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Items: 1 to 50 of 161

1.

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.

2.

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 Jun 15. doi: 10.1007/s00259-019-04382-9. [Epub ahead of print]

PMID:
31203421
3.

SIGN: Similarity identification in gene expression.

Madani Tonekaboni SA, Kumar Manem VS, El-Hachem N, Haibe-Kains B.

Bioinformatics. 2019 Jun 14. pii: btz485. doi: 10.1093/bioinformatics/btz485. [Epub ahead of print]

PMID:
31198954
4.

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. pii: canres.0349.2019. doi: 10.1158/0008-5472.CAN-19-0349. [Epub ahead of print]

PMID:
31142512
5.

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.

6.

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, Côté JF.

Oncotarget. 2019 Mar 12;10(21):2055-2067. doi: 10.18632/oncotarget.26725. eCollection 2019 Mar 12.

7.

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.

8.

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. pii: btz158. doi: 10.1093/bioinformatics/btz158. [Epub ahead of print]

PMID:
30850846
9.

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. eCollection 2019.

10.

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.

11.

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.

PMID:
30720033
12.

ONECUT2 is a driver of neuroendocrine prostate cancer.

Guo H, Ci X, Ahmed M, Hua JT, Soares F, Lin D, Puca L, Vosoughi A, Xue H, Li E, Su P, Chen S, Nguyen T, Liang Y, Zhang Y, Xu X, Xu J, Sheahan AV, Ba-Alawi W, Zhang S, Mahamud O, Vellanki RN, Gleave M, Bristow RG, Haibe-Kains B, Poirier JT, Rudin CM, Tsao MS, Wouters BG, Fazli L, Feng FY, Ellis L, van der Kwast T, Berlin A, Koritzinsky M, Boutros PC, Zoubeidi A, Beltran H, Wang Y, He HH.

Nat Commun. 2019 Jan 17;10(1):278. doi: 10.1038/s41467-018-08133-6.

13.

Whole genomes define concordance of matched primary, xenograft, and organoid models of pancreas cancer.

Gendoo DMA, Denroche RE, Zhang A, Radulovich N, Jang GH, Lemire M, Fischer S, Chadwick D, Lungu IM, Ibrahimov E, Cao PJ, 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. doi: 10.1371/journal.pcbi.1006596. eCollection 2019 Jan.

14.

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. eCollection 2018.

15.

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.

16.

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.

17.

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
18.

Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma.

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. Epub 2018 Jul 3.

PMID:
30084834
19.

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.

20.

Scoring of tumor-infiltrating lymphocytes: From visual estimation to machine learning.

Klauschen F, Müller KR, Binder A, Bockmayr M, Hägele M, Seegerer P, Wienert S, Pruneri G, de Maria S, Badve S, Michiels S, Nielsen TO, Adams S, Savas P, Symmans F, Willis S, Gruosso T, Park M, Haibe-Kains B, Gallas B, Thompson AM, Cree I, Sotiriou C, Solinas C, Preusser M, Hewitt SM, Rimm D, Viale G, Loi S, Loibl S, Salgado R, Denkert C; International Immuno-Oncology Biomarker Working Group.

Semin Cancer Biol. 2018 Oct;52(Pt 2):151-157. doi: 10.1016/j.semcancer.2018.07.001. Epub 2018 Jul 7. Review.

PMID:
29990622
21.

Gene expression signatures prognostic for relapse in stage I testicular germ cell tumours.

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 Nov;122(5):814-822. doi: 10.1111/bju.14372. Epub 2018 May 31.

PMID:
29726090
22.

Publisher Correction: 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. 2018 Apr 10;9:16194. doi: 10.1038/ncomms16194.

23.

Rational design and identification of immuno-oncology drug combinations.

Iafolla MAJ, Selby H, Warner K, Ohashi PS, Haibe-Kains B, Siu LL.

Eur J Cancer. 2018 May;95:38-51. doi: 10.1016/j.ejca.2018.02.027. Epub 2018 Apr 7. Review.

PMID:
29631102
24.

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 JR, Aerts HJ, Waldron JN, Haibe-Kains B, O'Sullivan B, Bratman SV, Liu FF.

Int J Radiat Oncol Biol Phys. 2018 Nov 15;102(4):1107-1116. doi: 10.1016/j.ijrobp.2018.01.057. Epub 2018 Feb 1.

PMID:
29506884
25.

Administration of Hypoxia-Activated Prodrug Evofosfamide after Conventional Adjuvant Therapy Enhances Therapeutic Outcome and Targets Cancer-Initiating Cells in Preclinical Models of Colorectal Cancer.

Haynes J, McKee TD, Haller A, 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 May 1;24(9):2116-2127. doi: 10.1158/1078-0432.CCR-17-1715. Epub 2018 Feb 23.

26.

CrosstalkNet: A Visualization Tool for Differential Co-expression Networks and Communities.

Manem V, Adam GA, Gruosso T, Gigoux M, Bertos N, Park M, Haibe-Kains B.

Cancer Res. 2018 Apr 15;78(8):2140-2143. doi: 10.1158/0008-5472.CAN-17-1383. Epub 2018 Feb 19.

27.

Disruption of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer.

Thu KL, Silvester J, Elliott MJ, Ba-Alawi W, Duncan MH, Elia AC, Mer AS, Smirnov P, Safikhani Z, Haibe-Kains B, Mak TW, Cescon DW.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):E1570-E1577. doi: 10.1073/pnas.1719577115. Epub 2018 Jan 29.

