I am currentlyworking on computationaltheory for de novo assembly of short DNA sequencing reads (eg. Illumina, 454).
Current activities:
MAPPI project (ANR): Mapping and assemby of metagenomic and metatranscriptomic data, linked with the Tara Oceans expedition.
Alcovnaproject (ARC): ALgorithms for COmparing and Visualizing Non Assembled data
Publications:
[9]G. Sacomoto, J. Kielbassa, R. Chikhi, R. Uricaru, P.
Antoniou, M-F. Sagot, P. Peterlongo and V. Lacroix, KisSplice: de-novo calling alternative splicing events from RNA-seq data,to appear in the proceedings of RECOMB-seq, BMC Bioinformatics (2012) [PDF]
[8]Dent A. Earl et al,Assemblathon 1: A competitive assessment of de novo short read assembly methods,Genome Research (2011) [PDF]
[7]G. Chapuis, R. Chikhi, D. Lavenier.Parallel and memory-e fficient reads indexing for genome assembly,PPAM Parallel Bio-Computing Workshop(2011)[PDF]
[6]R. Chikhi, D. Lavenier.Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph, Algorithms in Bioinformatics, LNCS 6833 (2011) [PDF]
[5] R. Chikhi, L. Sael, & D. Kihara,
Protein binding ligand prediction using moment-based methods., Protein function prediction for omis era, D. Kihara ed., Chapter 8, pp. 145-163, Springer. (2011) [PDF]
[4] D. Kihara, L. Sael, R. Chikhi, & J. Esquivel-Rodriguez,
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking., Curr. Protein and Peptide Science, 12: 520-530. (2010) [PDF]
[3] R. Chikhi, L. Sael,
D. Kihara.Real-time ligand
binding pocket
database search using local surface descriptors. Proteins:
Structure, Function, and Bioinformatics, Volume
78 Issue 9, Pages 2007 - 2028. (2010) [PDF]
[2] R. Chikhi, D. Lavenier. Paired-end read length lower bounds for genome re-sequencing.(Meeting Abstract) BMC Bioinformatics,
10(Suppl 13):O2 (2009) [PDF]
[1] R. Chikhi, S. Derrien, A. Noumsi, P. Quinton. Combining flash memory and FPGAs to efficiently implement a massively parallel algorithm for content-based image retrieval. International Journal of Electronics, Volume 95, Number 7, pp. 621-635(15) (2008) [PDF]
Talks:
Localized genome assembly from reads to scaffolds: practical traversal of the paired string graph
,WABI, 2011. [PDF]
de novo assembly tools, Monument, Mapsembler,IBL, Lille, 2011. [PDF]
Paired-end read length lower bounds for genome re-sequencing,ISCB Student Council Symposium, 2009. [PDF]
Reports:
R. Chikhi. Study of Unentanglement in Quantum Computing. Manuscript, research internship at MIT, Spring 2008.[PDF]
Summary: We investigate the conjecture that one cannot simulate QMA(2) protocols in QMA using a quantum operation called a disentangler. Our results show that, when exponential precision is required, this conjecture holds unless P = NP. Moreover, also in the exponential precision case, we show that one only needs a stronger hypothesis to prove the conjecture.
R.Chikhi. Protein surface descriptors for binding sites comparison and ligand prediction. Manuscript, research internship at Purdue University, Summer 2007. [PDF]
Summary: We present a model for two dimensional ligand binding pockets representation and we apply it to pocket-pocket matching and binding ligand prediction.
Targeted assembly on a desktop computer
Pocket-Surfer: http://dragon.bio.purdue.edu/pocket-surfer/index.php Protein ligand binding pocket type prediction using a database of known binding sites. See [3] for more details.
Software package for computing the ratio of single and paired (as in paired NGS reads) exact repetitions within a genome. Useful for obtaining re-sequencing lower bounds inspired by [Whiteford 05]. See [2] and the corresponding talk for sample results and details.
Hash table-free implementation of the de Bruijn graph for a set of reads.Also includes a tool that computes the union of two de Bruijn graphs and the cartesian product of abundances, useful for construction a multi-dataset de Bruijn graph.
