Bibliography

Major publications by the team in recent years

• 1S. Z. Alborzi, M.-D. Devignes, D. W. Ritchie.
  
  ECDomainMiner: discovering hidden associations between enzyme commission numbers and Pfam domains, in: BMC Bioinformatics, December 2017, vol. 18, n^o 1, 107 p. [ DOI : 10.1186/s12859-017-1519-x ]
  
  https://hal.inria.fr/hal-01466842
• 2S. Z. Alborzi, D. Ritchie, M.-D. Devignes.
  
  Computational Discovery of Direct Associations between GO terms and Protein Domains, in: BMC Bioinformatics, November 2018, vol. 19, n^o Suppl 14, 413 p. [ DOI : 10.1186/s12859-018-2380-2 ]
  
  https://hal.inria.fr/hal-01777508
• 3A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  Spatial clustering of protein binding sites for template based protein docking, in: Bioinformatics, August 2011, vol. 27, n^o 20, pp. 2820-2827. [ DOI : 10.1093/bioinformatics/btr493 ]
  
  https://hal.inria.fr/inria-00617921
• 4A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  Protein Docking Using Case-Based Reasoning, in: Proteins, October 2013, vol. 81, n^o 12, pp. 2150-2158. [ DOI : 10.1002/prot.24433 ]
  
  https://hal.inria.fr/hal-00880341
• 5A. W. Ghoorah, M.-D. Devignes, M. Smaïl-Tabbone, D. Ritchie.
  
  KBDOCK 2013: A spatial classification of 3D protein domain family interactions, in: Nucleic Acids Research, January 2014, vol. 42, n^o D1, pp. 389-395.
  
  https://hal.inria.fr/hal-00920612
• 6T. V. Hoang, X. Cavin, D. Ritchie.
  
  gEMfitter: A highly parallel FFT-based 3D density fitting tool with GPU texture memory acceleration, in: Journal of Structural Biology, September 2013. [ DOI : 10.1016/j.jsb.2013.09.010 ]
  
  https://hal.inria.fr/hal-00866871
• 7G. Macindoe, L. Mavridis, V. Venkatraman, M.-D. Devignes, D. Ritchie.
  
  HexServer: an FFT-based protein docking server powered by graphics processors, in: Nucleic Acids Research, May 2010, vol. 38, pp. W445-W449. [ DOI : 10.1093/nar/gkq311 ]
  
  https://hal.inria.fr/inria-00522712
• 8D. W. Ritchie, S. Grudinin.
  
  Spherical polar Fourier assembly of protein complexes with arbitrary point group symmetry, in: Journal of Applied Crystallography, February 2016, vol. 49, n^o 1, pp. 158-167. [ DOI : 10.1107/S1600576715022931 ]
  
  https://hal.inria.fr/hal-01261402
• 9D. Ritchie.
  
  Calculating and scoring high quality multiple flexible protein structure alignments, in: Bioinformatics, May 2016, vol. 32, n^o 17, pp. 2650-2658. [ DOI : 10.1093/bioinformatics/btw300 ]
  
  https://hal.inria.fr/hal-01371083
• 10D. W. Ritchie, V. Venkatraman.
  
  Ultra-fast FFT protein docking on graphics processors, in: Bioinformatics, August 2010, vol. 26, n^o 19, pp. 2398-2405. [ DOI : 10.1093/bioinformatics/btq444 ]
  
  https://hal.inria.fr/inria-00537988
• 11B. Sarker, D. Ritchie, S. Aridhi.
  
  GrAPFI: Graph Based Inference for Automatic Protein Function Annotation, September 2018, ECCB 2018 - 17th European Conference on Computational Biology, Poster.
  
  https://hal.inria.fr/hal-01876907
• 12B. Sarker, D. W. Ritchie, S. Aridhi.
  
  Exploiting Complex Protein Domain Networks for Protein Function Annotation, in: Complex Networks 2018 - 7th International Conference on Complex Networks and Their Applications, Cambridge, United Kingdom, December 2018.
  
  https://hal.inria.fr/hal-01920595

Publications of the year

Articles in International Peer-Reviewed Journals

• 13E. Bresso, D. Fernandez, D. X. Amora, P. Noel, A.-S. Petitot, M.-E. Lisei De Sa, E. V. S. Albuquerque, E. Danchin, B. Maigret, N. F. Martins.
  
