Publications

A complete list of publications by Dr. Haibe-Kains can be reviewed on Google Scholar and PubMed.

 

Publication Highlights:

2017

Nature

Network Science in Clinical Trials: A patient-centered approach.
Manem V, Salgado R, Aftimos P, Sotiriou C, Haibe-Kains B.
Semin Cancer Biol. 2017 Dec 23. doi: 10.1016/j.semcancer.2017.12.006.
pii: S1044-579X(17)30236-5.
PMID: 29278737


Nature

PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies.
Smirnov P, Kofia V, Maru A, Freeman M, Ho C, El-Hachem N, Adam GA, Ba-alawi W, Safikhani Z, Haibe-Kains B.
Nucleic Acids Res. 2017 Oct 9. doi: 10.1093/nar/gkx911.



Nature

Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins.
Yu R, Longo J, van Leeuwen JE, Mullen PJ, Ba-Alawi W, Haibe-Kains B, Penn LZ.
Cancer Res. 2017 Dec 11. doi: 10.1158/0008-5472.CAN-17-1231.
pii: canres.1231.2017.
PMID: 29229608


Nature

The international MAQC Society launches to enhance reproducibility of high-throughput technologies.
Shi L, Kusko R, Wolfinger RD, Haibe-Kains B, Fischer M, Sansone SA, Mason CE, Furlanello C, Jones WD, Ning B, Tong W.
Nat Biotechnol. 2017 Dec 8;35(12):1127-1128. doi: 10.1038/nbt.4029.
PMID: 29220036


Nature

Integrative cancer pharmacogenomics to establish drug mechanism of action: drug repurposing.
El-Hachem N, Ba-Alawi W, Smith I, Mer AS, Haibe-Kains B.
Pharmacogenomics. 2017 Oct 23. doi: 10.2217/pgs-2017-0132.
PMID: 29057710


Nature

Defining the biological basis of radiomic phenotypes in lung cancer.
Grossmann P, Stringfield O, El-Hachem N, Bui MM, Rios Velazquez E, Parmar C, Leijenaar RT, Haibe-Kains B,Lambin P, Gillies R, Aerts HJ.
Elife. 2017 Jul 21;6. pii: e23421. doi: 10.7554/eLife.23421.
PMID: 28731408


Nature

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.
Safikhani Z, Smirnov P, Thu KL, Silvester J, El-Hachem N, Quevedo R, Lupien M, Mak TW, Cescon D, Haibe-Kains B.
Nat Commun. 2017 Oct 24;8(1):1126. doi: 10.1038/s41467-017-01153-8.
PMID: 29066719




Nature

Software for the integration of multi-omics experiments in Bioconductor.
Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L. Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.
PMID: 29092936



Nature

Tissue specificity of in vitro drug sensitivity.
Yao F, Tonekaboni SAM, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B. J Am Med Inform Assoc. 2017 July.




Nature

Consensus on Molecular Subtypes of Ovarian Cancer.
Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. BioRxiv 2017 July. doi: 10.1101/162685




Nature

Genomic biomarkers for precision radiation medicine.
Bratman SV, Milosevic MF, Liu FF, Haibe-Kains B.
Lancet Oncol. 2017 May;18(5):e238.
PMID: 28495284


Nature

Integrative cancer pharmacogenomics to infer large-scale drug taxonomy.
El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B.
Cancer Res. 2017 Mar 17. pii: canres.0096.2017. doi: 10.1158/0008-5472.CAN-17-0096.
PMID: 28314784


Nature

Bidirectional terminators in Saccharomyces cerevisiae prevent cryptic transcription from invading neighboring genes.
Uwimana N, Collin P, Jeronimo C, Haibe-Kains B, Robert F.
Nucleic Acids Res. 2017 Apr 5.
PMID: 28383698


