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Items: 1 to 50 of 52

1.

FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics.

Chanumolu SK, Albahrani M, Otu HH.

BMC Bioinformatics. 2019 Aug 15;20(1):424. doi: 10.1186/s12859-019-3015-y.

2.

Neutrophil activation in systemic capillary leak syndrome (Clarkson disease).

Xie Z, Kuhns DB, Gu X, Otu HH, Libermann TA, Gallin JI, Parikh SM, Druey KM.

J Cell Mol Med. 2019 Aug;23(8):5119-5127. doi: 10.1111/jcmm.14381. Epub 2019 Jun 18.

3.

Zebrafish macroH2A variants have distinct embryo localization and function.

Gonzalez-Munoz E, Arboleda-Estudillo Y, Chanumolu SK, Otu HH, Cibelli JB.

Sci Rep. 2019 Jun 14;9(1):8632. doi: 10.1038/s41598-019-45058-6.

4.

Identification of Genes Differentially Expressed in Simvastatin-Induced Alveolar Bone Formation.

Liu J, Chanumolu SK, Krei Z, Albahrani M, Akhtam A, Jia Z, Wang X, Wang D, Otu HH, Reinhardt RA, Nawshad A.

JBMR Plus. 2019 Jan 2;3(5):e10122. doi: 10.1002/jbm4.10122. eCollection 2019 May.

5.

Identification of Plasma Proteome Signatures Associated With Surgery Using SOMAscan.

Fong TG, Chan NY, Dillon ST, Zhou W, Tripp B, Ngo LH, Otu HH, Inouye SK, Vasunilashorn SM, Cooper Z, Xie Z, Marcantonio ER, Libermann TA.

Ann Surg. 2019 Mar 26. doi: 10.1097/SLA.0000000000003283. [Epub ahead of print]

PMID:
30946084
6.

Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression.

Workman AD, Nocera AL, Mueller SK, Otu HH, Libermann TA, Bleier BS.

Int Forum Allergy Rhinol. 2019 Jul;9(7):776-786. doi: 10.1002/alr.22315. Epub 2019 Feb 18.

PMID:
30775848
7.

Noninvasive exosomal proteomic biosignatures, including cystatin SN, peroxiredoxin-5, and glycoprotein VI, accurately predict chronic rhinosinusitis with nasal polyps.

Mueller SK, Nocera AL, Dillon ST, Gu X, Wendler O, Otu HH, Libermann TA, Bleier BS.

Int Forum Allergy Rhinol. 2019 Feb;9(2):177-186. doi: 10.1002/alr.22226. Epub 2018 Nov 28.

PMID:
30485711
8.

Development of a Dynamic Multi-Protein Signature of Postoperative Delirium.

Vasunilashorn SM, Ngo LH, Chan NY, Zhou W, Dillon ST, Otu HH, Inouye SK, Wyrobnik I, Kuchel GA, McElhaney JE, Xie Z, Alsop DC, Jones RN, Libermann TA, Marcantonio ER.

J Gerontol A Biol Sci Med Sci. 2019 Jan 16;74(2):261-268. doi: 10.1093/gerona/gly036.

9.

Correction: Genomic Counter-Stress Changes Induced by the Relaxation Response.

Dusek JA, Otu HH, Wohlhueter AL, Bhasin M, Zerbini LF, Joseph MG, Benson H, Libermann TA.

PLoS One. 2017 Feb 21;12(2):e0172845. doi: 10.1371/journal.pone.0172845. eCollection 2017.

10.

Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs.

Tomov ML, Olmsted ZT, Dogan H, Gongorurler E, Tsompana M, Otu HH, Buck M, Chang EA, Cibelli J, Paluh JL.

Sci Rep. 2016 Dec 5;6:37637. doi: 10.1038/srep37637.

11.

Higher C-Reactive Protein Levels Predict Postoperative Delirium in Older Patients Undergoing Major Elective Surgery: A Longitudinal Nested Case-Control Study.

Dillon ST, Vasunilashorn SM, Ngo L, Otu HH, Inouye SK, Jones RN, Alsop DC, Kuchel GA, Metzger ED, Arnold SE, Marcantonio ER, Libermann TA.

Biol Psychiatry. 2017 Jan 15;81(2):145-153. doi: 10.1016/j.biopsych.2016.03.2098. Epub 2016 Mar 25.

12.

Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier.

Bhasin MK, Ndebele K, Bucur O, Yee EU, Otu HH, Plati J, Bullock A, Gu X, Castan E, Zhang P, Najarian R, Muraru MS, Miksad R, Khosravi-Far R, Libermann TA.

