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Items: 1 to 50 of 58

1.

Co-expression network analysis identified hub genes critical to triglyceride and free fatty acid metabolism as key regulators of age-related vascular dysfunction in mice.

Li H, Wang X, Lu X, Zhu H, Li S, Duan S, Zhao X, Zhang F, Alterovitz G, Wang F, Li Q, Tian XL, Xu M.

Aging (Albany NY). 2019 Sep 12;11. doi: 10.18632/aging.102275. [Epub ahead of print]

2.

A CRISPR-Cas12a-derived biosensing platform for the highly sensitive detection of diverse small molecules.

Liang M, Li Z, Wang W, Liu J, Liu L, Zhu G, Karthik L, Wang M, Wang KF, Wang Z, Yu J, Shuai Y, Yu J, Zhang L, Yang Z, Li C, Zhang Q, Shi T, Zhou L, Xie F, Dai H, Liu X, Zhang J, Liu G, Zhuo Y, Zhang B, Liu C, Li S, Xia X, Tong Y, Liu Y, Alterovitz G, Tan GY, Zhang LX.

Nat Commun. 2019 Aug 14;10(1):3672. doi: 10.1038/s41467-019-11648-1.

3.

Application of Omics and Bioinformatics Tools in Streptococcus Research.

Liao M, Tong T, Zong Y, Zhou X, Cheng L, Huang R, Ren B, Alterovitz G.

Curr Issues Mol Biol. 2019 Jun 5;32:327-376. doi: 10.21775/cimb.032.327. [Epub ahead of print]

PMID:
31166175
4.

Enabling precision medicine via standard communication of HTS provenance, analysis, and results.

Alterovitz G, Dean D, Goble C, Crusoe MR, Soiland-Reyes S, Bell A, Hayes A, Suresh A, Purkayastha A, King CH, Taylor D, Johanson E, Thompson EE, Donaldson E, Morizono H, Tsang H, Vora JK, Goecks J, Yao J, Almeida JS, Keeney J, Addepalli K, Krampis K, Smith KM, Guo L, Walderhaug M, Schito M, Ezewudo M, Guimera N, Walsh P, Kahsay R, Gottipati S, Rodwell TC, Bloom T, Lai Y, Simonyan V, Mazumder R.

PLoS Biol. 2018 Dec 31;16(12):e3000099. doi: 10.1371/journal.pbio.3000099. eCollection 2018 Dec.

5.

SMART Cancer Navigator: A Framework for Implementing ASCO Workshop Recommendations to Enable Precision Cancer Medicine.

Warner JL, Prasad I, Bennett M, Arniella M, Beeghly-Fadiel A, Mandl KD, Alterovitz G.

JCO Precis Oncol. 2018;2018. doi: 10.1200/PO.17.00292. Epub 2018 May 1.

6.

Lovastatin synergizes with itraconazole against planktonic cells and biofilms of Candida albicans through the regulation on ergosterol biosynthesis pathway.

Zhou Y, Yang H, Zhou X, Luo H, Tang F, Yang J, Alterovitz G, Cheng L, Ren B.

Appl Microbiol Biotechnol. 2018 Jun;102(12):5255-5264. doi: 10.1007/s00253-018-8959-8. Epub 2018 Apr 25.

PMID:
29691631
7.

Overcoming the Straw Man Effect in Oncology: Visualization and Ranking of Chemotherapy Regimens Using an Information Theoretic Approach.

Warner JL, Yang PC, Alterovitz G.

JCO Clin Cancer Inform. 2017 Nov;1:1-9. doi: 10.1200/CCI.17.00079.

8.

Somatosensory Modulation of Salivary Gene Expression and Oral Feeding in Preterm Infants: Randomized Controlled Trial.

Barlow SM, Maron JL, Alterovitz G, Song D, Wilson BJ, Jegatheesan P, Govindaswami B, Lee J, Rosner AO.

JMIR Res Protoc. 2017 Jun 14;6(6):e113. doi: 10.2196/resprot.7712.

9.

Biobrick chain recommendations for genetic circuit design.