Nature

Transcriptome Analysis of Human Reninomas as an Approach to Understanding Juxtaglomerular Cell Biology.
Martini AG, Xa LK, Lacombe MJ,Blanchet-Cohen A, Mercure C, Haibe-Kains B, Friesema EC, van den Meiracker AH, Gross KW, Azizi M, Corvol P, Nguyen G, Reudelhuber TL, Danser AH.
Hypertension. 2017 Apr 10.
PMID: 28396539


bib

A review of connectivity map and computational approaches in pharmacogenomics.
Musa A, Ghoraie LS, Zhang SD, Galzko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.
Brief Bioinform. 2017 Jan 9. pii: bbw112. doi: 10.1093/bib/bbw112.
PMID: 28069634


2016

Nature

Consistency in large pharmacogenomic studies: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J,Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E2-E4. doi: 10.1038/nature19839.
PMID: 27905430


Nature

Drug response consistency in CCLE and CGP: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E11-E12. doi: 10.1038/nature20581.
PMID: 27905423


Nature

Consistency in drug response profiling: reply.
Safikhani Z, El-Hachem N, Smirnov P, Freeman M, Goldenberg A, Birkbak NJ, Beck AH, Aerts HJ, Quackenbush J, Haibe-Kains B.
Nature. 2016 Nov 30;540(7631):E6-E8. doi: 10.1038/nature20172.
PMID: 27905416


Bib

Predictive approaches for drug combination discovery in cancer
Madani Tonekaboni SA, Soltan Ghoraie L, Manem VS, Haibe-Kains B.
Brief Bioinform. 2016 Nov 22. pii: bbw104.
PMID: 27881431


F1000Research

Revisiting inconsistency in large pharmacogenomic studies.
Zhaleh Safikhani, Mark Freeman, Petr Smirnov, Nehme El-Hachem, Adrian She, Rene Quevedo, Anna Goldenberg, Nicolai Juul Birkbak, Leming Shi, Andrew H Beck, Hugo JWL Aerts, John Quackenbush,Benjamin Haibe-Kains.
F1000Research 2016, 5:2333, doi: 10.12688/f1000research.9611.1.



Genome_Biology

DNA replication stress: a source of APOBEC3B expression in breast cancer.
Cescon DW, Haibe-Kains B.
Genome Biol. 2016 Sep 30;17(1):202 10.1186/s13059-016-1069-y.
PMID: 27069505


Genome_Biology

BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE.
Bioinformatics. 2016 Aug 18. pii: btw538.
PMID: 27540268


pharmacogenomic

Assessment of pharmacogenomic agreement..
Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B.
F1000Res. 2016 May 9;5:825. doi: 10.12688/f1000research.8705.1.
PMID: 27408686


Biomed_Central

MM2S: personalized diagnosis of medulloblastoma patients and model systems.
Deena DM, Haibe-Kains B.
Source Code Biol Med. 2016 Apr 11;11:6. doi: 10.1186/s13029-016-0053-y. eCollection 2016.
PMID: 27716362


2015

Bioinformatics

PharmacoGx: an R package for analysis of large pharmacogenomic datasets.
Smirnov P, Safikhani Z, El-Hachem N, Wang D, She A, Olsen C, Freeman M, Selby H, Gendoo DM, Grossmann P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B.
Bioinformatics. 2015 Dec 9. pii: btv723.
PMID: 26656004


Bioinformatics

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer.
Gendoo DM, Ratanasirigulchai N, Schröder MS, Paré L, Parker JS, Prat A, Haibe-Kains B.
Bioinformatics. 2015 Nov 24. pii: btv693..
PMID: 26607490


Genomics Data

Using shRNA experiments to validate gene regulatory networks.
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B.
Genom Data. 2015 Apr 1;4:123-6. doi: 10.1016/j.gdata.2015.03.011.
PMID: 26484195


Brief Bioinformatics

Public data and open source tools for multi-assay genomic investigation of disease.
Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B. Waldron L.
Brief Bioinform. 2015 Oct 12. pii: bbv080.
PMID: 26463000

