Experts and Doctors on software in France


Locale: France
Topic: software

Top Publications

  1. Coullet P, Toniolo C, Tresser C. How much information can one store in a nonequilibrium medium?. Chaos. 2004;14:839-44 pubmed
  2. Gelly J, Chiche L, Gracy J. EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments. BMC Bioinformatics. 2005;6:4 pubmed
    ..The easy adaptation of EvDTree to any specific data set opens the way for class-specific structure-dependent substitution scores which can be used in threading-based remote homology searches. ..
  3. Foulley J, Jaffrezic F. Modelling and estimating heterogeneous variances in threshold models for ordinal discrete data via Winbugs/Openbugs. Comput Methods Programs Biomed. 2010;97:19-27 pubmed publisher
    ..In particular, it was found that adding a random subject effect in the variance model significantly improved the posterior predictive p-value criterion of the model. ..
  4. Meglecz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, et al. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics. 2010;26:403-4 pubmed publisher
    ..QDD is freely available under the GPL licence for Windows and Linux from the following web site: Supplementary data are available at Bioinformatics online. ..
  5. Iannuccelli E, Mompart F, Gellin J, Lahbib Mansais Y, Yerle M, Boudier T. NEMO: a tool for analyzing gene and chromosome territory distributions from 3D-FISH experiments. Bioinformatics. 2010;26:696-7 pubmed publisher
    ..NEMO is a stand-alone Java application available for Windows and Linux platforms. The program is distributed under the creative commons licence and can be freely downloaded from ..
  6. Ehrenmann F, Kaas Q, Lefranc M. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res. 2010;38:D301-7 pubmed publisher
    ..IMGT/3Dstructure-DB and IMGT/DomainGapAlign are freely available at ..
  7. Schramm T, Hester Z, Klinkert I, Both J, Heeren R, Brunelle A, et al. imzML--a common data format for the flexible exchange and processing of mass spectrometry imaging data. J Proteomics. 2012;75:5106-5110 pubmed publisher
    ..All technical details necessary to implement imzML and additional background information is available at ..
  8. Lemesle Varloot L, Ojasoo T, Mornon J, Raynaud J. A model for the determination of the 3D-spatial distribution of the functions of the hormone-binding domain of receptors that bind 3-keto-4-ene steroids. J Steroid Biochem Mol Biol. 1992;41:369-88 pubmed
    ..Indeed, the model has enabled the identification of a Rossmann-fold in SHRs that might bind ATP. Visualization of all these functions should help to interpret the chain of concerted events induced by steroid binding. ..
  9. Chiapello H, Ollivier E, Landès Devauchelle C, Nitschke P, Risler J. Codon usage as a tool to predict the cellular location of eukaryotic ribosomal proteins and aminoacyl-tRNA synthetases. Nucleic Acids Res. 1999;27:2848-51 pubmed
    ..A WWW interface has been developed, aimed at providing a user-friendly tool for codon usage pattern analysis. It is available from ..

More Information

Publications186 found, 100 shown here

  1. Melet A, Assrir N, Jean P, Pilar Lopez Garcia M, Marques Soares C, Jaouen M, et al. Substrate selectivity of human cytochrome P450 2C9: importance of residues 476, 365, and 114 in recognition of diclofenac and sulfaphenazole and in mechanism-based inactivation by tienilic acid. Arch Biochem Biophys. 2003;409:80-91 pubmed
    ..They also provide the first experimental evidence showing that Phe 476 plays a crucial role in substrate recognition and hydroxylation by CYP 2C9. ..
  2. Cottret L, Wildridge D, Vinson F, Barrett M, Charles H, Sagot M, et al. MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 2010;38:W132-7 pubmed publisher
    ..The MetExplore web server is freely accessible at ..
