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Items: 1 to 50 of 181

1.

Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty.

Imani M, Dehghannasiri R, Braga-Neto UM, Dougherty ER.

Cancer Inform. 2018 Aug 6;17:1176935118790247. doi: 10.1177/1176935118790247. eCollection 2018. Review.

2.

Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective.

Kim E, Ivanov I, Dougherty ER.

Bioinformatics. 2018 Jul 25. doi: 10.1093/bioinformatics/bty665. [Epub ahead of print]

PMID:
30052771
3.

Commentary to: a cross-validation-based approach for delimiting reliable home range estimates.

Dougherty ER, de Valpine P, Carlson CJ, Blackburn JK, Getz WM.

Mov Ecol. 2018 Jul 12;6:10. doi: 10.1186/s40462-018-0128-2. eCollection 2018.

4.

Constructing Pathway-based Priors Within a Gaussian Mixture Model for Bayesian Regression and Classification.

Boluki S, Shahrokh Esfahani M, Qian X, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Nov 30. doi: 10.1109/TCBB.2017.2778715. [Epub ahead of print]

PMID:
29990066
5.

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.

6.

Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks.

Karbalayghareh A, Braga-Neto U, Dougherty ER.

BMC Syst Biol. 2018 Mar 21;12(Suppl 3):23. doi: 10.1186/s12918-018-0549-y.

7.

Guest Editorial-Special Collection Topic: Statistical Systems Theory in Cancer Modeling, Diagnosis, and Therapy.

Dougherty ER, Boulesteix AL, Dalton LA, Zhang M.

Cancer Inform. 2018 Mar 5;17:1176935118760944. doi: 10.1177/1176935118760944. eCollection 2018.

8.

Going through the motions: incorporating movement analyses into disease research.

Dougherty ER, Seidel DP, Carlson CJ, Spiegel O, Getz WM.

Ecol Lett. 2018 Apr;21(4):588-604. doi: 10.1111/ele.12917. Epub 2018 Feb 14. Review.

9.

Genetic responsiveness of African buffalo to environmental stressors: A role for epigenetics in balancing autosomal and sex chromosome interactions?

van Hooft P, Dougherty ER, Getz WM, Greyling BJ, Zwaan BJ, Bastos ADS.

PLoS One. 2018 Feb 7;13(2):e0191481. doi: 10.1371/journal.pone.0191481. eCollection 2018.

10.

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors.

Boluki S, Esfahani MS, Qian X, Dougherty ER.

BMC Bioinformatics. 2017 Dec 28;18(Suppl 14):552. doi: 10.1186/s12859-017-1893-4.

11.

Correction to: A cross-validation-based approach for delimiting reliable home range estimates.

Dougherty ER, Carlson CJ, Blackburn JK, Getz WM.

Mov Ecol. 2017 Dec 5;5:26. doi: 10.1186/s40462-017-0116-y. eCollection 2017.

12.

Discrete stochastic analogs of Erlang epidemic models.

Getz WM, Dougherty ER.

J Biol Dyn. 2018 Dec;12(1):16-38. doi: 10.1080/17513758.2017.1401677.

13.

Classification of Single-cell Gene Expression Trajectories from Incomplete and Noisy Data.

Karbalayghareh A, Braga-Neto U, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Oct 16:1. doi: 10.1109/TCBB.2017.2763946. [Epub ahead of print]

PMID:
29053466
14.

Parasite biodiversity faces extinction and redistribution in a changing climate.

Carlson CJ, Burgio KR, Dougherty ER, Phillips AJ, Bueno VM, Clements CF, Castaldo G, Dallas TA, Cizauskas CA, Cumming GS, Doña J, Harris NC, Jovani R, Mironov S, Muellerklein OC, Proctor HC, Getz WM.

Sci Adv. 2017 Sep 6;3(9):e1602422. doi: 10.1126/sciadv.1602422. eCollection 2017 Sep.

15.

A cross-validation-based approach for delimiting reliable home range estimates.

Dougherty ER, Carlson CJ, Blackburn JK, Getz WM.

