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Items: 1 to 50 of 68

1.

Evaluation of a Semi-automatic Right Ventricle Segmentation Method on Short-Axis MR Images.

Yilmaz P, Wallecan K, Kristanto W, Aben JP, Moelker A.

J Digit Imaging. 2018 Mar 9. doi: 10.1007/s10278-018-0061-3. [Epub ahead of print]

PMID:
29524154
2.

Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2018 Feb 6;36(2):196. doi: 10.1038/nbt0218-196a. No abstract available.

3.

Adaptability as the key to success for the ubiquitous marine nitrite oxidizer Nitrococcus.

Füssel J, Lücker S, Yilmaz P, Nowka B, van Kessel MAHJ, Bourceau P, Hach PF, Littmann S, Berg J, Spieck E, Daims H, Kuypers MMM, Lam P.

Sci Adv. 2017 Nov 1;3(11):e1700807. doi: 10.1126/sciadv.1700807. eCollection 2017 Nov.

4.

SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees.

Beccati A, Gerken J, Quast C, Yilmaz P, Glöckner FO.

BMC Bioinformatics. 2017 Sep 30;18(1):433. doi: 10.1186/s12859-017-1841-3.

5.

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, Schulz F, Jarett J, Rivers AR, Eloe-Fadrosh EA, Tringe SG, Ivanova NN, Copeland A, Clum A, Becraft ED, Malmstrom RR, Birren B, Podar M, Bork P, Weinstock GM, Garrity GM, Dodsworth JA, Yooseph S, Sutton G, Glöckner FO, Gilbert JA, Nelson WC, Hallam SJ, Jungbluth SP, Ettema TJG, Tighe S, Konstantinidis KT, Liu WT, Baker BJ, Rattei T, Eisen JA, Hedlund B, McMahon KD, Fierer N, Knight R, Finn R, Cochrane G, Karsch-Mizrachi I, Tyson GW, Rinke C; Genome Standards Consortium, Lapidus A, Meyer F, Yilmaz P, Parks DH, Eren AM, Schriml L, Banfield JF, Hugenholtz P, Woyke T.

Nat Biotechnol. 2017 Aug 8;35(8):725-731. doi: 10.1038/nbt.3893.

PMID:
28787424
6.

25 years of serving the community with ribosomal RNA gene reference databases and tools.

Glöckner FO, Yilmaz P, Quast C, Gerken J, Beccati A, Ciuprina A, Bruns G, Yarza P, Peplies J, Westram R, Ludwig W.

J Biotechnol. 2017 Nov 10;261:169-176. doi: 10.1016/j.jbiotec.2017.06.1198. Epub 2017 Jun 23.

7.

A phylogenetic framework for the kingdom Fungi based on 18S rRNA gene sequences.

Yarza P, Yilmaz P, Panzer K, Glöckner FO, Reich M.

Mar Genomics. 2017 Dec;36:33-39. doi: 10.1016/j.margen.2017.05.009. Epub 2017 Jun 1.

8.

Inferior Rectus Transposition a Novel Procedure for Abducens Palsy.

Sener EC, Yilmaz PT.

Am J Ophthalmol. 2017 Jul;179:209-210. doi: 10.1016/j.ajo.2017.04.025. Epub 2017 May 17. No abstract available.

PMID:
28528085
9.

Klestadt Cyst: Magnetic Resonance Imaging.

Kadiyoran C, Yilmaz PD, Dadaci Z, Vatansev H.

J Craniofac Surg. 2017 May;28(3):e273-e274. doi: 10.1097/SCS.0000000000003523.

PMID:
28468219
10.

Plant specimen contextual data consensus.

Hoopen PT, Walls RL, Cannon EK, Cochrane G, Cole J, Johnston A, Karsch-Mizrachi I, Yilmaz P.

Gigascience. 2016 Dec 1;5(1):1-4. doi: 10.1093/gigascience/giw002.

11.

UniEuk: Time to Speak a Common Language in Protistology!

Berney C, Ciuprina A, Bender S, Brodie J, Edgcomb V, Kim E, Rajan J, Parfrey LW, Adl S, Audic S, Bass D, Caron DA, Cochrane G, Czech L, Dunthorn M, Geisen S, Glöckner FO, Mahé F, Quast C, Kaye JZ, Simpson AGB, Stamatakis A, Del Campo J, Yilmaz P, de Vargas C.