Yang J, Yu S, Gong B, An N, Alterovitz G.

Comput Biol Med. 2017 Jul 1;86:31-39. doi: 10.1016/j.compbiomed.2017.04.019. Epub 2017 May 3.

PMID:
28499216
10.

SNP by SNP by environment interaction network of alcoholism.

Zollanvari A, Alterovitz G.

BMC Syst Biol. 2017 Mar 14;11(Suppl 3):19. doi: 10.1186/s12918-017-0403-7.

11.

Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

Yang J, Wang H, Ding H, An N, Alterovitz G.

BMC Bioinformatics. 2017 Jan 19;18(1):47. doi: 10.1186/s12859-017-1484-4.

12.

Wrapper-based gene selection with Markov blanket.

Wang A, An N, Yang J, Chen G, Li L, Alterovitz G.

Comput Biol Med. 2017 Feb 1;81:11-23. doi: 10.1016/j.compbiomed.2016.12.002. Epub 2016 Dec 5.

PMID:
28006702
13.

HLA-B*51:01 is strongly associated with clindamycin-related cutaneous adverse drug reactions.

Yang Y, Chen S, Yang F, Zhang L, Alterovitz G, Zhu H, Xuan J, Yang X, Luo H, Mu J, He L, Luo X, Xing Q.

Pharmacogenomics J. 2017 Dec;17(6):501-505. doi: 10.1038/tpj.2016.61. Epub 2016 Aug 16.

PMID:
27527109
14.

Gene expression prediction using low-rank matrix completion.

Kapur A, Marwah K, Alterovitz G.

BMC Bioinformatics. 2016 Jun 17;17(1):243. doi: 10.1186/s12859-016-1106-6.

15.

SMART precision cancer medicine: a FHIR-based app to provide genomic information at the point of care.

Warner JL, Rioth MJ, Mandl KD, Mandel JC, Kreda DA, Kohane IS, Carbone D, Oreto R, Wang L, Zhu S, Yao H, Alterovitz G.

J Am Med Inform Assoc. 2016 Jul;23(4):701-10. doi: 10.1093/jamia/ocw015. Epub 2016 Mar 27.

16.

Classification of hospital acquired complications using temporal clinical information from a large electronic health record.

Warner JL, Zhang P, Liu J, Alterovitz G.

J Biomed Inform. 2016 Feb;59:209-17. doi: 10.1016/j.jbi.2015.12.008. Epub 2015 Dec 17.

17.

All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health.

Lawler M, Siu LL, Rehm HL, Chanock SJ, Alterovitz G, Burn J, Calvo F, Lacombe D, Teh BT, North KN, Sawyers CL; Clinical Working Group of the Global Alliance for Genomics and Health (GA4GH).

Cancer Discov. 2015 Nov;5(11):1133-6. doi: 10.1158/2159-8290.CD-15-0821.

18.

SMART on FHIR Genomics: facilitating standardized clinico-genomic apps.

Alterovitz G, Warner J, Zhang P, Chen Y, Ullman-Cullere M, Kreda D, Kohane IS.

J Am Med Inform Assoc. 2015 Nov;22(6):1173-8. doi: 10.1093/jamia/ocv045. Epub 2015 Jul 21.

PMID:
26198304
19.

Improving PLS-RFE based gene selection for microarray data classification.

Wang A, An N, Chen G, Li L, Alterovitz G.

Comput Biol Med. 2015 Jul;62:14-24. doi: 10.1016/j.compbiomed.2015.04.011. Epub 2015 Apr 17.

PMID:
25912984
20.

Computational gene expression modeling identifies salivary biomarker analysis that predict oral feeding readiness in the newborn.

Maron JL, Hwang JS, Pathak S, Ruthazer R, Russell RL, Alterovitz G.

J Pediatr. 2015 Feb;166(2):282-8.e5. doi: 10.1016/j.jpeds.2014.10.065.

21.

Seeing the forest through the trees: uncovering phenomic complexity through interactive network visualization.

Warner JL, Denny JC, Kreda DA, Alterovitz G.

