Publications and Reviews

Publications

I’ve been fortunate to have worked on several international and interesting research projects in the field of cancer genomics. Keep an eye on the space below to see the list of publications my work has contributed to (hopefully!) grow the knowledge of the field…

• Bruzos, AL; Santamarina, M; García, D; … Tubío, JMC. (2022) The evolution of two transmissible leukaemias colonizing the coasts of Europe. Biorxiv. * denotes first authorship. DOI: doi.org/10.1101/2022.08.06.503021. Available in BioRxiv. Accepted on Nature Cancer (publication due in early October).

Mosaic BRAF fusions are a recurrent cause of congenital melanocytic naevi targetable by MEK inhibition

Martin SB#, Polubothu S#, Bruzos AL# et al. (2023). "Mosaic BRAF fusions are a recurrent cause of congenital melanocytic naevi targetable by MEK inhibition." The Journal of Investigative Dermatology. doi: 10.1016/j.jid.2023.06.213 - IF(2021) = 7.590 (#equal contribution)

The first high-density genetic map of common cockle reveals a major QTL controlling shell color variation

Hermida M et al (includes Bruzos AL). (2022). "The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation." Scientific reports. 12:16971. doi: 10.1038/s41598-022-21214-3 - IF(2021) = 4.996

Mitochondrial genome sequencing of marine leukaemias reveals cancer contagion between clam species in the Seas of Southern Europe

García-Souto, D#, Bruzos, AL#; Díaz-Costas, S# et al. (2022). "Mitochondrial genome sequencing of marine leukemias reveals cancer contagion between clam species in the Seas of Southern Europe." eLife. 11:e66946. doi: 10.7554/eLife.66946 - IF(2021) = 8.713 (#equal contribution)

Assessing the elemental fingerprints of cockle shells (Cerastoderma edule) to confirm their geographic origin from regional to international spatial scales

Ricardo, F et al (includes Bruzos AL). (2022). "Assessing the elemental fingerprints of cockle shells (Cerastoderma edule) to confirm their geographic origin from regional to international spatial scales." STOTEN. 814:152304. doi: 10.1016/j.scitotenv.2021.152304 - IF(2021) = 10.753

Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture

Álvarez, EG et al (includes Bruzos AL). (2021). "Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture." Nature Communications. 12:6910. doi: 10.1038/s41467-021-26805-8 - IF(2021) = 17.694

Pan-Cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B et al (includes Bruzos AL). (2020). "Pan-Cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition." Nature Genetics. 52:306-319. doi: 10.1038/s41588-019-0562-0 - IF(2020) = 38.333

Pan-Cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (includes Bruzos AL). (2020). "Pan-Cancer analysis of whole genomes." Nature. 578:82-93. doi: 10.1038/s41586-020-1969-6 - IF(2020) = 49.962

Peer-reviewing activity

My scientific expertise has led me to several invitations to take part in the peer-review system that ensures the rigorous standards of the scientific process. In particular, I have reviewed articles for the following journals:

• 1 for *Science.* IF(2021)=63.8
• 1 for *Science Advances.* IF(2021)=14.9
• 1 for *Wiley Molecular Ecology.* IF(2022)=6.2
• 1 for *Proceedings of the Royal Society B - Biological Sciences.* IF(2022)=5.5

All stated reviews have been certified by Publons / Web of Science: D-7235-2018.

Consortia publications

Consortia’s work can lead us to important conclusions. Throughout my career, I have been part of the PCAWG consortium that has published the following articles in which the consortium is an author:

• Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Bailey et al. (2020) Nature communications Comments: lists my name
• Sex differences in oncogenic mutational processes Constance et al. (2020) Nature communications Comments: lists my name
• Patterns of somatic structural variation in human cancer genomes Li et al. (2020) Nature
• The repertoire of mutational signatures in human cancer Alexandrov et al. (2020) Nature
• The evolutionary history of 2,658 cancers Gerstung et al. (2020) Nature
• Genomic basis for RNA alterations in cancer Calabrese et al. (2020) Nature
• Analyses of non-coding somatic drivers in 2,658 cancer whole genomes Rheinbay et al. (2020) Nature
• Comprehensive molecular characterization of mitochondrial genomes in human cancers Yuan et al. (2020) Nature genetics
• Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer Akdemir et al. (2020) Nature genetics
• The landscape of viral associations in human cancers Zapatka et al. (2020) Nature genetics
• Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing Cortés et al. (2020) Nature genetics
• Butler enables rapid cloud-based analysis of thousands of human genomes Yakneen et al. (2020) Nature biotechnology
• Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis Carlevaro et al. (2020) Communications Biology
• Integrative pathway enrichment analysis of multivariate omics data Paczkowska et al. (2020) Nature communications
• Pathway and network analysis of more than 2500 whole cancer genomes Reyna et al. (2020) Nature Communications
• A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns Jiao et al. (2020) Nature Communications
• High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations Zhang et al. (2020) Nature communications
• Genomic footprints of activated telomere maintenance mechanisms in cancer Sieverling et al. (2020) Nature communications
• Combined burden and functional impact tests for cancer driver discovery using DriverPower Shuai et al. (2020) Nature Communications
• Inferring structural variant cancer cell fraction Cmero et al. (2020) Nature communications
• Divergent mutational processes distinguish hypoxic and normoxic tumours Bhandari et al. (2020) Nature communications
• Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig Rubanova et al. (2020) Nature Communications