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Items: 1 to 50 of 68

1.

De novo prediction of cell-type complexity in single-cell RNA-seq and tumor microenvironments.

Woo J, Winterhoff BJ, Starr TK, Aliferis C, Wang J.

Life Sci Alliance. 2019 Jul 2;2(4). pii: e201900443. doi: 10.26508/lsa.201900443. Print 2019 Aug.

2.

Developing a Clinico-Molecular Test for Individualized Treatment of Ovarian Cancer: The interplay of Precision Medicine Informatics with Clinical and Health Economics Dimensions.

Winterhoff B, Kommoss S, Heitz F, Konecny GE, Dowdy SC, Mullany SA, Park-Simon TW, Baumann K, Hilpert F, Brucker S, du Bois A, Schröder W, Burges A, Shen S, Wang J, Tourani R, Ma S, Pfisterer J, Aliferis CF.

AMIA Annu Symp Proc. 2018 Dec 5;2018:1093-1102. eCollection 2018.

3.

Machine learning methods to predict child posttraumatic stress: a proof of concept study.

Saxe GN, Ma S, Ren J, Aliferis C.

BMC Psychiatry. 2017 Jul 10;17(1):223. doi: 10.1186/s12888-017-1384-1.

4.

A Complex Systems Approach to Causal Discovery in Psychiatry.

Saxe GN, Statnikov A, Fenyo D, Ren J, Li Z, Prasad M, Wall D, Bergman N, Briggs EC, Aliferis C.

PLoS One. 2016 Mar 30;11(3):e0151174. doi: 10.1371/journal.pone.0151174. eCollection 2016.

5.

An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation.

Ma S, Kemmeren P, Aliferis CF, Statnikov A.

Sci Rep. 2016 Mar 4;6:22558. doi: 10.1038/srep22558.

6.

Plasma levels of interleukin-1 receptor antagonist (IL1Ra) predict radiographic progression of symptomatic knee osteoarthritis.

Attur M, Statnikov A, Samuels J, Li Z, Alekseyenko AV, Greenberg JD, Krasnokutsky S, Rybak L, Lu QA, Todd J, Zhou H, Jordan JM, Kraus VB, Aliferis CF, Abramson SB.

Osteoarthritis Cartilage. 2015 Nov;23(11):1915-24. doi: 10.1016/j.joca.2015.08.006.

7.

Low-grade inflammation in symptomatic knee osteoarthritis: prognostic value of inflammatory plasma lipids and peripheral blood leukocyte biomarkers.

Attur M, Krasnokutsky S, Statnikov A, Samuels J, Li Z, Friese O, Hellio Le Graverand-Gastineau MP, Rybak L, Kraus VB, Jordan JM, Aliferis CF, Abramson SB.

Arthritis Rheumatol. 2015 Nov;67(11):2905-15. doi: 10.1002/art.39279.

8.

Computational Methods for Unraveling Temporal Brain Connectivity Data.

Ray B, Statnikov A, Aliferis C.

AMIA Annu Symp Proc. 2015 Nov 5;2015:2043-52. eCollection 2015.

9.

Information content and analysis methods for multi-modal high-throughput biomedical data.

Ray B, Henaff M, Ma S, Efstathiadis E, Peskin ER, Picone M, Poli T, Aliferis CF, Statnikov A.

Sci Rep. 2014 Mar 21;4:4411. doi: 10.1038/srep04411.

10.

A comprehensive evaluation of multicategory classification methods for microbiomic data.

Statnikov A, Henaff M, Narendra V, Konganti K, Li Z, Yang L, Pei Z, Blaser MJ, Aliferis CF, Alekseyenko AV.

Microbiome. 2013 Apr 5;1(1):11. doi: 10.1186/2049-2618-1-11.

11.

Medical decision support using machine learning for early detection of late-onset neonatal sepsis.

Mani S, Ozdas A, Aliferis C, Varol HA, Chen Q, Carnevale R, Chen Y, Romano-Keeler J, Nian H, Weitkamp JH.

J Am Med Inform Assoc. 2014 Mar-Apr;21(2):326-36. doi: 10.1136/amiajnl-2013-001854. Epub 2013 Sep 16.

12.

Microbiomic signatures of psoriasis: feasibility and methodology comparison.

Statnikov A, Alekseyenko AV, Li Z, Henaff M, Perez-Perez GI, Blaser MJ, Aliferis CF.

Sci Rep. 2013;3:2620. doi: 10.1038/srep02620.

13.

Identifying unproven cancer treatments on the health web: addressing accuracy, generalizability and scalability.