  A Chemosensory GPCR as a Potential Target to Control the Root-Knot Nematode Meloidogyne incognita Parasitism in Plants, in: Molecules, 2019, vol. 24, n^o 20, 3798 p. [ DOI : 10.3390/molecules24203798 ]
  
  https://hal.archives-ouvertes.fr/hal-02324816
• 14I. R. G. Capoci, D. R. Faria, K. M. Sakita, F. A. V. Rodrigues-Vendramini, P. d. S. Bonfim-Mendonça, T. C. A. Becker, E. S. Kioshima, T. I. E. Svidzinski, B. Maigret.
  
  Repurposing approach identifies new treatment options for invasive fungal disease, in: Bioorganic Chemistry, March 2019, vol. 84, pp. 87-97. [ DOI : 10.1016/j.bioorg.2018.11.019 ]
  
  https://hal.inria.fr/hal-02151642
• 15J. Devignes, M. Smaïl-Tabbone, A. Hervé, G. Cagninacci, M.-D. Devignes, T. Lecompte, S. Zuily, D. Wahl.
  
  Extended persistence of antiphospholipid antibodies beyond the twelve‐week time interval: Association with baseline antiphospholipid antibodies titres, in: International Journal of Laboratory Hematology, September 2019, vol. 41, n^o 6, pp. 726-730. [ DOI : 10.1111/ijlh.13094 ]
  
  https://hal.inria.fr/hal-02395258
• 16J. P. Ferreira, A. Pizard, J.-L. Machu, E. Bresso, H.-P. Brunner-LaRocca, N. Girerd, L. Céline, A. González, J. Díez, S. Heymans, M.-D. Devignes.
  
  Plasma protein biomarkers and their association with mutually exclusive cardiovascular phenotypes: the FIBRO‑TARGETS case–control analyses, in: Clinical Research in Cardiology, April 2019, vol. 1. [ DOI : 10.1007/s00392-019-01480-4 ]
  
  https://hal.inria.fr/hal-02138814
• 17M. Lensink, G. Brysbaert, N. Nadzirin, S. Velankar, R. A. Chaleil, T. Gerguri, P. Bates, E. Laine, A. Carbone, S. Grudinin, R. Kong, R. Liu, X. Xu, H. Shi, S. Chang, M. Eisenstein, A. Karczynska, C. Czaplewski, E. Lubecka, A. Lipska, P. Krupa, M. Mozolewska, Ł. Golon, S. Samsonov, A. Liwo, S. Crivelli, G. Pagès, M. Karasikov, M. Kadukova, Y. Yan, S. Huang, M. Rosell, L. A. Rodríguez‐Lumbreras, M. Romero‐Durana, L. Díaz‐Bueno, J. Fernandez‐Recio, C. Christoffer, G. Terashi, W. Shin, T. Aderinwale, S. Raghavendra Maddhuri Venkata Subram, D. Kihara, D. Kozakov, S. Vajda, K. Porter, D. Padhorny, I. Desta, D. Beglov, M. Ignatov, S. Kotelnikov, I. Moal, D. Ritchie, I. Chauvot de Beauchêne, B. Maigret, M.-E. Ruiz-Echartea, D. Barradas‐Bautista, Z. Cao, L. Cavallo, R. Oliva, Y. Cao, Y. Shen, M. Baek, T. Park, H. Woo, C. Seok, M. Braitbard, L. Bitton, D. Scheidman‐Duhovny, J. Dapkūnas, K. Olechnovič, Č. Venclovas, P. J. Kundrotas, S. Belkin, D. Chakravarty, V. Badal, I. A. Vakser, T. Vreven, S. Vangaveti, T. M. Borrman, Z. Weng, J. D. Guest, R. Gowthaman, B. G. Pierce, X. Xu, R. Duan, L. Qiu, J. Hou, B. Ryan Merideth, Z. Ma, J. Cheng, X. Zou, P. Koukos, J. Roel‐Touris, F. Ambrosetti, C. Geng, J. Schaarschmidt, M. Trellet, A. S. Melquiond, L. Xue, B. Jiménez‐García, C. Noort, R. Honorato, A. M. Bonvin, S. J. Wodak.
  
