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


Publication Highlights:


Scientific Reports

MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.
Gendoo DMA, Zon M, Sandhu V, Manem VSK, Ratanasirigulchai N, Chen GM, Waldron L, Haibe-Kains B.
Sci Rep. 2019 Jun 19;9(1):8770; doi: 10.1038/s41598-019-45165-4
PMID: 31217513


SIGN: Similarity identification in gene expression.
Madani Tonekaboni SA, Kumar Manem VS, El-Hachem N, Haibe-Kains B.
Bioinformatics. 2019 Jun 14; doi: 10.1093/bioinformatics/btz485
PMID: 31198954

Cancer Research

Integrative pharmacogenomics analysis of patient-derived xenografts.
Mer AS, Ba-Alawi W, Smirnov P, Wang YX, Brew B, Ortmann J, Tsao MS, Cescon DW, Goldenberg A, Haibe-Kains B.
Cancer Res. 2019 May 29; doi: 10.1158/0008-5472.CAN-19-0349
PMID: 31142512

European Journal of Nuclear Medicine and Molecular Imaging

Why imaging data alone is not enough - AI-based integration of imaging, omics and clinical data.
Holzinger A, Haibe-Kains B, Jurisica I.
Eur J Nucl Med Mol Imaging, 2019 May 27; doi: 10.1007/s00259-019-04382-9
PMID: 31203421

JCO Clinical Cancer Informatics

Meta-Analysis of 1,200 Transcriptomic Profiles Identifies a Prognostic Model for Pancreatic Ductal Adenocarcinoma.
Sandhu V, Labori KJ, Borgida A, Lungu I, Bartlett J, Hafezi-Bakhtiari S, Denroche RE, Jang GH, Pasternack D, Mbaabali F, Watson M, Wilson J, Kure EH, Gallinger S, Haibe-Kains B.
JCO Clin Cancer Inform. 2019 May;(3):1-16; doi: 10.1200/CCI.18.00102
PMID: 31070984


Creating reproducible pharmacogenomic analysis pipelines.
Mammoliti A, Smirnov P, Safikhani Z, Ba-Alawi W, Haibe-Kains B.
BioRxiv 2019 Apr 19; doi: 10.1101/614560

Journal of Clinical Investigation

Spatially distinct tumor immune microenvironments stratify triple-negative breast cancers.
Gruosso T, Gigoux M, Manem VSK, Bertos N, Zuo D, Perlitch I, Saleh SMI, Zhao H, Souleimanova M, Johnson RM, Monette A, Ramos VM, Hallett MT, Stagg J, Lapointe R, Omeroglu A, Meterissian S, Buisseret L, Van den Eynden G, Salgado R, Guiot MC, Haibe-Kains B, Park M.
J Clin Invest. 2019 Apr 1;129(4):1785-1800. doi: 10.1172/JCI96313. Epub 2019 Mar 18; doi: 10.1172/JCI96313
PMID: 30753167

Journal for ImmunoTherapy of Cancer

An interim report on the investigator-initiated phase 2 study of pembrolizumab immunological response evaluation (INSPIRE).
Clouthier DL, Lien SC, Yang SYC, Nguyen LT, Manem VSK, Gray D, Ryczko M, Razak ARA, Lewin J, Lheureux S, Colombo I, Bedard PL, Cescon D, Spreafico A, Butler MO, Hansen AR, Jang RW, Ghai S, Weinreb I, Sotov V, Gadalla R, Noamani B, Guo M, Elston S, Giesler A, Hakgor S, Jiang H, McGaha T, Brooks DG, Haibe-Kains B, Pugh TJ, Ohashi PS, Siu LL.
J Immunother Cancer. 2019 Mar 13;7(1):72; doi: 10.1186/s40425-019-0541-0 PMID: 30867072


Karyotypic divergence confounds cellular phenotypes in large pharmacogenomic studies.
Rene Quevedo, El-Hachem N, Smirnov P, Safikhani Z, Pugh TJ, Haibe-Kains B.
BioRxiv 2019 Mar 11; doi: 10.1101/574350


Dr.VAE: Improving drug response prediction via modeling of drug perturbation effects.
Rampášek L, Hidru D, Smirnov P, Haibe-Kains B, Goldenberg A.
Bioinformatics. 2019 Mar 8; doi: 10.1093/bioinformatics/btz158
PMID: 30850846

