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Items: 1 to 50 of 94

1.

Analysis of the effects of COHb, lactate, and troponin levels on the clinical process and outcome in patients who were admitted to the emergency service due to carbon monoxide poisoning.

Yildiz MN, Eroglu SE, Ozen C, Yildiz HA, Sektioglu BK, Alkan C.

North Clin Istanb. 2019 May 29;6(2):141-145. doi: 10.14744/nci.2018.88709. eCollection 2019.

2.

Evaluation of genome scaffolding tools using pooled clone sequencing.

Dal E, Alkan C.

Turk J Biol. 2018 Dec 10;42(6):471-476. doi: 10.3906/biy-1805-42. eCollection 2018.

3.

Discovery of tandem and interspersed segmental duplications using high throughput sequencing.

Soylev A, Le T, Amini H, Alkan C, Hormozdiari F.

Bioinformatics. 2019 Apr 1. pii: btz237. doi: 10.1093/bioinformatics/btz237. [Epub ahead of print]

PMID:
30937433
4.

Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment.

Alser M, Hassan H, Kumar A, Mutlu O, Alkan C.

Bioinformatics. 2019 Mar 28. pii: btz234. doi: 10.1093/bioinformatics/btz234. [Epub ahead of print]

PMID:
30923804
5.

Fast characterization of segmental duplications in genome assemblies.

Numanagic I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F.

Bioinformatics. 2018 Sep 1;34(17):i706-i714. doi: 10.1093/bioinformatics/bty586.

6.

Hercules: a profile HMM-based hybrid error correction algorithm for long reads.

Firtina C, Bar-Joseph Z, Alkan C, Cicek AE.

Nucleic Acids Res. 2018 Nov 30;46(21):e125. doi: 10.1093/nar/gky724.

7.

Realizing the potential of blockchain technologies in genomics.

Ozercan HI, Ileri AM, Ayday E, Alkan C.

Genome Res. 2018 Sep;28(9):1255-1263. doi: 10.1101/gr.207464.116. Epub 2018 Aug 3.

8.

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth.

Kahveci F, Alkan C.

Methods Mol Biol. 2018;1833:61-72. doi: 10.1007/978-1-4939-8666-8_4.

PMID:
30039363
9.

GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies.

Kim JS, Senol Cali D, Xin H, Lee D, Ghose S, Alser M, Hassan H, Ergin O, Alkan C, Mutlu O.

BMC Genomics. 2018 May 9;19(Suppl 2):89. doi: 10.1186/s12864-018-4460-0.

10.

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions.

Senol Cali D, Kim JS, Ghose S, Alkan C, Mutlu O.

Brief Bioinform. 2018 Apr 2. doi: 10.1093/bib/bby017. [Epub ahead of print]

PMID:
29617724
11.

Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer.

Saatci Ö, Borgoni S, Akbulut Ö, Durmuş S, Raza U, Eyüpoğlu E, Alkan C, Akyol A, Kütük Ö, Wiemann S, Şahin Ö.

Oncogene. 2018 Apr;37(17):2251-2269. doi: 10.1038/s41388-017-0108-9. Epub 2018 Feb 2.

PMID:
29391599
12.

Isolation and sequencing of Dashli virus, a novel Sicilian-like virus in sandflies from Iran; genetic and phylogenetic evidence for the creation of one novel species within the Phlebovirus genus in the Phenuiviridae family.

Alkan C, Moin Vaziri V, Ayhan N, Badakhshan M, Bichaud L, Rahbarian N, Javadian EA, Alten B, de Lamballerie X, Charrel RN.

PLoS Negl Trop Dis. 2017 Dec 27;11(12):e0005978. doi: 10.1371/journal.pntd.0005978. eCollection 2017 Dec.

13.

Discovery and genotyping of novel sequence insertions in many sequenced individuals.

Kavak P, Lin YY, Numanagic I, Asghari H, Güngör T, Alkan C, Hach F.

