Compounds > hydrogen sulfite
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hydrogen sulfite and cytosine

hydrogen sulfite has been researched along with cytosine in 122 studies

Research

Studies (122)

TimeframeStudies, this research(%)All Research%
pre-19901 (0.82)18.7374
1990's9 (7.38)18.2507
2000's22 (18.03)29.6817
2010's59 (48.36)24.3611
2020's31 (25.41)2.80

Authors

AuthorsStudies
Carew, JA; Feldberg, RS1
Jost, JP; Raizis, AM; Schmitt, F1
Heinlein, M; Kunze, R; Wang, L1
Georgiev, O; Matsuo, K; Rother, KI; Schaffner, W; Silke, J1
Clark, SJ; Paul, CL1
DePamphilis, ML; Rein, T; Zorbas, H1
Buiting, K; Dittrich, B; Doerfler, W; Horsthemke, B; Schmitz, B; Zeschnigk, M1
Carbonaro, DA; Kohn, DB; Robbins, PB; Wang, L1
Burri, N; Chaubert, P1
Radlińska, M; Skowronek, K1
Hoffman, AR; Hu, JF; Li, T; Nguyen, BT; Nguyen, D; Vu, TH; Yao, XM1
Nagane, Y; Tohgi, H; Utsugisawa, K1
Grimes, SR; Singal, R1
Jackson, M; Lough, J; Morris, R; Moyer, R1
Baumer, A; Hornby, DP; Matin, MM1
Ohashi, H1
Clark, AD; Hansen, RS; Hassan, KM; Laird, CD; Manley, NC; Morgan, T; Pleasant, ND; Sneeden, JL; Stöger, R; Vary, JC1
El-Maarri, O1
Inoue, S; Oishi, M1
Ratnam, S; Shen, HM; Storb, U1
Cauchi, S; Han, W; Herman, JG; Spivack, SD1
Hayatsu, H; Negishi, K; Shiraishi, M1
Hayatsu, H; Negishi, K; Tsuji, K1
Okamoto, A; Tanaka, K1
Bacher, B; Budiman, A; Citek, RW; Jeddeloh, JA; Korshunova, Y; Lakey, N; Leon, J; Maloney, RK; McCombie, WR; McPherson, JD; Ordway, JM1
Chollet, D; Delucinge Vivier, C; Descombes, P; Paszkowski, J; Reinders, J; Theiler, G1
Nakatani, K; Oka, Y; Peng, T; Takei, F1
Burden, AF; Genereux, DP; Johnson, WC; Laird, CD; Stöger, R1
Dugast-Darzacq, C; Grange, T1
Hanna, K; Lyko, F; Pollex, T; Schaefer, M1
Engelhart, AE; Hatmal, MM; Haworth, IS; Houston, SI; Hud, NV; Lieber, MR; Tsai, AG1
Nakatani, K; Oka, Y; Takei, F1
Bailey, VJ; Baylin, SB; Brock, MV; Carraway, HE; Easwaran, H; Herman, JG; Ho, YP; Keeley, BP; Pelosky, KL; Wang, TH; Zhang, Y1
Huang, Y; Liu, DR; Pastor, WA; Rao, A; Shen, Y; Tahiliani, M1
Foerster, AM; Hetzl, J; Mittelsten Scheid, O; Müllner, C1
Boyko, A; Kovalchuk, I1
Blazkova, J; Burny, A; Calomme, C; Cardona, C; Colin, L; Dekoninck, A; Guiguen, A; Hirsch, I; Kettmann, R; Merimi, M; Nguyên, TL; Nuttinck, M; Pierard, V; Portetelle, D; Rohr, O; Twizere, JC; Van Driessche, B; Van Lint, C; Vanhulle, C; Vierendeel, V; Wijmeersch, G1
Dunican, D; Meehan, R; Nestor, C; Ruzov, A1
Aichinger, E; Köhler, C1
Ballinger, T; Bernstein, BE; Bock, C; Chung, WY; Coarfa, C; Costello, JF; Delaney, A; Downey, SL; Echipare, L; Ecker, JR; Epstein, CB; Farnham, PJ; Forsberg, KJ; Fouse, SD; Gnirke, A; Gu, H; Gu, J; Harris, RA; Haussler, D; Hawkins, RD; Hirst, M; Hong, C; Johnson, BE; Li, W; Lister, R; Marra, MA; Meissner, A; Milosavljevic, A; Nagarajan, RP; O'Geen, H; Olshen, A; Pelizzola, M; Ren, B; Wang, T; Waterland, RA; Xi, Y; Zhang, MQ; Zhao, Y; Zhou, X1
Hanna, K; Pollex, T; Schaefer, M1
Bonthron, DT; Carr, IM; Darst, RP; Hoffman, CJ; Kladde, MP; Markham, AF; Pardo, CE1
Andrews, SR; Krueger, F1
Haque, N; Nishiguchi, M1
Cowley, MJ; Cropley, JE; Li, CC; Martin, DI; Preiss, T; Suter, CM1
Fischer, RL; Hsieh, TF; Ibarra, C; Pedersen, B1
Paszkowski, J; Reinders, J1
Acevedo, LG; Jelinek, MA; Sanz, A1
Adey, A; Shendure, J1
Balasubramanian, S; Booth, MJ; Branco, MR; Ficz, G; Krueger, F; Oxley, D; Reik, W1
Harris, EY; Le Roch, KG; Lonardi, S; Ponts, N1
Dinh, HQ; Dubin, M; Lettner, N; Mittelsten Scheid, O; Sedlazeck, FJ; von Haeseler, A1
Miller, AK; Schüler, P1
Ecker, JR; Schmitz, RJ; Schultz, MD1
He, C; Hon, GC; Jin, P; Ren, B; Song, CX; Szulwach, KE; Yu, M1
Hu, D; Jin, L; Lü, J; Wang, W2
He, C; Jin, P; Lu, X; Song, CX; Szulwach, K; Wang, Z; Weidenbacher, P1
Bassil, CF; Huang, Z; Murphy, SK1
Bollig-Fischer, A; Cao, X; Chen, CC; Cingolani, P; Coon, M; Garfinkel, MD; Huang, Y; Hudson, ME; Khetani, RS; Land, S; Robinson, GE; Ruden, DM; Sammak, A; Zhong, S1
Mituyama, T; Saito, Y; Tsuji, J1
Bachman, M; Balasubramanian, S; Beraldi, D; Booth, MJ; Marsico, G1
Armano, G; Manca, E; Manconi, A; Milanesi, L; Orro, A1
Holbrook, JD; Lin, X; Ong, ML1
Beygo, J; Borgmann, J; Buiting, K; Gromoll, J; Horsthemke, B; Kliesch, S; Laurentino, S; Nordhoff, V; Wistuba, J1
Ecker, JR; Lister, R; Nery, JR; Schmitz, RJ; Urich, MA1
Bachman, M; Balasubramanian, S; Beck, S; Beraldi, D; Field, SF; Stewart, SK1
Yuan, BF1
Burgess, D; Eichten, SR; Greally, JM; Green, D; Hermanson, PJ; Jeddeloh, J; Li, Q; Patterson, N; Richmond, T; Rosenbaum, H; Springer, NM; Suzuki, M; Wendt, J1
Chin, C; Deciu, C; Ehrich, M; Gebhard, C; Jensen, TJ; Kim, SK; Lu, T; van den Boom, D; Zhu, Z1
Burden, CJ; Forêt, S; Lin, P; Wilson, SR1
Chung, DH; Groom, J; He, C; Ji, L; Neumann, DA; Schmitz, RJ; Westpheling, J; Yu, M1
Han, D; He, C; Jiang, X; Liu, M; Lu, X; Sun, Z; Xia, B; Xie, W; Yi, C; Yin, Q; Zeng, H; Zhou, A1
Fukuzawa, S; Suetake, I; Tachibana, K; Tajima, S1
Kenta, N; Lee, JH; Park, SJ1
Mituyama, T; Saito, Y1
Bianchessi, V; Capogrossi, MC; Farina, F; Gualdi, V; Lauri, A; Nigro, P; Pompilio, G; Rizzi, V; Vinci, MC1
Wu, H; Wu, X; Zhang, Y1
Incarnato, D; Krepelova, A; Neri, F; Oliviero, S; Parlato, C1
Fukuzawa, S; Suetake, I; Tachibana, K; Tajima, S; Takahashi, S1
Moran, S1
Asahara, H; Miyata, K; Miyata, T; Mokuda, S; Naito, M1
Chen, YR; Yu, S; Zhong, S1
Lee, HJ; Smallwood, SA1
Daviaud, C; Deleuze, JF; Mauger, F; Renault, V; Tost, J1
Cheng, J; Huang, D; Long, F; Yi, S1
Owa, C; Poulin, M; Shioda, T; Yan, L1
Giehr, P; Kyriakopoulos, C; Lepikhov, K; Wallner, S; Walter, J; Wolf, V1
Fujita, K; Hashimoto, M1
Corces, VG; Xu, C1
Kriegel, AJ; Liang, M; Liu, Y1
Garg, R; Gupta, K1
He, Q; He, Z; Liu, X; Liu, Y; Sun, Z; Wu, F; Zhao, M; Zhou, J1
Coppens, F; Schmidt, M; Van Bel, M; Van Lijsebettens, M; Woloszynska, M1
Boquete, MT; Mounger, J; Richards, CL; Vergeer, P; Wagemaker, NCAM1
Andersen, CL; Bramsen, JB; Jensen, SØ; Nielsen, HJ; Øgaard, N1
de Lourdes Muñoz, M; García-Hernández, N; Pérez-Muñoz, AA; Santander-Lucio, H1
Auch, B; Chen, J; Chen, Y; Colwell, M; De Flora, S; Faulk, C; Han, Q; Kassie, F; Kono, TJY; Kotandeniya, D; La Maestra, S; Ren, Y; Sarver, AL; Seiler, CL; Song, JUM; Tretyakova, NY; Upadhyaya, P1
Stöger, R1
Huang, Z; Kohli, RM; Meng, Y; Pfeifer, GP; Szabó, PE1
Branco, MR; De Borre, M1
Berrios, KN; Kohli, RM; Luo, M; Schutsky, EK; Wang, T; Wu, H1
Sang, F1
Gibas, P; Kriukienė, E; Ličytė, J; Rukšėnaitė, A; Skardžiūtė, K; Stankevičius, V1
Chédin, F; Hartono, SR; Heyer, WD; Shah, SS1
Asp, T; Eriksen, B; Eriksen, LB; Jahoor, A; Jensen, CS; Jensen, J; Krusell, L; Malinowska, M; Nagy, I; Ruud, AK; Svane, SF; Thorup-Kristensen, K; Wagemaker, CAM1
Minczuk, M; Van Haute, L1
Baubec, T; Butz, S; Caflisch, A; Ilie, IM; Karemaker, ID; Mallona, I; Manzo, M1
Catoni, M; Zabet, NR1
Balasubramanian, S; Booth, MJ1
Eden, HE; Huang, Z; Robertson, KD; Rothbart, SB; Tiedemann, RL1
Bai, L; Huang, N; Liu, W; Luo, F; Ni, P; Nie, F; Wang, J; Wu, B; Xiao, CL; Zhang, J; Zhang, Z1
Lee, H1
Feng, H; Lou, Z; Qian, Y; Teng, J; Xue, L; Zhang, Y; Zheng, B; Zhu, F1
Edsinger, E; Macchi, F; Sadler, KC1
Kim, H; Kim, J; Kwon, K; Park, N; Sim, M1
Hara, S; Higashimoto, K; Soejima, H1
Chen, KK; Feng, YQ; Ji, TT; Tang, F; Xie, C; Xie, NB; Xiong, J; Yu, SY; Yuan, BF1
Aranyi, T; Guan, Y; Hu, H; Liang, X; Liu, H; Susztak, K; Zhou, J1
Chen, KK; Feng, YQ; Guo, X; Ji, TT; Tang, F; Wang, M; Xie, C; Xie, NB; Xiong, J; Yu, SY; Yuan, BF1
Alonso, C; Medrano, M; Peña-Ponton, C; Troyee, AN; Verhoeven, KJF1
An, R; Bai, Y; Cao, Y; Fan, Y; Gu, Q; Peng, J; Ren, L; Song, L; Song, W; Xie, XS; Yuan, T; Zheng, Y1

