Publications | Princess Margaret Bioinformatics and Computational Genomics Laboratory

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

Publication Highlights by category:

Pharmacogenomics

Similarity bias from averaging signatures from the Connectivity Map
Ian Smith, Benjamin Haibe-Kains.
bioRxiv 2022; doi: 10.1101/2022.01.24.477615.

PharmacoDB 2.0: improving scalability and transparency of in vitro pharmacogenomics analysis.
Feizi N, Nair SK, Smirnov P, Beri G, Eeles C, Nasr Esfahani P, Nakano M, Tkachuk D, Mammoliti A, Gorobets E, Mer AS, Lin E, Yu Y, Martin S, Hafner M, Haibe-Kains B.
Nucleic Acids Res. 2021 Nov 26. [IF 16.97]; doi: https://doi.org/10.1093/nar/gkab1084

Assessing therapy response in patient-derived xenografts.
Ortmann J, Rampášek L, Tai E, Mer AS, Shi R, Stewart EL, Mascaux C, Fares A, Pham NA, Beri G, Eeles C, Tkachuk D, Ho C, Sakashita S, Weiss J, Jiang X, Liu G, Cescon DW, O’Brien CA, Guo S, Tsao MS, Haibe-Kains B, Goldenberg A.
Sci Transl Med. 2021 Nov 17. [IF 17.96]; doi: 10.1126/scitranslmed.abf4969
PMID: 34788078

Reporting guidelines for human microbiome research: the STORMS checklist.
Mirzayi C, Renson A; Genomic Standards Consortium; Massive Analysis and Quality Control Society, Zohra F, Elsafoury S, Geistlinger L, Kasselman LJ, Eckenrode K, van de Wijgert J, Loughman A, Marques FZ, MacIntyre DA, Arumugam M, Azhar R, Beghini F, Bergstrom K, Bhatt A, Bisanz JE, Braun J, Bravo HC, Buck GA, Bushman F, Casero D, Clarke G, Collado MC, Cotter PD, Cryan JF, Demmer RT, Devkota S, Elinav E, Escobar JS, Fettweis J, Finn RD, Fodor AA, Forslund S, Franke A, Furlanello C, Gilbert J, Grice E, Haibe-Kains B, Handley S, Herd P, Holmes S, Jacobs JP, Karstens L, Knight R, Knights D, Koren O, Kwon DS, Langille M, Lindsay B, McGovern D, McHardy AC, McWeeney S, Mueller NT, Nezi L, Olm M, Palm N, Pasolli E, Raes J, Redinbo MR, Rühlemann M, Balfour Sartor R, Schloss PD, Schriml L, Segal E, Shardell M, Sharpton T, Smirnova E, Sokol H, Sonnenburg JL, Srinivasan S, Thingholm LB, Turnbaugh PJ, Upadhyay V, Walls RL, Wilmes P, Yamada T, Zeller G, Zhang M, Zhao N, Zhao L, Bao W, Culhane A, Devanarayan V, Dopazo J, Fan X, Fischer M, Jones W, Kusko R, Mason CE, Mercer TR, Sansone SA, Scherer A, Shi L, Thakkar S, Tong W, Wolfinger R, Hunter C, Segata N, Huttenhower C, Dowd JB, Jones HE, Waldron L.
Nat Med 2021 Nov 17 [IF 53.44]; doi: https://doi.org/10.1038/s41591-021-01552-x

Proteogenomic characterization of pancreatic ductal adenocarcinoma.
Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H; Clinical Proteomic Tumor Analysis Consortium.
Cell 2021 Sep 16; doi: https://doi.org/10.1016/j.cell.2021.08.023

Transparency and reproducibility in artificial intelligence.
Haibe-Kains B, Adam GA, Hosny A, Khodakarami F; Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL.
Nature. 2020 Oct;586(7829):E14-E16; doi: 10.1038/s41586-020-2766-y
PMID: 33057217