J Eukaryot Microbiol. 2017 May;64(3):407-411. doi: 10.1111/jeu.12414. Epub 2017 Apr 21. Review.

12.

The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle.

Martínez-Pérez C, Mohr W, Löscher CR, Dekaezemacker J, Littmann S, Yilmaz P, Lehnen N, Fuchs BM, Lavik G, Schmitz RA, LaRoche J, Kuypers MM.

Nat Microbiol. 2016 Sep 12;1(11):16163. doi: 10.1038/nmicrobiol.2016.163.

PMID:
27617976
13.

MIxS-HCR: a MIxS extension defining a minimal information standard for sequence data from environments pertaining to hydrocarbon resources.

Tsesmetzis N, Yilmaz P, Marks PC, Kyrpides NC, Head IM, Lomans BP.

Stand Genomic Sci. 2016 Oct 12;11:78. eCollection 2016.

14.

BioVeL: a virtual laboratory for data analysis and modelling in biodiversity science and ecology.

Hardisty AR, Bacall F, Beard N, Balcázar-Vargas MP, Balech B, Barcza Z, Bourlat SJ, De Giovanni R, de Jong Y, De Leo F, Dobor L, Donvito G, Fellows D, Guerra AF, Ferreira N, Fetyukova Y, Fosso B, Giddy J, Goble C, Güntsch A, Haines R, Ernst VH, Hettling H, Hidy D, Horváth F, Ittzés D, Ittzés P, Jones A, Kottmann R, Kulawik R, Leidenberger S, Lyytikäinen-Saarenmaa P, Mathew C, Morrison N, Nenadic A, de la Hidalga AN, Obst M, Oostermeijer G, Paymal E, Pesole G, Pinto S, Poigné A, Fernandez FQ, Santamaria M, Saarenmaa H, Sipos G, Sylla KH, Tähtinen M, Vicario S, Vos RA, Williams AR, Yilmaz P.

BMC Ecol. 2016 Oct 20;16(1):49.

15.

The Global Genome Biodiversity Network (GGBN) Data Standard specification.

Droege G, Barker K, Seberg O, Coddington J, Benson E, Berendsohn WG, Bunk B, Butler C, Cawsey EM, Deck J, Döring M, Flemons P, Gemeinholzer B, Güntsch A, Hollowell T, Kelbert P, Kostadinov I, Kottmann R, Lawlor RT, Lyal C, Mackenzie-Dodds J, Meyer C, Mulcahy D, Nussbeck SY, O'Tuama É, Orrell T, Petersen G, Robertson T, Söhngen C, Whitacre J, Wieczorek J, Yilmaz P, Zetzsche H, Zhang Y, Zhou X.

Database (Oxford). 2016 Oct 2;2016. pii: baw125. Print 2016.

16.

Subtle Sensory Abnormalities Detected by Quantitative Sensory Testing in Patients with Trigeminal Neuralgia.

Flor H, Rasche D, Islamian AP, Rolko C, Yilmaz P, Ruppolt M, Capelle HH, Tronnier V, Krauss JK.

Pain Physician. 2016 Sep-Oct;19(7):507-18.

17.

Perovskite BiFeO3 thin film photocathode performance with visible light activity.

Yilmaz P, Yeo D, Chang H, Loh L, Dunn S.

Nanotechnology. 2016 Aug 26;27(34):345402. doi: 10.1088/0957-4484/27/34/345402. Epub 2016 Jul 15.

PMID:
27420393
18.

Phylogeny-aware identification and correction of taxonomically mislabeled sequences.

Kozlov AM, Zhang J, Yilmaz P, Glöckner FO, Stamatakis A.

Nucleic Acids Res. 2016 Jun 20;44(11):5022-33. doi: 10.1093/nar/gkw396. Epub 2016 May 10.

19.

Deficiency of depression in adduction: clinical characteristics and surgical management of the "inverted Brown pattern".

Marsh JD, Yilmaz PT, Guyton DL.

J AAPOS. 2016 Feb;20(1):7-11. doi: 10.1016/j.jaapos.2015.10.011.

PMID:
26917064
20.

Linezolid and dexamethasone experience in a serious case of listeria rhombencephalitis.

Yılmaz PÖ, Mutlu NM, Sertçelik A, Baştuğ A, Doğu C, Kışlak S.

J Infect Public Health. 2016 Sep-Oct;9(5):670-4. doi: 10.1016/j.jiph.2015.12.018. Epub 2016 Feb 6.