Reviews

6 review(s) available for hydrogen sulfite and cytosine

ArticleYear
Methods: DNA methylation.
    Advances in experimental medicine and biology, 2003, Volume: 544

    Topics: Base Sequence; CpG Islands; Cytosine; DNA; DNA Methylation; Methods; Polymerase Chain Reaction; Sulfites

2003
Bisulfite methylation profiling of large genomes.
    Epigenomics, 2010, Volume: 2, Issue:2

    Topics: 5-Methylcytosine; Animals; Arabidopsis; Cytosine; DNA Methylation; Epigenesis, Genetic; Genome; High-Throughput Nucleotide Sequencing; Humans; Mice; Nanopores; Sulfites

2010
Novel DNA binding domain-based assays for detection of methylated and nonmethylated DNA.
    Epigenomics, 2011, Volume: 3, Issue:1

    Topics: 5-Methylcytosine; Biomarkers; CpG Islands; Cytosine; DNA (Cytosine-5-)-Methyltransferases; DNA Methylation; DNA Primers; Humans; Immunoprecipitation; Polymerase Chain Reaction; Protein Interaction Domains and Motifs; Sensitivity and Specificity; Sulfites

2011
Measuring epigenetics as the mediator of gene/environment interactions in DOHaD.
    Journal of developmental origins of health and disease, 2015, Volume: 6, Issue:1

    Topics: Cytosine; Cytosine Nucleotides; Data Interpretation, Statistical; DNA Methylation; Epigenesis, Genetic; Gene-Environment Interaction; Genome-Wide Association Study; Humans; Phenotype; Polymorphism, Single Nucleotide; Sulfites

2015
5-methylcytosine and its derivatives.
    Advances in clinical chemistry, 2014, Volume: 67

    Topics: 5-Methylcytosine; Chromatography, Thin Layer; Cytosine; DNA Methylation; Electrophoresis, Capillary; Endonucleases; Epigenesis, Genetic; Gas Chromatography-Mass Spectrometry; Humans; Microarray Analysis; Oxidation-Reduction; Polymerase Chain Reaction; Sulfites

2014
Technologies for Deciphering Epigenomic DNA Patterns.
    Advances in experimental medicine and biology, 2017, Volume: 978

    Topics: 5-Methylcytosine; CpG Islands; Cytosine; DNA Methylation; Epigenomics; Formaldehyde; Humans; Microarray Analysis; Paraffin Embedding; Sulfites; Tissue Fixation; Uracil

