Grant Details
| Grant Number: | 1U24CA180996-01A1 Interpret this number |
| Primary Investigator: | Morgan, Martin |
| Organization: | Fred Hutchinson Cancer Research Center |
| Project Title: | Cancer Genomics:integrative and Scalable Solutions in R / Bioconductor |
| Fiscal Year: | 2014 |
Abstract
DESCRIPTION (provided by applicant): This proposal develops scalable R / Bioconductor software infrastructure and data resources to integrate complex, heterogeneous, and large cancer genomic experiments. The falling cost of genomic assays facilitates collection of multiple data types (e.g., gene and transcript expression, structural variation, copy number, methylation, and microRNA data) from a set of clinical specimens. Furthermore, substantial resources are now available from large consortium activities like The Cancer Genome Atlas (TCGA). Existing analysis pipelines focus on the treatment of a specific data type, leaving a critical need for tool for integrative analysis of multiple genomic assays for locally generated or publicly available data. R / Bioconductor has historically provided standardized genomic data structures and annotations that have enjoyed widespread adoption in the cancer genomics research community. This proposal adapts R / Bioconductor to meet the increasing conceptual and computational complexity of multi-assay cancer genomic experiments. We begin by developing software containers for coordinated representation, manipulation, and transformation of heterogeneous derived data from multiple cancer genomic assays. These containers are then extended to manage very large primary data resources. To facilitate integration of local experimental results with major public cancer genomics experiment data sets and annotations, we re-package public resources and provide software and cloud-based facilities for easy and fast programmatic access from within R/Bioconductor. This greatly simplifies cancer genomic analysis tasks that otherwise require significant, error-prone individual efforts. Finally, we provide software infrastructure to enable high-throughput computation using parallel and iterative approaches. The ability to manipulate multi-assay cancer genomic experiments, to understand individual experimental results in the context of public experiments and annotations, and facilities for improved high-throughput computational performance in a well-established computing environment greatly enhances opportunities for analysis and comprehension of large multi-assay cancer genomic experiments.
Publications
saseR: juggling offsets unlocks RNA-seq tools for fast and scalable differential usage, aberrant splicing and expression retrieval.
Authors: Segers A. , Gilis J. , Van Heetvelde M. , Risso D. , De Baere E. , Clement L. .
Source: Genome Biology, 2026-02-18 00:00:00.0; , .
EPub date: 2026-02-18 00:00:00.0.
PMID: 41709279
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Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.
Authors: Long K. , Gravel-Pucillo K. , Waldron L. , Davis S. , Oh S. .
Source: Database : The Journal Of Biological Databases And Curation, 2026-01-15 00:00:00.0; 2026, .
PMID: 42172141
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Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.
Authors: Long K. , Gravel-Pucillo K. , Waldron L. , Davis S. , Oh S. .
Source: Biorxiv : The Preprint Server For Biology, 2025-12-01 00:00:00.0; , .
EPub date: 2025-12-01 00:00:00.0.
PMID: 41377518
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Learning and teaching biological data science in the Bioconductor community.
Authors: Drnevich J. , Tan F.J. , Almeida-Silva F. , Castelo R. , Culhane A.C. , Davis S. , Doyle M.A. , Geistlinger L. , Ghazi A.R. , Holmes S. , et al. .
Source: Arxiv, 2025-03-11 00:00:00.0; , .
EPub date: 2025-03-11 00:00:00.0.
PMID: 40160449
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Bioconductor's Computational Ecosystem for Genomic Data Science in Cancer.
Authors: Ramos M. , Shepherd L. , Sheffield N.C. , Mahmoud A. , Pagès H. , Wokaty A. , Righelli D. , Risso D. , Davis S. , Oh S. , et al. .
Source: Methods In Molecular Biology (clifton, N.j.), 2025; 2932, p. 1-46.
PMID: 40779102
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bamSliceR: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis.
Authors: Huang Y.P. , Harmon L. , Deering-Gardner E. , Ma X. , Harsh J. , Xue Z. , Wen H. , Ramos M. , Davis S. , Triche T.J. .
Source: Biorxiv : The Preprint Server For Biology, 2024-11-27 00:00:00.0; , .
EPub date: 2024-11-27 00:00:00.0.
PMID: 37745420
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saseR: Juggling offsets unlocks RNA-seq tools for fast and Scalable differential usage, Aberrant Splicing and Expression Retrieval.
