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Mathematical Foundations in Bioinformatics


Registration and lectures will take place in room K3.11 (3rd Floor, King's Building). The Terrace Café will be used for coffee breaks and the evening reception (0 Floor, Macadam Building). Both rooms are located in the Strand Campus.

Date: 20th July 2016


The students of the Algorithms & Bioinformatics group at King’s College London invite post-graduate and post-doctoral students to the first Student Conference on Mathematical Foundations in Bioinformatics, sponsored by the Department of Informatics at King’s College London and the London Mathematical Society.

The aim of this Conference is to enable communication between early stage pioneers in the field and showcase applications of combinatorics, statistics and general mathematical principles to solving problems in Bioinformatics. It is expected this will inspire professional networking, collaboration and future advancements in the careers of the postgraduates involved; and it will also promote the sharing and development of methods and approaches to problem solving.  

We invite students to submit abstracts to be considered for oral presentation, using this form. Selected abstracts will be invited to submit full papers to a special issue of the International Journal of Foundations in Computer Science.

Each session of this one-day conference will feature an invited talk followed by oral presentations by students. Breaks will provide the opportunity to network and lunch will be hosted in a local restaurant. Students will be awarded for exceptional presentations.

Registration is free, please sign up here. Travel support can be provided upon acceptance of a successful application, please apply here. Please email any enquiries to, or



Nadia Pisanti, University of Pisa 

Hélène Touzet, CNRS, Lille

Simon Puglisi, University of Helsinki

Rajeev Raman, University of Leicester

Gregory Kucherov,  University Paris-Est Marne-la-Vallée


Ritu Kundu 

Ahmad Retha 

Fatima Vayani 


Registration open 1st May

Abstract submission open 1st May

Travel Support application open 1st May

Submission close 7th July (Extended)

Travel Support application close 8th July

Registration close 9th July

Conference: 20th July


08.30 - 09.00: Registration - K3.11

Session 1 - Chaired by Prof. Costas Iliopoulos

09.00 - 09.10: Welcome - K3.11 - Prof. Peter McBurney

09.10 - 09.50: Invited Talk - K3.11 - Prof. Rajeev Raman: 

Succinct Dynamic Tries

09.50 - 10.15: Student Talk - K3.11 - Vladimir Gligorijevic: 

Revealing modular organization in multi-layer biological networks by non-negative matrix factorization

10.15 - 10.55: Invited talk - K3.11 - Prof. Gregory Kucherov: 

Algorithms and data structures for large-scale metagenomic analysis

11.05 - 11.30: Morning Coffee Break - Terrace Café*

Session 2 - Chaired by Ahmad Retha

11.30 - 12.10: Invited talk  - K3.11 - Dr. Hélène Touzet: 

Some algorithms for RNA analysis

12.10 - 12.35: Student talk - K3.11 - Jamie Alnasir: 

Transcriptomics: Leveraging a MapReduce algorithm and Python for gene-expression analysis on Apache Spark

12.35 - 13.00: Student talk - K3.11 - Alice Heliou:

Combinatorial RNA Design

13.00 - 14.50: Lunch - Fire and Stone

Session 3 - Chaired by Ritu Kundu

14.50 - 15.30: Invited talk - K3.11 - Dr. Simon Puglisi:

Indexing for Pan-genomics

15.30 - 15.55: Student talk - K3.11 - Nicola Prezza:

A Randomized In-Place LCE Data Structure

15.55 - 16.20: Student talk - K3.11 - Jia Gao:

Optimal Computation of Avoided Words

16.20 - 16.40: Afternoon Tea Break - Terrace Café*

Session 4 - Chaired by Fatima Vayani

16.40 - 17.20: Invited Talk - K3.11 - Dr. Nadia Pisanti:

Dynamic Programming Approaches to Haplotype Assembly

17.20 - 17.45: Student talk - K3.11 - Sofia Teixeira:

SpliceTAPyR – Efficient method for transcriptome alignment

17.45 - 18.10: Student talk - K3.11 - Maryam Abdollahyan:

Transcription Factor Binding Site-based Alignment of Conserved Non-coding Sequences

18.10 - 18.20: Closing remarks & Award announcement - K3.11

18.20 - 19.30: Drinks Reception - Terrace Café*

19.45: Dinner L'ulivo


* K3.11 - King’s College, Strand Campus, King’s Building, 3rd floor

Terrace Cafe - King’s College, Strand Campus, Macadam Building, Ground floor

Follow the link to see the full programme.


Click on the following links to view the presentations:

Nadia Pisanti

Hélène Touzet

Nicola Prezza

Simon Puglisi

Rajeev Raman


To see a selection of photos from the MatBio 2016 conference please click here

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