Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Major publications by the team in recent years
[1]
M. Aite, M. Chevallier, C. Frioux, C. Trottier, J. Got, M.-P. Cortés, S. N. Mendoza, G. Carrier, O. Dameron, N. Guillaudeux, M. Latorre, N. Loira, G. V. Markov, A. Maass, A. Siegel.
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models, in: PLoS Computational Biology, May 2018, vol. 14, no 5, e1006146. [ DOI : 10.1371/journal.pcbi.1006146 ]
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01807842
[2]
C. Belleannée, O. Sallou, J. Nicolas.
Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling, in: PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Stockholm, Sweden, M. Comin, L. Kall, E. Marchiori, A. Ngom, J. Rajapakse (editors), Springer International Publishing, August 2014, vol. 8626, pp. 34-47. [ DOI : 10.1007/978-3-319-09192-1_4 ]
https://hal.inria.fr/hal-01059506
[3]
C. Bettembourg, C. Diot, O. Dameron.
Optimal Threshold Determination for Interpreting Semantic Similarity and Particularity: Application to the Comparison of Gene Sets and Metabolic Pathways Using GO and ChEBI, in: PLoS ONE, 2015, 30 p. [ DOI : 10.1371/journal.pone.0133579 ]
https://hal.inria.fr/hal-01184934
[4]
P. Bordron, M. Latorre, M.-P. Cortés, M. Gonzales, S. Thiele, A. Siegel, A. Maass, D. Eveillard.
Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, in: MicrobiologyOpen, 2015, vol. 5, no 1, pp. 106-117. [ DOI : 10.1002/mbo3.315 ]
https://hal.inria.fr/hal-01246173
[5]
J. Coquet, N. Théret, V. Legagneux, O. Dameron.
Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-β Signaling, in: CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology, Darmstadt, Lecture Notes in Computer Sciences, September 2017, 17 p.
https://hal.archives-ouvertes.fr/hal-01559249
[6]
F. Coste, G. Garet, A. Groisillier, J. Nicolas, T. Tonon.
Automated Enzyme classification by Formal Concept Analysis, in: ICFCA - 12th International Conference on Formal Concept Analysis, Cluj-Napoca, Romania, Springer, June 2014.
https://hal.inria.fr/hal-01063727
[7]
F. Coste, J. Nicolas.
Learning local substitutable context-free languages from positive examples in polynomial time and data by reduction, in: ICGI 2018 - 14th International Conference on Grammatical Inference, Wrocław, Poland, September 2018, vol. 93, pp. 155 - 168.
https://hal.inria.fr/hal-01872266
[8]
C. Frioux, E. Fremy, C. Trottier, A. Siegel.
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia, in: Bioinformatics, September 2018, vol. 34, no 17, pp. i934 - i943. [ DOI : 10.1093/bioinformatics/bty588 ]
https://hal.inria.fr/hal-01871600
[9]
C. Frioux, T. Schaub, S. Schellhorn, A. Siegel, P. Wanko.
Hybrid Metitebolic Network Completion, in: Theory and Practice of Logic Programming, November 2018, pp. 1-23.
https://hal.inria.fr/hal-01936778
[10]
S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, no 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]
https://hal.inria.fr/hal-01449100
[11]
S. Videla, J. Saez-Rodriguez, C. Guziolowski, A. Siegel.
caspo: a toolbox for automated reasoning on the response of logical signaling networks families, in: Bioinformatics, 2017. [ DOI : 10.1093/bioinformatics/btw738 ]
https://hal.inria.fr/hal-01426880
Publications of the year

Doctoral Dissertations and Habilitation Theses

[12]
L. Bourneuf.
A search space of graph motifs for graph compression : From Powergraphs to triplet concepts, Université Rennes 1, December 2019.
https://hal.inria.fr/tel-02399641

