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Items: 1 to 20 of 229

1.

Construction of a computable cell proliferation network focused on non-diseased lung cells.

Westra JW, Schlage WK, Frushour BP, Gebel S, Catlett NL, Han W, Eddy SF, Hengstermann A, Matthews AL, Mathis C, Lichtner RB, Poussin C, Talikka M, Veljkovic E, Van Hooser AA, Wong B, Maria MJ, Peitsch MC, Deehan R, Hoeng J.

BMC Syst Biol. 2011 Jul 2;5:105. doi: 10.1186/1752-0509-5-105.

2.

A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue.

Schlage WK, Westra JW, Gebel S, Catlett NL, Mathis C, Frushour BP, Hengstermann A, Van Hooser A, Poussin C, Wong B, Lietz M, Park J, Drubin D, Veljkovic E, Peitsch MC, Hoeng J, Deehan R.

BMC Syst Biol. 2011 Oct 19;5:168. doi: 10.1186/1752-0509-5-168.

3.

Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset.

Belcastro V, Poussin C, Gebel S, Mathis C, Schlage WK, Lichtner RB, Quadt-Humme S, Wagner S, Hoeng J, Peitsch MC.

Bioinform Biol Insights. 2013 Jul 23;7:217-30. doi: 10.4137/BBI.S12167. Print 2013.

4.

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks.

Martin F, Thomson TM, Sewer A, Drubin DA, Mathis C, Weisensee D, Pratt D, Hoeng J, Peitsch MC.

BMC Syst Biol. 2012 May 31;6:54. doi: 10.1186/1752-0509-6-54.

5.

Construction of a computable network model for DNA damage, autophagy, cell death, and senescence.

Gebel S, Lichtner RB, Frushour B, Schlage WK, Hoang V, Talikka M, Hengstermann A, Mathis C, Veljkovic E, Peck M, Peitsch MC, Deehan R, Hoeng J, Westra JW.

Bioinform Biol Insights. 2013;7:97-117. doi: 10.4137/BBI.S11154. Epub 2013 Mar 7.

6.

New Markov-Shannon Entropy models to assess connectivity quality in complex networks: from molecular to cellular pathway, Parasite-Host, Neural, Industry, and Legal-Social networks.

Riera-Fernández P, Munteanu CR, Escobar M, Prado-Prado F, Martín-Romalde R, Pereira D, Villalba K, Duardo-Sánchez A, González-Díaz H.

J Theor Biol. 2012 Jan 21;293:174-88. doi: 10.1016/j.jtbi.2011.10.016. Epub 2011 Oct 25.

PMID:
22037044
7.

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. doi: 10.1007/978-1-59745-243-4_24. Review.

PMID:
19381531
8.

Elementary signaling modes predict the essentiality of signal transduction network components.

Wang RS, Albert R.

BMC Syst Biol. 2011 Mar 22;5:44. doi: 10.1186/1752-0509-5-44.

9.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

Boué S, Talikka M, Westra JW, Hayes W, Di Fabio A, Park J, Schlage WK, Sewer A, Fields B, Ansari S, Martin F, Veljkovic E, Kenney R, Peitsch MC, Hoeng J.

Database (Oxford). 2015 Apr 17;2015:bav030. doi: 10.1093/database/bav030. Print 2015.

10.

Enhancement of COPD biological networks using a web-based collaboration interface.

sbv IMPROVER project team (in alphabetical order)., Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M; Challenge Best Performers (in alphabetical order)., Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M.

Version 1. F1000Res. 2015 Jan 29;4:32. doi: 10.12688/f1000research.5984.1. eCollection 2015.

PMID:
25767696
11.

Enhancement of COPD biological networks using a web-based collaboration interface.

sbv IMPROVER project team (in alphabetical order)., Boue S, Fields B, Hoeng J, Park J, Peitsch MC, Schlage WK, Talikka M; Challenge Best Performers (in alphabetical order)., Binenbaum I, Bondarenko V, Bulgakov OV, Cherkasova V, Diaz-Diaz N, Fedorova L, Guryanova S, Guzova J, Igorevna Koroleva G, Kozhemyakina E, Kumar R, Lavid N, Lu Q, Menon S, Ouliel Y, Peterson SC, Prokhorov A, Sanders E, Schrier S, Schwaitzer Neta G, Shvydchenko I, Tallam A, Villa-Fombuena G, Wu J, Yudkevich I, Zelikman M.

Version 2. F1000Res. 2015 Jan 29 [revised 2015 May 20];4:32. doi: 10.12688/f1000research.5984.2. eCollection 2015.

12.

Gene expression network reconstruction by convex feature selection when incorporating genetic perturbations.

Logsdon BA, Mezey J.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001014. doi: 10.1371/journal.pcbi.1001014.

13.

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes.

Vlaic S, Schmidt-Heck W, Matz-Soja M, Marbach E, Linde J, Meyer-Baese A, Zellmer S, Guthke R, Gebhardt R.

BMC Syst Biol. 2012 Nov 29;6:147. doi: 10.1186/1752-0509-6-147.

14.

Network analysis: a new approach to study endocrine disorders.

Stevens A, De Leonibus C, Hanson D, Dowsey AW, Whatmore A, Meyer S, Donn RP, Chatelain P, Banerjee I, Cosgrove KE, Clayton PE, Dunne MJ.

J Mol Endocrinol. 2013 Dec 19;52(1):R79-93. doi: 10.1530/JME-13-0112. Print 2014 Feb. Review.

PMID:
24085748
15.

Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models.

Martin F, Sewer A, Talikka M, Xiang Y, Hoeng J, Peitsch MC.

BMC Bioinformatics. 2014 Jul 11;15:238. doi: 10.1186/1471-2105-15-238.

16.

Constraint-based models predict metabolic and associated cellular functions.

Bordbar A, Monk JM, King ZA, Palsson BO.

Nat Rev Genet. 2014 Feb;15(2):107-20. doi: 10.1038/nrg3643. Epub 2014 Jan 16. Review.

PMID:
24430943
17.

A data integration approach for cell cycle analysis oriented to model simulation in systems biology.

Alfieri R, Merelli I, Mosca E, Milanesi L.

BMC Syst Biol. 2007 Aug 1;1:35.

18.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

19.
20.

Modular analysis of biological networks.

Kaltenbach HM, Stelling J.

Adv Exp Med Biol. 2012;736:3-17. doi: 10.1007/978-1-4419-7210-1_1. Review.

PMID:
22161320

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