Authors: Segers A. , Gilis J. , Van Heetvelde M. , Risso D. , De Baere E. , Clement L. .
Source: Biorxiv : The Preprint Server For Biology, 2024-10-16 00:00:00.0; , .
EPub date: 2024-10-16 00:00:00.0.
PMID: 39464066
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Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package.
Authors: Pirrotta S. , Masatti L. , Bortolato A. , Corrà A. , Pedrini F. , Aere M. , Esposito G. , Martini P. , Risso D. , Romualdi C. , et al. .
Source: Nar Genomics And Bioinformatics, 2024 Sep; 6(4), p. lqae138.
EPub date: 2024-10-03 00:00:00.0.
PMID: 39363890
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Best practices to evaluate the impact of biomedical research software-metric collection beyond citations.
Authors: Afiaz A. , Ivanov A.A. , Chamberlin J. , Hanauer D. , Savonen C.L. , Goldman M.J. , Morgan M. , Reich M. , Getka A. , Holmes A. , et al. .
Source: Bioinformatics (oxford, England), 2024-08-02 00:00:00.0; 40(8), .
PMID: 39067017
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The tidyomics ecosystem: Enhancing omic data analyses.
Authors: Hutchison W.J. , Keyes T.J. , tidyomics Consortium , Crowell H.L. , Serizay J. , Soneson C. , Davis E.S. , Sato N. , Moses L. , Tarlinton B. , et al. .
Source: Biorxiv : The Preprint Server For Biology, 2024-05-22 00:00:00.0; , .
EPub date: 2024-05-22 00:00:00.0.
PMID: 38826347
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A multi-organ map of the human immune system across age, sex and ethnicity.
Authors: Mangiola S. , Milton M. , Ranathunga N. , Li-Wai-Suen C. , Odainic A. , Yang E. , Hutchison W. , Garnham A. , Iskander J. , Pal B. , et al. .
Source: Biorxiv : The Preprint Server For Biology, 2024-04-29 00:00:00.0; , .
EPub date: 2024-04-29 00:00:00.0.
PMID: 38746418
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Defining and benchmarking open problems in single-cell analysis.
Authors: Luecken M.D. , Gigante S. , Burkhardt D.B. , Cannoodt R. , Strobl D.C. , Markov N.S. , Zappia L. , Palla G. , Lewis W. , Dimitrov D. , et al. .
Source: Research Square, 2024-04-04 00:00:00.0; , .
EPub date: 2024-04-04 00:00:00.0.
PMID: 38645152
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Removing unwanted variation between samples in Hi-C experiments.
Authors: Fletez-Brant K. , Qiu Y. , Gorkin D.U. , Hu M. , Hansen K.D. .
Source: Briefings In Bioinformatics, 2024-03-27 00:00:00.0; 25(3), .
PMID: 38711367
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International Society for Extracellular Vesicles Workshop. QuantitatEVs: multiscale analyses, from bulk to single extracellular vesicle.
Authors: Basso M. , Gori A. , Nardella C. , Palviainen M. , Holcar M. , Sotiropoulos I. , Bobis-Wozowicz S. , D'Agostino V.G. , Casarotto E. , Ciani Y. , et al. .
Source: Journal Of Extracellular Biology, 2024 Jan; 3(1), .
EPub date: 2024-01-24 00:00:00.0.
PMID: 38405579
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Differential detection workflows for multi-sample single-cell RNA-seq data.
Authors: Gilis J. , Perin L. , Malfait M. , Van den Berge K. , Takele Assefa A. , Verbist B. , Risso D. , Clement L. .
Source: Biorxiv : The Preprint Server For Biology, 2023-12-19 00:00:00.0; , .
EPub date: 2023-12-19 00:00:00.0.
PMID: 38187695
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BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures.
Authors: Geistlinger L. , Mirzayi C. , Zohra F. , Azhar R. , Elsafoury S. , Grieve C. , Wokaty J. , Gamboa-Tuz S.D. , Sengupta P. , Hecht I. , et al. .
Source: Nature Biotechnology, 2023-09-11 00:00:00.0; , .
EPub date: 2023-09-11 00:00:00.0.
PMID: 37697152
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Curated single cell multimodal landmark datasets for R/Bioconductor.