  3. Grieco L, Calzone L, Bernard Pierrot I, Radvanyi F, Kahn Perlès B, Thieffry D. Integrative modelling of the influence of MAPK network on cancer cell fate decision. PLoS Comput Biol. 2013;9:e1003286 pubmed publisher
  4. Rimour S, Hill D, Militon C, Peyret P. GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics. 2005;21:1094-103 pubmed
    ..cuniculi microarray will overcome the difficulty to discriminate the parasite mRNAs from the host cell mRNAs demonstrating the power of the microarray approach to elucidate the lifestyle of an intracellular pathogen using mix mRNAs. ..
  5. Berdagué J, Tournayre P, Cambou S. Novel multi-gas chromatography-olfactometry device and software for the identification of odour-active compounds. J Chromatogr A. 2007;1146:85-92 pubmed
    ..Synchronisation of olfactometry and mass spectrometry data enabled us to propose 44 structures to account for 44 out of these 46 odorous zones. ..
  6. Miele A, Blanchin N, Raynaud P, Quesne B, Giraud J, Fottorino R, et al. MEDOR, a didactic tool to support interpretation of bioassay data after internal contamination by actinides. Radiat Prot Dosimetry. 2007;127:350-5 pubmed
    ..This underlines the need to estimate systematically the number of deposited particles, as well as to do chest monitoring as long as possible...
  7. Bianchetti L, Wu Y, Guerin E, Plewniak F, Poch O. SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. Nucleic Acids Res. 2007;35:e122 pubmed
    ..SAGETTARIUS is web interfaced and freely accessible to academic users. ..
  8. Navaza J. Combining X-ray and electron-microscopy data to solve crystal structures. Acta Crystallogr D Biol Crystallogr. 2008;64:70-5 pubmed
    ..The technique is described in the case of viral and subviral particles as well as in the case of oligomeric proteins. ..
  9. Pencheva T, Lagorce D, Pajeva I, Villoutreix B, Miteva M. AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. BMC Bioinformatics. 2008;9:438 pubmed publisher
  10. Krebs A, Frontini M, Tora L. GPAT: retrieval of genomic annotation from large genomic position datasets. BMC Bioinformatics. 2008;9:533 pubmed publisher
    ..Through the different annotation data displayed, GPAT facilitates the interpretation of genome wide datasets for molecular biologists. ..
  11. Michel C, Pellegrini M, Pirillo G. Maximal dinucleotide and trinucleotide circular codes. J Theor Biol. 2016;389:40-6 pubmed publisher
    ..We give the same information for the maximal self-complementary dinucleotide and trinucleotide circular codes. The amino acid distribution of maximal trinucleotide circular codes is also determined. ..
  12. André L, Lamy E, Lutz P, Pernier M, Lespinard O, Pauss A, et al. Electrical resistivity tomography to quantify in situ liquid content in a full-scale dry anaerobic digestion reactor. Bioresour Technol. 2016;201:89-96 pubmed publisher
    ..ERT method showed a strong relevance to monitor and to optimize the dry batch anaerobic digestion process. ..
  13. Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211-7 pubmed publisher
    ..It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time. ..
  14. Foissac S, Schiex T. Integrating alternative splicing detection into gene prediction. BMC Bioinformatics. 2005;6:25 pubmed
    ..This automatic combination of experimental data analysis and ab initio gene finding offers an ideal integration of alternatively spliced gene prediction inside a single annotation pipeline. ..
  15. Angly F, Rodriguez Brito B, Bangor D, McNairnie P, Breitbart M, Salamon P, et al. PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC Bioinformatics. 2005;6:41 pubmed
    ..The estimates support the fact that the four phage communities were extremely diverse and that phage community biodiversity and structure may be correlated with that of their hosts. ..
  16. Lambert A, Legendre M, Fontaine J, Gautheret D. Computing expectation values for RNA motifs using discrete convolutions. BMC Bioinformatics. 2005;6:118 pubmed
    ..This method is now implemented into the ERPIN software, but it can be applied as well to any search procedure based on ungapped profiles with statistically independent columns. ..
  17. Jombart T, Devillard S, Dufour A, Pontier D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity (Edinb). 2008;101:92-103 pubmed publisher
    ..sPCA performed better than PCA to reveal spatial genetic patterns. The proposed methodology is implemented in the adegenet package of the free software R. ..
