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Items: 1 to 50 of 141

1.

Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine.

Rachid Zaim S, Kenost C, Berghout J, Vitali F, Zhang HH, Lussier YA.

BMC Med Genomics. 2019 Jul 11;12(Suppl 5):96. doi: 10.1186/s12920-019-0513-8.

2.

A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes.

Schissler AG, Aberasturi D, Kenost C, Lussier YA.

Front Genet. 2019 May 9;10:414. doi: 10.3389/fgene.2019.00414. eCollection 2019.

3.
4.

Precision drug repurposing via convergent eQTL-based molecules and pathway targeting independent disease-associated polymorphisms.

Vitali F, Berghout J, Fan J, Li J, Li Q, Li H, Lussier YA.

Pac Symp Biocomput. 2019;24:308-319.

5.

Novel disease syndromes unveiled by integrative multiscale network analysis of diseases sharing molecular effectors and comorbidities.

Li H, Fan J, Vitali F, Berghout J, Aberasturi D, Li J, Wilson L, Chiu W, Pumarejo M, Han J, Kenost C, Koripella PC, Pouladi N, Billheimer D, Bedrick EJ, Lussier YA.

BMC Med Genomics. 2018 Dec 31;11(Suppl 6):112. doi: 10.1186/s12920-018-0428-9.

6.

ICD-10 procedure codes produce transition challenges.

Boyd AD, Li J', Kenost C, Zaim SR, Krive J, Mittal M, Satava RA, Burton M, Smith J, Lussier YA.

AMIA Jt Summits Transl Sci Proc. 2018 May 18;2017:35-44. eCollection 2018.

7.

Word-of-Mouth Innovation: Hypothesis Generation for Supplement Repurposing based on Consumer Reviews.

Fan JW, Lussier YA.

AMIA Annu Symp Proc. 2018 Apr 16;2017:689-695. eCollection 2017.

8.

Physician nurse care: A new use of UMLS to measure professional contribution: Are we talking about the same patient a new graph matching algorithm?

Boyd AD, Dunn Lopez K, Lugaresi C, Macieira T, Sousa V, Acharya S, Balasubramanian A, Roussi K, Keenan GM, Lussier YA, Li J', Burton M, Di Eugenio B.

Int J Med Inform. 2018 May;113:63-71. doi: 10.1016/j.ijmedinf.2018.02.002. Epub 2018 Feb 9.

9.

Genome-Wide Association Study in African Americans with Acute Respiratory Distress Syndrome Identifies the Selectin P Ligand Gene as a Risk Factor.

Bime C, Pouladi N, Sammani S, Batai K, Casanova N, Zhou T, Kempf CL, Sun X, Camp SM, Wang T, Kittles RA, Lussier YA, Jones TK, Reilly JP, Meyer NJ, Christie JD, Karnes JH, Gonzalez-Garay M, Christiani DC, Yates CR, Wurfel MM, Meduri GU, Garcia JGN.

Am J Respir Crit Care Med. 2018 Jun 1;197(11):1421-1432. doi: 10.1164/rccm.201705-0961OC.

10.

Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes.

Vitali F, Li Q, Schissler AG, Berghout J, Kenost C, Lussier YA.

Brief Bioinform. 2019 May 21;20(3):789-805. doi: 10.1093/bib/bbx149.

11.
12.

Reading Between the Genes: Computational Models to Discover Function from Noncoding DNA.

Lussier YA, Berghout J, Vitali F, Ramos KS, Kann M, Moore JH.

Pac Symp Biocomput. 2018;23:507-511.

13.
14.

Single subject transcriptome analysis to identify functionally signed gene set or pathway activity.

Berghout J, Li Q, Pouladi N, Li J, Lussier YA.

Pac Symp Biocomput. 2018;23:400-411.

15.

Semantic Modeling for Exposomics with Exploratory Evaluation in Clinical Context.

Fan JW, Li J, Lussier YA.

J Healthc Eng. 2017;2017:3818302. doi: 10.1155/2017/3818302. Epub 2017 Aug 30.

16.

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.

17.

Exploring Wound-Healing Genomic Machinery with a Network-Based Approach.

