| Kim M, Liotta EM, Maas MB, Braun RI, Garcia-Canga B, Ganger DR, Ladner DP, Reid KJ, Zee PC. | Rest-activity rhythm disturbance in liver cirrhosis and association with cognitive impairment. Sleep. 2020 Dec 25;. doi: 10.1093/sleep/zsaa288. [Epub ahead of print] PubMed PMID: 33367862. | 2020 |
| Grimaldi D, Reid KJ, Papalambros NA, Braun RI, Malkani RG, Abbott SM, Ong JC, Zee PC. | Autonomic dysregulation and sleep homeostasis in insomnia. Sleep. 2020 Dec 9;. doi: 10.1093/sleep/zsaa274. [Epub ahead of print] PubMed PMID: 33295989. | 2020 |
| Maas MB, Iwanaszko M, Lizza BD, Reid KJ, Braun RI, Zee PC. | Circadian Gene Expression Rhythms During Critical Illness. Crit Care Med. 2020 Dec;48(12):e1294-e1299. doi: 10.1097/CCM.0000000000004697. PubMed PMID: 33031153; PubMed Central PMCID: PMC7708445. | 2020 |
| Ness-Cohn E, Iwanaszko M, Kath WL, Allada R, Braun R. | TimeTrial: An Interactive Application for Optimizing the Design and Analysis of Transcriptomic Time-Series Data in Circadian Biology Research. J Biol Rhythms. 2020 Oct;35(5):439-451. doi: 10.1177/0748730420934672. Epub 2020 Jul 2. PubMed PMID: 32613882; PubMed Central PMCID: PMC7534021. | 2020 |
| Levine DC, Hong H, Weidemann BJ, Ramsey KM, Affinati AH, Schmidt MS, Cedernaes J, Omura C, Braun R, Lee C, Brenner C, Peek CB, Bass J. | NAD+Controls Circadian Reprogramming through PER2 Nuclear Translocation to Counter Aging. Mol Cell. 2020 Jun 4;78(5):835-849.e7. doi: 10.1016/j.molcel.2020.04.010. Epub 2020 May 4. PubMed PMID: 32369735; PubMed Central PMCID: PMC7275919. | 2020 |
| Shah SD, Braun R. | GeneSurrounder: network-based identification of disease genes in expression data. BMC Bioinformatics. 2019 May 6;20(1):229. doi: 10.1186/s12859-019-2829-y. PubMed PMID: 31060502; PubMed Central PMCID: PMC6503437. | 2019 |
| Grimaldi D, Papalambros NA, Reid KJ, Abbott SM, Malkani RG, Gendy M, Iwanaszko M, Braun RI, Sanchez DJ, Paller KA, Zee PC. | Strengthening sleep-autonomic interaction via acoustic enhancement of slow oscillations. Sleep. 2019 May 1;42(5). doi: 10.1093/sleep/zsz036. PubMed PMID: 30753650; PubMed Central PMCID: PMC7729207 | 2019 |
| Braun R, Kath WL, Iwanaszko M, Kula-Eversole E, Abbott SM, Reid KJ, Zee PC, Allada R. | Reply to Laing et al.: Accurate prediction of circadian time across platforms. Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5206-5208. doi: 10.1073/pnas.1819173116. Epub 2019 Mar 14. PubMed PMID: 30872489; PubMed Central PMCID: PMC6431220. | 2019 |
| Wojdyla T, Mehta H, Glaubach T, Bertolusso R, Iwanaszko M, Braun R, Corey SJ, Kimmel M. | Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia. PLoS Comput Biol.2019 Jan;15(1):e1006664. doi: 10.1371/journal.pcbi.1006664. eCollection 2019 Jan. PubMed PMID: 30615612; PubMed Central PMCID: PMC6336352. | 2019 |
| Nguyen P, Braun R. | Time-lagged Ordered Lasso for network inference. BMC Bioinformatics. 2018 Dec 29;19(1):545. doi: 10.1186/s12859-018-2558-7. PubMed PMID: 30594121; PubMed Central PMCID: PMC6311035. | 2018 |
| Wilk G, Braun R. | regQTLs: Single nucleotide polymorphisms that modulate microRNA regulation of gene expression in tumors. PLoS Genet. 2018 Dec;14(12):e1007837. doi: 10.1371/journal.pgen.1007837. eCollection 2018 Dec. PubMed PMID: 30557297; PubMed Central PMCID: PMC6343932. | 2018 |