J Am Med Inform Assoc. 2015 Mar;22(2):324-9. doi: 10.1136/amiajnl-2014-002965. Epub 2014 Oct 21.

22.

Modified Anderson-Darling test-based target detector in non-homogenous environments.

Li Y, Wei Y, Li B, Alterovitz G.

Sensors (Basel). 2014 Aug 29;14(9):16046-61. doi: 10.3390/s140916046.

23.

Prevalence of halitosis in children considering oral hygiene, gender and age.

Villa A, Zollanvari A, Alterovitz G, Cagetti MG, Strohmenger L, Abati S.

Int J Dent Hyg. 2014 Aug;12(3):208-12. doi: 10.1111/idh.12077. Epub 2014 Mar 28.

PMID:
24674694
24.

On the Bayesian Derivation of a Treatment-based Cancer Ontology.

Gao M, Warner J, Yang P, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2014 Apr 7;2014:209-17. eCollection 2014.

25.

Robust prediction-based analysis for genome-wide association and expression studies.

K Koppula S, Zollanvari A, An N, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:104. eCollection 2013.

PMID:
24303313
26.

Order-disorder interface characterization reveals critical factors for disease and drug targets.

Kallenbach J, Hsu WL, Dunker AK, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:101. eCollection 2013.

PMID:
24303310
27.

Reversal of medical practices.

Warner JL, Yang P, Alterovitz G.

Mayo Clin Proc. 2013 Oct;88(10):1182-3. doi: 10.1016/j.mayocp.2013.08.010. No abstract available.

PMID:
24079691
28.

Automated synthesis and visualization of a chemotherapy treatment regimen network.

Warner J, Yang P, Alterovitz G.

Stud Health Technol Inform. 2013;192:62-6. Review.

29.

Temporal phenome analysis of a large electronic health record cohort enables identification of hospital-acquired complications.

Warner JL, Zollanvari A, Ding Q, Zhang P, Snyder GM, Alterovitz G.

J Am Med Inform Assoc. 2013 Dec;20(e2):e281-7. doi: 10.1136/amiajnl-2013-001861. Epub 2013 Aug 1.

30.

SNP-based Bayesian networks can predict oral mucositis risk in autologous stem cell transplant recipients.

Sonis S, Antin J, Tedaldi M, Alterovitz G.

Oral Dis. 2013 Oct;19(7):721-7. doi: 10.1111/odi.12146. Epub 2013 Jun 28.

PMID:
23809011
31.

External phenome analysis enables a rational federated query strategy to detect changing rates of treatment-related complications associated with multiple myeloma.

Warner JL, Alterovitz G, Bodio K, Joyce RM.

J Am Med Inform Assoc. 2013 Jul-Aug;20(4):696-9. doi: 10.1136/amiajnl-2012-001355. Epub 2013 Mar 20.

32.

Phenome based analysis as a means for discovering context dependent clinical reference ranges.

Warner JL, Alterovitz G.

AMIA Annu Symp Proc. 2012;2012:1441-9. Epub 2012 Nov 3.

33.

Network biology of tumor stem-like cells identified a regulatory role of CBX5 in lung cancer.

Yu YH, Chiou GY, Huang PI, Lo WL, Wang CY, Lu KH, Yu CC, Alterovitz G, Huang WC, Lo JF, Hsu HS, Chiou SH.

Sci Rep. 2012;2:584. doi: 10.1038/srep00584. Epub 2012 Aug 16.

34.

Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities.

Quo CF, Kaddi C, Phan JH, Zollanvari A, Xu M, Wang MD, Alterovitz G.

Brief Bioinform. 2012 Jul;13(4):430-45. doi: 10.1093/bib/bbs026.

35.

An automated bayesian framework for integrative gene expression analysis and predictive medicine.

Parikh N, Zollanvari A, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2012;2012:95-104. Epub 2012 Mar 19.

36.

Context-specific ontology integration: a bayesian approach.

Marwah K, Katzin D, Zollanvari A, Noy NF, Ramoni M, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2012;2012:79-86. Epub 2012 Mar 19.

37.

A bayesian translational framework for knowledge propagation, discovery, and integration under specific contexts.