2017

Other Studies

116 other study(ies) available for hydrogen sulfite and cytosine

ArticleYear
Recognition of a cytosine base lesion by a human damage-specific DNA binding protein.
    Nucleic acids research, 1985, Jan-11, Volume: 13, Issue:1

    Topics: Cytosine; DNA Glycosylases; DNA Repair; DNA-Binding Proteins; Humans; Hydrogen-Ion Concentration; Mutation; N-Glycosyl Hydrolases; Sulfites; Temperature; Uracil; Uracil-DNA Glycosidase

1985
A bisulfite method of 5-methylcytosine mapping that minimizes template degradation.
    Analytical biochemistry, 1995, Mar-20, Volume: 226, Issue:1

    Topics: 5-Methylcytosine; Base Sequence; Cytosine; DNA; DNA Modification Methylases; DNA Primers; Hydrogen-Ion Concentration; Methylation; Molecular Sequence Data; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites; Templates, Genetic

1995
Methylation pattern of Activator transposase binding sites in maize endosperm.
    The Plant cell, 1996, Volume: 8, Issue:4

    Topics: 5-Methylcytosine; Base Sequence; Chromatids; Cytosine; DNA; DNA Primers; DNA Transposable Elements; Methylation; Molecular Sequence Data; Recombination, Genetic; Sulfites; Zea mays

1996
Influence of DNA sequence and methylation status on bisulfite conversion of cytosine residues.
    Analytical biochemistry, 1995, Oct-10, Volume: 231, Issue:1

    Topics: Base Sequence; Cytosine; DNA; Methylation; Molecular Sequence Data; Sequence Analysis; Sulfites

1995
Cytosine methylation: quantitation by automated genomic sequencing and GENESCAN analysis.
    BioTechniques, 1996, Volume: 21, Issue:1

    Topics: Autoanalysis; Base Sequence; Coloring Agents; Cytosine; Deoxyribonuclease HpaII; DNA Methylation; DNA Primers; DNA-Directed DNA Polymerase; Magnetics; Microspheres; Molecular Sequence Data; Plasmids; Polymerase Chain Reaction; Sequence Analysis, DNA; Software; Sulfites; Taq Polymerase

1996
Active mammalian replication origins are associated with a high-density cluster of mCpG dinucleotides.
    Molecular and cellular biology, 1997, Volume: 17, Issue:1

    Topics: 5-Methylcytosine; Animals; CHO Cells; CpG Islands; Cricetinae; Cytosine; Dinucleoside Phosphates; DNA; DNA Methylation; Molecular Sequence Data; Replication Origin; Ribosomal Proteins; Sulfites

1997
Imprinted segments in the human genome: different DNA methylation patterns in the Prader-Willi/Angelman syndrome region as determined by the genomic sequencing method.
    Human molecular genetics, 1997, Volume: 6, Issue:3

    Topics: 5-Methylcytosine; Angelman Syndrome; Autoantigens; Chromosomes, Human, Pair 15; Cloning, Molecular; CpG Islands; Cytosine; Dinucleoside Phosphates; DNA Methylation; Female; Genomic Imprinting; Humans; Male; Plasmids; Polymerase Chain Reaction; Prader-Willi Syndrome; Promoter Regions, Genetic; Restriction Mapping; Ribonucleoproteins, Small Nuclear; Sequence Analysis, DNA; Sequence Deletion; snRNP Core Proteins; Sulfites

1997
High-resolution analysis of cytosine methylation in the 5ĺong terminal repeat of retroviral vectors.
    Human gene therapy, 1998, Nov-01, Volume: 9, Issue:16

    Topics: Animals; Blotting, Northern; Carcinoma, Embryonal; CpG Islands; Cytosine; DNA Methylation; DNA Primers; Gene Expression Regulation, Viral; Genetic Vectors; Mice; Moloney murine leukemia virus; Retroviridae; Sequence Analysis, DNA; Sulfites; Terminal Repeat Sequences; Thy-1 Antigens; Tumor Cells, Cultured

1998
Complex methylation patterns analyzed by single-strand conformation polymorphism.
    BioTechniques, 1999, Volume: 26, Issue:2

    Topics: Cloning, Molecular; Cytosine; DNA Methylation; DNA Primers; DNA, Neoplasm; Genome; HT29 Cells; Humans; Polymorphism, Single-Stranded Conformational; Sulfites

1999
Novel procedure for the detection of 5-methylcytosine.
    Acta microbiologica Polonica, 1998, Volume: 47, Issue:4

    Topics: 5-Methylcytosine; Base Composition; Cytosine; DNA; DNA Methylation; DNA Modification Methylases; Genetic Techniques; Molecular Sequence Data; Plasmids; Sequence Analysis, DNA; Sulfites

1998
Symmetric and asymmetric DNA methylation in the human IGF2-H19 imprinted region.
    Genomics, 2000, Mar-01, Volume: 64, Issue:2

    Topics: Adult; Alleles; CpG Islands; Cytosine; DNA; DNA Methylation; Exons; Fetus; Genomic Imprinting; Humans; Insulin-Like Growth Factor II; Kidney; Molecular Sequence Data; Mosaicism; Muscle Proteins; Myocardium; Polymerase Chain Reaction; Promoter Regions, Genetic; RNA, Long Noncoding; RNA, Untranslated; Sequence Analysis, DNA; Sulfites

2000
PCR amplification in bisulfite methylcytosine mapping in the GC-rich promoter region of amyloid precursor protein gene in autopsy human brain.
    Brain research. Brain research protocols, 2000, Volume: 5, Issue:2

    Topics: Aged; Aged, 80 and over; Aging; Amyloid beta-Protein Precursor; Base Sequence; Cadaver; Cerebral Cortex; Cytosine; DNA Methylation; Genome; Humans; Male; Molecular Sequence Data; Polymerase Chain Reaction; Promoter Regions, Genetic; Sensitivity and Specificity; Sulfites; Temperature; Tissue Distribution

2000
Microsoft Word macro for analysis of cytosine methylation by the bisulfite deamination reaction.
    BioTechniques, 2001, Volume: 30, Issue:1

    Topics: Base Sequence; CpG Islands; Cytosine; Deamination; DNA; DNA Methylation; Molecular Sequence Data; Sequence Analysis, DNA; Software; Sulfites

2001
Bisulfite-induced cytosine deamination rates in E. coli SSB:DNA complexes.
    Mutation research, 2001, Jul-01, Volume: 478, Issue:1-2

    Topics: Cytosine; Deamination; DNA-Binding Proteins; DNA, Single-Stranded; Escherichia coli; Gene Frequency; Macromolecular Substances; Mutation; Sulfites

2001
An analytical method for the detection of methylation differences at specific chromosomal loci using primer extension and ion pair reverse phase HPLC.
    Human mutation, 2002, Volume: 20, Issue:4

    Topics: Ampicillin Resistance; Angelman Syndrome; Base Sequence; Chromatography, High Pressure Liquid; Chromatography, Ion Exchange; CpG Islands; Cytosine; Deamination; DNA; DNA Methylation; DNA Primers; Genetic Markers; Genomic Imprinting; Humans; Molecular Sequence Data; Mutagenesis, Site-Directed; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction; Prader-Willi Syndrome; Sulfites; Uracil

2002
Methylation-specific PCR.
    Methods in molecular biology (Clifton, N.J.), 2002, Volume: 192

    Topics: Base Sequence; Cytosine; DNA; DNA Methylation; DNA Primers; Indicators and Reagents; Polymerase Chain Reaction; Sensitivity and Specificity; Sulfites