Bioinformatics. 2017 Jul 15;33(14):i161-i169. doi: 10.1093/bioinformatics/btx254.

14.

Toolkit for automated and rapid discovery of structural variants.

Soylev A, Kockan C, Hormozdiari F, Alkan C.

Methods. 2017 Oct 1;129:3-7. doi: 10.1016/j.ymeth.2017.05.030. Epub 2017 Jun 2.

PMID:
28583483
15.

GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping.

Alser M, Hassan H, Xin H, Ergin O, Mutlu O, Alkan C.

Bioinformatics. 2017 Nov 1;33(21):3355-3363. doi: 10.1093/bioinformatics/btx342.

16.

Discovery of large genomic inversions using long range information.

Eslami Rasekh M, Chiatante G, Miroballo M, Tang J, Ventura M, Amemiya CT, Eichler EE, Antonacci F, Alkan C.

BMC Genomics. 2017 Jan 10;18(1):65. doi: 10.1186/s12864-016-3444-1.

17.

Inter-varietal structural variation in grapevine genomes.

Cardone MF, D'Addabbo P, Alkan C, Bergamini C, Catacchio CR, Anaclerio F, Chiatante G, Marra A, Giannuzzi G, Perniola R, Ventura M, Antonacci D.

Plant J. 2016 Nov;88(4):648-661. doi: 10.1111/tpj.13274. Epub 2016 Sep 16.

18.

On genomic repeats and reproducibility.

Firtina C, Alkan C.

Bioinformatics. 2016 Aug 1;32(15):2243-7. doi: 10.1093/bioinformatics/btw139. Epub 2016 Mar 11.

PMID:
27153582
19.

Sandfly-Borne Phlebovirus Isolations from Turkey: New Insight into the Sandfly fever Sicilian and Sandfly fever Naples Species.

Alkan C, Erisoz Kasap O, Alten B, de Lamballerie X, Charrel RN.

PLoS Negl Trop Dis. 2016 Mar 23;10(3):e0004519. doi: 10.1371/journal.pntd.0004519. eCollection 2016 Mar.

20.

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs.

Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J.

PLoS Genet. 2016 Mar 4;12(3):e1005851. doi: 10.1371/journal.pgen.1005851. eCollection 2016 Mar.

21.

Thermal energy storage characteristics of micro-nanoencapsulated heneicosane and octacosane with poly(methylmethacrylate) shell.

Sarı A, Alkan C, Biçer A.

J Microencapsul. 2016 May;33(3):221-8. doi: 10.3109/02652048.2016.1144820. Epub 2016 Feb 19.

PMID:
26892748
22.

Isolation, full genomic characterization and neutralization-based human seroprevalence of Medjerda Valley virus, a novel sandfly-borne phlebovirus belonging to the Salehabad virus complex in northern Tunisia.

Bichaud L, Dachraoui K, Alwassouf S, Alkan C, Mensi M, Piorkowski G, Sakhria S, Seston M, Fares W, De Lamballerie X, Zhioua E, Charrel RN.

J Gen Virol. 2016 Mar;97(3):602-10. doi: 10.1099/jgv.0.000389. Epub 2015 Dec 24.

PMID:
26704069
23.

Optimal seed solver: optimizing seed selection in read mapping.

Xin H, Nahar S, Zhu R, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O.

Bioinformatics. 2016 Jun 1;32(11):1632-42. doi: 10.1093/bioinformatics/btv670. Epub 2015 Nov 14.

24.

Determining the origin of synchronous multifocal bladder cancer by exome sequencing.

Acar Ö, Özkurt E, Demir G, Saraç H, Alkan C, Esen T, Somel M, Lack NA.

BMC Cancer. 2015 Nov 9;15:871. doi: 10.1186/s12885-015-1859-8.

25.

An integrated map of structural variation in 2,504 human genomes.

Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO.

Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394.

26.

Robustness of Massively Parallel Sequencing Platforms.

