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Items: 1 to 50 of 172

1.

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;10(1):4409. doi: 10.1038/s41598-020-61236-3.

2.

Assessment of modelling strategies for drug response prediction in cell lines and xenografts.

Kurilov R, Haibe-Kains B, Brors B.

Sci Rep. 2020 Feb 18;10(1):2849. doi: 10.1038/s41598-020-59656-2.

3.

Author Correction: Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.

Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F.

Nat Genet. 2020 Apr;52(4):463. doi: 10.1038/s41588-020-0588-3.

PMID:
32051610
4.

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

St Paul M, Saibil SD, Lien SC, Han S, Sayad A, Mulder DT, Garcia-Batres CR, Elford AR, Israni-Winger K, Robert-Tissot C, Zon M, Katz SR, Shaw PA, Clarke BA, Bernardini MQ, Nguyen LT, Haibe-Kains B, Pugh TJ, Ohashi PS.

Cancer Immunol Res. 2020 Mar;8(3):321-333. doi: 10.1158/2326-6066.CIR-19-0521. Epub 2020 Jan 21.

PMID:
31964625
5.

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution.

Chan-Seng-Yue M, Kim JC, Wilson GW, Ng K, Figueroa EF, O'Kane GM, Connor AA, Denroche RE, Grant RC, McLeod J, Wilson JM, Jang GH, Zhang A, Dodd A, Liang SB, Borgida A, Chadwick D, Kalimuthu S, Lungu I, Bartlett JMS, Krzyzanowski PM, Sandhu V, Tiriac H, Froeling FEM, Karasinska JM, Topham JT, Renouf DJ, Schaeffer DF, Jones SJM, Marra MA, Laskin J, Chetty R, Stein LD, Zogopoulos G, Haibe-Kains B, Campbell PJ, Tuveson DA, Knox JJ, Fischer SE, Gallinger S, Notta F.

Nat Genet. 2020 Feb;52(2):231-240. doi: 10.1038/s41588-019-0566-9. Epub 2020 Jan 13. Erratum in: Nat Genet. 2020 Feb 12;:.

PMID:
31932696
6.

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
7.

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. 2020 Mar 1;26(5):1162-1174. doi: 10.1158/1078-0432.CCR-19-1376. Epub 2019 Nov 6.

PMID:
31694835
8.

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
9.

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. Epub 2019 Sep 26.

PMID:
31558563
10.

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. Epub 2019 Sep 18.

11.

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.

12.

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.

13.

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 Dec;46(13):2722-2730. doi: 10.1007/s00259-019-04382-9. Epub 2019 Jun 15.

PMID:
31203421
14.

SIGN: similarity identification in gene expression.

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

Bioinformatics. 2019 Nov 1;35(22):4830-4833. doi: 10.1093/bioinformatics/btz485.

PMID:
31198954
15.

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 Sep 1;79(17):4539-4550. doi: 10.1158/0008-5472.CAN-19-0349. Epub 2019 May 29.

PMID:
31142512
16.

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.

17.

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.

18.

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.

19.

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 Oct 1;35(19):3743-3751. doi: 10.1093/bioinformatics/btz158.

20.

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.

21.

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.

22.

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
23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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
32.

Gene Expression Analyses in Breast Cancer: Sample Matters.

Haibe-Kains B, Cescon DW.

JNCI Cancer Spectr. 2018 May 22;2(2):pky019. doi: 10.1093/jncics/pky019. eCollection 2018 Apr. No abstract available.

33.

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.

34.

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.

35.

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
36.

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
37.

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.

38.

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.

39.

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.

40.

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.

41.

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
42.

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.

43.

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
44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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

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