Selected publications that used or cited MethPrimer program

Manning K, Tor M, Poole M, et al. A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening 
NATURE GENETICS 38 (8): 948-952 AUG 2006

Ferres-Marco D, Gutierrez-Garcia I, Vallejo DM, Bolivar J, Gutierrez-Avino FJ, Dominguez M. Epigenetic silencers and Notch collaborate to promote malignant tumours by Rb silencing. Nature. 2006 Jan 26;439(7075):430-6. (Cited in Supplementary Information)

Grigg SP, Canales C, Hay A, Tsiantis M. SERRATE coordinates shoot meristem function and leaf axial patterning in Arabidopsis.
Nature. 2005 Oct 13;437(7061):1022-6. (Cited in Supplementary Information)

Wu H, Chen Y, Liang J, Shi B, Wu G, Zhang Y, Wang D, Li R, Yi X, Zhang H, Sun L, Shang Y. Hypomethylation-linked activation of PAX2 mediates tamoxifen-stimulated endometrial carcinogenesis. Nature. 2005 Dec 15;438(7070):981-7. (Figure 5b was generated by MethPrimer)

Simonsson S, Gurdon J. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat Cell Biol. 2004 Oct;6(10):984-90. Epub 2004 Sep 26.

Lund P, Weisshaupt K, Mikeska T, et al.
Oncogenic HRAS suppresses clusterin expression through promoter hypermethylation 
ONCOGENE 25 (35): 4890-4903 AUG 10 2006

Park CW, Park J, Kren BT, et al.
Sleeping Beauty transposition in the mouse genome is associated with changes in DNA methylation at the site of insertion 
GENOMICS 88 (2): 204-213 AUG 2006

Wang YQ, Fan PS, Kahaleh B
Association between enhanced type I collagen expression and epigenetic repression of the FLI1 gene in scleroderma fibroblasts 
ARTHRITIS AND RHEUMATISM 54 (7): 2271-2279 JUL 2006

Cheng Q, Cheng C, Crews KR, et al.
Epigenetic regulation of human gamma-glutamyl hydrolase activity in acute lymphoblastic leukemia cells 
AMERICAN JOURNAL OF HUMAN GENETICS 79 (2): 264-274 AUG 2006

Li HW, Rauch T, Chen ZX, et al.
The histone methyltransferase SETDB1 and the DNA methyltransferase DNMT3A interact directly and localize to promoters silenced in cancer cells 
JOURNAL OF BIOLOGICAL CHEMISTRY 281 (28): 19489-19500 JUL 14 2006

Boyd VL, Moody KI, Karger AE, et al.
Methylation-dependent fragment separation: Direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA 
ANALYTICAL BIOCHEMISTRY 354 (2): 266-273 JUL 15 2006

Paixao VA, Vidal DO, Caballero OL, et al.
Hypermethylation of CpG island in the promoter region of CALCA in acute lymphoblastic leukemia with central nervous system (CNS) infiltration correlates with poorer prognosis 
LEUKEMIA RESEARCH 30 (7): 891-894 JUL 2006

Macheiner D, Heller G, Kappel S, et al.
NORE1B, a candidate tumor suppressor, is epigenetically silenced in human hepatocellular carcinoma 
JOURNAL OF HEPATOLOGY 45 (1): 81-89 JUL 2006

Kriaucionis S, Paterson A, CurtiS J, et al.
Gene expression analysis exposes mitochondrial abnormalities in a mouse model of Rett syndrome 
MOLECULAR AND CELLULAR BIOLOGY 26 (13): 5033-5042 JUL 2006

Ho SM, Tang WY, de Frausto JB, et al.
Developmental exposure to estradiol and bisphenol A increases susceptibility to prostate carcinogenesis and epigenetically regulates phosphodiesterase type 4 variant 4 
CANCER RESEARCH 66 (11): 5624-5632 JUN 1 2006

Zawlik I, Witusik M, Hulas-Bigoszewska K, et al.
Regulation of PrPc expression: Nerve growth factor (NGF) activates the prion gene promoter through the MEK1 pathway in PC12 cells 
NEUROSCIENCE LETTERS 400 (1-2): 58-62 MAY 29 2006

Luo W, Wang X, Kageshita T, et al.
Regulation of high molecular weight-melanoma associated antigen (HMW-MAA) gene expression by promoter DNA methylation in human melanoma cells 
ONCOGENE 25 (20): 2873-2884 MAY 2006

Tong YK, Lo YMD
Plasma epigenetic markers for cancer detection and prenatal diagnosis 
FRONTIERS IN BIOSCIENCE 11: 2647-2656 SEP 1 2006

Qiu G, Fan JC, He YS
5 ' CpG island methylation analysis identifies the MAGE-A1 and MAGE-A3 genes as potential markers of HCC 
CLINICAL BIOCHEMISTRY 39 (3): 259-266 MAR 2006

Brena RM, Auer H, Kornacker K, et al.
Accurate quantification of DNA methylation using combined bisulfite restriction analysis coupled with the Agilent 2100 Bioanalyzer platform 
NUCLEIC ACIDS RESEARCH 34 (3): Art. No. e17 2006

