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Items: 50

1.

How accurate can genetic predictions be?

Dreyfuss JM, Levner D, Galagan JE, Church GM, Ramoni MF.

BMC Genomics. 2012 Jul 24;13:340. doi: 10.1186/1471-2164-13-340.

2.

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
3.

Glycosaminoglycans and glucose prevent apoptosis in 4-methylumbelliferone-treated human aortic smooth muscle cells.

Vigetti D, Rizzi M, Moretto P, Deleonibus S, Dreyfuss JM, Karousou E, Viola M, Clerici M, Hascall VC, Ramoni MF, De Luca G, Passi A.

J Biol Chem. 2011 Oct 7;286(40):34497-503. doi: 10.1074/jbc.M111.266312. Epub 2011 Jul 18.

4.

Inferring cell cycle feedback regulation from gene expression data.

Ferrazzi F, Engel FB, Wu E, Moseman AP, Kohane IS, Bellazzi R, Ramoni MF.

J Biomed Inform. 2011 Aug;44(4):565-75. doi: 10.1016/j.jbi.2011.02.002. Epub 2011 Feb 16.

5.

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.

6.

Association of linear growth impairment in pediatric Crohn's disease and a known height locus: a pilot study.

Lee JJ, Essers JB, Kugathasan S, Escher JC, Lettre G, Butler JL, Stephens MC, Ramoni MF, Grand RJ, Hirschhorn J.

Ann Hum Genet. 2010 Nov;74(6):489-97. doi: 10.1111/j.1469-1809.2010.00606.x. Epub 2010 Sep 15.

7.

A transcriptional network signature characterizes lung cancer subtypes.

Chang HH, Dreyfuss JM, Ramoni MF.

Cancer. 2011 Jan 15;117(2):353-60. doi: 10.1002/cncr.25592. Epub 2010 Sep 13.

8.

Genome-wide association for smoking cessation success in a trial of precessation nicotine replacement.

Uhl GR, Drgon T, Johnson C, Ramoni MF, Behm FM, Rose JE.

Mol Med. 2010 Nov-Dec;16(11-12):513-26. doi: 10.2119/molmed.2010.00052. Epub 2010 Aug 24.

9.

A systems biology approach to modeling vibrio cholerae gene expression under virulence-inducing conditions.

Kanjilal S, Citorik R, LaRocque RC, Ramoni MF, Calderwood SB.

J Bacteriol. 2010 Sep;192(17):4300-10. doi: 10.1128/JB.00182-10. Epub 2010 Jul 2.

10.

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.

11.

Integrative predictive model of coronary artery calcification in atherosclerosis.

McGeachie M, Ramoni RL, Mychaleckyj JC, Furie KL, Dreyfuss JM, Liu Y, Herrington D, Guo X, Lima JA, Post W, Rotter JI, Rich S, Sale M, Ramoni MF.

Circulation. 2009 Dec 15;120(24):2448-54. doi: 10.1161/CIRCULATIONAHA.109.865501.

12.

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.

13.

Dynamic gene expression analysis links melanocyte growth arrest with nevogenesis.

Yang G, Thieu K, Tsai KY, Piris A, Udayakumar D, Njauw CN, Ramoni MF, Tsao H.

Cancer Res. 2009 Dec 1;69(23):9029-37. doi: 10.1158/0008-5472.CAN-09-0783. Epub 2009 Nov 10.

14.

Transcriptional network classifiers.

Chang HH, Ramoni MF.

BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S1. doi: 10.1186/1471-2105-10-S9-S1.

15.

Predicting response to short-acting bronchodilator medication using Bayesian networks.

Himes BE, Wu AC, Duan QL, Klanderman B, Litonjua AA, Tantisira K, Ramoni MF, Weiss ST.

Pharmacogenomics. 2009 Sep;10(9):1393-412. doi: 10.2217/pgs.09.93.

16.

Prediction of chronic obstructive pulmonary disease (COPD) in asthma patients using electronic medical records.

Himes BE, Dai Y, Kohane IS, Weiss ST, Ramoni MF.

J Am Med Inform Assoc. 2009 May-Jun;16(3):371-9. doi: 10.1197/jamia.M2846. Epub 2009 Mar 4.

17.

A testable prognostic model of nicotine dependence.

