Home Page



CONTACT INFORMATION:

Adrian Caciula,

Limited-Term Assistant Professor

Department of Computer Science
Georgia Southern University
Room 2305, P.O. Box 7997, Statesboro, GA 30460 USA
E-mail: acaciula [at] georgiasouthern [dot] edu
Webaddress: www.cs.gsu.edu/~acaciula1

SUMMARY OF QUALIFICATIONS:
  • Developing, designing and implementing optimization tools for RNA-Seq data analysis
  • Experienced with many programming languages, bioinformatics tools, and high-throughput sequencing.
  • Excellent communication, teaching and leadership skills
RESEARCH INTERESTS Bioinformatics, High Throughput Genomics, RNA-Seq Data, Discrete Algorithms and Combinatorial Optimization, Scheduling Algorithms.
EDUCATION:
    2008 – 2014: Georgia State University, Atlanta, GA USA
           MS in Computer Science
           PhD in Bioinformatics
           Dissertation Title: Optimization Techniques For Next-Generation Sequencing Data Analysis
           Advisor: Prof. Dr. Alexander Zelikovsky
    2003 - 2008: The Transilvania University of Brasov, Brasov, Romania
           Bachelor of Science, Electrical Engineering and Computer Science:
           Thesis Topic: Java Tools For MIDlet Analyses
           Area of Study: Parallel Distribution
AWARDS:
  • 2012 - 2013: Molecular Basis of Disease Fellowship, Georgia State University.
  • 2012, May - ISBRA 2012 NSF Travel Fellowship, Dallas, TX
  • 2011 - Outstanding Teaching By A Graduate Student Award , from Dept. Of Computer Science, Georgia State University.
  • 2008 - Full scholarship under the framework of Socrates-Erasmus European. Program to develop the final project in 'Distributed And Parallel Approximations Of The Security Of Java Code Developed For Mobile Phones' in France at the University of Franche-Comte, Besancon.
ACADEMIC EXPERIENCE:
    Fall 2012 - Summer 2014: University of North Georgia, Dahlonega, GA, USA
  • Limited Term Faculty - Department of Computer Science
  • Courses taught:
    • Bioinformatics (CSCI 4860) - Fall 2012
    • Computer Science I (CSCI 1301) - Spring 2013, Fall 2013
    • Computer Science II (CSCI 1302) - Spring 2013, Spring 2014
    • Information Technologies (CSCI 1250) - Fall 2012, Spring 2013, Fall 2013, Spring 2014
    • Systems Analysis & Design (CSCI 3300) - Fall 2012
    2007 - 2008: Transilvania University of Brasov, Brasov, Romania
  • Energy Efficiency Project at Transilvania University of Brasov. Assignments: electrical measurements, data analysis and computational parameters.
  • Instructor: Trained in-class undergraduate teaching assistants in laboratory procedure.
PUBLICATIONS:
    Book Chapters:
  • S. Al Seesi, S. Mangul, A. Caciula, A. Zelikovsky and I.I. Mandoiu, Transcriptome reconstruction and quantification from RNA sequencing data, In Maria Poptsova, Genome Analysis: Current Procedures and Applications, Caister Academic Press, pp. 39-60, 2014.
  • S. Mangul, A. Caciula, O. Glebova, I. Mandoiu and A. Zelikovsky "RNA-Seq based transcriptome quantification and reconstruction guided by protein coding gene annotation", book chapter in Algorithmic and AI Methods for Protein Bioinformatics, 2013.
    Refereed Journal Articles
  • S. Mangul, A. Caciula, O. Glebova, I. Mandoiu and A. Zelikovsky "Improved Transcriptome Quantification and Reconstruction from RNA-Seq Reads using Partial Annotations" (submitted), In Silico Biology(ISB), An International Journal on Computational Molecular Biology, 2012.
    Refereed Articles in Conference Proceedings:
  • S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Rouf Banday, R. Kanadia, I.I. Mandoiu and A. Zelikovsky, "Flexible Approach for Novel Transcript Reconstruction from RNA-Seq Data using Maximum Likelihood Integer Programming", Proc. 5th International Conference on Bioinformatics and Computational Biology (BICoB), 2013.
  • S. Mangul, A. Caciula, S. Al Seesi, D. Brinza, A. Rouf Banday, R. Kanadia, I.I. Mandoiu and A. Zelikovsky, ”An Integer Programming Approach to Novel Transcript Reconstruction from Paired-End RNA-Seq Reads”, Proc. ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), pp. 369-376, 2012.
  • S. Mangul, A. Caciula, I. Mandoiu and A. Zelikovsky, "RNA-Seq based discovery and reconstruction of unannotated transcripts in partially annotated genomes", Proc. 1st Workshop on Computational Advances in Molecular Epidemiology (CAME 2011), pp. 118-123, 2011.
  • Y. Wang, X. Cao, A. Caciula, Q. Hu: “Batch scheduling in optical networks with feedback/feed-forward fiber delay lines”. Global Communications Conference (GLOBECOM), 2012 IEEE: 2965-2970
  • X. Cao, Y. Wang, A. Caciula and Yichuan Wang, “Developing a Multifunctional Network Laboratory for Teaching and Research”, Proceedings of the 10th ACM conference on SIG-information technology education (ACM-SIGITE). Fairfax, Virginia, USA, ACM: 155-160.
    Workshop Articles and Conference Abstracts:
  • A. Caciula, A. Zelikovsky, S. Mangul, J. Lindsay and I. Mandoiu, "Monte-Carlo Regression Algorithm for Isoform Frequency Estimation from RNA-Seq Data",Proc. 3rd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2013)
  • S. Mangul, S. Al Seesi, A. Caciula, D. Brinza, I. Mandoiu and A. Zelikovsky, "Transcriptome Assembly and Quantification from Ion Torrent RNA-Seq Data", Proc. 3rd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2013)
  • A. Caciula, S. Mangul, I. Mandoiu and A. Zelikovsky, "Transcriptome Reconstruction from Single RNA-Seq Reads Using Expectation Maximization Algorithm with Expected Deviation Minimization Enhancement", 9th International Symposium on Bioinformatics Research and Applications (ISBRA 2013)
  • S. Mangul, A. Caciula, D. Brinza, I. I. Mandoiu, A. Zelikovsky, “TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads,” BMC Bioinformatics 13(S-18): A11 (2012)
  • S. Mangul, A. Caciula, I. Mandoiu and A. Zelikovsky, "Novel Transcript Reconstruction from Paired-End RNA-Seq Reads Using Fragment Length Distribution", Proc. 2nd Workshop on Computational Advances for Next Generation Sequencing (CANGS 2012)
  • Y. Wang, X. Cao, A. Caciula, Q. Hu: “On-line Batch Scheduling in Distributed Optical Networks”. IPDPS Workshops 2012: 886-893
    Presentations and Posters:
  • 7 posters, including 2 best poster awards
  • 2 invited talks