Authors: Eckenrode K.B. , Righelli D. , Ramos M. , Argelaguet R. , Vanderaa C. , Geistlinger L. , Culhane A.C. , Gatto L. , Carey V. , Morgan M. , et al. .
Source: Plos Computational Biology, 2023 Aug; 19(8), p. e1011324.
EPub date: 2023-08-25 00:00:00.0.
PMID: 37624866
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Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
Authors: Afiaz A. , Ivanov A.A. , Chamberlin J. , Hanauer D. , Savonen C.L. , Goldman M.J. , Morgan M. , Reich M. , Getka A. , Holmes A. , et al. .
Source: Arxiv, 2023-06-05 00:00:00.0; , .
EPub date: 2023-06-05 00:00:00.0.
PMID: 37332562
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CO-CLUSTERING OF SPATIALLY RESOLVED TRANSCRIPTOMIC DATA.
Authors: Sottosanti A. , Risso D. .
Source: The Annals Of Applied Statistics, 2023 Jun; 17(2), p. 1444-1468.
EPub date: 2023-05-01 00:00:00.0.
PMID: 37811520
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RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.
Authors: Ramos M. , Morgan M. , Geistlinger L. , Carey V.J. , Waldron L. .
Source: Bioinformatics (oxford, England), 2023-05-19 00:00:00.0; , .
EPub date: 2023-05-19 00:00:00.0.
PMID: 37208161
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signifinder enables the identification of tumor cell states and cancer expression signatures in bulk, single-cell and spatial transcriptomic data.
Authors: Pirrotta S. , Masatti L. , Corrà A. , Pedrini F. , Esposito G. , Martini P. , Risso D. , Romualdi C. , Calura E. .
Source: Biorxiv : The Preprint Server For Biology, 2023-03-10 00:00:00.0; , .
EPub date: 2023-03-10 00:00:00.0.
PMID: 36945491
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Designing spatial transcriptomic experiments.
Authors: Righelli D. , Sottosanti A. , Risso D. .
Source: Nature Methods, 2023-03-02 00:00:00.0; , .
EPub date: 2023-03-02 00:00:00.0.
PMID: 36864198
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A Bartlett-type correction for likelihood ratio tests with application to testing equality of Gaussian graphical models.
Authors: Banzato E. , Chiogna M. , Djordjilović V. , Risso D. .
Source: Statistics & Probability Letters, 2023 Feb; 193, .
EPub date: 2022-11-09 00:00:00.0.
PMID: 38584807
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benchdamic: benchmarking of differential abundance methods for microbiome data.
Authors: Calgaro M. , Romualdi C. , Risso D. , Vitulo N. .
Source: Bioinformatics (oxford, England), 2023-01-01 00:00:00.0; 39(1), .
PMID: 36477500
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GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases.
Authors: Oh S. , Geistlinger L. , Ramos M. , Blankenberg D. , van den Beek M. , Taroni J.N. , Carey V.J. , Greene C.S. , Waldron L. , Davis S. .
Source: Nature Communications, 2022-06-27 00:00:00.0; 13(1), p. 3695.
EPub date: 2022-06-27 00:00:00.0.
PMID: 35760813
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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor.
Authors: Righelli D. , Weber L.M. , Crowell H.L. , Pardo B. , Collado-Torres L. , Ghazanfar S. , Lun A.T.L. , Hicks S.C. , Risso D. .
Source: Bioinformatics (oxford, England), 2022-04-28 00:00:00.0; , .
EPub date: 2022-04-28 00:00:00.0.
PMID: 35482478
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SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor.
Authors: Righelli D. , Weber L.M. , Crowell H.L. , Pardo B. , Collado-Torres L. , Ghazanfar S. , Lun A.T.L. , Hicks S.C. , Risso D. .
Source: Bioinformatics (oxford, England), 2022-04-28 00:00:00.0; , .
EPub date: 2022-04-28 00:00:00.0.
PMID: 35482478
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NewWave: a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data.
Authors: Agostinis F. , Romualdi C. , Sales G. , Risso D. .
Source: Bioinformatics (oxford, England), 2022-03-10 00:00:00.0; , .
EPub date: 2022-03-10 00:00:00.0.
PMID: 35266509
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Open-source Software Sustainability Models: Initial White Paper From the Informatics Technology for Cancer Research Sustainability and Industry Partnership Working Group.
