H. C. Bravo

发表

Tackling the widespread and critical impact of batch effects in high-throughput data

David M. Simcha, D. Geman, B. Langmead, 2010, Nature Reviews Genetics.

Transcriptome Remodeling in Trypanosoma cruzi and Human Cells during Intracellular Infection

C. Clayton, M. Temanni, N. El-Sayed, 2016, PLoS pathogens.

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Evan Z. Macosko, Trygve E Bakken, Staci A. Sorensen, 2021, Nature.

Orchestrating high-throughput genomic analysis with Bioconductor

Raphael Gottardo, Robert Gentleman, Wolfgang Huber, 2015, Nature Methods.

Improving Deep Learning Interpretability by Saliency Guided Training pdf

Soheil Feizi, Aya Abdelsalam Ismail, H'ector Corrada Bravo, 2021, NeurIPS.

Benchmarking Deep Learning Interpretability in Time Series Predictions pdf

Soheil Feizi, Mohamed K. Gunady, Aya Abdelsalam Ismail, 2020, NeurIPS.

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2014, Bioinform..

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

A. Regev, Gabriele Scalia, J. Kaminker, 2023, bioRxiv.

Robust methods for differential abundance analysis in marker gene surveys

Mihai Pop, Héctor Corrada Bravo, Joseph N Paulson, 2013, Nature Methods.

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

Nick C Fox, Razvan V. Marinescu, Aya Abdelsalam Ismail, 2020, Machine Learning for Biomedical Imaging.

Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures

H. Bravo, Laura A. L. Dillon, N. El-Sayed, 2016, mBio.

Multivariable association discovery in population-scale meta-omics studies

Timothy L. Tickle, C. Huttenhower, L. Waldron, 2021, bioRxiv.

metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data

Héctor Corrada Bravo, Joseph N. Paulson, Jayaram Kancherla, 2018, bioRxiv.

Graph-based data analysis: tree-structured covariance estimation, prediction by regularized kernel estimation and aggregate database query processing for probabilistic inference

Raghu Ramakrishnan, Grace Wahba, Héctor Corrada Bravo, 2008 .

Increased methylation variation in epigenetic domains across cancer types

A. Feinberg, B. Langmead, K. Hansen, 2011, Nature Genetics.

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.

Nathan D. Olson, H. Bravo, M. Salit, 2020, Microbiome.

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Mihai Pop, Julian Parkhill, Hector Corrada Bravo, 2014, Genome Biology.

Capturing discrete latent structures: choose LDs over PCs.

H. Bravo, R. Irizarry, Theresa A Alexander, 2021, Biostatistics.

Heterogeneity of transcription factor binding specificity models within and across cell lines

H. Bravo, S. Hannenhalli, Mahfuza Sharmin, 2015, bioRxiv.

Intensity normalization improves color calling in SOLiD sequencing

Héctor Corrada Bravo, Rafael A Irizarry, H. Bravo, 2010, Nature Methods.

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

Evan Z. Macosko, A. S. Booeshaghi, Ricky S. Adkins, 2021, Nature.

Epiviz File Server: Query, transform and interactively explore data from indexed genomic files

Yifan Yang, Héctor Corrada Bravo, Jayaram Kancherla, 2019, bioRxiv.

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

M. Pop, H. Bravo, J. Parkhill, 2016, BMC Genomics.

gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

Owen White, Amiel A. Dror, Carlo Colantuoni, 2020, Nature Methods.

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Evan Z. Macosko, Trygve E Bakken, Staci A. Sorensen, 2021, Nature.

BatchQC: interactive software for evaluating sample and batch effects in genomic data

Benjamin Haibe-Kains, John Quackenbush, Jeffrey T. Leek, 2016, Bioinform..

Gene expression anti-profiles as a basis for accurate universal cancer signatures

Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, 2012, BMC Bioinformatics.

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Winston Timp, Rafael A Irizarry, Hector Corrada Bravo, 2014, Genome Medicine.

Reporting guidelines for human microbiome research: the STORMS checklist

Chris I. Hunter, Jennifer M. Fettweis, F. Bushman, 2021, Nature Medicine.

A multimodal cell census and atlas of the mammalian primary motor cortex

Satrajit S. Ghosh, Nicholas N. Foster, Evan Z. Macosko, 2020, Nature.

Gene Expression Signatures Based on Variability can Robustly Predict Tumor Progression and Prognosis

Héctor Corrada Bravo, H. Bravo, Wikum Dinalankara, 2015, Cancer informatics.

Epiviz: a view inside the design of an integrated visual analysis software for genomics

Florin Chelaru, Héctor Corrada Bravo, H. Bravo, 2015, BMC Bioinformatics.

