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Benchmarking strategies for cross-species integration of single-cell RNA sequencing data.
- Published in:
- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-41855-w
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- Publication type:
- Article
Simulating structurally variable nuclear pore complexes for microscopy.
- Published in:
- Bioinformatics, 2023, v. 39, n. 10, p. 1, doi. 10.1093/bioinformatics/btad587
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- Publication type:
- Article
RNAget: an API to securely retrieve RNA quantifications.
- Published in:
- Bioinformatics, 2023, v. 39, n. 4, p. 1, doi. 10.1093/bioinformatics/btad126
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- Publication type:
- Article
PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. D1, p. D543, doi. 10.1093/nar/gkab1038
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- Publication type:
- Article
Single-Cell Analysis Reveals the Immune Characteristics of Myeloid Cells and Memory T Cells in Recovered COVID-19 Patients With Different Severities.
- Published in:
- Frontiers in Immunology, 2022, v. 12, p. 1, doi. 10.3389/fimmu.2021.781432
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- Publication type:
- Article
Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.
- Published in:
- Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-00121-z
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- Publication type:
- Article
An integrated landscape of protein expression in human cancer.
- Published in:
- Scientific Data, 2021, v. 8, n. 1, p. 1, doi. 10.1038/s41597-021-00890-2
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- Publication type:
- Article
Guidelines for reporting single-cell RNA-seq experiments.
- Published in:
- 2020
- By:
- Publication type:
- Letter
Using Deep Learning to Extrapolate Protein Expression Measurements.
- Published in:
- Proteomics, 2020, v. 20, n. 21/22, p. 1, doi. 10.1002/pmic.202000009
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- Publication type:
- Article
Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.
- Published in:
- Microorganisms, 2020, v. 8, n. 8, p. 1196, doi. 10.3390/microorganisms8081196
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- Publication type:
- Article
Dysregulation at multiple points of the kynurenine pathway is a ubiquitous feature of renal cancer: implications for tumour immune evasion.
- Published in:
- 2020
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- Publication type:
- journal article
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13885-w
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- Publication type:
- Article
Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks.
- Published in:
- NPJ Vaccines, 2019, v. 4, n. 1, p. 1, doi. 10.1038/s41541-019-0145-1
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- Publication type:
- Article
Dynamics of gene regulatory networks and their dependence on network topology and quantitative parameters – the case of phage λ.
- Published in:
- BMC Bioinformatics, 2019, v. 20, n. 1, p. 1, doi. 10.1186/s12859-019-2909-z
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- Publication type:
- Article
ArrayExpress update – from bulk to single-cell expression data.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. D1, p. D711, doi. 10.1093/nar/gky964
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- Publication type:
- Article
clustComp, a bioconductor package for the comparison of clustering results.
- Published in:
- Bioinformatics, 2017, v. 33, n. 24, p. 4001, doi. 10.1093/bioinformatics/btx532
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- Publication type:
- Article
The RNASeq-er API--a gateway to systematically updated analysis of public RNA-seq data.
- Published in:
- Bioinformatics, 2017, v. 33, n. 14, p. 2218, doi. 10.1093/bioinformatics/btx143
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- Publication type:
- Article
Orchestrating differential data access for translational research: a pilot implementation.
- Published in:
- 2017
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- Publication type:
- journal article
Subtype-specific micro-RNA expression signatures in breast cancer progression.
- Published in:
- International Journal of Cancer, 2016, v. 139, n. 5, p. 1117, doi. 10.1002/ijc.30142
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- Publication type:
- Article
Identification of Cancer Related Genes Using a Comprehensive Map of Human Gene Expression.
- Published in:
- PLoS ONE, 2016, v. 11, n. 6, p. 1, doi. 10.1371/journal.pone.0157484
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- Publication type:
- Article
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
- Published in:
- Nature Communications, 2016, v. 7, n. 6, p. 11778, doi. 10.1038/ncomms11778
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- Publication type:
- Article
Modelling-based experiment retrieval: a case study with gene expression clustering.
- Published in:
- Bioinformatics, 2016, v. 32, n. 9, p. 1388, doi. 10.1093/bioinformatics/btv762
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- Publication type:
- Article
The BioStudies database.
- Published in:
- Molecular Systems Biology, 2015, v. 11, n. 12, p. n/a, doi. 10.15252/msb.20156658
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- Publication type:
- Article
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
- Published in:
- Skeletal Muscle, 2015, v. 5, n. 1, p. 1, doi. 10.1186/s13395-015-0059-1
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- Publication type:
- Article
A novel atlas of gene expression in human skeletal muscle reveals molecular changes associated with aging.
- Published in:
- Skeletal Muscle, 2015, v. 5, p. 1, doi. 10.1186/s13395-015-0059-1
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- Publication type:
- Article
Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
- Published in:
- PLoS ONE, 2015, v. 10, n. 9, p. 1, doi. 10.1371/journal.pone.0137367
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- Publication type:
- Article
Cellular phenotype database: a repository for systems microscopy data.