Ramoni RB, Saccone NL, Hatsukami DK, Bierut LJ, Ramoni MF.

J Neurogenet. 2009;23(3):283-92. doi: 10.1080/01677060802572911. Epub 2009 Jan 31. Review.

18.

Predictive genomics of cardioembolic stroke.

Ramoni RB, Himes BE, Sale MM, Furie KL, Ramoni MF.

Stroke. 2009 Mar;40(3 Suppl):S67-70. doi: 10.1161/STROKEAHA.108.533273. Epub 2008 Dec 8.

19.
20.

Use of Bayesian networks to probabilistically model and improve the likelihood of validation of microarray findings by RT-PCR.

English SB, Shih SC, Ramoni MF, Smith LE, Butte AJ.

J Biomed Inform. 2009 Apr;42(2):287-95. doi: 10.1016/j.jbi.2008.08.009. Epub 2008 Aug 26.

21.

System-wide peripheral biomarker discovery using information theory.

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

Pac Symp Biocomput. 2008:231-42.

22.

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
23.

Economic evaluation of a Bayesian model to predict late-phase success of new chemical entities.

Schachter AD, Ramoni MF, Baio G, Roberts TG Jr, Finkelstein SN.

Value Health. 2007 Sep-Oct;10(5):377-85.

24.

Bayesian methods for proteomics.

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

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

PMID:
17654463
25.

Paediatric drug development.

Schachter AD, Ramoni MF.

Nat Rev Drug Discov. 2007 Jun;6(6):429-30. No abstract available.

PMID:
17633788
26.

Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks.

Ferrazzi F, Sebastiani P, Ramoni MF, Bellazzi R.

BMC Bioinformatics. 2007 May 24;8 Suppl 5:S2.

27.

A novel, single nucleotide polymorphism-based assay to detect 22q11 deletions.

Funke BH, Brown AC, Ramoni MF, Regan ME, Baglieri C, Finn CT, Babcock M, Shprintzen RJ, Morrow BE, Kucherlapati R.

Genet Test. 2007 Spring;11(1):91-100.

PMID:
17394398
28.

Geography and genography: prediction of continental origin using randomly selected single nucleotide polymorphisms.

Allocco DJ, Song Q, Gibbons GH, Ramoni MF, Kohane IS.

BMC Genomics. 2007 Mar 10;8:68.

29.

Clinical forecasting in drug development.

Schachter AD, Ramoni MF.

Nat Rev Drug Discov. 2007 Feb;6(2):107-8. No abstract available.

PMID:
17342862
30.

Transcription factor CHF1/Hey2 regulates the global transcriptional response to platelet-derived growth factor in vascular smooth muscle cells.

Shirvani SM, Mookanamparambil L, Ramoni MF, Chin MT.

Physiol Genomics. 2007 Jun 19;30(1):61-8. Epub 2007 Feb 27.

PMID:
17327490
31.

Discovering biological guilds through topological abstraction.

Alterovitz G, Ramoni MF.

AMIA Annu Symp Proc. 2006:1-5.

32.

Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease.

Aivado M, Spentzos D, Germing U, Alterovitz G, Meng XY, Grall F, Giagounidis AA, Klement G, Steidl U, Otu HH, Czibere A, Prall WC, Iking-Konert C, Shayne M, Ramoni MF, Gattermann N, Haas R, Mitsiades CS, Fung ET, Libermann TA.

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1307-12. Epub 2007 Jan 12.

33.

GO PaD: the Gene Ontology Partition Database.

Alterovitz G, Xiang M, Mohan M, Ramoni MF.

Nucleic Acids Res. 2007 Jan;35(Database issue):D322-7. Epub 2006 Nov 10.

34.

Regulation of myogenic progenitor proliferation in human fetal skeletal muscle by BMP4 and its antagonist Gremlin.

Frank NY, Kho AT, Schatton T, Murphy GF, Molloy MJ, Zhan Q, Ramoni MF, Frank MH, Kohane IS, Gussoni E.

J Cell Biol. 2006 Oct 9;175(1):99-110. Epub 2006 Oct 2.

35.

Melanoma cell adhesion molecule is a novel marker for human fetal myogenic cells and affects myoblast fusion.