Kavak P, Yüksel B, Aksu S, Kulekci MO, Güngör T, Hach F, Şahinalp SC; Turkish Human Genome Project, Alkan C, Sağıroğlu MŞ.

PLoS One. 2015 Sep 18;10(9):e0138259. doi: 10.1371/journal.pone.0138259. eCollection 2015.

27.

Ecuador Paraiso Escondido Virus, a New Flavivirus Isolated from New World Sand Flies in Ecuador, Is the First Representative of a Novel Clade in the Genus Flavivirus.

Alkan C, Zapata S, Bichaud L, Moureau G, Lemey P, Firth AE, Gritsun TS, Gould EA, de Lamballerie X, Depaquit J, Charrel RN.

J Virol. 2015 Dec;89(23):11773-85. doi: 10.1128/JVI.01543-15. Epub 2015 Sep 9.

28.

Virus isolation, genetic characterization and seroprevalence of Toscana virus in Algeria.

Alkan C, Allal-Ikhlef AB, Alwassouf S, Baklouti A, Piorkowski G, de Lamballerie X, Izri A, Charrel RN.

Clin Microbiol Infect. 2015 Nov;21(11):1040.e1-9. doi: 10.1016/j.cmi.2015.07.012. Epub 2015 Jul 30.

29.

Isolation, genetic characterization, and seroprevalence of Adana virus, a novel phlebovirus belonging to the Salehabad virus complex, in Turkey.

Alkan C, Alwassouf S, Piorkowski G, Bichaud L, Tezcan S, Dincer E, Ergunay K, Ozbel Y, Alten B, de Lamballerie X, Charrel RN.

J Virol. 2015 Apr;89(8):4080-91. doi: 10.1128/JVI.03027-14. Epub 2015 Feb 4.

30.

Activating mutations of STAT5B and STAT3 in lymphomas derived from γδ-T or NK cells.

Küçük C, Jiang B, Hu X, Zhang W, Chan JK, Xiao W, Lack N, Alkan C, Williams JC, Avery KN, Kavak P, Scuto A, Sen E, Gaulard P, Staudt L, Iqbal J, Zhang W, Cornish A, Gong Q, Yang Q, Sun H, d'Amore F, Leppä S, Liu W, Fu K, de Leval L, McKeithan T, Chan WC.

Nat Commun. 2015 Jan 14;6:6025. doi: 10.1038/ncomms7025.

PMID:
25586472
31.

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.

Xin H, Greth J, Emmons J, Pekhimenko G, Kingsford C, Alkan C, Mutlu O.

Bioinformatics. 2015 May 15;31(10):1553-60. doi: 10.1093/bioinformatics/btu856. Epub 2015 Jan 10.

32.

Fast and accurate mapping of Complete Genomics reads.

Lee D, Hormozdiari F, Xin H, Hach F, Mutlu O, Alkan C.

Methods. 2015 Jun;79-80:3-10. doi: 10.1016/j.ymeth.2014.10.012. Epub 2014 Oct 22.

33.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

Montague MJ, Li G, Gandolfi B, Khan R, Aken BL, Searle SM, Minx P, Hillier LW, Koboldt DC, Davis BW, Driscoll CA, Barr CS, Blackistone K, Quilez J, Lorente-Galdos B, Marques-Bonet T, Alkan C, Thomas GW, Hahn MW, Menotti-Raymond M, O'Brien SJ, Wilson RK, Lyons LA, Murphy WJ, Warren WC.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17230-5. doi: 10.1073/pnas.1410083111. Epub 2014 Nov 10.

34.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.

Alkan C, Kavak P, Somel M, Gokcumen O, Ugurlu S, Saygi C, Dal E, Bugra K, Güngör T, Sahinalp SC, Özören N, Bekpen C.

BMC Genomics. 2014 Nov 7;15:963. doi: 10.1186/1471-2164-15-963.

35.