21.

Expanding the World of Marine Bacterial and Archaeal Clades.

Yilmaz P, Yarza P, Rapp JZ, Glöckner FO.

Front Microbiol. 2016 Jan 8;6:1524. doi: 10.3389/fmicb.2015.01524. eCollection 2015.

22.

Expression and function of purinergic receptors in platelets from apheresis-derived platelet concentrates.

Koessler J, Weber K, Koessler A, Yilmaz P, Boeck M, Kobsar A.

Blood Transfus. 2015 Nov 17;14(6):545-551. doi: 10.2450/2015.0073-15. [Epub ahead of print]

23.

The magnitude of gonadotoxicity of chemotherapy drugs on ovarian follicles and granulosa cells varies depending upon the category of the drugs and the type of granulosa cells.

Yuksel A, Bildik G, Senbabaoglu F, Akin N, Arvas M, Unal F, Kilic Y, Karanfil I, Eryılmaz B, Yilmaz P, Ozkanbaş C, Taskiran C, Aksoy S, Guzel Y, Balaban B, Ince U, Iwase A, Urman B, Oktem O.

Hum Reprod. 2015 Dec;30(12):2926-35. doi: 10.1093/humrep/dev256. Epub 2015 Oct 13.

PMID:
26466914
24.

Evaluation of Carotid Intima Media Thickness and Renal Artery Resistive Index in Patients With Pseudoexfoliation Syndrome: A Prospective Case-Control Study.

Gökce SE, Deren T, Köz ÖG, Yilmaz P, Başkan C, Duman R, Yarangümeli AA, Kural G.

J Glaucoma. 2016 May;25(5):e559-61. doi: 10.1097/IJG.0000000000000327.

PMID:
26372158
25.

Minimum Information about a Biosynthetic Gene cluster.

Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, de Bruijn I, Chooi YH, Claesen J, Coates RC, Cruz-Morales P, Duddela S, Düsterhus S, Edwards DJ, Fewer DP, Garg N, Geiger C, Gomez-Escribano JP, Greule A, Hadjithomas M, Haines AS, Helfrich EJ, Hillwig ML, Ishida K, Jones AC, Jones CS, Jungmann K, Kegler C, Kim HU, Kötter P, Krug D, Masschelein J, Melnik AV, Mantovani SM, Monroe EA, Moore M, Moss N, Nützmann HW, Pan G, Pati A, Petras D, Reen FJ, Rosconi F, Rui Z, Tian Z, Tobias NJ, Tsunematsu Y, Wiemann P, Wyckoff E, Yan X, Yim G, Yu F, Xie Y, Aigle B, Apel AK, Balibar CJ, Balskus EP, Barona-Gómez F, Bechthold A, Bode HB, Borriss R, Brady SF, Brakhage AA, Caffrey P, Cheng YQ, Clardy J, Cox RJ, De Mot R, Donadio S, Donia MS, van der Donk WA, Dorrestein PC, Doyle S, Driessen AJ, Ehling-Schulz M, Entian KD, Fischbach MA, Gerwick L, Gerwick WH, Gross H, Gust B, Hertweck C, Höfte M, Jensen SE, Ju J, Katz L, Kaysser L, Klassen JL, Keller NP, Kormanec J, Kuipers OP, Kuzuyama T, Kyrpides NC, Kwon HJ, Lautru S, Lavigne R, Lee CY, Linquan B, Liu X, Liu W, Luzhetskyy A, Mahmud T, Mast Y, Méndez C, Metsä-Ketelä M, Micklefield J, Mitchell DA, Moore BS, Moreira LM, Müller R, Neilan BA, Nett M, Nielsen J, O'Gara F, Oikawa H, Osbourn A, Osburne MS, Ostash B, Payne SM, Pernodet JL, Petricek M, Piel J, Ploux O, Raaijmakers JM, Salas JA, Schmitt EK, Scott B, Seipke RF, Shen B, Sherman DH, Sivonen K, Smanski MJ, Sosio M, Stegmann E, Süssmuth RD, Tahlan K, Thomas CM, Tang Y, Truman AW, Viaud M, Walton JD, Walsh CT, Weber T, van Wezel GP, Wilkinson B, Willey JM, Wohlleben W, Wright GD, Ziemert N, Zhang C, Zotchev SB, Breitling R, Takano E, Glöckner FO.

Nat Chem Biol. 2015 Sep;11(9):625-31. doi: 10.1038/nchembio.1890. No abstract available.

