List of Publications

    Journal Articles

  1. Vasunilashorn SM, Dillon ST, Chan NY, Fong TG, Joseph M, Tripp B, Inouye SK, Xie Z, Ngo LH, Lee C, Elias JA, Otu HH, Marcantonio ER, Libermann TA. "Proteome-wide analysis using SOMAscan identifies and validates Chitinase 3-Like Protein 1 as a risk and disease marker of postoperative Delirium" The Journal of Gerontology: Series A, 2020. DOI:10.1093/gerona/glaa326.
  2. Tripp BA, Dillon ST, Yuan M, Asara JM, Vasunilashorn SM, Fong TG, Inouye SK, Metzger ED, Xie Z, Ngo LH, Marcantonio E, Libermann T, Otu HH. "Targeted metabolomics analysis identifies risk and disease markers of postoperative Delirium" Scientific Reports, 2021; 11(1):1521. DOI:10.1038/s41598-020-80412-z.
  3. Yakah W, Singh P, Brown J, Stoll B, Burrin D, Premkumar MH, Otu HH, Gu X, Dillon ST, Liberman TA, Freedman SD, and Martin CR. "Parenteral lipid emulsions induce unique ileal fatty acid and metabolomic profiles but do not increase the risk of necrotizing enterocolitis in preterm pigs" Am J Physiol Gastrointest Liver Physiol, 2021; 320(2):G227-G239. DOI: 10.1152/ajpgi.00311.2020
  4. Chanumolu SK, Albahrani M, Can H, Otu HH. "KEGG2Net: deducing gene interaction networks and acyclic graphs from KEGG pathways" EMBnet.journal, 2021,26:e949. DOI: 10.14806/ej.26.0.949
  5. Yalcin D and Otu HH. "An unbiased predictive model to detect DNA methylation propensity of CpG islands in the human genome" Current Bioinformatics, 2021; 16(2):179-196. DOI: 10.2174/1574893615999200724145835
  6. Liu J, Chanumolu SK, White KM, ALbahrani M, Otu HH, Nawshad A. "Transcriptional analysis of cleft palate in TGF-B3 mutant mice" Scientific Reports, 2020; 10(1):14940. DOI:10.1038/s41598-020-71636-0
  7. Can H, Chanumolu SK, Gonzalez-Munoz E, Prukudom S, Otu HH*, Cibelli JB*. "Comparative analysis of single-cell transcriptomics in human and zebrafish oocytes" BMC Genomics, 2020 21(1):471 DOI: 10.1186/s12864-020-06860-z (*Co-senior authors)
  8. Morad G, Daisy CC, Otu HH, Liebermann TA, Dillon S, Moses M. "Cdc42-Dependent Transfer of mir301 from Breast Cancer-Derived Extracellular Vesicles Regulates the Matrix Modulating Ability of Astrocytes at the Blood–Brain Barrier" Int. J. Mol. Sci., 2020 21(11):3851 DOI: 10.3390/ijms21113851
  9. Shainker SA, Silver BM, Modest AM, Hacker MR, Hecht JH, Salahuddin S, Dillon ST, Ciampa EJ, D'Alton ME, Otu HH, Abuhamad AZ, Einserson BD, Branch DW, Wylie BJ, Libermann TA, Karumanchi SA. "Placenta Accreta Spectrum: Biomarker Discovery using Plasma Proteomics" Am J Obstet Gynecol., 2020 223(3):433.e1-433.e14. DOI: 10.1016/j.ajog.2020.03.019.
  10. Workman AD, Miyake M, Nocera AL, Mueller SK, Finn K, Otu HH, Libermann TA, Bleier BS. "Unexpected effects of systemic steroids on the CRSwNP proteome: Is protein upregulation more important than inhibition?" Int. Forum Allergy Rhinol., 2020 10(3):334-342. DOI: 10.1002/alr.22497.
  11. Chanumolu, Sree K., Mustafa Albahrani, and Hasan H. Otu. "FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics." BMC Bioinformatics. (2019); 20(1):424. DOI: 10.1186/s12859-019-3015-y
  12. Xie, Zhihui, Douglas B. Kuhns, Xuesong Gu, Hasan H. Otu, Towia A. Libermann, John I. Gallin, Samir M. Parikh, and Kirk M. Druey. "Neutrophil activation in systemic capillary leak syndrome (Clarkson disease)." Journal of Cellular and Molecular Medicine. (2019); 23(8):5119-5127. DOI: 10.1111/jcmm.14381
  13. Gonzalez-Munoz, E., Y. Arboleda-Estudillo, S. K. Chanumolu, Hasan H. Otu, and J. B. Cibelli. "Zebrafish macroH2A variants have distinct embryo localization and function." Scientific Reports. (2019); 9(1):8632. DOI: 10.1038/s41598-019-45058-6
  14. Liu, J., S. K. Chanumolu, Z. Krei, M. Albahrani, A. Akhtam, Z. Jia, X. Wang et al. "Identification of Genes Differentially Expressed in Simvastatin‐Induced Alveolar Bone Formation." JBMR Plus. (2019); 3(5):e10122. DOI: 10.1002/jbm4.10122
  15. Fong, Tamara G., Noel Y. Chan, Simon T. Dillon, Wenxiao Zhou, Bridget Tripp, Long H. Ngo, Hasan H. Otu et al. "Identification of Plasma Proteome Signatures Associated With Surgery Using SOMAscan." Annals of Surgery (2019). DOI: 10.1097/SLA.0000000000003283
  16. Workman, Alan D., Angela L. Nocera, Sarina K. Mueller, Hasan H. Otu, Towia A. Libermann, and Benjamin S. Bleier. "Translating transcription: proteomics in chronic rhinosinusitis with nasal polyps reveals significant discordance with messenger RNA expression." International Forum of Allergy & Rhinology. (2019); 9(7):776-786. DOI: 10.1002/alr.22315
  17. Mueller, Sarina K., Angela L. Nocera, Simon T. Dillon, Xuesong Gu, Olaf Wendler, Hasan H. Otu, Towia A. Libermann, and Benjamin S. Bleier. "Noninvasive exosomal proteomic biosignatures, including cystatin SN, peroxiredoxin‐5, and glycoprotein VI, accurately predict chronic rhinosinusitis with nasal polyps." International Forum of Allergy & Rhinolog. (2019); 9(2):177-186. DOI: 10.1002/alr.22226
  18. Vasunilashorn, Sarinnapha M., Long H. Ngo, Noel Y. Chan, Wenxiao Zhou, Simon T. Dillon, Hasan H. Otu, Sharon K. Inouye et al. "Development of a Dynamic Multi-Protein Signature of Postoperative Delirium." The Journals of Gerontology: Series A. (2018); 74(2):261-268. DOI: 10.1093/gerona/gly036
  19. Dillon, Simon T., Sarinnapha M. Vasunilashorn, Long Ngo, Hasan H. Otu, Sharon K. Inouye, Richard N. Jones, David C. Alsop et al. "Higher C-reactive protein levels predict postoperative delirium in older patients undergoing major elective surgery: a longitudinal nested case-control study." Biological Psychiatry. (2017); 81(2):145-153. DOI: 10.1016/j.biopsych.2016.03.2098
  20. Tomov, Martin L., Zachary T. Olmsted, Haluk Dogan, Eda Gongorurler, Maria Tsompana, Hasan H. Otu, Michael Buck, Eun-Ah Chang, Jose Cibelli, and Janet L. Paluh. "Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs." Scientific Reports. (2016); 6:37637. DOI: 10.1038/srep37637 (2016).
