Hasan Otu

Hasan Otu

Contact Information:

City Campus (Lincoln)
SEC C290D
(402) 472-3771
hotu2@unl.edu

Personal Links:

• Google Scholar Page
• OtuLab

Professional Memberships:

• International Society for Computational Biology
• American Association for the Advancement of Science

Professor

Academic Degrees

  • Ph.D., University of Nebraska-Lincoln, 2002
  • M.S., Bogazici University, 1997
  • B.S., Bogazici University, 1996

Certifications

  • PhD

Experience

Academic Appointments:
  • 2013-present, Professor - University of Nebraska-Lincoln, Department of Electrical Engineering
  • 2010-2013, Assistant Prof. - Istanbul Bilgi University Department of Bioengineering, Istanbul, Turkey
  • 2003- 2012, Instructor of Medicine - Harvard Medical School, Boston, MA
  • 2002-2003, Research Fellow - Harvard Medical School, Boston, MA
  • 2000-2002, Instructor of EE - University of Nebraska-Lincoln, Department of Electrical Engineering
Visiting and Other Academic Appointments:
  • 2005- 2008, Adjunct Instructor - Boston Uni. Bioinformatics Program, Boston, MA
  • 2005- 2006, Teaching Instructor - Northeastern University Department of Biology, Graduate Program in Bionformatics, Boston, MA
  • 2006-2007, Assistant Prof. - Yeditepe University Department of Genetics and Bioengineering, Istanbul, Turkey
  • 2008, Assistant Prof. - Sabanci University Department of Biological Sciences and Bioengineering, Istanbul, Turkey
Major Administrative Responsibilities:
  • 2003-2007, Director - Bioinformatics Core, BIDMC Genomics Center
  • 2004-2012, Associate Director - Dana-Farber/Harvard Cancer Center Proteomics Core
  • 2006-2008, Steering Committee - Biotechnology Institute, Yeditepe University 
  • 2007-2012, Associate Director - Bioinformatics Core, BIDMC Genomics Center
  • 2010-2013, Chair - Department of Bioengineering, Istanbul Bilgi U.
  • 2016-           Advisory Committee - Department of Bioengineering, Istanbul Bilgi U.
Editorial Boards and Program Committees:
  • 2000: Ad hoc reviewer - IEEE Transactions on Communications, Bioinformatics, Systematic Biology, Journal of Computational Chemistry, Journal of Molecular Modeling, Cancer Informatics, Journal of Molecular Evolution, BMC Bioinformatics, BMC Medical Genomics, Journal of Computational Biology, Molecular Simulation, The Computer Journal, African Journal of Biotechnology, European Journal of Human Genetics, Journal of Theoretical Biology, Acta Biotheoretica, Journal of Heredity
  • 2010-2017: Associate Editor - EURASIP Journal on Bioinformatics and Systems Biology
  • 2011: PC Co-chair The 6th International Symposium on Health Informatics and Bioinformatics, (HIBIT)
  • 2012: Organizer - Workshop, “Bioinformatics Approaches for Analysis of High-throughput Biological Data”, International Centre for Genetic Engineering and Biotechnology
  • 2013-2017: Associate Editor - Advances in Biology
  • 2014-2018: Editor in Chief - Journal of Bioinformatics, Computational and Systems Biology
  • 2014- : Associate Editor - Journal of Bioinformatics, Proteomics and Imaging Analysis
  • 2017: Member - Technical Program Committee Electro-Information Technology Conference
  • 2017: Member - Program Committee International Symposium on Integrative Bioinformatics
  • 2018- 2020: Associate Editor - Advances in Bioinformatics
  • 2020- : Associate Editor - Cells
  • 2023- : Editorial Board Member - Frontiers in Plant Science - Plant Bioinformatics

Curriculum Vitae (CV):

HHO_CV.pdf

Areas of Research and Professional Interest

  • Bioinformatics
  • Systems Biology
  • Bayesian Networks
  • Genetic Variations

Research Profiles:

In the News: Powered by the Nebraska Engineering News

Inventions/Patents

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

About Hasan Otu

Hasan H. Otu obtained his B.S. degree in 1996 and his M.S. degree in 1997, both from Bogazici University, Department of Electrical and Electronics Engineering. In 2002, he graduated from the University of Nebraska-Lincoln with a Ph.D. in Electrical Engineering focusing on Bioinformatics.

He has been a faculty member at Harvard Medical School (2003 - 2012), where he was a research fellow between 2002-2003. Dr. Otu is the founding director of Bioinformatics Core at Beth Israel Deaconess Medical Center, Harvard Medical School and Associate Director of Proteomics Core at Dana Farber Harvard Cancer Center. Between 2010-2013, Dr. Otu was the founding chair of the Department of Genetics and Bioengineering at Istanbul Bilgi University.

