Fogarty EA, Kraus WL.

Mol Endocrinol. 2012 May;26(5):736-47. doi: 10.1210/me.2011-1158. Epub 2012 Mar 22.

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