Aphinyanaphongs Y, Fu LD, Aliferis CF.

Stud Health Technol Inform. 2013;192:667-71.

14.

Algorithms for Discovery of Multiple Markov Boundaries.

Statnikov A, Lytkin NI, Lemeire J, Aliferis CF.

J Mach Learn Res. 2013 Feb;14:499-566.

15.

New methods for separating causes from effects in genomics data.

Statnikov A, Henaff M, Lytkin NI, Aliferis CF.

BMC Genomics. 2012;13 Suppl 8:S22. doi: 10.1186/1471-2164-13-S8-S22. Epub 2012 Dec 17.

16.

Regression of atherosclerosis is characterized by broad changes in the plaque macrophage transcriptome.

Feig JE, Vengrenyuk Y, Reiser V, Wu C, Statnikov A, Aliferis CF, Garabedian MJ, Fisher EA, Puig O.

PLoS One. 2012;7(6):e39790. doi: 10.1371/journal.pone.0039790. Epub 2012 Jun 27.

17.

Trends and developments in bioinformatics in 2010: prospects and perspectives.

Aliferis CF, Alekseyenko AV, Aphinyanaphongs Y, Brown S, Fenyo D, Fu L, Shen S, Statnikov A, Wang J.

Yearb Med Inform. 2011;6:146-55. Review.

PMID:
21938341
18.

Expanding the understanding of biases in development of clinical-grade molecular signatures: a case study in acute respiratory viral infections.

Lytkin NI, McVoy L, Weitkamp JH, Aliferis CF, Statnikov A.

PLoS One. 2011;6(6):e20662. doi: 10.1371/journal.pone.0020662. Epub 2011 Jun 1.

19.

Causal graph-based analysis of genome-wide association data in rheumatoid arthritis.

Alekseyenko AV, Lytkin NI, Ai J, Ding B, Padyukov L, Aliferis CF, Statnikov A.

Biol Direct. 2011 May 18;6:25. doi: 10.1186/1745-6150-6-25.

20.

A comparison of evaluation metrics for biomedical journals, articles, and websites in terms of sensitivity to topic.

Fu LD, Aphinyanaphongs Y, Wang L, Aliferis CF.

J Biomed Inform. 2011 Aug;44(4):587-94. doi: 10.1016/j.jbi.2011.03.006. Epub 2011 Mar 17.

21.

Using gene expression profiles from peripheral blood to identify asymptomatic responses to acute respiratory viral infections.

Statnikov A, Lytkin NI, McVoy L, Weitkamp JH, Aliferis CF.

BMC Res Notes. 2010 Oct 20;3:264. doi: 10.1186/1756-0500-3-264.

22.

A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks.

Narendra V, Lytkin NI, Aliferis CF, Statnikov A.

Genomics. 2011 Jan;97(1):7-18. doi: 10.1016/j.ygeno.2010.10.003. Epub 2010 Oct 14.

23.

Analysis and computational dissection of molecular signature multiplicity.

Statnikov A, Aliferis CF.

PLoS Comput Biol. 2010 May 20;6(5):e1000790. doi: 10.1371/journal.pcbi.1000790.

24.

Improving development of the molecular signature for diagnosis of acute respiratory viral infections.

Statnikov A, McVoy L, Lytkin N, Aliferis CF.

Cell Host Microbe. 2010 Feb 18;7(2):100-1; author reply 102. doi: 10.1016/j.chom.2010.01.003. No abstract available.

25.

The FAST-AIMS Clinical Mass Spectrometry Analysis System.

Fananapazir N, Statnikov A, Aliferis CF.

Adv Bioinformatics. 2009:598241. doi: 10.1155/2009/598241. Epub 2009 Jul 9.

26.

A novel information retrieval model for high-throughput molecular medicine modalities.

Wehbe FH, Brown SH, Massion PP, Gadd CS, Masys DR, Aliferis CF.

Cancer Inform. 2009 Feb 9;8:1-17.

27.

Factors influencing the statistical power of complex data analysis protocols for molecular signature development from microarray data.

Aliferis CF, Statnikov A, Tsamardinos I, Schildcrout JS, Shepherd BE, Harrell FE Jr.

PLoS One. 2009;4(3):e4922. doi: 10.1371/journal.pone.0004922. Epub 2009 Mar 17.

28.

Models for predicting and explaining citation count of biomedical articles.

Fu LD, Aliferis C.

AMIA Annu Symp Proc. 2008 Nov 6:222-6.

29.
30.

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification.

Statnikov A, Wang L, Aliferis CF.