  18. Gouzy J, Carrère S, Schiex T. FrameDP: sensitive peptide detection on noisy matured sequences. Bioinformatics. 2009;25:670-1 pubmed publisher
    ..FrameDP for Linux (web-server and underlying pipeline) is available at {{}} for direct use or a standalone installation. ..
  19. Paradis E. pegas: an R package for population genetics with an integrated-modular approach. Bioinformatics. 2010;26:419-20 pubmed publisher
    ..pegas is distributed through the Comprehensive R Archive Network (CRAN): Further information may be found at: ..
  20. Abel S, Dupradeau F, Raman E, MacKerell A, Marchi M. Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J Phys Chem B. 2011;115:487-99 pubmed publisher
    ..5 times slower than that of bulk water due to the entrapment of the water in the micelle crevices. This retardation is independent of the headgroup in α- or β-anomers. ..
  21. Sallet E, Roux B, Sauviac L, Jardinaud M, Carrère S, Faraut T, et al. Next-generation annotation of prokaryotic genomes with EuGene-P: application to Sinorhizobium meliloti 2011. DNA Res. 2013;20:339-54 pubmed publisher
    ..meliloti RpoE2 regulon by ?3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes. ..
  22. Lefresne G, Latrille E, Irlinger F, Grimont P. Repeatability and reproducibility of ribotyping and its computer interpretation. Res Microbiol. 2004;155:154-61 pubmed
    ..Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained...
  23. Vacher C, Brown S, Hochberg M. Avoid, attack or do both? Behavioral and physiological adaptations in natural enemies faced with novel hosts. BMC Evol Biol. 2005;5:60 pubmed
    ..We discuss the implications of our findings for the management of invasive plant species and the management of pest resistance to new crop protectants or varieties. ..
  24. Vivares D, Arnoux P, Pignol D. A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. Proc Natl Acad Sci U S A. 2005;102:18848-53 pubmed
    ..GSH hydrolase and PCS activities of the enzyme are discussed in the light of both structures. ..
  25. Thompson J, Muller A, Waterhouse A, Procter J, Barton G, Plewniak F, et al. MACSIMS: multiple alignment of complete sequences information management system. BMC Bioinformatics. 2006;7:318 pubmed
    ..A web server and the source code are available at ..
  26. Durand P, Mahé F, Valin A, Nicolas J. Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics. 2006;7:477 pubmed
    ..By proposing a new visualization environment to analyse repeated sequences, this application aims to increase the efficiency of laboratories involved in investigating repeat organization in single genomes or across several genomes. ..
  27. Le Fevre F, Smidtas S, Combe C, Durot M, d Alché Buc F, Schachter V. CycSim--an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics. 2009;25:1987-8 pubmed publisher
    ..CycSim also functions as an online repository of genome-scale metabolic models. ..
  28. Nguyen V, Lavenier D. PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics. 2009;10:329 pubmed publisher
    ..A parallel algorithmic approach driven by the knowledge of the internal microprocessor architecture allows significant speedup to be obtained while preserving standard sensitivity for similarity search problems. ..
  29. Shi X, Marie D, Jardillier L, Scanlan D, Vaulot D. Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE. 2009;4:e7657 pubmed publisher
  30. Guindon S, Dufayard J, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307-21 pubmed publisher
    ..Overall, our tests show that the last version (3.0) of PhyML is fast, accurate, stable, and ready to use. A Web server and binary files are available from ..
  31. Abby S, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics. 2010;11:324 pubmed publisher
    ..Prunier is implemented in C++, using the Bio++ library and the phylogeny program Treefinder. It is available at: ..
  32. Ueno S, Le Provost G, Léger V, Klopp C, Noirot C, Frigerio J, et al. Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. BMC Genomics. 2010;11:650 pubmed publisher This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations. ..