Oncotarget. 2016 Apr 26;7(17):23263-81. doi: 10.18632/oncotarget.8139.

13.

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota.

Wang F, Kaplan JL, Gold BD, Bhasin MK, Ward NL, Kellermayer R, Kirschner BS, Heyman MB, Dowd SE, Cox SB, Dogan H, Steven B, Ferry GD, Cohen SA, Baldassano RN, Moran CJ, Garnett EA, Drake L, Otu HH, Mirny LA, Libermann TA, Winter HS, Korolev KS.

Cell Rep. 2016 Feb 2;14(4):945-955. doi: 10.1016/j.celrep.2015.12.088. Epub 2016 Jan 21.

14.

Nicotine Exposure During Pregnancy Results in Persistent Midline Epithelial Seam With Improper Palatal Fusion.

Ozturk F, Sheldon E, Sharma J, Canturk KM, Otu HH, Nawshad A.

Nicotine Tob Res. 2016 May;18(5):604-12. doi: 10.1093/ntr/ntv227. Epub 2015 Oct 6.

15.

Bioinformatics approaches to single-cell analysis in developmental biology.

Yalcin D, Hakguder ZM, Otu HH.

Mol Hum Reprod. 2016 Mar;22(3):182-92. doi: 10.1093/molehr/gav050. Epub 2015 Sep 10. Review.

PMID:
26358759
16.

Bayesian pathway analysis of cancer microarray data.

Korucuoglu M, Isci S, Ozgur A, Otu HH.

PLoS One. 2014 Jul 18;9(7):e102803. doi: 10.1371/journal.pone.0102803. eCollection 2014.

17.

Cell reprogramming. Histone chaperone ASF1A is required for maintenance of pluripotency and cellular reprogramming.

Gonzalez-Muñoz E, Arboleda-Estudillo Y, Otu HH, Cibelli JB.

Science. 2014 Aug 15;345(6198):822-5. doi: 10.1126/science.1254745. Epub 2014 Jul 17.

18.

Whole genome sequence of a Turkish individual.

Dogan H, Can H, Otu HH.

PLoS One. 2014 Jan 9;9(1):e85233. doi: 10.1371/journal.pone.0085233. eCollection 2014.

19.

Bayesian network prior: network analysis of biological data using external knowledge.

Isci S, Dogan H, Ozturk C, Otu HH.

Bioinformatics. 2014 Mar 15;30(6):860-7. doi: 10.1093/bioinformatics/btt643. Epub 2013 Nov 9.

20.

Objective functions.

Doğan H, Otu HH.

Methods Mol Biol. 2014;1079:45-58. doi: 10.1007/978-1-62703-646-7_3.

PMID:
24170394
21.

Prediction of peptides binding to MHC class I and II alleles by temporal motif mining.

Meydan C, Otu HH, Sezerman OU.

BMC Bioinformatics. 2013;14 Suppl 2:S13. doi: 10.1186/1471-2105-14-S2-S13. Epub 2013 Jan 21.

22.

Gene expression profiling of granulosa cells from PCOS patients following varying doses of human chorionic gonadotropin.

Coskun S, Otu HH, Awartani KA, Al-Alwan LA, Al-Hassan S, Al-Mayman H, Kaya N, Inan MS.

J Assist Reprod Genet. 2013 Mar;30(3):341-52. doi: 10.1007/s10815-013-9935-y. Epub 2013 Feb 5.

23.

Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. using the relative complexity measure.

Bakış Y, Otu HH, Taşçı N, Meydan C, Bilgin N, Yüzbaşıoğlu S, Sezerman OU.

BMC Bioinformatics. 2013 Jan 17;14:20. doi: 10.1186/1471-2105-14-20.

24.

Identification of a novel gene set in human cumulus cells predictive of an oocyte's pregnancy potential.

Iager AE, Kocabas AM, Otu HH, Ruppel P, Langerveld A, Schnarr P, Suarez M, Jarrett JC, Conaghan J, Rosa GJ, Fernández E, Rawlins RG, Cibelli JB, Crosby JA.

Fertil Steril. 2013 Mar 1;99(3):745-752.e6. doi: 10.1016/j.fertnstert.2012.10.041. Epub 2012 Nov 29.

PMID:
23200692
25.

Reprogrammed transcriptome in rhesus-bovine interspecies somatic cell nuclear transfer embryos.

