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Items: 42

1.

Synthetic Biology Open Language (SBOL) Version 2.3.

Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, Pocock M, Samineni M, Scott-Brown J, Tarter Y, Zhang M, Zhang Z, Zundel Z, Beal J, Bissell M, Clancy K, Gennari JH, Misirli G, Myers C, Oberortner E, Sauro H, Wipat A.

J Integr Bioinform. 2019 Jun 13. pii: /j/jib.ahead-of-print/jib-2019-0025/jib-2019-0025.xml. doi: 10.1515/jib-2019-0025. [Epub ahead of print]

PMID:
31199770
2.

SBOL-OWL: An Ontological Approach for Formal and Semantic Representation of Synthetic Biology Information.

Mısırlı G, Taylor R, Goñi-Moreno A, McLaughlin JA, Myers C, Gennari JH, Lord P, Wipat A.

ACS Synth Biol. 2019 Jul 19;8(7):1498-1514. doi: 10.1021/acssynbio.8b00532. Epub 2019 May 14.

PMID:
31059645
3.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087.

4.

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.

Waites W, Mısırlı G, Cavaliere M, Danos V, Wipat A.

ACS Synth Biol. 2018 Dec 21;7(12):2812-2823. doi: 10.1021/acssynbio.8b00201. Epub 2018 Nov 20.

5.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

Misirli G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones TS, Densmore D, Myers C, Wipat A.

ACS Synth Biol. 2019 Jul 19;8(7):1548-1559. doi: 10.1021/acssynbio.7b00459. Epub 2018 Jun 5.

PMID:
29782151
6.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2018 Apr 2;15(1). pii: /j/jib.2018.15.issue-1/jib-2018-0001/jib-2018-0001.xml. doi: 10.1515/jib-2018-0001.

7.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A.

ACS Synth Biol. 2018 Feb 16;7(2):682-688. doi: 10.1021/acssynbio.7b00403. Epub 2018 Jan 30.

PMID:
29316788
8.

A standard-enabled workflow for synthetic biology.

Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Mısırlı G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z.

Biochem Soc Trans. 2017 Jun 15;45(3):793-803. doi: 10.1042/BST20160347. Review.

PMID:
28620041
9.

Synthetic Biology Open Language (SBOL) Version 2.1.0.

Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari J, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2016 Dec 18;13(3):291. doi: 10.2390/biecoll-jib-2016-291.

PMID:
28187407
10.

Data Integration and Mining for Synthetic Biology Design.

Mısırlı G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A.

ACS Synth Biol. 2016 Oct 21;5(10):1086-1097. Epub 2016 Jun 20.

11.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Madsen C, McLaughlin JA, Mısırlı G, Pocock M, Flanagan K, Hallinan J, Wipat A.

ACS Synth Biol. 2016 Jun 17;5(6):487-97. doi: 10.1021/acssynbio.5b00210. Epub 2016 Jun 8.

12.

Sharing Structure and Function in Biological Design with SBOL 2.0.

Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ.

ACS Synth Biol. 2016 Jun 17;5(6):498-506. doi: 10.1021/acssynbio.5b00215. Epub 2016 May 4.

PMID:
27111421
13.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

McLaughlin JA, Pocock M, Mısırlı G, Madsen C, Wipat A.

ACS Synth Biol. 2016 Aug 19;5(8):874-6. doi: 10.1021/acssynbio.5b00244. Epub 2016 Feb 9.

PMID:
26808703
14.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A.

Bioinformatics. 2016 Mar 15;32(6):908-17. doi: 10.1093/bioinformatics/btv660. Epub 2015 Nov 11.

15.

Synthetic Biology Open Language (SBOL) Version 2.0.0.

Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H.

J Integr Bioinform. 2015 Sep 4;12(2):272. doi: 10.2390/biecoll-jib-2015-272.

PMID:
26528570
16.

Estimating the chance of success in IVF treatment using a ranking algorithm.

Güvenir HA, Misirli G, Dilbaz S, Ozdegirmenci O, Demir B, Dilbaz B.

Med Biol Eng Comput. 2015 Sep;53(9):911-20. doi: 10.1007/s11517-015-1299-2. Epub 2015 Apr 17.

17.

The synthetic biology open language.

Myers C, Clancy K, Misirli G, Oberortner E, Pocock M, Quinn J, Roehner N, Sauro HM.

Methods Mol Biol. 2015;1244:323-36. doi: 10.1007/978-1-4939-1878-2_16.

PMID:
25487105
18.

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.

Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A.

J Integr Bioinform. 2014 Jul 8;11(2):244. doi: 10.2390/biecoll-jib-2014-244.

PMID:
25001169
19.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM.

Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6.

PMID:
24911500
20.

Proposed data model for the next version of the synthetic biology open language.

Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ.

ACS Synth Biol. 2015 Jan 16;4(1):57-71. doi: 10.1021/sb500176h. Epub 2014 Jun 16.

PMID:
24896221
21.

Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins.

Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM.

Proteomics. 2013 Nov;13(22):3298-308. doi: 10.1002/pmic.201300183. Epub 2013 Oct 27.

PMID:
24115457
22.

The authors reply.

Misirli G, Benetou V, Lagiou P, Bamia C, Trichopoulos D, Trichopoulou A.

Am J Epidemiol. 2013 Aug 15;178(4):661-2. No abstract available.

PMID:
24073441
23.

BacillOndex: an integrated data resource for systems and synthetic biology.

Misirli G, Wipat A, Mullen J, James K, Pocock M, Smith W, Allenby N, Hallinan JS.

J Integr Bioinform. 2013 Apr 10;10(2):224. doi: 10.2390/biecoll-jib-2013-224.

PMID:
23571273
24.

Relation of the traditional Mediterranean diet to cerebrovascular disease in a Mediterranean population.

Misirli G, Benetou V, Lagiou P, Bamia C, Trichopoulos D, Trichopoulou A.

Am J Epidemiol. 2012 Dec 15;176(12):1185-92. doi: 10.1093/aje/kws205. Epub 2012 Nov 27.

PMID:
23186748
25.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion.

Misirli G, Hallinan JS, Yu T, Lawson JR, Wimalaratne SM, Cooling MT, Wipat A.

Bioinformatics. 2011 Apr 1;27(7):973-9. doi: 10.1093/bioinformatics/btr048. Epub 2011 Feb 4.

26.

Fruit and vegetable intake and mortality from ischaemic heart disease: results from the European Prospective Investigation into Cancer and Nutrition (EPIC)-Heart study.

Crowe FL, Roddam AW, Key TJ, Appleby PN, Overvad K, Jakobsen MU, Tjønneland A, Hansen L, Boeing H, Weikert C, Linseisen J, Kaaks R, Trichopoulou A, Misirli G, Lagiou P, Sacerdote C, Pala V, Palli D, Tumino R, Panico S, Bueno-de-Mesquita HB, Boer J, van Gils CH, Beulens JW, Barricarte A, Rodríguez L, Larrañaga N, Sánchez MJ, Tormo MJ, Buckland G, Lund E, Hedblad B, Melander O, Jansson JH, Wennberg P, Wareham NJ, Slimani N, Romieu I, Jenab M, Danesh J, Gallo V, Norat T, Riboli E; European Prospective Investigation into Cancer and Nutrition (EPIC)-Heart Study Collaborators.

Eur Heart J. 2011 May;32(10):1235-43. doi: 10.1093/eurheartj/ehq465. Epub 2011 Jan 18.

27.

Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits.

Hallinan JS, Misirli G, Wipat A.

Conf Proc IEEE Eng Med Biol Soc. 2010;2010:768-74. doi: 10.1109/IEMBS.2010.5626353.

PMID:
21095906
28.

Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A.

Bioinformatics. 2010 Apr 1;26(7):925-31. doi: 10.1093/bioinformatics/btq063. Epub 2010 Feb 16.

PMID:
20160009
29.

Risk factors and drug interactions predisposing to statin-induced myopathy: implications for risk assessment, prevention and treatment.

Chatzizisis YS, Koskinas KC, Misirli G, Vaklavas C, Hatzitolios A, Giannoglou GD.

Drug Saf. 2010 Mar 1;33(3):171-87. doi: 10.2165/11319380-000000000-00000. Review.

PMID:
20158283
30.

Association between pre-diagnostic circulating vitamin D concentration and risk of colorectal cancer in European populations:a nested case-control study.

Jenab M, Bueno-de-Mesquita HB, Ferrari P, van Duijnhoven FJ, Norat T, Pischon T, Jansen EH, Slimani N, Byrnes G, Rinaldi S, Tjønneland A, Olsen A, Overvad K, Boutron-Ruault MC, Clavel-Chapelon F, Morois S, Kaaks R, Linseisen J, Boeing H, Bergmann MM, Trichopoulou A, Misirli G, Trichopoulos D, Berrino F, Vineis P, Panico S, Palli D, Tumino R, Ros MM, van Gils CH, Peeters PH, Brustad M, Lund E, Tormo MJ, Ardanaz E, Rodríguez L, Sánchez MJ, Dorronsoro M, Gonzalez CA, Hallmans G, Palmqvist R, Roddam A, Key TJ, Khaw KT, Autier P, Hainaut P, Riboli E.

BMJ. 2010 Jan 21;340:b5500. doi: 10.1136/bmj.b5500.

31.

Dietary fat intake in the European Prospective Investigation into Cancer and Nutrition: results from the 24-h dietary recalls.