26.

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data.

Panzer K, Yilmaz P, Weiß M, Reich L, Richter M, Wiese J, Schmaljohann R, Labes A, Imhoff JF, Glöckner FO, Reich M.

PLoS One. 2015 Jul 30;10(7):e0134377. doi: 10.1371/journal.pone.0134377. eCollection 2015.

27.

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.

Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group.

Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121.

28.

Chemical constituents and biological activities of Cirsium leucopsis, C. sipyleum, and C. eriophorum.

Boğa M, Yilmaz PK, Cebe DB, Fatima M, Siddiqui BS, Kolak U.

Z Naturforsch C. 2014 Sep-Oct;69(9-10):381-90.

PMID:
25711039
29.

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs.

Klatt JM, Haas S, Yilmaz P, de Beer D, Polerecky L.

Environ Microbiol. 2015 Sep;17(9):3301-13. doi: 10.1111/1462-2920.12791. Epub 2015 Mar 4.

PMID:
25630511
30.

Anoxygenic photosynthesis controls oxygenic photosynthesis in a cyanobacterium from a sulfidic spring.

Klatt JM, Al-Najjar MA, Yilmaz P, Lavik G, de Beer D, Polerecky L.

Appl Environ Microbiol. 2015 Mar;81(6):2025-31. doi: 10.1128/AEM.03579-14. Epub 2015 Jan 9.

31.

Genomic standards consortium projects.

Field D, Sterk P, Kottmann R, De Smet JW, Amaral-Zettler L, Cochrane G, Cole JR, Davies N, Dawyndt P, Garrity GM, Gilbert JA, Glöckner FO, Hirschman L, Klenk HP, Knight R, Kyrpides N, Meyer F, Karsch-Mizrachi I, Morrison N, Robbins R, San Gil I, Sansone S, Schriml L, Tatusova T, Ussery D, Yilmaz P, White O, Wooley J, Caporaso G.

Stand Genomic Sci. 2014 Feb 15;9(3):599-601. doi: 10.4056/sigs.5559680. eCollection 2014 Jun 15.

32.

The effect of immunoadsorption with the Immusorba TR-350 column on coagulation compared to plasma exchange.

Koessler J, Kobsar A, Kuhn S, Koessler A, Yilmaz P, Weinig E, Putz E, Boeck M, Klinker E.

Vox Sang. 2015 Jan;108(1):46-51. doi: 10.1111/vox.12191. Epub 2014 Aug 14.

PMID:
25131310
33.

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences.

Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R.

Nat Rev Microbiol. 2014 Sep;12(9):635-45. doi: 10.1038/nrmicro3330. Review.

PMID:
25118885
34.

In vitro biological activities and fatty acid profiles of Pistacia terebinthus fruits and Pistacia khinjuk seeds.

Hacıbekiroğlu I, Yılmaz PK, Haşimi N, Kılınç E, Tolan V, Kolak U.

Nat Prod Res. 2015;29(5):444-6. doi: 10.1080/14786419.2014.947492. Epub 2014 Aug 12.

PMID:
25115646
35.
36.

Lethal autoimmune hemagglutination due to an immunoglobulin A autoagglutinin with Band 3 specificity.

Salama A, Janvier D, Mayer B, Saison C, Moscatelli H, Aucouturier F, Yilmaz P, Arnaud L, Wild V, Knop S, Cartron JP.

Transfusion. 2014 Aug;54(8):1988-95. doi: 10.1111/trf.12638. Epub 2014 Apr 2.

PMID:
24697848
37.

Increasing susceptibility of nitric oxide-mediated inhibitory platelet signaling during storage of apheresis-derived platelet concentrates.

Kobsar A, Klinker E, Kuhn S, Koessler A, Yilmaz P, Boeck M, Koessler J.

Transfusion. 2014 Jul;54(7):1782-9. doi: 10.1111/trf.12584. Epub 2014 Feb 27.

PMID:
24576258
38.

The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO.

Nucleic Acids Res. 2014 Jan;42(Database issue):D643-8. doi: 10.1093/nar/gkt1209. Epub 2013 Nov 28.

39.

MIxS-BE: a MIxS extension defining a minimum information standard for sequence data from the built environment.

Glass EM, Dribinsky Y, Yilmaz P, Levin H, Van Pelt R, Wendel D, Wilke A, Eisen JA, Huse S, Shipanova A, Sogin M, Stajich J, Knight R, Meyer F, Schriml LM.

