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Research Output 1993 2019

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2019
5 Citations (Scopus)

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

Kim, D. S., Camacho, C. V., Nagari, A., Malladi, V. S., Challa, S. & Kraus, W. L., Sep 19 2019, In : Molecular cell. 75, 6, p. 1270-1285.e14

Research output: Contribution to journalArticle

Small Nucleolar RNA
RNA Helicases
Ribosomes
Ribosomal DNA
Adenosine Diphosphate
2018
13 Citations (Scopus)

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

Danko, C. G., Choate, L. A., Marks, B. A., Rice, E. J., Wang, Z., Chu, T., Martins, A. L., Dukler, N., Coonrod, S. A., Tait Wojno, E. D., Lis, J. T., Kraus, W. L. & Siepel, A., Jan 29 2018, (Accepted/In press) In : Nature Ecology and Evolution. p. 1-12 12 p.

Research output: Contribution to journalArticle

primate
RNA
Primates
transcription (genetics)
T-lymphocytes
12 Citations (Scopus)

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

Franco, H. L., Nagari, A., Malladi, V. S., Li, W., Xi, Y., Richardson, D., Allton, K. L., Tanaka, K., Li, J., Murakami, S., Keyomarsi, K., Bedford, M. T., Shi, X., Li, W., Barton, M. C., Dent, S. Y. R. & Kraus, W. L., Feb 1 2018, In : Genome Research. 28, 2, p. 159-170 12 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Gene Expression
Triple Negative Breast Neoplasms
Transcription Factors
Cell Line
4 Citations (Scopus)

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

Xi, Y., Shi, J., Li, W., Tanaka, K., Allton, K. L., Richardson, D., Li, J., Franco, H. L., Nagari, A., Malladi, V. S., Coletta, L. D., Simper, M. S., Keyomarsi, K., Shen, J., Bedford, M. T., Shi, X., Barton, M. C., Lee Kraus, W., Li, W. & Dent, S. Y. R., Feb 20 2018, In : BMC Genomics. 19, 1, 150.

Research output: Contribution to journalArticle

Histone Code
Epigenomics
Chromatin
Breast Neoplasms
Cell Line
27 Citations (Scopus)

Metabolic regulation of transcription through compartmentalized NAD+ biosynthesis

Ryu, K. W., Nandu, T., Kim, J., Challa, S., DeBerardinis, R. J. & Lee Kraus, W., May 11 2018, In : Science. 360, 6389, Y.

Research output: Contribution to journalArticle

NAD
Nicotinamide Mononucleotide
Physiological Phenomena
Poly Adenosine Diphosphate Ribose
Adipogenesis
12 Citations (Scopus)

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

Willcockson, A. R., Nandu, T., Liu, C. L., Nallasamy, S., Kraus, W. L. & Mahendroo, M., Mar 1 2018, In : Biology of Reproduction. 98, 3, p. 408-421 14 p.

Research output: Contribution to journalArticle

Premature Birth
Transcriptome
Lipopolysaccharides
Peptide Hydrolases
Elastic Tissue
2017
24 Citations (Scopus)

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

Liu, Z. & Kraus, W. L., Feb 16 2017, In : Molecular Cell. 65, 4, p. 589-603.e9

Research output: Contribution to journalArticle

Transcription Factors
Nucleosomes
Chromatin
Binding Sites
Embryonic Stem Cells
5 Citations (Scopus)

Computational approaches for mining GRO-seq data to identify and characterize active enhancers

Nagari, A., Murakami, S., Malladi, V. S. & Kraus, W. L., 2017, In : Methods in Molecular Biology. 1468, p. 121-138 18 p.

Research output: Contribution to journalArticle

Transcription Factors
RNA Polymerase II
DNA-Directed RNA Polymerases
Molecular Biology
Binding Sites
14 Citations (Scopus)

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

Murakami, S., Nagari, A. & Kraus, W. L., Aug 1 2017, In : Genes and Development. 31, 15, p. 1535-1548 14 p.

Research output: Contribution to journalArticle

Estrogen Receptors
Steroid Receptors
Maintenance
Hormones
Breast Neoplasms
11 Citations (Scopus)

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

Gibson, B. A., Conrad, L. B., Huang, D. & Kraus, W. L., Dec 5 2017, In : Biochemistry. 56, 48, p. 6305-6316 12 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate Ribose
Carrier Proteins
Antibodies
Adenosine Diphosphate
Assays
20 Citations (Scopus)

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

Luo, X., Ryu, K. W., Kim, D. S., Nandu, T., Medina, C. J., Gupte, R., Gibson, B. A., Soccio, R. E., Yu, Y., Gupta, R. K. & Kraus, W. L., Jan 19 2017, In : Molecular Cell. 65, 2, p. 260-271 12 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate
Poly C
Adipogenesis
Post Translational Protein Processing
Transcription Factors
2016
129 Citations (Scopus)