Scientific Reports

Radiomic feature clusters and prognostic signatures specific for Lung and Head & Neck cancer.
Parmar C, Leijenaar RT, Grossmann P, Rios Velazquez E, Bussink J, Rietveld D, Rietbergen MM, Haibe-Kains B, Lambin P, Aerts HJ.
Sci Rep. 2015 Jun 5;5:11044. doi: 10.1038/srep11044.
PMID: 26251068

EHP

Characterization of Conserved Toxicogenomic Responses in Chemically Exposed Hepatocytes across Species and Platforms.
El-Hachem N, Grossmann P, Blanchet-Cohen A, Bateman AR, Bouchard N, Archambault J, Aerts HJ, Haibe-Kains B.
Environ Health Perspect. 2015 Jul 14.
PMID: 26173225

Bioinformatics

ABC: a tool to identify SNVs causing allele-specific transcription factor binding from ChIP-Seq experiments.
Bailey SD, Virtanen C, Haibe-Kains B, Lupien M.
Bioinformatics. 2015 Sep 15;31(18):3057-9. doi: 10.1093/bioinformatics/btv321.
PMID: 25995231


Genomics

Personalized diagnosis of medulloblastoma subtypes across patients and model systems.
Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B.
Genomics. 2015 Aug;106(2):96-106. doi: 10.1016/j.ygeno.2015.05.002.
PMID: 25979459


BMC Bioinformatics

A network model for angiogenesis in ovarian cancer.
Glass K, Quackenbush J, Spentzos D, Haibe-Kains B, Yuan GC.
BMC Bioinformatics. 2015 Apr 11;16(1):115.
PMID: 25888305


Bioinformatics

Test set bias affects reproducibility of gene signatures.
Patil P, Bachant-Winner PO, Haibe-Kains B, Leek JT.
Bioinformatics. 2015 Mar 18. pii: btv157.
PMID: 25788628


Nature Communications

CT-based radiomic signature predicts distant metastasis in lung adenocarcinoma.
Coroller TP, Grossmann P, Hou Y, Rios Velazquez E, Leijenaar RT, Hermann G, Lambin P, Haibe-Kains B, Mak RH, Aerts HJ.
Radiother Oncol. 2015 Mar;114(3):345-50. doi: 10.1016/j.radonc.2015.02.015.
PMID: 25746350

Proceedings of the National Academy of Sciences of the United States of America

APOBEC3B expression in breast cancer reflects cellular proliferation while a deletion polymorphism is associated with immune activation.
David W. Cescon, Benjamin Haibe-Kains and Tak W. Mak
Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2841-6. doi: 10.1073/pnas.1424869112,
PMID: 25730878

Nature Communications

ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.
Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M.
Nat Commun. 2015 Feb 3;2:6186.
PMID: 25645053

2014

BMC Genomics

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology.
Fumagalli D, Blanchet-Cohen A, Brown D, Desmedt C, Gacquer D, Michiels S, Rothé F, Majjaj S, Salgado R, Larsimont D, Ignatiadis M, Maetens M,Piccart M,Detours V, Sotiriou C,Haibe-Kains B.
BMC Genomics. 2014 Nov 21;15(1):1008.
PMID: 25412710

Frontiers in Genetics

Untangling statistical and biological models to understand network inference: the need for a genomics network ontology.
Emmert-Streib F, Dehmer M, Haibe-Kains B
Front Genet. 2014 Aug 29;5:299. doi: 10.3389/fgene.2014.00299. eCollection 2014. Review.
PMID: 25221572

Frontiers in Cell and Developmental Biology

Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks.
Emmert-Streib F, Dehmer M, Haibe-Kains B
Front Cell Dev Biol. 2014 Aug 19;2:38. doi: 10.3389/fcell.2014.00038 eCollection 2014 Review
PMID: 25364745