Evaluation of statistical approaches for association testing in noisy drug screening data.
Smirnov P, Smith I, Safikhani Z, Ba-alawi W, Khodakarami F, Lin E, Yu Y, Martin S, Ortmann J, Aittokallio T, Hafner M, Haibe-Kains B
arXiv 2021 Apr 28; arXiv:2104.14036

Orchestrating and sharing large multimodal data for transparent and reproducible research.
Mammoliti A, Smirnov P, Nakano M, Safikhani Z, Ho C, Eeles C, Seo H, Nair SK, Mer AS, Beri G, Rebecca Kusko, MAQC Society, Benjamin Haibe-Kains
BioRxiv 2021 Apr 20; doi: 10.1101/2020.09.18.303842

Biological and therapeutic implications of a unique subtype of NPM1 mutated AML.
Mer AS, Heath EM, Madani Tonekaboni SA, Dogan-Artun N, Nair SK, Murison A, Garcia-Prat L, Shlush L, Hurren R, Voisin V, Bader GD, Nislow C, Rantalainen M, Lehmann S, Gower M, Guidos CJ, Lupien M, Dick JE, Minden MD, Schimmer AD, Haibe-Kains B
Nature Comm 2021 Feb 16 10.1038/s41467-021-21233-0

PRMT5 inhibition disrupts splicing and stemness in glioblastoma
Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB
Nature Comm 2021 Feb 12 10.1038/s41467-021-21204-5

Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations.
Madani Tonekaboni SA, Haibe-Kains B, Lupien M
Nature Comm 2021 Jan 21 10.1038/s41467-020-20830-9
PMID: 33479238

Single-cell chromatin accessibility profiling of glioblastoma identifies an invasive cancer stem cell population associated with lower survival.
Guilhamon P, Chesnelong C, Kushida MM, Nikolic A, Singhal D, MacLeod G, Madani Tonekaboni SA, Cavalli FM, Arlidge C, Rajakulendran N, Rastegar N, Hao X, Hassam R, Smith LJ, Whetstone H, Coutinho FJ, Nadorp B, Ellestad KI, Luchman AH, Chan JA, Shoichet MS, Taylor MD, Haibe-Kains B, Weiss S, Angers S, Gallo M, Dirks PB, Lupien M.
Elife. 2021 Jan 11;10:e64090; doi: 10.7554/eLife.64090
PMID: 33427645

Assessment of Genetic Drift in Large Pharmacogenomic Studies.
Quevedo R, Smirnov P, Tkachuk D, Ho C, El-Hachem N, Safikhani Z, Pugh TJ, Haibe-Kains B
Cell Systems. 2020 Oct 21;11(4):393-401; doi: 10.1016/j.cels.2020.08.012
PMID: 32937114

Nonesterified Fatty Acids and Depression in Cancer Patients and Caregivers.
McCusker MR, Bazinet RP, Metherel AH, Klein RY, Kundra A, Haibe-Kains B, Li M.
Curr Dev Nutr. 2020 Oct 13;4(11); doi: 10.1093/cdn/nzaa156
PMID: 33447694

Pathway-Based Drug Response Prediction Using Similarity Identification in Gene Expression.
Madani Tonekaboni SA, Beri G, Haibe-Kains B, Dai P.
Front Genet. 2020 Sep 9; doi: 10.3389/fgene.2020.01016
PMID: 3033492

Computational pharmacogenomics screen identifies synergistic statin-compound combinations as anti-breast cancer therapies.
Leeuwen J, Ba-Alawi W, Branchard E, Longo J, Silvester J, Cescon DW, Haibe-Kains B, Penn LZ, Gendoo DMA.
BioRxiv 2020 Sep 09; doi: 10.1101/2020.09.07.286922

Bimodality of gene expression in cancer patient tumors as interpretable biomarkers for drug sensitivity.
Ba-Alawi W, Nair SK, Li B, Mammoliti A, Smirnov P, Mer AS, Penn L, Haibe-Kains B.
BioRxiv 2020 Sep 09; doi: 10.1101/2020.09.08.288688

