Denis C. Shields, PhD - Publications

Complex and Adaptive Systems Laboratory University College Dublin, Dublin, County Dublin, Ireland 
Genetics, Bioinformatics

157 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Um J, Manguy J, Anes J, Jacquier JC, Hurley D, Dillon ET, Wynne K, Fanning S, O'Sullivan M, Shields DC. Enriching antimicrobial peptides from milk hydrolysates using pectin/alginate food-gels. Food Chemistry. 352: 129220. PMID 33684717 DOI: 10.1016/j.foodchem.2021.129220  0.92
2021 Mészáros B, Sámano-Sánchez H, Alvarado-Valverde J, Čalyševa J, Martínez-Pérez E, Alves R, Shields DC, Kumar M, Rippmann F, Chemes LB, Gibson TJ. Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications. Science Signaling. 14. PMID 33436497 DOI: 10.1126/scisignal.abd0334  0.72
2020 O'Brien KT, Mooney C, Lopez C, Pollastri G, Shields DC. Prediction of polyproline II secondary structure propensity in proteins. Royal Society Open Science. 7: 191239. PMID 32218953 DOI: 10.1098/Rsos.191239  0.6
2019 Manguy J, Shields DC. Implications of kappa-casein evolutionary diversity for the self-assembly and aggregation of casein micelles. Royal Society Open Science. 6: 190939. PMID 31824707 DOI: 10.1098/Rsos.190939  0.92
2019 Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, ... ... Shields DC, et al. An intrinsically disordered proteins community for ELIXIR. F1000research. 8. PMID 31824649 DOI: 10.12688/F1000Research.20136.1  0.92
2019 O'Brien KT, Golla K, Kranjc T, O'Donovan D, Allen S, Maguire P, Simpson JC, O'Connell D, Moran N, Shields DC. Computational and experimental analysis of bioactive peptide linear motifs in the integrin adhesome. Plos One. 14: e0210337. PMID 30689642 DOI: 10.1371/Journal.Pone.0210337  0.6
2018 Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH. Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Communications. 9: 1887. PMID 29760453 DOI: 10.1038/S41467-018-04374-7  0.96
2018 Drummond E, Flynn S, Whelan H, Nongonierma AB, Holton TA, Robinson A, Egan T, Cagney G, Shields DC, Gibney ER, Newsholme P, Gaudel C, Jacquier JC, Noronha N, Fitzgerald RJ, et al. A casein hydrolysate with glycaemic control properties: evidence from cell, animal models and humans. Journal of Agricultural and Food Chemistry. PMID 29638124 DOI: 10.1021/Acs.Jafc.7B05550  0.84
2016 Manguy J, Jehl P, Dillon ET, Davey NE, Shields DC, Holton TA. Peptigram: A Web-Based Application for Peptidomics Data Visualization. Journal of Proteome Research. PMID 27997202 DOI: 10.1021/Acs.Jproteome.6B00751  0.92
2016 Postmus I, Warren HR, Trompet S, Arsenault BJ, Avery CL, Bis JC, Chasman DI, de Keyser CE, Deshmukh HA, Evans DS, Feng Q, Li X, Smit RA, Smith AV, Sun F, ... ... Shields DC, et al. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins. Journal of Medical Genetics. PMID 27587472 DOI: 10.1136/Jmedgenet-2016-103966  1
2016 Jehl P, Manguy J, Shields DC, Higgins DG, Davey NE. ProViz-a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. Nucleic Acids Research. PMID 27085803 DOI: 10.1093/Nar/Gkw265  0.92
2015 Olorin E, O'Brien KT, Palopoli N, Pérez-Bercoff Å, Shields DC, Edwards RJ. SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks. F1000research. 4: 477. PMID 26674271 DOI: 10.12688/F1000Research.6773.1  0.92
2015 Bianchin A, Bell A, Chubb AJ, Doolan N, Leneghan D, Stavropoulos I, Shields DC, Mooney C. Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to erythrocyte invasion. Plos One. 10: e0127383. PMID 26039561 DOI: 10.1371/Journal.Pone.0127383  0.6
2015 Lombardi F, Golla K, Fitzpatrick DJ, Casey FP, Moran N, Shields DC. Discovering anti-platelet drug combinations with an integrated model of activator-inhibitor relationships, activator-activator synergies and inhibitor-inhibitor synergies. Plos Computational Biology. 11: e1004119. PMID 25875950 DOI: 10.1371/Journal.Pcbi.1004119  1
2015 Fitzpatrick DJ, Ryan CJ, Shah N, Greene D, Molony C, Shields DC. Genome-wide epistatic expression quantitative trait loci discovery in four human tissues reveals the importance of local chromosomal interactions governing gene expression. Bmc Genomics. 16: 109. PMID 25765234 DOI: 10.1186/S12864-015-1300-3  1
2015 Duffy FJ, O'Donovan D, Devocelle M, Moran N, O'Connell DJ, Shields DC. Virtual screening using combinatorial cyclic peptide libraries reveals protein interfaces readily targetable by cyclic peptides. Journal of Chemical Information and Modeling. 55: 600-13. PMID 25668361 DOI: 10.1021/Ci500431Q  1
2015 Bianchin A, Bell A, Chubb AJ, Doolan N, Leneghan D, Stavropoulos I, Shields DC, Mooney C. Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to erythrocyte invasion Plos One. 10. DOI: 10.1371/journal.pone.0127383  1
2015 Duffy FJ, Devocelle M, Shields DC. Computational approaches to developing short cyclic peptide modulators of protein–protein interactions Methods in Molecular Biology. 1268: 241-271. DOI: 10.1007/978-1-4939-2285-7_11  1