2002
Hairpin-bisulfite PCR: assessing epigenetic methylation patterns on complementary strands of individual DNA molecules.
    Proceedings of the National Academy of Sciences of the United States of America, 2004, Jan-06, Volume: 101, Issue:1

    Topics: Alleles; Base Sequence; Chromosomes, Human, X; CpG Islands; Cytosine; DNA; DNA Methylation; DNA Transposable Elements; Dosage Compensation, Genetic; Epigenesis, Genetic; Female; Fragile X Mental Retardation Protein; Humans; Molecular Sequence Data; Nerve Tissue Proteins; Nucleic Acid Conformation; Polymerase Chain Reaction; RNA-Binding Proteins; Sequence Homology, Nucleic Acid; Sulfites

2004
Effects of methylation of non-CpG sequence in the promoter region on the expression of human synaptotagmin XI (syt11).
    Gene, 2005, Mar-28, Volume: 348

    Topics: Animals; Base Sequence; Binding Sites; Binding, Competitive; Calcium-Binding Proteins; Cell Line; Cell Line, Tumor; CHO Cells; CpG Islands; Cricetinae; Cricetulus; Cytosine; DNA; DNA Methylation; DNA-Binding Proteins; Electrophoretic Mobility Shift Assay; Gene Expression Regulation; Humans; Luciferases; Membrane Glycoproteins; Molecular Sequence Data; Nerve Tissue Proteins; Oligonucleotides; Plasmids; Polymerase Chain Reaction; Promoter Regions, Genetic; Sequence Analysis, DNA; Sp1 Transcription Factor; Sp3 Transcription Factor; Sulfites; Synaptotagmins; Transcription Factors; Transcription Initiation Site; Transcription, Genetic; Transfection

2005
Targeting of the activation-induced cytosine deaminase is strongly influenced by the sequence and structure of the targeted DNA.
    Molecular and cellular biology, 2005, Volume: 25, Issue:24

    Topics: Ampicillin Resistance; Base Sequence; Cytidine Deaminase; Cytosine; Cytosine Deaminase; Deamination; DNA; Humans; Kanamycin Resistance; Mutagenesis; Mutation; Nucleic Acid Conformation; Sulfites; Transcription, Genetic

2005
DNA methylation mapping by tag-modified bisulfite genomic sequencing.
    Analytical biochemistry, 2006, Aug-01, Volume: 355, Issue:1

    Topics: Base Sequence; Cells, Cultured; CpG Islands; Cytosine; DNA; DNA Methylation; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2006
Accelerated bisulfite-deamination of cytosine in the genomic sequencing procedure for DNA methylation analysis.
    Nucleic acids symposium series (2004), 2004, Issue:48

    Topics: Animals; Base Composition; Chromatography, High Pressure Liquid; Cytosine; Deamination; DNA Methylation; Genome; Male; Nucleosides; Salmon; Sequence Analysis, DNA; Sulfites; Testis

2004
Does urea promote the bisulfite-mediated deamination of cytosine in DNA? Investigation aiming at speeding-up the procedure for DNA methylation analysis.
    Nucleic acids symposium series (2004), 2006, Issue:50

    Topics: 5-Methylcytosine; Cell Line, Tumor; Cytosine; Deamination; DNA; DNA Methylation; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites; Urea

2006
Degradation of DNA by bisulfite treatment.
    Bioorganic & medicinal chemistry letters, 2007, Apr-01, Volume: 17, Issue:7

    Topics: Absorption; Chemistry, Pharmaceutical; Cytosine; DNA; Drug Design; Epigenesis, Genetic; Gene Expression; Models, Chemical; Molecular Conformation; Polymerase Chain Reaction; Polymers; Reverse Transcriptase Polymerase Chain Reaction; Sulfites; Time Factors

2007
Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA.
    Genome research, 2008, Volume: 18, Issue:1

    Topics: Biomarkers, Tumor; Breast Neoplasms; Cytosine; DNA Methylation; DNA, Neoplasm; Female; Humans; Quantitative Trait Loci; Sequence Analysis, DNA; Sulfites

2008
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion.
    Genome research, 2008, Volume: 18, Issue:3

    Topics: Arabidopsis; Cytosine; DNA Methylation; Genomics; Nucleic Acid Amplification Techniques; Oligonucleotide Array Sequence Analysis; Polymorphism, Genetic; Sulfites

2008
The reaction of cytosine with bisulfite by base flipping from the duplex.
    Nucleic acids symposium series (2004), 2008, Issue:52

    Topics: 5-Methylcytosine; Base Pair Mismatch; Carbamates; Chromatography, High Pressure Liquid; Cytosine; DNA; Hydroxylamine; Naphthyridines; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Sulfites

2008
Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies.
    Nucleic acids research, 2008, Volume: 36, Issue:22

    Topics: 5-Methylcytosine; Cytosine; DNA; DNA Methylation; DNA, Single-Stranded; Nucleic Acid Conformation; Oligonucleotides; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites; Temperature

2008
MethylQuant: a real-time PCR-based method to quantify DNA methylation at single specific cytosines.
    Methods in molecular biology (Clifton, N.J.), 2009, Volume: 507

    Topics: CpG Islands; Cytosine; DNA; DNA Methylation; DNA Primers; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Sulfites

2009
RNA cytosine methylation analysis by bisulfite sequencing.
    Nucleic acids research, 2009, Volume: 37, Issue:2

    Topics: 5-Methylcytosine; Animals; Cytosine; Drosophila melanogaster; Methylation; RNA; RNA, Ribosomal, 16S; RNA, Transfer, Asp; Sequence Analysis, RNA; Sulfites

2009
Conformational variants of duplex DNA correlated with cytosine-rich chromosomal fragile sites.
    The Journal of biological chemistry, 2009, Mar-13, Volume: 284, Issue:11

    Topics: Chromosome Fragility; Chromosomes, Human; Circular Dichroism; Crystallography, X-Ray; Cytosine; DNA; DNA, Superhelical; Exons; Genes, bcl-1; Genes, bcl-2; Genes, myc; Humans; Lymphoma; Nucleic Acid Conformation; Oligodeoxyribonucleotides; Plasmids; Sulfites

2009
Reaction of cytosine with bisulfite and hydroxylamine.
    Nucleic acids symposium series (2004), 2009, Issue:53

    Topics: Cytosine; Hydroxylamine; Oligodeoxyribonucleotides; Sulfites; Sulfonic Acids; Uracil

2009
Enzymatic incorporation of multiple dyes for increased sensitivity in QD-FRET sensing for DNA methylation detection.
    Chembiochem : a European journal of chemical biology, 2010, Jan-04, Volume: 11, Issue:1

    Topics: Cell Line, Tumor; Cytosine; DNA; DNA Methylation; Enzymes; Fluorescence Resonance Energy Transfer; Fluorescent Dyes; Humans; Quantum Dots; Sulfites; Tumor Suppressor Protein p14ARF

2010
The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing.
    PloS one, 2010, Jan-26, Volume: 5, Issue:1

    Topics: 5-Methylcytosine; Base Sequence; Chromatography, Liquid; Cytosine; Mass Spectrometry; Molecular Sequence Data; Polymerase Chain Reaction; Sulfites

2010
Analysis of bisulfite sequencing data from plant DNA using CyMATE.
    Methods in molecular biology (Clifton, N.J.), 2010, Volume: 631

    Topics: Cytosine; DNA Methylation; DNA, Plant; Inverted Repeat Sequences; Plants; Sequence Alignment; Sequence Analysis, DNA; Software; Sulfites

