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Items: 1 to 50 of 62

1.

Using Chou's 5-steps rule to Model Feedback in Lung Cancer.

Vundavilli H, Datta A, Sima C, Hua J, Lopes R, Bittner ML.

IEEE J Biomed Health Inform. 2019 Dec 6. doi: 10.1109/JBHI.2019.2958042. [Epub ahead of print]

PMID:
31825884
2.

In Silico Design and Experimental Validation of Combination Therapy for Pancreatic Cancer.

Vundavilli H, Datta A, Sima C, Hua J, Lopes R, Bittner ML.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep 28. doi: 10.1109/TCBB.2018.2872573. [Epub ahead of print]

PMID:
30281473
3.

A Gaussian Mixture-Model Exploiting Pathway Knowledge for Dissecting Cancer Heterogeneity.

Kapoor R, Datta A, Sima C, Hua J, Lopes R, Bittner ML.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep 12. doi: 10.1109/TCBB.2018.2869813. [Epub ahead of print]

PMID:
30222582
4.

Phenotype Classification Using Moment Features of Single-Cell Data.

Sima C, Hua J, Bittner ML, Kim S, Dougherty ER.

Cancer Inform. 2018 Apr 23;17:1176935118771701. doi: 10.1177/1176935118771701. eCollection 2018.

5.

A Bayesian approach to determine the composition of heterogeneous cancer tissue.

Katiyar A, Mohanty A, Hua J, Chao S, Lopes R, Datta A, Bittner ML.

BMC Bioinformatics. 2018 Mar 21;19(Suppl 3):90. doi: 10.1186/s12859-018-2062-0.

6.

Systems biology for organotypic cell cultures.

Grego S, Dougherty ER, Alexander FJ, Auerbach SS, Berridge BR, Bittner ML, Casey W, Cooley PC, Dash A, Ferguson SS, Fennell TR, Hawkins BT, Hickey AJ, Kleensang A, Liebman MNJ, Martin F, Maull EA, Paragas J, Qiao GG, Ramaiahgari S, Sumner SJ, Yoon M.

ALTEX. 2017;34(2):301-310. doi: 10.14573/altex.1608221. Epub 2016 Nov 14.

7.

Assessing Combinational Drug Efficacy in Cancer Cells by Using Image-based Dynamic Response Analysis.

Sima C, Hua J, Cypert M, Miller T, Wilson-Robles HM, Trent JM, Dougherty ER, Bittner ML.

Cancer Inform. 2016 Mar 9;14(Suppl 5):33-43. doi: 10.4137/CIN.S30799. eCollection 2015.

8.

Evaluating gene set enrichment analysis via a hybrid data model.

Hua J, Bittner ML, Dougherty ER.

Cancer Inform. 2014 Feb 12;13(Suppl 1):1-16. doi: 10.4137/CIN.S13305. eCollection 2014.

9.

Newton, laplace, and the epistemology of systems biology.

Bittner ML, Dougherty ER.

Cancer Inform. 2012;11:185-90. doi: 10.4137/CIN.S10630. Epub 2012 Oct 30.

10.

Assessing the efficacy of molecularly targeted agents on cell line-based platforms by using system identification.

Li X, Qian L, Hua J, Bittner ML, Dougherty ER.

BMC Genomics. 2012;13 Suppl 6:S11. doi: 10.1186/1471-2164-13-S6-S11. Epub 2012 Oct 26.

11.

Identifying mechanistic similarities in drug responses.

Zhao C, Hua J, Bittner ML, Ivanov I, Dougherty ER.

Bioinformatics. 2012 Jul 15;28(14):1902-10. doi: 10.1093/bioinformatics/bts290. Epub 2012 May 15.

PMID:
22592382
12.

Tracking transcriptional activities with high-content epifluorescent imaging.

Hua J, Sima C, Cypert M, Gooden GC, Shack S, Alla L, Smith EA, Trent JM, Dougherty ER, Bittner ML.

J Biomed Opt. 2012 Apr;17(4):046008. doi: 10.1117/1.JBO.17.4.046008.

13.

A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens-a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems.

Li X, Qian L, Bittner ML, Dougherty ER.

Cancer Inform. 2012;11:41-60. doi: 10.4137/CIN.S8185. Epub 2012 Feb 27.

14.

Causality, randomness, intelligibility, and the epistemology of the cell.

Dougherty ER, Bittner ML.

Curr Genomics. 2010 Jun;11(4):221-37. doi: 10.2174/138920210791233072.

15.

Characterization of drug efficacy regions based on dosage and frequency schedules.

Li XL, Qian L, Bittner ML, Dougherty ER.

IEEE Trans Biomed Eng. 2011 Mar;58(3):488-98. doi: 10.1109/TBME.2010.2090660. Epub 2010 Nov 9.

PMID:
21095860
16.
17.