KuLGaP: A Selective Measure for Assessing Therapy Response in Patient-Derived Xenografts.
Ortmann J, Rampášek L, Tai E, Mer AS, Shi R, Stewart EL, Mascaux C, Fares A, Pham N, Beri G, Eeles C, Tkachuk D, Ho C, Sakashita S, Weiss J, Jiang X, Liu G, Cescon DW, O’Brien C, Guo S, Tsao MS, Haibe-Kains B, Goldenberg A.
BioRxiv 2020 Sep 09; doi: 10.1101/2020.09.08.287573

Machine learning approaches to drug response prediction: challenges and recent progress.
Adam G, Rampášek L, Safikhani Z, Smirnov P, Haibe-Kains B, Goldenberg A*.
NPJ Precis Oncol. 2020 Jun 15;4(1):1-0; doi: 10.1038/s41698-020-0122-1
PMID: 7296033

Gene isoforms as expression-based biomarkers predictive of drug response in vitro.
Safikhani Z, Smirnov P, Thu KL, Silvester J, 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

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 Jun 1;77(11):3057-69; doi: 10.1158/0008-5472.CAN-17-0096
PMID: 28314784

Revisiting inconsistency in large pharmacogenomic studies.
Safikhani Z, Freeman M, Smirnov P, El-Hachem N, She A, Quevedo R, Goldenberg A, Birkbak NJ, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B.
F1000Res. 2016 Sep 16; doi: 10.12688/f1000research.9611.2
PMID: 28928933

Radiomics

Evaluating clinical acceptability of organ-at-risk segmentation In head & neck cancer using a compendium of open-source 3D convolutional neural networks.
Joseph Marsilla, Jun Won Kim, Sejin Kim, Denis Tkachuck, Katrina Rey-McIntyre, Tirth Patel, Tony Tadic, Fei-Fei Liu, Scott Bratman, Andrew Hope, Benjamin Haibe-Kains.
medRxiv 2022; doi: 10.1101/2022.01.15.22269276

Lymph Node Graph Neural Networks for Cancer Metastasis Prediction.
Michal Kazmierski, Benjamin Haibe-Kains.
arXiv 2021 Jun 3; doi: arxiv.org/abs/2106.01711

Automated detection of dental artifacts for large-scale radiomic analysis in radiation oncology.
Arrowsmith C, Reiazi R, Welch M, Kazmierski M, Patel T, Rezaie A, Tadic T, Bratman S, Haibe-Kains B
Phys Imaging Radiat Oncol 2021 Apr 21; doi: 10.1016/j.phro.2021.04.001

The impact of the variation of imaging parameters on the robustness of Computed Tomography radiomic features: A review.
Reiazi R, Abbas E, Famiyeh P, Rezaie A, Kwan JYY, Patel T, Bratman SV, Tadic T, Liu FF, Haibe-Kains B
Comput Biol Med. 2021 Apr 16;133:104400; doi: 10.1016/j.compbiomed.2021.104400
PMID: 33930766

The Impact of the Variation of CT Scanner on the Prediction of Human Papillomavirus (HPV) Association of Oropharyngeal Cancer (OPC) using Radiomic Models.
Reiazi R, Arrowsmith C, Welch M, Abbas-Aghababazadeh F, Eeles C, Tadic T, Hope AJ, Bratman SV, Haibe-Kains B
medRxiv 2021 Mar 08; doi: 10.1186/10.1101/2021.03.04.21252908

Development of web-based quality-assurance tool for radiotherapy target delineation for head and neck cancer: quality evaluation of nasopharyngeal carcinoma.
Kim JW, Marsilla J, Kazmierski M , Tkachuk D, Huang SH, Xu W, Cho J, Ringash J, Bratman S, Hope A, Haibe-Kains B
medRxiv 2021 Feb 24; doi: 10.1101/2021.02.24.21252123