  21. Bhasin, Manoj K., Kenneth Ndebele, Octavian Bucur, Eric U. Yee, Hasan H. Otu, Jessica Plati, Andrea Bullock et al. "Meta-analysis of transcriptome data identifies a novel 5-gene pancreatic adenocarcinoma classifier." Oncotarget. (2016); 7(17):23263-81. DOI: 10.18632/oncotarget.8139
  22. Ozturk, Ferhat, Elizabeth Sheldon, Janki Sharma, Kemal Murat Canturk, Hasan H. Otu, and Ali Nawshad. "Nicotine exposure during pregnancy results in persistent midline epithelial seam with improper palatal fusion." Nicotine & Tobacco Research. (2015); 18(5):604-612. DOI: 10.1093/ntr/ntv227
  23. Wang, Feng, Jess L. Kaplan, Benjamin D. Gold, Manoj K. Bhasin, Naomi L. Ward, Richard Kellermayer, Barbara S. Kirschner, Melvin B. Heyman, Scot E. Dowd, Stephen B. Cox, Haluk Dogan, Blaire Steven, George D. Ferry, Stanley A. Cohen, Robert N. Baldassano, Christopher J. Moran, Elizabeth A. Garnett, Lauren Drake, Hasan H. Otu, Leonid A. Mirny, Towia A. Libermann, Harland S. Winter, Kirill S. Korolev."Detecting microbial dysbiosis associated with pediatric Crohn disease despite the high variability of the gut microbiota." Cell Reports. (2016); 14(4):945-955. DOI: 10.1016/j.celrep.2015.12.088
  24. Yalcin, Dicle, Zeynep M. Hakguder, and Hasan H. Otu. "Bioinformatics approaches to single-cell analysis in developmental biology." Molecular Human Reproduction. (2015); 22(3):182-192. DOI: 10.1093/molehr/gav050
  25. Gonzalez-Muñoz, Elena, Yohanna Arboleda-Estudillo, Hasan H. Otu, and Jose B. Cibelli. "Histone chaperone ASF1A is required for maintenance of pluripotency and cellular reprogramming." Science. (2014); 345(6198):822-825. DOI: 10.1126/science.1254745
  26. Korucuoglu, Melike, Senol Isci, Arzucan Ozgur, and Hasan H. Otu. "Bayesian pathway analysis of cancer microarray data." PloS One. (2014); 9(7):e102803. DOI: 10.1371/journal.pone.0102803
  27. Dogan, Haluk, Handan Can, and Hasan H. Otu. "Whole genome sequence of a Turkish individual." PloS One. (2014); 9(1):e85233. DOI: 10.1371/journal.pone.0085233
  28. Isci, Senol, Haluk Dogan, Cengizhan Ozturk, and Hasan H. Otu. "Bayesian network prior: network analysis of biological data using external knowledge." Bioinformatics. (2013); 30(6):860-867. DOI: 10.1093/bioinformatics/btt643
  29. Coskun, Serdar, Hasan H. Otu, Khalid A. Awartani, Laila A. Al-Alwan, Saad Al-Hassan, Hend Al-Mayman, Namik Kaya, and Mehmet S. Inan. "Gene expression profiling of granulosa cells from PCOS patients following varying doses of human chorionic gonadotropin." Journal of Assisted Reproduction and Genetics. (2013); 30(3):341-352. DOI: 10.1007/s10815-013-9935-y
  30. Bakış, Yasin, Hasan H. Otu, Nivart Taşçı, Cem Meydan, Sırrı Yüzbaşıoğlu, and O. Uğur Sezerman. "Testing robustness of relative complexity measure method constructing robust phylogenetic trees for Galanthus L. Using the relative complexity measure." BMC Bioinformatics. (2013); 14:20. DOI: 10.1186/1471-2105-14-20
  31. Meydan, Cem, Hasan H. Otu, and Osman Uğur Sezerman. "Prediction of peptides binding to MHC class I and II alleles by temporal motif mining." BMC Bioinformatics. (2013); 14(Suppl 2):S13. DOI: 10.1186/1471-2105-14-S2-S13
  32. Otu, Hasan H.*, Amy E. Iager*, Arif M. Kocabas*, Patricia Ruppel, Anna Langerveld, Patricia Schnarr, Mariluz Suarez et al. "Identification of a novel gene set in human cumulus cells predictive of an oocyte's pregnancy potential." Fertility and Sterility. (2013); 99(3):745-752. DOI: 10.1016/j.fertnstert.2012.10.041 *Equal Contribution