Linseisen J, Welch AA, Ocké M, Amiano P, Agnoli C, Ferrari P, Sonestedt E, Chajès V, Bueno-de-Mesquita HB, Kaaks R, Weikert C, Dorronsoro M, Rodríguez L, Ermini I, Mattiello A, van der Schouw YT, Manjer J, Nilsson S, Jenab M, Lund E, Brustad M, Halkjaer J, Jakobsen MU, Khaw KT, Crowe F, Georgila C, Misirli G, Niravong M, Touvier M, Bingham S, Riboli E, Slimani N.

Eur J Clin Nutr. 2009 Nov;63 Suppl 4:S61-80. doi: 10.1038/ejcn.2009.75.

PMID:
19888281
32.

Intake of total, animal and plant proteins, and their food sources in 10 countries in the European Prospective Investigation into Cancer and Nutrition.

Halkjaer J, Olsen A, Bjerregaard LJ, Deharveng G, Tjønneland A, Welch AA, Crowe FL, Wirfält E, Hellstrom V, Niravong M, Touvier M, Linseisen J, Steffen A, Ocké MC, Peeters PH, Chirlaque MD, Larrañaga N, Ferrari P, Contiero P, Frasca G, Engeset D, Lund E, Misirli G, Kosti M, Riboli E, Slimani N, Bingham S.

Eur J Clin Nutr. 2009 Nov;63 Suppl 4:S16-36. doi: 10.1038/ejcn.2009.73.

PMID:
19888272
33.

Anthropometry and esophageal cancer risk in the European prospective investigation into cancer and nutrition.

Steffen A, Schulze MB, Pischon T, Dietrich T, Molina E, Chirlaque MD, Barricarte A, Amiano P, Quirós JR, Tumino R, Mattiello A, Palli D, Vineis P, Agnoli C, Misirli G, Boffetta P, Kaaks R, Rohrmann S, Bueno-de-Mesquita HB, Peeters PH, May AM, Spencer EA, Allen NE, Bingham S, Tjønneland A, Halkjaer J, Overvad K, Stegger J, Manjer J, Lindkvist B, Hallmanns G, Stenling R, Lund E, Riboli E, Gonzalez CA, Boeing H.

Cancer Epidemiol Biomarkers Prev. 2009 Jul;18(7):2079-89. doi: 10.1158/1055-9965.EPI-09-0265. Epub 2009 Jun 30.

34.

Physical activity and risk of prostate cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort.

Johnsen NF, Tjønneland A, Thomsen BL, Christensen J, Loft S, Friedenreich C, Key TJ, Allen NE, Lahmann PH, Mejlvig L, Overvad K, Kaaks R, Rohrmann S, Boing H, Misirli G, Trichopoulou A, Zylis D, Tumino R, Pala V, Bueno-de-Mesquita HB, Kiemeney LA, Suárez LR, Gonzalez CA, Sánchez MJ, Huerta JM, Gurrea AB, Manjer J, Wirfält E, Khaw KT, Wareham N, Boffetta P, Egevad L, Rinaldi S, Riboli E.

Int J Cancer. 2009 Aug 15;125(4):902-8. doi: 10.1002/ijc.24326.

35.

Fruit, vegetables, and colorectal cancer risk: the European Prospective Investigation into Cancer and Nutrition.

van Duijnhoven FJ, Bueno-De-Mesquita HB, Ferrari P, Jenab M, Boshuizen HC, Ros MM, Casagrande C, Tjønneland A, Olsen A, Overvad K, Thorlacius-Ussing O, Clavel-Chapelon F, Boutron-Ruault MC, Morois S, Kaaks R, Linseisen J, Boeing H, Nöthlings U, Trichopoulou A, Trichopoulos D, Misirli G, Palli D, Sieri S, Panico S, Tumino R, Vineis P, Peeters PH, van Gils CH, Ocké MC, Lund E, Engeset D, Skeie G, Suárez LR, González CA, Sánchez MJ, Dorronsoro M, Navarro C, Barricarte A, Berglund G, Manjer J, Hallmans G, Palmqvist R, Bingham SA, Khaw KT, Key TJ, Allen NE, Boffetta P, Slimani N, Rinaldi S, Gallo V, Norat T, Riboli E.

Am J Clin Nutr. 2009 May;89(5):1441-52. doi: 10.3945/ajcn.2008.27120. Epub 2009 Apr 1.

PMID:
19339391
36.

Lifestyle factors and serum androgens among 636 middle aged men from seven countries in the European Prospective Investigation into Cancer and Nutrition (EPIC).