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

Gibson, B. A., Zhang, Y., Jiang, H., Hussey, K. M., Shrimp, J. H., Lin, H., Schwede, F., Yu, Y. & Kraus, W. L., Jul 1 2016, In : Science. 353, 6294, p. 45-50 6 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate Ribose
Poly Adenosine Diphosphate Ribose
Adenosine Diphosphate
NAD
Proteome
14 Citations (Scopus)

miR-200 regulates endometrial development during early pregnancy

Jimenez, P. T., Mainigi, M. A., Word, R. A., Kraus, W. L. & Mendelson, C. R., Sep 1 2016, In : Molecular Endocrinology. 30, 9, p. 977-987 11 p.

Research output: Contribution to journalArticle

MicroRNAs
Pregnancy
Stromal Cells
Superovulation
Epithelial-Mesenchymal Transition
9 Citations (Scopus)

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, W. L., Ueda, H. & Ito, T., Feb 18 2016, In : Scientific Reports. 6, 20179.

Research output: Contribution to journalArticle

CREB-Binding Protein
Acetylation
Adenosine Triphosphate
Histones
Nucleosomes
2015
1 Citation (Scopus)

A PreSTIGEous use of LncRNAs to predict enhancers

Murakami, S., Gadad, S. S. & Kraus, W. L., Jan 1 2015, In : Cell Cycle. 14, 11, p. 1619-1620 2 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
74 Citations (Scopus)

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

Sun, M., Gadad, S. S., Kim, D. S. & Kraus, W. L., Aug 20 2015, In : Molecular Cell. 59, 4, p. 698-711 14 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
cdc Genes
Breast Neoplasms
Gene Expression
Histone Code
2 Citations (Scopus)

Editorial: Would you like a hypothesis with those data? Omics and the age of discovery science

Lee Kraus, W., Nov 1 2015, In : Molecular Endocrinology. 29, 11, p. 1531-1534 4 p.

Research output: Contribution to journalArticle

Metabolomics
Gene Expression Profiling
Microarray Analysis
Genomics
Proteomics
143 Citations (Scopus)

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

Sun, M. & Kraus, W. L., 2015, In : Endocrine Reviews. 36, 1, p. 25-64 40 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Muscle Neoplasms
Neurobiology
Endocrinology
Gene Expression Regulation
17 Citations (Scopus)
Fibroblasts
Transcription
Lung
Cardiac Myocytes
Sequencing
63 Citations (Scopus)

Identification of active transcriptional regulatory elements from GRO-seq data

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., Cheung, V. G., Kraus, W. L., Lis, J. T. & Siepel, A., Apr 29 2015, In : Nature Methods. 12, 5, p. 433-438 6 p.

Research output: Contribution to journalArticle

RNA Caps
Transcriptional Regulatory Elements
Polymorphism
Gene expression
Histones
26 Citations (Scopus)

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

Winans, B., Nagari, A., Chae, M., Post, C. M., Ko, C. I., Puga, A., Kraus, W. L. & Lawrence, B. P., May 1 2015, In : Journal of Immunology. 194, 9, p. 4446-4457 12 p.

Research output: Contribution to journalArticle

Aryl Hydrocarbon Receptors
DNA Methylation
Antiviral Agents
T-Lymphocytes
Infection
54 Citations (Scopus)

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

Ryu, K. W., Kim, D. S. & Kraus, W. L., Mar 25 2015, In : Chemical Reviews. 115, 6, p. 2453-2481 29 p.

Research output: Contribution to journalArticle

Poly(ADP-ribose) Polymerases
Gene expression
NAD
Adenosine Diphosphate
Adenosine Diphosphate Ribose
14 Citations (Scopus)

No Driver behind the Wheel? Targeting Transcription in Cancer

Franco, H. L. & Kraus, W. L., Sep 24 2015, In : Cell. 163, 1, p. 28-30 3 p.

Research output: Contribution to journalArticle

Transcription
Wheels
Triple Negative Breast Neoplasms
Cyclin-Dependent Kinases
Cell death
56 Citations (Scopus)

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

Kraus, W. L., Jun 18 2015, In : Molecular Cell. 58, 6, p. 902-910 9 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate
DNA Damage
Poly Adenosine Diphosphate Ribose
Biological Phenomena
Transferases
2 Citations (Scopus)

PARPs and ADP-Ribosylation Come Into Focus

Kraus, W. L., Jun 18 2015, In : Molecular Cell. 58, 6, p. 901 1 p.

Research output: Contribution to journalArticle

Adenosine Diphosphate Ribose
Poly Adenosine Diphosphate Ribose
Poly(ADP-ribose) Polymerases
Post Translational Protein Processing
Adenosine Diphosphate
53 Citations (Scopus)

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

Liu, X., Kraus, W. L. & Bai, X., Sep 1 2015, In : Trends in Biochemical Sciences. 40, 9, p. 516-525 10 p.