  33. Bakış, Yasin, Hasan H. Otu, and O. Uğur Sezerman. "Inferring phylogenies from physico-chemical properties of DNA." American Journal of Bioinformatics Research. (2012); 2(1):1-6. DOI: 10.5923/j.bioinformatics.20120201.01
  34. Wang, Kai, Hasan H. Otu, Ying Chen, Young Lee, Keith Latham, and Jose B. Cibelli. "Reprogrammed transcriptome in rhesus-bovine interspecies somatic cell nuclear transfer embryos." PLoS One. (2011); 6(7):e22197. DOI: 10.1371/journal.pone.0022197
  35. Isci, Senol, Cengizhan Ozturk, Jon Jones, and Hasan H. Otu. "Pathway analysis of high-throughput biological data within a Bayesian network framework." Bioinformatics. (2011); 27(12):1667-1674. DOI: 10.1093/bioinformatics/btr269
  36. Albayrak, Aydin, Hasan H. Otu, and Ugur O. Sezerman. "Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets." BMC Bioinformatics. (2010); 11: 428. DOI: 10.1186/1471-2105-11-428
  37. Kang, Jinjoo, Jaehyuk Yoo, Sunju Lee, Wanli Tang, Berenice Aguilar, Swapnika Ramu, Inho Choi et al. "An exquisite cross-control mechanism among endothelial cell fate regulators directs the plasticity and heterogeneity of lymphatic endothelial cells." Blood. (2010); 116(1):140-150. DOI: 10.1182/blood-2009-11-252270
  38. Ho, Karen J., Nhue L. Do, Hasan H. Otu, Martin J. Dib, Xianghui Ren, Keiichi Enjyoji, Simon C. Robson, Ernest F. Terwilliger, and Seth J. Karp. "Tob1 is a constitutively expressed repressor of liver regeneration." Journal of Experimental Medicine. (2010); 207(6):1197-1208. DOI: 10.1084/jem.20092434
  39. Bhasin, Manoj, Lei Yuan, Derin B. Keskin, Hasan H. Otu, Towia A. Libermann, and Peter Oettgen. "Bioinformatic identification and characterization of human endothelial cell-restricted genes." BMC Genomics. (2010); 11:342. DOI: 10.1186/1471-2164-11-342
  40. Al-Swailem, Abdulaziz M., Maher M. Shehata, Faisel M. Abu-Duhier, Essam J. Al-Yamani, Khalid A. Al-Busadah, Mohammed S. Al-Arawi, Ali Y. Al-Khider et al. "Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius." PLoS One. (2010); 5(5):e10720. DOI: 10.1371/journal.pone.0010720
  41. Ramlawi, Basel, Hasan Otu, Mark J. Russo, Richard J. Novick, Cesario Bianchi, and Frank W. Sellke. "Aprotinin attenuates genomic expression variability following cardiac surgery." Journal of Cardiac Surgery. (2009); 24(6):772-780. DOI: 10.1111/j.1540-8191.2009.00924.x
  42. Prall, Wolf C., Akos Czibere, Franck Grall, Dimitrios Spentzos, Ulrich Steidl, Aristoteles Achilles Nikolaus Giagounidis, Andrea Kuendgen et al. "Differential gene expression of bone marrow-derived CD34+ cells is associated with survival of patients suffering from myelodysplastic syndrome." International Journal of Hematology. (2009); 89(2):173-187. View Article
  43. Haram, Kerstyn M., Heidi J. Peltier, Bin Lu, Manoj Bhasin, Hasan H. Otu, Bob Choy, Meredith Regan et al. "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." The Prostate. (2008); 68(14):1517-1530. DOI: 10.1002/pros.20803
  44. Russell, David J., Hasan H. Otu, and Khalid Sayood. "Grammar-based distance in progressive multiple sequence alignment." BMC Bioinformatics. (2008); 9:306. DOI: 10.1186/1471-2105-9-306
  45. Otu, Hasan H.*, Jeffery A. Dusek*, Ann L. Wohlhueter, Manoj Bhasin, Luiz F. Zerbini, Marie G. Joseph, Herbert Benson, and Towia A. Libermann. "Genomic counter-stress changes induced by the relaxation response." PloS One. (2008); 3(7):e2576. DOI: 10.1371/journal.pone.0002576. *Equal Contribution.
