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Research Output

  • 11956 Citations
  • 31 Article
  • 1 Letter
  • 1 Review article
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Article
2020

NAD+ Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging

Levine, D. C., Hong, H., Weidemann, B. J., Ramsey, K. M., Affinati, A. H., Schmidt, M. S., Cedernaes, J., Omura, C., Braun, R., Lee, C., Brenner, C., Peek, C. B. & Bass, J., Jun 4 2020, In : Molecular cell. 78, 5, p. 835-849.e7

Research output: Contribution to journalArticle

3 Scopus citations
2019

GeneSurrounder: Network-based identification of disease genes in expression data

Shah, S. D. & Braun, R., May 6 2019, In : BMC bioinformatics. 20, 1, 229.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia

Wojdyla, T., Mehta, H., Glaubach, T., Bertolusso, R., Iwanaszko, M., Braun, R., Corey, S. J. & Kimmel, M., 2019, In : PLoS computational biology. 15, 1, e1006664.

Research output: Contribution to journalArticle

1 Scopus citations

Strengthening sleep-autonomic interaction via acoustic enhancement of slow oscillations

Grimaldi, D., Papalambros, N. A., Reid, K. J., Abbott, S. M., Malkani, R. G., Gendy, M., Iwanaszko, M., Braun, R. I., Sanchez, D. J., Paller, K. A. & Zee, P. C., May 1 2019, In : Sleep. 42, 5, zsz036.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations
2018

Habitual light exposure relative to circadian timing in delayed sleep-wake phase disorder

Wilson, J., Reid, K. J., Braun, R. I., Abbott, S. M. & Zee, P. C., Nov 1 2018, In : Sleep. 41, 11

Research output: Contribution to journalArticle

3 Scopus citations

Integrative analysis reveals disrupted pathways regulated by MicroRNAs in cancer

Wilk, G. & Braun, R., Feb 16 2018, In : Nucleic acids research. 46, 3, p. 1089-1101 13 p.

Research output: Contribution to journalArticle

7 Scopus citations

Next steps for modelling the evolution of ornamental signals

Clifton, S. M., Braun, R. I. & Abrams, D. M., Jan 1 2018, (Accepted/In press) In : Animal Behaviour.

Research output: Contribution to journalArticle

Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes

Janus, P., Szołtysek, K., Zając, G., Stokowy, T., Walaszczyk, A., Widłak, W., Wojtaś, B., Gielniewski, B., Iwanaszko, M., Braun, R., Cockell, S., Perkins, N. D., Kimmel, M. & Widlak, P., Jun 2018, In : Cellular Signalling. 46, p. 23-31 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors

Wilk, G. & Braun, R., Dec 2018, In : PLoS genetics. 14, 12, e1007837.

Research output: Contribution to journalArticle

8 Scopus citations

Semi-supervised network inference using simulated gene expression dynamics

Nguyen, P. & Braun, R., Apr 1 2018, In : Bioinformatics. 34, 7, p. 1148-1156 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Time-lagged Ordered Lasso for network inference

Nguyen, P. & Braun, R., Dec 29 2018, In : BMC bioinformatics. 19, 1, 545.

Research output: Contribution to journalArticle

2 Scopus citations
30 Scopus citations
2017
64 Scopus citations
2016

Handicap principle implies emergence of dimorphic ornaments

Clifton, S. M., Braun, R. I. & Abrams, D. M., Nov 30 2016, In : Proceedings of the Royal Society B: Biological Sciences. 283, 1843, 20161970.

Research output: Contribution to journalArticle

4 Scopus citations
2014

Network methods for pathway analysis of gene expression data

Braun, R. & Shah, S., Nov 2014, In : arXiv preprint. p. 1993 1 p.

Research output: Contribution to journalArticle

Systems analysis of high-throughput data

Braun, R., 2014, In : Advances in experimental medicine and biology. 844, p. 153-187 35 p.

