| DESCRIPTION | - ALTSCHUL SF et al., J Mol Biol., (19900000), vol. 215, no. 3, pages 403 - 410 | - |
| DESCRIPTION | - BECKMANN et al., "Detecting epigenetic motifs in low coverage and metagenomics settings.", BMC Bioinformatics, (20140000), vol. 15 | - |
| DESCRIPTION | - BLOW, M.J. et al., "The Epigenomic Landscape of Prokaryotes.", PLOS Genet., (20160000), vol. 12 | - |
| DESCRIPTION | - BREIMAN, L., Random Forests. Mach. Learn., (20010000), vol. 45, pages 5 - 32 | - |
| DESCRIPTION | - BRIOUDE et al., Nat Rev Endocrinol., (20180000), vol. 14, pages 229 - 249 | - |
| DESCRIPTION | - CADIEUX et al., Cancer Res., (20060000), vol. 66, pages 8469 - 76 | - |
| DESCRIPTION | - CHIU et al., Am J Pathol., (20070000), vol. 170, pages 941 - 950 | - |
| DESCRIPTION | - CLARK, T.A. et al., "Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.", Nucleic Acids Res., (20120000), vol. 40, page 29 | - |
| DESCRIPTION | - CLARK, T.A. et al., "Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tetl oxidation.", BMC Biol., (20130000), vol. 11, no. 4 | - |
| DESCRIPTION | - COSTELLO et al., Nat Genet., (20000000), vol. 24, pages 132 - 8 | - |
| DESCRIPTION | - DE MAIO et al., Micob Genom., (20190000), vol. 5, no. 9 | - |
| DESCRIPTION | - DIDIER W et al., Nat Rev Micorbiol., (20090000), vol. 4, pages 183 - 192 | - |
| DESCRIPTION | - EDGE et al., Genome Res., (20170000), vol. 27, pages 801 - 812 | - |
| DESCRIPTION | - "Feature selection, L 1 vs. L 2 regularization, and rotational invariance.", NG, A. Y., Twenty-first International Conference on Machine Learning - ICML '04, ACM Press, (20040000), page 78 | - |
| DESCRIPTION | - FEINBERG, A.P.IRIZARRY, R.A., "Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease.", Proc. Natl. Acad. Sci., (20100000), vol. 107, pages 1757 - 1764 | - |
| DESCRIPTION | - FENG, Z. et al., "Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.", PLoS Comput Biol., (20130000), vol. 9 | - |
| DESCRIPTION | - FERNANDEZ et al., Genome Res., (20090000), vol. 19, pages 438 - 51 | - |
| DESCRIPTION | - FLUSBERG et al., Nat Methods, (20100000), vol. 7, pages 461 - 465 | - |
| DESCRIPTION | - GAI, W. et al., "Liver- and colon-specific DNA methylation markers in plasma for investigation of colorectal cancers with or without liver metastases.", Clin. Chem., (20180000), vol. 64, pages 1239 - 1249 | - |
| DESCRIPTION | - GRAFF et al., Cancer Res., (19950000), vol. 55, pages 5195 - 9 | - |
| DESCRIPTION | - GRUNAU, C., "Bisulfite genomic sequencing: systematic investigation of critical experimental parameters.", Nucleic Acids Res., (20010000), vol. 29 | - |
| DESCRIPTION | - HUBER et al., Nucleic Acids Res., (20160000), vol. 44, pages 9881 - 9890 | - |
| DESCRIPTION | - JAIN et al., Sci Rep., (20150000), vol. 5, page 10478 | - |
| DESCRIPTION | - J D ENGEL et al., J Biol Chem., (19780000), vol. 253, pages 927 - 34 | - |
| DESCRIPTION | - JIANG, P. et al., "Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis.", PLoS One, (20140000), vol. 9 | - |
| DESCRIPTION | - KENT WJ, Genome Res., (20020000), vol. 12, no. 4, pages 656 - 664 | - |
| DESCRIPTION | - KIELBASA SM et al., Genome Res., (20110000), vol. 21, no. 3, pages 487 - 493 | - |
| DESCRIPTION | - KINDE et al., PLOS One, (20120000), vol. 7, no. 7, page 41162 | - |
| DESCRIPTION | - LECUN, Y. et al., "Backpropagation Applied to Handwritten Zip Code Recognition.", Neural Comput., (19890000), vol. 1, pages 541 - 551, XP000789854 | - |
| DESCRIPTION | - LEE, E.-J. et al., "Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.", Nucleic Acids Res., (20110000), vol. 39, page 127 | - |