Research output: Contribution to journalArticle

Cell signaling
RNA Polymerase II
Biological systems
Transcription
Genes
54 Citations (Scopus)

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

Franco, H. L., Nagari, A. & Kraus, W. L., Apr 2 2015, In : Molecular Cell. 58, 1, p. 21-34 14 p.

Research output: Contribution to journalArticle

Transcriptome
Estrogen Receptors
Binding Sites
Breast Neoplasms
Gene Expression
2014
21 Citations (Scopus)

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

Luo, X., Chae, M., Krishnakumar, R., Danko, C. G. & Kraus, W. L., Feb 24 2014, In : BMC Genomics. 15, 1, 155.

Research output: Contribution to journalArticle

Transcriptome
Cardiac Myocytes
Tumor Necrosis Factor-alpha
Amanitins
Genes
13 Citations (Scopus)

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

Lee Kraus, W., Mar 2014, In : Molecular Endocrinology. 28, 3, p. 277-280 4 p.

Research output: Contribution to journalArticle

Scientific Misconduct
Quality Improvement
Reproducibility of Results
Biomedical Research
91 Citations (Scopus)

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

Allen, M. A., Andrysik, Z., Dengler, V. L., Mellert, H. S., Guarnieri, A., Freeman, J. A., Sullivan, K. D., Galbraith, M. D., Luo, X., Lee Kraus, W., Dowell, R. D. & Espinosa, J. M., May 27 2014, In : eLife. 2014, 3, e02200.

Research output: Contribution to journalArticle

p53 Genes
Transcription
Genes
RNA
Null Lymphocytes
44 Citations (Scopus)

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

Hah, N. & Kraus, W. L., Jan 25 2014, In : Molecular and Cellular Endocrinology. 382, 1, p. 652-664 13 p.

Research output: Contribution to journalArticle

Transcriptome
Estrogens
Cells
Hormones
Breast Neoplasms
11 Citations (Scopus)

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

Hussey, K. M., Chen, H., Yang, C., Park, E., Hah, N., Erdjument-Bromage, H., Tempst, P., Gamble, M. J. & Kraus, W. L., 2014, In : Molecular and Cellular Biology. 34, 13, p. 2437-2449 13 p.

Research output: Contribution to journalArticle

Histones
Gene Expression
Chromatin
Ligands
Chromatin Immunoprecipitation
2013
248 Citations (Scopus)

Enhancer transcripts mark active estrogen receptor binding sites

Hah, N., Murakami, S., Nagari, A., Danko, C. G. & Lee Kraus, W., Aug 2013, In : Genome Research. 23, 8, p. 1210-1223 14 p.

Research output: Contribution to journalArticle

alvocidib
Estrogen Receptors
Binding Sites
Estrogen Receptor alpha
Genes

Erratum to Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells [Molecular Cell 50, (2013) 778]

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A. & Kraus, W. L., Jun 6 2013, In : Molecular Cell. 50, 5, p. 778 1 p.

Research output: Contribution to journalArticle

RNA Polymerase II
10 Citations (Scopus)

Mapping ERβ Genomic Binding Sites Reveals Unique Genomic Features and Identifies EBF1 as an ERβ Interactor

Le, T. P., Sun, M., Luo, X., Kraus, W. L. & Greene, G. L., Aug 8 2013, In : PLoS One. 8, 8, e71355.

Research output: Contribution to journalArticle

binding sites
Binding Sites
genomics
Physiology
Estrogen Receptors
27 Citations (Scopus)

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

Sun, M. & Lee Kraus, W., Sep 1 2013, In : Molecular Endocrinology. 27, 9, p. 1390-1402 13 p.

Research output: Contribution to journalArticle

Long Noncoding RNA
Endocrinology
Gene Expression
RNA
Untranslated RNA
144 Citations (Scopus)

PARP-1 and gene regulation: Progress and puzzles

Kraus, W. L. & Hottiger, M. O., Dec 2013, In : Molecular Aspects of Medicine. 34, 6, p. 1109-1123 15 p.

Research output: Contribution to journalArticle

Poly(ADP-ribose) Polymerases
Gene expression
Genes
Transcription
Regulator Genes
164 Citations (Scopus)

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

Danko, C. G., Hah, N., Luo, X., Martins, A. L., Core, L., Lis, J. T., Siepel, A. & Kraus, W. L., Apr 25 2013, In : Molecular Cell. 50, 2, p. 212-222 11 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Long Noncoding RNA
Transcriptional Activation
Genes
Estradiol
2012
5 Citations (Scopus)
JNK Mitogen-Activated Protein Kinases
Uterine Cervical Neoplasms
Estrogen Receptors
Epithelial Cells
Chemical activation
11 Citations (Scopus)

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

Sun, M., Isaacs, G. D., Hah, N., Heldring, N., Fogarty, E. A. & Lee Kraus, W., May 2012, In : Molecular Endocrinology. 26, 5, p. 736-747 12 p.