Mov Ecol. 2017 Sep 6;5:19. doi: 10.1186/s40462-017-0110-4. eCollection 2017. Erratum in: Mov Ecol. 2017 Dec 5;5:26.

16.

Bayesian Regression with Network Prior: Optimal Bayesian Filtering Perspective.

Qian X, Dougherty ER.

IEEE Trans Signal Process. 2016 Dec 1;64(23):6243-6253. doi: 10.1109/TSP.2016.2605072. Epub 2016 Sep 1.

17.

Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach.

Oduola WO, Li XL, Duan C, Qian L, Dougherty ER.

IEEE Trans Biomed Eng. 2018 Apr;65(4):866-874. doi: 10.1109/TBME.2017.2723957. Epub 2017 Jul 6.

PMID:
28692960
18.

Review of stochastic hybrid systems with applications in biological systems modeling and analysis.

Li X, Omotere O, Qian L, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2017 Dec;2017(1):8. doi: 10.1186/s13637-017-0061-5. Epub 2017 Jun 30. Review.

19.

The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data.

Kim E, Ivanov I, Hua J, Lampe JW, Hullar MA, Chapkin RS, Dougherty ER.

Cancer Inform. 2017 Jun 12;16:1176935117710530. doi: 10.1177/1176935117710530. eCollection 2017.

20.

Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy.

Oduola WO, Li X, Duan C, Qian L, Wu F, Dougherty ER.

Cancer Inform. 2017 May 10;16:1176935117706888. doi: 10.1177/1176935117706888. eCollection 2017.

21.

Parasite vulnerability to climate change: an evidence-based functional trait approach.

Cizauskas CA, Carlson CJ, Burgio KR, Clements CF, Dougherty ER, Harris NC, Phillips AJ.

R Soc Open Sci. 2017 Jan 11;4(1):160535. doi: 10.1098/rsos.160535. eCollection 2017 Jan. Review.

22.

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.

23.

Accelerated search for BaTiO3-based piezoelectrics with vertical morphotropic phase boundary using Bayesian learning.

Xue D, Balachandran PV, Yuan R, Hu T, Qian X, Dougherty ER, Lookman T.

Proc Natl Acad Sci U S A. 2016 Nov 22;113(47):13301-13306. Epub 2016 Nov 7.

24.

Classification of State Trajectories in Gene Regulatory Networks.

Karbalayghareh A, Braga-Neto U, Hua J, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):68-82. doi: 10.1109/TCBB.2016.2616470. Epub 2016 Oct 11.

PMID:
27740496
25.

Big data need big theory too.

Coveney PV, Dougherty ER, Highfield RR.

Philos Trans A Math Phys Eng Sci. 2016 Nov 13;374(2080). pii: 20160153. Review.

26.

Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error.

Mohsenizadeh DN, Dehghannasiri R, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Jan-Feb;15(1):218-230. doi: 10.1109/TCBB.2016.2602873. Epub 2016 Aug 25.

PMID:
27576263
27.

An Ecological Assessment of the Pandemic Threat of Zika Virus.

Carlson CJ, Dougherty ER, Getz W.

PLoS Negl Trop Dis. 2016 Aug 26;10(8):e0004968. doi: 10.1371/journal.pntd.0004968. eCollection 2016 Aug.

28.

Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations.

Zollanvari A, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2016 Jan 20;2016(1):2. eCollection 2016 Dec.

29.

Integrating Multiscale Modeling with Drug Effects for Cancer Treatment.

Li XL, Oduola WO, Qian L, Dougherty ER.

Cancer Inform. 2016 Jan 13;14(Suppl 5):21-31. doi: 10.4137/CIN.S30797. eCollection 2015. Review.

31.

Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks.

Dehghannasiri R, Yoon BJ, Dougherty ER.

BMC Bioinformatics. 2015 Dec 14;16:410. doi: 10.1186/s12859-015-0839-y. No abstract available.

32.

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification.

Knight JM, Ivanov I, Triff K, Chapkin RS, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2018 Mar-Apr;15(2):484-493. doi: 10.1109/TCBB.2015.2485223. Epub 2015 Oct 1.