2010
Analysis of locus-specific changes in methylation patterns using a COBRA (combined bisulfite restriction analysis) assay.
    Methods in molecular biology (Clifton, N.J.), 2010, Volume: 631

    Topics: Cytosine; DNA; DNA Methylation; DNA Restriction Enzymes; Genetic Loci; Sequence Analysis, DNA; Sulfites

2010
DNA cytosine methylation in the bovine leukemia virus promoter is associated with latency in a lymphoma-derived B-cell line: potential involvement of direct inhibition of cAMP-responsive element (CRE)-binding protein/CRE modulator/activation transcription
    The Journal of biological chemistry, 2010, Jun-18, Volume: 285, Issue:25

    Topics: Activating Transcription Factor 1; B-Lymphocytes; Chromatin; Cyclic AMP; Cyclic AMP Response Element Modulator; Cyclic AMP Response Element-Binding Protein; Cytosine; DNA; DNA Methylation; Enzyme-Linked Immunosorbent Assay; Humans; Leukemia Virus, Bovine; Lymphoma; Plasmids; Promoter Regions, Genetic; Sulfites

2010
Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA.
    BioTechniques, 2010, Volume: 48, Issue:4

    Topics: 5-Methylcytosine; CpG Islands; Cytosine; DNA; DNA Methylation; DNA Restriction Enzymes; Genes, BRCA1; Humans; Octamer Transcription Factor-3; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2010
Bisulphite sequencing of plant genomic DNA.
    Methods in molecular biology (Clifton, N.J.), 2010, Volume: 655

    Topics: 5-Methylcytosine; Base Sequence; Cytosine; DNA Methylation; DNA, Plant; DNA, Single-Stranded; Epigenomics; Genome, Plant; Plants; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites; Uracil

2010
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
    Nature biotechnology, 2010, Volume: 28, Issue:10

    Topics: Alleles; Cell Line; CpG Islands; Cytosine; DNA Methylation; Embryonic Stem Cells; Epigenesis, Genetic; Gene Expression Regulation; Humans; Sequence Analysis, DNA; Sulfites

2010
Detection of cytosine methylation in RNA using bisulfite sequencing.
    Cold Spring Harbor protocols, 2010, Oct-01, Volume: 2010, Issue:10

    Topics: Cytosine; Methylation; RNA; RNA Processing, Post-Transcriptional; Sequence Analysis, RNA; Sulfites

2010
MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.
    Nucleic acids research, 2011, Volume: 39, Issue:1

    Topics: Adaptor Proteins, Signal Transducing; Cell Line, Tumor; Chromatin; Computational Biology; CpG Islands; Cytidine; Cytosine; DNA; DNA (Cytosine-5-)-Methyltransferases; DNA Methylation; Humans; Image Enhancement; MutL Protein Homolog 1; Nuclear Proteins; Sequence Alignment; Sequence Analysis, DNA; Software; Sulfites

2011
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications.
    Bioinformatics (Oxford, England), 2011, Jun-01, Volume: 27, Issue:11

    Topics: Cytosine; DNA; DNA Methylation; Sequence Analysis, DNA; Software; Sulfites

2011
Bisulfite sequencing for cytosine-methylation analysis in plants.
    Methods in molecular biology (Clifton, N.J.), 2011, Volume: 744

    Topics: Base Sequence; Cytosine; DNA Methylation; Genes, Plant; Molecular Sequence Data; Plants, Genetically Modified; Polymerase Chain Reaction; RNA Interference; Sequence Analysis, DNA; Sulfites

2011
A sustained dietary change increases epigenetic variation in isogenic mice.
    PLoS genetics, 2011, Volume: 7, Issue:4

    Topics: 5-Methylcytosine; Alleles; Animals; CpG Islands; Cytosine; Dietary Supplements; DNA Methylation; Environment; Epigenesis, Genetic; Gene Expression; Genetic Loci; Genetic Variation; Mice; Mice, Inbred C57BL; Phenotype; Principal Component Analysis; Promoter Regions, Genetic; Repetitive Sequences, Nucleic Acid; Stochastic Processes; Sulfites

2011
MethylCoder: software pipeline for bisulfite-treated sequences.
    Bioinformatics (Oxford, England), 2011, Sep-01, Volume: 27, Issue:17

    Topics: Cytosine; DNA; DNA Methylation; Genomics; Sequence Alignment; Sequence Analysis, DNA; Software; Sulfites

2011
Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing.
    Genome research, 2012, Volume: 22, Issue:6

    Topics: Base Sequence; Cell Line, Transformed; CpG Islands; Cytosine; DNA; DNA Methylation; Gene Library; Genome, Human; Humans; Lymphocytes; Molecular Sequence Data; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites; Transposases

2012
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution.
    Science (New York, N.Y.), 2012, May-18, Volume: 336, Issue:6083

    Topics: 5-Methylcytosine; Animals; CpG Islands; Cytosine; DNA; DNA Methylation; Embryonic Stem Cells; Epigenesis, Genetic; Genes, Intracisternal A-Particle; High-Throughput Nucleotide Sequencing; Long Interspersed Nucleotide Elements; Mice; Oxidation-Reduction; Rhenium; Sequence Analysis, DNA; Sulfites; Transcription, Genetic; Uracil

2012
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
    Bioinformatics (Oxford, England), 2012, Jul-01, Volume: 28, Issue:13

    Topics: Cytosine; DNA Methylation; Genome; High-Throughput Nucleotide Sequencing; Sequence Analysis, DNA; Software; Sulfites

2012
Advanced methylome analysis after bisulfite deep sequencing: an example in Arabidopsis.
    PloS one, 2012, Volume: 7, Issue:7

    Topics: Arabidopsis; Base Sequence; Cytosine; DNA Methylation; Genome, Plant; High-Throughput Nucleotide Sequencing; Reference Standards; Reproducibility of Results; Sequence Alignment; Sequence Analysis, DNA; Sulfites

2012
Sequencing the sixth base (5-hydroxymethylcytosine): selective DNA oxidation enables base-pair resolution.
    Angewandte Chemie (International ed. in English), 2012, Oct-22, Volume: 51, Issue:43

    Topics: 5-Methylcytosine; Base Pairing; Cytosine; Deamination; DNA; Oxidation-Reduction; Sequence Analysis, DNA; Sulfites

2012
'Leveling' the playing field for analyses of single-base resolution DNA methylomes.
    Trends in genetics : TIG, 2012, Volume: 28, Issue:12

    Topics: Cytosine; DNA Methylation; Genome; Sequence Analysis, DNA; Sulfites

2012
Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine.
    Nature protocols, 2012, Volume: 7, Issue:12

    Topics: 5-Methylcytosine; Animals; Chromatography, High Pressure Liquid; Cytosine; DNA-Binding Proteins; Glucosyltransferases; Mice; Polymerase Chain Reaction; Proto-Oncogene Proteins; Sequence Analysis, DNA; Sulfites

2012
The conversion of protonated cytosine-SO3(-) to uracil-SO3(-): insights into the novel induced hydrolytic deamination through bisulfite catalysis.
    Physical chemistry chemical physics : PCCP, 2013, Jun-21, Volume: 15, Issue:23

    Topics: Catalysis; Cytosine; Deamination; Hydrolysis; Models, Molecular; Protons; Sulfites; Sulfur Oxides; Uracil

2013
Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA.
    Journal of the American Chemical Society, 2013, Jun-26, Volume: 135, Issue:25