  46. Ijiri, Kosei, Luiz F. Zerbini, Haibing Peng, Hasan H. Otu, Kaneyuki Tsuchimochi, Miguel Otero, Cecilia Dragomir et al. "Differential expression of GADD45β in normal and osteoarthritic cartilage: potential role in homeostasis of articular chondrocytes." Arthritis & Rheumatism. (2008); 58(7):2075-2087. DOI: 10.1002/art.23504
  47. Nikolova-Krstevski, Vesna, Manoj Bhasin, Hasan H. Otu, Towia Libermann, and Peter Oettgen. "Gene expression analysis of embryonic stem cells expressing VE-cadherin (CD144) during endothelial differentiation." BMC Genomics. (2008); 9:240. DOI: 10.1186/1471-2164-9-240
  48. Marselli, Lorella, Jeffrey Thorne, Yu-Bae Ahn, Abdulkadir Omer, Dennis C. Sgroi, Towia Libermann, Hasan H. Otu, Arun Sharma, Susan Bonner-Weir, and Gordon C. Weir. "Gene expression of purified β-cell tissue obtained from human pancreas with laser capture microdissection." The Journal of Clinical Endocrinology & Metabolism. (2008); 93(3):1046-1053. DOI: 10.1210/jc.2007-0931
  49. Jones, Jon, Hasan H. Otu, Franck Grall, Dimitrios Spentzos, Handan Can, Manuel Aivado, Arie S. Belldegrun, Allan J. Pantuck, and Towia A. Libermann. "Proteomic identification of interleukin-2 therapy response in metastatic renal cell cancer." The Journal of Urology. (2008); 179(2):730-736. DOI: 10.1016/j.juro.2007.09.016
  50. Zinkin, Noah T., Franck Grall, Killimangalam Bhaskar, Hasan H. Otu, Dimitrios Spentzos, Brett Kalmowitz, Meghan Wells et al. "Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver disease." Clinical Cancer Research. (2008); 14(2):470-477. DOI: 10.1158/1078-0432.CCR-07-0586
  51. Ramlawi, Basel, Hasan Otu, James L. Rudolph, Shigetoshi Mieno, Isaac S. Kohane, Handan Can, Towia A. Libermann, Edward R. Marcantonio, Cesario Bianchi, and Frank W. Sellke. "Genomic expression pathways associated with brain injury after cardiopulmonary bypass." The Journal of Thoracic and Cardiovascular Surgery. (2007); 134(4):996-1005. DOI: 10.1016/j.jtcvs.2007.01.096
  52. Zhang, Xiaoping, Liang Zhang, Hongmei Yang, Xu Huang, Hasan Otu, Towia A. Libermann, William C. DeWolf, Roya Khosravi-Far, and Aria F. Olumi. "c-Fos as a proapoptotic agent in TRAIL-induced apoptosis in prostate cancer cells." Cancer Research. (2007); 67(19):9425-9434. DOI: 10.1158/0008-5472.CAN-07-1310
  53. Ramlawi, Basel, Hasan Otu, Shigetoshi Mieno, Munir Boodhwani, Neel R. Sodha, Richard T. Clements, Cesario Bianchi, and Frank W. Sellke. "Oxidative stress and atrial fibrillation after cardiac surgery: a case-control study." The Annals of Thoracic Surgery. (2007); 84(4):1166-1173. DOI: 10.1016/j.athoracsur.2007.04.126
  54. Kennedy, Adam R., Pavlos Pissios, Hasan Otu, Bingzhong Xue, Kenji Asakura, Noburu Furukawa, Frank E. Marino et al. "A high-fat, ketogenic diet induces a unique metabolic state in mice." American Journal of Physiology-Endocrinology and Metabolism. (2007); 292(6):E1724-E1739. DOI: 10.1152/ajpendo.00717.2006
  55. Gu, Xuesong, Luiz F. Zerbini, Hasan H. Otu, Manoj Bhasin, Quanli Yang, Marie G. Joseph, Franck Grall, Tomi Onatunde, Ricardo G. Correa, and Towia A. Libermann. "Reduced PDEF expression increases invasion and expression of mesenchymal genes in prostate cancer cells." Cancer Research. (2007); 67(9):4219-4226. DOI: 10.1158/0008-5472.CAN-06-3689
  56. Otu, Hasan H., Kamila Naxerova, Karen Ho, Handan Can, Nicole Nesbitt, Towia A. Libermann, and Seth J. Karp. "Restoration of liver mass after injury requires proliferative and not embryonic transcriptional patterns." Journal of Biological Chemistry. (2007); 282(15):11197-11204. DOI: 10.1074/jbc.M608441200
  57. Otu, Hasan H., Handan Can, Dimitrios Spentzos, Robert G. Nelson, Robert L. Hanson, Helen C. Looker, William C. Knowler et al. "Prediction of diabetic nephropathy using urine proteomic profiling 10 years prior to development of nephropathy." Diabetes Care. (2007); 30(3): 638-643. DOI: 10.2337/dc06-1656
  58. Aivado, Manuel, Dimitrios Spentzos, Ulrich Germing, Gil Alterovitz, Xiao-Ying Meng, Franck Grall, Aristoteles AN Giagounidis et al. "Serum proteome profiling detects myelodysplastic syndromes and identifies CXC chemokine ligands 4 and 7 as markers for advanced disease." Proceedings of the National Academy of Sciences. (2007); 104(4):1307-1312. DOI: 10.1073/pnas.0610330104
  59. Zerbini, Luiz F., Akos Czibere, Yihong Wang, Ricardo G. Correa, Hasan Otu, Marie Joseph, Yuko Takayasu et al. "A Novel Pathway Involving Melanoma Differentiation Associated Gene-7/Interleukin-24 Mediates Nonsteroidal Anti-inflammatory Drug–Induced Apoptosis and Growth Arrest of Cancer Cells." Cancer Research. (2006); 66(24):11922-11931. DOI: 10.1158/0008-5472.CAN-06-2068