Wang K, Otu HH, Chen Y, Lee Y, Latham K, Cibelli JB.

PLoS One. 2011;6(7):e22197. doi: 10.1371/journal.pone.0022197. Epub 2011 Jul 25. Erratum in: PLoS One. 2012;7(10). doi:10.1371/annotation/5aa90741-1a8a-4443-83b1-c5abcb59bb51.

26.

Pathway analysis of high-throughput biological data within a Bayesian network framework.

Isci S, Ozturk C, Jones J, Otu HH.

Bioinformatics. 2011 Jun 15;27(12):1667-74. doi: 10.1093/bioinformatics/btr269. Epub 2011 May 5.

PMID:
21551144
27.

Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets.

Albayrak A, Otu HH, Sezerman UO.

BMC Bioinformatics. 2010 Aug 18;11:428. doi: 10.1186/1471-2105-11-428.

28.

Tob1 is a constitutively expressed repressor of liver regeneration.

Ho KJ, Do NL, Otu HH, Dib MJ, Ren X, Enjyoji K, Robson SC, Terwilliger EF, Karp SJ.

J Exp Med. 2010 Jun 7;207(6):1197-208. doi: 10.1084/jem.20092434. Epub 2010 May 31.

29.

Bioinformatic identification and characterization of human endothelial cell-restricted genes.

Bhasin M, Yuan L, Keskin DB, Otu HH, Libermann TA, Oettgen P.

BMC Genomics. 2010 May 28;11:342. doi: 10.1186/1471-2164-11-342.

30.

Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius.

Al-Swailem AM, Shehata MM, Abu-Duhier FM, Al-Yamani EJ, Al-Busadah KA, Al-Arawi MS, Al-Khider AY, Al-Muhaimeed AN, Al-Qahtani FH, Manee MM, Al-Shomrani BM, Al-Qhtani SM, Al-Harthi AS, Akdemir KC, Inan MS, Otu HH.

PLoS One. 2010 May 19;5(5):e10720. doi: 10.1371/journal.pone.0010720.

31.

An exquisite cross-control mechanism among endothelial cell fate regulators directs the plasticity and heterogeneity of lymphatic endothelial cells.

Kang J, Yoo J, Lee S, Tang W, Aguilar B, Ramu S, Choi I, Otu HH, Shin JW, Dotto GP, Koh CJ, Detmar M, Hong YK.

Blood. 2010 Jul 8;116(1):140-50. doi: 10.1182/blood-2009-11-252270. Epub 2010 Mar 29.

32.

Gene expression profile of mouse prostate tumors reveals dysregulations in major biological processes and identifies potential murine targets for preclinical development of human prostate cancer therapy.

Haram KM, Peltier HJ, Lu B, Bhasin M, Otu HH, Choy B, Regan M, Libermann TA, Latham GJ, Sanda MG, Arredouani MS.

Prostate. 2008 Oct 1;68(14):1517-30. doi: 10.1002/pros.20803.

PMID:
18668517
33.

Grammar-based distance in progressive multiple sequence alignment.

Russell DJ, Otu HH, Sayood K.

BMC Bioinformatics. 2008 Jul 10;9:306. doi: 10.1186/1471-2105-9-306.

34.

Genomic counter-stress changes induced by the relaxation response.

Dusek JA, Otu HH, Wohlhueter AL, Bhasin M, Zerbini LF, Joseph MG, Benson H, Libermann TA.

PLoS One. 2008 Jul 2;3(7):e2576. doi: 10.1371/journal.pone.0002576. Erratum in: PLoS One. 2017 Feb 21;12 (2):e0172845.

35.

Differential expression of GADD45beta in normal and osteoarthritic cartilage: potential role in homeostasis of articular chondrocytes.

Ijiri K, Zerbini LF, Peng H, Otu HH, Tsuchimochi K, Otero M, Dragomir C, Walsh N, Bierbaum BE, Mattingly D, van Flandern G, Komiya S, Aigner T, Libermann TA, Goldring MB.

Arthritis Rheum. 2008 Jul;58(7):2075-87. doi: 10.1002/art.23504.

36.

Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation.

Nikolova-Krstevski V, Bhasin M, Otu HH, Libermann T, Oettgen P.

BMC Genomics. 2008 May 22;9:240. doi: 10.1186/1471-2164-9-240.

37.

Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver disease.

Zinkin NT, Grall F, Bhaskar K, Otu HH, Spentzos D, Kalmowitz B, Wells M, Guerrero M, Asara JM, Libermann TA, Afdhal NH.

