ArticleGenome biology2018
ROP: dumpster diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues.
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Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers, 1 of them a synthesis that pooled it.
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32citing papers in PubMed, 1 pooled it
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32 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- RnaXtract, a tool for extracting gene expression, variants, and cell-type composition from bulk RNA sequencing.Scientific reports · 2025Article
- A brain microbiome in salmonids at homeostasis.Science advances · 2024Article
- Computational approaches and challenges in the analysis of circRNA data.BMC genomics · 2024Review
- Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach.Scientific reports · 2024Article
- Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis.Arthritis research & therapy · 2024Article
- Airborne fine particulate matter exposure induces transcriptomic alterations resembling asthmatic signatures: insights from integrated omics analysis.Environmental epigenetics · 2024Article
- New insight into circRNAs: characterization, strategies, and biomedical applications.Experimental hematology & oncology · 2023Review
- capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable elements.Communications biology · 2023Article
- Whole blood RNA extraction efficiency contributes to variability in RNA sequencing data sets.PloS one · 2023Article
- Brain-inhabiting bacteria and neurodegenerative diseases: the "brain microbiome" theory.Frontiers in aging neuroscience · 2023Review
- Functional genomics data: privacy risk assessment and technological mitigation.Nature reviews. Genetics · 2022Review
- Landscape of adenosine-to-inosine RNA recoding across human tissues.Nature communications · 2022Article
- Joint Analysis of Microbial and Immune Cell Abundance in Liver Cancer Tissue Using a Gene Expression Profile Deconvolution Algorithm Combined With Foreign Read Remapping.Frontiers in immunology · 2022Article
- Baiting out a full length sequence from unmapped RNA-seq data.BMC genomics · 2021Article
- The role of noncoding RNAs in Parkinson's disease: biomarkers and associations with pathogenic pathways.Journal of biomedical science · 2021Review
- Detection of viral gene expression in risk-stratified biopsies reveals no active HPV in cutaneous squamous cell carcinoma.Experimental dermatology · 2021Article
- CAMPAREE: a robust and configurable RNA expression simulator.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
24 authors.
Serghei MangulDepartment of Computer Science, University of California, Los Angeles, CA, USA. smangul@ucla.edu.
Harry Taegyun YangDepartment of Computer Science, University of California, Los Angeles, CA, USA.
Nicolas StrauliBiomedical Sciences Graduate Program, University of California, San Francisco, CA, USA.
Franziska GruhlCenter for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
Hagit T PorathThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
Kevin HsiehDepartment of Computer Science, University of California, Los Angeles, CA, USA.
Linus ChenDepartment of Bioengineering, University of California, Los Angeles, CA, USA.
Timothy DaleyMolecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
Stephanie ChristensonDivision of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
Agata Wesolowska-AndersenCenter for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
Roberto SpreaficoInstitute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA, USA.
Cydney RiosCenter for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.
Celeste EngDepartment of Medicine, University of California, San Francisco, CA, USA.
Andrew D SmithMolecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
Ryan D HernandezDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Roel A OphoffCenter for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University California, Los Angeles, CA, USA.
Jose Rodriguez SantanaCentro de Neumología Pediátrica, San Juan, Puerto Rico.
Erez Y LevanonThe Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
Prescott G WoodruffDivision of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA.
Esteban BurchardSchools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
Max A SeiboldDepartment of Pediatrics, National Jewish Health, Denver, CO, USA.
Sagiv ShifmanDepartment of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
Eleazar EskinDepartment of Computer Science, University of California, Los Angeles, CA, USA.
Noah ZaitlenDivision of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, and Cardiovascular Research Institute, University of California, San Francisco, CA, USA. Noah.Zaitlen@ucsf.edu.