| Wilson J 4th, Reid KJ, Braun RI, Abbott SM, Zee PC. | Habitual light exposure relative to circadian timing in delayed sleep-wake phase disorder.Sleep. 2018 Nov 1;41(11). doi: 10.1093/sleep/zsy166. PubMed PMID: 30423177; PubMed Central PMCID: PMC6231529. | 2018 |
| Braun R, Kath WL, Iwanaszko M, Kula-Eversole E, Abbott SM, Reid KJ, Zee PC, Allada R. | Universal method for robust detection of circadian state from gene expression. Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):E9247-E9256. doi: 10.1073/pnas.1800314115. Epub 2018 Sep 10. PubMed PMID: 30201705; PubMed Central PMCID: PMC6166804. | 2018 |
| Janus P, Szołtysek K, Zając G, Stokowy T, Walaszczyk A, Widłak W, Wojtaś B, Gielniewski B, Iwanaszko M, Braun R, Cockell S, Perkins ND, Kimmel M, Widlak P. | Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes. Cell Signal. 2018 Jun;46:23-31. doi: 10.1016/j.cellsig.2018.02.011. Epub 2018 Feb 21. PubMed PMID: 29476964. | 2018 |
| Papalambros NA, Grimaldi D, Reid KJ, Abbott SM, Malkani RG, Santostasi G, Gendy M, Ritger A, Braun RI, Sanchez D, Paller KA, Zee PC. | Acoustically induced changes in sleep spindle and autonomic activity predict memory consolidation. Sleep. 2018 April; 41(suppl_1):A34. doi: 10.1093/sleep/zsy061.082. | 2018 |
| Nguyen P, Braun R. | Semi-supervised network inference using simulated gene expression dynamics. Bioinformatics. 2018 Apr 1;34(7):1148-1156. doi: 10.1093/bioinformatics/btx748. PubMed PMID: 29186340; PubMed Central PMCID: PMC6455938. | 2018 |
| Clifton SM, Braun RI, Abrams DM. | Next steps for modelling the evolution of ornamental signals. Animal behaviour. 2018 March; doi: 10.1016/j.anbehav.2018.01.017. | 2018 |
| Wilk G, Braun R. | Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer. Nucleic Acids Res. 2018 Feb 16;46(3):1089-1101. doi: 10.1093/nar/gkx1250. PubMed PMID: 29294105; PubMed Central PMCID: PMC5814839. | 2018 |
| Papalambros NA, Santostasi G, Malkani RG, Braun R, Weintraub S, Paller KA, Zee PC. | Acoustic Enhancement of Sleep Slow Oscillations and Concomitant Memory Improvement in Older Adults. Front Hum Neurosci. 2017;11:109. doi: 10.3389/fnhum.2017.00109. eCollection 2017. PubMed PMID: 28337134; PubMed Central PMCID: PMC5340797. | 2017 |
| Clifton SM, Braun RI, Abrams DM. | Handicap principle implies emergence of dimorphic ornaments. Proc Biol Sci. 2016 Nov 30;283(1843). doi: 10.1098/rspb.2016.1970. PubMed PMID: 27903876; PubMed Central PMCID: PMC5136597. | 2016 |
| Kennedy M, Garibay C, Sanford C, Braun R, Koerner J, Lewin J, Daugherty R. | Science Club: Bridging In-SchooAl and Out-of-School STEM Learning Through a Collaborative, Community-Based After-School Program. Connected Science Learning. 2016 March; 1(1). | 2016 |
| Braun R, Shah S. | Network Methods for Pathway Analysis of Genomic Data. arXiv:1411.1993. 2014 November; | 2014 |
| Braun R. | Systems analysis of high-throughput data. Adv Exp Med Biol. 2014;844:153-87. doi: 10.1007/978-1-4939-2095-2_8. Review. PubMed PMID: 25480641; PubMed Central PMCID: PMC4426208. | 2014 |
