Hector Bravo - Publications

2012-2019 Anatomy and Neurobiology UPR School of Medicine 

48 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics (Oxford, England). PMID 34467372 DOI: 10.1093/biostatistics/kxab030  1
2021 Orvis J, Gottfried B, Kancherla J, Adkins RS, Song Y, Dror AA, Olley D, Rose K, Chrysostomou E, Kelly MC, Milon B, Matern MS, Azaiez H, Herb B, Colantuoni C, ... Bravo HC, et al. gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration. Nature Methods. PMID 34172972 DOI: 10.1038/s41592-021-01200-9  1
2020 Sarkar H, Srivastava A, Bravo HC, Love MI, Patro R. Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data. Bioinformatics (Oxford, England). 36: i102-i110. PMID 32657377 DOI: 10.1093/Bioinformatics/Btaa448  0.01
2020 Kancherla J, Yang Y, Chae H, Bravo HC. Epiviz File Server: Query, Transform and Interactively Explore Data from Indexed Genomic Files. Bioinformatics (Oxford, England). PMID 32618995 DOI: 10.1093/Bioinformatics/Btaa591  1
2020 Olson ND, Kumar MS, Li S, Braccia DJ, Hao S, Timp W, Salit ML, Stine OC, Bravo HC. A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures. Microbiome. 8: 35. PMID 32169095 DOI: 10.1186/S40168-020-00812-1  1
2019 Williams J, Bravo HC, Tom J, Paulson JN. : Simulating longitudinal differential abundance for microbiome data. F1000research. 8: 1769. PMID 32148761 DOI: 10.12688/F1000Research.20660.2  1
2019 Cui Z, Kancherla J, Chang KW, Elmqvist N, Bravo HC. Proactive Visual and Statistical Analysis of Genomic Data in Epiviz. Bioinformatics (Oxford, England). PMID 31782758 DOI: 10.1093/Bioinformatics/Btz883  1
2018 Kancherla J, Zhang A, Gottfried B, Bravo HC. Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets. F1000research. 7: 1096. PMID 30135734 DOI: 10.12688/F1000Research.15433.1  1
2017 Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics (Oxford, England). PMID 29036413 DOI: 10.1093/Biostatistics/Kxx028  1
2016 Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE. BatchQC: interactive software for evaluating sample and batch effects in genomic data. Bioinformatics (Oxford, England). PMID 27540268 DOI: 10.1093/Bioinformatics/Btw538  1
2016 Sharmin M, Bravo HC, Hannenhalli S. Heterogeneity of transcription factor binding specificity models within and across cell lines. Genome Research. PMID 27311443 DOI: 10.1101/Gr.199166.115  1
2016 Pop M, Paulson JN, Chakraborty S, Astrovskaya I, Lindsay BR, Li S, Bravo HC, Harro C, Parkhill J, Walker AW, Walker RI, Sack DA, Stine OC. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. Bmc Genomics. 17: 440. PMID 27277524 DOI: 10.1186/S12864-016-2777-0  1
2016 Fernandes MC, Dillon LA, Belew AT, Bravo HC, Mosser DM, El-Sayed NM. Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures. Mbio. 7. PMID 27165796 DOI: 10.1128/Mbio.00027-16  0.01
2015 Sharmin M, Bravo HC, Hannenhalli S. Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer. Bmc Cancer. 16: 88. PMID 26868017 DOI: 10.1186/S12885-016-2128-1  1
2015 Dinalankara W, Bravo HC. Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis. Cancer Informatics. 14: 71-81. PMID 26078586 DOI: 10.4137/Cin.S23862  0.01
2015 Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 12: 115-21. PMID 25633503 DOI: 10.1038/Nmeth.3252  1
2014 Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Medicine. 6: 61. PMID 25191524 DOI: 10.1186/S13073-014-0061-Y  1
2014 Chelaru F, Smith L, Goldstein N, Bravo HC. Epiviz: interactive visual analytics for functional genomics data. Nature Methods. 11: 938-40. PMID 25086505 DOI: 10.1038/Nmeth.3038  0.01
2014 Paulson JN, Bravo HC, Pop M. Reply to: "a fair comparison". Nature Methods. 11: 359-60. PMID 24681718 DOI: 10.1038/Nmeth.2898  1
2013 Paulson JN, Stine OC, Bravo HC, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nature Methods. 10: 1200-2. PMID 24076764 DOI: 10.1038/Nmeth.2658  1
2013 Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G. A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics. 69: 614-23. PMID 23909925 DOI: 10.1111/Biom.12060  1
2013 He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C. Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding. Bmc Genomics. 14: 428. PMID 23805837 DOI: 10.1186/1471-2164-14-428  1
2013 Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HC, Fredrikson KM, Harkins TT, Milos P, Zbar B, Linehan WM, Yeager M, Andresson T, et al. Somatic alterations contributing to metastasis of a castration-resistant prostate cancer. Human Mutation. 34: 1231-41. PMID 23636849 DOI: 10.1002/Humu.22346  1
2012 Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. Bmc Bioinformatics. 13: 272. PMID 23088656 DOI: 10.1186/1471-2105-13-272  1
2012 Shi W, Wahba G, Irizarry RA, Bravo HC, Wright SJ. The partitioned LASSO-patternsearch algorithm with application to gene expression data. Bmc Bioinformatics. 13: 98. PMID 22587526 DOI: 10.1186/1471-2105-13-98  1
