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High resolution analysis of follicular lymphoma genomes reveals somatic recurrent sites of copy-neutral loss of heterozygosity and copy number alterations that target single genes.
- Published in:
- Genes, Chromosomes & Cancer, 2010, v. 49, n. 8, p. 669, doi. 10.1002/gcc.20780
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- Publication type:
- Article
Fast, light, and scalable: harnessing data-mined line annotations for automated tumor segmentation on brain MRI.
- Published in:
- European Radiology, 2023, v. 33, n. 9, p. 6582, doi. 10.1007/s00330-023-09583-3
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- Publication type:
- Article
Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector.
- Published in:
- Nature Communications, 2023, n. 1, p. 1, doi. 10.1038/s41467-023-39985-2
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- Publication type:
- Article
DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer.
- Published in:
- Genome Biology, 2012, v. 13, n. 12, p. 1, doi. 10.1186/gb-2012-13-12-r124
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- Publication type:
- Article
Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer.
- Published in:
- Nature Communications, 2015, v. 6, n. 11, p. 8760, doi. 10.1038/ncomms9760
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- Publication type:
- Article
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
- Published in:
- Nature Communications, 2015, v. 6, n. 10, p. 8554, doi. 10.1038/ncomms9554
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- Publication type:
- Article
Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma.
- Published in:
- Science Translational Medicine, 2017, v. 9, n. 396, p. 1, doi. 10.1126/scitranslmed.aak9969
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- Publication type:
- Article
Identification of the epigenetic reader CBX2 as a potential drug target in advanced prostate cancer.
- Published in:
- Clinical Epigenetics, 2016, v. 8, p. 1, doi. 10.1186/s13148-016-0182-9
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- Publication type:
- Article
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.
- Published in:
- Nature, 2012, v. 486, n. 7403, p. 346, doi. 10.1038/nature10983
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- Publication type:
- Article
The clonal and mutational evolution spectrum of primary triple-negative breast cancers.
- Published in:
- Nature, 2012, v. 486, n. 7403, p. 395, doi. 10.1038/nature10933
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- Publication type:
- Article
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers.
- Published in:
- Nature, 2011, v. 471, n. 7338, p. 377, doi. 10.1038/nature09754
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- Publication type:
- Article
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.
- Published in:
- Nature, 2009, v. 461, n. 7265, p. 809, doi. 10.1038/nature08489
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- Publication type:
- Article
Somatic mutation detection and classification through probabilistic integration of clonal population information.
- Published in:
- Communications Biology, 2019, v. 2, n. 1, p. N.PAG, doi. 10.1038/s42003-019-0291-z
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- Publication type:
- Article
Spatial genomic heterogeneity within localized, multifocal prostate cancer.
- Published in:
- Nature Genetics, 2015, v. 47, n. 7, p. 736, doi. 10.1038/ng.3315
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- Publication type:
- Article
Corrigendum: Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.
- Published in:
- Nature Genetics, 2014, v. 46, n. 7, p. 759, doi. 10.1038/ng0714-759a
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- Publication type:
- Article
Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4.
- Published in:
- Nature Genetics, 2014, v. 46, n. 5, p. 427, doi. 10.1038/ng.2928
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- Publication type:
- Article
Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma.
- Published in:
- Nature Genetics, 2014, v. 46, n. 4, p. 329, doi. 10.1038/ng.2900
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- Publication type:
- Article
Synchronous Endometrial and Ovarian Carcinomas: Evidence of Clonality.
- Published in:
- 2016
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- Publication type:
- journal article
Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.
- Published in:
- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-04368-5
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- Publication type:
- Article
Atlas -- a data warehouse for integrative bioinformatics.
- Published in:
- BMC Bioinformatics, 2005, v. 6, p. 1, doi. 10.1186/1471-2105-6-34
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- Publication type:
- Article
Pegasys: software for executing and integrating analyses of biological sequences.
- Published in:
- BMC Bioinformatics, 2004, v. 5, p. 40, doi. 10.1186/1471-2105-5-40
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- Publication type:
- Article
deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.
- Published in:
- PLoS Computational Biology, 2011, v. 7, n. 5, p. 1, doi. 10.1371/journal.pcbi.1001138
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- Publication type:
- Article
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.
