List of works by Benjamin Haibe-Kains

4-IBP, a sigma1 receptor agonist, decreases the migration of human cancer cells, including glioblastoma cells, in vitro and sensitizes them in vitro and in vivo to cytotoxic insults of proapoptotic and proautophagic drugs

scientific article published on May 2007

A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all?

scientific article

A fuzzy gene expression-based computational approach improves breast cancer prognostication

scientific article

A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets

scientific article published on 27 November 2013

A network model for angiogenesis in ovarian cancer

scientific article published on 11 April 2015

A three-gene model to robustly identify breast cancer molecular subtypes

scientific article published on 18 January 2012

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments

scientific article

APOBEC3B expression in breast cancer reflects cellular proliferation, while a deletion polymorphism is associated with immune activation

scientific article

Adenosine 2B Receptor Expression on Cancer Cells Promotes Metastasis

scientific article published on 24 May 2016

Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer

scientific article

An imprinted non-coding genomic cluster at 14q32 defines clinically relevant molecular subtypes in osteosarcoma across multiple independent datasets

scientific article

Analysis of Array Data and Clinical Validation of Array-Based Assays

Angiogenic mRNA and microRNA gene expression signature predicts a novel subtype of serous ovarian cancer

scientific article (publication date: 2012)

Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials

scientific article

Assessment of pharmacogenomic agreement

scientific article

Author Correction: Gene isoforms as expression-based biomarkers predictive of drug response in vitro.

scientific article published on 9 January 2018

BatchQC: interactive software for evaluating sample and batch effects in genomic data

scientific article

Biological Processes Associated with Breast Cancer Clinical Outcome Depend on the Molecular Subtypes

article published in 2008

Biological and therapeutic implications of a unique subtype of NPM1 mutated AML

scientific article published on 16 February 2021

CD4⁺ follicular helper T cell infiltration predicts breast cancer survival

scientific article published on 17 June 2013

CD73 is associated with poor prognosis in high-grade serous ovarian cancer

scientific article published on 11 September 2015

CD73 promotes anthracycline resistance and poor prognosis in triple negative breast cancer

scientific article published on 17 June 2013

CT-based radiomic signature predicts distant metastasis in lung adenocarcinoma

scientific article

Characterization and clinical evaluation of CD10+ stroma cells in the breast cancer microenvironment

scientific article published on 10 January 2012

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms.

scientific article published on 14 July 2015

Chromosomal instability as a prognostic marker in cervical cancer

scientific article published on 6 May 2015

Classification Models for Breast Cancer Molecular Subtyping: What is the Best Candidate for a Translation into Clinic? ⬇️

scientific article published on September 1, 2010

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer

scientific article

Comparison and validation of genomic predictors for anticancer drug sensitivity

scientific article published on 26 January 2013

Comparison of prognostic gene expression signatures for breast cancer

scientific article

Computational Intelligence in Clinical Oncology: Lessons Learned from an Analysis of a Clinical Study

Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma

Consensus on Molecular Subtypes of Ovarian Cancer

Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response

scientific article

Corrigendum: Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

scientific article published on 7 August 2014

Creating reproducible pharmacogenomic analysis pipelines

scientific article published on 03 September 2019

CrosstalkNet: A visualization tool for differential co-expression networks and communities

scientific article published on 19 February 2018

DNA methylation profiling reveals a predominant immune component in breast cancers.

scientific article

DNA replication stress: a source of APOBEC3B expression in breast cancer

scientific article

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach

scientific article

Definition of clinically distinct molecular subtypes in estrogen receptor-positive breast carcinomas through genomic grade

scientific article

Dr.VAE: improving drug response prediction via modeling of drug perturbation effects

scientific article published on 01 October 2019

Elucidating prognosis and biology of breast cancer arising in young women using gene expression profiling.

scientific article

Enhancing reproducibility in cancer drug screening: how do we move forward?