Cancer Research

Enhancing Reproducibility in Cancer Drug Screening: How Do We Move Forward?
Hatzis C, Bedard PL, Juul-Birkbak N, Beck AH, Aerts HJWL, Stern DF, Shi L, Clarke R, Quackenbush J, Haibe-Kains B
Cancer Res 2014 August 1; 74(15):4016-4023. Epub 2014 July 11. Review.
PMID: 25015668


Frontiers in Genetics

Quantitative assessment and validation of network inference methods in bioinformatics.
Haibe-Kains B, Emmert-Streib F.
Front Genet. 2014 July 26; 5:221. doi: 10.3389/fgene.2014.00221. eCollection 2014.
PMID: 25076966


Frontiers in Genetics

Relevance of different prior knowledge sources for inferring gene interaction networks
Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B
Front Genet. 2014 June 24; 5:177. doi: 10.3389/fgene.2014.00177.
PMID: 25009552


Nature Communications

Decoding the tumor phenotype by non-invasive imaging using a quantitative radionics approach
Aerts HJ, Velazquez ER, Leijenaar R, Parmar C, Grossmann P, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen M, Leemans M, Dekker A, Quackenbush J, Gillies R, Lambin P
Nat Commun. 2014 June 3; 5:4006. doi: 10.1038/ncomms5006.
PMID: 24892406

Journal of the National Cancer Institute

Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer
Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G
J Natl Cancer Inst. 2014 Apr 3; 106(5). pii: dju049. doi: 10.1093/jnci/dju049.Review.
PMID: 24700801

Nature Methods

Similarity network fusion for aggregating data types on a genomic scale
Wang B, Mezlini AM, Demir F, Fiume M, Tu Z, Brudno M, Haibe-Kains B, Goldenberg A
Nat Methods. 2014 Mar; 11(3):333-7. doi: 10.1038/nmeth.2810. Epub 2014 Jan 26.
PMID: 24464287


Genomics

Inference and validation of predictive gene networks from biomedical literature and gene expression data
Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J
Genomics. 2014 Mar 29. pii: S0888-7543(14)00033-0. doi: 10.1016/j.ygeno.2014.03.004.
[Epub ahead of print]
PMID: 24691108

Scientific Reports

Importance of collection in gene set enrichment analysis of drug response in cancer cell lines
Bateman AR, El-Hachem N, Beck AH, Aerts HJ, Haibe-Kains B
Sci Rep. 2014 Feb 13;4:4092. doi: 10.1038/srep04092.
PMID: 24522610

2013

Nature

Inconsistency in large pharmacogenomic studies
Haibe-Kains B, El-Hachem N, Birkbak NJ, Jin AC, Beck AH, Aerts HJ, Quackenbush J
Nature. 2013 Dec 19; 504(7480):389-93. doi: 10.1038/nature12831. Epub 2013 Nov 27.
PMID: 24284626


Bioinformatics

mRMRe: an R package for parallelized mRMR ensemble feature selection
De Jay N, Papillon-Cavanagh S, Olsen C, El-Hachem N, Bontempi G, Haibe-Kains B
Bioinformatics. 2013 Sep 15;29(18):2365-8. doi: 10.1093/bioinformatics/btt383. Epub 2013 Jul 3.
PMID: 23825369


PLOS Computational Biology - www.ploscompbiol.org

Significance analysis of prognostic signatures
Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B
PLoS Comput Biol. 2013; 9(1):e1002875. doi: 10.1371/journal.pcbi.1002875. Epub 2013 Jan 24.
PMID: 23365551

J. Am. Med. Inform. Assoc.

Comparison and validation of genomic predictors for anticancer drug sensitivity
Papillon-Cavanagh S, De Jay N, Hachem N, Olsen C, Bontempi G, Aerts HJ, Quackenbush J, Haibe-Kains B
J Am Med Inform Assoc. 2013 Jul-Aug; 20(4):597-602. doi: 10.1136/amiajnl-2012-001442. Epub 2013 Jan 26.
PMID: 23355484