  60. Abid, Md Ruhul, Shu-Ching Shih, Hasan H. Otu, Katherine C. Spokes, Yoshiaki Okada, David T. Curiel, Takashi Minami, and William C. Aird. "A novel class of vascular endothelial growth factor-responsive genes that require forkhead activity for expression." Journal of Biological Chemistry. (2006); 281(46):35544-35553. DOI: 10.1074/jbc.M608620200
  61. Steidl, Ulrich, Frank Rosenbauer, Roel GW Verhaak, Xuesong Gu, Alexander Ebralidze, Hasan H. Otu, Steffen Klippel et al. "Essential role of Jun family transcription factors in PU. 1 knockdown–induced leukemic stem cells." Nature Genetics. (2006); 38(11):1269-77. DOI: 10.1038/ng1898
  62. Kocabas, Arif Murat, Javier Crosby, Pablo J. Ross, Hasan H. Otu, Zeki Beyhan, Handan Can, Wai-Leong Tam et al. "The transcriptome of human oocytes." Proceedings of the National Academy of Sciences. (2006); 103(38):14027-14032. DOI: 10.1073/pnas.0603227103
  63. El Essawy, Basset, Hasan H. Otu, Bob Choy, Xin Xiao Zheng, Towia A. Libermann, and Terry B. Strom. "Proteomic analysis of the allograft response." Transplantation. (2006) 82(2):267-274. DOI: 10.1097/01.tp.0000226254.89987.ec
  64. Ramnarain, Deepti B., Seongmi Park, Diana Y. Lee, Kimmo J. Hatanpaa, Shane O. Scoggin, Hasan Otu, Towia A. Libermann et al. "Differential gene expression analysis reveals generation of an autocrine loop by a mutant epidermal growth factor receptor in glioma cells." Cancer Research. (2006); 66(2):867-874. DOI: 10.1158/0008-5472.CAN-05-2753
  65. Ijiri, Kosei, Luiz F. Zerbini, Haibing Peng, Ricardo G. Correa, Binfeng Lu, Nicole Walsh, Yani Zhao et al. "A novel role for GADD45β as a mediator of MMP-13 gene expression during chondrocyte terminal differentiation." Journal of Biological Chemistry. (2005); 280(46):38544-38555. DOI: 10.1074/jbc.M504202200
  66. Wada, Youichiro, Hasan Otu, Shengqian Wu, Md Ruhul Abid, Hitomi Okada, Towia Libermann, Tatsuhiko Kodama, Shu-Ching Shih, Takashi Minami, and William C. Aird. "Preconditioning of primary human endothelial cells with inflammatory mediators alters the “set point” of the cell." The FASEB Journal. (2005); 19(13):1914-1916. DOI: 10.1096/fj.05-4037fje
  67. Spentzos, Dimitrios, Douglas A. Levine, Shakirahmed Kolia, Hasan Otu, Jeff Boyd, Towia A. Libermann, and Stephen A. Cannistra. "Unique gene expression profile based on pathologic response in epithelial ovarian cancer." Journal of Clinical Oncology. (2005); 23(31):7911-7918. DOI: 10.1200/JCO.2005.02.9363
  68. Jones, Jon, Hasan Otu, Dimitrios Spentzos, Shakirahmed Kolia, Mehmet Inan, Wolf D. Beecken, Christian Fellbaum et al. "Gene signatures of progression and metastasis in renal cell cancer." Clinical Cancer Research. (2005); 11(16):5730-5739. DOI: 10.1158/1078-0432.CCR-04-2225
  69. Aivado, Manuel, Dimitrios Spentzos, Gil Alterovitz, Hasan H. Otu, Franck Grall, Aristoteles AN Giagounidis, Meghan Wells, Je-Yoel Cho, Ulrich Germing, Akos Czibere, Wolf C. Prall, Chris Porter, Marco F. Ramoni, Towia A. Libermann. "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." Clinical Chemistry and Laboratory Medicine. (2005); 43(2):133-140. DOI: 10.1515/CCLM.2005.022
  70. von Stechow, D., D. Zurakowski, A. R. Pettit, Ralph Müller, G. Gronowicz, M. Chorev, H. Otu, T. Libermann, and Joseph M. Alexander. "Differential transcriptional effects of PTH and estrogen during anabolic bone formation." Journal of Cellular Biochemistry. (2004); 93(3):476-490. DOI: 10.1002/jcb.20174
  71. Voisine, Pierre, Marc Ruel, Tanveer A. Khan, Cesario Bianchi, Shu-Hua Xu, Isaac Kohane, Towia A. Libermann, Hasan Otu, Alan R. Saltiel, and Frank W. Sellke. "Differences in gene expression profiles of diabetic and nondiabetic patients undergoing cardiopulmonary bypass and cardioplegic arrest." Circulation. (2004); 110(11 Suppl 1):II-280. DOI: 10.1161/01.CIR.0000138974.18839.02
  72. Bastola, Dhundy R., Hasan H. Otu, Sarah E. Doukas, Khalid Sayood, Steven H. Hinrichs, Peter C. Iwen. "Utilization of the relative complexity measure to construct a phylogenetic tree for fungi." Mycological Research. (2004); 108(2):117-125. DOI: 10.1017/S0953756203009079. [This journal is called “Fungal Biology” as of Jan. 2010]
  73. Otu, Hasan H., and Khalid Sayood. "A new sequence distance measure for phylogenetic tree construction." Bioinformatics. (2003); 19(16):2122-2130. DOI: 10.1093/bioinformatics/btg295
  74. Otu, Hasan H.*, Nicolas O. Fortunel*, Huck-Hui Ng, Jinhui Chen, Xiuqian Mu, Timothy Chevassut, Xiaoyu Li, Marie Joseph, Charles Bailey, Jacques A. Hatzfeld, Antoinette Hatzfeld, Fatih Usta, Vinsensius B. Vega, Philip M. Long, Towia A. Libermann, Bing Lim. "Comment on ‘Stemness: Transcriptional Profiling of Embryonic and Adult Stem Cells’ and ‘A Stem Cell Molecular Signature’." Science. (2003); 302:393b. DOI: 110.1126/science.1086384 *Equal Contribution.