28.

Author Correction: 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. 2018 Jan 9;9(1):166. doi: 10.1038/s41467-017-02136-5.

29.

Network science in clinical trials: A patient-centered approach.

Manem VSK, Salgado R, Aftimos P, Sotiriou C, Haibe-Kains B.

Semin Cancer Biol. 2018 Oct;52(Pt 2):135-150. doi: 10.1016/j.semcancer.2017.12.006. Epub 2017 Dec 24. Review.

PMID:
29278737
30.

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. 2018 Mar 1;78(5):1347-1357. doi: 10.1158/0008-5472.CAN-17-1231. Epub 2017 Dec 11.

31.

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. No abstract available.

PMID:
29220036
32.

Software for the Integration of Multiomics 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.

33.

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. Erratum in: Nat Commun. 2018 Jan 9;9(1):166.

34.

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 Nov;18(16):1469-1472. doi: 10.2217/pgs-2017-0132. Epub 2017 Oct 23. No abstract available.

35.

Tissue specificity of in vitro drug sensitivity.

Yao F, Madani Tonekaboni SA, Safikhani Z, Smirnov P, El-Hachem N, Freeman M, Manem VSK, Haibe-Kains B.

J Am Med Inform Assoc. 2018 Feb 1;25(2):158-166. doi: 10.1093/jamia/ocx062.

36.

Revisiting inconsistency in large pharmacogenomic studies.

Safikhani Z, Smirnov P, Freeman M, El-Hachem N, She A, Rene Q, Goldenberg A, Birkbak NJ, Hatzis C, Shi L, Beck AH, Aerts HJWL, Quackenbush J, Haibe-Kains B.

Version 3. F1000Res. 2016 Sep 16 [revised 2017 Jan 1];5:2333. doi: 10.12688/f1000research.9611.3. eCollection 2016.

37.

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 RJ, Aerts HJ.

Elife. 2017 Jul 21;6. pii: e23421. doi: 10.7554/eLife.23421.

38.

AutoDock and AutoDockTools for Protein-Ligand Docking: Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1(BACE1) as a Case Study.

El-Hachem N, Haibe-Kains B, Khalil A, Kobeissy FH, Nemer G.

Methods Mol Biol. 2017;1598:391-403. doi: 10.1007/978-1-4939-6952-4_20.

PMID:
28508374
39.

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

Hill KE, Kelly AD, Kuijjer ML, Barry W, Rattani A, Garbutt CC, Kissick H, Janeway K, Perez-Atayde A, Goldsmith J, Gebhardt MC, Arredouani MS, Cote G, Hornicek F, Choy E, Duan Z, Quackenbush J, Haibe-Kains B, Spentzos D.

J Hematol Oncol. 2017 May 15;10(1):107. doi: 10.1186/s13045-017-0465-4.

40.

Genomic biomarkers for precision radiation medicine.

Bratman SV, Milosevic MF, Liu FF, Haibe-Kains B.

Lancet Oncol. 2017 May;18(5):e238. doi: 10.1016/S1470-2045(17)30263-2. No abstract available.

PMID:
28495284
41.

Study of Meta-analysis strategies for network inference using information-theoretic approaches.

Pham NC, Haibe-Kains B, Bellot P, Bontempi G, Meyer PE.

BioData Min. 2017 May 6;10:15. doi: 10.1186/s13040-017-0136-6. eCollection 2017.

42.

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 ECH, van den Meiracker AH, Gross KW, Azizi M, Corvol P, Nguyen G, Reudelhuber TL, Danser AHJ.

Hypertension. 2017 Jun;69(6):1145-1155. doi: 10.1161/HYPERTENSIONAHA.117.09179. Epub 2017 Apr 10.

43.

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 Jun 20;45(11):6417-6426. doi: 10.1093/nar/gkx242.

44.

A review of connectivity map and computational approaches in pharmacogenomics.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.

Brief Bioinform. 2017 Sep 1;18(5):903. doi: 10.1093/bib/bbx023. No abstract available.

45.

Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.

El-Hachem N, Gendoo DMA, Ghoraie LS, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader GD, Goldenberg A, Haibe-Kains B.

Cancer Res. 2017 Jun 1;77(11):3057-3069. doi: 10.1158/0008-5472.CAN-17-0096. Epub 2017 Mar 17.

46.

The Cdc42/Rac1 regulator CdGAP is a novel E-cadherin transcriptional co-repressor with Zeb2 in breast cancer.

He Y, Northey JJ, Pelletier A, Kos Z, Meunier L, Haibe-Kains B, Mes-Masson AM, Côté JF, Siegel PM, Lamarche-Vane N.

Oncogene. 2017 Jun 15;36(24):3490-3503. doi: 10.1038/onc.2016.492. Epub 2017 Jan 30.

47.

A review of connectivity map and computational approaches in pharmacogenomics.

Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F.

Brief Bioinform. 2018 May 1;19(3):506-523. doi: 10.1093/bib/bbw112. Review. Erratum in: Brief Bioinform. 2017 Sep 1;18(5):903.

48.

Safikhani et al. 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. No abstract available.

PMID:
27905430
49.

Safikhani et al. 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. No abstract available.

PMID:
27905423
50.

Safikhani et al. 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. No abstract available.

PMID:
27905416

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