Cerletti M, Molloy MJ, Tomczak KK, Yoon S, Ramoni MF, Kho AT, Beggs AH, Gussoni E.

J Cell Sci. 2006 Aug 1;119(Pt 15):3117-27. Epub 2006 Jul 11.

36.

Automation, parallelism, and robotics for proteomics.

Alterovitz G, Liu J, Chow J, Ramoni MF.

Proteomics. 2006 Jul;6(14):4016-22. Review.

PMID:
16786489
37.

The gene expression profile in refractory periodontitis patients.

Kim DM, Ramoni MF, Nevins M, Fiorellini JP.

J Periodontol. 2006 Jun;77(6):1043-50.

PMID:
16734580
38.

A Bayesian dynamic model for influenza surveillance.

Sebastiani P, Mandl KD, Szolovits P, Kohane IS, Ramoni MF.

Stat Med. 2006 Jun 15;25(11):1803-16; discussion 1817-25.

39.

SELDI-TOF MS of quadruplicate urine and serum samples to evaluate changes related to storage conditions.

Traum AZ, Wells MP, Aivado M, Libermann TA, Ramoni MF, Schachter AD.

Proteomics. 2006 Mar;6(5):1676-80.

40.

Factors affecting automated syndromic surveillance.

Wang L, Ramoni MF, Mandl KD, Sebastiani P.

Artif Intell Med. 2005 Jul;34(3):269-78.

PMID:
16023563
41.

Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling.

Aivado M, Spentzos D, Alterovitz G, Otu HH, Grall F, Giagounidis AA, Wells M, Cho JY, Germing U, Czibere A, Prall WC, Porter C, Ramoni MF, Libermann TA.

Clin Chem Lab Med. 2005;43(2):133-40.

PMID:
15843205
42.

Genetic dissection and prognostic modeling of overt stroke in sickle cell anemia.

Sebastiani P, Ramoni MF, Nolan V, Baldwin CT, Steinberg MH.

Nat Genet. 2005 Apr;37(4):435-40. Epub 2005 Mar 20.

43.

Robust transmission/disequilibrium test for incomplete family genotypes.

Sebastiani P, Abad MM, Alpargu G, Ramoni MF.

Genetics. 2004 Dec;168(4):2329-37.

44.

Gene expression signature with independent prognostic significance in epithelial ovarian cancer.

Spentzos D, Levine DA, Ramoni MF, Joseph M, Gu X, Boyd J, Libermann TA, Cannistra SA.

J Clin Oncol. 2004 Dec 1;22(23):4700-10. Epub 2004 Oct 25. Erratum in: J Clin Oncol. 2005 Jan 1;23(1):248.

PMID:
15505275
45.

Bayesian approach to discovering pathogenic SNPs in conserved protein domains.

Cai Z, Tsung EF, Marinescu VD, Ramoni MF, Riva A, Kohane IS.

Hum Mutat. 2004 Aug;24(2):178-84.

PMID:
15241800
46.

Identification of a transcriptional profile associated with in vitro invasion in non-small cell lung cancer cell lines.

Lader AS, Ramoni MF, Zetter BR, Kohane IS, Kwiatkowski DJ.

Cancer Biol Ther. 2004 Jul;3(7):624-31. Epub 2004 Jul 9.

PMID:
15153803
47.

Bayesian machine learning and its potential applications to the genomic study of oral oncology.

Sebastiani P, Yu YH, Ramoni MF.

Adv Dent Res. 2003 Dec;17:104-8.

PMID:
15126219
48.

Expression profiling and identification of novel genes involved in myogenic differentiation.

Tomczak KK, Marinescu VD, Ramoni MF, Sanoudou D, Montanaro F, Han M, Kunkel LM, Kohane IS, Beggs AH.

FASEB J. 2004 Feb;18(2):403-5. Epub 2003 Dec 19.

PMID:
14688207
49.

Minimal haplotype tagging.

Sebastiani P, Lazarus R, Weiss ST, Kunkel LM, Kohane IS, Ramoni MF.

Proc Natl Acad Sci U S A. 2003 Aug 19;100(17):9900-5. Epub 2003 Aug 4.

50.

Cluster analysis of gene expression dynamics.

Ramoni MF, Sebastiani P, Kohane IS.

Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9121-6. Epub 2002 Jun 24.

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