- Published in:
- Bioinformatics, 2015, v. 31, n. 16, p. 2736, doi. 10.1093/bioinformatics/btv199
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- Publication type:
- Article
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.
- Published in:
- BMC Genomics, 2015, v. 16, p. 1, doi. 10.1186/1471-2164-16-S8-S2
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- Publication type:
- Article
ArrayExpress update—simplifying data submissions.
- Published in:
- Nucleic Acids Research, 2015, v. 43, n. D1, p. D1113, doi. 10.1093/nar/gku1057
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- Publication type:
- Article
RNA-Seq Gene Profiling - A Systematic Empirical Comparison.
- Published in:
- PLoS ONE, 2014, v. 9, n. 9, p. 1, doi. 10.1371/journal.pone.0107026
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- Publication type:
- Article
Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants.
- Published in:
- PLoS ONE, 2014, v. 9, n. 8, p. 1, doi. 10.1371/journal.pone.0104567
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- Publication type:
- Article
Updates to BioSamples database at European Bioinformatics Institute.
- Published in:
- Nucleic Acids Research, 2014, v. 42, n. D1, p. D50, doi. 10.1093/nar/gkt1081
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- Publication type:
- Article
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
- Published in:
- Nature Biotechnology, 2013, v. 31, n. 11, p. 1015, doi. 10.1038/nbt.2702
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- Publication type:
- Article
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.
- Published in:
- Genome Biology, 2013, v. 14, n. 7, p. 1, doi. 10.1186/gb-2013-14-7-r70
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- Publication type:
- Article
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum.
- Published in:
- BMC Systems Biology, 2013, v. 7, n. 1, p. 1, doi. 10.1186/1752-0509-7-52
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- Publication type:
- Article
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.
- Published in:
- Nucleic Acids Research, 2013, v. 41, n. 10, p. e110, doi. 10.1093/nar/gkt229
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- Publication type:
- Article
Reuse of public genome-wide gene expression data.
- Published in:
- Nature Reviews Genetics, 2013, v. 14, n. 2, p. 89, doi. 10.1038/nrg3394
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- Publication type:
- Article
Tools for mapping high-throughput sequencing data.
- Published in:
- Bioinformatics, 2012, v. 28, n. 24, p. 3169, doi. 10.1093/bioinformatics/bts605
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- Publication type:
- Article
MageComet—web application for harmonizing existing large-scale experiment descriptions.
- Published in:
- Bioinformatics, 2012, v. 28, n. 10, p. 1402, doi. 10.1093/bioinformatics/bts148
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- Publication type:
- Article
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma.
- Published in:
- Bioinformatics, 2012, v. 28, n. 2, p. 246, doi. 10.1093/bioinformatics/btr634
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- Publication type:
- Article
The BioSample Database (BioSD) at the European Bioinformatics Institute.
- Published in:
- Nucleic Acids Research, 2012, p. D64, doi. 10.1093/nar/gkr937
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- Publication type:
- Article
Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes.
- Published in:
- Nature Genetics, 2011, v. 43, n. 10, p. 948, doi. 10.1038/ng.906
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- Publication type:
- Article
A pipeline for RNA-seq data processing and quality assessment.
- Published in:
- Bioinformatics, 2011, v. 27, n. 6, p. 867, doi. 10.1093/bioinformatics/btr012
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- Publication type:
- Article
SAIL—a software system for sample and phenotype availability across biobanks and cohorts.
- Published in:
- Bioinformatics, 2011, v. 27, n. 4, p. 589, doi. 10.1093/bioinformatics/btq693
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- Publication type:
- Article
Annotare—a tool for annotating high-throughput biomedical investigations and resulting data.
- Published in:
- Bioinformatics, 2010, v. 26, n. 19, p. 2470, doi. 10.1093/bioinformatics/btq462
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- Publication type:
- Article
A CD8<sup>+</sup> T cell transcription signature predicts prognosis in autoimmune disease.
- Published in:
- Nature Medicine, 2010, v. 16, n. 5, p. 586, doi. 10.1038/nm.2130
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- Publication type:
- Article
Modeling sample variables with an Experimental Factor Ontology.
- Published in:
- Bioinformatics, 2010, v. 26, n. 8, p. 1112, doi. 10.1093/bioinformatics/btq099
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- Publication type:
- Article
A global map of human gene expression.
- Published in:
- Nature Biotechnology, 2010, v. 28, n. 4, p. 322, doi. 10.1038/nbt0410-322
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- Publication type:
- Article
Gene Expression Atlas at the European Bioinformatics Institute.
- Published in:
- Nucleic Acids Research, 2010, v. 38, p. D690, doi. 10.1093/nar/gkp936
- By:
- Publication type:
- Article
The IronChip evaluation package: a package ofperl modules for robust analysis of custommicroarrays.
- Published in:
- 2010
- By:
- Publication type:
- Product Review