  75. Otu, Hasan H., and Khalid Sayood. "A divide-and-conquer approach to fragment assembly." Bioinformatics. (2003); 19(1):22-29. DOI: 10.1093/bioinformatics/19.1.22
  76. Sayood, Khalid, Hasan H. Otu, and Nejat Demir. "Joint source/channel coding for variable length codes." IEEE Transactions on Communications. (2000); 48(5):787-794. DOI: 10.1109/26.843191
  77. Otu, Hasan H., and Khalid Sayood. "A joint source/channel coder with block constraints." IEEE Transactions on Communications. (1999); 47(11):1615-1618. DOI: 10.1109/26.803493
  78. Conference Proceedings

  79. Vasunilashorn SM, Ngo LH, Zhou W, Dillon ST, Otu HH, Tripp BA, Inouye SK, Libermann TA, Marcantonio ER. "An Inflammatory Signature of Postoperative Delirium" The Gerontological Society of America (GSA) Annual Scientific Meeting, 2019, Innovation in Aging 3(S1):S820-S821. DOI: 10.1093/geroni/igz038.3027
  80. Vasunilashorn SM, Ngo LH, Dillon ST, Otu HH, Tripp BA, Fong TG, Arnold SE, Xie Z, Inouye SK, Libermann TA, Marcantonio ER. "Inflammation as a Potential Shared Mechanism for Postoperative Delirium and Long-Term Cognitive Decline in Older Adults Undergoing Major Surgery" Alzheimer's Association International Conference, 2019 Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 15(7):P1607. DOI: 10.1016/j.jalz.2019.06.4826
  81. Tripp BA, Dillon ST, Vasunilashorn SM, Ngo LH, Fong TG, Marcantonio ER, Libermann TA, Otu HH. "Metabolomics of Delirium: A Case-Control Study" The Gerontological Society of America (GSA) Annual Scientific Meeting, 2019, Innovation in Aging 3(S1):S92. DOI: 10.1093/geroni/igz038.350
  82. Morhardt, Tina, Simon T. Dillon, Hasan H. Otu, Gabor Veres, Emma Li, Xuesong Gu, Towia A. Libermann, and Harland Winter. "SOMAscan As a Discovery Platform to Identify Predictive Serum Proteomic Biomarkers of Infliximab Response in Pediatric Patients with Crohn's Disease." Gastroenterology. (2019); 156(6):S-394. DOI: 10.1016/S0016-5085(19)37834-5
  83. Dillon, Simon T., Hasan H. Otu, Tina L. Morhardt, Xuesong Gu, Emma Li, Jess Kaplan, Christopher J. Moran, Harland Winter, and Towia A. Libermann. "Identification of Serum Protein Biomarkers for Non-Invasive Diagnosis of Pediatric IBD Using Somascan." Gastroenterology. (2019); 156(6):S-657. DOI: 10.1016/S0016-5085(19)38548-8
  84. Libermann, T. A., S. T. Dillon, H. H. Otu, S. M. Vasunilashorn, W. Zhou, L. H. Ngo, S. K. Inouye, and E. R. Marcantonio. "SOMAscan as a discovery platform to identify plasma protein biomarkers for postoperative delirium." Innovation in Aging. (2018); 2(Suppl 1):204. DOI: 10.1093/geroni/igy023.750
  85. Morad, Golnaz, Hasan H. Otu, Simon T. Dillon, and Marsha A. Moses. "Using proteomics profiling to elucidate the interactions of breast cancer-derived exosomes with the blood-brain barrier." Cancer Research. (2018); 78(13 Supplement):5083. DOI: 10.1158/1538-7445.AM2018-5083
  86. Lai, M., H. Otu, L. Ngo, S. Dillon, X. Gu, N. Afdhal, and T. Libermann. "Identification of serum protein biomarkers for non-invasive discrimination between NASH and simple steatosis using SOMAscan." Journal of Hepatology. (2018); 68:S98-S99. DOI: 10.1016/S0168-8278(18)30417-3
  87. Yalcin, Dicle, and Hasan H. Otu. "Comparative analysis of human and mouse CpG islands using dbCGI." In 2017 IEEE International Conference on Electro Information Technology (EIT), pp. 211-216. IEEE, 2017. DOI: 10.1109/EIT.2017.8053357
  88. Yalcin, Dicle, and Hasan H. Otu. “CpG Island (CGI) Annotation Database and Analysis of CGIs in Human Genome.” Proceedings of the Festival of Genomics; 2016 June 27-29; Boston, MA.
  89. Ağyüz, Umut, Şenol İşçi, Cengizhan Öztürk, Ahmet Ademoğlu, and Hasan H. Otu. "A dynamic Bayesian framwork to learn temporal gene interactions using external knowledge." In 2013 8th International Symposium on Health Informatics and Bioinformatics, pp. 1-5. IEEE, 2013. DOI: 10.1109/HIBIT.2013.6661680
  90. Iager, A. E., A. M. Kocabas, H. H. Otu, E. Fernández, J. B. Cibelli, and J. A. Crosby. "Pregnancy outcome following IVF can be predicted by a gene expression signature in human cumulus cells." Fertility and Sterility. (2012); 345(6198):S101. DOI: 10.1016j.fertnstert.2012.07.371
  91. Isci, Senol, Umut Agyuz, Cengizhan Ozturk, and Hasan H. Otu. "Detecting gene interactions within a bayesian network framework using external knowledge." In 2012 7th International Symposium on Health Informatics and Bioinformatics, pp. 82-87. IEEE, 2012. DOI: 10.1109/HIBIT.2012.6209047
  92. Iager, A. E., A. M. Kocabas, H. H. Otu, P. Ruppel, A. Langerveld, P. Schnarr, M. Suarez, J. C. Jarrett, J. Conaghan, G. J. M. Rosa, E. Fernández, R. G. Rawlins, J. B. Cibelli, J. Crosby. "A novel biomarker signature expressed in human cumulus cells predicts oocyte pregnancy potential during ART." Human Reproduction. (2012); 27(Suppl 2):ii1-ii3. DOI: 10.1093/humrep/27.s2.2
  93. Meydan, Cem, Hasan Otu, and Ugur Sezerman. "Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, pp. 315-318. IEEE, 2009. DOI: 10.1109/IJCBS.2009.122
  94. Bakiş, Yasin, O. Uğur Sezerman, and Hasan H. Otu. “Resampling techniques for non-alignment based sequence distance methods” Proceedings of the 16th National Biotechnology Conference S-D5: 235-237, 2009; Antalya, Turkey.
  95. Bakiş, Yasin, O. Uğur Sezerman, and Hasan H. Otu. "Physico-chemical properties of DNA in phylogeny construction." In 2010 5th International Symposium on Health Informatics and Bioinformatics, pp. 27-30. IEEE, 2010. DOI: 10.1109/HIBIT.2010.5478912
  96. Ramlawi, Basel, Hasan Otu, Sirisha Emani, Cesario Bianchi, and Frank W. Sellke. "Tissue permeability associated with chemokine-class inflammatory response following cardiac surgery." Journal of the American College of Surgeons. (2009); 209(3):S29-S30.DOI: 10.1016/j.jamcollsurg.2009.06.060
  97. Jones, Jon, Hasan H. Otu, Dimitrios Spentzos, Arie S. Belldegrun, Towia A. Libermann, and Allan J. Pantuck. "Proteomic identification and validation of interleukin-2 therapy response in metastatic renal cell cancer." The Journal of Urology. (2008); 179(4S):35-36. DOI: 10.1016/S0022-5347(08)60108-1
  98. Marselli L, Sgroi DC, Thorne J, Dahiya S, Torri S, Omer A, Del Prato S, Libermann T, Otu HH, Sharma A, Bonner-Weir S, Marchetti P, Weir GC. “Evidence of inflammatory markers in beta cells of type 2 diabetic subjects” 43rd Annual Meeting of the European Association for the Study of Diabetes, Diabetologia 50: Suppl 1, pp. S178-S179, September 2007; Amsterdam, Netherlands.