Conditioning-based modeling of contextual genomic regulation.

Dougherty ER, Brun M, Trent JM, Bittner ML.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):310-20. doi: 10.1109/TCBB.2007.70247.

PMID:
19407354
18.

Validation of computational methods in genomics.

Doughtery ER, Jianping H, Bittner ML.

Curr Genomics. 2007 Mar;8(1):1-19.

19.

Normalization benefits microarray-based classification.

Hua J, Balagurunathan Y, Chen Y, Lowey J, Bittner ML, Xiong Z, Suh E, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2006:43056. doi: 10.1155/BSB/2006/43056.

20.

Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen.

Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, Trent JM, Bittner ML, Meltzer PS, Fornace AJ Jr.

Cancer Res. 2008 Jan 15;68(2):415-24. doi: 10.1158/0008-5472.CAN-07-2120.

21.

A cell proliferation and chromosomal instability signature in anaplastic thyroid carcinoma.

Salvatore G, Nappi TC, Salerno P, Jiang Y, Garbi C, Ugolini C, Miccoli P, Basolo F, Castellone MD, Cirafici AM, Melillo RM, Fusco A, Bittner ML, Santoro M.

Cancer Res. 2007 Nov 1;67(21):10148-58.

22.

Optimization of oligonucleotide microarray fabricated by spotting 65-mer.

Lee M, Trent JM, Bittner ML.

Anal Biochem. 2007 Sep 1;368(1):61-9. Epub 2007 Jun 8.

23.

Performance characteristics of 65-mer oligonucleotide microarrays.

Lee M, Xiang CC, Trent JM, Bittner ML.

Anal Biochem. 2007 Sep 1;368(1):70-8. Epub 2007 May 13.

24.

Intervention in a family of Boolean networks.

Choudhary A, Datta A, Bittner ML, Dougherty ER.

Bioinformatics. 2006 Jan 15;22(2):226-32. Epub 2005 Nov 12.

PMID:
16286362
25.

Generating Boolean networks with a prescribed attractor structure.

Pal R, Ivanov I, Datta A, Bittner ML, Dougherty ER.

Bioinformatics. 2005 Nov 1;21(21):4021-5. Epub 2005 Sep 8.

PMID:
16150807
26.

Stress-specific signatures: expression profiling of p53 wild-type and -null human cells.

Amundson SA, Do KT, Vinikoor L, Koch-Paiz CA, Bittner ML, Trent JM, Meltzer P, Fornace AJ Jr.

Oncogene. 2005 Jun 30;24(28):4572-9.

PMID:
15824734
27.

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.

Pal R, Datta A, Fornace AJ Jr, Bittner ML, Dougherty ER.

Bioinformatics. 2005 Apr 15;21(8):1542-9. Epub 2004 Dec 14.

PMID:
15598836
28.

Intervention in context-sensitive probabilistic Boolean networks.

Pal R, Datta A, Bittner ML, Dougherty ER.

Bioinformatics. 2005 Apr 1;21(7):1211-8. Epub 2004 Nov 5.

PMID:
15531600
29.

Which is better for cDNA-microarray-based classification: ratios or direct intensities.

Attoor S, Dougherty ER, Chen Y, Bittner ML, Trent JM.

Bioinformatics. 2004 Nov 1;20(16):2513-20. Epub 2004 Sep 28.

PMID:
15454406
30.

Noise factor analysis for cDNA microarrays.

Balagurunathan Y, Wang N, Dougherty ER, Nguyen D, Chen Y, Bittner ML, Trent J, Carroll R.

J Biomed Opt. 2004 Jul-Aug;9(4):663-78.

31.

Functional genomics of UV radiation responses in human cells.

Koch-Paiz CA, Amundson SA, Bittner ML, Meltzer PS, Fornace AJ Jr.

Mutat Res. 2004 May 18;549(1-2):65-78.

PMID:
15120963
32.

Growing genetic regulatory networks from seed genes.

Hashimoto RF, Kim S, Shmulevich I, Zhang W, Bittner ML, Dougherty ER.

Bioinformatics. 2004 May 22;20(8):1241-7. Epub 2004 Feb 10.

PMID:
14871865
33.

External control in Markovian genetic regulatory networks: the imperfect information case.

Datta A, Choudhary A, Bittner ML, Dougherty ER.

Bioinformatics. 2004 Apr 12;20(6):924-30. Epub 2004 Jan 29.

PMID:
14751971
34.

Gene expression profile in multiple sclerosis patients and healthy controls: identifying pathways relevant to disease.

Bomprezzi R, Ringnér M, Kim S, Bittner ML, Khan J, Chen Y, Elkahloun A, Yu A, Bielekova B, Meltzer PS, Martin R, McFarland HF, Trent JM.

Hum Mol Genet. 2003 Sep 1;12(17):2191-9. Epub 2003 Jul 8.

PMID:
12915464
35.

