CoMetGeNe: mining conserved neighborhood patterns in metabolic and genomic contexts

Autor: Alexandra Zaharia, Bernard Labedan, Christine Froidevaux, Alain Denise

Publikováno v: BMC Bioinformatics, Vol 20, Iss 1, Pp 1-20 (2019)

Abstract Background In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways and genomic context of

Externí odkaz: https://doaj.org/article/63556fd6ff5b4a0b8cf9e2bc0d3cac91

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies.

Autor: Mélanie Boudard, Julie Bernauer, Dominique Barth, Johanne Cohen, Alain Denise

Publikováno v: PLoS ONE, Vol 10, Iss 8, p e0136444 (2015)

Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is

Externí odkaz: https://doaj.org/article/a3bbc53c2dab4653b7a61beefdf16351

Efficient, robust and effective rank aggregation for massive biological datasets

Autor: Alain Denise, Laurent Bulteau, Bryan Brancotte, Pierre Andrieu, Adeline Pierrot, Stéphane Vialette, Sarah Cohen-Boulakia

Publikováno v: Future Generation Computer Systems
Future Generation Computer Systems, 2021, 124, pp.406-421. ⟨10.1016/j.future.2021.06.013⟩
Future Generation Computer Systems, Elsevier, 2021, 124, pp.406-421. ⟨10.1016/j.future.2021.06.013⟩

International audience; Massive biological datasets are available in various sources. To answer a biological question (e.g., ''which are the genes involved in a given disease?''), life scientists query and mine such datasets using various techniques.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::14f8ab4123bfded52a7169925afab50d
https://hal.science/hal-03388443/document

Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families

Autor: Alain Denise, Vladimir Reinharz, Jérôme Waldispühl, Antoine Soulé, Eric Westhof

Publikováno v: Nucleic Acids Research

The wealth of the combinatorics of nucleotide base pairs enables RNA molecules to assemble into sophisticated interaction networks, which are used to create complex 3D substructures. These interaction networks are essential to shape the 3D architectu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c8a8ba6638d33b76b75991db4899f92e
https://doi.org/10.1093/nar/gky197

Rank aggregation with ties

Autor: Sylvie Hamel, Bryan Brancotte, Guillaume Blin, Sarah Cohen-Boulakia, Alain Denise, Bo Yang

Publikováno v: The 41st International Conference on Very Large Data Bases
The 41st International Conference on Very Large Data Bases, Aug 2015, Kohala Coast, Hawaï, United States
Scopus-Elsevier
HAL
Proceedings of the VLDB Endowment (PVLDB)
41. International Conference of Very Large Data Bases
Proceedings of the VLDB Endowment (PVLDB), VLDB Endowment, 2015, Proceedings of the VLDB Endowment (PVLDB), 8 (11), pp.1202-1213. ⟨10.14778/2809974.2809982⟩
Proceedings of the VLDB Endowment (PVLDB), VLDB Endowment, 2015, 8 (11), pp.1202-1213. ⟨10.14778/2809974.2809982⟩
Proceedings of the VLDB Endowment (PVLDB), 2015, Proceedings of the VLDB Endowment (PVLDB), 8 (11), pp.1202-1213. ⟨10.14778/2809974.2809982⟩
Proceedings of the VLDB Endowment (PVLDB), VLDB Endowment, 2015, pp.2051

The problem of aggregating multiple rankings into one consensus ranking is an active research topic especially in the database community. Various studies have implemented methods for rank aggregation and may have come up with contradicting conclusion

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a537ee7a5180c648f362915c350e0ba3
https://doi.org/10.14778/2809974.2809982