Hector Corrada Bravo - Publications

Computer Science University of Maryland, College Park, College Park, MD 
Bioinformatics and Computational Biology,Data Science

26/60 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
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
2014 Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain MA, Oundo J, Tamboura B, Mai V, Astrovskaya I, Corrada Bravo H, Rance R, Stares M, Levine MM, Panchalingam S, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biology. 15: R76. PMID 24995464 DOI: 10.1186/Gb-2014-15-6-R76  0.68
2014 Paulson JN, Bravo HC, Pop M. Reply to: "a fair comparison". Nature Methods. 11: 359-60. PMID 24681718 DOI: 10.1038/Nmeth.2898  0.68
2014 Alemu EY, Carl JW, Corrada Bravo H, Hannenhalli S. Determinants of expression variability. Nucleic Acids Research. 42: 3503-14. PMID 24435799 DOI: 10.1093/Nar/Gkt1364  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.36
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  0.68
2007 Bravo HC, Ramakrishnan R. Optimizing mpf queries: Decision support and probabilistic inference Proceedings of the Acm Sigmod International Conference On Management of Data. 701-712. DOI: 10.1145/1247480.1247558  0.68
Low-probability matches
2018 Wagner J, Chelaru F, Kancherla J, Paulson JN, Zhang A, Felix V, Mahurkar A, Elmqvist N, Corrada Bravo H. Metaviz: interactive statistical and visual analysis of metagenomic data. Nucleic Acids Research. PMID 29529268 DOI: 10.1093/Nar/Gky136  0.04
2015 Dillon LA, Okrah K, Hughitt VK, Suresh R, Li Y, Fernandes MC, Belew AT, Corrada Bravo H, Mosser DM, El-Sayed NM. Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation. Nucleic Acids Research. PMID 26150419 DOI: 10.1093/Nar/Gkv656  0.04
2014 Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (Oxford, England). 30: 1363-9. PMID 24478339 DOI: 10.1093/Bioinformatics/Btu049  0.04
2020 Wagner J, Kancherla J, Braccia D, Matsumara J, Felix V, Crabtree J, Mahurkar A, Corrada Bravo H. Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz. F1000research. 9: 601. PMID 32742640 DOI: 10.12688/F1000Research.24345.1  0.01
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  0.04
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  0.04
2020 Kancherla J, Bravo HC. Quickly compose custom interactive genomic visualization apps in R/Bioc with epiviz components F1000research. 9. DOI: 10.7490/F1000Research.1118127.1  0.01
2020 Boca S, Bhuvaneshwar K, Fernandez-Vega V, Kancherla J, Rao S, Madhavan S, Riggins R, Beckman RA, Corrada Bravo H, Scampavia L, Spicer T. Prioritizing targeted therapies in an evidence-based manner, integrating biological context and functional precision medicine. Journal of Clinical Oncology. 38: e14065-e14065. DOI: 10.1200/Jco.2020.38.15_Suppl.E14065  0.01
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  0.08
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  0.08
2019 Gunady MK, Mount SM, Corrada Bravo H. Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis. Bmc Bioinformatics. 20: 421. PMID 31409274 DOI: 10.1186/S12859-019-2947-6  0.01
2019 Olson ND, Shah N, Kancherla J, Wagner J, Paulson JN, Corrada-Bravo H. metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data. Bioinformatics (Oxford, England). PMID 30821316 DOI: 10.1093/Bioinformatics/Btz136  0.01
2019 Williams J, Bravo HC, Tom J, Paulson JN. microbiomeDASim: Simulating longitudinal differential abundance for microbiome data F1000research. 8: 1769. DOI: 10.12688/f1000research.20660.1  0.01
2018 Kumar MS, Slud EV, Okrah K, Hicks SC, Hannenhalli S, Corrada Bravo H. Analysis and correction of compositional bias in sparse sequencing count data. Bmc Genomics. 19: 799. PMID 30400812 DOI: 10.1186/S12864-018-5160-5  0.01
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  0.08
2017 Braid SM, Okrah K, Shetty A, Corrada Bravo H. DNA Methylation Patterns in Cord Blood of Neonates Across Gestational Age: Association With Cell-Type Proportions. Nursing Research. PMID 28125511 DOI: 10.1097/Nnr.0000000000000210  0.01
2017 Dorri F, Mendelowitz L, Corrada Bravo H. methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing. Bioinformatics (Oxford, England). 32: 1618-24. PMID 27246923 DOI: 10.1093/Bioinformatics/Btw287  0.01
2017 Heath LS, Corrada Bravo H, Caccamo M, Schatz M. Bioinformatics of DNA Proceedings of the Ieee. 105: 419-421. DOI: 10.1109/JPROC.2017.2652958  0.01
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  0.04
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
2016 Li Y, Shah-Simpson S, Okrah K, Belew AT, Choi J, Caradonna KL, Padmanabhan P, Ndegwa DM, Temanni MR, Corrada Bravo H, El-Sayed NM, Burleigh BA. Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection. Plos Pathogens. 12: e1005511. PMID 27046031 DOI: 10.1371/Journal.Ppat.1005511  0.01
2016 Wagner J, Paulson JN, Wang X, Bhattacharjee B, Bravo HC. Privacy-Preserving Microbiome Analysis Using Secure Computation. Bioinformatics (Oxford, England). PMID 26873931 DOI: 10.1093/Bioinformatics/Btw073  0.04
2015 Dillon LA, Suresh R, Okrah K, Corrada Bravo H, Mosser DM, El-Sayed NM. Simultaneous transcriptional profiling of Leishmania major and its murine macrophage host cell reveals insights into host-pathogen interactions. Bmc Genomics. 16: 1108. PMID 26715493 DOI: 10.1186/S12864-015-2237-2  0.01
2015 Chelaru F, Bravo HC. Epiviz: a view inside the design of an integrated visual analysis software for genomics Bmc Bioinformatics. 16: 1-14. PMID 26328750 DOI: 10.1186/1471-2105-16-S11-S4  0.01
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 Okrah K, Bravo HC. Shape analysis of high-throughput transcriptomics experiment data Biostatistics. 16: 627-640. PMID 25964664 DOI: 10.1093/Biostatistics/Kxv018  0.08
2014 Parker HS, Corrada Bravo H, Leek JT. Removing batch effects for prediction problems with frozen surrogate variable analysis. Peerj. 2: e561. PMID 25332844 DOI: 10.7717/Peerj.561  0.01
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 Ye C, Hsiao C, Corrada Bravo H. BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution. Bioinformatics (Oxford, England). 30: 1214-9. PMID 24413520 DOI: 10.1093/Bioinformatics/Btu010  0.01
2011 Paulson JN, Pop M, Bravo HC. Metastats: an improved statistical method for analysis of metagenomic data Genome Biology. 12. DOI: 10.1186/Gb-2011-12-S1-P17  0.01
2010 Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Medicine. 2: 87. PMID 21144010 DOI: 10.1186/Gm208  0.01
2009 Acevedo MA, Corrada-Bravo CJ, Corrada-Bravo H, Villanueva-Rivera LJ, Aide TM. Automated classification of bird and amphibian calls using machine learning: A comparison of methods Ecological Informatics. 4: 206-214. DOI: 10.1016/J.Ecoinf.2009.06.005  0.01
2006 Churnside J, Bravo H, Naugolnykh K, Fuks J. Acousto‐optic interactions at a surface perturbed by acoustic and gravity waves The Journal of the Acoustical Society of America. 120: 3369-3369. DOI: 10.1121/1.4781543  0.01
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