Presence of sandfly-borne phleboviruses of two antigenic complexes (Sandfly fever Naples virus and Sandfly fever Sicilian virus) in two different bio-geographical regions of Tunisia demonstrated by a microneutralisation-based seroprevalence study in dogs.

Sakhria S, Alwassouf S, Fares W, Bichaud L, Dachraoui K, Alkan C, Zoghlami Z, de Lamballerie X, Zhioua E, Charrel RN.

Parasit Vectors. 2014 Oct 12;7:476. doi: 10.1186/s13071-014-0476-8.

36.

Arthropods as a source of new RNA viruses.

Bichaud L, de Lamballerie X, Alkan C, Izri A, Gould EA, Charrel RN.

Microb Pathog. 2014 Dec;77:136-41. doi: 10.1016/j.micpath.2014.09.002. Epub 2014 Sep 18. Review.

PMID:
25239874
37.

Annotated features of domestic cat - Felis catus genome.

Tamazian G, Simonov S, Dobrynin P, Makunin A, Logachev A, Komissarov A, Shevchenko A, Brukhin V, Cherkasov N, Svitin A, Koepfli KP, Pontius J, Driscoll CA, Blackistone K, Barr C, Goldman D, Antunes A, Quilez J, Lorente-Galdos B, Alkan C, Marques-Bonet T, Menotti-Raymond M, David VA, Narfström K, O'Brien SJ.

Gigascience. 2014 Aug 5;3:13. doi: 10.1186/2047-217X-3-13. eCollection 2014.

38.

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications.

Hach F, Sarrafi I, Hormozdiari F, Alkan C, Eichler EE, Sahinalp SC.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W494-500. doi: 10.1093/nar/gku370. Epub 2014 May 8.

39.

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair.

Dal GM, Ergüner B, Sağıroğlu MS, Yüksel B, Onat OE, Alkan C, Özçelik T.

J Med Genet. 2014 Jul;51(7):455-9. doi: 10.1136/jmedgenet-2013-102197. Epub 2014 Apr 24.

PMID:
24764354
40.

The emergence of Schmallenberg virus across Culicoides communities and ecosystems in Europe.

Balenghien T, Pagès N, Goffredo M, Carpenter S, Augot D, Jacquier E, Talavera S, Monaco F, Depaquit J, Grillet C, Pujols J, Satta G, Kasbari M, Setier-Rio ML, Izzo F, Alkan C, Delécolle JC, Quaglia M, Charrel R, Polci A, Bréard E, Federici V, Cêtre-Sossah C, Garros C.

Prev Vet Med. 2014 Oct 15;116(4):360-9. doi: 10.1016/j.prevetmed.2014.03.007. Epub 2014 Mar 18.

PMID:
24698329
41.

Genome sequencing highlights the dynamic early history of dogs.

Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, Han E, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Beale H, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Wilton A, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Ostrander EA, Marques-Bonet T, Wayne RK, Novembre J.

PLoS Genet. 2014 Jan;10(1):e1004016. doi: 10.1371/journal.pgen.1004016. Epub 2014 Jan 16. Erratum in: PLoS Genet. 2014 Aug;10(8):e1004631. Wilton, Alan [added].

42.

Reconstructing complex regions of genomes using long-read sequencing technology.

Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE.

Genome Res. 2014 Apr;24(4):688-96. doi: 10.1101/gr.168450.113. Epub 2014 Jan 13.

43.

Rates and patterns of great ape retrotransposition.

Hormozdiari F, Konkel MK, Prado-Martinez J, Chiatante G, Herraez IH, Walker JA, Nelson B, Alkan C, Sudmant PH, Huddleston J, Catacchio CR, Ko A, Malig M, Baker C; Great Ape Genome Project, Marques-Bonet T, Ventura M, Batzer MA, Eichler EE.

Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13457-62. doi: 10.1073/pnas.1310914110. Epub 2013 Jul 24.

44.