| DESCRIPTION | - LEHMANN-WERMAN, R. et al., "Identification of tissue-specific cell death using methylation patterns of circulating DNA.", Proc. Natl. Acad. Sci., (20160000), vol. 113, pages 1826 - 1834 | - |
| DESCRIPTION | - LI H, Bioinformatics., (20180000), vol. 34, no. 18, pages 3094 - 3100 | - |
| DESCRIPTION | - LI H et al., Bioinformatics., (20090000), vol. 25, pages 1754 - 60 | - |
| DESCRIPTION | - LI H et al., Bioinformatics., (20100000), vol. 26, no. 5, pages 589 - 595 | - |
| DESCRIPTION | - LISTER et al., Nature., (20090000), vol. 462, pages 315 - 322 | - |
| DESCRIPTION | - LUN et al., Clin Chem., (20130000), vol. 59, pages 1583 - 94 | - |
| DESCRIPTION | - MARK J CHAISSON et al., BMC Bioinformatics., (20120000), vol. 13, page 238 | - |
| DESCRIPTION | - NATTESTAD, M. et al., "Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line.", Genome Res., (20180000), vol. 28, pages 1126 - 1135 | - |
| DESCRIPTION | - OKOU, D. T. et al., "Microarray-based genomic selection for high-throughput resequencing.", Nat., (20070000), vol. 4, pages 907 - 909 | - |
| DESCRIPTION | - OLOVA, N. et al., "Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data", Genome Biol., (20180000), vol. 19, no. 33 | - |
| DESCRIPTION | - PICKAR-OLIVER et al., Nat Rev Mol Cell, (20190000), vol. 20, pages 490 - 507 | - |
| DESCRIPTION | - RODRIGUEZ et al., Nucleic Acids Res., (20080000), vol. 36, pages 770 - 784 | - |
| DESCRIPTION | - ROSS et al., Epigenomics., (20100000), vol. 2, pages 245 - 69 | - |
| DESCRIPTION | - SCHADT, E.E. et al., "Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.", Genome Res., (20130000), vol. 23, no. 1, pages 129 - 41 | - |
| DESCRIPTION | - SCHREIBER et al., Proc Natl Acad Sci, (20130000), vol. 110, pages 18910 - 18915 | - |
| DESCRIPTION | - SEDLAZECK FJ et al., Nat Methods., (20180000), vol. 15, no. 6, pages 461 - 468 | - |
| DESCRIPTION | - SMITH, Z.D.MEISSNER, A., "DNA methylation: roles in mammalian development.", Nat. Rev. Genet., (20130000), vol. 14, pages 204 - 20 | - |
| DESCRIPTION | - STEVENS et al., PLOS One, (20190000), vol. 14, no. 4 | - |
| DESCRIPTION | - STRECKER et al., Science, (20190000), vol. 365, pages 48 - 53 | - |
| DESCRIPTION | - SUZUKI, Y., "Agin: measuring the landscape of CpG methylation of individual repetitive elements.", Bioinformatics, (20160000), vol. 32, pages 2911 - 2919 | - |
| DESCRIPTION | - WATSON et al., Lab Invest, (20200000), vol. 100, pages 135 - 146 | - |
| DESCRIPTION | - WENGER et al., Nat Biotechnol., (20190000), vol. 37, pages 1155 - 1162 | - |
| DESCRIPTION | - XIAO CL et al., Mol Cell, (20180000), vol. 71, pages 306 - 318 | - |
| DESCRIPTION | - XIAO CL et al., Mol Cell., (20180000), vol. 71, pages 306 - 318 | - |
| DESCRIPTION | - XIE et al., Cell., (20180000), vol. 1175, pages 1228 - 1243 | - |
| DESCRIPTION | - LISTER, R, "Human DNA methylomes at base resolution show widespread epigenomic differences.", Nature, (20090000), vol. 462, doi:10.1038/nature08514, pages 315 - 322, XP055076298 | |
| DESCRIPTION | - ALBERT, T.J. et al., "Direct selection of human genomic loci by microarray hybridization.", Nat. Methods, (20070000), vol. 4, doi:10.1038/NMETH1111, pages 903 - 905, XP002499757 | |
| DESCRIPTION | - FLUSBERG, B.A. et al., "Direct detection of DNA methylation during single-molecule, real-time sequencing.", Nat. Methods, (20100000), vol. 7, doi:10.1038/nmeth.1459, pages 461 - 465, XP009526141 | |
| DESCRIPTION | - ROBERTSON, K.D., "DNA methylation and human disease.", Nat. Rev. Genet., (20050000), vol. 6, doi:10.1038/NRG1655, pages 597 - 610, XP002570215 | |
| DESCRIPTION | - WATSON, C.M. et al., "Cas9-based enrichment and single-molecule sequencing for precise characterization of genomic duplications.", Lab. Investig, (20190000), vol. 100, doi:10.1038/s41374-019-0283-0, pages 135 - 146, XP036966479 | |