| Chen QR, Braun R, Hu Y, Yan C, Brunt EM, Meerzaman D, Sanyal AJ, Buetow K. | Multi-SNP analysis of GWAS data identifies pathways associated with nonalcoholic fatty liver disease. PLoS One. 2013;8(7):e65982. doi: 10.1371/journal.pone.0065982. Print 2013. PubMed PMID: 23894275; PubMed Central PMCID: PMC3716806. | 2013 |
| Braun R, Finney R, Yan C, Chen QR, Hu Y, Edmonson M, Meerzaman D, Buetow K. | Discovery analysis of TCGA data reveals association between germline genotype and survival in ovarian cancer patients. PLoS One. 2013;8(3):e55037. doi: 10.1371/journal.pone.0055037. Epub 2013 Mar 21. PubMed PMID: 23555554; PubMed Central PMCID: PMC3605427. | 2013 |
| Braun R, Leibon G, Pauls S, Rockmore D. | Partition decoupling for multi-gene analysis of gene expression profiling data. BMC Bioinformatics. 2011 Dec 30;12:497. doi: 10.1186/1471-2105-12-497. PubMed PMID: 22208906; PubMed Central PMCID: PMC3276603. | 2011 |
| Braun R, Buetow K. | Pathways of distinction analysis: a new technique for multi-SNP analysis of GWAS data. PLoS Genet. 2011 Jun;7(6):e1002101. doi: 10.1371/journal.pgen.1002101. Epub 2011 Jun 9. PubMed PMID: 21695280; PubMed Central PMCID: PMC3111473. | 2011 |
| Braun R, Rowe W, Schaefer C, Zhang J, Buetow K. | Needles in the haystack: identifying individuals present in pooled genomic data. PLoS Genet.2009 Oct;5(10):e1000668. doi: 10.1371/journal.pgen.1000668. Epub 2009 Oct 2. PubMed PMID: 19798441; PubMed Central PMCID: PMC2747273. | 2009 |
| Mathé EA, Nguyen GH, Bowman ED, Zhao Y, Budhu A, Schetter AJ, Braun R, Reimers M, Kumamoto K, Hughes D, Altorki NK, Casson AG, Liu CG, Wang XW, Yanaihara N, Hagiwara N, Dannenberg AJ, Miyashita M, Croce CM, Harris CC. | MicroRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: associations with survival. Clin Cancer Res. 2009 Oct 1;15(19):6192-200. doi: 10.1158/1078-0432.CCR-09-1467. Epub 2009 Sep 29. PubMed PMID: 19789312; PubMed Central PMCID: PMC2933109. | 2009 |
| Braun R, Cope L, Parmigiani G. | Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008 Nov 18;9:488. doi: 10.1186/1471-2105-9-488. PubMed PMID: 19017408; PubMed Central PMCID: PMC2613418. | 2008 |
| Cohen J, Arkhipov A, Braun R, Schulten K. | Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin. Biophys J. 2006 Sep 1;91(5):1844-57. doi: 10.1529/biophysj.106.085746. Epub 2006 Jun 2. PubMed PMID: 16751246; PubMed Central PMCID: PMC1544290. | 2006 |
| Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. | Scalable molecular dynamics with NAMD. J Comput Chem. 2005 Dec;26(16):1781-802. doi: 10.1002/jcc.20289. PubMed PMID: 16222654; PubMed Central PMCID: PMC2486339. | 2005 |
| Braun R, Engelman DM, Schulten K. | Molecular Dynamics Simulations of Micelle Formation around Dimeric Glycophorin A Transmembrane Helices. Biophys J. 2004 Aug;87(2):754-63. doi: 10.1529/biophysj.104.040279. PubMed PMID: 15298884; PubMed Central PMCID: PMC1304485. | 2004 |
| Braun R, Sarikaya M, Schulten K. | Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics. J Biomater Sci Polym Ed. 2002;13(7):747-57. doi: 10.1163/156856202760197384. PubMed PMID: 12296441; NIHMSID:NIHMS465086. | 2002 |
| Gullingsrud J, Braun R, Schulten K. | Reconstrucing Potentials of Mean Force through Time Series Anaylsis of Steered Molecular Dynamics Simulations. Journal of Computational Physics. 1999; 151:190-211. doi:10.1006/jcph.1999.6218. | 1999 |