Frontiers in Pharmacology

A Comparative Study of Cluster Detection Algorithms in Protein-Protein Interaction for Drug Target Discovery and Drug Repurposing.
Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Dai P.
Front Pharmacol. 2019 Feb 19;10:109; doi: 10.3389/fphar.2019.00109
PMID: 30837876

Nature Communications

A cancer pharmacogenomic screen powering crowd-sourced advancement of drug combination prediction.
Menden MP, Wang D, Guan Y, Mason M, Szalai B, Bulusu KC, Yu T, Kang J, Jeon M, Wolfinger R, Nguyen T, Zaslavskiy M, AstraZeneca-Sanger Drug Combination DREAM Consortium, Jang S, Ghazoui Z, Ahsen ME, Vogel R, Neto EC, Norman T, Tang E KY, Garnett MJ, Di Veroli G, Fawell S, Stolovitzky G, Guinney J, Dry JR, Saez-Rodriguez J.
Nature Comm 2019 Feb 15; doi: 10.1101/200451

Molecular Omics

Network-based approach to identify principal isoforms among four cancer types.
Ma J, Wang J, Ghoraie LS, Men X, Haibe-Kains B, Dai P.
Mol Omics. 2019 Apr 1;15(2):117-129. doi: 10.1039/c8mo00234g. Epub 2019 Feb 5; doi: 10.1039/c8mo00234g
PMID: 30720033

PLOS Computational Biology

Whole Genomes Define Concordance of Matched Primary, Xenograft, and Organoid Models of Pancreas Cancer.
Gendoo DMA, Denroche RE, Zhang A, Jang GH, Lemire M, Fischer S, Radulovich N, Chadwick D, Lungu LM, Stein LD, Wilson JM, Bartlett JMS, Tsao MS, Dhani N, Hedley D, Gallinger S, Haibe-Kains B.
PLoS Comput Biol. 2019 Jan 10;15(1):e1006596. [IF 3.96]; doi: 10.1371/journal.pcbi.1006596
PMID: 30629588



Radiotherapy Oncology

Vulnerabilities of radiomic signature development: The need for safeguards.
Welch ML, McIntosh C, Haibe-Kains B, Milosevic MF, Wee L, Dekker A, Huang SH, Purdie TG, O'Sullivan B, Aerts HJWL, Jaffray DA.
Radiother Oncol. 2019 Jan;130:2-9. doi: 10.1016/j.radonc.2018.10.027. Epub 2018 Nov 8. doi: 10.1016/j.radonc.2018.10.027
PMID: 30416044

Scientific Reports

The Antiarrhythmic Drug, Dronedarone, Demonstrates Cytotoxic Effects in Breast Cancer Independent of Thyroid Hormone Receptor Alpha 1 (THRα1) Antagonism.
Elliott MJ, Jerzak KJ, Cockburn JG, Safikhani Z, Gwynne WD, Hassell JA, Bane A, Silvester J, Thu KL, Haibe-Kains B, Mak TW, Cescon DW.
Sci Rep. 2018 Nov 8;8(1):16562. doi: 10.1038/s41598-018-34348-0
PMID: 30410118

Nature Metabolism

Metabolic Perturbation of Dermal Fibroblasts Regulates Skin Extracellular Matrix Homeostasis and Fibrosis.
Zhao X*, Psarianos P, Ghoraie LS, Yip K, Goldstein D, Gilbert R, Witterick I, Pang H, Hussain A, Lee JH, Williams J, Bratman S, Ailles L, Haibe-Kains B, Liu FF.
Nature Metabolism. 2018 Oct 29.