- Published in:
- Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1645-z
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- Publication type:
- Article
ReMixT: clone-specific genomic structure estimation in cancer.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1267-2
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- Publication type:
- Article
Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research.
- Published in:
- PLoS ONE, 2013, v. 8, n. 9, p. 1, doi. 10.1371/journal.pone.0072162
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- Publication type:
- Article
The genomic landscape of epithelioid sarcoma cell lines and tumours.
- Published in:
- Journal of Pathology, 2016, v. 238, n. 1, p. 63, doi. 10.1002/path.4636
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- Publication type:
- Article
Multifocal endometriotic lesions associated with cancer are clonal and carry a high mutation burden.
- Published in:
- Journal of Pathology, 2015, v. 236, n. 2, p. 201, doi. 10.1002/path.4516
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- Publication type:
- Article
Recurrent genomic rearrangements in primary testicular lymphoma.
- Published in:
- Journal of Pathology, 2015, v. 236, n. 2, p. 136, doi. 10.1002/path.4522
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- Publication type:
- Article
Use of mutation profiles to refine the classification of endometrial carcinomas.
- Published in:
- Journal of Pathology, 2012, v. 228, n. 1, p. 20, doi. 10.1002/path.4056
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- Publication type:
- Article
Using next-generation sequencing for the diagnosis of rare disorders: a family with retinitis pigmentosa and skeletal abnormalities.
- Published in:
- Journal of Pathology, 2011, v. 225, n. 1, p. 12, doi. 10.1002/path.2941
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- Publication type:
- Article
Subtype-specific mutation of PPP2R1A in endometrial and ovarian carcinomas.
- Published in:
- Journal of Pathology, 2011, v. 223, n. 5, p. 567, doi. 10.1002/path.2848
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- Publication type:
- Article
PyClone: statistical inference of clonal population structure in cancer.
- Published in:
- Nature Methods, 2014, v. 11, n. 4, p. 396, doi. 10.1038/nmeth.2883
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- Publication type:
- Article
Kronos: a workflow assembler for genome analytics and informatics.
- Published in:
- GigaScience, 2017, v. 6, n. 7, p. 1, doi. 10.1093/gigascience/gix042
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- Publication type:
- Article
Enhancing knowledge discovery from cancer genomics data with Galaxy.
- Published in:
- GigaScience, 2017, v. 6, n. 5, p. 1, doi. 10.1093/gigascience/gix015
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- Publication type:
- Article
CDK12 regulates alternative last exon mRNA splicing and promotes breast cancer cell invasion.
- Published in:
- Nucleic Acids Research, 2017, v. 45, n. 11, p. 6698, doi. 10.1093/nar/gkx187
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- Publication type:
- Article
Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells.
- Published in:
- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-46710-0
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- Publication type:
- Article
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data.
- Published in:
- Bioinformatics, 2012, v. 28, n. 7, p. 907, doi. 10.1093/bioinformatics/bts053
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- Publication type:
- Article
Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data.
- Published in:
- Bioinformatics, 2012, v. 28, n. 2, p. 167, doi. 10.1093/bioinformatics/btr629
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- Publication type:
- Article
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
- Published in:
- Bioinformatics, 2010, v. 26, n. 6, p. 730, doi. 10.1093/bioinformatics/btq040
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- Publication type:
- Article
Model-based clustering of array CGH data.
- Published in:
- Bioinformatics, 2009, v. 25, n. 12, p. i30, doi. 10.1093/bioinformatics/btp205
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- Publication type:
- Article
Modeling recurrent DNA copy number alterations in array CGH data.
- Published in:
- Bioinformatics, 2007, v. 23, n. 13, p. i450, doi. 10.1093/bioinformatics/btm221
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- Publication type:
- Article
Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15951-0
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- Publication type:
- Article
Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models.
- Published in:
- PLoS Computational Biology, 2019, v. 15, n. 2, p. 1, doi. 10.1371/journal.pcbi.1006799
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- Publication type:
- Article
ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data.
- Published in:
- Genome Biology, 2017, v. 18, p. 1, doi. 10.1186/s13059-017-1169-3
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- Publication type:
- Article
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
- Published in:
- Genome Biology, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s13059-015-0648-7
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- Publication type:
- Article
Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data.
- Published in:
- PLoS Computational Biology, 2020, v. 16, n. 9, p. 1, doi. 10.1371/journal.pcbi.1008270
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- Publication type:
- Article