Suzuki R, Allen NE, Appleby PN, Key TJ, Dossus L, Tjønneland A, Føns Johnsen N, Overvad K, Sacerdote C, Palli D, Krogh V, Tumino R, Rohrmann S, Linseisen J, Boeing H, Trichopoulou A, Makrygiannis G, Misirli G, Bueno-de-Mesquita HB, May AM, Díaz MJ, Sánchez MJ, Barricarte Gurrea A, Rodríguez Suárez L, Buckland G, Larrañaga N, Bingham S, Khaw KT, Rinaldi S, Slimani N, Jenab M, Riboli E, Kaaks R.

Cancer Causes Control. 2009 Aug;20(6):811-21. doi: 10.1007/s10552-009-9326-y. Epub 2009 Mar 21. Erratum in: Cancer Causes Control. 2009 Aug;20(6):823-4.

PMID:
19306067
37.

Ethanol intake and the risk of pancreatic cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC).

Rohrmann S, Linseisen J, Vrieling A, Boffetta P, Stolzenberg-Solomon RZ, Lowenfels AB, Jensen MK, Overvad K, Olsen A, Tjonneland A, Boutron-Ruault MC, Clavel-Chapelon F, Fagherazzi G, Misirli G, Lagiou P, Trichopoulou A, Kaaks R, Bergmann MM, Boeing H, Bingham S, Khaw KT, Allen N, Roddam A, Palli D, Pala V, Panico S, Tumino R, Vineis P, Peeters PH, Hjartåker A, Lund E, Redondo Cornejo ML, Agudo A, Arriola L, Sánchez MJ, Tormo MJ, Barricarte Gurrea A, Lindkvist B, Manjer J, Johansson I, Ye W, Slimani N, Duell EJ, Jenab M, Michaud DS, Mouw T, Riboli E, Bueno-de-Mesquita HB.

Cancer Causes Control. 2009 Jul;20(5):785-94. doi: 10.1007/s10552-008-9293-8. Epub 2009 Jan 16.

38.

Plasma selenium concentration and prostate cancer risk: results from the European Prospective Investigation into Cancer and Nutrition (EPIC).

Allen NE, Appleby PN, Roddam AW, Tjønneland A, Johnsen NF, Overvad K, Boeing H, Weikert S, Kaaks R, Linseisen J, Trichopoulou A, Misirli G, Trichopoulos D, Sacerdote C, Grioni S, Palli D, Tumino R, Bueno-de-Mesquita HB, Kiemeney LA, Barricarte A, Larrañaga N, Sánchez MJ, Agudo A, Tormo MJ, Rodriguez L, Stattin P, Hallmans G, Bingham S, Khaw KT, Slimani N, Rinaldi S, Boffetta P, Riboli E, Key TJ; European Prospective Investigation into Cancer and Nutrition.

Am J Clin Nutr. 2008 Dec;88(6):1567-75. doi: 10.3945/ajcn.2008.26205.

PMID:
19064517
39.

The syndrome of rhabdomyolysis: complications and treatment.

Chatzizisis YS, Misirli G, Hatzitolios AI, Giannoglou GD.

Eur J Intern Med. 2008 Dec;19(8):568-74. doi: 10.1016/j.ejim.2007.06.037. Epub 2008 Apr 28. Review.

PMID:
19046720
40.

A prospective analysis of the association between dietary fiber intake and prostate cancer risk in EPIC.

Suzuki R, Allen NE, Key TJ, Appleby PN, Tjønneland A, Johnsen NF, Jensen MK, Overvad K, Boeing H, Pischon T, Kaaks R, Rohrmann S, Trichopoulou A, Misirli G, Trichopoulos D, Bueno-de-Mesquita HB, van Duijnhoven F, Sacerdote C, Pala V, Palli D, Tumino R, Ardanaz E, Quirós JR, Larrañaga N, Sánchez MJ, Tormo MJ, Jakszyn P, Johansson I, Stattin P, Berglund G, Manjer J, Bingham S, Khaw KT, Egevad L, Ferrari P, Jenab M, Riboli E.

Int J Cancer. 2009 Jan 1;124(1):245-9. doi: 10.1002/ijc.23908.

41.

In vivo comparative study of linear versus geometrically correct three-dimensional reconstruction of coronary arteries.

Chatzizisis YS, Giannoglou GD, Sianos G, Ziakas A, Tsikaderis D, Dardas P, Matakos A, Basdekidou C, Misirli G, Zamboulis C, Louridas GE, Parcharidis GE.

Am J Cardiol. 2008 Jan 15;101(2):263-7. doi: 10.1016/j.amjcard.2007.07.070.

PMID:
18178419
42.

The syndrome of rhabdomyolysis: Pathophysiology and diagnosis.

Giannoglou GD, Chatzizisis YS, Misirli G.

Eur J Intern Med. 2007 Mar;18(2):90-100.

PMID:
17338959

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