Articles in International Peer-Reviewed Journals

[13]
S. Blanquart, A.-S. Borowiec, P. Delcourt, M. Figeac, C. A. Emerling, A. S. Meseguer, M. Roudbaraki, N. Prevarskaya, G. Bidaux.
Evolution of the human cold/menthol receptor, TRPM8, in: Molecular Phylogenetics and Evolution, July 2019, vol. 136, pp. 104-118. [ DOI : 10.1016/j.ympev.2019.04.011 ]
https://hal.inria.fr/hal-02284919
[14]
V. Delannée, S. Langouët, A. Siegel, N. Théret.
In silico prediction of Heterocyclic Aromatic Amines metabolism susceptible to form DNA adducts in humans, in: Toxicology Letters, January 2019, vol. 300, pp. 18-30. [ DOI : 10.1016/j.toxlet.2018.10.011 ]
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01903264
[15]
W. Dyrka, M. Pyzik, F. Coste, H. Talibart.
Estimating probabilistic context-free grammars for proteins using contact map constraints, in: PeerJ, March 2019, vol. 7, pp. 1-35. [ DOI : 10.7717/peerj.6559 ]
https://hal.archives-ouvertes.fr/hal-02400871
[16]
M. Folschette, V. Legagneux, A. Poret, L. Chebouba, C. Guziolowski, N. Théret.
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma, in: BMC Bioinformatics, January 2020. [ DOI : 10.1186/s12859-019-3316-1 ]
https://hal.archives-ouvertes.fr/hal-02095930
[17]
D. Nègre, M. Aite, A. Belcour, C. Frioux, L. Brillet-Guéguen, X. Liu, P. Bordron, O. Godfroy, A. P. Lipinska, C. Leblanc, A. Siegel, S. M. Dittami, E. Corre, G. V. Markov.
Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus, in: Antioxidants, November 2019, vol. 8, no 11, 564 p. [ DOI : 10.3390/antiox8110564 ]
https://hal.inria.fr/hal-02395080
[18]
Y. Rivault, O. Dameron, N. Le Meur.
queryMed: Semantic Web functions for linking pharmacological and medical knowledge to data, in: Bioinformatics, January 2019, vol. 35, no 17, pp. 3203-3205. [ DOI : 10.1093/bioinformatics/btz034 ]
https://hal.archives-ouvertes.fr/hal-01988699
[19]
K. Straub, M. Linde, C. Kropp, S. Blanquart, P. Babinger, R. Merkl.
Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase, in: Biological Chemistry, February 2019, vol. 400, no 3, pp. 367-381. [ DOI : 10.1515/hsz-2018-0344 ]
https://hal.inria.fr/hal-02284913
[20]
M. Wery, O. Dameron, J. Nicolas, E. Rémy, A. Siegel.
Formalizing and enriching phenotype signatures using Boolean networks, in: Journal of Theoretical Biology, 2019, vol. 467, pp. 66-79. [ DOI : 10.1016/j.jtbi.2019.01.015 ]
https://hal.inria.fr/hal-02018724

Invited Conferences

[21]
A. Siegel.
Learning boolean regulations based on prior-knowledge data: a logical-based viewpoint, in: SASB 2019 - 10th International Workshop on Static Analysis for Systems Biology, Porto, Portugal, October 2019.
https://hal.inria.fr/hal-02412421
[22]
A. Siegel.
Using automated reasoning to explore unconventional organisms: a first step to explore host-microbial interactions, in: MPA 2019 - Conference on Metabolic Pathway Analysis, Riga, Latvia, August 2019.
https://hal.inria.fr/hal-02412419

International Conferences with Proceedings

[23]
J. Bakalara, T. Guyet, O. Dameron, E. Oger, A. Happe.
Temporal models of care sequences for the exploration of medico-administrative data, in: 2019 - Workshop IA&Santé, PFIA, Toulouse, France, July 2019, pp. 1-8.
https://hal.archives-ouvertes.fr/hal-02265743
[24]
L. Bourneuf, J. Nicolas.
Concept Lattices as a Search Space for Graph Compression, in: ICFCA 2019 - 15th International Conference on Formal Concept Analysis, Francfort, Germany, D. C. L. B. Sertkaya (editor), ICFCA: International Conference on Formal Concept Analysis, Springer, May 2019, vol. 15th International Conference, no 15, pp. 274-289. [ DOI : 10.1007/978-3-030-21462-3_18 ]
https://hal.inria.fr/hal-02399578
[25]
M. Louarn, F. Chatonnet, X. Garnier, T. Fest, A. Siegel, O. Dameron.
Increasing life science resources re-usability using Semantic Web technologies, in: eScience 2019 - 15th International eScience Conference, San Diego, United States, September 2019, pp. 1-9.
https://hal.inria.fr/hal-02274982

Conferences without Proceedings

[26]
L. Bourneuf.
Biseau: An Answer Set Programming Environment for High-Level Specification and Graph Visualization applied to FCA, in: ICFCA 2019 - International Conference on Formal Concept Analysis, Frankfort, Germany, June 2019, pp. 1-6.
https://hal.inria.fr/hal-02399610
[27]
X. Garnier, A. Bretaudeau, F. Legeai, A. Siegel, O. Dameron.
AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019, 1 p.
https://hal.archives-ouvertes.fr/hal-02401750
[28]
V. J. Henry, G. Bassignana, V. Zujovic, F. De Vico Fallani, O. Dameron, I. Moszer, O. Colliot.
Conciliation of process description and molecular interaction networks using logical properties of ontology, in: JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Nantes, France, July 2019.
https://hal.archives-ouvertes.fr/hal-02301702
[29]
N. Le Meur, Y. Rivault, O. Dameron.
Linking pharmacological and medical knowledge using semantic Web technologies, in: useR! 2019 - Conférence internationale des utilisateurs de R, Toulouse, France, July 2019.
https://hal.archives-ouvertes.fr/hal-02294364
[30]
H. Talibart, F. Coste.
Using residues coevolution to search for protein homologs through alignment of Potts models, in: CECAM 2019 - workshop on Co-evolutionary methods for the prediction and design of protein structure and interactions, Lausanne, Switzerland, CECAM-HQ-EPFL, June 2019, pp. 1-2.
https://hal.inria.fr/hal-02402646