Authors: Ye Y. , Barapatre S. , Davis M.K. , Elliston K.O. , Davatzikos C. , Fedorov A. , Fillion-Robin J.C. , Foster I. , Gilbertson J.R. , Lasso A. , et al. .
Source: Journal Of Medical Internet Research, 2021-12-02 00:00:00.0; 23(12), p. e20028.
EPub date: 2021-12-02 00:00:00.0.
PMID: 34860667
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A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development.
Authors: Modzelewski A.J. , Shao W. , Chen J. , Lee A. , Qi X. , Noon M. , Tjokro K. , Sales G. , Biton A. , Anand A. , et al. .
Source: Cell, 2021-10-28 00:00:00.0; 184(22), p. 5541-5558.e22.
EPub date: 2021-10-12 00:00:00.0.
PMID: 34644528
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PsiNorm: a scalable normalization for single-cell RNA-seq data.
Authors: Borella M. , Martello G. , Risso D. , Romualdi C. .
Source: Bioinformatics (oxford, England), 2021-09-09 00:00:00.0; , .
EPub date: 2021-09-09 00:00:00.0.
PMID: 34499096
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Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles.
Authors: Risso D. , Pagnotta S.M. .
Source: Bioinformatics (oxford, England), 2021-02-09 00:00:00.0; , .
EPub date: 2021-02-09 00:00:00.0.
PMID: 33560368
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A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.
Authors: Joglekar A. , Prjibelski A. , Mahfouz A. , Collier P. , Lin S. , Schlusche A.K. , Marrocco J. , Williams S.R. , Haase B. , Hayes A. , et al. .
Source: Nature Communications, 2021-01-19 00:00:00.0; 12(1), p. 463.
EPub date: 2021-01-19 00:00:00.0.
PMID: 33469025
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Toward a gold standard for benchmarking gene set enrichment analysis.
Authors: Geistlinger L. , Csaba G. , Santarelli M. , Ramos M. , Schiffer L. , Turaga N. , Law C. , Davis S. , Carey V. , Morgan M. , et al. .
Source: Briefings In Bioinformatics, 2021-01-18 00:00:00.0; 22(1), p. 545-556.
PMID: 32026945
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SIMON: Open-Source Knowledge Discovery Platform.
Authors: Tomic A. , Tomic I. , Waldron L. , Geistlinger L. , Kuhn M. , Spreng R.L. , Dahora L.C. , Seaton K.E. , Tomaras G. , Hill J. , et al. .
Source: Patterns (new York, N.y.), 2021-01-08 00:00:00.0; 2(1), p. 100178.
EPub date: 2021-01-08 00:00:00.0.
PMID: 33511368
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Transparency and reproducibility in artificial intelligence.
Authors: Haibe-Kains B. , Adam G.A. , Hosny A. , Khodakarami F. , Massive Analysis Quality Control (MAQC) Society Board of Directors , Waldron L. , Wang B. , McIntosh C. , Goldenberg A. , Kundaje A. , et al. .
Source: Nature, 2020 10; 586(7829), p. E14-E16.
EPub date: 2020-10-14 00:00:00.0.
PMID: 33057217
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Multiomic Integration of Public Oncology Databases in Bioconductor.
Authors: Ramos M. , Geistlinger L. , Oh S. , Schiffer L. , Azhar R. , Kodali H. , de Bruijn I. , Gao J. , Carey V.J. , Morgan M. , et al. .
Source: Jco Clinical Cancer Informatics, 2020 Oct; 4, p. 958-971.
PMID: 33119407
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Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.
Authors: Calgaro M. , Romualdi C. , Waldron L. , Risso D. , Vitulo N. .
Source: Genome Biology, 2020-08-03 00:00:00.0; 21(1), p. 191.
EPub date: 2020-08-03 00:00:00.0.
PMID: 32746888
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Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma.
Authors: Geistlinger L. , Oh S. , Ramos M. , Schiffer L. , LaRue R.S. , Henzler C.M. , Munro S.A. , Daughters C. , Nelson A.C. , Winterhoff B.J. , et al. .
Source: Cancer Research, 2020-08-03 00:00:00.0; , .
EPub date: 2020-08-03 00:00:00.0.