A Machine Learning Challenge for Prognostic Modelling in Head and Neck Cancer Using Multi-modal Data.
Kazmierski M, Welch M, Kim S, McIntosh C, Rey-McIntyre K, Huang SH, Patel T, Tadic T, Milosevic M, Liu FF, Hope A, Bratman S, Haibe-Kains B
arXiv 2021 Jan 28; arxiv.org/abs/2101.11935

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
PMID: 30416044

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:e23421; doi: 10.7554/eLife.23421
PMID: 28731408

Automatic classification of dental artifact status for efficient image veracity checks: effects of image resolution and convolutional neural network depth.
Welch ML, McIntosh C, Purdie TG, Wee L, Traverso A, Dekker A, Haibe-Kains B, Jaffray DA.
Phys Med Biol. 2020 Jan 10;65(1):015005; doi: 10.1088/1361-6560/ab5427
PMID: 31683260

Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.
Aerts HJ, Velazquez ER, Leijenaar RT, Parmar C, Grossmann P, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin P.
Nat Commun. 2014 Jun 3;5:4006; doi: 10.1038/ncomms5006
PMID: 24892406

Software Development

SYNERGxDB: an integrative pharmacogenomic portal to identify synergistic drug combinations for precision oncology.
Seo H, Tkachuk D, Ho C, Mammoliti A, Rezaie A, Madani Tonekaboni SA, Haibe-Kains B.
Nucleic Acids Res. 2020 Jul 2;48(W1):W494-W501; doi: 10.1093/nar/gkaa421
PMID: 32442307

ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets.
Nair SK, Eeles C, Ho C, Beri G, Yoo E, Tkachuk D, Tang A, Nijrabi P, Smirnov P, Seo H, Jennen D,Haibe-Kains B.
Nucleic Acids Res. 2020 Jul 2;48(W1):W455-W462; doi: 10.1093/nar/gkaa390
PMID: 32421831

Creating reproducible pharmacogenomic analysis pipelines.
Mammoliti A, Smirnov P, Safikhani Z, Ba-Alawi W, Haibe-Kains B.
Sci Data. 2019 Sep 3;6(1):166; doi: 10.1038/s41597-019-0174-7
PMID: 31481707

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. 2018 Jan 4;46(D1):D994-D1002; doi: 10.1093/nar/gkx911
PMID: 30053271

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, Grossman P, Beck AH, Aerts HJ, Lupien M, Goldenberg A, Haibe-Kains B.
Bioinformatics. 2016 Apr 15;32(8):1244-6; doi: 10.1093/bioinformatics/btv723
PMID: 26656004

Publication Highlights by year:

2022

Similarity bias from averaging signatures from the Connectivity Map
Ian Smith, Benjamin Haibe-Kains.
bioRxiv 2022; doi: 10.1101/2022.01.24.477615.

2021

Lymph Node Graph Neural Networks for Cancer Metastasis Prediction.
Michal Kazmierski, Benjamin Haibe-Kains.
arXiv 2021 Jun 3; doi: arxiv.org/abs/2106.01711

2020

Centromeric cohesion failure invokes a conserved choreography of chromosomal mis-segregations in pancreatic neuroendocrine tumor.
Quevedo R, Spreafico A, Bruce J, Danesh A, El Ghamrasni S, Giesler A, Hanna Y, Have C, Li T, Yang SYC, Zhang T, Asa SL, Haibe-Kains B, Krzyzanowska M, Smith AC, Singh S, Siu LL, Pugh TJ.
Genome Med. 2020 Apr 28;12(1):38; doi: 10.1186/s13073-020-00730-9
PMID: 32345369

Modeling germline mutations in pineoblastoma uncovers lysosome disruption-based therapy.
Chung PED, Gendoo DMA, Ghanbari-Azarnier R, Liu JC, Jiang Z, Tsui J, Wang DY, Xiao X, Li B, Dubuc A, Shih D, Remke M, Ho B, Garzia L, Ben-David Y, Kang SG, Croul S, Haibe-Kains B, Huang A, Taylor MD, Zacksenhaus E.
Nat Commun. 2020 Apr 14;11(1):1825; doi: 10.1038/s41467-020-15585-2
PMID: 32286280