    Topics: Amides; Catalysis; Cytosine; DNA; Ethyldimethylaminopropyl Carbodiimide; Molecular Structure; Sulfites

2013
Bisulfite pyrosequencing.
    Methods in molecular biology (Clifton, N.J.), 2013, Volume: 1049

    Topics: Cytosine; DNA Methylation; Genome, Human; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2013
Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees.
    BMC genomics, 2013, Sep-30, Volume: 14

    Topics: 5-Methylcytosine; Africa; Alternative Splicing; Animals; Bees; Behavior, Animal; CpG Islands; Cytosine; DNA Methylation; Europe; Exons; Gene Expression Regulation; Genes, Insect; Honey; Introns; Reproducibility of Results; RNA Splice Sites; RNA, Messenger; Sequence Analysis, DNA; Sulfites

2013
A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study.
    Physical chemistry chemical physics : PCCP, 2014, Feb-28, Volume: 16, Issue:8

    Topics: Cytosine; Deamination; Gases; Hydrogen Bonding; Isomerism; Models, Molecular; Solvents; Sulfites; Thermodynamics; Water

2014
Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions.
    Nucleic acids research, 2014, Volume: 42, Issue:6

    Topics: Cytosine; DNA Methylation; Sequence Alignment; Sequence Analysis, DNA; Software; Sulfites

2014
Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.
    Nature chemistry, 2014, Volume: 6, Issue:5

    Topics: Animals; Cytosine; DNA; Embryonic Stem Cells; Mice; Sulfites

2014
GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
    PloS one, 2014, Volume: 9, Issue:5

    Topics: Animals; Cytosine; DNA Methylation; Humans; Sequence Analysis, DNA; Sulfites

2014
Epigenetic germline mosaicism in infertile men.
    Human molecular genetics, 2015, Mar-01, Volume: 24, Issue:5

    Topics: Adult; Alleles; Cytosine; DNA Methylation; Epigenesis, Genetic; Epigenomics; Genomic Imprinting; Germ-Line Mutation; High-Throughput Nucleotide Sequencing; Humans; Infertility, Male; Male; Mosaicism; Potassium Channels, Voltage-Gated; Proteins; Spermatozoa; Sulfites

2015
MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.
    Nature protocols, 2015, Volume: 10, Issue:3

    Topics: Cytosine; DNA Fragmentation; DNA Methylation; Genomic Library; Genomics; Sequence Analysis, DNA; Sulfites

2015
Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array).
    PloS one, 2015, Volume: 10, Issue:2

    Topics: 5-Methylcytosine; Adult; Cerebellum; Cytosine; DNA; DNA Methylation; Humans; Male; Oligonucleotide Array Sequence Analysis; Oxidation-Reduction; Reproducibility of Results; Sulfites

2015
Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.
    Nucleic acids research, 2015, Jul-13, Volume: 43, Issue:12

    Topics: 5-Methylcytosine; Alleles; Animals; Cell Line; Cytosine; DNA Methylation; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; Humans; Mice; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Sulfites

2015
Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains.
    Genome biology, 2015, Apr-15, Volume: 16

    Topics: CpG Islands; Cytosine; DNA; DNA Fragmentation; DNA Methylation; Epigenesis, Genetic; Female; Fetus; Gene Library; Genomics; Humans; Immunoprecipitation; Placenta; Pregnancy; Sequence Analysis, DNA; Sulfites

2015
Estimation of the methylation pattern distribution from deep sequencing data.
    BMC bioinformatics, 2015, May-06, Volume: 16

    Topics: Algorithms; Animals; Bees; Brain; Cytosine; DNA Methylation; Documentation; High-Throughput Nucleotide Sequencing; Models, Statistical; Programming Languages; Sulfites

2015
Base-resolution detection of N4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing.
    Nucleic acids research, 2015, Dec-02, Volume: 43, Issue:21

    Topics: 5-Methylcytosine; Animals; Cytosine; DNA-Binding Proteins; DNA, Bacterial; Firmicutes; Genome, Bacterial; Mice; Nucleotide Motifs; Proto-Oncogene Proteins; Sequence Analysis, DNA; Sulfites

2015
Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale.
    Nature methods, 2015, Volume: 12, Issue:11

    Topics: 5-Methylcytosine; Animals; Cell Line; CpG Islands; Cytosine; DNA Methylation; DNA Primers; Epigenomics; Gene Expression Regulation; Genome; Mice; Mice, Transgenic; Oligonucleotides; Oxygen; Polymerase Chain Reaction; Sequence Analysis, DNA; Stem Cells; Sulfites

2015
Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution.
    Bioorganic & medicinal chemistry letters, 2015, Dec-15, Volume: 25, Issue:24

    Topics: 5-Methylcytosine; Base Sequence; Catalysis; Cytosine; Mass Spectrometry; Micelles; Oxidation-Reduction; Sulfites

2015
An integrative approach for efficient analysis of whole genome bisulfite sequencing data.
    BMC genomics, 2015, Volume: 16 Suppl 12

    Topics: Algorithms; Computational Biology; CpG Islands; Cytosine; DNA Methylation; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Sequence Analysis, DNA; Sulfites

2015
Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions.
    BMC genomics, 2015, Volume: 16 Suppl 12

    Topics: Algorithms; Binomial Distribution; Computational Biology; Cytosine; DNA Methylation; Genome-Wide Association Study; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Markov Chains; Sequence Analysis, DNA; Sulfites

2015
Methylation profiling by bisulfite sequencing analysis of the mtDNA Non-Coding Region in replicative and senescent Endothelial Cells.
    Mitochondrion, 2016, Volume: 27

    Topics: 5-Methylcytosine; Cytosine; DNA, Intergenic; DNA, Mitochondrial; Endothelial Cells; Humans; Mitochondria; Sequence Analysis, DNA; Sulfites

2016
Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq.
    Nature protocols, 2016, Volume: 11, Issue:6

    Topics: 5-Methylcytosine; Animals; Cell Line; Cytosine; DNA; DNA Methylation; DNA Modification Methylases; Mice; Sequence Analysis, DNA; Sulfites

2016
Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis.
    Nature protocols, 2016, Volume: 11, Issue:7

    Topics: 5-Methylcytosine; Animals; Base Sequence; Cell Line; CpG Islands; Cytosine; DNA; DNA Methylation; Epigenesis, Genetic; Humans; Mice; Sequence Analysis, DNA; Sulfites

2016
Simple and accurate single base resolution analysis of 5-hydroxymethylcytosine by catalytic oxidative bisulfite sequencing using micelle incarcerated oxidants.
    Bioorganic & medicinal chemistry, 2016, 09-15, Volume: 24, Issue:18

    Topics: 5-Methylcytosine; Adamantane; Animals; Cyclic N-Oxides; Cytosine; DNA, Single-Stranded; Embryonic Stem Cells; Iodobenzenes; Mice; Micelles; Onium Compounds; Oxidants; Oxidation-Reduction; Sequence Analysis, DNA; Sodium Dodecyl Sulfate; Sulfites; Temperature

2016
Bisulfite Sequencing for DNA Methylation Analysis of Primary Muscle Stem Cells.
    Methods in molecular biology (Clifton, N.J.), 2017, Volume: 1668

    Topics: Cytosine; DNA; DNA Methylation; DNA, Single-Stranded; Genome-Wide Association Study; Genome, Human; Humans; Primary Cell Culture; RNA; Satellite Cells, Skeletal Muscle; Sequence Analysis, DNA; Sulfites; Transcriptome

