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Items: 1 to 20 of 34

1.

Silencing of ANKRD12 circRNA induces molecular and functional changes associated with invasive phenotypes.

Karedath T, Ahmed I, Al Ameri W, Al-Dasim FM, Andrews SS, Samuel S, Al-Azwani IK, Mohamoud YA, Rafii A, Malek JA.

BMC Cancer. 2019 Jun 11;19(1):565. doi: 10.1186/s12885-019-5723-0.

2.

High-resolution protein-protein interaction mapping using all-versus-all sequencing (AVA-Seq).

Andrews SS, Schaefer-Ramadan S, Al-Thani NM, Ahmed I, Mohamoud YA, Malek JA.

J Biol Chem. 2019 Jul 26;294(30):11549-11558. doi: 10.1074/jbc.RA119.008792. Epub 2019 Jun 10.

PMID:
31182485
3.

Rule-Based Modeling Using Wildcards in the Smoldyn Simulator.

Andrews SS.

Methods Mol Biol. 2019;1945:179-202. doi: 10.1007/978-1-4939-9102-0_8.

PMID:
30945247
4.

Transferring information without distortion.

Andrews SS, Brent R, Bal√°zsi G.

Elife. 2018 Oct 25;7. pii: e41894. doi: 10.7554/eLife.41894.

5.

Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.

Andrews SS.

Bioinformatics. 2017 Mar 1;33(5):710-717. doi: 10.1093/bioinformatics/btw700.

PMID:
28365760
6.

Push-Pull and Feedback Mechanisms Can Align Signaling System Outputs with Inputs.

Andrews SS, Peria WJ, Yu RC, Colman-Lerner A, Brent R.

Cell Syst. 2016 Nov 23;3(5):444-455.e2. doi: 10.1016/j.cels.2016.10.002. Epub 2016 Oct 27.

7.

Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma.

Ahmed I, Karedath T, Andrews SS, Al-Azwani IK, Mohamoud YA, Querleu D, Rafii A, Malek JA.

Oncotarget. 2016 Jun 14;7(24):36366-36381. doi: 10.18632/oncotarget.8917.

8.

Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli.

Emiola A, Andrews SS, Heller C, George J.

Proc Natl Acad Sci U S A. 2016 Mar 15;113(11):3108-13. doi: 10.1073/pnas.1521168113. Epub 2016 Feb 29.

9.

A Method and On-Line Tool for Maximum Likelihood Calibration of Immunoblots and Other Measurements That Are Quantified in Batches.

Andrews SS, Rutherford S.

PLoS One. 2016 Feb 23;11(2):e0149575. doi: 10.1371/journal.pone.0149575. eCollection 2016.

10.

A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli.

Emiola A, George J, Andrews SS.

PLoS One. 2015 Apr 28;10(4):e0121216. doi: 10.1371/journal.pone.0121216. eCollection 2014.

11.

Multiscale reaction-diffusion simulations with Smoldyn.

Robinson M, Andrews SS, Erban R.

Bioinformatics. 2015 Jul 15;31(14):2406-8. doi: 10.1093/bioinformatics/btv149. Epub 2015 Mar 18.

12.

An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding.

Schmidt HG, Sewitz S, Andrews SS, Lipkow K.

PLoS One. 2014 Oct 21;9(10):e108575. doi: 10.1371/journal.pone.0108575. eCollection 2014.

13.

Identifying risk factors for severe hypoglycemia in hospitalized patients with diabetes.

Dendy JA, Chockalingam V, Tirumalasetty NN, Dornelles A, Blonde L, Bolton PM, Meadows RY, Andrews SS.

Endocr Pract. 2014 Oct;20(10):1051-6. doi: 10.4158/EP13467.OR.

PMID:
24936545
14.

Methods for modeling cytoskeletal and DNA filaments.

Andrews SS.

Phys Biol. 2014 Feb;11(1):011001. doi: 10.1088/1478-3975/11/1/011001. Epub 2014 Jan 29. Review.

PMID:
24476634
15.

The autoregulation of a eukaryotic DNA transposon.

Claeys Bouuaert C, Lipkow K, Andrews SS, Liu D, Chalmers R.

Elife. 2013 Jun 18;2:e00668. doi: 10.7554/eLife.00668.

16.

Label transfer reagents to probe p38 MAPK binding partners.

Andrews SS, Hill ZB, Perera BG, Maly DJ.

Chembiochem. 2013 Jan 21;14(2):209-16. doi: 10.1002/cbic.201200673. Epub 2013 Jan 14.

17.

Targeting diverse signaling interaction sites allows the rapid generation of bivalent kinase inhibitors.

Hill ZB, Perera BG, Andrews SS, Maly DJ.

ACS Chem Biol. 2012 Mar 16;7(3):487-95. doi: 10.1021/cb200387g. Epub 2011 Dec 22.

18.

Spatial and stochastic cellular modeling with the Smoldyn simulator.

Andrews SS.

Methods Mol Biol. 2012;804:519-42. doi: 10.1007/978-1-61779-361-5_26.

PMID:
22144170
19.

Detailed simulations of cell biology with Smoldyn 2.1.

Andrews SS, Addy NJ, Brent R, Arkin AP.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000705. doi: 10.1371/journal.pcbi.1000705.

20.

Accurate particle-based simulation of adsorption, desorption and partial transmission.

Andrews SS.

Phys Biol. 2009 Nov 12;6(4):046015. doi: 10.1088/1478-3975/6/4/046015.

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