2014 Holton TA, Vijayakumar V, Dallas DC, Guerrero A, Borghese RA, Lebrilla CB, German JB, Barile D, Underwood MA, Shields DC, Khaldi N. Following the digestion of milk proteins from mother to baby. Journal of Proteome Research. 13: 5777-83. PMID 25385259 DOI: 10.1021/Pr5006907  1
2014 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, ... ... Shields DC, et al. Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. Nature Communications. 5: 5068. PMID 25350695 DOI: 10.1038/ncomms6068  1
2014 Duffy FJ, Devocelle M, Croucher DR, Shields DC. Computational survey of peptides derived from disulphide-bonded protein loops that may serve as mediators of protein-protein interactions. Bmc Bioinformatics. 15: 305. PMID 25231912 DOI: 10.1186/1471-2105-15-305  1
2014 Nongonierma AB, Mooney C, Shields DC, Fitzgerald RJ. In silico approaches to predict the potential of milk protein-derived peptides as dipeptidyl peptidase IV (DPP-IV) inhibitors Peptides. 57: 43-51. PMID 24793774 DOI: 10.1016/J.Peptides.2014.04.018  1
2014 Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB. Predicting the important enzymes in human breast milk digestion. Journal of Agricultural and Food Chemistry. 62: 7225-32. PMID 24620897 DOI: 10.1021/Jf405601E  0.52
2014 Ruhanen H, Hurley D, Ghosh A, O'Brien KT, Johnston CR, Shields DC. Potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey. Frontiers in Microbiology. 5: 4. PMID 24478765 DOI: 10.3389/Fmicb.2014.00004  1
2014 Khaldi N, Holton TA, Shields DC. Amino acid enrichment and compositional changes among mammalian milk proteins and the resulting nutritional consequences. Journal of Dairy Science. 97: 1248-58. PMID 24472131 DOI: 10.3168/Jds.2013-7317  1
2014 Khaldi N, Vijayakumar V, Dallas DC, Guerrero A, Wickramasinghe S, Smilowitz JT, Medrano JF, Lebrilla CB, Shields DC, German JB. Predicting the important enzymes in human breast milk digestion Journal of Agricultural and Food Chemistry. 62: 7225-7232. DOI: 10.1021/jf405601e  1
2014 Phelan M, Khaldi N, Shields DC, Kerins DM. Angiotensin converting enzyme and nitric oxide inhibitory activities ofnovel milk derived peptides International Dairy Journal. 35: 38-42. DOI: 10.1016/J.Idairyj.2013.10.008  1
2013 Holton TA, Pollastri G, Shields DC, Mooney C. CPPpred: prediction of cell penetrating peptides. Bioinformatics (Oxford, England). 29: 3094-6. PMID 24064418 DOI: 10.1093/Bioinformatics/Btt518  1
2013 Khan W, Duffy F, Pollastri G, Shields DC, Mooney C. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains. Plos One. 8: e72838. PMID 24019881 DOI: 10.1371/Journal.Pone.0072838  1
2013 Yadav S, Cotlarciuc I, Munroe PB, Khan MS, Nalls MA, Bevan S, Cheng YC, Chen WM, Malik R, McCarthy NS, Holliday EG, Speed D, Hasan N, Pucek M, Rinne PE, ... ... Shields DC, et al. Genome-wide analysis of blood pressure variability and ischemic stroke. Stroke; a Journal of Cerebral Circulation. 44: 2703-9. PMID 23929743 DOI: 10.1161/Strokeaha.113.002186  1
2013 O'Brien KT, Haslam NJ, Shields DC. SLiMScape: A protein short linear motif analysis plugin for Cytoscape Bmc Bioinformatics. 14. PMID 23855714 DOI: 10.1186/1471-2105-14-224  1
2013 Nongonierma AB, Mooney C, Shields DC, FitzGerald RJ. Inhibition of dipeptidyl peptidase IV and xanthine oxidase by amino acids and dipeptides Food Chemistry. 141: 644-653. PMID 23768405 DOI: 10.1016/J.Foodchem.2013.02.115  1
2013 Pushker R, Mooney C, Davey NE, Jacqué JM, Shields DC. Marked variability in the extent of protein disorder within and between viral families. Plos One. 8: e60724. PMID 23620725 DOI: 10.1371/Journal.Pone.0060724  1
2013 Mooney C, Cessieux A, Shields DC, Pollastri G. SCL-Epred: a generalised de novo eukaryotic protein subcellular localisation predictor. Amino Acids. 45: 291-9. PMID 23568340 DOI: 10.1007/S00726-013-1491-3  1
2013 Mooney C, Haslam NJ, Holton TA, Pollastri G, Shields DC. PeptideLocator: prediction of bioactive peptides in protein sequences. Bioinformatics (Oxford, England). 29: 1120-6. PMID 23505299 DOI: 10.1093/Bioinformatics/Btt103  1
2013 O'Brien RP, Phelan PJ, Conroy J, O'Kelly P, Green A, Keogan M, O'Neill D, Jennings S, Traynor C, Casey J, McCormack M, Conroy R, Chubb A, Ennis S, Shields DC, et al. A genome-wide association study of recipient genotype and medium-term kidney allograft function. Clinical Transplantation. 27: 379-87. PMID 23432519 DOI: 10.1111/Ctr.12093  1
2012 Vijayakumar V, Guerrero AN, Davey N, Lebrilla CB, Shields DC, Khaldi N. EnzymePredictor: a tool for predicting and visualizing enzymatic cleavages of digested proteins. Journal of Proteome Research. 11: 6056-65. PMID 23098558 DOI: 10.1021/Pr300721F  1
2012 Asselbergs FW, Guo Y, van Iperen EP, Sivapalaratnam S, Tragante V, Lanktree MB, Lange LA, Almoguera B, Appelman YE, Barnard J, Baumert J, Beitelshees AL, Bhangale TR, Chen YD, Gaunt TR, ... ... Shields DC, et al. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci. American Journal of Human Genetics. 91: 823-38. PMID 23063622 DOI: 10.1016/J.Ajhg.2012.08.032  1
