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Items: 23

1.

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.

Frochaux MV, Bou Sleiman M, Gardeux V, Dainese R, Hollis B, Litovchenko M, Braman VS, Andreani T, Osman D, Deplancke B.

Genome Biol. 2020 Jan 17;21(1):6. doi: 10.1186/s13059-019-1912-z.

2.

Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle.

Friman ET, Deluz C, Meireles-Filho AC, Govindan S, Gardeux V, Deplancke B, Suter DM.

Elife. 2019 Dec 3;8. pii: e50087. doi: 10.7554/eLife.50087.

3.

Sex-dependent and sex-independent regulatory systems of size variation in natural populations.

Okada H, Yagi R, Gardeux V, Deplancke B, Hafen E.

Mol Syst Biol. 2019 Nov;15(11):e9012. doi: 10.15252/msb.20199012.

4.

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing.

Alpern D, Gardeux V, Russeil J, Mangeat B, Meireles-Filho ACA, Breysse R, Hacker D, Deplancke B.

Genome Biol. 2019 Apr 19;20(1):71. doi: 10.1186/s13059-019-1671-x.

5.

A genome-by-environment interaction classifier for precision medicine: personal transcriptome response to rhinovirus identifies children prone to asthma exacerbations.

Gardeux V, Berghout J, Achour I, Schissler AG, Li Q, Kenost C, Li J, Shang Y, Bosco A, Saner D, Halonen MJ, Jackson DJ, Li H, Martinez FD, Lussier YA.

J Am Med Inform Assoc. 2017 Nov 1;24(6):1116-1126. doi: 10.1093/jamia/ocx069.

6.

Profiling of Single-Cell Transcriptomes.

Chen W, Gardeux V, Meireles-Filho A, Deplancke B.

Curr Protoc Mouse Biol. 2017 Sep 8;7(3):145-175. doi: 10.1002/cpmo.30.

PMID:
28884792
7.

N-of-1-pathways MixEnrich: advancing precision medicine via single-subject analysis in discovering dynamic changes of transcriptomes.

Li Q, Schissler AG, Gardeux V, Achour I, Kenost C, Berghout J, Li H, Zhang HH, Lussier YA.

BMC Med Genomics. 2017 May 24;10(Suppl 1):27. doi: 10.1186/s12920-017-0263-4.

8.

ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data.

Gardeux V, David FPA, Shajkofci A, Schwalie PC, Deplancke B.

Bioinformatics. 2017 Oct 1;33(19):3123-3125. doi: 10.1093/bioinformatics/btx337.

9.

Dissecting the brown adipogenic regulatory network using integrative genomics.

Pradhan RN, Bues JJ, Gardeux V, Schwalie PC, Alpern D, Chen W, Russeil J, Raghav SK, Deplancke B.

Sci Rep. 2017 Feb 9;7:42130. doi: 10.1038/srep42130.

10.

kMEn: Analyzing noisy and bidirectional transcriptional pathway responses in single subjects.

Li Q, Schissler AG, Gardeux V, Berghout J, Achour I, Kenost C, Li H, Zhang HH, Lussier YA.

J Biomed Inform. 2017 Feb;66:32-41. doi: 10.1016/j.jbi.2016.12.009. Epub 2016 Dec 19.

11.

Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions.

Li H, Achour I, Bastarache L, Berghout J, Gardeux V, Li J, Lee Y, Pesce L, Yang X, Ramos KS, Foster I, Denny JC, Moore JH, Lussier YA.

NPJ Genom Med. 2016;1. pii: 16006. Epub 2016 Apr 27.

12.

The Genetics of Transcription Factor DNA Binding Variation.

Deplancke B, Alpern D, Gardeux V.

Cell. 2016 Jul 28;166(3):538-554. doi: 10.1016/j.cell.2016.07.012. Review.

13.

eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs.

Li H, Pouladi N, Achour I, Gardeux V, Li J, Li Q, Zhang HH, Martinez FD, 'Skip' Garcia JGN, Lussier YA.

