Meta-analysis with MMUPHin and Multi-omics Integration with Cooperative Learning

DESCRIPTION

@@ -29,50 +29,50 @@ Depends:
 Imports:
     mia
 Suggests:
-    rebook, 
+    ALDEx2, 
+    ANCOMBC, 
+    ape, 
+    BiocParallel, 
+    Biostrings, 
+    bluster, 
+    curatedMetagenomicData, 
+    dplyr, 
+    DT, 
+    fido,
+    dendextend, 
+    ggplot2, 
+    ggsignif, 
+    ggtree, 
     glue, 
-    sessioninfo, 
+    gtools, 
+    knitr, 
     miaTime, 
-    microbiomeDataSets,
     microbiome,
-    curatedMetagenomicData, 
-    ggplot2, 
-    BiocParallel, 
-    Biostrings, 
+    microbiomeDataSets,
+    miaViz, 
+    MLeval, 
+    patchwork, 
+    pheatmap, 
     phyloseq, 
-    gtools, 
+    plotly, 
     purrr, 
-    vegan, 
-    fido,
+    rebook, 
     rgl, 
-    plotly, 
-    knitr, 
-    dplyr, 
     scales, 
-    DT, 
     scater, 
-    bluster, 
-    patchwork, 
-    miaViz, 
-    ggsignif, 
-    pheatmap, 
-    ape, 
-    ggtree, 
+    sessioninfo, 
+    vegan, 
     kableExtra, 
-    dendextend, 
     NbClust, 
     cobiclust, 
     biclust, 
-    ALDEx2, 
     tidyverse, 
-    ANCOMBC, 
     Maaslin2, 
     MicrobiomeStat, 
     GUniFrac, 
     randomcoloR,
     DirichletMultinomial, 
     mikropml,
-    MLeval, 
     sechm, 
     ggpubr, 
     stringr, 
@@ -82,6 +82,18 @@ Suggests:
     corpcor, 
     circlize, 
     BiocBook,
+    SuperLearner,
+    WGCNA,
+    reshape2,
+    gsEasy,
+    topGO,
+    caret,
+    multiview,
+    glmnet,
+    forcats,
+    ROCR,
+    MMUPHin,
+    cowplot    
     BiocManager,
     stats,
     reshape2,