PMID:
26441451
33.

Dynamical modeling of uncertain interaction-based genomic networks.

Mohsenizadeh DN, Hua J, Bittner M, Dougherty ER.

BMC Bioinformatics. 2015;16 Suppl 13:S3. doi: 10.1186/1471-2105-16-S13-S3. Epub 2015 Sep 25.

34.

Efficient experimental design for uncertainty reduction in gene regulatory networks.

Dehghannasiri R, Yoon BJ, Dougherty ER.

BMC Bioinformatics. 2015;16 Suppl 13:S2. doi: 10.1186/1471-2105-16-S13-S2. Epub 2015 Sep 25. Erratum in: BMC Bioinformatics. 2015;16:410.

35.

Paradigms for parasite conservation.

Dougherty ER, Carlson CJ, Bueno VM, Burgio KR, Cizauskas CA, Clements CF, Seidel DP, Harris NC.

Conserv Biol. 2016 Aug;30(4):724-33. doi: 10.1111/cobi.12634. Epub 2015 Dec 18.

36.

Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty.

Dehghannasiri R, Yoon BJ, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug;12(4):938-50. doi: 10.1109/TCBB.2014.2377733.

PMID:
26357334
37.

Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida.

Fedrizzi N, Stiassny ML, Boehm JT, Dougherty ER, Amato G, Mendez M.

PLoS One. 2015 Jul 22;10(7):e0132308. doi: 10.1371/journal.pone.0132308. eCollection 2015.

38.

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.

39.

MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.

Knight JM, Ivanov I, Dougherty ER.

BMC Bioinformatics. 2014 Dec 10;15:401. doi: 10.1186/s12859-014-0401-3.

40.

Modeling and systematic analysis of biomarker validation using selected reaction monitoring.

Atashpaz-Gargari E, Braga-Neto UM, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2014 Nov 15;2014:17. doi: 10.1186/s13637-014-0017-y. eCollection 2014 Dec.

41.

Unbiased bootstrap error estimation for linear discriminant analysis.

Vu T, Sima C, Braga-Neto UM, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2014 Oct 3;2014:15. doi: 10.1186/s13637-014-0015-0. eCollection 2014 Dec.

42.

Cross-validation under separate sampling: strong bias and how to correct it.

Braga-Neto UM, Zollanvari A, Dougherty ER.

Bioinformatics. 2014 Dec 1;30(23):3349-55. doi: 10.1093/bioinformatics/btu527. Epub 2014 Aug 13.

43.

Learning restricted Boolean network model by time-series data.

Ouyang H, Fang J, Shen L, Dougherty ER, Liu W.

EURASIP J Bioinform Syst Biol. 2014;2014(1):10. doi: 10.1186/s13637-014-0010-5. Epub 2014 Jul 15.

44.

Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms.

Fang J, Ouyang H, Shen L, Dougherty ER, Liu W.

EURASIP J Bioinform Syst Biol. 2014 Jul 3;2014:13. doi: 10.1186/s13637-014-0013-2. eCollection 2014 Dec.

45.
46.

A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty.

Yousefi MR, Dougherty ER.

EURASIP J Bioinform Syst Biol. 2014 Apr 3;2014(1):6. doi: 10.1186/1687-4153-2014-6.

47.

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.

48.

Validation of gene regulatory network inference based on controllability.

Qian X, Dougherty ER.

Front Genet. 2013 Dec 12;4:272. doi: 10.3389/fgene.2013.00272. eCollection 2013.

49.

Incorporation of Biological Pathway Knowledge in the Construction of Priors for Optimal Bayesian Classification.

Esfahani MS, Dougherty ER.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):202-18. doi: 10.1109/TCBB.2013.143.

PMID:
26355519
50.

Effect of separate sampling on classification accuracy.

Shahrokh Esfahani M, Dougherty ER.

Bioinformatics. 2014 Jan 15;30(2):242-50. doi: 10.1093/bioinformatics/btt662. Epub 2013 Nov 20.

PMID:
24257187

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