  33. Ye T, Krebs A, Choukrallah M, Keime C, Plewniak F, Davidson I, et al. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 2011;39:e35 pubmed publisher
  34. Brancotte B, Biton A, Bernard Pierrot I, Radvanyi F, Reyal F, Cohen Boulakia S. Gene List significance at-a-glance with GeneValorization. Bioinformatics. 2011;27:1187-9 pubmed publisher
    ..To illustrate how helpful GeneValorization is, we will consider the gene list of the OncotypeDX prognostic marker test. Supplementary data are available at Bioinformatics online. ..
  35. Godard P, Allain M, Chamard V, Rodenburg J. Noise models for low counting rate coherent diffraction imaging. Opt Express. 2012;20:25914-34 pubmed publisher
    ..Based on this analysis, we develop a hybrid strategy which works efficiently in the absence of an informed initial guess. Our work emphasises issues which should be considered carefully when inverting experimental data. ..
  36. Charles L, Van Opstal F, Marti S, Dehaene S. Distinct brain mechanisms for conscious versus subliminal error detection. Neuroimage. 2013;73:80-94 pubmed publisher
    ..We propose the existence of two distinct brain mechanisms for metacognitive judgements: a conscious all-or-none process of single-trial response evaluation, and a non-conscious statistical assessment of confidence. ..
  37. Prague M, Commenges D, Guedj J, Drylewicz J, Thiebaut R. NIMROD: a program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations. Comput Methods Programs Biomed. 2013;111:447-58 pubmed publisher
    ..Then, we illustrate NIMROD use on Amprenavir pharmacokinetics data from the PUZZLE clinical trial in HIV infected patients. ..
  38. Lensink M, Wodak S. Docking, scoring, and affinity prediction in CAPRI. Proteins. 2013;81:2082-95 pubmed publisher
  39. Bizien T, Durand D, Roblina P, Thureau A, Vachette P, Pérez J. A Brief Survey of State-of-the-Art BioSAXS. Protein Pept Lett. 2016;23:217-31 pubmed
    ..The great potential of these multi-pronged approaches is illustrated by a series of very recent studies covering the various ways and means of using BioSAXS. ..
  40. Vidal F, Villard P. Development and validation of real-time simulation of X-ray imaging with respiratory motion. Comput Med Imaging Graph. 2016;49:1-15 pubmed publisher
  41. Robic A, Seroude V, Jeon J, Yerle M, Wasungu L, Andersson L, et al. A radiation hybrid map of the RN region in pigs demonstrates conserved gene order compared with the human and mouse genomes. Mamm Genome. 1999;10:565-8 pubmed
    ..The order of other genes already mapped in the mouse (FN1, IGFBP5, TNP1, VIL1, INHA/AE3, and PAX3) was identical in pigs. We found no clear difference between the gene order on pig Chr 15 and human Chr 2q. ..
  42. Délye C, Straub C, Michel S, Le Corre V. Nucleotide variability at the acetyl coenzyme A carboxylase gene and the signature of herbicide selection in the grass weed Alopecurus myosuroides (Huds.). Mol Biol Evol. 2004;21:884-92 pubmed
    ..This study provides the first evidence for the signature of ongoing, recent, pesticide selection upon variation at the gene encoding the targeted enzyme in natural plant populations. ..
  43. Prigent V, Thierry J, Poch O, Plewniak F. DbW: automatic update of a functional family-specific multiple alignment. Bioinformatics. 2005;21:1437-42 pubmed
    ..The DbW software is available for download at and online at CONTACT: ..
  44. Bui Q, Delaurière L, Casse N, Nicolas V, Laulier M, Chénais B. Molecular characterization and phylogenetic position of a new mariner-like element in the coastal crab, Pachygrapsus marmoratus. Gene. 2007;396:248-56 pubmed
    ..Furthermore, molecular phylogeny analyses have shown that Pacmmar elements constitute a new lineage of the irritans subfamily within the mariner family. ..