Scalable querying of human cell atlases via a foundational model reveals commonalities across fibrosis-associated macrophages

A. Regev, Gabriele Scalia, J. Kaminker, 2023, bioRxiv.

An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types

Evan Z. Macosko, A. S. Booeshaghi, Ricky S. Adkins, 2020, bioRxiv.

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

J. Stamatoyannopoulos, H. Bravo, R. Chatterjee, 2013, BMC Genomics.

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Christof Koch, Brian D. Aevermann, Richard H. Scheuermann, 2020, bioRxiv.

Analysis and correction of compositional bias in sparse sequencing count data

Stephanie C. Hicks, Sridhar Hannenhalli, Eric V. Slud, 2017, BMC Genomics.

Smooth Quantile Normalization

John Quackenbush, H. Bravo, R. Irizarry, 2016, bioRxiv.

Reply to: "A fair comparison"

J. Paulson, Mihai Pop, H. C. Bravo, 2014, Nature Methods.

Somatic Alterations Contributing to Metastasis of a Castration‐Resistant Prostate Cancer

Karin M. Fredrikson, H. Bravo, T. Harkins, 2013, Human mutation.

Metastats: an improved statistical method for analysis of metagenomic data

M. Pop, H. Bravo, J. Paulson, 2011, Genome Biology.

A Decision‐Theory Approach to Interpretable Set Analysis for High‐Dimensional Data

Brian Caffo, Jeffrey T Leek, Giovanni Parmigiani, 2013, Biometrics.

Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models

Héctor Corrada Bravo, Kristine E Lee, Barbara E K Klein, 2009, Proceedings of the National Academy of Sciences.

scGAIN: Single Cell RNA-seq Data Imputation using Generative Adversarial Networks

Soheil Feizi, Héctor Corrada Bravo, Jayaram Kancherla, 2019, bioRxiv.

Fast and interpretable alternative splicing and differential gene-level expression analysis using transcriptome segmentation with Yanagi

Héctor Corrada Bravo, Stephen M. Mount, Mohamed K Gunady, 2018, bioRxiv.

Distinct genomic and epigenomic features demarcate hypomethylated blocks in colon cancer

H. Bravo, S. Hannenhalli, Mahfuza Sharmin, 2015, BMC Cancer.

Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data

Rob Patro, Avi Srivastava, Hirak Sarkar, 2020, bioRxiv.

methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing

Héctor Corrada Bravo, Faezeh Dorri, Lee Mendelowitz, 2016, Bioinform..

Epiviz: interactive visual analytics for functional genomics data

Héctor Corrada Bravo, Florin Chelaru, Naomi Goldstein, 2014, Nature Methods.

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis

Héctor Corrada Bravo, Mohamed K. Gunady, Stephen M. Mount, 2019, BMC Bioinformatics.

Privacy-preserving microbiome analysis using secure computation

Xiao Wang, Bobby Bhattacharjee, Justin Wagner, 2015, bioRxiv.

Estimating Tree-Structured Covariance Matrices via Mixed-Integer Programming

Stephen J. Wright, Grace Wahba, Héctor Corrada Bravo, 2009, AISTATS.

Optimizing mpf queries: decision support and probabilistic inference

Raghu Ramakrishnan, Héctor Corrada Bravo, R. Ramakrishnan, 2007, SIGMOD '07.

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Martin J. Aryee, A. Feinberg, K. Hansen, 2014, Bioinform..

Model‐Based Quality Assessment and Base‐Calling for Second‐Generation Sequencing Data

R. Irizarry, H. C. Bravo, 2010, Biometrics.

Anomaly Classification with the Anti-Profile Support Vector Machine

H. Bravo, W. Dinalankara, Wikum Dinalankara, 2013, 1301.3514.

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures.

Nathan D. Olson, H. Bravo, M. Salit, 2020, Microbiome.

BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution

Chengxi Ye, Chiaowen Hsiao, Héctor Corrada Bravo, 2014, Bioinform..

Influence of Host Gene Transcription Level and Orientation on HIV-1 Latency in a Primary-Cell Model

R. Siliciano, J. Margolick, H. Bravo, 2011, Journal of Virology.

Examining the relative influence of familial, genetic, and environmental covariate information in flexible risk models

G. Wahba, B. Klein, Kristine E. Lee, 2009, Proceedings of the National Academy of Sciences.

microbiomeDASim: Simulating longitudinal differential abundance for microbiome data

H. Bravo, J. Paulson, J. Tom, 2019, F1000Research.

Sherpa: Leveraging User Attention for Computational Steering in Visual Analytics

Niklas Elmqvist, Zhe Cui, Héctor Corrada Bravo, 2019, 2019 IEEE Visualization in Data Science (VDS).