  Blind prediction of homo‐ and hetero‐ protein complexes: The CASP13‐CAPRI experiment, in: Proteins - Structure, Function and Bioinformatics, October 2019, vol. 87, n^o 12, pp. 1200-1221. [ DOI : 10.1002/prot.25838 ]
  
  https://hal.inria.fr/hal-02320974
• 18F. A. V. Rodrigues-Vendramini, D. R. Faria, G. S. Arita, I. R. G. Capoci, K. M. Sakita, S. M. Caparroz-Assef, T. C. A. Becker, P. de Souza Bonfim-Mendonça, M. S. Felipe, T. I. E. Svidzinski, B. Maigret, E. S. Kioshima, P. Small.
  
  Antifungal activity of two oxadiazole compounds for the paracoccidioidomycosis treatment, in: PLoS Neglected Tropical Diseases, June 2019, vol. 13, n^o 6, e0007441 p. [ DOI : 10.1371/journal.pntd.0007441 ]
  
  https://hal.inria.fr/hal-02151638
• 19M. E. Ruiz­ Echartea, I. Chauvot de Beauchêne, D. Ritchie.
  
  EROS-DOCK: Protein-Protein Docking Using Exhaustive Branch-and-Bound Rotational Search, in: Bioinformatics, 2019, forthcoming. [ DOI : 10.1093/bioinformatics/btz434 ]
  
  https://hal.archives-ouvertes.fr/hal-02269812
• 20M. Smaïl-Tabbone, M. Smaïl-Tabbone, B. Rance.
  
  Contributions from the 2018 Literature on Bioinformatics and Translational Informatics, in: IMIA Yearbook of Medical Informatics, August 2019, vol. 28, n^o 01, pp. 190-193. [ DOI : 10.1055/s-0039-1677945 ]
  
  https://hal.inria.fr/hal-02413623
• 21N. Soler, E. Robert, I. Chauvot de Beauchêne, P. Monteiro, V. Libante, B. Maigret, J. Staub, D. W. Ritchie, G. Guédon, S. Payot, M.-D. Devignes, N. N. Leblond-Bourget.
  
  Characterization of a relaxase belonging to the MOBT family, a widespread family in Firmicutes mediating the transfer of ICEs, in: Mobile DNA, December 2019, vol. 10, n^o 1. [ DOI : 10.1186/s13100-019-0160-9 ]
  
  https://hal.inria.fr/hal-02138843
• 22U. Uciechowska-Kaczmarzyk, I. Chauvot de Beauchêne, S. Samsonov.
  
  Docking software performance in protein-glycosaminoglycan systems, in: Journal of Molecular Graphics and Modelling, April 2019, vol. 90, pp. 42-50. [ DOI : 10.1016/j.jmgm.2019.04.001 ]
  