MicroRNA-mRNA networks define translatable molecular outcome phenotypes in osteosarcoma.
Lietz CE, Garbutt C, Barry WT, Deshpande V, Chen YL, Lozano-Calderon SA, Wang Y, Lawney B, Ebb D, Cote GM, Duan Z, Hornicek FJ, Choy E, Petur Nielsen G, Haibe-Kains B, Quackenbush J, Spentzos D.
Sci Rep. 2020 Mar 10;9(1):8770; doi: 10.1038/s41598-020-61236-3
PMID: 31217513

External validation and transfer learning of convolutional neural networks for computed tomography dental artifact classification.
Welch ML, McIntosh C, Traverso A, Wee L, Purdie TG, Dekker A, Haibe-Kains B, Jaffray DA.
Phys Med Biol. 2020 Feb 5;65(3):035017; doi: 10.1088/1361-6560/ab63ba
PMID: 31851961

2019

Modeling Cellular Response in Large-Scale Radiogenomic Databases to Advance Precision Radiotherapy.
Manem VS, Lambie M, Smith I, Smirnov P, Kofia V, Freeman M, Koritzinsky M, Abazeed ME, Haibe-Kains B, Bratman SV.
Cancer Res. 2019 Dec 15;79(24):6227-6237; doi: 10.1158/0008-5472.CAN-19-0179
PMID: 31558563

Organoid Cultures as Preclinical Models of Non-Small Cell Lung Cancer.
Shi R, Radulovich N, Ng C,Liu N, Notsuda H, Cabanero M,Martins-Filho SN, Raghavan V, Li Q,Mer AS, Rosen JC,Li M,Wang YH, Tamblyn L, Pham NA,Haibe-Kains B,Liu G, Moghal N, Tsao MS.
Clin Cancer Res. 2019 Nov 6; doi: 10.1158/1078-0432.CCR-19-1376
PMID: 31694835

Identifying clusters of cis-regulatory elements underpinning TAD structures and lineage-specific regulatory networks.
Madani Tonekaboni SA, Mazrooei P, Kofia V, Haibe-Kains B, Lupien M.
Genome Res. 2019 Oct;29(10):1733-1743; doi: 10.1101/gr.248658.119
PMID: 31533978

GLUT1 inhibition blocks growth of RB1-positive Triple Negative Breast Cancer.
Qin Wu,Wail Ba-alawi, Genevieve Deblois, Jennifer Cruickshank, Shili Duan, Evelyne Lima-Fernandes, Jillian Haight, Seyed Ali Madani Tonekaboni, Anne-Marie Fortier, Hellen Kuasne, Trevor D. McKee,Hassan Mahmoud, Sarina Cameron, Nergiz Dogan-Artun, WenJun Chen, Ravi N. Vellanki, Stanley Zhou, Susan J. Done, Morag Park, David W. Cescon,Benjamin Haibe-Kains, Mathieu Lupien, Cheryl H. Arrowsmith.
BioRxiv 2019 Sep 11; doi: 10.1101/764944

Creating reproducible pharmacogenomic analysis pipelines.
Mammoliti A, Smirnov P, Safikhani Z, Ba-Alawi W, Haibe-Kains B.
Sci Data. 2019 Sep 3;6(1):166; doi: 10.1038/s41597-019-0174-7
PMID: 31481707

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

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

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

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

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

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

AXL knockdown gene signature reveals a drug repurposing opportunity for a class of antipsychotics to reduce growth and metastasis of triple-negative breast cancer.
Goyette MA, Cusseddu R, Elkholi I,Abu-Thuraia A, El-Hachem N,Haibe-Kains B,Gratton JP, Cote JF.
Oncotarget. 2019 Mar 12;10(21):2055-2067; doi: 10.18632/oncotarget.26725
PMID: 31007848

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

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

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

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

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

2018

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

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

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. https://www.nature.com/articles/s42255-018-0008-5

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

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

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. https://arxiv.org/abs/1808.06645

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

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

2017

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

2016

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

2015

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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