Funding
ULTRASTRUCTURE OF THE INTIMA IN EARLY LESION FORMATIONP01HL030568 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FOGELMAN, ALAN M · 1985 to 2019
$55.2MSystems genomics of metabolic syndrome traitsP01HL028481 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUSIS, ALDONS JAKE · 1985 to 2019
$50.2MUnderstanding Asthma EndotypesU19AI077439 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Nirav Rati Bhakta · 2008 to 2026
$41.1MRole of miRNAs in Th2-Driven inflammation in AsthmaP01HL107202 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANSEL, KARL MARK · 2012 to 2023
$23.3MSubstance Abuse & Behavioral Disinhibition: Integrating Genes & EnvironmentU01DA024417 · NIDA · UNIVERSITY OF MINNESOTA · PI IACONO, WILLIAM G. · 2007 to 2010
$10.8MThe Airway Functional Genomics of Bronchodilator Drug Response in Minority Children with AsthmaR01HL117004 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI AHITUV, NADAV, SEIBOLD, MAX A · 2013 to 2022
$9.3MSocial Interventions to address disparities In young adult tobacco useP60MD006902 · NIMHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BIBBINS-DOMINGO, KIRSTEN · 2012 to 2016
$6.4MGenomic Studies of Bipolar Disorder in a Large Cohort from The NetherlandsR01MH090553 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI OPHOFF, ROEL A · 2010 to 2014
$6.0MTranscriptomic and Pharmacogenetic Asthma Endotypes in Minority ChildrenR01HL135156 · NHLBI · NATIONAL JEWISH HEALTH · PI SEIBOLD, MAX A, ZIV, ELAD · 2017 to 2021
$4.1MINTEGRATIVE GENETIC APPROACHES TO GENE-AIR POLLUTION INTERACTIONS IN ASTHMAR01ES021801 · NIEHS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI AKBARI, OMID, ALLAYEE, HOOMAN · 2012 to 2016
$3.9MGenes, air pollution, and asthma severity in minority childrenR01MD010443 · NIMHD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SEIBOLD, MAX A, ZIV, ELAD · 2016 to 2020
$3.8MMolecular Phenotyping of AsthmaR01HL095372 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI WOODRUFF, PRESCOTT G · 2008 to 2011
$3.1MNHGRI NIH HHS R01 HG007644NHGRI NIH HHS R01 HG007650NHLBI NIH HHS K23 HL123778NHLBI NIH HHS K24 HL137013NHLBI NIH HHS K25 HL080079NHLBI NIH HHS K25 HL121295NHLBI NIH HHS P01 HL028481NHLBI NIH HHS P01 HL030568NHLBI NIH HHS P01 HL107202NHLBI NIH HHS R01 HL095372NHLBI NIH HHS R01 HL117004NHLBI NIH HHS R01 HL121774NHLBI NIH HHS R01 HL128439NHLBI NIH HHS R01 HL135156NIAID NIH HHS U19 AI077439NIDA NIH HHS U01 DA024417NIDCR NIH HHS R03 DE025665NIEHS NIH HHS R01 ES021801NIEHS NIH HHS R01 ES022282NIEHS NIH HHS R21 ES024844NIGMS NIH HHS R01 GM083198NIMHD NIH HHS P60 MD006902NIMHD NIH HHS R01 MD010443NIMH NIH HHS R01 MH090553NIMH NIH HHS R01 MH101782
Abstract
High-throughput RNA-sequencing (RNA-seq) technologies provide an unprecedented opportunity to explore the individual transcriptome. Unmapped reads are a large and often overlooked output of standard RNA-seq analyses. Here, we present Read Origin Protocol (ROP), a tool for discovering the source of all reads originating from complex RNA molecules. We apply ROP to samples across 2630 individuals from 54 diverse human tissues. Our approach can account for 99.9% of 1 trillion reads of various read length. Additionally, we use ROP to investigate the functional mechanisms underlying connections between the immune system, microbiome, and disease. ROP is freely available at https://github.com/smangul1/rop/wiki .
Indexed as
SoftwareAdultAlgorithmsAsthmaBacteriaCell LineGene Expression ProfilingGenes, ImmunoglobulinGenes, T-Cell ReceptorHigh-Throughput Nucleotide SequencingHumansSequence Analysis, RNA
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.