J Biomed Inform. 2015 Dec;58:226-234. doi: 10.1016/j.jbi.2015.10.010. Epub 2015 Oct 30.

14.

Dynamic changes of RNA-sequencing expression for precision medicine: N-of-1-pathways Mahalanobis distance within pathways of single subjects predicts breast cancer survival.

Schissler AG, Gardeux V, Li Q, Achour I, Li H, Piegorsch WW, Lussier YA.

Bioinformatics. 2015 Jun 15;31(12):i293-302. doi: 10.1093/bioinformatics/btv253.

15.

Computing molecular signatures as optima of a bi-objective function: method and application to prediction in oncogenomics.

Gardeux V, Chelouah R, Wanderley MF, Siarry P, Braga AP, Reyal F, Rouzier R, Pusztai L, Natowicz R.

Cancer Inform. 2015 Apr 19;14:33-45. doi: 10.4137/CIN.S21111. eCollection 2015.

16.

Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes.

Gardeux V, Bosco A, Li J, Halonen MJ, Jackson D, Martinez FD, Lussier YA.

J Biomed Inform. 2015 Jun;55:94-103. doi: 10.1016/j.jbi.2015.03.003. Epub 2015 Mar 19.

17.

Are we able to predict survival in ER-positive HER2-negative breast cancer? A comparison of web-based models.

Laas E, Mallon P, Delomenie M, Gardeux V, Pierga JY, Cottu P, Lerebours F, Stevens D, Rouzier R, Reyal F.

Br J Cancer. 2015 Mar 3;112(5):912-7. doi: 10.1038/bjc.2014.641. Epub 2015 Jan 15.

18.

'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine.

Gardeux V, Achour I, Li J, Maienschein-Cline M, Li H, Pesce L, Parinandi G, Bahroos N, Winn R, Foster I, Garcia JG, Lussier YA.

J Am Med Inform Assoc. 2014 Nov-Dec;21(6):1015-25. doi: 10.1136/amiajnl-2013-002519. Epub 2014 Jun 12.

19.

In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment.

Yang X, Huang Y, Lee Y, Gardeux V, Achour I, Regan K, Rebman E, Li H, Lussier YA.

BMC Med Genomics. 2014;7 Suppl 1:S2. doi: 10.1186/1755-8794-7-S1-S2. Epub 2014 May 8.

20.

Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study.

Gardeux V, Arslan AD, Achour I, Ho TT, Beck WT, Lussier YA.

BMC Med Genomics. 2014;7 Suppl 1:S1. doi: 10.1186/1755-8794-7-S1-S1. Epub 2014 May 8.

21.

ARTS: automated randomization of multiple traits for study design.

Maienschein-Cline M, Lei Z, Gardeux V, Abbasi T, Machado RF, Gordeuk V, Desai AA, Saraf S, Bahroos N, Lussier Y.

Bioinformatics. 2014 Jun 1;30(11):1637-9. doi: 10.1093/bioinformatics/btu075. Epub 2014 Feb 3.

22.

COPD Hospitalization Risk Increased with Distinct Patterns of Multiple Systems Comorbidities Unveiled by Network Modeling.

Lee YJ, Boyd AD, Li JJ, Gardeux V, Kenost C, Saner D, Li H, Abraham I, Krishnan JA, Lussier YA.

AMIA Annu Symp Proc. 2014 Nov 14;2014:855-64. eCollection 2014.

23.

The discriminatory cost of ICD-10-CM transition between clinical specialties: metrics, case study, and mitigating tools.

Boyd AD, Li JJ, Burton MD, Jonen M, Gardeux V, Achour I, Luo RQ, Zenku I, Bahroos N, Brown SB, Vanden Hoek T, Lussier YA.

J Am Med Inform Assoc. 2013 Jul-Aug;20(4):708-17. doi: 10.1136/amiajnl-2012-001358. Epub 2013 May 5.

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