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Items: 1 to 50 of 140

1.

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.

2.

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 Apr 6;95:38-51. doi: 10.1016/j.ejca.2018.02.027. [Epub ahead of print]

PMID:
29631102
3.

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 Feb 1. pii: S0360-3016(18)30129-9. doi: 10.1016/j.ijrobp.2018.01.057. [Epub ahead of print]

PMID:
29506884
4.

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 Feb 23. doi: 10.1158/1078-0432.CCR-17-1715. [Epub ahead of print]

PMID:
29476017
5.

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.

PMID:
29459407
6.

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.

PMID:
29378962
7.

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.

8.

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

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

Semin Cancer Biol. 2017 Dec 24. pii: S1044-579X(17)30236-5. doi: 10.1016/j.semcancer.2017.12.006. [Epub ahead of print] Review.

PMID:
29278737
9.

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. pii: canres.1231.2017. doi: 10.1158/0008-5472.CAN-17-1231. [Epub ahead of print]

PMID:
29229608
10.

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
11.

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.

PMID:
29092936
12.

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.

13.

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.

14.

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.

PMID:
29016819
15.

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.

16.

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.

17.

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
18.

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.

19.

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
20.

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.

21.

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.

PMID:
28396539
22.

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.

23.

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.

PMID:
28334173
24.

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.

PMID:
28314784
25.

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.

26.

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 Jan 9. pii: bbw112. doi: 10.1093/bib/bbw112. [Epub ahead of print] Erratum in: Brief Bioinform. 2017 Sep 1;18(5):903.

PMID:
28069634
27.

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
28.

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
29.

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
30.

Predictive approaches for drug combination discovery in cancer.

Madani Tonekaboni SA, Soltan Ghoraie L, Manem VSK, Haibe-Kains B.

Brief Bioinform. 2018 Mar 1;19(2):263-276. doi: 10.1093/bib/bbw104.

PMID:
27881431
31.

The molecular basis of breast cancer pathological phenotypes.

Heng YJ, Lester SC, Tse GM, Factor RE, Allison KH, Collins LC, Chen YY, Jensen KC, Johnson NB, Jeong JC, Punjabi R, Shin SJ, Singh K, Krings G, Eberhard DA, Tan PH, Korski K, Waldman FM, Gutman DA, Sanders M, Reis-Filho JS, Flanagan SR, Gendoo DM, Chen GM, Haibe-Kains B, Ciriello G, Hoadley KA, Perou CM, Beck AH.

J Pathol. 2017 Feb;241(3):375-391. doi: 10.1002/path.4847. Epub 2016 Dec 29.

32.

Older adults with heart failure treated with carvedilol, bisoprolol, or metoprolol tartrate: risk of mortality.

Perreault S, de Denus S, White M, White-Guay B, Bouvier M, Dorais M, Dubé MP, Rouleau JL, Tardif JC, Jenna S, Haibe-Kains B, Leduc R, Deblois D.

Pharmacoepidemiol Drug Saf. 2017 Jan;26(1):81-90. doi: 10.1002/pds.4132. Epub 2016 Nov 16.

PMID:
27859924
33.

DNA replication stress: a source of APOBEC3B expression in breast cancer.

Cescon DW, Haibe-Kains B.

Genome Biol. 2016 Sep 30;17(1):202. Review.

34.

Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer.

Bailey SD, Desai K, Kron KJ, Mazrooei P, Sinnott-Armstrong NA, Treloar AE, Dowar M, Thu KL, Cescon DW, Silvester J, Yang SY, Wu X, Pezo RC, Haibe-Kains B, Mak TW, Bedard PL, Pugh TJ, Sallari RC, Lupien M.

Nat Genet. 2016 Oct;48(10):1260-6. doi: 10.1038/ng.3650. Epub 2016 Aug 29.

35.

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 Dec 15;32(24):3836-3838. Epub 2016 Aug 18.

36.

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. eCollection 2016.

37.

Adenosine 2B Receptor Expression on Cancer Cells Promotes Metastasis.

Mittal D, Sinha D, Barkauskas D, Young A, Kalimutho M, Stannard K, Caramia F, Haibe-Kains B, Stagg J, Khanna KK, Loi S, Smyth MJ.

Cancer Res. 2016 Aug 1;76(15):4372-82. doi: 10.1158/0008-5472.CAN-16-0544. Epub 2016 May 24.

38.

MM2S: personalized diagnosis of medulloblastoma patients and model systems.

Gendoo DM, Haibe-Kains B.

Source Code Biol Med. 2016 Apr 11;11:6. doi: 10.1186/s13029-016-0053-y. eCollection 2016.

39.

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. 2016 Apr 15;32(8):1244-6. doi: 10.1093/bioinformatics/btv723. Epub 2015 Dec 9.

PMID:
26656004
40.

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. 2016 Apr 1;32(7):1097-9. doi: 10.1093/bioinformatics/btv693. Epub 2015 Nov 24.

PMID:
26607490
41.

Association of Treatment with Carvedilol, Bisoprolol and Metoprolol on the Risk of Mortality and Hospital Admission Among Older Adults with Heart Failure.

Perreault S, de Denus S, White M, White-Guay B, Bouvier M, Dorais M, Dubé M, Rouleau J, Tardif J, Jenna S, Haibe-Kains B, Leduc R, Deblois D.

Value Health. 2015 Nov;18(7):A379. doi: 10.1016/j.jval.2015.09.801. Epub 2015 Oct 20. No abstract available.

42.

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. eCollection 2015 Jun.

43.

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. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.

44.

CD73 is associated with poor prognosis in high-grade serous ovarian cancer.

Turcotte M, Spring K, Pommey S, Chouinard G, Cousineau I, George J, Chen GM, Gendoo DM, Haibe-Kains B, Karn T, Rahimi K, Le Page C, Provencher D, Mes-Masson AM, Stagg J.

Cancer Res. 2015 Nov 1;75(21):4494-503. doi: 10.1158/0008-5472.CAN-14-3569. Epub 2015 Sep 11.

45.

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.

46.

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. 2016 Mar;124(3):313-20. doi: 10.1289/ehp.1409157. Epub 2015 Jul 14.

47.

Extensive rewiring of epithelial-stromal co-expression networks in breast cancer.

Oh EY, Christensen SM, Ghanta S, Jeong JC, Bucur O, Glass B, Montaser-Kouhsari L, Knoblauch NW, Bertos N, Saleh SM, Haibe-Kains B, Park M, Beck AH.

Genome Biol. 2015 Jun 19;16:128. doi: 10.1186/s13059-015-0675-4.

48.

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. Epub 2015 May 20.

49.

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. Epub 2015 May 12.

PMID:
25979459
50.

Prognostic microRNAs modulate the RHO adhesion pathway: A potential therapeutic target in undifferentiated pleomorphic sarcomas.

Wong P, Hui A, Su J, Yue S, Haibe-Kains B, Gokgoz N, Xu W, Bruce J, Williams J, Catton C, Wunder JS, Andrulis IL, Gladdy R, Dickson B, O'Sullivan B, Liu FF.

Oncotarget. 2015 Nov 17;6(36):39127-39. doi: 10.18632/oncotarget.3926.

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