  99. Ramlawi B, Otu HH, Mieno S, Boodhwani M, Sodha NR, Clements RT, Bianchi C, Sellke FW. “Oxidative stress and postoperative atrial fibrillation after cardiac surgery” Canadian Cardiovascular Congress, Canadian Journal of Cardiology 23: p. 292C, October 2007; Quebec, Canada.
  100. Otu, Hasan H., Handan Can, Namik Kaya, Laila Al-alwan, Pinar Ozand, and Mehmet S. Inan. "Computational Analysis of Transcriptional Profiling in Dysmorphic Syndrome." In 2007 IEEE 15th Signal Processing and Communications Applications, pp. 1-4. IEEE, 2007. DOI: 10.1109/SIU.2007.4298831
  101. Haram, Kerstyn, Heidi Peltier, Bin Lu, Towia Libermann, Bob Choy, Hasan Otu, Gary Latham, and Martin Sanda. "Gene expression profile of Transgenic Adenocarcinoma of the Mouse Prostate (TRAMP) reveals murine targets for preclinical development of human prostate cancer therapy." Cancer Research. (2007); 67(9):3882. AACR Annual Meeting.
  102. Kang, Jinjoo, Nynke MS van den Akker, Bernice Aguilar, Wanli Tang, Darren Kafka, Sunju Lee, Swapnika Ramu, Sathish K. Ganesan, Hasan H. Otu, John M. G. van Vugt, Jay W. Shin, G. Paolo Dotto, Michael Detmar, Adriana C. Gittenberger-de Groot, Young-Kwon Hong. "Dysregulated Notch signaling induces pathological arterialization of developing lymphatics in Down syndrome fetus." The FASEB Journal. (2007); 21(5): A15-A15. View Article
  103. Ramlawi B, Otu HH, Kohane IS, Bianchi C, Sellke FW. “Genomic expression pathways associated to brain injury after cardiopulmonary bypass” 79th Annual Scientific Session of the American-Heart-Association, Circulation 114 (18): Suppl. S, p. 402 November 2006; Chicago, Illinois. View Article
  104. Zhang, Xiaoping, Hongmei Yang, Liang Zhang, Xu Huang, Hasan Otu, Towia Libermann, Roya Khosravi-Far, William C. DeWolf, and Aria F. Olumi. "C-FOS Promotes Trail-Induced Apoptosis by Repressing C-Flip (L)." The Journal of Urology. (2007); 177(4S):222. DOI: 10.1016/S0022-5347(18)30901-7
  105. Abid MR, Shih SC, Otu HH, Spokes KC, Okada Y, Curiel DT, Minami T, Aird WC. “A novel class of VEGF-responsive genes that require forkhead aactivity for expression.” 7th Annual Conference on Arteriosclerosis, Thrombosis and Vascular Biology, Arteriosclerosis Thrombosis and Vascular Biology 26 (5): p. E45, April 2006; Denver, Colorado.
  106. Singh, Ajita V., Hasan Otu, Towia Libermann, and Jin-Rong Zhou. "Modulation of gene expression by soy phytochemicals in orthotopic bladder tumors in mice by using affymetrix microarray assay." Cancer Research. (2006); 66(8S):1297-1297. View Article
  107. Jones, J., H. Otu, D. Spentzos, S. Kolia, R. Blaheta, D. Jonas, and T. A. Libermann. "Gene Signatures of Progression and Metastasis in Renal Cell Cancer." Aktuelle Urologie. (2006); 37(S1):V1. DOI: 10.1055/s-2006-947390
  108. Steidl, Ulrich, Frank Rosenbauer, Roel GW Verhaak, Xuesong Gu, Hasan H. Otu, Shakir Kolia, Bronwyn M. Owens et al. "Essential Role of Jun Family Transcription Factors in PU. 1-Induced Leukemic Stem Cell Transformation." Blood. (2005); 106(11):463-463. View Article
  109. Otu, Hasan H., Shakirahmed Kolia, Jon Jones, Osman Osman, and Towia A. Libermann. "Significance analysis of clustering high throughput biological data." In 2005 IEEE International Conference on Electro Information Technology, pp. 6-pp. IEEE, 2005. DOI: 10.1109/EIT.2005.1627001
  110. Jones J, Spentzos D, Otu H, Aivado M, Kolia S, Paullus J, Belldegrun AS, Figlin RA, Libermann TA, Pantuck AJ. “Proteomic identification of interleukin-2 therapy responders in metastatic renal cell cancer.” Annual Meeting of the American Urological Association, Journal of Urology 173 (4): Suppl. S, pp. 171-172, May 2005; San Antonio, Texas.
  111. Zinkin NT, Otu HH, Spentzos D, Aivado M, Wells M, Kalmowitz BD, Bhaskar KK, Libermann TA, Afdhal NH. “A combined proteomic and serologic approach to diagnosis of hepatocellular carcinoma.” 56th Annual Meeting of the American Association for the Study of Liver Diseases, Hepatology 42 (4): Suppl. 1, p. 239A, November 2005; San Fransisco, California.
  112. Zinkin NT, Otu HH, Spentzos D, Aivado M, Wells M, Libermann TA, Afdhal NH. “Proteomic profiling of hepatocellular carcinoma with seldi-tof mass spectrometry in patients with chronic liver disease.” 106th Annual Meeting of the American Gastroenterological Association, Gastroenterology 128 (4): Suppl. 2, p. A30 May 2005; Chicago, Illinois.
