Author

Alvis Brazma

Broad Institute

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Genomics· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 4 Research Focus:differential expression· 3 Approach:statistical model· 3 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Research Focus:cell type annotation· 1 Research Focus:clustering· 1 Organism:human· 1

Frequent Co-Authors

Nuno A. FonsecaiD· 2 shared Adrian Baez‐OrtegaiD· 1 shared Akinyemi I. OjesinaiD· 1 shared Alvis BrāzmaiD· 1 shared Ana Dueso-BarrosoiD· 1 shared André KahlesiD· 1 shared Andrew J DunfordiD· 1 shared Angela Norie BrooksiD· 1 shared

Activity by Year

2014-2020 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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2 shared papersGenomics

Nuno A. FonsecaORCID

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Author profile →

4 papers

Recent·Most cited

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

Yiqun Zhang, Fengju Chen, Nuno A. Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brāzma, PCAWG Transcriptome Working Group, Samirkumar B. Amin, Philip Awadalla, Peter J. Bailey, Alvis Brazma, Angela Norie Brooks, Claudia Calabrese, , Paul Alan Edwards

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nature Communications · Feb 5, 2020Peer-reviewedGenomics

RNA-seq gene profiling - a systematic empirical comparison

Nuno A Fonseca, John A Marioni, Alvis Brazma

This paper evaluates 50 RNA-seq gene profiling pipelines using simulated data to assess their accuracy in inferring gene expression levels.

bioRxiv · Jul 16, 2014Bioinformatics

iRAP - an integrated RNA-seq Analysis Pipeline

Nuno A. Fonseca, Robert Petryszak, John C. Marioni, Alvis Brazma

iRAP is an RNA-seq analysis pipeline that integrates multiple tools for read mapping, expression quantification, differential expression testing, and gene set enrichment analysis, providing customizable and user-friendly workflows.

bioRxiv · Jun 6, 2014 · PreprintBioinformatics

Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq

Mar Gonzàlez-Porta, Alvis Brazma

SwitchSeq identifies and visualizes extreme splicing changes from RNA-seq data, aiding in the interpretation of differential splicing events.

bioRxiv · Jun 6, 2014 · PreprintBioinformatics