BMC Bioinformatics. 2008 Jul 22;9:319. doi: 10.1186/1471-2105-9-319.

31.

A statistical reappraisal of the findings of an esophageal cancer genome-wide association study.

Statnikov A, Li C, Aliferis CF.

Cancer Res. 2008 Apr 15;68(8):3074-5; author reply 3075. doi: 10.1158/0008-5472.CAN-07-2999. No abstract available.

32.

Text categorization models for identifying unproven cancer treatments on the web.

Aphinyanaphongs Y, Aliferis C.

Stud Health Technol Inform. 2007;129(Pt 2):968-72.

PMID:
17911859
33.

Learning causal and predictive clinical practice guidelines from data.

Mani S, Aliferis C, Krishnaswami S, Kotchen T.

Stud Health Technol Inform. 2007;129(Pt 2):850-4.

PMID:
17911836
34.

A comparison of impact factor, clinical query filters, and pattern recognition query filters in terms of sensitivity to topic.

Fu LD, Wang L, Aphinyanagphongs Y, Aliferis CF.

Stud Health Technol Inform. 2007;129(Pt 1):716-20.

PMID:
17911810
35.
36.

Genomics and proteomics of lung disease: conference summary.

Raj JU, Aliferis C, Caprioli RM, Cowley AW Jr, Davies PF, Duncan MW, Erle DJ, Erzurum SC, Finn PW, Ischiropoulos H, Kaminski N, Kleeberger SR, Leikauf GD, Loyd JE, Martin TR, Matalon S, Moore JH, Quackenbush J, Sabo-Attwood T, Shapiro SD, Schnitzer JE, Schwartz DA, Schwiebert LM, Sheppard D, Ware LB, Weiss ST, Whitsett JA, Wurfel MM, Matthay MA.

Am J Physiol Lung Cell Mol Physiol. 2007 Jul;293(1):L45-51. Epub 2007 Apr 27. No abstract available.

38.
40.

Formative evaluation of a prototype system for automated analysis of mass spectrometry data.

Fananapazir N, Li M, Spentzos D, Aliferis CF.

AMIA Annu Symp Proc. 2005:241-5.

41.

Extracting drug-drug interaction articles from MEDLINE to improve the content of drug databases.

Duda S, Aliferis C, Miller R, Statnikov A, Johnson K.

AMIA Annu Symp Proc. 2005:216-20.

42.

A comparison of citation metrics to machine learning filters for the identification of high quality MEDLINE documents.

Aphinyanaphongs Y, Statnikov A, Aliferis CF.

J Am Med Inform Assoc. 2006 Jul-Aug;13(4):446-55. Epub 2006 Apr 18.

43.

Using citation data to improve retrieval from MEDLINE.

Bernstam EV, Herskovic JR, Aphinyanaphongs Y, Aliferis CF, Sriram MG, Hersh WR.

J Am Med Inform Assoc. 2006 Jan-Feb;13(1):96-105. Epub 2005 Oct 12.

44.

Predicting dire outcomes of patients with community acquired pneumonia.

Cooper GF, Abraham V, Aliferis CF, Aronis JM, Buchanan BG, Caruana R, Fine MJ, Janosky JE, Livingston G, Mitchell T, Monti S, Spirtes P.

J Biomed Inform. 2005 Oct;38(5):347-66. Epub 2005 Mar 17.

45.

GEMS: a system for automated cancer diagnosis and biomarker discovery from microarray gene expression data.

Statnikov A, Tsamardinos I, Dosbayev Y, Aliferis CF.

Int J Med Inform. 2005 Aug;74(7-8):491-503.

PMID:
15967710
46.

Text categorization models for high-quality article retrieval in internal medicine.

Aphinyanaphongs Y, Tsamardinos I, Statnikov A, Hardin D, Aliferis CF.

J Am Med Inform Assoc. 2005 Mar-Apr;12(2):207-16. Epub 2004 Nov 23.

47.

A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis.

Statnikov A, Aliferis CF, Tsamardinos I, Hardin D, Levy S.

Bioinformatics. 2005 Mar 1;21(5):631-43. Epub 2004 Sep 16.

PMID:
15374862
48.
49.

A novel algorithm for scalable and accurate Bayesian network learning.

Brown LE, Tsamardinos I, Aliferis CF.

Stud Health Technol Inform. 2004;107(Pt 1):711-5.

PMID:
15360905
50.

Learning Boolean queries for article quality filtering.

Aphinyanaphongs Y, Aliferis CF.

Stud Health Technol Inform. 2004;107(Pt 1):263-7.

PMID:
15360815

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