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SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks.

Olorin E, O'Brien KT, Palopoli N, Pérez-Bercoff Å, Shields DC, Edwards RJ.

F1000Res. 2015 Aug 5;4:477. doi: 10.12688/f1000research.6773.1. eCollection 2015.


Inhibition of Calpain Activation Protects MPTP-Induced Nigral and Spinal Cord Neurodegeneration, Reduces Inflammation, and Improves Gait Dynamics in Mice.

Samantaray S, Knaryan VH, Shields DC, Cox AA, Haque A, Banik NL.

Mol Neurobiol. 2015 Oct;52(2):1054-66. doi: 10.1007/s12035-015-9255-6. Epub 2015 Jun 25.


Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to erythrocyte invasion.

Bianchin A, Bell A, Chubb AJ, Doolan N, Leneghan D, Stavropoulos I, Shields DC, Mooney C.

PLoS One. 2015 Jun 3;10(6):e0127383. doi: 10.1371/journal.pone.0127383. eCollection 2015.


Lateralization of mesial temporal lobe epilepsy with chronic ambulatory electrocorticography.

King-Stephens D, Mirro E, Weber PB, Laxer KD, Van Ness PC, Salanova V, Spencer DC, Heck CN, Goldman A, Jobst B, Shields DC, Bergey GK, Eisenschenk S, Worrell GA, Rossi MA, Gross RE, Cole AJ, Sperling MR, Nair DR, Gwinn RP, Park YD, Rutecki PA, Fountain NB, Wharen RE, Hirsch LJ, Miller IO, Barkley GL, Edwards JC, Geller EB, Berg MJ, Sadler TL, Sun FT, Morrell MJ.

Epilepsia. 2015 Jun;56(6):959-67. doi: 10.1111/epi.13010. Epub 2015 May 19.


Discovering anti-platelet drug combinations with an integrated model of activator-inhibitor relationships, activator-activator synergies and inhibitor-inhibitor synergies.

Lombardi F, Golla K, Fitzpatrick DJ, Casey FP, Moran N, Shields DC.

PLoS Comput Biol. 2015 Apr 15;11(4):e1004119. doi: 10.1371/journal.pcbi.1004119. eCollection 2015 Apr.


Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression.

Fitzpatrick DJ, Ryan CJ, Shah N, Greene D, Molony C, Shields DC.

BMC Genomics. 2015 Feb 21;16:109. doi: 10.1186/s12864-015-1300-3.


Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides.

Duffy FJ, O'Donovan D, Devocelle M, Moran N, O'Connell DJ, Shields DC.

J Chem Inf Model. 2015 Mar 23;55(3):600-13. doi: 10.1021/ci500431q. Epub 2015 Feb 20.


Long-term treatment with responsive brain stimulation in adults with refractory partial seizures.

Bergey GK, Morrell MJ, Mizrahi EM, Goldman A, King-Stephens D, Nair D, Srinivasan S, Jobst B, Gross RE, Shields DC, Barkley G, Salanova V, Olejniczak P, Cole A, Cash SS, Noe K, Wharen R, Worrell G, Murro AM, Edwards J, Duchowny M, Spencer D, Smith M, Geller E, Gwinn R, Skidmore C, Eisenschenk S, Berg M, Heck C, Van Ness P, Fountain N, Rutecki P, Massey A, O'Donovan C, Labar D, Duckrow RB, Hirsch LJ, Courtney T, Sun FT, Seale CG.

Neurology. 2015 Feb 24;84(8):810-7. doi: 10.1212/WNL.0000000000001280. Epub 2015 Jan 23.


Computational approaches to developing short cyclic peptide modulators of protein-protein interactions.

Duffy FJ, Devocelle M, Shields DC.

Methods Mol Biol. 2015;1268:241-71. doi: 10.1007/978-1-4939-2285-7_11.


Following the digestion of milk proteins from mother to baby.

Holton TA, Vijayakumar V, Dallas DC, Guerrero A, Borghese RA, Lebrilla CB, German JB, Barile D, Underwood MA, Shields DC, Khaldi N.

J Proteome Res. 2014 Dec 5;13(12):5777-83. doi: 10.1021/pr5006907. Epub 2014 Nov 11.


Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins.

Postmus I, Trompet S, Deshmukh HA, Barnes MR, Li X, Warren HR, Chasman DI, Zhou K, Arsenault BJ, Donnelly LA, Wiggins KL, Avery CL, Griffin P, Feng Q, Taylor KD, Li G, Evans DS, Smith AV, de Keyser CE, Johnson AD, de Craen AJ, Stott DJ, Buckley BM, Ford I, Westendorp RG, Slagboom PE, Sattar N, Munroe PB, Sever P, Poulter N, Stanton A, Shields DC, O'Brien E, Shaw-Hawkins S, Chen YD, Nickerson DA, Smith JD, Dubé MP, Boekholdt SM, Hovingh GK, Kastelein JJ, McKeigue PM, Betteridge J, Neil A, Durrington PN, Doney A, Carr F, Morris A, McCarthy MI, Groop L, Ahlqvist E; Welcome Trust Case Control Consortium, Bis JC, Rice K, Smith NL, Lumley T, Whitsel EA, Stürmer T, Boerwinkle E, Ngwa JS, O'Donnell CJ, Vasan RS, Wei WQ, Wilke RA, Liu CT, Sun F, Guo X, Heckbert SR, Post W, Sotoodehnia N, Arnold AM, Stafford JM, Ding J, Herrington DM, Kritchevsky SB, Eiriksdottir G, Launer LJ, Harris TB, Chu AY, Giulianini F, MacFadyen JG, Barratt BJ, Nyberg F, Stricker BH, Uitterlinden AG, Hofman A, Rivadeneira F, Emilsson V, Franco OH, Ridker PM, Gudnason V, Liu Y, Denny JC, Ballantyne CM, Rotter JI, Adrienne Cupples L, Psaty BM, Palmer CN, Tardif JC, Colhoun HM, Hitman G, Krauss RM, Wouter Jukema J, Caulfield MJ.

Nat Commun. 2014 Oct 28;5:5068. doi: 10.1038/ncomms6068.


Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions.

Duffy FJ, Devocelle M, Croucher DR, Shields DC.

BMC Bioinformatics. 2014 Sep 17;15:305. doi: 10.1186/1471-2105-15-305.


Cadherin juxtamembrane region derived peptides inhibit TGFβ1 induced gene expression.

Stavropoulos I, Golla K, Moran N, Martin F, Shields DC.

Bioarchitecture. 2014;4(3):103-10. doi: 10.4161/bioa.32143. Epub 2014 Aug 9.


In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors.

Nongonierma AB, Mooney C, Shields DC, FitzGerald RJ.

Peptides. 2014 Jul;57:43-51. doi: 10.1016/j.peptides.2014.04.018. Epub 2014 May 2.


Reward and reinforcement activity in the nucleus accumbens during learning.

Gale JT, Shields DC, Ishizawa Y, Eskandar EN.

Front Behav Neurosci. 2014 Apr 3;8:114. doi: 10.3389/fnbeh.2014.00114. eCollection 2014.


Predicting the important enzymes in human breast milk digestion.

Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB.

J Agric Food Chem. 2014 Jul 23;62(29):7225-32. doi: 10.1021/jf405601e. Epub 2014 Jul 10.


Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey.

Ruhanen H, Hurley D, Ghosh A, O'Brien KT, Johnston CR, Shields DC.

Front Microbiol. 2014 Jan 21;5:4. doi: 10.3389/fmicb.2014.00004. eCollection 2014.


Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences.

Khaldi N, Holton TA, Shields DC.

J Dairy Sci. 2014 Mar;97(3):1248-58. doi: 10.3168/jds.2013-7317. Epub 2014 Jan 25.


A historical perspective: stereotactic lesions for the treatment of epilepsy.

Leiphart JW, Young RM, Shields DC.

Seizure. 2014 Jan;23(1):1-5. doi: 10.1016/j.seizure.2013.10.006. Epub 2013 Oct 19. Review.


CPPpred: prediction of cell penetrating peptides.

Holton TA, Pollastri G, Shields DC, Mooney C.

Bioinformatics. 2013 Dec 1;29(23):3094-6. doi: 10.1093/bioinformatics/btt518. Epub 2013 Sep 23.

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