Vitali F, Marini S, Balli M, Grosemans H, Sampaolesi M, Lussier YA, Cusella De Angelis MG, Bellazzi R.

Pharmaceuticals (Basel). 2017 Jun 21;10(2). pii: E55. doi: 10.3390/ph10020055.

18.

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.

19.

Testing for differentially expressed genetic pathways with single-subject N-of-1 data in the presence of inter-gene correlation.

Schissler AG, Piegorsch WW, Lussier YA.

Stat Methods Med Res. 2018 Dec;27(12):3797-3813. doi: 10.1177/0962280217712271. Epub 2017 May 29.

PMID:
28552011
20.

Microbes Are Associated with Host Innate Immune Response in Idiopathic Pulmonary Fibrosis.

Huang Y, Ma SF, Espindola MS, Vij R, Oldham JM, Huffnagle GB, Erb-Downward JR, Flaherty KR, Moore BB, White ES, Zhou T, Li J, Lussier YA, Han MK, Kaminski N, Garcia JGN, Hogaboam CM, Martinez FJ, Noth I; COMET-IPF Investigators.

Am J Respir Crit Care Med. 2017 Jul 15;196(2):208-219. doi: 10.1164/rccm.201607-1525OC.

21.

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.

22.

Biomechanisms of Comorbidity: Reviewing Integrative Analyses of Multi-omics Datasets and Electronic Health Records.

Pouladi N, Achour I, Li H, Berghout J, Kenost C, Gonzalez-Garay ML, Lussier YA.

Yearb Med Inform. 2016 Nov 10;(1):194-206. Review.

23.

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.

24.

Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells.

Schissler AG, Li Q, Chen JL, Kenost C, Achour I, Billheimer DD, Li H, Piegorsch WW, Lussier YA.

Bioinformatics. 2016 Jun 15;32(12):i80-i89. doi: 10.1093/bioinformatics/btw248.

25.

Simulation of ICD-9 to ICD-10-CM Transition for Family Medicine: Simple or Convoluted?

Grief SN, Patel J, Kochendorfer KM, Green LA, Lussier YA, Li J, Burton M, Boyd AD.

J Am Board Fam Med. 2016 Jan-Feb;29(1):29-36. doi: 10.3122/jabfm.2016.01.150146.

26.

A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis.

Huang Y, Ma SF, Vij R, Oldham JM, Herazo-Maya J, Broderick SM, Strek ME, White SR, Hogarth DK, Sandbo NK, Lussier YA, Gibson KF, Kaminski N, Garcia JG, Noth I.

BMC Pulm Med. 2015 Nov 21;15:147. doi: 10.1186/s12890-015-0142-8.

27.

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.

28.

Wnt7a is a novel inducer of β-catenin-independent tumor-suppressive cellular senescence in lung cancer.

Bikkavilli RK, Avasarala S, Van Scoyk M, Arcaroli J, Brzezinski C, Zhang W, Edwards MG, Rathinam MK, Zhou T, Tauler J, Borowicz S, Lussier YA, Parr BA, Cool CD, Winn RA.

Oncogene. 2015 Oct 16;34(42):5406. doi: 10.1038/onc.2015.165. No abstract available.

PMID:
26473947
29.

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.

30.

Evidence Suggesting That Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors.

Amin AD, Rajan SS, Liang WS, Pongtornpipat P, Groysman MJ, Tapia EO, Peters TL, Cuyugan L, Adkins J, Rimsza LM, Lussier YA, Puvvada SD, Schatz JH.

Cancer Res. 2015 Jul 15;75(14):2916-27. doi: 10.1158/0008-5472.CAN-14-3437. Epub 2015 May 27.

31.

Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing.

Pouladi N, Bime C, Garcia JGN, Lussier YA.

Transl Res. 2016 Feb;168:22-39. doi: 10.1016/j.trsl.2015.04.016. Epub 2015 May 7. Review.

32.

The complexity and challenges of the International Classification of Diseases, Ninth Revision, Clinical Modification to International Classification of Diseases, 10th Revision, Clinical Modification transition in EDs.

Krive J, Patel M, Gehm L, Mackey M, Kulstad E, Li JJ, Lussier YA, Boyd AD.