Other Publications

[31]
A. Abel.
Faster SPARQL Federated Queries, Université Rennes1, June 2019.
https://hal.inria.fr/hal-02269417
[32]
P. Beaudier.
Evaluation of the public databases' relevance as comprehensive tools for pharmacological mechanisms, Université de Rennes 1, June 2019.
https://hal.inria.fr/hal-02191210
[33]
A. Belcour, C. Frioux, M. Aite, A. Bretaudeau, A. Siegel.
Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species, December 2019, working paper or preprint. [ DOI : 10.1101/803056 ]
https://hal.inria.fr/hal-02395024
[34]
B. Burgunter-Delamare, H. Kleinjan, C. Frioux, E. Fremy, M. Wagner, E. Corre, A. Le Salver, C. Leroux, C. Leblanc, A. Siegel, S. M. Dittami.
Metabolic complementarity between a brown alga and associated 1 cultivable bacteria provide indications of beneficial interactions, October 2019, working paper or preprint. [ DOI : 10.1101/813683 ]
https://hal.sorbonne-universite.fr/hal-02333039
[35]
F. Casse Encadrée.
Regulation of genes regulating fecondity and early embryonic development by miRNAs in the Medaka fish, Univ Rennes, Inria, CNRS, IRISA, June 2019.
https://hal.inria.fr/hal-02192476
[36]
F. Coste.
Deep learning languages: a key fundamental shift from probabilities to weights?, August 2019, https://arxiv.org/abs/1908.00785 - working paper or preprint.
https://hal.inria.fr/hal-02235207
[37]
O. Dennler.
Caractérisation en modules fonctionnels de la famille de protéines ADAMTS / ADAMTSL, Univ Rennes, June 2019.
https://hal.inria.fr/hal-02403084
[38]
S. M. Dittami, E. Corre, L. Brillet-Guéguen, A. P. Lipinska, M. Aite, K. Avia, C. Caron, C. H. Cho, J. Collen, A. Cormier, L. Delage, S. Doubleau, C. Frioux, A. Gobet, I. González-Navarrete, A. Groisillier, C. Hervé, D. Jollivet, H. Kleinjan, C. Leblanc, X. Liu, D. Marie, G. V. Markov, A. E. Minoche, P. Pericard, M.-M. Perrineau, A. F. Peters, A. Siegel, C. Trottier, H. S. Yoon, H. Himmelbauer, C. Boyen, T. Tonon.
The genome of Ectocarpus subulatus -a highly stress-tolerant brown alga, October 2019, working paper or preprint. [ DOI : 10.1101/307165 ]
https://hal.sorbonne-universite.fr/hal-02333021
[39]
N. Guillaudeux, C. Belleannée, S. Blanquart, J.-S. Varré.
Predicting isoform transcripts: What does the comparison of known transcripts in human, mouse and dog tell us?, July 2019, vol. 8, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster présenté à JOBIM 2019 (https://jobim2019.sciencesconf.org/) qui s'est déroulé du 2 au 5 juillet 2019 et à ISMB/ECCB 2019 (https://www.iscb.org/ismbeccb2019) qui s'est déroulé du 21 au 25 juillet 2019. [ DOI : 10.7490/f1000research.1117311.1 ]
https://hal.inria.fr/hal-02267357
[40]
H. Talibart, F. Coste.
Using residues coevolution to search for protein homologs through alignment of Potts models, July 2019, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
https://hal.inria.fr/hal-02402687
[41]
K. Thuillier.
Linear programming for metabolic network completion, Inria Rennes - Bretagne Atlantique and University of Rennes 1, France, December 2019.
https://hal.inria.fr/hal-02408003
[42]
M. Wery, E. Becker, F. Auge, C. Bettembourg, O. Dameron, A. Siegel.
Identification of causal signature using omics data integration and network reasoning-based analysis, July 2019, 1 p, JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Poster.
https://hal.inria.fr/hal-02193860
References in notes
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An integrative modeling framework reveals plasticity of TGF-Beta signaling, in: BMC Systems Biology, 2014, vol. 8, no 1, 30 p. [ DOI : 10.1186/1752-0509-8-30 ]
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[45]
C. Bettembourg, C. Diot, O. Dameron.
Semantic particularity measure for functional characterization of gene sets using gene ontology, in: PLoS ONE, 2014, vol. 9, no 1, e86525. [ DOI : 10.1371/journal.pone.0086525 ]
https://hal.inria.fr/hal-00941850
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Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism, in: BMC Systems Biology, 2014, vol. 8, no 1, 32 p. [ DOI : 10.1186/1752-0509-8-32 ]
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Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, in: MicrobiologyOpen, 2015, vol. 5, no 1, pp. 106-117. [ DOI : 10.1002/mbo3.315 ]
