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Items: 50

1.

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.

Zhan YA, Wray CG, Namburi S, Glantz ST, Laubenbacher R, Chuang JH.

PLoS Comput Biol. 2019 Jun 13;15(6):e1007026. doi: 10.1371/journal.pcbi.1007026. eCollection 2019 Jun.

2.

Topological Data Analysis.

Laubenbacher R, Hastings A.

Bull Math Biol. 2019 May 7. doi: 10.1007/s11538-019-00610-3. [Epub ahead of print] No abstract available.

PMID:
31066000
3.

Editorial.

Laubenbacher R, Hastings A.

Bull Math Biol. 2018 Dec;80(12):3069-3070. doi: 10.1007/s11538-018-0501-8. No abstract available.

PMID:
30171473
4.

An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study.

Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P.

Mol Microbiol. 2018 Nov;110(3):357-369. doi: 10.1111/mmi.14086. Epub 2018 Sep 16.

PMID:
30047562
5.

A Systems Biology Approach to Understanding the Pathophysiology of High-Grade Serous Ovarian Cancer: Focus on Iron and Fatty Acid Metabolism.

Konstorum A, Lynch ML, Torti SV, Torti FM, Laubenbacher RC.

OMICS. 2018 Jul;22(7):502-513. doi: 10.1089/omi.2018.0060.

6.

The innate immune response to ischemic injury: a multiscale modeling perspective.

Dimitrova E, Caromile LA, Laubenbacher R, Shapiro LH.

BMC Syst Biol. 2018 Apr 10;12(1):50. doi: 10.1186/s12918-018-0580-z.

7.

Applications of network analysis to routinely collected health care data: a systematic review.

Brunson JC, Laubenbacher RC.

J Am Med Inform Assoc. 2018 Feb 1;25(2):210-221. doi: 10.1093/jamia/ocx052.

PMID:
29025116
8.

Addressing current challenges in cancer immunotherapy with mathematical and computational modelling.

Konstorum A, Vella AT, Adler AJ, Laubenbacher RC.

J R Soc Interface. 2017 Jun;14(131). pii: 20170150. doi: 10.1098/rsif.2017.0150. Review.

9.

Effects of research complexity and competition on the incidence and growth of coauthorship in biomedicine.

Brunson JC, Wang X, Laubenbacher RC.

PLoS One. 2017 Mar 22;12(3):e0173444. doi: 10.1371/journal.pone.0173444. eCollection 2017.

10.

Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective.

Chifman J, Arat S, Deng Z, Lemler E, Pino JC, Harris LA, Kochen MA, Lopez CF, Akman SA, Torti FM, Torti SV, Laubenbacher R.

PLoS Comput Biol. 2017 Feb 6;13(2):e1005352. doi: 10.1371/journal.pcbi.1005352. eCollection 2017 Feb.

11.

Optimization and Control of Agent-Based Models in Biology: A Perspective.

An G, Fitzpatrick BG, Christley S, Federico P, Kanarek A, Neilan RM, Oremland M, Salinas R, Laubenbacher R, Lenhart S.

Bull Math Biol. 2017 Jan;79(1):63-87. doi: 10.1007/s11538-016-0225-6. Epub 2016 Nov 8.

12.

Editorial.

Hastings A, Laubenbacher R.

Bull Math Biol. 2016 Dec;78(12):2303. doi: 10.1007/s11538-016-0223-8. No abstract available.

PMID:
27796721
13.

Identification of control targets in Boolean molecular network models via computational algebra.

Murrugarra D, Veliz-Cuba A, Aguilar B, Laubenbacher R.

BMC Syst Biol. 2016 Sep 23;10(1):94.

14.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

Hosny A, Vera-Licona P, Laubenbacher R, Favre T.

Bioinformatics. 2016 Aug 1;32(15):2396-8. doi: 10.1093/bioinformatics/btw120. Epub 2016 Mar 2.

15.

A computational model of invasive aspergillosis in the lung and the role of iron.

Oremland M, Michels KR, Bettina AM, Lawrence C, Mehrad B, Laubenbacher R.

BMC Syst Biol. 2016 Apr 21;10:34. doi: 10.1186/s12918-016-0275-2.

16.

Editorial.

Laubenbacher R, Hastings A.

Bull Math Biol. 2016 Jan;78(1):1-3. doi: 10.1007/s11538-015-0134-0. No abstract available.

PMID:
26754090
17.

Costimulation Endows Immunotherapeutic CD8 T Cells with IL-36 Responsiveness during Aerobic Glycolysis.

Tsurutani N, Mittal P, St Rose MC, Ngoi SM, Svedova J, Menoret A, Treadway FB, Laubenbacher R, Suárez-Ramírez JE, Cauley LS, Adler AJ, Vella AT.