Clin Cancer Res. 2008 Jan 15;14(2):470-7. doi: 10.1158/1078-0432.CCR-07-0586.

38.

Proteomic identification of interleukin-2 therapy response in metastatic renal cell cancer.

Jones J, Otu HH, Grall F, Spentzos D, Can H, Aivado M, Belldegrun AS, Pantuck AJ, Libermann TA.

J Urol. 2008 Feb;179(2):730-6. Epub 2007 Dec 20.

39.

Gene expression of purified beta-cell tissue obtained from human pancreas with laser capture microdissection.

Marselli L, Thorne J, Ahn YB, Omer A, Sgroi DC, Libermann T, Otu HH, Sharma A, Bonner-Weir S, Weir GC.

J Clin Endocrinol Metab. 2008 Mar;93(3):1046-53. Epub 2007 Dec 11.

40.

Reduced PDEF expression increases invasion and expression of mesenchymal genes in prostate cancer cells.

Gu X, Zerbini LF, Otu HH, Bhasin M, Yang Q, Joseph MG, Grall F, Onatunde T, Correa RG, Libermann TA.

Cancer Res. 2007 May 1;67(9):4219-26.

41.

Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy.

Otu HH, Can H, Spentzos D, Nelson RG, Hanson RL, Looker HC, Knowler WC, Monroy M, Libermann TA, Karumanchi SA, Thadhani R.

Diabetes Care. 2007 Mar;30(3):638-43.

PMID:
17327333
42.

Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns.

Otu HH, Naxerova K, Ho K, Can H, Nesbitt N, Libermann TA, Karp SJ.

J Biol Chem. 2007 Apr 13;282(15):11197-204. Epub 2007 Jan 16.

43.

Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease.

Aivado M, Spentzos D, Germing U, Alterovitz G, Meng XY, Grall F, Giagounidis AA, Klement G, Steidl U, Otu HH, Czibere A, Prall WC, Iking-Konert C, Shayne M, Ramoni MF, Gattermann N, Haas R, Mitsiades CS, Fung ET, Libermann TA.

Proc Natl Acad Sci U S A. 2007 Jan 23;104(4):1307-12. Epub 2007 Jan 12.

44.

Essential role of Jun family transcription factors in PU.1 knockdown-induced leukemic stem cells.

Steidl U, Rosenbauer F, Verhaak RG, Gu X, Ebralidze A, Otu HH, Klippel S, Steidl C, Bruns I, Costa DB, Wagner K, Aivado M, Kobbe G, Valk PJ, Passegué E, Libermann TA, Delwel R, Tenen DG.

Nat Genet. 2006 Nov;38(11):1269-77. Epub 2006 Oct 15.

PMID:
17041602
45.

A novel class of vascular endothelial growth factor-responsive genes that require forkhead activity for expression.

Abid MR, Shih SC, Otu HH, Spokes KC, Okada Y, Curiel DT, Minami T, Aird WC.

J Biol Chem. 2006 Nov 17;281(46):35544-53. Epub 2006 Sep 15.

46.

The transcriptome of human oocytes.

Kocabas AM, Crosby J, Ross PJ, Otu HH, Beyhan Z, Can H, Tam WL, Rosa GJ, Halgren RG, Lim B, Fernandez E, Cibelli JB.

Proc Natl Acad Sci U S A. 2006 Sep 19;103(38):14027-32. Epub 2006 Sep 12.

47.

Proteomic analysis of the allograft response.

El Essawy B, Otu HH, Choy B, Zheng XX, Libermann TA, Strom TB.

Transplantation. 2006 Jul 27;82(2):267-74.

PMID:
16858291
48.

Optimization and evaluation of surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) with reversed-phase protein arrays for protein profiling.

Aivado M, Spentzos D, Alterovitz G, Otu HH, Grall F, Giagounidis AA, Wells M, Cho JY, Germing U, Czibere A, Prall WC, Porter C, Ramoni MF, Libermann TA.

Clin Chem Lab Med. 2005;43(2):133-40.

PMID:
15843205
49.

Utilization of the relative complexity measure to construct a phylogenetic tree for fungi.

Bastola DR, Otu HH, Doukas SE, Sayood K, Hinrichs SH, Iwen PC.

Mycol Res. 2004 Feb;108(Pt 2):117-25.

PMID:
15119348
50.

A new sequence distance measure for phylogenetic tree construction.

Otu HH, Sayood K.

Bioinformatics. 2003 Nov 1;19(16):2122-30.

PMID:
14594718

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