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TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

BMC bioinformatics, 2010-03, Vol.11 (1), p.154-154, Article 154

2010

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TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

Nucleic acids research, 2016-05, Vol.44 (8), p.e71

2016

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Machine learning prediction of oncology drug targets based on protein and network properties

BMC bioinformatics, 2020-03, Vol.21 (1), p.104-104, Article 104

2020

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Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators

Journal of translational medicine, 2023-01, Vol.21 (1), p.55-55, Article 55

2023

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RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

Cell reports (Cambridge), 2019-02, Vol.26 (6), p.1627-1640.e7

2019

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Evolution of Metastases in Space and Time under Immune Selection

Cell, 2018-10, Vol.175 (3), p.751-765.e16

2018

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Deep learning predicts short non-coding RNA functions from only raw sequence data

PLoS computational biology, 2020-11, Vol.16 (11), p.e1008415-e1008415

2020

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Learning gene regulatory networks from only positive and unlabeled data

BMC bioinformatics, 2010-05, Vol.11 (1), p.228-228, Article 228

2010

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A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data

Nature communications, 2023-02, Vol.14 (1), p.1074-1074, Article 1074

2023

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A metabolic function of FGFR3-TACC3 gene fusions in cancer

Nature (London), 2018-01, Vol.553 (7687), p.222-227

2018

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Single-cell transcriptome analysis of lineage diversity in high-grade glioma

Genome medicine, 2018-07, Vol.10 (1), p.57-15, Article 57

2018

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TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]

F1000 research, 2016, Vol.5, p.1542-1542

2016

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Pancancer network analysis reveals key master regulators for cancer invasiveness

Journal of translational medicine, 2023-08, Vol.21 (1), p.1-558, Article 558

2023

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Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions

Journal of translational medicine, 2024-03, Vol.22 (1), p.281-281

2024

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Specific gene expression signatures induced by the multiple oncogenic alterations that occur within the PTEN/PI3K/AKT pathway in lung cancer

PloS one, 2017-06, Vol.12 (6), p.e0178865-e0178865

2017

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The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

Journal of translational medicine, 2023-12, Vol.21 (1), p.893-893, Article 893

2023

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Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial

Nature communications, 2023-09, Vol.14 (1), p.5914-5914, Article 5914

2023

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Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics

BMC bioinformatics, 2018-11, Vol.19 (1), p.407-407, Article 407

2018

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Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis

Oncoimmunology, 2017-02, Vol.6 (2), p.e1253654-e1253654

2017

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Epigenetic remodeling to improve the efficacy of immunotherapy in human glioblastoma: pre-clinical evidence for development of new immunotherapy approaches

Journal of translational medicine, 2024-03, Vol.22 (1), p.223-223

2024

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A novel microRNA signature for the detection of melanoma by liquid biopsy

Journal of translational medicine, 2022-10, Vol.20 (1), p.1-469, Article 469

2022

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Signaling networks associated with AKT activation in non-small cell lung cancer (NSCLC): new insights on the role of phosphatydil-inositol-3 kinase

PloS one, 2012-02, Vol.7 (2), p.e30427

2012

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Preface: In memory of Alfredo Petrosino

Pattern recognition letters, 2020-10, Vol.138, p.657-658

Ceccarelli, Michele

2020

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Immune Escape Mechanisms in Colorectal Cancer Pathogenesis and Liver Metastasis

Journal of immunology research, 2014-01, Vol.2014, p.686879-11

2014

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TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach

TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data

Machine learning prediction of oncology drug targets based on protein and network properties

Pan-cancer onco-signatures reveal a novel mitochondrial subtype of luminal breast cancer with specific regulators

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

Evolution of Metastases in Space and Time under Immune Selection

Deep learning predicts short non-coding RNA functions from only raw sequence data

Learning gene regulatory networks from only positive and unlabeled data

A variational algorithm to detect the clonal copy number substructure of tumors from scRNA-seq data

A metabolic function of FGFR3-TACC3 gene fusions in cancer

Single-cell transcriptome analysis of lineage diversity in high-grade glioma

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages [version 2; peer review: 1 approved, 2 approved with reservations]

Pancancer network analysis reveals key master regulators for cancer invasiveness

Transcriptional regulatory networks of tumor-associated macrophages that drive malignancy in mesenchymal glioblastoma

Identification of therapeutic targets in osteoarthritis by combining heterogeneous transcriptional datasets, drug-induced expression profiles, and known drug-target interactions

Specific gene expression signatures induced by the multiple oncogenic alterations that occur within the PTEN/PI3K/AKT pathway in lung cancer

The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses

Guadecitabine plus ipilimumab in unresectable melanoma: five-year follow-up and integrated multi-omic analysis in the phase 1b NIBIT-M4 trial

Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics

Identification of genetic determinants of breast cancer immune phenotypes by integrative genome-scale analysis

Epigenetic remodeling to improve the efficacy of immunotherapy in human glioblastoma: pre-clinical evidence for development of new immunotherapy approaches

A novel microRNA signature for the detection of melanoma by liquid biopsy

Signaling networks associated with AKT activation in non-small cell lung cancer (NSCLC): new insights on the role of phosphatydil-inositol-3 kinase

Preface: In memory of Alfredo Petrosino

Immune Escape Mechanisms in Colorectal Cancer Pathogenesis and Liver Metastasis

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