J Immunol. 2016 Jan 1;196(1):124-34. doi: 10.4049/jimmunol.1501217. Epub 2015 Nov 16.

18.

Iron acquisition and oxidative stress response in aspergillus fumigatus.

Brandon M, Howard B, Lawrence C, Laubenbacher R.

BMC Syst Biol. 2015 Apr 24;9:19. doi: 10.1186/s12918-015-0163-1.

19.

A network biology approach to denitrification in Pseudomonas aeruginosa.

Arat S, Bullerjahn GS, Laubenbacher R.

PLoS One. 2015 Feb 23;10(2):e0118235. doi: 10.1371/journal.pone.0118235. eCollection 2015.

20.

Optimal harvesting for a predator-prey agent-based model using difference equations.

Oremland M, Laubenbacher R.

Bull Math Biol. 2015 Mar;77(3):434-59. doi: 10.1007/s11538-014-0060-6. Epub 2015 Jan 6.

PMID:
25559457
21.

A systems biology approach to iron metabolism.

Chifman J, Laubenbacher R, Torti SV.

Adv Exp Med Biol. 2014;844:201-25. doi: 10.1007/978-1-4939-2095-2_10. Review.

22.

A mathematical model of skeletal muscle disease and immune response in the mdx mouse.

Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R.

Biomed Res Int. 2014;2014:871810. doi: 10.1155/2014/871810. Epub 2014 Jun 11.

23.

Steady state analysis of Boolean molecular network models via model reduction and computational algebra.

Veliz-Cuba A, Aguilar B, Hinkelmann F, Laubenbacher R.

BMC Bioinformatics. 2014 Jun 26;15:221. doi: 10.1186/1471-2105-15-221.

24.

An algebra-based method for inferring gene regulatory networks.

Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R.

BMC Syst Biol. 2014 Mar 26;8:37. doi: 10.1186/1752-0509-8-37.

25.

The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide.

Sha W, Martins AM, Laubenbacher R, Mendes P, Shulaev V.

PLoS One. 2013 Sep 20;8(9):e74939. doi: 10.1371/journal.pone.0074939. eCollection 2013.

26.

Stabilizing gene regulatory networks through feedforward loops.

Kadelka C, Murrugarra D, Laubenbacher R.

Chaos. 2013 Jun;23(2):025107. doi: 10.1063/1.4808248.

PMID:
23822505
27.

Modeling stochasticity and variability in gene regulatory networks.

Murrugarra D, Veliz-Cuba A, Aguilar B, Arat S, Laubenbacher R.

EURASIP J Bioinform Syst Biol. 2012 Jun 6;2012(1):5. doi: 10.1186/1687-4153-2012-5.

28.

The core control system of intracellular iron homeostasis: a mathematical model.

Chifman J, Kniss A, Neupane P, Williams I, Leung B, Deng Z, Mendes P, Hower V, Torti FM, Akman SA, Torti SV, Laubenbacher R.

J Theor Biol. 2012 May 7;300:91-9. doi: 10.1016/j.jtbi.2012.01.024. Epub 2012 Jan 23.

29.

Bioinformatics tools for cancer metabolomics.

Blekherman G, Laubenbacher R, Cortes DF, Mendes P, Torti FM, Akman S, Torti SV, Shulaev V.

Metabolomics. 2011 Sep;7(3):329-343. Epub 2011 Jan 12.

30.

Regulatory patterns in molecular interaction networks.

Murrugarra D, Laubenbacher R.

J Theor Biol. 2011 Nov 7;288:66-72. doi: 10.1016/j.jtbi.2011.08.015. Epub 2011 Aug 24.

PMID:
21872607
31.

ADAM: analysis of discrete models of biological systems using computer algebra.

Hinkelmann F, Brandon M, Guang B, McNeill R, Blekherman G, Veliz-Cuba A, Laubenbacher R.

BMC Bioinformatics. 2011 Jul 20;12:295. doi: 10.1186/1471-2105-12-295.

32.

Algebraic methods in mathematical biology.

Laubenbacher R.

Bull Math Biol. 2011 Apr;73(4):701-5. doi: 10.1007/s11538-011-9643-7. No abstract available.

PMID:
21400021
33.

Differential gene expression in normal and transformed human mammary epithelial cells in response to oxidative stress.

Cortes DF, Sha W, Hower V, Blekherman G, Laubenbacher R, Akman S, Torti SV, Shulaev V.

Free Radic Biol Med. 2011 Jun 1;50(11):1565-74. doi: 10.1016/j.freeradbiomed.2011.03.002. Epub 2011 Mar 29.

34.

A mathematical framework for agent based models of complex biological networks.