  https://hal.archives-ouvertes.fr/hal-02391852
• 23N. Zhou, Y. Jiang, T. Bergquist, A. Lee, B. Kacsoh, A. Crocker, K. Lewis, G. Georghiou, H. Nguyen, M. N. Hamid, L. Davis, T. Dogan, V. Atalay, A. Rifaioglu, A. Dalkıran, R. Cetin Atalay, C. Zhang, R. Hurto, P. Freddolino, Y. Zhang, P. Bhat, F. Supek, J. Fernandez, B. Gemovic, V. Perovic, R. Davidović, N. Sumonja, N. Veljkovic, E. Asgari, M. R. Mofrad, G. Profiti, C. Savojardo, P. L. Martelli, R. Casadio, F. Boecker, H. Schoof, I. Kahanda, N. Thurlby, A. C. McHardy, A. Renaux, R. Saidi, J. Gough, A. Freitas, M. Antczak, F. Fabris, M. Wass, J. Hou, J. Cheng, Z. Wang, A. Romero, A. Paccanaro, H. Yang, T. Goldberg, C. Zhao, L. Holm, P. Törönen, A. J. Medlar, E. Zosa, I. Borukhov, I. Novikov, A. Wilkins, O. Lichtarge, P.-H. Chi, W.-C. Tseng, M. Linial, P. Rose, C. Dessimoz, V. Vidulin, S. Dzeroski, I. Sillitoe, S. Das, J. G. Lees, D. Jones, C. Wan, D. Cozzetto, R. Fa, M. Torres, A. Warwick Vesztrocy, J. M. Rodriguez, M. Tress, M. Frasca, M. Notaro, G. Grossi, A. Petrini, M. Re, G. Valentini, M. Mesiti, D. S. Roche, J. Reeb, D. Ritchie, S. Aridhi, S. Z. Alborzi, M.-D. Devignes, D. C. E. Koo, R. Bonneau, V. Gligorijević, M. Barot, H. Fang, S. Toppo, E. Lavezzo, M. Falda, M. Berselli, S. C. Tosatto, M. Carraro, D. Piovesan, H. Ur Rehman, Q. Mao, S. Zhang, S. Vucetic, G. Black, D. Jo, E. Suh, J. Dayton, D. Larsen, A. Omdahl, L. McGuffin, D. Brackenridge, P. Babbitt, J. Yunes, P. Fontana, F. Zhang, S. Zhu, R. You, Z. Zhang, S. Dai, S. Yao, W. Tian, R. Cao, C. Chandler, M. Amezola, D. Johnson, J.-M. Chang, W.-H. Liao, Y.-W. Liu, S. Pascarelli, Y. Frank, R. Hoehndorf, M. Kulmanov, I. Boudellioua, G. Politano, S. Di Carlo, A. Benso, K. Hakala, F. Ginter, F. Mehryary, S. Kaewphan, J. Björne, H. Moen, M. E. Tolvanen, T. Salakoski, D. Kihara, A. Jain, T. Šmuc, A. M. Altenhoff, A. Ben-Hur, B. Rost, S. Brenner, C. Orengo, C. Jeffery, G. Bosco, D. Hogan, M. Martin, C. O’Donovan, S. Mooney, C. Greene, P. Radivojac, I. Friedberg.
  
  The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens, in: Genome Biology, December 2019, vol. 20, n^o 1. [ DOI : 10.1186/s13059-019-1835-8 ]
  
  https://hal.inria.fr/hal-02393202
• 24M. Zoghlami, S. Aridhi, M. Maddouri, E. Mephu Nguifo.
  
  Multiple instance learning for sequence data with across bag dependencies, in: International journal of machine learning and cybernetics, 2019, https://arxiv.org/abs/1602.00163, forthcoming. [ DOI : 10.1007/s13042-019-01021-5 ]
  
  https://hal.inria.fr/hal-02393742

International Conferences with Proceedings

• 25B. Sarker, D. W. Ritchie, S. Aridhi.
  
  Functional Annotation of Proteins using Domain Embedding based Sequence Classification, in: KDIR 2019 - 11th International Conference on Knowledge Discovery and Information Retrieval, Vienna, Austria, September 2019.
  
  https://hal.inria.fr/hal-02283430
• 26M. Zoghlami, S. Aridhi, M. Maddouri, E. M. Nguifo.
  
  A Structure Based Multiple Instance Learning Approach for Bacterial Ionizing Radiation Resistance Prediction, in: KES 2019 - 23rd International Conference on Knowledge-Based and Intelligent Information & Engineering Systems, Budapest, Hungary, September 2019.
  
  https://hal.inria.fr/hal-02307048

National Conferences with Proceedings

• 27K. Dalleau, M. Couceiro, M. Smaïl-Tabbone.
  
  Les forêts d'arbres extrêmement aléatoires : utilisation dans un cadre non supervisé, in: EGC 2019 - 19ème Conférence Francophone sur l'Extraction et Gestion des connaissances, Metz, France, Hermann-Éditions, January 2019, vol. RNTI E-35, pp. 395-400.
  
  https://hal.inria.fr/hal-02099532

Conferences without Proceedings

• 28M.-E. Ruiz-Echartea, I. Chauvot de Beauchêne, D. Ritchie.
  