Research output: Contribution to journalArticle

Estrogens
Phosphotransferases
Breast Neoplasms
Gene Expression
Estrogen Receptors
552 Citations (Scopus)

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

Gibson, B. A. & Kraus, W. L., Jul 2012, In : Nature Reviews Molecular Cell Biology. 13, 7, p. 411-424 14 p.

Research output: Contribution to journalArticle

Poly Adenosine Diphosphate Ribose
Poly(ADP-ribose) Polymerases
Adenosine Diphosphate Ribose
Proteins
Adenosine Diphosphate
375 Citations (Scopus)

On par with PARP: Cellular stress signaling through poly(ADP-ribose) and PARP-1

Luo, X. & Lee Kraus, W., Mar 1 2012, In : Genes and Development. 26, 5, p. 417-432 16 p.

Research output: Contribution to journalArticle

NAD
Adenosine Diphosphate Ribose
Physiological Stress
Metabolome
Metabolic Diseases
47 Citations (Scopus)

Regulation of poly(ADP-ribose) polymerase-1-dependent gene expression through promoter-directed recruitment of a nuclear NAD + synthase

Zhang, T., Berrocal, J. G., Yao, J., DuMond, M. E., Krishnakumar, R., Ruhl, D. D., Ryu, K. W., Gamble, M. J. & Kraus, W. L., Apr 6 2012, In : Journal of Biological Chemistry. 287, 15, p. 12405-12416 12 p.

Research output: Contribution to journalArticle

Poly(ADP-ribose) Polymerases
Gene expression
Genes
Gene Expression
NAD
2011
11 Citations (Scopus)

A one and a two ... expanding roles for poly(ADP-ribose) polymerases in metabolism

Luo, X. & Kraus, W. L., Apr 6 2011, In : Cell Metabolism. 13, 4, p. 353-355 3 p.

Research output: Contribution to journalArticle

Poly(ADP-ribose) Polymerases
NAD
Energy Metabolism
Obesity
Diet
290 Citations (Scopus)

A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T. & Kraus, W. L., May 13 2011, In : Cell. 145, 4, p. 622-634 13 p.

Research output: Contribution to journalArticle

Transient analysis
Estrogens
Cells
Breast Neoplasms
Transcriptome

Erratum: A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells (Cell (2011) 145 (622-634))

Hah, N., Danko, C. G., Core, L., Waterfall, J. J., Siepel, A., Lis, J. T. & Kraus, W. L., Jun 24 2011, In : Cell. 145, 7, p. 1156 1 p.

Research output: Contribution to journalArticle

Estrogens
Breast Neoplasms
29 Citations (Scopus)

Evolution of ligand specificity in vertebrate corticosteroid receptors

Arterbery, A. S., Fergus, D. J., Fogarty, E. A., Mayberry, J., Deitcher, D. L., Kraus, W. L. & Bass, A. H., 2011, In : BMC Evolutionary Biology. 11, 1, 14.

Research output: Contribution to journalArticle

mineralocorticoids
adrenal cortex hormones
teleost
ligand
vertebrate
58 Citations (Scopus)

Genome-Wide analysis reveals PADI4 cooperates with Elk-1 to activate C-Fos expression in breast cancer cells

Zhang, X., Gamble, M. J., Stadler, S., Cherrington, B. D., Causey, C. P., Thompson, P. R., Roberson, M. S., Kraus, W. L. & Coonrod, S. A., Jun 2011, In : PLoS Genetics. 7, 6, e1002112.

Research output: Contribution to journalArticle

elks
breast neoplasms
cancer
genome
Genome
35 Citations (Scopus)

Multiple sequence-specific DNA-binding proteins mediate estrogen receptor signaling through a tethering pathway

Heldring, N., Isaacs, G. D., Diehl, A. G., Sun, M., Cheung, E., Ranish, J. A. & Lee Kraus, W., Apr 2011, In : Molecular Endocrinology. 25, 4, p. 564-574 11 p.

Research output: Contribution to journalArticle

DNA-Binding Proteins
Estrogen Receptors
Transcription Factors
Estrogens
Transcription Factor AP-1
11 Citations (Scopus)

Small Molecules, Big Effects: A Role for Chromatin-Localized Metabolite Biosynthesis in Gene Regulation

Gibson, B. A. & Kraus, W. L., Mar 4 2011, In : Molecular Cell. 41, 5, p. 497-499 3 p.

Research output: Contribution to journalArticle

Chromatin
S-Adenosylmethionine
Co-Repressor Proteins
Genes
Enzymes