Ahmad Retha

PhD Student in Bioinformatics

King's College London

About Me

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. 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
Strand Campus
Bush House
30 Aldwych
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.

Publications


2017
[7]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. [bibtex] [pdf] [doi]
2016
[6]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. [bibtex] [pdf] [doi]
[5]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. [bibtex] [pdf] [doi]
2015
[4]S. 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. [bibtex] [pdf] [doi]
[3]R. Grossi, C. S. Iliopoulos, R. Merca\cs, N. Pisanti, S. P. Pissis, A. Retha, F. Vayani, Circular Sequence Comparison with q-grams, Berlin, Heidelberg: Springer Berlin Heidelberg, 2015, pp. 203-216. [bibtex] [pdf] [doi]
[2]C. Barton, C. S. Iliopoulos, R. Kundu, S. P. Pissis, A. Retha, F. Vayani, Accurate and Efficient Methods to Improve Multiple Circular Sequence Alignment, Cham: Springer International Publishing, 2015, pp. 247-258. [bibtex] [pdf] [doi]
2014
[1]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. [bibtex] [pdf] [doi]

Conferences Organised & Talks Delivered

Papers Reviewed

Research Grants & Awards

Module Teaching

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:

Professional Certifications

11 Apr 2017 - Associate Fellow of The Higher Education Academy.

Other Stuff

Sometimes I put code on Github, write helpful code Gists, and sometimes I blog.