Dr. Otu’s research interests are in the area of Bioinformatics focusing on macromolecular sequence analysis, microarrays, biomarker discovery, genetic variations and systems biology, analyzing high throughput biological data within the context of networks. Dr. Otu has published over 70 journal articles and ~50 conference proceedings, which have received over 5,000 citations. Dr. Otu has written 5 book chapters and holds 6 U.S. patents.

Funding

Last Ten Years (prior funding $~3M in seven projects funded by NIH, MSU, and KACST):
  • 2009-2012       The Dubai Harvard Foundation for Medical Research; “Analysis of high-throughput genomic data using an integrated approach; Otu (PI); ~$182,000
  • 2011-2013       Istanbul Bilgi University Research Fund; “Human Whole Genome Sequencing” Otu (PI); ~$25,000                   
  • 2011-2013       The Scientific and Technological Research Council of Turkey; Project No: 111E042; “Bayesian Network Analysis of High Throughput Biological Data: A Systems Biology Approach”; Otu (PI); ~$85,000
  • 2016-2021       NIH/NIA; Project No: R01AG051658; “Advancing the Understanding of Postoperative Delirium Mechanisms via Multi-Omics”;  Marcantonio/Libermann (MPI’s), Otu (Co-PI); ~$2.3M
  • 2018-2024       NIH/NIA; Project No: P01AG031720; “Delirium, Dementia, and the Vulnerable Brain: An Integrative Approach”; Inouye (PI); “The role of inflammation in the pathophysiology of delirium and its associated long term cognitive decline (Project2)”; Marcantonio/Libermann (MPI’s), Otu (Co-PI); ~$13.6M
  • 2018-2021       NIH/NLM; Project No: 1R21LM012759; “Identification and characterization of interaction atlases in human”; Otu (PI); ~$450,000
  • 2020-2021       The University of Nebraska Foundation, Jane Robertson Layman Fund; "Integrating Meta-Multiomic Data Using Probabilistic Graph Representations"; Otu (PI); $10,000
  • 2022-2027       NIH/NIA; Project No: R01AG051658; “AD/ADRD and biological aging proteomic signatures in the etiopathology of delirium and its associated long-term cognitive decline”; Marcantonio/Libermann (MPI’s), Otu (Co-PI); ~$4.2M

Selected Publications

  • 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, Al-Manee MM, Al-Shomrani BM, Al-Qhtani SM, Al-Harthi AS, Akdemir KC, Inan MS, Otu HH. “Sequencing, analysis, and annotation of expressed sequence tags for camelus dromedaries” PLoS ONE, 2010 5(5):e10720.
  • Isci S, Jones J, Ozturk C, Otu HH. “Pathway analysis of high throughput biological data within a Bayesian Network framework” Bioinformatics, 2011 27(12):1667-1674.
  • Isci S, Dogan H, Ozturk C, Otu HH. “Bayesian Network Prior: Network Analysis of Biological Data Using External Knowledge” Bioinformatics, 2014 30(6):860-867.
  • Dogan H, Can H, Otu HH. “Whole Genome Sequencing of a Turkish Individual” PLoS One, 2014 9(1): e85233.
  • Gonzalez-Muñoz E, Arboleda-Estudillo Y, Otu HH, Cibelli JB. “Histone chaperone ASF1A is required for maintenance of pluripotency and cellular reprogramming” Science, 2014 Jul 17. DOI:10.1126/science.1254745.
  • Yalcin D, Hakguder ZM, Otu HH. “Bioinformatics approaches to single-cell analysis in developmental biology” Mol Hum Reprod., 2016 22(3):182-192.
  • Chanumolu SK, Albahrani M, Otu HH. “FQStat: a parallel architecture for very high-speed assessment of sequencing quality metrics” BMC Bioinformatics, 2019 20(1):424.
  • Can H, Chanumolu SK, Gonzalez-Munoz E, Prukudom S, Otu HH*, Cibelli JB*. “Comparative analysis of single-cell transcriptomics of human and zebrafish oocytes” BMC Genomics, 2020 21(1):471. (*Co-senior authors)
  • Yalcin D, 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.
  • Chanumolu SK, Albahrani M, Can H, Otu HH. “KEGG2Net: deducing gene interaction networks and acyclic graphs from KEGG pathways” EMBnet.journal, 2021, 26:e949.
  • 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.
  • Tripp BA, Otu HH. “Integration of Multi-omics Data Using Probabilistic Graph Models and External Knowledge” Current Bioinformatics, 2022; 17(1):37-47.
  • Chanumolu SK, Otu HH. “Identifying large scale interaction atlases using probabilistic graphs and external knowledge” J. Clin. Transl. Sci., 2022; 6(1):e27.
  • Can H, Chanumolu SK, Nielsen B, Alvarez S, Naldrett MJ, Unlu G, Otu HH*. “Integration of Meta-Multi-Omics Data Using Probabilistic Graphs and External Knowledge” Cells 2023; 12(15):1998.
  • Bioinformatics: A One Semester Course, Khalid Sayood and Hasan H. Otu, Springer, 1st Edition (2023) ISBN: 978-3-031-20016-8.