2017
Profiling DNA Methylation Using Bisulfite Sequencing (BS-Seq).
    Methods in molecular biology (Clifton, N.J.), 2018, Volume: 1675

    Topics: Arabidopsis; Cytosine; DNA Methylation; Epigenesis, Genetic; Genome, Plant; High-Throughput Nucleotide Sequencing; Sulfites; Whole Genome Sequencing

2018
Genome-Wide Analysis of DNA Methylation in Single Cells Using a Post-bisulfite Adapter Tagging Approach.
    Methods in molecular biology (Clifton, N.J.), 2018, Volume: 1712

    Topics: Animals; Cytosine; DNA; DNA Methylation; Epigenomics; Gene Library; Genome-Wide Association Study; High-Throughput Nucleotide Sequencing; Humans; Mice; Sequence Analysis, DNA; Single-Cell Analysis; Sulfites; Whole Genome Sequencing

2018
Whole-Genome Bisulfite Sequencing Using the Ovation® Ultralow Methyl-Seq Protocol.
    Methods in molecular biology (Clifton, N.J.), 2018, Volume: 1708

    Topics: Computational Biology; Cytosine; DNA Methylation; Epigenesis, Genetic; Genome, Human; High-Throughput Nucleotide Sequencing; Humans; Polymerase Chain Reaction; Sulfites; Whole Genome Sequencing

2018
An optimized rapid bisulfite conversion method with high recovery of cell-free DNA.
    BMC molecular biology, 2017, Dec-19, Volume: 18, Issue:1

    Topics: Cell-Free Nucleic Acids; Cytosine; Deamination; DNA; DNA Methylation; Humans; Molecular Biology; Real-Time Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2017
Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: Sources and avoidance of false-positive detection.
    PloS one, 2018, Volume: 13, Issue:2

    Topics: Animals; CpG Islands; Cytosine; DNA Methylation; DNA, Mitochondrial; Humans; Mice; Sequence Analysis, DNA; Sulfites

2018
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing.
    Nucleic acids research, 2018, 09-06, Volume: 46, Issue:15

    Topics: 5-Methylcytosine; Animals; Cytosine; DNA; DNA (Cytosine-5-)-Methyltransferase 1; DNA Methylation; DNA-Binding Proteins; Embryonic Stem Cells; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Mice; Oxidation-Reduction; Proto-Oncogene Proteins; Sulfites

2018
Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites.
    Electrophoresis, 2019, Volume: 40, Issue:2

    Topics: Cytosine; DNA; DNA Methylation; Fluorescence Resonance Energy Transfer; Guanine; HeLa Cells; Humans; Sulfites

2019
Resolution of the DNA methylation state of single CpG dyads using in silico strand annealing and WGBS data.
    Nature protocols, 2019, Volume: 14, Issue:1

    Topics: Animals; Base Sequence; Computational Biology; Computer Simulation; CpG Islands; Cytosine; DNA; DNA Methylation; Embryo, Mammalian; Epigenesis, Genetic; Genome; High-Throughput Nucleotide Sequencing; Mice; Models, Genetic; Sequence Alignment; Sulfites; Whole Genome Sequencing

2019
Library Preparation for Multiplexed Reduced Representation Bisulfite Sequencing with a Universal Adapter.
    Methods in molecular biology (Clifton, N.J.), 2019, Volume: 2018

    Topics: 5-Methylcytosine; Animals; CpG Islands; Cytosine; DNA Methylation; DNA Primers; Gene Library; Rats; Sequence Analysis, DNA; Sulfites

2019
Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes.
    Methods in molecular biology (Clifton, N.J.), 2020, Volume: 2107

    Topics: Cytosine; DNA Methylation; DNA, Plant; Epigenesis, Genetic; Fabaceae; High-Throughput Nucleotide Sequencing; Molecular Sequence Annotation; Sulfites; Whole Genome Sequencing

2020
BCREval: a computational method to estimate the bisulfite conversion ratio in WGBS.
    BMC bioinformatics, 2020, Jan-31, Volume: 21, Issue:1

    Topics: Algorithms; Computational Biology; Cytosine; DNA; DNA Methylation; Genome; High-Throughput Nucleotide Sequencing; Humans; Sulfites; Whole Genome Sequencing

2020
Plant-RRBS: DNA Methylome Profiling Adjusted to Plant Genomes, Utilizing Efficient Endonuclease Combinations, for Multi-Sample Studies.
    Methods in molecular biology (Clifton, N.J.), 2020, Volume: 2093

    Topics: Breeding; Cytosine; DNA Fingerprinting; DNA Methylation; DNA, Plant; Endonucleases; Epigenome; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; Oryza; Plants; Sulfites; Whole Genome Sequencing

2020
Epigenetic Approaches in Non-Model Plants.
    Methods in molecular biology (Clifton, N.J.), 2020, Volume: 2093

    Topics: Cytosine; DNA Methylation; DNA, Plant; Epigenesis, Genetic; Epigenomics; Genetic Variation; Genome, Plant; Genomics; High-Throughput Nucleotide Sequencing; Plants; Sulfites

2020
Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion.
    Clinical chemistry, 2020, 07-01, Volume: 66, Issue:7

    Topics: Aged; Biomarkers, Tumor; Circulating Tumor DNA; Colorectal Neoplasms; Cytosine; DNA Methylation; DNA, Antisense; Female; Humans; KCNQ Potassium Channels; Male; Membrane Proteins; Polymerase Chain Reaction; Sulfites

2020
A New Approach to Identify the Methylation Sites in the Control Region of Mitochondrial DNA.
    Current molecular medicine, 2021, Volume: 21, Issue:2

    Topics: CpG Islands; Cytosine; DNA Methylation; DNA, Mitochondrial; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2021
Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung.
    Scientific reports, 2020, 07-09, Volume: 10, Issue:1

    Topics: Animals; Carcinogens; Cell Proliferation; Chromatography, High Pressure Liquid; CpG Islands; Cytosine; DNA; DNA Methylation; Epigenesis, Genetic; Female; High-Throughput Nucleotide Sequencing; Histones; Inflammation; Inhalation Exposure; Lung; Lung Neoplasms; Mice; Mice, Inbred Strains; Nicotiana; Nitrosamines; Smoke; Smoking; Sulfites; Tobacco Products

2020
Hairpin-Bisulfite PCR.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2198

    Topics: Cytosine; DNA; DNA Methylation; DNA, Complementary; Humans; Inverted Repeat Sequences; Nucleic Acid Conformation; Oligonucleotides; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2021
High-Resolution Analysis of 5-Hydroxymethylcytosine by TET-Assisted Bisulfite Sequencing.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2198

    Topics: 5-Methylcytosine; Animals; Cytosine; Dioxygenases; DNA; DNA Methylation; Epigenesis, Genetic; Epigenomics; Genome; Humans; Oxidation-Reduction; Sequence Analysis, DNA; Sulfites

2021
Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2198

    Topics: 5-Methylcytosine; Animals; Computational Biology; Cytosine; Dioxygenases; DNA; DNA Methylation; High-Throughput Nucleotide Sequencing; Humans; Oxidation-Reduction; Oxidative Stress; Sequence Analysis, DNA; Sulfites

2021
Bisulfite-Free Sequencing of 5-Hydroxymethylcytosine with APOBEC-Coupled Epigenetic Sequencing (ACE-Seq).
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2198

    Topics: 5-Methylcytosine; Animals; Computational Biology; Cytidine Deaminase; Cytosine; DNA; DNA Methylation; Epigenomics; Humans; Proteins; Sequence Analysis, DNA; Single Molecule Imaging; Sulfites