Am J Emerg Med. 2015 May;33(5):713-8. doi: 10.1016/j.ajem.2015.03.001. Epub 2015 Mar 7.

33.

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.

34.

Wnt7a is a novel inducer of β-catenin-independent tumor-suppressive cellular senescence in lung cancer.

Bikkavilli RK, Avasarala S, Van Scoyk M, Arcaroli J, Brzezinski C, Zhang W, Edwards MG, Rathinam MK, Zhou T, Tauler J, Borowicz S, Lussier YA, Parr BA, Cool CD, Winn RA.

Oncogene. 2015 Oct 16;34(42):5317-28. doi: 10.1038/onc.2015.2. Epub 2015 Mar 2. Erratum in: Oncogene. 2015 Oct 16;34(42):5406.

35.

Metrics and tools for consistent cohort discovery and financial analyses post-transition to ICD-10-CM.

Boyd AD, Li JJ, Kenost C, Joese B, Yang YM, Kalagidis OA, Zenku I, Saner D, Bahroos N, Lussier YA.

J Am Med Inform Assoc. 2015 May;22(3):730-7. doi: 10.1093/jamia/ocu003. Epub 2015 Feb 12.

36.

Prognostic implication of pulmonary function at the beginning of postoperative radiotherapy in non-small cell lung cancer.

Kim H, Lussier YA, Noh OK, Li H, Oh YT, Heo J.

Radiother Oncol. 2014 Dec;113(3):374-8. doi: 10.1016/j.radonc.2014.11.007. Epub 2014 Nov 28.

37.
38.

'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.

39.

Role of FAM18B in diabetic retinopathy.

Wang AL, Rao VR, Chen JJ, Lussier YA, Rehman J, Huang Y, Jager RD, Grassi MA.

Mol Vis. 2014 Aug 4;20:1146-59. eCollection 2014.

40.

Challenges and remediation for Patient Safety Indicators in the transition to ICD-10-CM.

Boyd AD, Yang YM, Li J, Kenost C, Burton MD, Becker B, Lussier YA.

J Am Med Inform Assoc. 2015 Jan;22(1):19-28. doi: 10.1136/amiajnl-2013-002491. Epub 2014 Sep 3.

41.

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.

42.

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.

43.

The transition to ICD-10-CM: challenges for pediatric practice.

Caskey R, Zaman J, Nam H, Chae SR, Williams L, Mathew G, Burton M, Li JJ, Lussier YA, Boyd AD.

Pediatrics. 2014 Jul;134(1):31-6. doi: 10.1542/peds.2013-4147. Epub 2014 Jun 2.

44.

The mitochondrial cardiolipin remodeling enzyme lysocardiolipin acyltransferase is a novel target in pulmonary fibrosis.

Huang LS, Mathew B, Li H, Zhao Y, Ma SF, Noth I, Reddy SP, Harijith A, Usatyuk PV, Berdyshev EV, Kaminski N, Zhou T, Zhang W, Zhang Y, Rehman J, Kotha SR, Gurney TO, Parinandi NL, Lussier YA, Garcia JG, Natarajan V.

Am J Respir Crit Care Med. 2014 Jun 1;189(11):1402-15. doi: 10.1164/rccm.201310-1917OC.

45.

Identifying clinically disruptive International Classification of Diseases 10th Revision Clinical Modification conversions to mitigate financial costs using an online tool.

Venepalli NK, Qamruzzaman Y, Li JJ, Lussier YA, Boyd AD.

J Oncol Pract. 2014 Mar;10(2):97-103. doi: 10.1200/JOP.2013.001156. Epub 2014 Feb 11.

PMID:
24520143
46.

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.

47.

Conquering computational challenges of omics data and post-ENCODE paradigms.

Lussier YA, Li H, Maienschein-Cline M.

Genome Biol. 2013 Aug 23;14(8):310. doi: 10.1186/gb-2013-14-8-310.

48.

Curation-free biomodules mechanisms in prostate cancer predict recurrent disease.

Chen JL, Hsu A, Yang X, Li J, Lee Y, Parinandi G, Li H, Lussier YA.

BMC Med Genomics. 2013;6 Suppl 2:S4. doi: 10.1186/1755-8794-6-S2-S4. Epub 2013 May 7.

49.

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.

50.

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