Differential responses of stress genes to low dose-rate gamma irradiation.

Amundson SA, Lee RA, Koch-Paiz CA, Bittner ML, Meltzer P, Trent JM, Fornace AJ Jr.

Mol Cancer Res. 2003 Apr;1(6):445-52.

36.

Ratio statistics of gene expression levels and applications to microarray data analysis.

Chen Y, Kamat V, Dougherty ER, Bittner ML, Meltzer PS, Trent JM.

Bioinformatics. 2002 Sep;18(9):1207-15.

PMID:
12217912
37.

Simulation of cDNA microarrays via a parameterized random signal model.

Balagurunathan Y, Dougherty ER, Chen Y, Bittner ML, Trent JM.

J Biomed Opt. 2002 Jul;7(3):507-23.

38.

Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices.

Wahde M, Klus GT, Bittner ML, Chen Y, Szallasi Z.

Bioinformatics. 2002 Mar;18(3):389-94.

PMID:
11934737
39.

Strong feature sets from small samples.

Kim S, Dougherty ER, Barrera J, Chen Y, Bittner ML, Trent JM.

J Comput Biol. 2002;9(1):127-46.

PMID:
11911798
40.

Gene expression profiling in cancer using cDNA microarrays.

Khan J, Saal LH, Bittner ML, Jiang Y, Gooden GC, Glatfelter AA, Meltzer PS.

Methods Mol Med. 2002;68:205-22. No abstract available.

PMID:
11901504
41.

Human prostate cancer and benign prostatic hyperplasia: molecular dissection by gene expression profiling.

Luo J, Duggan DJ, Chen Y, Sauvageot J, Ewing CM, Bittner ML, Trent JM, Isaacs WB.

Cancer Res. 2001 Jun 15;61(12):4683-8.

42.

Down-regulation of the desmosomal cadherin desmocollin 3 in human breast cancer.

Klus GT, Rokaeus N, Bittner ML, Chen Y, Korz DM, Sukumar S, Schick A, Szallasi Z.

Int J Oncol. 2001 Jul;19(1):169-74.

PMID:
11408939
43.

Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer.

Monni O, Barlund M, Mousses S, Kononen J, Sauter G, Heiskanen M, Paavola P, Avela K, Chen Y, Bittner ML, Kallioniemi A.

Proc Natl Acad Sci U S A. 2001 May 8;98(10):5711-6. Epub 2001 May 1.

44.

General nonlinear framework for the analysis of gene interaction via multivariate expression arrays.

Kim S, Dougherty ER, Bittner ML, Chen Y, Sivakumar K, Meltzer P, Trent JM.

J Biomed Opt. 2000 Oct;5(4):411-24. Review.

45.

Monitoring the expression profiles of doxorubicin-induced and doxorubicin-resistant cancer cells by cDNA microarray.

Kudoh K, Ramanna M, Ravatn R, Elkahloun AG, Bittner ML, Meltzer PS, Trent JM, Dalton WS, Chin KV.

Cancer Res. 2000 Aug 1;60(15):4161-6.

46.

Detecting activation of ribosomal protein S6 kinase by complementary DNA and tissue microarray analysis.

Bärlund M, Forozan F, Kononen J, Bubendorf L, Chen Y, Bittner ML, Torhorst J, Haas P, Bucher C, Sauter G, Kallioniemi OP, Kallioniemi A.

J Natl Cancer Inst. 2000 Aug 2;92(15):1252-9.

PMID:
10922410
47.

Identification of tumor-suppressor genes using human melanoma cell lines UACC903, UACC903(+6), and SRS3 by comparison of expression profiles.

Su YA, Bittner ML, Chen Y, Tao L, Jiang Y, Zhang Y, Stephan DA, Trent JM.

Mol Carcinog. 2000 Jun;28(2):119-27.

PMID:
10900469
48.

Positional cloning utilizing genomic DNA microarrays: the Niemann-Pick type C gene as a model system.

Stephan DA, Chen Y, Jiang Y, Malechek L, Gu JZ, Robbins CM, Bittner ML, Morris JA, Carstea E, Meltzer PS, Adler K, Garlick R, Trent JM, Ashlock MA.

Mol Genet Metab. 2000 May;70(1):10-8.

PMID:
10833327
49.

Detection of gene amplification by genomic hybridization to cDNA microarrays.

Heiskanen MA, Bittner ML, Chen Y, Khan J, Adler KE, Trent JM, Meltzer PS.

Cancer Res. 2000 Feb 15;60(4):799-802.

50.

cDNA microarrays detect activation of a myogenic transcription program by the PAX3-FKHR fusion oncogene.

Khan J, Bittner ML, Saal LH, Teichmann U, Azorsa DO, Gooden GC, Pavan WJ, Trent JM, Meltzer PS.

Proc Natl Acad Sci U S A. 1999 Nov 9;96(23):13264-9.

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