Publications by authors named "Alvis Brazma"

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Expression Atlas in 2026: enabling FAIR and open expression data through community collaboration and integration.
Pedro Madrigal, Anil S Thanki, Silvie Fexova, Iris D Yu, Arsenios Chatzigeorgiou, Alvis Brazma

Nucleic Acids Res· December 2025

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bia-binder: a web-native cloud compute service for the bioimage analysis community.
Craig T Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Alvis Brazma

Bioinformatics· August 2025

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Alleviating batch effects in cell type deconvolution with SCCAF-D.
Shuo Feng, Liangfeng Huang, Anna Vathrakokoili Pournara, Ziliang Huang, Xinlu Yang, Alvis Brazma

Nat Commun· December 2024

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bia-binder: A web-native cloud compute service for the bioimage analysis community.
Craig T Russell, Jean-Marie Burel, Awais Athar, Simon Li, Ugis Sarkans, Alvis Brazma

ArXiv· November 2024

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The evolution of computational research in a data-centric world.
Dhrithi Deshpande, Karishma Chhugani, Tejasvene Ramesh, Matteo Pellegrini, Sagiv Shifman, Alvis Brazma

Cell· August 2024

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CATD: a reproducible pipeline for selecting cell-type deconvolution methods across tissues.
Anna Vathrakokoili Pournara, Zhichao Miao, Ozgur Yilimaz Beker, Nadja Nolte, Alvis Brazma

Bioinform Adv· March 2024

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Expression Atlas update: insights from sequencing data at both bulk and single cell level.
Nancy George, Silvie Fexova, Alfonso Munoz Fuentes, Pedro Madrigal, Yalan Bi, Alvis Brazma

Nucleic Acids Res· January 2024

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Canonical Wnt and TGF-β/BMP signaling enhance melanocyte regeneration but suppress invasiveness, migration, and proliferation of melanoma cells.
Esra Katkat, Yeliz Demirci, Guillaume Heger, Doga Karagulle, Irene Papatheodorou, Alvis Brazma

Front Cell Dev Biol· November 2023

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Simulating structurally variable nuclear pore complexes for microscopy.
Maria Theiss, Jean-Karim Hériché, Craig Russell, David Helekal, Alisdair Soppitt, Alvis Brazma

Bioinformatics· October 2023

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Benchmarking strategies for cross-species integration of single-cell RNA sequencing data.
Yuyao Song, Zhichao Miao, Alvis Brazma, Irene Papatheodorou

Nat Commun· October 2023

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Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma.
Naveen S Vasudev, Ghislaine Scelo, Kate I Glennon, Michelle Wilson, Louis Letourneau, Alvis Brazma

Clin Cancer Res· April 2023

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Author Correction: Genomic basis for RNA alterations in cancer.

Nature· February 2023

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Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Yiqun Zhang, Fengju Chen, Nuno A Fonseca, Yao He, Masashi Fujita, Alvis Brazma

Nat Commun· December 2022

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The BioImage Archive - Building a Home for Life-Sciences Microscopy Data.
Matthew Hartley, Gerard J Kleywegt, Ardan Patwardhan, Ugis Sarkans, Jason R Swedlow, Alvis Brazma

J Mol Biol· June 2022

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Author Correction: Tumour gene expression signature in primary melanoma predicts long-term outcomes.
Manik Garg, Dominique-Laurent Couturier, Jérémie Nsengimana, Nuno A Fonseca, Matthew Wongchenko, Alvis Brazma

Nat Commun· May 2022

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Brain Regeneration Resembles Brain Cancer at Its Early Wound Healing Stage and Diverges From Cancer Later at Its Proliferation and Differentiation Stages.
Yeliz Demirci, Guillaume Heger, Esra Katkat, Irene Papatheodorou, Alvis Brazma

Front Cell Dev Biol· February 2022

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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
Yasset Perez-Riverol, Jingwen Bai, Chakradhar Bandla, David García-Seisdedos, Suresh Hewapathirana, Alvis Brazma

Nucleic Acids Res· January 2022

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Expression Atlas update: gene and protein expression in multiple species.
Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Alvis Brazma

Nucleic Acids Res· January 2022

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Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.
Xu Li, Manik Garg, Tingting Jia, Qijun Liao, Lifang Yuan, Alvis Brazma

Front Immunol· January 2022

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REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
Ugis Sarkans, Wah Chiu, Lucy Collinson, Michele C Darrow, Jan Ellenberg, Alvis Brazma

Nat Methods· December 2021

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A proteomics sample metadata representation for multiomics integration and big data analysis.
Chengxin Dai, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M Solovyeva, Jingwen Deng, Alvis Brazma

Nat Commun· October 2021

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Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
Manik Garg, Xu Li, Pablo Moreno, Irene Papatheodorou, Yuelong Shu, Alvis Brazma

Sci Rep· October 2021

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User-friendly, scalable tools and workflows for single-cell RNA-seq analysis.
Pablo Moreno, Ni Huang, Jonathan R Manning, Suhaib Mohammed, Andrey Solovyev, Alvis Brazma

Nat Methods· April 2021

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An integrated landscape of protein expression in human cancer.
Andrew F Jarnuczak, Hanna Najgebauer, Mitra Barzine, Deepti J Kundu, Fatemeh Ghavidel, Alvis Brazma

Sci Data· April 2021

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Tumour gene expression signature in primary melanoma predicts long-term outcomes.
Manik Garg, Dominique-Laurent Couturier, Jérémie Nsengimana, Nuno A Fonseca, Matthew Wongchenko, Alvis Brazma

Nat Commun· February 2021

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