2012 Mooney C, Haslam NJ, Pollastri G, Shields DC. Towards the improved discovery and design of functional peptides: common features of diverse classes permit generalized prediction of bioactivity. Plos One. 7: e45012. PMID 23056189 DOI: 10.1371/Journal.Pone.0045012  1
2012 Haslam NJ, Shields DC. Peptide-binding domains: Are limp handshakes safest? Science Signaling. 5. PMID 23012652 DOI: 10.1126/Scisignal.2003372  1
2012 Davey NE, Cowan JL, Shields DC, Gibson TJ, Coldwell MJ, Edwards RJ. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions. Nucleic Acids Research. 40: 10628-41. PMID 22977176 DOI: 10.1093/Nar/Gks854  1
2012 Stavropoulos I, Khaldi N, Davey NE, O'Brien K, Martin F, Shields DC. Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins. Plos One. 7: e44389. PMID 22962613 DOI: 10.1371/Journal.Pone.0044389  1
2012 Sudol M, Shields DC, Farooq A. Structures of YAP protein domains reveal promising targets for development of new cancer drugs. Seminars in Cell & Developmental Biology. 23: 827-33. PMID 22609812 DOI: 10.1016/J.Semcdb.2012.05.002  1
2012 Haslam NJ, Shields DC. Profile-based short linear protein motif discovery Bmc Bioinformatics. 13. PMID 22607209 DOI: 10.1186/1471-2105-13-104  1
2012 Deshmukh HA, Colhoun HM, Johnson T, McKeigue PM, Betteridge DJ, Durrington PN, Fuller JH, Livingstone S, Charlton-Menys V, Neil A, Poulter N, Sever P, Shields DC, Stanton AV, Chatterjee A, et al. Genome-wide association study of genetic determinants of LDL-c response to atorvastatin therapy: importance of Lp(a). Journal of Lipid Research. 53: 1000-11. PMID 22368281 DOI: 10.1194/Jlr.P021113  1
2012 Lombardi F, De Chaumont C, Shields DC, Moran N. Platelet signalling networks: Pathway perturbation demonstrates differential sensitivity of ADP secretion and fibrinogen binding Platelets. 23: 17-25. PMID 22129436 DOI: 10.3109/09537104.2011.594190  1
2012 Rue-Albrecht K, Shields DC, Khaldi N. Correlation of disorder between S. cerevisiae interacting proteins Molecular Biosystems. 8: 417-425. PMID 22108582 DOI: 10.1039/C1Mb05214D  1
2012 Mooney C, Pollastri G, Shields DC, Haslam NJ. Prediction of short linear protein binding regions. Journal of Molecular Biology. 415: 193-204. PMID 22079048 DOI: 10.1016/J.Jmb.2011.10.025  1
2012 Casey JP, Magalhaes T, Conroy JM, Regan R, Shah N, Anney R, Shields DC, Abrahams BS, Almeida J, Bacchelli E, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, et al. A novel approach of homozygous haplotype sharing identifies candidate genes in autism spectrum disorder. Human Genetics. 131: 565-79. PMID 21996756 DOI: 10.1007/S00439-011-1094-6  1
2012 Edwards RJ, Davey NE, O'Brien K, Shields DC. Interactome-wide prediction of short, disordered protein interaction motifs in humans. Molecular Biosystems. 8: 282-95. PMID 21879107 DOI: 10.7490/F1000Research.1089989.1  1
2012 Norris R, Casey F, FitzGerald RJ, Shields D, Mooney C. Predictive modelling of angiotensin converting enzyme inhibitory dipeptides Food Chemistry. 133: 1349-1354. DOI: 10.1016/J.Foodchem.2012.02.023  1
2011 Johnson T, Gaunt TR, Newhouse SJ, Padmanabhan S, Tomaszewski M, Kumari M, Morris RW, Tzoulaki I, O'Brien ET, Poulter NR, Sever P, Shields DC, Thom S, Wannamethee SG, Whincup PH, et al. Blood pressure loci identified with a gene-centric array. American Journal of Human Genetics. 89: 688-700. PMID 22100073 DOI: 10.1016/J.Ajhg.2011.10.013  1
2011 Montanari F, Shields DC, Khaldi N. Differences in the number of intrinsically disordered regions between yeast duplicated proteins, and their relationship with functional divergence. Plos One. 6: e24989. PMID 21949823 DOI: 10.1371/Journal.Pone.0024989  1
2011 Khaldi N, Shields DC. Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species. Biology Direct. 6: 40. PMID 21801421 DOI: 10.1186/1745-6150-6-40  0.52
2011 Mooney C, Davey N, Martin AJ, Walsh I, Shields DC, Pollastri G. In silico protein motif discovery and structural analysis. Methods in Molecular Biology (Clifton, N.J.). 760: 341-53. PMID 21780007 DOI: 10.1007/978-1-61779-176-5_21  1
2011 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch 2.0: biological context for short linear motifs in proteins. Nucleic Acids Research. 39: W56-60. PMID 21622654 DOI: 10.1093/Nar/Gkr402  1
2011 Vangjeli C, Dicker P, Tregouet DA, Shields DC, Evans A, Stanton AV. A polymorphism in ACE2 is associated with a lower risk for fatal cardiovascular events in females: The MORGAM project Jraas - Journal of the Renin-Angiotensin-Aldosterone System. 12: 504-509. PMID 21490025 DOI: 10.1177/1470320311405557  1
2011 Duffy FJ, Verniere M, Devocelle M, Bernard E, Shields DC, Chubb AJ. CycloPs: Generating virtual libraries of cyclized and constrained peptides including nonnatural amino acids Journal of Chemical Information and Modeling. 51: 829-836. PMID 21434641 DOI: 10.1021/Ci100431R  1