scientific article

Epigenetic switch-induced viral mimicry evasion in chemotherapy resistant breast cancer

scientific article published on 16 June 2020

Estrogen receptor negative/progesterone receptor positive breast cancer is not a reproducible subtype

scientific article published on January 2013

Evidence of galectin-1 involvement in glioma chemoresistance

scientific article

Exploiting high-throughput cell line drug screening studies to identify candidate therapeutic agents in head and neck cancer

scientific article

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer

scientific article published on 19 June 2015

Functional and genetic analysis of the colon cancer network

scientific article

Galectin 1 proangiogenic and promigratory effects in the Hs683 oligodendroglioma model are partly mediated through the control of BEX2 expression

scientific article published on May 2009

Gene expression profiling identifies activated growth factor signaling in poor prognosis (Luminal-B) estrogen receptor positive breast cancer

scientific article

Gene expression profiling reveals differences in microenvironment interaction between patients with chronic lymphocytic leukemia expressing high versus low ZAP70 mRNA

scientific article published on 18 April 2009

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.

scientific article published on 24 October 2017

Gene modules and response to neoadjuvant chemotherapy in breast cancer subtypes: a pooled analysis.

scientific article

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks

scientific article published on 19 August 2014

GeneSigDB: a manually curated database and resource for analysis of gene expression signatures

scientific article published on 21 November 2011

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.

scientific article published on 24 November 2015

Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients

scientific article

Genomic grade index is associated with response to chemotherapy in patients with breast cancer

scientific article published on 13 April 2009

IL6 Induces an IL22+ CD8+ T-cell Subset with Potent Antitumor Function

scientific article published on 21 January 2020

Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.

scientific article published on 13 February 2014

Improvement of the clinical applicability of the Genomic Grade Index through a qRT-PCR test performed on frozen and formalin-fixed paraffin-embedded tissues

scientific article

In Reply

Inconsistency in large pharmacogenomic studies

scientific article

Inference and validation of predictive gene networks from biomedical literature and gene expression data

scientific article

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy

scientific article

Integrative Pharmacogenomics Analysis of Patient-Derived Xenografts

scientific article published on 29 May 2019

Knocking down galectin 1 in human hs683 glioblastoma cells impairs both angiogenesis and endoplasmic reticulum stress responses

scientific article

Long-term in vitro treatment of human glioblastoma cells with temozolomide increases resistance in vivo through up-regulation of GLUT transporter and aldo-keto reductase enzyme AKR1C expression

scientific article

Long-term temozolomide treatment induces marked amino metabolism modifications and an increase in TMZ sensitivity in Hs683 oligodendroglioma cells

scientific article

Loss of Pgc-1α expression in aging mouse muscle potentiates glucose intolerance and systemic inflammation

scientific article

Low CD10 mRNA expression identifies high-risk ductal carcinoma in situ (DCIS).

scientific article

Low residual proliferation after short-term letrozole therapy is an early predictive marker of response in high proliferative ER-positive breast cancer.

scientific article published on 14 November 2011

MM2S: personalized diagnosis of medulloblastoma patients and model systems

scientific article published on 11 April 2016

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis

article

Medulloblastoma subgroups remain stable across primary and metastatic compartments

scientific article

Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures

scientific article published on 28 July 2008

MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.

scientific article published on 22 January 2013

Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status

scientific article

Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy

scientific article published on 26 September 2019

Modeling invasive breast cancer: growth factors propel progression of HER2-positive premalignant lesions

scientific article published on 5 December 2011

Molecular profiling of CD3-CD4+ T cells from patients with the lymphocytic variant of hypereosinophilic syndrome reveals targeting of growth control pathways.

scientific article

Multifactorial approach to predicting resistance to anthracyclines

scientific article published on 21 March 2011

Multiple-input multiple-output causal strategies for gene selection

scientific article

NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML

scientific article

Network statistics of genetically-driven gene co-expression modules in mouse crosses

scientific article published on 26 December 2013

Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.