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TGF-β signaling intersects with CD103 integrin signaling to promote T lymphocyte accumulation and antitumor activity in the lung tumor microenvironment, in: Cancer Research, 2016, vol. 76, no 7, pp. 1757-69. [ DOI : 10.1158/0008-5472.CAN-15-1545 ]
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282442
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[51]
J. Coquet, N. Théret, V. Legagneux, O. Dameron.
Identifying Functional Families of Trajectories in Biological Pathways by Soft Clustering: Application to TGF-β Signaling, in: CMSB 2017 - 15th International Conference on Computational Methods in Systems Biology, Darmstadt, France, Lecture Notes in Computer Sciences, September 2017, 17 p.
https://hal.archives-ouvertes.fr/hal-01559249
[52]
M.-P. Cortés, S. N. Mendoza, D. Travisany, A. Gaete, A. Siegel, V. Cambiazo, A. Maass.
Analysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing, in: Frontiers in Microbiology, December 2017, vol. 8, 15 p. [ DOI : 10.3389/fmicb.2017.02462 ]
https://hal.inria.fr/hal-01661270
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Automated Enzyme classification by Formal Concept Analysis, in: ICFCA - 12th International Conference on Formal Concept Analysis, Cluj-Napoca, Romania, Springer, June 2014.
https://hal.inria.fr/hal-01063727
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V. Delannée, S. Langouët, N. Théret, A. Siegel.
A modeling approach to evaluate the balance between bioactivation and detoxification of MeIQx in human hepatocytes, in: PeerJ, 2017, vol. 5, e3703 p. [ DOI : 10.7717/peerj.3703 ]
https://hal.inria.fr/hal-01575579
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Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae, in: Frontiers in Genetics, 2014, vol. 5, 241 p. [ DOI : 10.3389/fgene.2014.00241 ]
https://hal.inria.fr/hal-01079739
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K. Faust, J. Raes.
Microbial interactions: from networks to models, in: Nat. Rev. Microbiol., Jul 2012, vol. 10, no 8, pp. 538–550.
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https://hal.archives-ouvertes.fr/hal-01210940
[60]
F. Herault, A. Vincent, O. Dameron, P. Le Roy, P. Cherel, M. Damon.
The longissimus and semimembranosus muscles display marked differences in their gene expression profiles in pig, in: PLoS ONE, 2014, vol. 9, no 5, e96491. [ DOI : 10.1371/journal.pone.0096491 ]
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M.-A. Laurent, D. Bonnier, N. Théret, P. Tufféry, G. Moroy.
In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1, in: Computational Biology and Chemistry, April 2016, vol. 61, pp. 155-161. [ DOI : 10.1016/j.compbiolchem.2016.01.012 ]
https://hal.archives-ouvertes.fr/hal-02394687
[62]
S. Prigent, G. Collet, S. M. Dittami, L. Delage, F. Ethis de Corny, O. Dameron, D. Eveillard, S. Thiele, J. Cambefort, C. Boyen, A. Siegel, T. Tonon.
The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, in: Plant Journal, September 2014, pp. 367-81. [ DOI : 10.1111/tpj.12627 ]
https://hal.archives-ouvertes.fr/hal-01057153
[63]
S. Prigent, C. Frioux, S. M. Dittami, S. Thiele, A. Larhlimi, G. Collet, G. Fabien, J. Got, D. Eveillard, J. Bourdon, F. Plewniak, T. Tonon, A. Siegel.
Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, in: PLoS Computational Biology, January 2017, vol. 13, no 1, 32 p. [ DOI : 10.1371/journal.pcbi.1005276 ]
https://hal.inria.fr/hal-01449100
[64]
Y. Rivault.
Care trajectory analysis using medico-administrative data : contribution of a knowledge-based enrichment from the Linked Data, Université Rennes 1, January 2019.
https://tel.archives-ouvertes.fr/tel-02137442
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M. H. Saier, V. S. Reddy, B. V. Tsu, M. S. Ahmed, C. Li, G. Moreno-Hagelsieb.
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Big Data: Astronomical or Genomical?, in: PLoS biology, 2015, vol. 13, no 7, e1002195 p.
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Triple Pattern Fragments: a Low-cost Knowledge Graph Interface for the Web, in: Journal of Web Semantics, March 2016, vol. 37–38, pp. 184–206. [ DOI : doi:10.1016/j.websem.2016.03.003 ]
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