Deng M, Zollanvari A, Alterovitz G.

AMIA Jt Summits Transl Sci Proc. 2012;2012:25-34. Epub 2012 Mar 19.

38.

Genomic studies of GVHD-lessons learned thus far.

Ting C, Alterovitz G, Merlob A, Abdi R.

Bone Marrow Transplant. 2013 Jan;48(1):4-9. doi: 10.1038/bmt.2012.9. Epub 2012 Feb 20. Review.

PMID:
22343675
39.

Is the reduction of dimensionality to a small number of features always necessary in constructing predictive models for analysis of complex diseases or behaviours?

Zollanvari A, Saccone NL, Bierut LJ, Ramoni MF, Alterovitz G.

Conf Proc IEEE Eng Med Biol Soc. 2011;2011:3573-6. doi: 10.1109/IEMBS.2011.6090596.

PMID:
22255111
40.

Personalized medicine for mucositis: Bayesian networks identify unique gene clusters which predict the response to gamma-D-glutamyl-L-tryptophan (SCV-07) for the attenuation of chemoradiation-induced oral mucositis.

Alterovitz G, Tuthill C, Rios I, Modelska K, Sonis S.

Oral Oncol. 2011 Oct;47(10):951-5. doi: 10.1016/j.oraloncology.2011.07.006. Epub 2011 Aug 6.

PMID:
21824803
41.

Mapping transcription mechanisms from multimodal genomic data.

Chang HH, McGeachie M, Alterovitz G, Ramoni MF.

BMC Bioinformatics. 2010 Oct 28;11 Suppl 9:S2. doi: 10.1186/1471-2105-11-S9-S2.

42.

Genomic characterization of Wilms' tumor suppressor 1 targets in nephron progenitor cells during kidney development.

Hartwig S, Ho J, Pandey P, Macisaac K, Taglienti M, Xiang M, Alterovitz G, Ramoni M, Fraenkel E, Kreidberg JA.

Development. 2010 Apr;137(7):1189-203. doi: 10.1242/dev.045732.

43.

High-throughput discovery and characterization of fetal protein trafficking in the blood of pregnant women.

Maron JL, Alterovitz G, Ramoni M, Johnson KL, Bianchi DW.

Proteomics Clin Appl. 2009 Dec;3(12):1389-96. doi: 10.1002/prca.200900109.

44.

Ontology engineering.

Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF.

Nat Biotechnol. 2010 Feb;28(2):128-30. doi: 10.1038/nbt0210-128. No abstract available.

45.

The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms.

Alterovitz G, Muso T, Ramoni MF.

Brief Bioinform. 2010 Jan;11(1):80-95. doi: 10.1093/bib/bbp054. Epub 2009 Nov 11. Review.

46.

An artificial intelligence tool to predict fluid requirement in the intensive care unit: a proof-of-concept study.

Celi LA, Hinske LC, Alterovitz G, Szolovits P.

Crit Care. 2008;12(6):R151. doi: 10.1186/cc7140. Epub 2008 Dec 1.

47.

System-wide peripheral biomarker discovery using information theory.

Alterovitz G, Xiang M, Liu J, Chang A, Ramoni MF.

Pac Symp Biocomput. 2008:231-42.

48.

Automated programming for bioinformatics algorithm deployment.

Alterovitz G, Jiwaji A, Ramoni MF.

Bioinformatics. 2008 Feb 1;24(3):450-1. doi: 10.1093/bioinformatics/btm602. Epub 2008 Jan 3.

PMID:
18174185
49.

Gene expression analysis in pregnant women and their infants identifies unique fetal biomarkers that circulate in maternal blood.

Maron JL, Johnson KL, Slonim D, Lai CQ, Ramoni M, Alterovitz G, Jarrah Z, Yang Z, Bianchi DW.

J Clin Invest. 2007 Oct;117(10):3007-19.

50.

Bayesian methods for proteomics.

Alterovitz G, Liu J, Afkhami E, Ramoni MF.

Proteomics. 2007 Aug;7(16):2843-55. Review.

PMID:
17654463

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