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Permanent associate researcher (CRCN).

Short resume

Phone: +33 (0)5 61 28 54 93

Mail: [Matthias.Zytnicki(-at-)]

I joined MIAT in sep. 2013.

  • PhD in MIAT in 2004-2007 on weighted constraints for non-coding RNA identification.
  • Post-doc in 2008 with Cédric Notredame (CRG, Barcelona) on bio-informatics for transcriptomics.
  • First position in 2009-2013 at the URGI (INRA, Versailles) on transposable element and epigenetics.

I am currently working on the following topics:

  • epigenetics,
  • text algorithms for high-throughput data.

Publications (2009-2019)

  • Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW (2018). Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Molecular Ecology, Advance Access.
  • Charbonnel C, Niazi AK, Elvira-Matelot É, Nowak E, Zytnicki M, de Bures A, Jobet É, Opsomer A, Shamandi N, Nowotny M, Carapito C, Reichheld J-P, Vaucheret H, Sáez-Vásquez J (2017). The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain. Nucleic Acids Research, 45: 11891–11907.
  • Zytnicki M (2017). mmquant: how to count multi-mapping reads? BMC Bioinformatics, 18: 411.
  • Molitor A, Latrasse D, Zytnicki M, Andrey P, Houba-Hérin N, Hachet M, Battail C, Del Prete S, Alberti A, Quesneville H, Gaudin V (2016). The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes. The Plant Cell, 28:2197--2211.
  • Elvira-Matelot E, Hachet M, Shamandi N, Comella P, Saez-Vasquez J, Zytnicki M, Vaucheret H (2016). Arabidopsis RNASE THREE LIKE2 modulates the expression of protein-coding genes via 24-nt siRNA-directed DNA methylation. The Plant Cell, 28(2): 406-425.
  • Shamandi N, Zytnicki M, Charbonnel C, Elvira-Matelot E, Bochnakian A, Comella P, Mallory AC, Lepère G, Sáez-Vásquez J, Vaucheret H (2015). Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. PLoS Biology, 13(12):e1002326.
  • Allouche D, De Givry S, Katsirelos G, Schiex T, Zytnicki M (2015). Anytime Hybrid Best-First Search with Tree Decomposition for Weighted CSP. CP'15, 12-29.
  • Willing EM, Rawat V, Mandàkovà T, Maumus F, James G, Nordström, K, Becker C, Warthmann N, Chica C, Szarzynska B et al. (2015). Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants, 1 (2).
  • Parent JS, Jauvion V, Bouché N, Béclin C, Hachet M, Zytnicki M, Vaucheret H (2015). Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes. Nucleic Acids Research, gkv753.
  • Geering A, Maumus F, Copetti D, Choisne N, Zwickl D, Zytnicki M, McTaggart A, Scalabrin S, Vezzulli S, Wing R et al. (2014). Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature communications, 5.
  • International Wheat Genome Sequencing Consortium (IWGSC) (2014). A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science, 345 (6194), 1251788.
  • Zytnicki, M, Akhunov, E, Quesneville, H (2014). Tedna: a transposable element de novo assembler. Bioinformatics, 30 (18), 2656 - 2658.
  • Toffano-Nioche, C, Luo, Y, Kuchly, C, Wallon, C, Steinbach, D, Zytnicki, M, Jacq, A, Gautheret, D (2013). Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline. Methods, 63 (1), 60 - 65.
  • Zanni, V, Eymery, A, Coiffet, M, Zytnicki, M, Luyten, I, Quesneville, H, Vaury, C, Jensen, S (2013). Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters. Proceedings of the National Academy of Sciences of the United States of America.
  • Zytnicki, M, Luo, Y, Quesneville, H (2013). Efficient comparison of sets of intervals with NC-lists. Bioinformatics, 29 (7), 933-939.
  • Campo, S, Peris-Peris, C, Siré, C, Moreno, A, Donaire, L, Zytnicki, M, Notredame, C, Llave, C, San Segundo, B (2013). Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. New Phytologist, 199 (1), 212-27.
  • Toffano-Nioche, C, Ott, A, Crozat, E, Nguyen, A, Zytnicki, M, Leclerc, F, Forterre, P, Bouloc, P, Gautheret, D (2013). RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi. RNA Biology, 10 (7), 1211-1220.
  • Schbath, S, Martin, V, Zytnicki, M, Fayolle, J, Loux, V, Gibrat, JF (2012). Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. Journal of Computational Biology, 19 (6), 796-813.
  • Bussotti, G, Raineri, E, Erb, I., Zytnicki, M, Wilm, A, Beaudoing, E, Bucher, P, Notredame, C (2011). BlastR-fast and accurate database searches for non-coding RNAs. Nucleic Acids Research, 39 (16), 6886-6895.
  • Zytnicki, M, Quesneville, H (2011). S-MART, a software toolbox to aid RNA-seq data analysis. Plos One, 6 (10), 1-3.
  • Ørom, U, Derrien, T, Beringer, M, Gumireddy, K, Gardini, A, Bussotti, G, Lai, F, Zytnicki, M, Notredame, C, Huang, Q, Guigo, R, Shiekhattar, R (2010). Long noncoding RNAs with enhancer-like function in human cells. Cell, 143 (1), 46-58.
  • Cooper, M, De Givry, S, Sanchez, M, Schiex, T, Zytnicki, M, Werner, T (2010). Soft arc consistency revisited. Artificial Intelligence (174), 449-478.
  • Zytnicki, M, Gaspin, C, De Givry, S, Schiex, T (2009). Bounds arc consistency for weighted CSPs. Journal of Artificial Intelligence Research, 35, 593-621.

PhD Students

Leila Khajavi

2017 -- 2021: Transcriptional regulation of narcolepsy.

Walid Ben Saoud Benjerri

2016 -- 2018: Text algorithms for short-RNA mapping.


Pierre Guenzi-Tibéri

2021: Pipe-line de détection et d'annotation de petits ARN.

Cyril Kurylo

2019: Detection of differential compartments with Hi-C.

Leila Khajavi

2017: Analysis of ChIP-Seq for brain deseases.

Aurélien Cottin

2015: Text algorithms for short-RNA mapping.

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