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Items: 23

1.

Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets using protocol-specific bias modeling.

Karabacak Calviello A, Hirsekorn A, Wurmus R, Yusuf D, Ohler U.

Genome Biol. 2019 Feb 21;20(1):42. doi: 10.1186/s13059-019-1654-y.

2.

Levodropropizine suppresses seizure activity in rats with pentylenetetrazol-induced epilepsy.

Erdogan MA, Yusuf D, Erdogan A, Erbas O.

Epilepsy Res. 2019 Feb;150:32-37. doi: 10.1016/j.eplepsyres.2018.12.011. Epub 2018 Dec 29.

PMID:
30610970
3.

Deciphering human ribonucleoprotein regulatory networks.

Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U.

Nucleic Acids Res. 2019 Jan 25;47(2):570-581. doi: 10.1093/nar/gky1185.

4.

Community-Driven Data Analysis Training for Biology.

Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D; Galaxy Training Network, Taylor J, Backofen R, Nekrutenko A, Grüning B.

Cell Syst. 2018 Jun 27;6(6):752-758.e1. doi: 10.1016/j.cels.2018.05.012.

5.

Highly selective SGLT2 inhibitor dapagliflozin reduces seizure activity in pentylenetetrazol-induced murine model of epilepsy.

Erdogan MA, Yusuf D, Christy J, Solmaz V, Erdogan A, Taskiran E, Erbas O.

BMC Neurol. 2018 Jun 7;18(1):81. doi: 10.1186/s12883-018-1086-4.

6.

Small RNA profiling of low biomass samples: identification and removal of contaminants.

Heintz-Buschart A, Yusuf D, Kaysen A, Etheridge A, Fritz JV, May P, de Beaufort C, Upadhyaya BB, Ghosal A, Galas DJ, Wilmes P.

BMC Biol. 2018 May 14;16(1):52. doi: 10.1186/s12915-018-0522-7.

7.

A case report of nifedipine-induced hepatitis with jaundice.

Yusuf D, Christy J, Owen D, Ho M, Li D, Fishman MJ.

BMC Res Notes. 2018 Apr 3;11(1):228. doi: 10.1186/s13104-018-3322-9.

8.

Strategies for analyzing bisulfite sequencing data.

Wreczycka K, Gosdschan A, Yusuf D, Grüning B, Assenov Y, Akalin A.

J Biotechnol. 2017 Nov 10;261:105-115. doi: 10.1016/j.jbiotec.2017.08.007. Epub 2017 Aug 16. Review.

9.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

10.

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A.

Nucleic Acids Res. 2017 Jun 2;45(10):e91. doi: 10.1093/nar/gkx120.

11.

Study of γ-H2AX as DNA double strand break biomarker in resident living in high natural radiation area of Mamuju, West Sulawesi.

Hasan Basri IK, Yusuf D, Rahardjo T, Nurhayati S, Tetriana D, Ramadhani D, Alatas Z, Purnami S, Kisnanto T, Lusiyanti Y, Syaifudin M.

J Environ Radioact. 2017 May;171:212-216. doi: 10.1016/j.jenvrad.2017.02.012. Epub 2017 Mar 8.

PMID:
28282532
12.

Fear of future terrorism: Associated psychiatric burden.

Abiola T, Udofia O, Sheikh TL, Yusuf DA.

Asian J Psychiatr. 2018 Dec;38:53-56. doi: 10.1016/j.ajp.2017.01.028. Epub 2017 Feb 4.

PMID:
28223059
13.

The extracellular RNA complement of Escherichia coli.

Ghosal A, Upadhyaya BB, Fritz JV, Heintz-Buschart A, Desai MS, Yusuf D, Huang D, Baumuratov A, Wang K, Galas D, Wilmes P.

Microbiologyopen. 2015 Apr;4(2):252-266. doi: 10.1002/mbo3.235. Epub 2015 Jan 21.

14.

Effect of physical activity and sun exposure on vitamin D status of Saudi children and adolescents.

Al-Othman A, Al-Musharaf S, Al-Daghri NM, Krishnaswamy S, Yusuf DS, Alkharfy KM, Al-Saleh Y, Al-Attas OS, Alokail MS, Moharram O, Sabico S, Chrousos GP.

BMC Pediatr. 2012 Jul 3;12:92. doi: 10.1186/1471-2431-12-92.

15.