Sandfly-borne phleboviruses of Eurasia and Africa: epidemiology, genetic diversity, geographic range, control measures.

Alkan C, Bichaud L, de Lamballerie X, Alten B, Gould EA, Charrel RN.

Antiviral Res. 2013 Oct;100(1):54-74. doi: 10.1016/j.antiviral.2013.07.005. Epub 2013 Jul 19. Review.

45.

Great ape genetic diversity and population history.

Prado-Martinez J, Sudmant PH, Kidd JM, Li H, Kelley JL, Lorente-Galdos B, Veeramah KR, Woerner AE, O'Connor TD, Santpere G, Cagan A, Theunert C, Casals F, Laayouni H, Munch K, Hobolth A, Halager AE, Malig M, Hernandez-Rodriguez J, Hernando-Herraez I, Prüfer K, Pybus M, Johnstone L, Lachmann M, Alkan C, Twigg D, Petit N, Baker C, Hormozdiari F, Fernandez-Callejo M, Dabad M, Wilson ML, Stevison L, Camprubí C, Carvalho T, Ruiz-Herrera A, Vives L, Mele M, Abello T, Kondova I, Bontrop RE, Pusey A, Lankester F, Kiyang JA, Bergl RA, Lonsdorf E, Myers S, Ventura M, Gagneux P, Comas D, Siegismund H, Blanc J, Agueda-Calpena L, Gut M, Fulton L, Tishkoff SA, Mullikin JC, Wilson RK, Gut IG, Gonder MK, Ryder OA, Hahn BH, Navarro A, Akey JM, Bertranpetit J, Reich D, Mailund T, Schierup MH, Hvilsom C, Andrés AM, Wall JD, Bustamante CD, Hammer MF, Eichler EE, Marques-Bonet T.

Nature. 2013 Jul 25;499(7459):471-5. doi: 10.1038/nature12228. Epub 2013 Jul 3.

46.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

Prado-Martinez J, Hernando-Herraez I, Lorente-Galdos B, Dabad M, Ramirez O, Baeza-Delgado C, Morcillo-Suarez C, Alkan C, Hormozdiari F, Raineri E, Estellé J, Fernandez-Callejo M, Valles M, Ritscher L, Schöneberg T, de la Calle-Mustienes E, Casillas S, Rubio-Acero R, Melé M, Engelken J, Caceres M, Gomez-Skarmeta JL, Gut M, Bertranpetit J, Gut IG, Abello T, Eichler EE, Mingarro I, Lalueza-Fox C, Navarro A, Marques-Bonet T.

BMC Genomics. 2013 May 31;14:363. doi: 10.1186/1471-2164-14-363.

47.

Accelerating read mapping with FastHASH.

Xin H, Lee D, Hormozdiari F, Yedkar S, Mutlu O, Alkan C.

BMC Genomics. 2013;14 Suppl 1:S13. doi: 10.1186/1471-2164-14-S1-S13. Epub 2013 Jan 21.

48.

Refinement and discovery of new hotspots of copy-number variation associated with autism spectrum disorder.

Girirajan S, Dennis MY, Baker C, Malig M, Coe BP, Campbell CD, Mark K, Vu TH, Alkan C, Cheng Z, Biesecker LG, Bernier R, Eichler EE.

Am J Hum Genet. 2013 Feb 7;92(2):221-37. doi: 10.1016/j.ajhg.2012.12.016. Epub 2013 Jan 31.

49.

SCALCE: boosting sequence compression algorithms using locally consistent encoding.

Hach F, Numanagic I, Alkan C, Sahinalp SC.

Bioinformatics. 2012 Dec 1;28(23):3051-7. doi: 10.1093/bioinformatics/bts593. Epub 2012 Oct 9.

50.

A high-coverage genome sequence from an archaic Denisovan individual.

Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S.

Science. 2012 Oct 12;338(6104):222-6. doi: 10.1126/science.1224344. Epub 2012 Aug 30.

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