2011 Alendé N, Nielsen JE, Shields DC, Khaldi N. Evolution of the isoelectric point of mammalian proteins as a consequence of indels and adaptive evolution. Proteins. 79: 1635-48. PMID 21387414 DOI: 10.1002/Prot.22990  1
2011 Casey F, Krogan N, Shields DC, Cagney G. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs Bmc Systems Biology. 5. DOI: 10.1186/1752-0509-5-133  1
2011 Khaldi N, Shields DC. Shift in the isoelectric-point of milk proteins as a consequence of adaptive divergence between the milks of mammalian species Biology Direct. 6. DOI: 10.1186/1745-6150-6-40  1
2010 Padmanabhan S, Melander O, Johnson T, Di Blasio AM, Lee WK, Gentilini D, Hastie CE, Menni C, Monti MC, Delles C, Laing S, Corso B, Navis G, Kwakernaak AJ, van der Harst P, ... ... Shields DC, et al. Genome-wide association study of blood pressure extremes identifies variant near UMOD associated with hypertension. Plos Genetics. 6: e1001177. PMID 21082022 DOI: 10.1371/journal.pgen.1001177  1
2010 Davey NE, Edwards RJ, Shields DC. Computational identification and analysis of protein short linear motifs. Frontiers in Bioscience (Landmark Edition). 15: 801-25. PMID 20515727 DOI: 10.2741/3647  1
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs. Nucleic Acids Research. 38: W534-9. PMID 20497999 DOI: 10.1093/Nar/Gkq440  1
2010 Maree AO, Vangjeli C, Jneid H, Ryan J, Cox D, Cannon CP, Shields DC, Fitzgerald DJ. G-protein β3 subunit polymorphism and bleeding in the orbofiban in patients with unstable coronary syndromes-thrombolysis in myocardial infarction 16 trial Journal of Thrombosis and Haemostasis. 8: 934-941. PMID 20096003 DOI: 10.1111/J.1538-7836.2010.03775.X  1
2010 Pushker R, Jacqué JM, Shields DC. Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression Journal of Virology. 84: 3644-3653. PMID 20071583 DOI: 10.1128/Jvi.01959-09  1
2010 Davey NE, Edwards RJ, Shields DC. Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. Bmc Bioinformatics. 11: 14. PMID 20055997 DOI: 10.1186/1471-2105-11-14  1
2010 Davey NE, Haslam NJ, Shields DC, Edwards RJ. SLiMSearch: A webserver for finding novel occurrences of short linear motifs in proteins, incorporating sequence context Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 6282: 50-61. DOI: 10.1007/978-3-642-16001-1_5  1
2009 Casey FP, Pihan E, Shields DC. Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization Journal of Chemical Information and Modeling. 49: 2708-2717. PMID 19994847 DOI: 10.1021/Ci900294X  1
2009 Talmud PJ, Drenos F, Shah S, Shah T, Palmen J, Verzilli C, Gaunt TR, Pallas J, Lovering R, Li K, Casas JP, Sofat R, Kumari M, Rodriguez S, Johnson T, ... ... Shields DC, et al. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. American Journal of Human Genetics. 85: 628-42. PMID 19913121 DOI: 10.1016/J.Ajhg.2009.10.014  1
2009 Bernard E, Parthasarathi L, Cho MK, Aylward K, Raab M, Daxecker H, O'Dushlaine CT, Shields DC, Devocelle M, Keyes T, Cosgrave L, O'Neill S, Mok KH, Moran N. Ligand switching in cell-permeable peptides: Manipulation of the α-integrin signature motif Acs Chemical Biology. 4: 457-471. PMID 19371094 DOI: 10.1021/Cb8002623  1
2009 Davey NE, Shields DC, Edwards RJ. Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery. Bioinformatics (Oxford, England). 25: 443-50. PMID 19136552 DOI: 10.1093/Bioinformatics/Btn664  1
2009 O'Halloran AM, Patterson CC, Horan P, Maree A, Curtin R, Stanton A, McKeown PP, Shields DC. Genetic polymorphisms in platelet-related proteins and coronary artery disease: Investigation of candidate genes, including N-acetylgalactosaminyltransferase 4 (GALNT4) and sulphotransferase 1A1/2 (SULT1A1/2) Journal of Thrombosis and Thrombolysis. 27: 175-184. PMID 18259693 DOI: 10.1007/S11239-008-0196-Z  1
2008 Parthasarathi L, Casey F, Stein A, Aloy P, Shields DC. Approved drug mimics of short peptide ligands from protein interaction motifs Journal of Chemical Information and Modeling. 48: 1943-1948. PMID 18826301 DOI: 10.1021/Ci800174C  1
2008 Casey FP, Cagney G, Krogan NJ, Shields DC. Optimal stepwise experimental design for pairwise functional interaction studies. Bioinformatics (Oxford, England). 24: 2733-9. PMID 18805797 DOI: 10.1093/Bioinformatics/Btn472  1
2008 Grisoni ML, Proust C, Alanne M, DeSuremain M, Salomaa V, Kuulasmaa K, Cambien F, Nicaud V, Stegmayr B, Virtamo J, Shields D, Kee F, Tiret L, Evans A, Tregouet DA. Haplotypic analysis of tag SNPs of the interleukin-18 gene in relation to cardiovascular disease events: The MORGAM Project European Journal of Human Genetics. 16: 1512-1520. PMID 18628791 DOI: 10.1038/Ejhg.2008.127  1
2008 Casey FP, Davey NE, Baran I, Varekova RS, Shields DC. Web server to identify similarity of amino acid motifs to compounds (SAAMCO). Journal of Chemical Information and Modeling. 48: 1524-9. PMID 18570372 DOI: 10.1021/Ci8000474  1