2021
Bioinformatics Analysis of DNA Methylation Through Bisulfite Sequencing Data.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2198

    Topics: Animals; Computational Biology; Cytosine; DNA; DNA Methylation; Epigenesis, Genetic; Epigenomics; Genome; Genomics; High-Throughput Nucleotide Sequencing; Humans; Polymerase Chain Reaction; Sequence Analysis, DNA; Sulfites

2021
A Bisulfite-free Approach for Base-Resolution Analysis of Genomic 5-Carboxylcytosine.
    Cell reports, 2020, 09-15, Volume: 32, Issue:11

    Topics: Animals; Binding Sites; Cell Line; Cytosine; Genome; Humans; Mice; Mice, Knockout; Mouse Embryonic Stem Cells; Pluripotent Stem Cells; Reproducibility of Results; Sulfites; Transcription Factors; Transcription, Genetic

2020
Bisulfite treatment and single-molecule real-time sequencing reveal D-loop length, position, and distribution.
    eLife, 2020, 11-13, Volume: 9

    Topics: Cytosine; DNA Repair; DNA, Single-Stranded; Nucleic Acid Amplification Techniques; Single Molecule Imaging; Sulfites; Uracil

2020
The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth.
    The plant genome, 2020, Volume: 13, Issue:3

    Topics: Cytosine; DNA Methylation; Hordeum; Sulfites

2020
Detection of 5-formylcytosine in Mitochondrial Transcriptome.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2192

    Topics: Cytosine; DNA, Mitochondrial; Gene Expression Profiling; Mitochondria; Nucleotides; RNA Processing, Post-Transcriptional; RNA-Seq; RNA, Mitochondrial; Sulfites; Transcriptome

2021
Flanking sequence preference modulates de novo DNA methylation in the mouse genome.
    Nucleic acids research, 2021, 01-11, Volume: 49, Issue:1

    Topics: Amino Acid Substitution; Animals; Arginine; Base Sequence; CpG Islands; Crystallography, X-Ray; Cytosine; Datasets as Topic; DNA (Cytosine-5-)-Methyltransferases; DNA Methylation; DNA Methyltransferase 3A; DNA Methyltransferase 3B; Embryonic Stem Cells; Gene Knockout Techniques; Guanine; Humans; Lysine; Mice; Molecular Dynamics Simulation; Substrate Specificity; Sulfites; Whole Genome Sequencing

2021
Analysis of Plant DNA Methylation Profiles Using R.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2250

    Topics: Algorithms; Chromosome Mapping; Chromosomes, Plant; Computational Biology; Cytosine; DNA Methylation; Epigenesis, Genetic; Gene Expression Regulation, Plant; Genome, Plant; Genomics; Plants; Software; Sulfites; Whole Genome Sequencing

2021
Reduced Bisulfite Sequencing: Quantitative Base-Resolution Sequencing of 5-Formylcytosine.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2272

    Topics: Animals; Cytosine; DNA; DNA Methylation; Epigenomics; Humans; Sequence Analysis, DNA; Sulfites

2021
Distinguishing Active Versus Passive DNA Demethylation Using Illumina MethylationEPIC BeadChip Microarrays.
    Methods in molecular biology (Clifton, N.J.), 2021, Volume: 2272

    Topics: 5-Methylcytosine; Computational Biology; Cytosine; DNA; DNA Demethylation; DNA Methylation; Epigenesis, Genetic; High-Throughput Nucleotide Sequencing; Humans; Microarray Analysis; Oxidation-Reduction; Sulfites

2021
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning.
    Nature communications, 2021, 10-13, Volume: 12, Issue:1

    Topics: Arabidopsis; CpG Islands; Cytosine; Deep Learning; DNA Methylation; DNA, Plant; Epigenesis, Genetic; Genome, Plant; High-Throughput Nucleotide Sequencing; Nanopores; Oryza; Sequence Analysis, DNA; Sulfites

2021
Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions.
    Methods in molecular biology (Clifton, N.J.), 2022, Volume: 2443

    Topics: Cytosine; DNA Methylation; Epigenesis, Genetic; Sulfites

2022
Effects of salinity stress on methylation of the liver genome and complement gene in large yellow croaker (Larimichthys crocea).
    Fish & shellfish immunology, 2022, Volume: 129

    Topics: Animals; Complement C7; Complement System Proteins; Cytosine; DNA Methylation; Fish Proteins; Liver; Perciformes; RNA, Messenger; Salt Stress; Sulfites

2022
Epigenetic machinery is functionally conserved in cephalopods.
    BMC biology, 2022, 09-14, Volume: 20, Issue:1

    Topics: Animals; Cephalopoda; Cytosine; DNA Transposable Elements; Epigenesis, Genetic; Sulfites

2022
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data.
    BMC bioinformatics, 2022, Sep-19, Volume: 23, Issue:1

    Topics: Cytosine; Sequence Analysis, DNA; Sulfites; Whole Genome Sequencing

2022
DNA Methylation Analysis Using Bisulfite Pyrosequencing.
    Methods in molecular biology (Clifton, N.J.), 2023, Volume: 2577

    Topics: Animals; CpG Islands; Cytosine; DNA Methylation; DNA Primers; High-Throughput Nucleotide Sequencing; Mammals; Polymorphism, Single Nucleotide; Sequence Analysis, DNA; Sulfites; Thymine

2023
Bisulfite-Free and Single-Base Resolution Detection of Epigenetic DNA Modification of 5-Methylcytosine by Methyltransferase-Directed Labeling with APOBEC3A Deamination Sequencing.
    Analytical chemistry, 2022, 11-08, Volume: 94, Issue:44

    Topics: 5-Methylcytosine; Animals; Cytosine; Deamination; DNA; DNA Methylation; Epigenesis, Genetic; Humans; Mammals; Methyltransferases; Sequence Analysis, DNA; Sulfites

2022
Tet2- and Tet3- Mediated Cytosine Hydroxymethylation in Six2 Progenitor Cells in Mice Is Critical for Nephron Progenitor Differentiation and Nephron Endowment.
    Journal of the American Society of Nephrology : JASN, 2023, 04-01, Volume: 34, Issue:4

    Topics: Animals; Cell Differentiation; Cytosine; Dioxygenases; DNA Methylation; Female; Homeodomain Proteins; Humans; Mice; Mixed Function Oxygenases; Nephrons; Nerve Tissue Proteins; Perinatal Death; Pregnancy; Proto-Oncogene Proteins; Renal Insufficiency; Stem Cells

2023
Engineered APOBEC3C Sequencing Enables Bisulfite-Free and Direct Detection of DNA Methylation at a Single-Base Resolution.
    Analytical chemistry, 2023, 01-17, Volume: 95, Issue:2

    Topics: 5-Methylcytosine; Cytidine Deaminase; Cytosine; DNA; DNA Methylation; Epigenesis, Genetic; Humans; Sequence Analysis, DNA; Sulfites

2023
Herbivory induced methylation changes in the Lombardy poplar: A comparison of results obtained by epiGBS and WGBS.
    PloS one, 2023, Volume: 18, Issue:9

    Topics: Cytosine; DNA Methylation; DNA, Intergenic; Herbivory; Populus

2023
Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability.
    Proceedings of the National Academy of Sciences of the United States of America, 2023, Dec-05, Volume: 120, Issue:49

    Topics: 5-Methylcytosine; Animals; Cytosine; DNA Methylation; Mice; Sequence Analysis, DNA; Sulfites

2023