  45. Kamgoue A, Ohayon J, Usson Y, Riou L, Tracqui P. Quantification of cardiomyocyte contraction based on image correlation analysis. Cytometry A. 2009;75:298-308 pubmed publisher
    ..Thus, our algorithmic approach provides a fast and efficient tool for analyzing the correlation between global cell dynamical behavior and mechanosensitive intracellular processes. ..
  46. Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009;25:1974-5 pubmed publisher
    ..VARNA is a free software, released under the terms of the GPLv3.0 license and available at Supplementary data are available at Bioinformatics online. ..
  47. Teste M, Duquenne M, Francois J, Parrou J. Validation of reference genes for quantitative expression analysis by real-time RT-PCR in Saccharomyces cerevisiae. BMC Mol Biol. 2009;10:99 pubmed publisher
    ..In contrast, we invalidated and discourage the use of ACT1 as well as other commonly used reference genes (PDA1, TDH3, RDN18, etc) as internal controls for quantitative gene expression analysis in yeast. ..
  48. Desquilbet L, Mariotti F. Dose-response analyses using restricted cubic spline functions in public health research. Stat Med. 2010;29:1037-57 pubmed publisher
  49. Grangeon M, Guillot A, Collet C. Postural control during visual and kinesthetic motor imagery. Appl Psychophysiol Biofeedback. 2011;36:47-56 pubmed publisher
    ..Finally, our data showed that kinesthetic and visual imagery differentially impacted the postural regulation. ..
  50. Gramfort A, Papadopoulo T, Olivi E, Clerc M. Forward field computation with OpenMEEG. Comput Intell Neurosci. 2011;2011:923703 pubmed publisher
    ..OpenMEEG is open source and multiplatform. It can be used from Python and Matlab in conjunction with toolboxes that solve the inverse problem; its integration within FieldTrip is operational since release 2.0. ..
  51. Royer P, Marchesi V, Rousseau V, Buchheit I, Wolf D, Peiffert D, et al. [Evaluation of transit in vivo dosimetry using portal imaging and comparison with measurements using diodes]. Cancer Radiother. 2014;18:183-90 pubmed publisher
    ..A comparative evaluation was conducted between a commercial solution, EPIgray(®) and an in vivo dosimetry control reference using semiconductors diodes...
  52. Poirier S, Desmond Le Quéméner E, Madigou C, Bouchez T, Chapleur O. Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes. Bioresour Technol. 2016;207:92-101 pubmed publisher
    ..0 and 25.0g/L respectively, while Syntrophomonas and Ruminococcus groups declined. In 25.0g/L assays, Caldicoprobacter were dominant. This study highlights the emergence of AD key phylotypes at extreme ammonia concentrations. ..
  53. Ruas M, Guignon V, Sempere G, Sardos J, Hueber Y, Duvergey H, et al. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. Database (Oxford). 2017;2017: pubmed publisher
  54. Massoubre C, Bonnefond H, Grosselin A, Nelva A, Pellet J, Lang F. [Preliminary comparative study of the personality disorder evaluation DIP instrument with the semi-structured SCID-II interview]. Encephale. 2009;35:544-53 pubmed publisher
    ..The main interest of our work was to make the first French translation of the DIP known and to compare it to another instrument, which has often been evaluated previously. ..
  55. Coutant S, Cabot C, Lefebvre A, Leonard M, Prieur Gaston E, Campion D, et al. EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics. BMC Bioinformatics. 2012;13 Suppl 14:S9 pubmed publisher
    ..Thereby, it provides a response to new needs at the expanding era of medical genomics investigated by WES for both fundamental research and clinical diagnostics. ..
  56. Negre V, Hotelier T, Volkoff A, Gimenez S, Cousserans F, Mita K, et al. SPODOBASE: an EST database for the lepidopteran crop pest Spodoptera. BMC Bioinformatics. 2006;7:322 pubmed
    ..SPODOBASE is available from URL: ..
  57. Splendiani A. RDFScape: Semantic Web meets systems biology. BMC Bioinformatics. 2008;9 Suppl 4:S6 pubmed publisher
    ..This allows the use of ontologies not only as annotations, but as a knowledge-base from which new information relevant for specific analysis can be derived. ..