2008 O'Dushlaine CT, Shields DC. Marked variation in predicted and observed variability of tandem repeat loci across the human genome Bmc Genomics. 9. PMID 18416815 DOI: 10.1186/1471-2164-9-175  1
2008 Edwards RJ, Davey NE, Shields DC. CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics (Oxford, England). 24: 1307-9. PMID 18375965 DOI: 10.1093/Bioinformatics/Btn105  1
2008 Ryan AW, O'Brien E, Shields D, McManus R. Lack of association between NFKBIL1/LTA polymorphisms and hypertension, myocardial infarct, unstable angina and stable angina in a large Irish population sample Atherosclerosis. 197: 465-466. PMID 17485095 DOI: 10.1016/J.Atherosclerosis.2007.03.032  1
2008 Shields DC, Johnston CR, Wallace IM, Edwards RJ. Evolution of specificity and diversity Ancestral Sequence Reconstruction. DOI: 10.1093/acprof:oso/9780199299188.003.0019  1
2007 Lavin PJ, Laing ME, O'Kelly P, Moloney FJ, Gopinathan D, Aradi AA, Shields DC, Murphy GM, Conlon PJ. Improved renal allograft survival with vitamin D receptor polymorphism Renal Failure. 29: 785-789. PMID 17994444 DOI: 10.1080/08860220701540417  1
2007 Edwards RJ, Davey NE, Shields DC. SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. Plos One. 2: e967. PMID 17912346 DOI: 10.1371/Journal.Pone.0000967  1
2007 Laing ME, Dicker P, Moloney FJ, Ho WL, Murphy GM, Conlon P, Whitehead AS, Shields DC. Association of methylenetetrahydrofolate reductase polymorphism and the risk of squamous cell carcinoma in renal transplant patients. Transplantation. 84: 113-6. PMID 17627246 DOI: 10.1097/01.Tp.0000266069.41882.28  1
2007 Davey NE, Edwards RJ, Shields DC. The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Research. 35: W455-9. PMID 17576682 DOI: 10.1093/Nar/Gkm400  1
2007 Moore N, Dicker P, O'Brien JK, Stojanovic M, Conroy RM, Treumann A, O'Brien ET, Fitzgerald D, Shields D, Stanton AV. Renin gene polymorphisms and haplotypes, blood pressure, and responses to renin-angiotensin system inhibition Hypertension. 50: 340-347. PMID 17562974 DOI: 10.1161/Hypertensionaha.106.085563  1
2007 Iohom G, Ni Chonghaile M, O'Brien JK, Cunningham AJ, Fitzgerald DF, Shields DC. An investigation of potential genetic determinants of propofol requirements and recovery from anaesthesia European Journal of Anaesthesiology. 24: 912-919. PMID 17555608 DOI: 10.1017/S0265021507000476  1
2007 Baran I, Varekova RS, Parthasarathi L, Suchomel S, Casey F, Shields DC. Identification of potential small molecule peptidomimetics similar to motifs in proteins. Journal of Chemical Information and Modeling. 47: 464-74. PMID 17309247 DOI: 10.1021/Ci600404Q  1
2007 Edwards RJ, Moran N, Devocelle M, Kiernan A, Meade G, Signac W, Foy M, Park SD, Dunne E, Kenny D, Shields DC. Bioinformatic discovery of novel bioactive peptides. Nature Chemical Biology. 3: 108-12. PMID 17220901 DOI: 10.1038/Nchembio854  1
2007 Johnston CR, O'Dushlaine C, Fitzpatrick DA, Edwards RJ, Shields DC. Evaluation of whether accelerated protein evolution in chordates has occurred before, after, or simultaneously with gene duplication. Molecular Biology and Evolution. 24: 315-23. PMID 17065596 DOI: 10.1093/Molbev/Msl162  1
2006 O'Dushlaine CT, Shields DC. Tools for the identification of variable and potentially variable tandem repeats. Bmc Genomics. 7: 290. PMID 17107618 DOI: 10.1186/1471-2164-7-290  1
2006 O'Halloran AM, Stanton A, O'Brien E, Shields DC. The impact on coronary artery disease of common polymorphisms known to modulate responses to pathogens. Annals of Human Genetics. 70: 934-45. PMID 17044867 DOI: 10.1111/J.1469-1809.2006.00281.X  1
2006 Parthasarathi L, Devocelle M, Søndergaard C, Baran I, O'Dushlaine CT, Davey NE, Edwards RJ, Moran N, Kenny D, Shields DC. Absolute net charge and the biological activity of oligopeptides. Journal of Chemical Information and Modeling. 46: 2183-90. PMID 16995748 DOI: 10.1021/Ci0600760  1
2006 Moran N, Kiernan A, Dunne E, Edwards RJ, Shields DC, Kenny D. Monitoring modulators of platelet aggregation in a microtiter plate assay. Analytical Biochemistry. 357: 77-84. PMID 16920064 DOI: 10.1016/J.Ab.2006.06.037  1
2006 Davey NE, Shields DC, Edwards RJ. SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Research. 34: 3546-54. PMID 16855291 DOI: 10.1093/Nar/Gkl486  1
2006 Moloney FJ, Dicker P, Conlon PJ, Shields DC, Murphy GM. The frequency and significance of thiopurine S-methyltransferase gene polymorphisms in azathioprine-treated renal transplant recipients. The British Journal of Dermatology. 154: 1199-200. PMID 16704656 DOI: 10.1111/J.1365-2133.2006.07239.X  1
2006 Hillmann AG, Harmon S, Park SD, O'brien J, Shields DC, Kenny D. Comparative RNA expression analyses from small-scale, single-donor platelet samples. Journal of Thrombosis and Haemostasis : Jth. 4: 349-56. PMID 16420564 DOI: 10.1111/J.1538-7836.2006.01684.X  1