  EROS-DOCK for Pairwise and Multi-body Protein-Protein Docking, in: Journée MASIM2019 (Méthodes Algorithmiques pour les Structures et Interactions Macromoléculaires), Paris, France, November 2019.
  
  https://hal.archives-ouvertes.fr/hal-02391973
• 29A. Vaginay, M. Smaïl-Tabbone, T. Boukhobza.
  
  Towards an automatic conversion from SBML core to SBML qual, in: Journées Ouvertes Biologie, Informatique et Mathématiques, JOBIM 2019, Nantes, France, July 2019, Présentation Poster.
  
  https://hal.archives-ouvertes.fr/hal-02407443

Other Publications

• 30F.-É. Calvier, P. Monnin, M. Boland, P. Jarnot, E. Bresso, M. Smaïl-Tabbone, A. Coulet, C. Bousquet.
  
  Providing Molecular Characterization for Unexplained Adverse Drug Reactions : Podium Abstract, July 2019, Podium Abstract at MedInfo 2019, Lyon, France.
  
  https://hal.inria.fr/hal-02196134
• 31K. Dalleau, M. Couceiro, M. Smaïl-Tabbone.
  
  Clustering graphs using random trees, September 2019, working paper or preprint.
  
  https://hal.inria.fr/hal-02282207
• 32K. Dalleau, M. Couceiro, M. Smaïl-Tabbone.
  
  Computing Vertex-Vertex Dissimilarities Using Random Trees: Application to Clustering in Graphs, November 2019, working paper or preprint.
  
  https://hal.inria.fr/hal-02427563
• 33K. Dalleau, M. Couceiro, M. Smaïl-Tabbone.
  
  Unsupervised Extra Trees: a stochastic approach to compute similarities in heterogeneous data, January 2019, working paper or preprint.
  
  https://hal.inria.fr/hal-01982232
• 34W. Inoubli, S. Aridhi, H. Mezni, M. Mondher, E. M. Nguifo.
  
  A Distributed Algorithm for Large-Scale Graph Clustering, August 2019, working paper or preprint.
  
  https://hal.inria.fr/hal-02190913
• 35M.-E. Ruiz-Echartea, I. Chauvot de Beauchêne, D. Ritchie.
  
  EROS: A Protein Docking Algorithm Using a Quaternion pi- Ball Representation for Exhaustive and Accelerated Exploration of 3D Rotational Space, April 2019, GGMM (groupe de graphisme et modélisation moléculaire ), Poster.
  
  https://hal.archives-ouvertes.fr/hal-02392106

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  Docking essential dynamics eigenstructures, in: Proteins: Structure, Function, and Genetics, 2005, vol. 60, pp. 269-274. [ DOI : 10.1002/prot.20569 ]
  
  https://hal.inria.fr/inria-00434271
• 58S. Orchard, S. Kerrien, S. Abbani, B. Aranda, J. Bhate, S. Bidwell, A. Bridge, L. Briganti, F. S. L. Brinkman, G. Cesareni, A. Chatraryamontri, E. Chautard, C. Chen, M. Dumousseau, J. Goll, R. E. W. Hancock, L. I. Hannick, I. Jurisica, J. Khadake, D. J. Lynn, U. Mahadevan, L. Perfetto, A. Raghunath, S. Ricard-Blum, B. Roechert, L. Salwinski, V. Stümpflen, M. Tyers, P. Uetz, I. Xenarios, H. Hermjakob.
  
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• 59B. Pierce, W. Tong, Z. Weng.
  
  M-ZDOCK: A Grid-Based Approach for $C_n$ Symmetric Multimer Docking, in: Bioinformatics, 2005, vol. 21, n^o 8, pp. 1472–1478.
• 60D. Ritchie, G. J. Kemp.
  
  Protein docking using spherical polar Fourier correlations, in: Proteins: Structure, Function, and Genetics, 2000, vol. 39, pp. 178-194.
  
  https://hal.inria.fr/inria-00434273
• 61D. Ritchie, D. Kozakov, S. Vajda.
  
  Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions, in: Bioinformatics, June 2008, vol. 24, n^o 17, pp. 1865-1873. [ DOI : 10.1093/bioinformatics/btn334 ]
  
  https://hal.inria.fr/inria-00434264
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