2012 Hamidi SA, Bravo HR, Klump JV, Beletsky D, Schwab DJ. Hydrodynamic model for Green Bay, Lake Michigan World Environmental and Water Resources Congress 2012: Crossing Boundaries, Proceedings of the 2012 Congress. 1438-1446. DOI: 10.1061/9780784412312.144  1
2011 Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T. Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biology. 12: R93. PMID 21955804 DOI: 10.1186/Gb-2011-12-9-R93  1
2011 Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43: 768-75. PMID 21706001 DOI: 10.1038/Ng.865  1
2011 Rivas A, Boahene KD, Bravo HC, Tan M, Tamargo RJ, Francis HW. A model for early prediction of facial nerve recovery after vestibular schwannoma surgery. Otology & Neurotology : Official Publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology. 32: 826-33. PMID 21527865 DOI: 10.1097/Mao.0B013E31821B0Afd  1
2011 Shan L, Yang HC, Rabi SA, Bravo HC, Shroff NS, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. Journal of Virology. 85: 5384-93. PMID 21430059 DOI: 10.1128/Jvi.02536-10  1
2011 Ghanbari RN, Bravo HR. Coherence among climate signals, precipitation, and groundwater. Ground Water. 49: 476-90. PMID 21087250 DOI: 10.1111/j.1745-6584.2010.00772.x  1
2010 Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews. Genetics. 11: 733-9. PMID 20838408 DOI: 10.1038/Nrg2825  1
2010 Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nature Methods. 7: 336-7. PMID 20431543 DOI: 10.1038/Nmeth0510-336  1
2010 Bravo HC, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 66: 665-74. PMID 19912177 DOI: 10.1111/J.1541-0420.2009.01353.X  1
2009 Bravo HC, Wright S, Eng KH, Keles S, Wahba G. Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming. Journal of Machine Learning Research : Jmlr. 5: 41-48. PMID 22081761  1
2009 Eng KH, Bravo HC, KeleÅŸ S. A phylogenetic mixture model for the evolution of gene expression. Molecular Biology and Evolution. 26: 2363-72. PMID 19602540 DOI: 10.1093/Molbev/Msp149  1
2009 Bravo HC, Lee KE, Klein BE, Klein R, Iyengar SK, Wahba G. Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models. Proceedings of the National Academy of Sciences of the United States of America. 106: 8128-33. PMID 19420224 DOI: 10.1073/Pnas.0902906106  1
2009 Ghanbari RN, Bravo HR. Trend and oscillations in the ice-cover duration of Lake Mendota, Wisconsin, USA Hydrological Sciences Journal. 54: 497-512. DOI: 10.1623/hysj.54.3.497  1
2009 Ghanbari RN, Bravo HR, Magnuson JJ, Hyzer WG, Benson BJ. Coherence between lake ice cover, local climate and teleconnections (Lake Mendota, Wisconsin) Journal of Hydrology. 374: 282-293. DOI: 10.1016/J.Jhydrol.2009.06.024  1
2008 Bravo HR, Villarroel E, Copaja SV, Argandoña VH. Chemical basis for the phytotoxicity of N-aryl hydroxamic acids and acetanilide analogues. Zeitschrift Fur Naturforschung. C, Journal of Biosciences. 63: 389-94. PMID 18669025  1
2008 Ghanbari RN, Bravo HR. Coherence between atmospheric teleconnections, Great Lakes water levels, and regional climate Advances in Water Resources. 31: 1284-1298. DOI: 10.1016/j.advwatres.2008.05.002  1
2007 Bravo HR, Gulliver JS, Hondzo M. Development of a commercial code-based two-fluid model for bubble plumes Environmental Modelling and Software. 22: 536-547. DOI: 10.1016/J.Envsoft.2006.02.009  1
2006 Silva H, Copaja SV, Bravo HR, Argandoña VH. Relationship between grain yield, osmotic adjustment and benzoxazinone content in Triticum aestivum L. cultivars. Zeitschrift Fur Naturforschung. C, Journal of Biosciences. 61: 704-8. PMID 17137117  1
2006 Copaja SV, Villarroel E, Bravo HR, Pizarro L, Argandoña VH. Hydroxamic acids in Secale cereale L. and the relationship with their antifeedant and allelopathic properties. Zeitschrift Fur Naturforschung. C, Journal of Biosciences. 61: 670-6. PMID 17137112  1
2005 Bravo HR, Copaja SV, Figueroa-Duarte S, Lamborot M, San Martín J. 1,4-benzoxazin-3-one, 2-benzoxazolinone and gallic acid from Calceolaria thyrsiflora Graham and their antibacterial activity. Zeitschrift Fur Naturforschung. C, Journal of Biosciences. 60: 389-93. PMID 16042337  1
2004 Bravo HR, Copaja SV, San Martín J. Contents of 1,4-benzoxazin-3-ones and 2-benzoxazolinone from Stenandrium dulce (Nees). Zeitschrift Fur Naturforschung. C, Journal of Biosciences. 59: 177-80. PMID 15241920  1
2004 Machol JL, Ayers T, Schwenz KT, Koenig KW, Hardesty RM, Senff CJ, Krainak MA, Abshire JB, Bravo HE, Sandberg SP. Preliminary measurements with an automated compact differential absorption lidar for the profiling of water vapor. Applied Optics. 43: 3110-21. PMID 15176200 DOI: 10.1364/AO.43.003110  1
2004 Bravo HR, Copaja SV, Argandoña VH. Chemical basis for the antifeedant activity of natural hydroxamic acids and related compounds. Journal of Agricultural and Food Chemistry. 52: 2598-601. PMID 15113164 DOI: 10.1021/jf030766t  1
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