2006 O'Halloran AM, Curtin R, O'Connor F, Dooley M, Fitzgerald A, O'Brien JK, Fitzgerald DJ, Shields DC. The impact of genetic variation in the region of the GPIIIa gene, on Pl expression bias and GPIIb/IIIa receptor density in platelets. British Journal of Haematology. 132: 494-502. PMID 16412022 DOI: 10.1111/J.1365-2141.2005.05897.X  1
2005 Hawi Z, Segurado R, Conroy J, Sheehan K, Lowe N, Kirley A, Shields D, Fitzgerald M, Gallagher L, Gill M. Preferential transmission of paternal alleles at risk genes in attention-deficit/hyperactivity disorder American Journal of Human Genetics. 77: 958-965. PMID 16380908 DOI: 10.1086/498174  1
2005 Dolan C, Shields DC, Stanton A, O'Brien E, Lambert DM, O'Brien JK, Treacy EP. Polymorphisms of the Flavin containing monooxygenase 3 (FMO3) gene do not predispose to essential hypertension in Caucasians. Bmc Medical Genetics. 6: 41. PMID 16324215 DOI: 10.1186/1471-2350-6-41  1
2005 Cagney G, Park S, Chung C, Tong B, O'Dushlaine C, Shields DC, Emili A. Human tissue profiling with multidimensional protein identification technology. Journal of Proteome Research. 4: 1757-67. PMID 16212430 DOI: 10.1021/Pr0500354  1
2005 Edwards RJ, Shields DC. BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinformatics (Oxford, England). 21: 4190-1. PMID 16159912 DOI: 10.1093/Bioinformatics/Bti678  1
2005 Maree AO, Curtin RJ, Chubb A, Dolan C, Cox D, O'Brien J, Crean P, Shields DC, Fitzgerald DJ. Cyclooxygenase-1 haplotype modulates platelet response to aspirin. Journal of Thrombosis and Haemostasis : Jth. 3: 2340-5. PMID 16150050 DOI: 10.1111/J.1538-7836.2005.01555.X  1
2005 O'Dushlaine CT, Edwards RJ, Park SD, Shields DC. Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biology. 6: R69. PMID 16086851 DOI: 10.1186/Gb-2005-6-8-R69  1
2005 Johnston CR, Shields DC. A sequence sub-sampling algorithm increases the power to detect distant homologues. Nucleic Acids Research. 33: 3772-8. PMID 16006623 DOI: 10.1093/Nar/Gki687  1
2005 Dolan C, O'Halloran A, Bradley DG, Croke DT, Evans A, O'Brien JK, Dicker P, Shields DC. Genetic stratification of pathogen-response-related and other variants within a homogeneous Caucasian Irish population. European Journal of Human Genetics : Ejhg. 13: 798-806. PMID 15785776 DOI: 10.1038/Sj.Ejhg.5201382  1
2005 Kelly H, Ennis S, Yoneda A, Bermingham C, Shields DC, Molony C, Green AJ, Puri P, Barton DE. Uroplakin III is not a major candidate gene for primary vesicoureteral reflux. European Journal of Human Genetics : Ejhg. 13: 500-2. PMID 15523493 DOI: 10.1038/Sj.Ejhg.5201322  1
2005 Molony CM, Fitzgerald AP, Shields DC. Overdispersion of allele frequency differences between populations: implications for meta-analyses of genotypic disease associations. European Journal of Human Genetics : Ejhg. 13: 79-85. PMID 15470368 DOI: 10.1038/Sj.Ejhg.5201275  1
2004 Edwards RJ, Shields DC. GASP: Gapped Ancestral Sequence Prediction for proteins. Bmc Bioinformatics. 5: 123. PMID 15350199 DOI: 10.1186/1471-2105-5-123  1
2004 Byrne CE, Fitzgerald A, Cannon CP, Fitzgerald DJ, Shields DC. Elevated white cell count in acute coronary syndromes: relationship to variants in inflammatory and thrombotic genes. Bmc Medical Genetics. 5: 13. PMID 15171792 DOI: 10.1186/1471-2350-5-13  1
2004 McRedmond JP, Park SD, Reilly DF, Coppinger JA, Maguire PB, Shields DC, Fitzgerald DJ. Integration of proteomics and genomics in platelets: a profile of platelet proteins and platelet-specific genes. Molecular & Cellular Proteomics : McP. 3: 133-44. PMID 14645502 DOI: 10.1074/Mcp.M300063-Mcp200  1
2003 Martin K, Meade G, Moran N, Shields DC, Kenny D. A palmitylated peptide derived from the glycoprotein Ib beta cytoplasmic tail inhibits platelet activation. Journal of Thrombosis and Haemostasis : Jth. 1: 2643-52. PMID 14675101 DOI: 10.1046/J.1538-7836.2003.00478.X  1
2003 Shields DC. Molecular evolution of CXC chemokines and receptors. Trends in Immunology. 24: 355; author reply 35. PMID 12860523 DOI: 10.1016/S1471-4906(03)00138-8  1
2003 Seoighe C, Johnston CR, Shields DC. Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation. Molecular Biology and Evolution. 20: 484-90. PMID 12654935 DOI: 10.1093/Molbev/Msg059  1
2003 Hokamp K, Shields DC, Wolfe KH, Caffrey DR. Wrapping up BLAST and other applications for use on Unix clusters. Bioinformatics (Oxford, England). 19: 441-2. PMID 12584141 DOI: 10.1093/Bioinformatics/Btg007  1
2002 Shields DC, O'Halloran AM. Integrating genotypic data with transcriptomic and proteomic data. Comparative and Functional Genomics. 3: 22-7. PMID 18628875 DOI: 10.1002/Cfg.135  1
2002 Muckian C, Fitzgerald A, O'Neill A, O'Byrne A, Fitzgerald DJ, Shields DC. Genetic variability in the extracellular matrix as a determinant of cardiovascular risk: association of type III collagen COL3A1 polymorphisms with coronary artery disease. Blood. 100: 1220-3. PMID 12149201 DOI: 10.1182/Blood-2002-01-0283  1