| DESCRIPTION | - LIU, Q. et al., "Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.", Nature Commun., (20190000), vol. 10, doi:10.1038/s41467-019-10168-2, page 2449, XP093015041 | |
| DESCRIPTION | - BEAULAURIER, J. et al., "Deciphering bacterial epigenomes using modern sequencing technologies.", Nature Reviews Genetics, (20190000), vol. 20, doi:10.1038/s41576-018-0081-3, pages 157 - 172, XP036703128 | |
| DESCRIPTION | - LIU, Y. et al., "Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution.", Nat. Biotechnol., (20190000), vol. 37, doi:10.1038/s41587-019-0041-2, pages 424 - 429, XP055737047 | |
| DESCRIPTION | - GOUIL, Q. et al., "Latest techniques to study DNA methylation.", Essays Biochem., (20190000), vol. 63, no. 6, doi:10.1042/EBC20190027, pages 639 - 648, XP055850135 | |
| DESCRIPTION | - CHAN, K.C.A. et al., "Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing.", Proc. Natl. Acad. Sci. U. S. A., (20130000), vol. 110, doi:10.1073/pnas.1313995110, pages 18761 - 8, XP055181312 | |
| DESCRIPTION | - SUN, K. et al., "Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments.", Proc. Natl. Acad. Sci., (20150000), vol. 112, doi:10.1073/pnas.1508736112, XP055373988 | |
| DESCRIPTION | - FROMMER, M. et al., "A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.", Proc. Natl. Acad. Sci., (19920000), vol. 89, doi:10.1073/pnas.89.5.1827, pages 1827 - 1831, XP002941272 | |
| DESCRIPTION | - HERMAN, J.G. et al., "Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands.", Proc. Natl. Acad. Sci. U. S. A., (19960000), vol. 93, doi:10.1073/pnas.93.18.9821, pages 9821 - 9826, XP002542477 | |
| DESCRIPTION | - NI, P. et al., "DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.", Bioinformatics, (20190000), vol. 35, doi:10.1093/bioinformatics/btz276, pages 4586 - 4595, XP055850617 | |
| DESCRIPTION | - EID, J. et al., "Real-Time DNA Sequencing from Single Polymerase Molecules.", Science, (20090000), vol. 323, doi:10.1126/science.1162986, pages 133 - 138, XP055333285 | |
| DESCRIPTION | - ZHANG, W. et al., "Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements", Genome Biol., (20150000), vol. 16, no. 14, doi:10.1186/s13059-015-0581-9, XP002743924 | |
| DESCRIPTION | - LUN, F.M.F. et al., "Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA.", Clin. Chem., (20130000), vol. 59, doi:10.1373/clinchem.2013.212274, pages 1583 - 1594, XP055246177 | |
| OPPOSITION | - "BAM format specification for PacBio — PacBioFileFormats 5.0.0 documentation", Waybackmachine, (20170916), pages 1 - 9, Waybackmachine, URL: https://web.archive.org/web/20170916112547/http://pacbiofileformats.readthedocs.io/en/5.0/BAM.html, XP093266169 | - |
| OPPOSITION | - D007 - PACBIO TEMPLATE GUIDE | - |
| OPPOSITION | - Benjamin A Flusberg, "Direct detection of DNA methylation during single-molecule, real-time sequencing", Nature Methods, New York, (20100601), vol. 7, no. 6, doi:10.1038/nmeth.1459, ISSN 1548-7091, pages 461 - 465, XP093165435 | |
| OPPOSITION | - Ni Peng, Huang Neng, Zhang Zhi, Wang De-Peng, Liang Fan, Miao Yu, Xiao Chuan-Le, Luo Feng, Wang Jianxin, "DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning", Bioinformatics, GB, (20190417), doi:10.1093/bioinformatics/btz276, pages 4586 - 4595, XP055850617 | |
| SEARCH | - BENJAMIN A FLUSBERG ET AL, "Direct detection of DNA methylation during single-molecule, real-time sequencing", NATURE METHODS, NATURE PUB. GROUP, NEW YORK, vol. 7, no. 6, doi:10.1038/NMETH.1459, ISSN 1548-7091, (20100509), pages 461 - 465, (20100509), XP009526141 [A] 1-19 * the whole document * * in particular * * page 462 - page 464; figures 1, 3 * | |