inst/assets/bibliography.bib

@@ -1908,3 +1908,286 @@ @article{yaverouglu2014revealing
 volume = {4},
 year = {2014}
 }
+
+
+
+
+
+
+
+
+
+@article{Lee2019,
+    author = {Lee YH},
+    title = {Strengths and Limitations of Meta-Analysis},
+    journal = {The Korean Journal of Internal Medicine},
+    volume = {94},
+    number = {5},
+    pages = {391-395},
+    url = {https://www.ekjm.org/journal/view.php?number=25636},
+    year = {2019}
+}
+
+
+@article{Finckh2008,
+    author = {Finckh A},
+    title = {Primer: strengths and weaknesses of meta-analysis},
+    journal = {Nature Clinical Practice Rheumatology},
+    volume = {4},
+    number = {3},
+    pages = {146-152},
+    url = {https://www.nature.com/articles/ncprheum0732},
+    year = {2008}
+}
+
+
+@article{Israel2011,
+    author = {Israel H},
+    title = {A guide to understanding meta-analysis},
+    journal = {Journal of Orthopaedic & Sports Physical Therapy},
+    volume = {41},
+    number = {7},
+    pages = {496-504},
+    url = {https://www.jospt.org/doi/10.2519/jospt.2011.3333?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},
+    year = {2011}
+}
+
+
+@article{Hoffman2019,
+    author = {Hoffman JIE},
+    title = {Basic biostatistics for medical & biomedical practitioners},
+    journal = {Indian Journal of Medical Research},
+    volume = {154},
+    number = {6},
+    pages = {899–900},
+    url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9347243/},
+    year = {2019}
+}
+
+
+@article{Haidich2010,
+    author = {Haidich AB},
+    title = {Meta-analysis in medical research},
+    journal = {Hippokratia},
+    volume = {14},
+    number = {Suppl 1},
+    pages = {29-37},
+    url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3049418/},
+    year = {2010}
+}
+
+
+@article{Ma2022,
+    author = {Ma S},
+    title = {Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin},
+    journal = {Genome Biology},
+    volume = {23},
+    number = {1},
+    pages = {208},
+    url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02753-4},
+    year = {2022}
+}
+
+
+@article{Pasolli2017,
+    author = {Pasolli E},
+    title = {Accessible, curated metagenomic data through ExperimentHub},
+    journal = {Nature Methods},
+    volume = {14},
+    number = {11},
+    pages = {1023-1024},
+    url = {https://www.nature.com/articles/nmeth.4468},
+    year = {2017}
+}
+
+
+@article{Mallick2021,
+    author = {Mallick H},
+    title = {Multivariable Association Discovery in Population-scale Meta-omics Studies},
+    journal = {PLOS Computational Biology},
+    volume = {17},
+    number = {11},
+    pages = {e1009442},
+    url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009442},
+    year = {2021}
+}
+
+
+@article{Frankel2017,
+    author = {Frankel AE},
+    title = {Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients},
+    journal = {Neoplasia},
+    volume = {19},
+    number = {10},
+    pages = {848-855},
+    url = {https://www.clinicalkey.com/#!/content/playContent/1-s2.0-S1476558617302385?returnurl=https:%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1476558617302385%3Fshowall%3Dtrue&referrer=https:%2F%2Fpubmed.ncbi.nlm.nih.gov%2F},
+    year = {2017}
+}
+
+
+@article{Lee2022,
+    author = {Lee KA},
+    title = {Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma},
+    journal = {Nature Medicine},
+    volume = {28},
+    number = {3},
+    pages = {535-544},
+    url = {https://www.nature.com/articles/s41591-022-01695-5},
+    year = {2022}
+}
+
+
+@article{Matson2018,
+    author = {Matson V},
+    title = {The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients},
+    journal = {Science},
+    volume = {359},
+    number = {6371},
+    pages = {104-108},
+    url = {https://www.science.org/doi/10.1126/science.aao3290?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},
+    year = {2018}
+}
+
+
+@article{Peters2019,
+    author = {Peters BA},
+    title = {Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients},
+    journal = {Genome Medicine},
+    volume = {11},
+    number = {1},
+    pages = {61},
+    url = {https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-019-0672-4},
+    year = {2019}
+}
+
+
+@article{Wind2020,
+    author = {Wind TT},
+    title = {Gut microbial species and metabolic pathways associated with response to treatment with immune checkpoint inhibitors in metastatic melanoma},
+    journal = {Melanoma Research},
+    volume = {30},
+    number = {3},
+    pages = {235-246},
+    url = {https://journals.lww.com/melanomaresearch/fulltext/2020/06000/gut_microbial_species_and_metabolic_pathways.2.aspx},
+    year = {2020}
+}
+
+
+@article{Tang2016,
+    author = {Tang ZZ},
+    title = {PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances},
+    journal = {Bioinformatics},
+    volume = {32},
+    number = {17},
+    pages = {2618-2625},
+    url = {https://academic.oup.com/bioinformatics/article/32/17/2618/2450751?login=true},
+    year = {2016}
+}
+
+
+@article{Mallick2022,
+    author = {Mallick H},
+    title = {Differential expression of single-cell RNA-seq data using Tweedie models},
+    journal = {Statistics in Medicine},
+    volume = {41},
+    number = {18},
+    pages = {3492-3510},
+    url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288986/},
+    year = {2022}
+}
+
+
+@article{Ding2022,
+    author = {Ding DY},
+    title = {Cooperative learning for multiview analysis},
+    journal = {Proceedings of the National Academy of Sciences},
+    volume = {119},
+    number = {38},
+    pages = {e2202113119},
+    url = {https://www.pnas.org/doi/full/10.1073/pnas.2202113119},
+    year = {2022}
+}
+
+
+@article{Van2007,
+    author = {Van der Laan MJ},
+    title = {Super learner},
+    journal = {Statistical Applications in Genetics and Molecular Biology},
+    volume = {6},
+    number = {},
+    pages = {Article25},
+    url = {https://www.degruyter.com/document/doi/10.2202/1544-6115.1309/html},
+    year = {2007}
+}
+
+
+@article{Mallick2023,
+    author = {Mallick H},
+    title = {An integrated Bayesian framework for multi-omics prediction and classification},
+    journal = {Statistics in Medicine},
+    volume = {43},
+    number = {5},
+    pages = {983-1002},
+    url = {https://pubmed.ncbi.nlm.nih.gov/38146838/},
+    year = {2023}
+}
+
+
+@article{Lloyd-Price2019,
+    author = {Lloyd-Price J},
+    title = {Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases},
+    journal = {Nature},
+    volume = {569},
+    number = {7758},
+    pages = {655-662},
+    url = {},
+    year = {2019}
+}
+
+
+@article{Subramanian2005,
+    author = {Subramanian A},
+    title = {Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles},
+    journal = {Proceedings of the National Academy of Sciences},
+    volume = {102},
+    number = {43},
+    pages = {15545-15550},
+    url = {https://www.pnas.org/doi/10.1073/pnas.0506580102?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed},
+    year = {2005}
+}
+
+
+@article{Kou2020,
+    author = {Kou Y},
+    title = {Microbe-set enrichment analysis facilitates functional interpretation of microbiome profiling data},
+    journal = {Scientific Reports},
+    volume = {10},
+    number = {1},
+    pages = {21466},
+    url = {https://www.nature.com/articles/s41598-020-78511-y},
+    year = {2020}
+}
+
+
+@article{Langfelder2008,
+    author = {Langfelder},
+    title = {WGCNA: an R package for weighted correlation network analysis},
+    journal = {BMC Bioinformatics},
+    volume = {9},
+    number = {},
+    pages = {559},
+    url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-559},
+    year = {2008}
+}
+
+
+@article{Geistlinger2023,
+    author = {Geistlinger L},
+    title = {BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures},
+    journal = {Nature Biotechnology},
+    volume = {},
+    number = {},
+    pages = {},
+    url = {https://doi.org/10.1038/s41587-023-01872-y},
+    year = {2023}
+}

inst/pages/90_acknowledgments.qmd

@@ -89,6 +89,10 @@ key authors/contributors include:
 - *Jacques Serizay* converted the _OMA_ book to the `BiocBook` format. This 
 allows the _OMA_ book to be built and distributed by Bioconductor. 
 
+- *Himel Mallick, PhD, FASA*, principal investigator and tenure-track faculty at Cornell University’s Department of Population Health Sciences and an adjunct faculty of Statistics and Data Science at Bowers College of Computing and Information Science. He contributed to the chapters on meta-analyses, microbe set enrichment analysis (MSEA) and multi-omics prediction and classification.
+
+- *Yihan Liu*, assisted Dr. Mallick in writing the chapters on meta-anlayses, MSEA and multi-omics prediction and classification. 
+
 ### Acknowledgments {-}
 
 This work would not have been possible without the countless