PMID: 32747365
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Global Alliance for Genomics and Health Meets Bioconductor: Toward Reproducible and Agile Cancer Genomics at Cloud Scale.
Authors: Carey V.J. , Ramos M. , Stubbs B.J. , Gopaulakrishnan S. , Oh S. , Turaga N. , Waldron L. , Morgan M. .
Source: Jco Clinical Cancer Informatics, 2020 May; 4, p. 472-479.
PMID: 32453635
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Reliable Analysis of Clinical Tumor-Only Whole-Exome Sequencing Data.
Authors: Oh S. , Geistlinger L. , Ramos M. , Morgan M. , Waldron L. , Riester M. .
Source: Jco Clinical Cancer Informatics, 2020 04; 4, p. 321-335.
PMID: 32282230
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The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer.
Authors: Schwede M. , Waldron L. , Mok S.C. , Wei W. , Basunia A. , Merritt M.A. , Mitsiades C.S. , Parmigiani G. , Harrington D.P. , Quackenbush J. , et al. .
Source: Cancer Epidemiology, Biomarkers & Prevention : A Publication Of The American Association For Cancer Research, Cosponsored By The American Society Of Preventive Oncology, 2020 02; 29(2), p. 509-519.
EPub date: 2019-12-23 00:00:00.0.
PMID: 31871106
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Editorial: Multi-omic Data Integration in Oncology.
Authors: Finotello F. , Calura E. , Risso D. , Hautaniemi S. , Romualdi C. .
Source: Frontiers In Oncology, 2020; 10, p. 1768.
EPub date: 2020-09-15 00:00:00.0.
PMID: 33042824
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Orchestrating single-cell analysis with Bioconductor.
Authors: Amezquita R.A. , Lun A.T.L. , Becht E. , Carey V.J. , Carpp L.N. , Geistlinger L. , Martini F. , Rue-Albrecht K. , Risso D. , Soneson C. , et al. .
Source: Nature Methods, 2019-12-02 00:00:00.0; , .
EPub date: 2019-12-02 00:00:00.0.
PMID: 31792435
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MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.
Authors: Gendoo D.M.A. , Zon M. , Sandhu V. , Manem V.S.K. , Ratanasirigulchai N. , Chen G.M. , Waldron L. , Haibe-Kains B. .
Source: Scientific Reports, 2019-06-19 00:00:00.0; 9(1), p. 8770.
EPub date: 2019-06-19 00:00:00.0.
PMID: 31217513
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HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.
Authors: Schiffer L. , Azhar R. , Shepherd L. , Ramos M. , Geistlinger L. , Huttenhower C. , Dowd J.B. , Segata N. , Waldron L. .
Source: American Journal Of Epidemiology, 2019-06-01 00:00:00.0; 188(6), p. 1023-1026.
PMID: 30649166
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Waldron et al. Reply to "Commentary on the HMP16SData Bioconductor Package".
Authors: Waldron L. , Schiffer L. , Azhar R. , Ramos M. , Geistlinger L. , Segata N. .
Source: American Journal Of Epidemiology, 2019-06-01 00:00:00.0; 188(6), p. 1031-1032.
PMID: 30689687
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Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study.
Authors: Beghini F. , Renson A. , Zolnik C.P. , Geistlinger L. , Usyk M. , Moody T.U. , Thorpe L. , Dowd J.B. , Burk R. , Segata N. , et al. .
Source: Annals Of Epidemiology, 2019 Jun; 34, p. 18-25.e3.
EPub date: 2019-03-28 00:00:00.0.
PMID: 31076212
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Sociodemographic variation in the oral microbiome.
Authors: Renson A. , Jones H.E. , Beghini F. , Segata N. , Zolnik C.P. , Usyk M. , Moody T.U. , Thorpe L. , Burk R. , Waldron L. , et al. .
Source: Annals Of Epidemiology, 2019-05-08 00:00:00.0; , .
EPub date: 2019-05-08 00:00:00.0.
PMID: 31151886
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Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation.
Authors: Thomas A.M. , Manghi P. , Asnicar F. , Pasolli E. , Armanini F. , Zolfo M. , Beghini F. , Manara S. , Karcher N. , Pozzi C. , et al. .
Source: Nature Medicine, 2019 04; 25(4), p. 667-678.
EPub date: 2019-04-01 00:00:00.0.
PMID: 30936548
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