  58. Corblin F, Fanchon E, Trilling L. Applications of a formal approach to decipher discrete genetic networks. BMC Bioinformatics. 2010;11:385 pubmed publisher
    ..Last, the constraint approach promotes an integration of model and experimental data in a single framework. ..
  59. Coroller L, Kan King Yu D, Leguerinel I, Mafart P, Membre J. Modelling of growth, growth/no-growth interface and nonthermal inactivation areas of Listeria in foods. Int J Food Microbiol. 2012;152:139-52 pubmed publisher
    ..It might also be used to optimise a food formulation or storage condition in the case of a targeted increase or decrease of the bacterial population. ..
  60. Aubertot J, Robin M. Injury Profile SIMulator, a qualitative aggregative modelling framework to predict crop injury profile as a function of cropping practices, and the abiotic and biotic environment. I. Conceptual bases. PLoS ONE. 2013;8:e73202 pubmed publisher
    ..In addition, IPSIM could also be used to help make diagnoses on commercial fields. It is important to point out that the presented concepts are not crop- or pest-specific and that IPSIM can be used on any crop. ..
  61. Bédubourg G, Le Strat Y. Evaluation and comparison of statistical methods for early temporal detection of outbreaks: A simulation-based study. PLoS ONE. 2017;12:e0181227 pubmed publisher
    ..5% to 68.4%. Multivariate Poisson regression models showed that performance measures were strongly influenced by the characteristics of time series. Past or current outbreak size and duration strongly influenced detection performances. ..
  62. Friedrich A, Garnier N, Gagniere N, Nguyen H, Albou L, Biancalana V, et al. SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases. Hum Mutat. 2010;31:127-35 pubmed publisher
    ..The entire content of SM2PH-db is regularly and automatically updated thanks to a computational grid data federation facilities provided in the context of the Decrypthon program. ..
  63. Lelong C, Chevallet M, Diemer H, Luche S, Van Dorsselaer A, Rabilloud T. Improved proteomic analysis of nuclear proteins, as exemplified by the comparison of two myeloid cell lines nuclear proteomes. J Proteomics. 2012;77:577-602 pubmed publisher
  64. Cohen J, Goo J, Yoo R, Park S, van Ginneken B, Ferretti G, et al. The effect of late-phase contrast enhancement on semi-automatic software measurements of CT attenuation and volume of part-solid nodules in lung adenocarcinomas. Eur J Radiol. 2016;85:1174-80 pubmed publisher
    ..05). As most volumetric and attenuation measurements changed significantly after contrast enhancement, care should be taken in comparing unenhanced and enhanced CT in the evaluation of PSNs. ..
  65. Cebo C, Durier V, Lagant P, Maes E, Florea D, Lefebvre T, et al. Function and molecular modeling of the interaction between human interleukin 6 and its HNK-1 oligosaccharide ligands. J Biol Chem. 2002;277:12246-52 pubmed
    ..Stahl, M., and Seehra, J. S. (1997) EMBO J. 16, 989-997), already known to be involved in interactions with gp130. ..
  66. Cros M, de Monte A, Mariette J, Bardou P, Grenier Boley B, Gautheret D, et al. An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA. 2011;17:1947-56 pubmed publisher It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project ( ..
  67. Venail F, Legris E, Vaerenberg B, Puel J, Govaerts P, Ceccato J. Validation of the French-language version of the OTOSPEECH automated scoring software package for speech audiometry. Eur Ann Otorhinolaryngol Head Neck Dis. 2016;133:101-6 pubmed publisher
    ..76, P<0.01, respectively), with DTW scores ranging from 24.17 to 53.24. Automated scoring of customized self-voice recorded lists for speech audiometry displayed results similar to conventional audiometric techniques. ..
  68. Gautier R, Douguet D, Antonny B, Drin G. HELIQUEST: a web server to screen sequences with specific alpha-helical properties. Bioinformatics. 2008;24:2101-2 pubmed publisher
    ..This server is also dedicated to mutating helices manually or automatically by genetic algorithm to design analogues of defined features. ..