Orchestrating a community-developed computational workshop and accompanying training materials.
Davis S, Ramos M, Shepherd L, Turaga N, Geistlinger L, Morgan MT, Haibe-Kains B, Waldron L.
F1000Res. 2018 Oct 17;7:1656. doi: 10.12688/f1000research.16516.1
PMID: 30473781

Clinical Cancer Research

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.
Clin Cancer Res 2018 Oct 15;24(20):5037-5047. doi: 10.1158/1078-0432.CCR-18-0784

Cancer Cell

MYC Interacts with the G9a Histone Methyltransferase to Drive Transcriptional Repression and Tumorigenesis.
Tu WB, Shiah YJ, Lourenco C, Mullen PJ, Dingar D, Redel C, Tamachi A, Ba-Alawi W, Aman A, Al-Awar R, Cescon DW, Haibe-Kains B, Arrowsmith CH, Raught B, Boutros PC, Penn LZ.
Cancer Cell. 2018 Oct 8; 34(4):579-595.e8. doi: 10.1016/j.ccell.2018.09.001
PMID: 30300580


Stochastic Combinatorial Ensembles for Defending Against Adversarial Examples.
Adam GA, Smirnov P, Duvenaud D, Haibe-Kains B, Goldenberg A.
arXiv 2018 Aug 20.

BJU International

Gene Expression Signatures Prognostic for Relapse in Stage I Testicular Germ Cell Tumors (TGCT).
Lewin J, Soltan Ghoraie L, Bedard PL, Hamilton RJ, Chung P, Moore M, Jewett MAS, Anson-Cartwright L, Virtanen C, Winegarden N, Tsao J, Warde P, Sweet J, Haibe-Kains B, Hansen AR.
BJU Int. 2018 May 3; 122(5):814-822. doi: bju.14372
PMID: 29726090

European Journal of Cancer

Rational design and identification of immuno-oncology drug combinations.
Lafolla MAJ, Selby H, Warner K, Ohashi PM, Haibe-Kains B, Siu LL.
Eur J Cancer. 2018 Apr 6. doi: 10.1016/j.ejca.2018.02.027
PMID: 29631102


Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer.
Deblois G, Tonekaboni SAM, Kao Y, Tai F, Liu X, Ettayebi I, Grillo G, Guilhamon P, Ba-alawi W, Fedor A, Murison A, Cescon DW, Arrowsmith C, DeCarvalho D, Park M, Haibe-Kains B, Locasale JW, Lupien M.
BioRxiv 2018 Mar 28. doi: 10.1101/286054


Administration of Hypoxia-Activated Prodrug Evofosfamide after Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Colorectal Cancer.
Haynes J, McKee TD, Haller AC, Wang Y, Leung C, Gendoo DMA, Lima-Fernandes E, Kreso A, Wolman R, Szentgyorgyi E, Vines DC, Haibe-Kains B, Wouters BG, Metser U, Jaffray DA, Smith M, O’Brien CA.
Clin Cancer Res. 2018 Feb 23. doi: 10.1158/1078-0432.CCR-17-1715.
PMID: 29476017


Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer.
Thu KL, Silvester J, Elliott M, Ba-alawi W, Elia A, Duncan MH, Mer AS, Smirnov P, Safikhani Z, Haibe-Kains B, Mak TW, Cescon DW.
Proc Natl Acad Sci U S A. 2018 Jan 29 doi: 10.1073/pnas.1719577115.
PMID: 29378962


Radiomic Biomarkers to Refine Risk Models for Distant Metastasis in HPV-related Oropharyngeal Carcinoma.
Kwan JYY, Su J, Huang SH, Ghoraie LS, Xu W, Chan B, Yip KW, Giuliani M, Bayley A, Kim J, Hope AJ, Ringash J, Cho J, McNiven A, Hansen A, Goldstein D, de Almeida J, Aerts HJW, Waldron JN, Haibe-Kains B, O’Sullivan B, Bratman SV, Liu FF.
Int J Radiat Oncol Biol Phys. 2018 Jan 14. doi: 10.1016/j.ijrobp.2018.01.057.
pii: S0360-3016(18)30129-9
PMID: 29506884


CrosstalkNet: mining large-scale bipartite co-expression networks to characterize epi-stroma crosstalk.
Manem VSK, Adam GA, Gruosso T, Mathieu Gigoux M, Bertos N, Park M, Haibe-Kains B.
Cancer Res. 2018 Jan 2. doi: 10.1158/0008-5472.CAN-17-1383.
PMID: 29459407




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



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.



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



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



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



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



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



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



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.



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



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



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



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



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



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




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



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



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



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



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.



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



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



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



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




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



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


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


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



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



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


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



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



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



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 -

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