2002 Shields DC, Fitzgerald AP, O'Neill PA, Muckian C, Kenny D, Moran B, Cannon CP, Byrne CE, Fitzgerald DJ. The contribution of genetic factors to thrombotic and bleeding outcomes in coronary patients randomised to IIb/IIIa antagonists. The Pharmacogenomics Journal. 2: 182-90. PMID 12082590 DOI: 10.1038/Sj.Tpj.6500100  1
2002 Kenny D, Muckian C, Fitzgerald DJ, Cannon CP, Shields DC. Platelet glycoprotein Ib alpha receptor polymorphisms and recurrent ischaemic events in acute coronary syndrome patients. Journal of Thrombosis and Thrombolysis. 13: 13-9. PMID 11994555 DOI: 10.1023/A:1015307823578  1
2002 Cotter PJ, Caffrey DR, Shields DC. Improved database searches for orthologous sequences by conditioning on outgroup sequences. Bioinformatics (Oxford, England). 18: 83-91. PMID 11836215 DOI: 10.1093/Bioinformatics/18.1.83  1
2001 O'Connor FF, Shields DC, Fitzgerald A, Cannon CP, Braunwald E, Fitzgerald DJ. Genetic variation in glycoprotein IIb/IIIa (GPIIb/IIIa) as a determinant of the responses to an oral GPIIb/IIIa antagonist in patients with unstable coronary syndromes. Blood. 98: 3256-60. PMID 11719362 DOI: 10.1182/Blood.V98.12.3256  1
2001 Murphy VE, Mynett-Johnson LA, Claffey E, Shields DC, McKeon P. No association between 5HT-2A and bipolar disorder irrespective of genomic imprinting. American Journal of Medical Genetics. 105: 422-5. PMID 11449393 DOI: 10.1002/Ajmg.1435  1
2001 Cahill M, Karabatzaki M, Donoghue C, Meleady R, Mynett-Johnson LA, Mooney D, Graham IM, Whitehead AS, Shields DC. Thermolabile MTHFR genotype and retinal vascular occlusive disease. The British Journal of Ophthalmology. 85: 88-90. PMID 11133719 DOI: 10.1136/Bjo.85.1.88  1
2000 Malcuit I, de Jong W, Baulcombe DC, Shields DC, Kavanagh TA. Acquisition of multiple virulence/avirulence determinants by potato virus X (PVX) has occurred through convergent evolution rather than through recombination. Virus Genes. 20: 165-72. PMID 10872879 DOI: 10.1023/A:1008178800366  1
2000 Shields DC, Ramsbottom D, Donoghue C, Pinjon E, Kirke PN, Molloy AM, Edwards YH, Mills JL, Mynett-Johnson L, Weir DG, Scott JM, Whitehead AS. Association between historically high frequencies of neural tube defects and the human T homologue of mouse T (Brachyury). American Journal of Medical Genetics. 92: 206-11. PMID 10817656 DOI: 10.1002/(Sici)1096-8628(20000529)92:3<206::Aid-Ajmg9>3.0.Co;2-W  1
2000 Caffrey DR, O'Neill LA, Shields DC. A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. Protein Science : a Publication of the Protein Society. 9: 655-70. PMID 10794408 DOI: 10.1110/Ps.9.4.655  1
2000 Shields DC. Gene conversion among chemokine receptors Gene. 246: 239-245. PMID 10767545 DOI: 10.1016/S0378-1119(00)00072-X  1
2000 Muckian C, Hillmann A, Kenny D, Shields DC. A novel variant of the platelet glycoprotein Ibα macroglycopeptide region lacks any copies of the 'Perfect' 13 amino acid repeat Thrombosis and Haemostasis. 83: 513-514. PMID 10744166 DOI: 10.1055/S-0037-1613849  1
2000 O'Connor FF, Shields DC, Fitzgerald DJ. Factor v leiden and thermolabile mthfr and the response to the oral glycoprotein (gp) hbmiia antagonist orbofiban in acute coronary syndromes Blood. 96: 53a.  1
2000 Hillmann A, Shields DC, Fitzgerald DJ, Kenny D. Polymorphisms in glycoprotein (GP) 1b alpha are not associated with adverse outcomes in primigravidae Journal of Obstetrics and Gynaecology. 20: 250-255.  1
1999 Caffrey DR, O'Neill LAJ, Shields DC. The evolution of the map kinase pathways: Coduplication of interacting proteins leads to new signaling cascades Journal of Molecular Evolution. 49: 567-582. PMID 10552038 DOI: 10.1007/Pl00006578  1
1999 Harmon DL, Shields DC, Woodside JV, McMaster D, Yarnell JWG, Young IS, Peng K, Shane B, Evans AE, Whitehead AS. Methionine synthase D919G polymorphism is a significant but modest determinant of circulating homocysteine concentrations Genetic Epidemiology. 17: 298-309. PMID 10520212 DOI: 10.1002/(Sici)1098-2272(199911)17:4<298::Aid-Gepi5>3.0.Co;2-V  1
1999 Shields DC, Kirke PN, Mills JL, Ramsbottom D, Molloy AM, Burke H, Weir DG, Scott JM, Whitehead AS. The "thermolabile" variant of methylenetetrahydrofolate reductase and neural tube defects: An evaluation of genetic risk and the relative importance of the genotypes of the embryo and the mother. American Journal of Human Genetics. 64: 1045-55. PMID 10090889 DOI: 10.1086/302310  1
1999 Harmon DL, Doyle RM, Meleady R, Doyle M, Shields DC, Barry R, Coakley D, Graham IM, Whitehead AS. Genetic analysis of the thermolabile variant of 5,10- methylenetetrahydrofolate reductase as a risk factor for ischemic stroke Arteriosclerosis, Thrombosis, and Vascular Biology. 19: 208-211. PMID 9974399 DOI: 10.1161/01.Atv.19.2.208  1
1998 Mynett-Johnson LA, Murphy VE, Claffey E, Shields DC, McKeon P. Preliminary evidence of an association between bipolar disorder in females and the catechol-O-methyltransferase gene Psychiatric Genetics. 8: 221-225. PMID 9861640  1