  69. Gamm M, Héloir M, Kelloniemi J, Poinssot B, Wendehenne D, Adrian M. Identification of reference genes suitable for qRT-PCR in grapevine and application for the study of the expression of genes involved in pterostilbene synthesis. Mol Genet Genomics. 2011;285:273-85 pubmed publisher
    ..cinerea, respectively. Next, we have highlighted that the expression of ROMT is induced in P. viticola-infected leaves and also in B. cinerea-infected berries, confirming the involvement of pterostilbene in grapevine defenses. ..
  70. Busset J, Cabau C, Meslin C, Pascal G. PhyleasProg: a user-oriented web server for wide evolutionary analyses. Nucleic Acids Res. 2011;39:W479-85 pubmed publisher
    ..This connection between different domains of phylogenetics opens the way to new biological analyses for the discovery of the function and structure of proteins. ..
  71. Basse M, Betzi S, Morelli X, Roche P. 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. Database (Oxford). 2016;2016: pubmed publisher
    ..Database URL: ..
  72. Claudel Renard C, Chevalet C, Faraut T, Kahn D. Enzyme-specific profiles for genome annotation: PRIAM. Nucleic Acids Res. 2003;31:6633-9 pubmed
    ..The results of this automated method were compared with the original genome annotation and visualised on KEGG graphs in order to facilitate the interpretation of metabolic pathways and to highlight potentially missing enzymes. ..
  73. Chalmel F, Primig M. The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. BMC Bioinformatics. 2008;9:86 pubmed publisher
    ..We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program. ..
  74. Rizk G, Lavenier D. GASSST: global alignment short sequence search tool. Bioinformatics. 2010;26:2534-40 pubmed publisher
    ..GASSST is distributed under the CeCILL software license at; Supplementary data are available at Bioinformatics online. ..
  75. Gramfort A, Papadopoulo T, Olivi E, Clerc M. OpenMEEG: opensource software for quasistatic bioelectromagnetics. Biomed Eng Online. 2010;9:45 pubmed publisher
    ..Moreover, our software development strategies have made it handy to use and to integrate with other packages. The bioelectromagnetic research community should therefore be able to benefit from OpenMEEG with a limited development effort. ..
  76. Gauthier F, Martin O, Falque M. CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes. BMC Bioinformatics. 2011;12:27 pubmed publisher
    ..CODA implements that model's complex physics and mathematics, and uses a summary statistic to overcomes the lack of a computable likelihood which has hampered its use till now. ..
  77. Naville M, Ghuillot Gaudeffroy A, Marchais A, Gautheret D. ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol. 2011;8:11-3 pubmed
    ..The ARNold Web server is available at : ..
  78. Barakat M, Ortet P, Whitworth D. P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. BMC Genomics. 2013;14:269 pubmed publisher
    ..P2RP is the first publicly available tool for predicting and analysing RP proteins in users' sequences. The server is freely available and can be accessed along with documentation at ..
  79. Benabderrahmane S, Smail Tabbone M, Poch O, Napoli A, Devignes M. IntelliGO: a new vector-based semantic similarity measure including annotation origin. BMC Bioinformatics. 2010;11:588 pubmed publisher
    ..An on-line version of the IntelliGO similarity measure is available at: ..
  80. Fievet J, Dillmann C, Lagniel G, Davanture M, Negroni L, Labarre J, et al. Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis. Proteomics. 2004;4:1939-49 pubmed
    ..Absolute quantification of most glycolytic enzymes was carried out in two yeast strains. ..
  81. Rousseau C, Gonnet M, Le Romancer M, Nicolas J. CRISPI: a CRISPR interactive database. Bioinformatics. 2009;25:3317-8 pubmed publisher
    ..CRISPI free access at; ..
  82. Simon A, Biot E. ANAIS: analysis of NimbleGen arrays interface. Bioinformatics. 2010;26:2468-9 pubmed publisher
    .. ..
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