scientific article published on 29 August 2016

Novel Effects of Chromosome Y on Cardiac Regulation, Chromatin Remodeling, and Neonatal Programming in Male Mice

article

Nucleolus and c-Myc: potential targets of cardenolide-mediated antitumor activity

scientific article published in May 2008

Older adults with heart failure treated with carvedilol, bisoprolol, or metoprolol tartrate: risk of mortality

scientific article published on 16 November 2016

Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer

scientific article published in 2021

Organoid Cultures as Preclinical Models of Non-Small Cell Lung Cancer

scientific article published on 06 November 2019

PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer

scientific article

Personalized diagnosis of medulloblastoma subtypes across patients and model systems

scientific article published on 12 May 2015

PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis

scientific article published on 01 January 2022

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.

scientific article published on 9 December 2015

Predicting prognosis using molecular profiling in estrogen receptor-positive breast cancer treated with tamoxifen

scientific article

Predictive approaches for drug combination discovery in cancer

scientific article published on 22 November 2016

Predictive networks: a flexible, open source, web application for integration and analysis of human gene networks

scientific article published on 16 November 2011

Prognostic microRNAs modulate the RHO adhesion pathway: A potential therapeutic target in undifferentiated pleomorphic sarcomas

scientific article published on 23 April 2015

Proliferation and estrogen signaling can distinguish patients at risk for early versus late relapse among estrogen receptor positive breast cancers

scientific article published on January 2013

Public data and open source tools for multi-assay genomic investigation of disease

scientific article

Quantification of ZAP70 mRNA in B Cells by Real-Time PCR Is a Powerful Prognostic Factor in Chronic Lymphocytic Leukemia

Quantitative assessment and validation of network inference methods in bioinformatics

scientific article published on 16 July 2014

REFLECTions on Combination Therapies Empowered by Data Sharing

scientific article published in 2022

Rac-specific guanine nucleotide exchange factor DOCK1 is a critical regulator of HER2-mediated breast cancer metastasis

scientific article published on 16 April 2013

Radiomic feature clusters and prognostic signatures specific for Lung and Head & Neck cancer

scientific article

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface

scientific article published on 6 January 2013

Relevance of different prior knowledge sources for inferring gene interaction networks

scientific article published on 24 June 2014

Robust Radiomics feature quantification using semiautomatic volumetric segmentation

scientific article

Significance analysis of prognostic signatures

scientific article

Similarity network fusion for aggregating data types on a genomic scale

scientific article

Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis

scientific article

Strong time dependence of the 76-gene prognostic signature for node-negative breast cancer patients in the TRANSBIG multicenter independent validation series

scientific article published in June 2007

Test set bias affects reproducibility of gene signatures

scientific article published on 18 March 2015

The Gene expression Grade Index: a potential predictor of relapse for endocrine-treated breast cancer patients in the BIG 1-98 trial

scientific article

The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks

scientific article published on 03 February 2014

The mevalonate pathway is an actionable vulnerability of t(4;14)-positive multiple myeloma

scientific article published on 14 July 2020

Time to move forward from “first-generation” prognostic gene signatures in early breast cancer

article

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

scientific article

Transparency and reproducibility in artificial intelligence

scientific article published on 14 October 2020

UNBS5162, a novel naphthalimide that decreases CXCL chemokine expression in experimental prostate cancers

scientific article published on June 2008

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology ⬇️

scientific article published on 29 August 2014

Using shRNA experiments to validate gene regulatory networks

scientific article

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters

scientific article published on 3 February 2015

curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

scientific article

mRMRe: an R package for parallelized mRMR ensemble feature selection

scientific article

microRNA-29c and microRNA-223 down-regulation has in vivo significance in chronic lymphocytic leukemia and improves disease risk stratification

scientific article

survcomp: an R/Bioconductor package for performance assessment and comparison of survival models

scientific article published on 7 September 2011

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