I started as a PhD student in Bioinformatics at Kings College London in the Department of Informatics, Faculty of Natural & Mathematical Sciences, in October 2014. I will be submitting my thesis before September 2018. My supervisor is Dr Solon P. Pissis. My email is ahmad.rethakcl.ac.uk. I am a Graduate Teaching Assistant/Scholar - please see below for my experience. My physical location is:(N)5.11
Department of Informatics
King's College London
London WC2B 4BG
My research is about applying string algorithms to solve bioinformatics problems. Biological sequences such as RNA, DNA and Proteins can be represented as a sequence or string of characters. I implement new exact, approximate and heuristic algorithms and modify existing algorithms to perform exact and approximate pattern matching and alignment on biological sequences. These algorithms will help improve bioinformatics processes and pipelines making them run faster and give more accurate results.
|||S. P. Pissis, A. Retha, "Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line", in 17th International Symposium on Experimental Algorithms (SEA 2018), G. D'Angelo, Ed., Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, pp. 16:1-16:14.|
|||R. Grossi, C. S. Iliopoulos, C. Liu, N. Pisanti, S. P. Pissis, A. Retha, G. Rosone, F. Vayani, L. Versari, "On-Line Pattern Matching on Similar Texts", in 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017), J. R. Juha Kärkkäinen, W. Rytter, Eds., Dagstuhl, Germany: Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, pp. 9:1-9:14.|
|||R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani, "Circular sequence comparison: algorithms and applications", Algorithms for Molecular Biology, vol. 11, no. 1, 2016, pp. 1-14.|
|||L. A. Ayad, S. P. Pissis and A. Retha, "libFLASM: a software library for fixed-length approximate string matching", BMC Bioinformatics, vol. 17, no. 1, 2016, pp. 454.|
|||S. P. Pissis, A. Retha, "Generalised Implementation for Fixed-Length Approximate String Matching Under Hamming Distance and Applications", in Proceedings of the 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, Washington, DC, USA: IEEE Computer Society, pp. 367-374.|
|||R. Grossi, C. S. Iliopoulos, R. Mercas, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani, "Circular Sequence Comparison with q-grams", in Algorithms in Bioinformatics: 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings, M. Pop, H. Touzet, Eds., Berlin, Heidelberg: Springer Berlin Heidelberg, pp. 203-216.|
|||C. Barton, C. S. Iliopoulos, R. Kundu, S. P. Pissis, A. Retha, F. Vayani, "Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment", in Experimental Algorithms: 14th International Symposium, SEA 2015, Paris, France, June 29 -- July 1, 2015, Proceedings, E. Bampis, Ed., Cham: Springer International Publishing, pp. 247-258.|
|||G. Koscielny, G. Yaikhom, V. Iyer, T. F. Meehan, H. Morgan, J. Atienza-Herrero, A. Blake, C. Chen, R. Easty, A. Di Fenza, T. Fiegel, M. Grifiths, A. Horne, N. A. Karp, N. Kurbatova, J. C. Mason, P. Matthews, D. J. Oakley, A. Qazi, J. Regnart, A. Retha, L. A. Santos, D. J. Sneddon, J. Warren, H. Westerberg, R. J. Wilson, D. G. Melvin, D. Smedley, S. D. M. Brown, P. Flicek, W. C. Skarnes, A. Mallon, H. Parkinson, "The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data", Nucleic Acids Research, vol. 42, no. D1, 2014, pp. D802-D809.|
Conferences Organised & Talks Delivered
- 02 Aug 2018 MatBio 2018 (Student Symposium on Mathematical Foundations in Bioinformatics), KCL, London, UK. Presented "Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line" paper.
- 21 - 23 June 2017 SEA 2017, KCL, London, UK. Part of organising committee.
- 2017, 2015 LSD&LAW, KCL, London, UK. Part of organising committee.
- 20 Jul 2016 MatBio 2016 (Student Symposium on Mathematical Foundations in Bioinformatics), KCL, London, UK. Co-chair/organiser.
- 25 - 29 May 2015 IEEE IPDPS 2015, Hyderabad, India. Presented "Generalised Implementation for Fixed-Length Approximate String Matching Under Hamming Distance and Applications" paper in HiCOMB 15 workshop.
- Oct 2017 for Journal of Software: Practice and Experience.
- Feb 2017 for Journal of Experimental Algorithmics.
- Sep 2016 for ALENEX '17 Conference.
- Jan 2016 for Journal of Frontiers in Bioengineering and Biotechnology.
Research Grants & Awards
- London Mathematical Society scheme 8 conference organisation fund, MatBio 2016.
- Erasmus Student Mobility Grant 2015-16.
- NSF/TCPP Travel grant for participation in IEEE IPDPS 2015.
- King's College London Graduate School conference fund, 2015.
I am a Graduate Teaching Assistant for first and second year Computer Science and Masters in Data Science students at KCL and do small and large group teaching, labs and/or marking for the following modules:
- 7CCSMBDT - Big Data Technologies (R, Amazon AWS, Cloudera, Hadoop, Map-Reduce with Python + MRJob, Apache Sqoop, Apache Hive, Apache Spark, MongoDB)
- 7CCSMSDV - Simulation and Data Visualisation (Tableau, Python + Pandas + Matplotlib, Processing, Discrete Event Simulation, Monte Carlo Simulation, Agent-based Modelling, Flocking, Network Modelling)
- 7CCSMCMP - Computer Programming for Data Scientists (Python)
- 7CCSMDDW/5CCS02DB/4CCS1DBS - Database Systems (ER Diagrams, Database design and normalisation, SQL, NOSQL, Relational Algebra, MySQL, Data Warehousing)
- 4CCS1DST - Data Structures (Java)
- 4CCS1PRP - Programming Practice (Java, Python, C)
- 4CCS1PRA - Programming Applications (Java, UI design)
- 4CCS1PEP - Practical Experiences of Programming (Java, Prolog)
Associate Fellow of The Higher Education Academy (obtained 11 Apr 2017)