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Items: 18

1.

PyBioNetFit and the Biological Property Specification Language.

Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS.

iScience. 2019 Aug 28;19:1012-1036. doi: 10.1016/j.isci.2019.08.045. [Epub ahead of print]

2.

A Step-by-Step Guide to Using BioNetFit.

Hlavacek WS, Csicsery-Ronay JA, Baker LR, Ramos Álamo MDC, Ionkov A, Mitra ED, Suderman R, Erickson KE, Dias R, Colvin J, Thomas BR, Posner RG.

Methods Mol Biol. 2019;1945:391-419. doi: 10.1007/978-1-4939-9102-0_18.

PMID:
30945257
3.

Using RuleBuilder to Graphically Define and Visualize BioNetGen-Language Patterns and Reaction Rules.

Suderman R, Fricke GM, Hlavacek WS.

Methods Mol Biol. 2019;1945:33-42. doi: 10.1007/978-1-4939-9102-0_2.

PMID:
30945241
4.

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor.

Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS.

PLoS Comput Biol. 2019 Jan 17;15(1):e1006706. doi: 10.1371/journal.pcbi.1006706. eCollection 2019 Jan.

5.

Intrinsic limits of information transmission in biochemical signalling motifs.

Suderman R, Deeds EJ.

Interface Focus. 2018 Dec 6;8(6):20180039. doi: 10.1098/rsfs.2018.0039. Epub 2018 Oct 19.

PMID:
30443336
6.

Preassembled GPCR signaling complexes mediate distinct cellular responses to ultralow ligand concentrations.

Civciristov S, Ellisdon AM, Suderman R, Pon CK, Evans BA, Kleifeld O, Charlton SJ, Hlavacek WS, Canals M, Halls ML.

Sci Signal. 2018 Oct 9;11(551). pii: eaan1188. doi: 10.1126/scisignal.aan1188.

PMID:
30301787
7.

Generalizing Gillespie's Direct Method to Enable Network-Free Simulations.

Suderman R, Mitra ED, Lin YT, Erickson KE, Feng S, Hlavacek WS.

Bull Math Biol. 2019 Aug;81(8):2822-2848. doi: 10.1007/s11538-018-0418-2. Epub 2018 Mar 28.

PMID:
29594824
8.

Fundamental trade-offs between information flow in single cells and cellular populations.

Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):5755-5760. doi: 10.1073/pnas.1615660114. Epub 2017 May 12.

9.

Development of polyol-responsive antibody mimetics for single-step protein purification.

Suderman RJ, Rice DA, Gibson SD, Strick EJ, Chao DM.

Protein Expr Purif. 2017 Jun;134:114-124. doi: 10.1016/j.pep.2017.04.008. Epub 2017 Apr 17.

10.

Theory and application of shapelets to the analysis of surface self-assembly imaging.

Suderman R, Lizotte DJ, Abukhdeir NM.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Mar;91(3):033307. Epub 2015 Mar 25.

PMID:
25871246
11.

Machines vs. ensembles: effective MAPK signaling through heterogeneous sets of protein complexes.

Suderman R, Deeds EJ.

PLoS Comput Biol. 2013;9(10):e1003278. doi: 10.1371/journal.pcbi.1003278. Epub 2013 Oct 10.

12.

Polydnavirus Ank proteins bind NF-κB homodimers and inhibit processing of Relish.

Bitra K, Suderman RJ, Strand MR.

PLoS Pathog. 2012;8(5):e1002722. doi: 10.1371/journal.ppat.1002722. Epub 2012 May 24.

13.

Model reactions for insect cuticle sclerotization: participation of amino groups in the cross-linking of Manduca sexta cuticle protein MsCP36.

Suderman RJ, Dittmer NT, Kramer KJ, Kanost MR.

Insect Biochem Mol Biol. 2010 Mar;40(3):252-8. doi: 10.1016/j.ibmb.2010.02.008. Epub 2010 Feb 26.

PMID:
20219676
14.

Protein tyrosine phosphatase-H2 from a polydnavirus induces apoptosis of insect cells.

Suderman RJ, Pruijssers AJ, Strand MR.

J Gen Virol. 2008 Jun;89(Pt 6):1411-20. doi: 10.1099/vir.0.2008/000307-0.

PMID:
18474557
15.

An insulin-like peptide regulates egg maturation and metabolism in the mosquito Aedes aegypti.

Brown MR, Clark KD, Gulia M, Zhao Z, Garczynski SF, Crim JW, Suderman RJ, Strand MR.

Proc Natl Acad Sci U S A. 2008 Apr 15;105(15):5716-21. doi: 10.1073/pnas.0800478105. Epub 2008 Apr 7.

16.

Model reactions for insect cuticle sclerotization: cross-linking of recombinant cuticular proteins upon their laccase-catalyzed oxidative conjugation with catechols.

Suderman RJ, Dittmer NT, Kanost MR, Kramer KJ.

Insect Biochem Mol Biol. 2006 Apr;36(4):353-65. Epub 2006 Jan 19. Erratum in: Insect Biochem Mol Biol. 2006 Jul;36(7):610-1.

PMID:
16551549
17.
18.

Characterization and cDNA cloning of three major proteins from pharate pupal cuticle of Manduca sexta.

Suderman RJ, Andersen SO, Hopkins TL, Kanost MR, Kramer KJ.

Insect Biochem Mol Biol. 2003 Mar;33(3):331-43.

PMID:
12609518

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