The transcription factor encyclopedia.

Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS, Schnabl JM, Ramos OH, Vasseur-Cognet M, de Leeuw CN, Simpson EM, Ryffel GU, Lam EW, Kist R, Wilson MS, Marco-Ferreres R, Brosens JJ, Beccari LL, Bovolenta P, Benayoun BA, Monteiro LJ, Schwenen HD, Grontved L, Wederell E, Mandrup S, Veitia RA, Chakravarthy H, Hoodless PA, Mancarelli MM, Torbett BE, Banham AH, Reddy SP, Cullum RL, Liedtke M, Tschan MP, Vaz M, Rizzino A, Zannini M, Frietze S, Farnham PJ, Eijkelenboom A, Brown PJ, Laperrière D, Leprince D, de Cristofaro T, Prince KL, Putker M, del Peso L, Camenisch G, Wenger RH, Mikula M, Rozendaal M, Mader S, Ostrowski J, Rhodes SJ, Van Rechem C, Boulay G, Olechnowicz SW, Breslin MB, Lan MS, Nanan KK, Wegner M, Hou J, Mullen RD, Colvin SC, Noy PJ, Webb CF, Witek ME, Ferrell S, Daniel JM, Park J, Waldman SA, Peet DJ, Taggart M, Jayaraman PS, Karrich JJ, Blom B, Vesuna F, O'Geen H, Sun Y, Gronostajski RM, Woodcroft MW, Hough MR, Chen E, Europe-Finner GN, Karolczak-Bayatti M, Bailey J, Hankinson O, Raman V, LeBrun DP, Biswal S, Harvey CJ, DeBruyne JP, Hogenesch JB, Hevner RF, Héligon C, Luo XM, Blank MC, Millen KJ, Sharlin DS, Forrest D, Dahlman-Wright K, Zhao C, Mishima Y, Sinha S, Chakrabarti R, Portales-Casamar E, Sladek FM, Bradley PH, Wasserman WW.

Genome Biol. 2012;13(3):R24. doi: 10.1186/gb-2012-13-3-r24.

16.

Vitamin D deficiency and calcium intake in reference to increased body mass index in children and adolescents.

Al-Musharaf S, Al-Othman A, Al-Daghri NM, Krishnaswamy S, Yusuf DS, Alkharfy KM, Al-Saleh Y, Al-Attas OS, Alokail MS, Moharram O, Yakout S, Sabico S, Chrousos GP.

Eur J Pediatr. 2012 Jul;171(7):1081-6. doi: 10.1007/s00431-012-1686-8. Epub 2012 Feb 7.

PMID:
22311168
17.

Animal snoRNAs and scaRNAs with exceptional structures.

Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.

RNA Biol. 2011 Nov-Dec;8(6):938-46. doi: 10.4161/rna.8.6.16603. Epub 2011 Nov 1.

18.

Bcheck: a wrapper tool for detecting RNase P RNA genes.

Yusuf D, Marz M, Stadler PF, Hofacker IL.

BMC Genomics. 2010 Jul 13;11:432. doi: 10.1186/1471-2164-11-432.

19.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles.

Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A.

Nucleic Acids Res. 2010 Jan;38(Database issue):D105-10. doi: 10.1093/nar/gkp950. Epub 2009 Nov 11.

20.

An alternative method for the evaluation of docking performance: RSR vs RMSD.

Yusuf D, Davis AM, Kleywegt GJ, Schmitt S.

J Chem Inf Model. 2008 Jul;48(7):1411-22. doi: 10.1021/ci800084x. Epub 2008 Jul 4.

PMID:
18598022
21.

Gene characterization index: assessing the depth of gene annotation.

Kemmer D, Podowski RM, Yusuf D, Brumm J, Cheung W, Wahlestedt C, Lenhard B, Wasserman WW.

PLoS One. 2008 Jan 23;3(1):e1440. doi: 10.1371/journal.pone.0001440.

22.

The Gene Set Builder: collation, curation, and distribution of sets of genes.

Yusuf D, Lim JS, Wasserman WW.

BMC Bioinformatics. 2005 Dec 21;6:305.

23.

Twins with moyamoya disease.

Sarenur T, Mehmet K, Vesile O, Nilgün Y, Yusuf D, Sabahattin K, Tugrul O.

Acta Paediatr Jpn. 1994 Dec;36(6):705-8.

PMID:
7871988

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