Research output: Contribution to journalArticle

17 Scopus citations
2013

Discovery Analysis of TCGA Data Reveals Association between Germline Genotype and Survival in Ovarian Cancer Patients

Braun, R., Finney, R., Yan, C., Chen, Q. R., Hu, Y., Edmonson, M., Meerzaman, D. & Buetow, K., Mar 21 2013, In : PloS one. 8, 3, e55037.

Research output: Contribution to journalArticle

22 Scopus citations

Multi-SNP Analysis of GWAS Data Identifies Pathways Associated with Nonalcoholic Fatty Liver Disease

Chen, Q. R., Braun, R., Hu, Y., Yan, C., Brunt, E. M., Meerzaman, D., Sanyal, A. J. & Buetow, K., Jul 19 2013, In : PloS one. 8, 7, e65982.

Research output: Contribution to journalArticle

16 Scopus citations
2011

Partition decoupling for multi-gene analysis of gene expression profiling data

Braun, R., Leibon, G., Pauls, S. & Rockmore, D., Dec 30 2011, In : BMC bioinformatics. 12, 1, 497.

Research output: Contribution to journalArticle

10 Scopus citations

Pathways of distinction analysis: A new technique for multi-SNP analysis of GWAS data

Braun, R. & Buetow, K., Jun 2011, In : PLoS genetics. 7, 6, e1002101.

Research output: Contribution to journalArticle

50 Scopus citations
2009

MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: Associations with survival

Mathé, E. A., Giang, H. N., Bowman, E. D., Zhao, Y., Budhu, A., Schetter, A. J., Braun, R., Reimers, M., Kumamoto, K., Hughes, D., Altorki, N., Casson, A. G., Liu, C. G., Xin, W. W., Yanaihara, N., Hagiwara, N., Dannenberg, A. J., Miyashita, M., Croce, C. M. & Harris, C. C., Oct 1 2009, In : Clinical Cancer Research. 15, 19, p. 6192-6200 9 p.

Research output: Contribution to journalArticle

324 Scopus citations

Needles in the Haystack: Identifying individuals present in pooled genomic data

Braun, R., Rowe, W., Schaefer, C., Zhang, J. & Buetow, K., Oct 2009, In : PLoS genetics. 5, 10, e1000668.

Research output: Contribution to journalArticle

37 Scopus citations
2008

Identifying differential correlation in gene/pathway combinations

Braun, R., Cope, L. & Parmigiani, G., Nov 18 2008, In : BMC Bioinformatics. 9, 488.

Research output: Contribution to journalArticle

19 Scopus citations
2006

Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin

Cohen, J., Arkhipov, A., Braun, R. & Schulten, K., Jan 1 2006, In : Biophysical Journal. 91, 5, p. 1844-1857 14 p.

Research output: Contribution to journalArticle

219 Scopus citations
2005
2004

Molecular dynamics simulations of micelle formation around dimeric glycophorin A transmembrane helices

Braun, R., Engelman, D. M. & Schulten, K., Aug 2004, In : Biophysical Journal. 87, 2, p. 754-763 10 p.

Research output: Contribution to journalArticle

74 Scopus citations
2003

Determining Force Fields

Amaro, R., Autenreith, F., Baudry, J., Braun, R. & Luthey-Schulten, Z., 2003, In : Technical report, Theoretical and Computational Biophysics Group, University of Illinois.

Research output: Contribution to journalArticle

2002

Genetically engineered gold-binding polypeptides: Structure prediction and molecular dynamics

Braun, R., Sarikaya, M. & Schulten, K., 2002, In : Journal of Biomaterials Science, Polymer Edition. 13, 7, p. 747-757 11 p.

Research output: Contribution to journalArticle

139 Scopus citations
1999

Reconstructing Potentials of Mean Force through Time Series Analysis of Steered Molecular Dynamics Simulations

Gullingsrud, J. R., Braun, R. & Schulten, K., May 1 1999, In : Journal of Computational Physics. 151, 1, p. 190-211 22 p.

Research output: Contribution to journalArticle

107 Scopus citations