1998 Mynett-Johnson L, Murphy V, McCormack J, Shields DC, Claffey E, Manley P, McKeon P. Evidence for an allelic association between bipolar disorder and a Na+, K+ adenosine triphosphatase alpha subunit gene (ATP1A3) Biological Psychiatry. 44: 47-51. PMID 9646882 DOI: 10.1016/S0006-3223(97)00343-0  1
1997 Mynett-Johnson LA, Murphy VE, Manley P, Shields DC, McKeon P. Lack of evidence for a major locus for bipolar disorder in the pericentromeric region of chromosome 18 in Irish pedigrees Biological Psychiatry. 42: 486-494. PMID 9285084 DOI: 10.1016/S0006-3223(96)00427-1  1
1997 Harmon DL, McMaster D, McCluskey DR, Shields DC, Whitehead AS. A common genetic variant affecting folate metabolism is not over-represented in chronic fatigue syndrome Annals of Clinical Biochemistry. 34: 427-429. PMID 9247678 DOI: 10.1177/000456329703400416  1
1997 Wolfe KH, Shields DC. Molecular evidence for an ancient duplication of the entire yeast genome. Nature. 387: 708-13. PMID 9192896 DOI: 10.1038/42711  1
1997 Harmon DL, McMaster D, Shields DC, Whitehead AS, Rea IM. MTHFR thermolabile genotype frequencies and longevity in Northern Ireland Atherosclerosis. 131: 137-138. PMID 9180255 DOI: 10.1016/S0021-9150(97)06096-6  1
1997 Shields DC, Wolfe KH. Accelerated evolution of sites undergoing mRNA editing in plant mitochondria and chloroplasts. Molecular Biology and Evolution. 14: 344-9. PMID 9066800 DOI: 10.1093/Oxfordjournals.Molbev.A025768  1
1997 Jensen LE, Hiney MP, Shields DC, Uhlar CM, Lindsay AJ, Whitehead AS. Acute Phase Proteins in Salmonids: Evolutionary Analyses and Acute Phase Response Journal of Immunology. 158: 384-392. PMID 8977214  1
1996 Shields DC, Butler A, Mosurski KR, Walsh MT, Whitehead AS. Mapping genes within a YAC by computer-assisted interpretation of partial restriction digestions Nucleic Acids Research. 24: 4495-4500. PMID 8948640 DOI: 10.1093/Nar/24.22.4495  1
1996 Gallagher PM, Meleady R, Shields DC, Tan KS, McMaster D, Rozen R, Evans A, Graham IM, Whitehead AS. Homocysteine and risk of premature coronary heart disease: Evidence for a common gene mutation Circulation. 94: 2154-2158. PMID 8901666 DOI: 10.1161/01.Cir.94.9.2154  1
1996 De Roux N, Shields DC, Misrahi M, Ratanachaiyavong S, McGregor AM, Milgrom E. Analysis of the thyrotropin receptor as a candidate gene in familial Graves' disease Journal of Clinical Endocrinology and Metabolism. 81: 3483-3486. PMID 8855789 DOI: 10.1210/Jcem.81.10.8855789  1
1996 Uhlar CM, Black IL, Shields DC, Brack CM, Schreiber G, Whitehead AS. Wallaby serum amyloid A protein: cDNA cloning, sequence and evolutionary analysis Scandinavian Journal of Immunology. 43: 271-276. PMID 8602460 DOI: 10.1046/J.1365-3083.1996.D01-34.X  1
1996 Shields DC, Harmon DL, Whitehead AS. Evolution of hemopoietic ligands and their receptors: Influence of positive selection on correlated replacements throughout ligand and receptor proteins Journal of Immunology. 156: 1062-1070. PMID 8557980  1
1995 Houlston RS, Collins A, Kee F, Collins BJ, Shields DC, Morton NE. Segregation analysis of colorectal cancer in Northern Ireland Human Heredity. 45: 41-48. PMID 7896299 DOI: 10.1159/000154253  1
1995 Shields DC, McDevitt D, Foster TJ. Evidence against concerted evolution in a tandem array in the clumping factor gene of Staphylococcus aureus Molecular Biology and Evolution. 12: 963-965. PMID 7476144 DOI: 10.1093/Oxfordjournals.Molbev.A040275  1
1994 Attwood J, Chiano M, Collins A, Donis-Keller H, Dracopoli N, Fountain J, Falk C, Goudie D, Gusella J, Haines J, Armour JAL, Jeffreys AJ, Kwiatkowski D, Lathrop M, Matise T, ... ... Shields D, et al. CEPH Consortium Map of Chromosome 9 Genomics. 19: 203-214. PMID 8188250 DOI: 10.1006/Geno.1994.1049  1
1992 Shields DC, Higgins DG, Sharp PM. GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Computer Applications in the Biosciences : Cabios. 8: 521-3. PMID 1422886 DOI: 10.1093/Bioinformatics/8.5.521  1
1990 Sharp PM, Higgins DG, Shields DC, Devine KM, Hoch JA. Bacillus Subtilis Gene Sequences Genetics and Biotechnology of Bacilli. 89-98. DOI: 10.1016/B978-0-12-274162-3.50013-X  1
1989 Sharp PM, Shields DC, Wolfe KH, Li WH. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science (New York, N.Y.). 246: 808-10. PMID 2683084 DOI: 10.1126/Science.2683084  1
1989 Shields DC, Sharp PM. Evidence that mutation patterns vary among Drosophila transposable elements. Journal of Molecular Biology. 207: 843-6. PMID 2547975 DOI: 10.1016/0022-2836(89)90252-0  1
1988 Shields DC, Sharp PM, Higgins DG, Wright F. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution. 5: 704-16. PMID 3146682 DOI: 10.1093/Oxfordjournals.Molbev.A040525  1
1988 Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Research. 16: 8207-11. PMID 3138659 DOI: 10.1093/Nar/16.17.8207  1
1987 Shields DC, Sharp PM. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Research. 15: 8023-40. PMID 3118331 DOI: 10.1093/Nar/15.19.8023  1
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