  113. Jones, Jon, Dimitrios Spentzos, Hasan Otu, Manuel Aivado, Arie Belldegrun, Robert Figlin, Allan Pantuck, and Towia Libermann. "Proteomic identification of interleukin-2 therapy response in metastatic renal cell cancer." Cancer Research. (2005); 65(9S):733-733. View Article
  114. Aivado, M., Dimitrios Spentzos, Ulrich Germing, Frank Grall, Aristoteles A. N. Giagounidis, Hasan H. Otu, Norbert Gattermann, Rainer Haas, Constantine S. Mitsiades, Eric Fung, Towia A. Libermann. "Noninvasive detection ofmyelodysplastic syndromes using serum proteome profiling." Leukemia Research. (2005); 29:S7. DOI: 10.1016/S0145-2126(05)80019-0
  115. Ijiri K, Peng H, Zerbini LFC, Walsh N, Wedig M, Gray M, Komiya S, Aigner T, Otu HH, Libermann TA, Goldring MB. “Growth arrest and dna damage-inducible gene 45β expression in normal and osteoarthiritic cartilage.” 9th World Congress of the Osteoarthritis Research Society International, Osteoarthritis and Cartilage 12: Suppl. B, p. S8-S9, December 2004; Chicago, Illinois.
  116. Jones J, Inan M, Otu HH, Spentzos D, Gu X, Joseph M, Beecken W, Jonas D, Libermann TA. “Gene expression profiles in Renal Cell Cancer: Characterization of gene signatures in various histological subtypes and application of a metastatic signature” 56th Congress of the German Urological Society, Der Urologe (A) Suppl 1: p. S23, 2004; Hamburg.
  117. Aivado, Manuel, Dimitrios Spentzos, Ulrich Germing, Gil Alterovitz, Xiao-Ying Meng, Franck Grall, Aristoteles AN Giagounidis et al. "Serum Protein Profiling with Mass Spectrometry for the Diagnosis of Myelodysplastic Syndromes." Blood. (2004); 104(11):2362-2362. View Article
  118. Jones J, Inan M, Otu HH, Cho JY, Gu X, Beecken W, Bailey C, Joseph M, Fellbaum C, Jonas D, Libermann TA. “Transcriptional Profiling for Detection of a Gene Signature in Renal Cell Cancer.” 55th Congress of the German Urological Society, Der Urologe (A) Suppl 1: p. S19, 2003; Hamburg.
  119. Jones J, Inan MS, Otu HH, Cho JY, Gu XS, Beecken WD, Joseph M, Fellbaum C, Libermann TA. “Gene Expression Analysis for Identification of a Gene Signature in Renal Cell Cancer.” 56th Congress of the German Urological Society, 36th Annual Meeting of the American Society of Nephrology, Journal of the American Society of Nephrology, 14: Suppl S p.367A, November 2003; San Diego, California.
  120. El Essawy B, Otu HH, Aivado M, Kim YS, Libermann T, Strom T. “Proteomic analysis of the allograft response.” American Transplant Congress, American Journal of Transplantation, 4: Spl. 8 p.512, May 2004; Boston, Massachusetts.
  121. Arnavut, Ziya, Hasan H. Otu. “Compressing Color-mapped Images with Burrows-Wheeler Transformation” Proceedings of Signal Processing Conference IASTED, pp.185-189, 2001 July; Rhodes, Greece.
  122. Otu HH, Sayood K. “A Joint Source Channel Coder with Block Constraints” Proceedings of 1998 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), pp. 3461-3464,1998 May; Seattle, Washington.
  123. Otu, Hasan H., and Khalid Sayood. "A compression algorithm that preserves NDVI and NDWI values." In Conference Record of the Thirty-First Asilomar Conference on Signals, Systems and Computers (Cat. No. 97CB36136), vol. 1, pp. 205-208. IEEE, 1997. DOI: 10.1109/ACSSC.1997.680056
  124. Book Chapters

  125. Otu, Hasan H. “Bioinformatics”. In: Dundar M. and Bagis H., Eds. Current Biotechnology and Applications, pp. 401-424. Erciyes University Press 2017. ISBN: 978-60567442-0-4
  126. Doğan, Haluk, and Hasan H. Otu. "Objective functions." In Multiple Sequence Alignment Methods, pp. 45-58. Humana Press, Totowa, NJ, 2014. ISBN: 1627036458. DOI: 10.1007/978-1-62703-646-7_3
  127. Otu, Hasan H. “Bioinformatics”. In: Dundar M. and Bagis H., Eds. Modern Biotechnology and Applications, pp. 425-462. Erciyes University Press 2010. ISBN: 9789756478639
  128. Thomson A, Hui NG, Robson P, Otu HH, Lim B. “Embryonic Stem cells as a model for Systems Biology”. In: Rigoutsos I. and Stephanoplous D., Eds. Systems Biology 2, pp. 297-319. Oxford University Press. 2007 ISBN: 0195300807
  129. Otu, Hasan H., and Towia A. Libermann. "From microarrays to gene networks." In Bioarrays, pp. 45-58. Humana Press, 2007. ISBN: 1588294765. DOI: 10.1007/978-1-59745-328-8_4
  130. Patents

  131. Protein biomarkers for early detection of Pancreatic Cancer, provisional.
  132. Markers for the diagnosis and treatment of non-alcoholic steatohepatitis (NASH) and advanced liver fibrosis. File Number: 2019099706
  133. Genes differentially expressed by cumulus cells and assays using same to identify pregnancy competent oocytes. File Number: 20130053261/20140296104
  134. Human Transcriptome Corresponding To Human Oocytes And Use Of Said Genes Or The Corresponding Polypeptides To Trans-Differentiate Somatic Cells. File Number: 20090028835
  135. System and Method for Sequence Distance Measure for Phylogenetic Tree Construction. File Number: 20070225918
  136. Divide and Conquer System and Method of DNA Sequence Assembly. File Number: 20030224384
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