ISME J. 2014 Jan;8(1):1-3. doi: 10.1038/ismej.2013.176. Epub 2013 Oct 24. No abstract available.

40.

A metagenomics portal for a democratized sequencing world.

Wilke A, Glass EM, Bartels D, Bischof J, Braithwaite D, D'Souza M, Gerlach W, Harrison T, Keegan K, Matthews H, Kottmann R, Paczian T, Tang W, Trimble WL, Yilmaz P, Wilkening J, Desai N, Meyer F.

Methods Enzymol. 2013;531:487-523. doi: 10.1016/B978-0-12-407863-5.00022-8.

PMID:
24060134
41.

Decreasing phosphodiesterase 5A activity contributes to platelet cGMP accumulation during storage of apheresis-derived platelet concentrates.

Kobsar A, Putz E, Yilmaz P, Weinig E, Boeck M, Koessler J.

Transfusion. 2014 Apr;54(4):1008-14. doi: 10.1111/trf.12360. Epub 2013 Aug 2.

PMID:
23909451
42.

Comparison of the serious injury pattern of adult bicyclists, between South-West Netherlands and the State of Victoria, Australia 2001-2009.

Yilmaz P, Gabbe BJ, McDermott FT, Van Lieshout EM, Rood PP, Mulligan TM, Patka P, Cameron PA.

Injury. 2013 Jun;44(6):848-54. doi: 10.1016/j.injury.2013.03.007. Epub 2013 Apr 6.

PMID:
23570703
43.

Ecogenomic perspectives on domains of unknown function: correlation-based exploration of marine metagenomes.

Buttigieg PL, Hankeln W, Kostadinov I, Kottmann R, Yilmaz P, Duhaime MB, Glöckner FO.

PLoS One. 2013;8(3):e50869. doi: 10.1371/journal.pone.0050869. Epub 2013 Mar 14.

44.

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012).

Tuama EÓ, Deck J, Dröge G, Döring M, Field D, Kottmann R, Ma J, Mori H, Morrison N, Sterk P, Sugawara H, Wieczorek J, Wu L, Yilmaz P.

Stand Genomic Sci. 2012 Oct 10;7(1):166-70. doi: 10.4056/sigs.3166513. Epub 2012 Sep 28.

45.

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.

Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO.

Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. doi: 10.1093/nar/gks1219. Epub 2012 Nov 28.

46.

Treatment-related changes in brain activation in patients with fibromyalgia syndrome.

Diers M, Yilmaz P, Rance M, Thieme K, Gracely RH, Rolko C, Schley MT, Kiessling U, Wang H, Flor H.

Exp Brain Res. 2012 May;218(4):619-28. doi: 10.1007/s00221-012-3055-2. Epub 2012 Mar 17.

PMID:
22427134
47.

Ecological structuring of bacterial and archaeal taxa in surface ocean waters.

Yilmaz P, Iversen MH, Hankeln W, Kottmann R, Quast C, Glöckner FO.

FEMS Microbiol Ecol. 2012 Aug;81(2):373-85. doi: 10.1111/j.1574-6941.2012.01357.x. Epub 2012 Apr 10.

48.

CDinFusion--submission-ready, on-line integration of sequence and contextual data.

Hankeln W, Wendel NJ, Gerken J, Waldmann J, Buttigieg PL, Kostadinov I, Kottmann R, Yilmaz P, Glöckner FO.

PLoS One. 2011;6(9):e24797. doi: 10.1371/journal.pone.0024797. Epub 2011 Sep 13.

49.

Data shopping in an open marketplace: Introducing the Ontogrator web application for marking up data using ontologies and browsing using facets.

Morrison N, Hancock D, Hirschman L, Dawyndt P, Verslyppe B, Kyrpides N, Kottmann R, Yilmaz P, Glöckner FO, Grethe J, Booth T, Sterk P, Nenadic G, Field D.

Stand Genomic Sci. 2011 Apr 29;4(2):286-92. doi: 10.4056/sigs.1344279.

50.

Analysis of 23S rRNA genes in metagenomes - a case study from the Global Ocean Sampling Expedition.

Yilmaz P, Kottmann R, Pruesse E, Quast C, Glöckner FO.

Syst Appl Microbiol. 2011 Sep;34(6):462-9. doi: 10.1016/j.syapm.2011.04.005. Epub 2011 Jun 14.

PMID:
21676569

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