Hinkelmann F, Murrugarra D, Jarrah AS, Laubenbacher R.

Bull Math Biol. 2011 Jul;73(7):1583-602. doi: 10.1007/s11538-010-9582-8. Epub 2010 Sep 29.

PMID:
20878493
35.

Discretization of time series data.

Dimitrova ES, Licona MP, McGee J, Laubenbacher R.

J Comput Biol. 2010 Jun;17(6):853-68. doi: 10.1089/cmb.2008.0023.

36.

Polynomial algebra of discrete models in systems biology.

Veliz-Cuba A, Jarrah AS, Laubenbacher R.

Bioinformatics. 2010 Jul 1;26(13):1637-43. doi: 10.1093/bioinformatics/btq240. Epub 2010 May 6.

PMID:
20448137
37.

The dynamics of conjunctive and disjunctive Boolean network models.

Jarrah AS, Laubenbacher R, Veliz-Cuba A.

Bull Math Biol. 2010 Aug;72(6):1425-47. doi: 10.1007/s11538-010-9501-z. Epub 2010 Jan 20.

PMID:
20087672
38.

Algebraic models of biochemical networks.

Laubenbacher R, Jarrah AS.

Methods Enzymol. 2009;467:163-196. doi: 10.1016/S0076-6879(09)67007-5.

PMID:
19897093
39.

Mathematical biology education: beyond calculus.

Robeva R, Laubenbacher R.

Science. 2009 Jul 31;325(5940):542-3. doi: 10.1126/science.1176016. No abstract available.

PMID:
19644095
40.

A systems biology view of cancer.

Laubenbacher R, Hower V, Jarrah A, Torti SV, Shulaev V, Mendes P, Torti FM, Akman S.

Biochim Biophys Acta. 2009 Dec;1796(2):129-39. doi: 10.1016/j.bbcan.2009.06.001. Epub 2009 Jun 6. Review.

41.

A general map of iron metabolism and tissue-specific subnetworks.

Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV.

Mol Biosyst. 2009 May;5(5):422-43. doi: 10.1039/b816714c. Epub 2009 Mar 6. Review.

42.

Nested Canalyzing, Unate Cascade, and Polynomial Functions.

Jarrah AS, Raposa B, Laubenbacher R.

Physica D. 2007 Sep 15;233(2):167-174.

43.

The effect of negative feedback loops on the dynamics of boolean networks.

Sontag E, Veliz-Cuba A, Laubenbacher R, Jarrah AS.

Biophys J. 2008 Jul;95(2):518-26. doi: 10.1529/biophysj.107.125021. Epub 2008 Mar 28.

44.

A virtual look at Epstein-Barr virus infection: simulation mechanism.

Shapiro M, Duca KA, Lee K, Delgado-Eckert E, Hawkins J, Jarrah AS, Laubenbacher R, Polys NF, Hadinoto V, Thorley-Lawson DA.

J Theor Biol. 2008 Jun 21;252(4):633-48. doi: 10.1016/j.jtbi.2008.01.032. Epub 2008 Feb 16.

45.

Using formal concept analysis for microarray data comparison.

Choi V, Huang Y, Lam V, Potter D, Laubenbacher R, Duca K.

J Bioinform Comput Biol. 2008 Feb;6(1):65-75.

PMID:
18324746
46.

A virtual look at Epstein-Barr virus infection: biological interpretations.

Duca KA, Shapiro M, Delgado-Eckert E, Hadinoto V, Jarrah AS, Laubenbacher R, Lee K, Luzuriaga K, Polys NF, Thorley-Lawson DA.

PLoS Pathog. 2007 Oct 19;3(10):1388-400.

47.

Comparison of reverse-engineering methods using an in silico network.

Camacho D, Vera Licona P, Mendes P, Laubenbacher R.

Ann N Y Acad Sci. 2007 Dec;1115:73-89. Epub 2007 Oct 9. Review.

PMID:
17925358
48.

Reverse engineering of dynamic networks.

Stigler B, Jarrah A, Stillman M, Laubenbacher R.

Ann N Y Acad Sci. 2007 Dec;1115:168-77. Epub 2007 Oct 9.

PMID:
17925347
49.

Simulating Epstein-Barr virus infection with C-ImmSim.

Castiglione F, Duca K, Jarrah A, Laubenbacher R, Hochberg D, Thorley-Lawson D.

Bioinformatics. 2007 Jun 1;23(11):1371-7. Epub 2007 Mar 6.

PMID:
17341499
50.

A computational algebra approach to the reverse engineering of gene regulatory networks.

Laubenbacher R, Stigler B.

J Theor Biol. 2004 Aug 21;229(4):523-37.

PMID:
15246788

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