Ushmorov A, Leithauser F, Sakk O, et al.
Epigenetic processes play a major role in B-cell-specitic gene silencing in classical Hodgkin lymphoma 
BLOOD 107 (6): 2493-2500 MAR 15 2006

Takami N, Osawa K, Miura Y, et al.
Hypermethylated promoter region of DR3, the death receptor 3 gene, in rheumatoid arthritis synovial cells 
ARTHRITIS AND RHEUMATISM 54 (3): 779-787 MAR 2006

Niculescu MD, Craciunescu CN, Zeisel SH
Dietary choline deficiency alters global and gene-specific DNA methylation in the developing hippocampus of mouse fetal brains 
FASEB JOURNAL 20 (1): 43-49 JAN 2006

Weeks RJ, Morison IM
Detailed methylation analysis of CpG islands on human chromosome region 9p21 
GENES CHROMOSOMES & CANCER 45 (4): 357-364 APR 2006

Seth G, Ozturk M, Hu WS
Reverting cholesterol auxotrophy of NS0 cells by altering epigenetic gene silencing 
BIOTECHNOLOGY AND BIOENGINEERING 93 (4): 820-827 MAR 5 2006

Heller G, Fong KM, Girard L, et al.
Expression and methylation pattern of TSLC1 cascade genes in lung carcinomas 
ONCOGENE 25 (6): 959-968 FEB 2006

Xi SC, Dyer KF, Kimak M, et al.
Decreased STAT1 expression by promoter methylation in squamous cell carcinogenesis 
JOURNAL OF THE NATIONAL CANCER INSTITUTE 98 (3): 181-189 FEB 1 2006

Tang L, Roberts PC, Kraniak JM, et al.
Stat1 expression is not sufficient to regulate the interferon signaling pathway in cellular immortalization 
JOURNAL OF INTERFERON AND CYTOKINE RESEARCH 26 (1): 14-26 JAN 2006

Visser R, Hasegawa T, Niikawa N, et al.
Analysis of the NSD1 promoter region in patients with a Sotos syndrome phenotype 
JOURNAL OF HUMAN GENETICS 51 (1): 15-20 2006

Sova P, Feng QH, Geiss G, et al.
Discovery of novel methylation biomarkers in cervical carcinoma by global demethylation and microarray analysis 
CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION 15 (1): 114-123 JAN 2006

Urakami S, Shiina H, Enokida H, et al.
Epigenetic inactivation of Wnt inhibitory factor-1 plays an important role in bladder cancer through aberrant canonical Wnt/beta-catenin signaling pathway 
CLINICAL CANCER RESEARCH 12 (2): 383-391 JAN 15 2006

Enokida H, Shiina H, Urakami S, et al.
Smoking influences aberrant CpG hypermethylation of multiple genes in human prostate carcinoma 
CANCER 106 (1): 79-86 JAN 1 2006 

Lindsey JC, Lusher ME, Strathdee G, et al.
Epigenetic inactivation of MCJ (DNAJD1) in malignant paediatric brain tumours 
INTERNATIONAL JOURNAL OF CANCER 118 (2): 346-352 JAN 15 2006 

Roberts PC, Mottillo EP, Baxa AC, et al.
Sequential molecular and cellular events during neoplastic progression: A mouse syngeneic ovarian cancer model 
NEOPLASIA 7 (10): 944-956 OCT 2005 

Corradi JP, Ravyn V, Robbins AK, et al.
Alternative transcripts and evidence of imprinting of GNAL on 18p11.2 
MOLECULAR PSYCHIATRY 10 (11): 1017-1025 NOV 2005 

Bock C, Reither S, Mikeska T, et al.
BiQ analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing 
BIOINFORMATICS 21 (21): 4067-4068 NOV 1 2005 

Wang YP, Yu QJ, Cho AH, et al.
Survey of differentially methylated promoters in prostate cancer cell lines 
NEOPLASIA 7 (8): 748-760 AUG 2005 

Ordway JM, Bedell JA, Citek RW, et al.
MethylMapper: a method for high-throughput, multilocus bisulfite sequence analysis and reporting 
BIOTECHNIQUES 39 (4): 464+ OCT 2005 

Lung HL, Bangarusamy DK, Xie D, et al.
THY1 is a candidate tumour suppressor gene with decreased expression in metastatic nasopharyngeal carcinoma 
ONCOGENE 24 (43): 6525-6532 SEP 2005 

Enokida H, Shiina H, Urakami S, et al.
Multigene methylation analysis for detection and staging of prostate cancer 
CLINICAL CANCER RESEARCH 11 (18): 6582-6588 SEP 15 2005 

Hamada T, Goto M, Tsutsumida H, et al.
Mapping of the methylation pattern of the MUC2 promoter in pancreatic cancer cell lines, using bisulfite genomic sequencing 
CANCER LETTERS 227 (2): 175-184 SEP 28 2005 

Tokizane T, Shiina H, Igawa M, et al.
Cytochrome P450 1B1 is overexpressed and regulated by hypomethylation in prostate cancer 
CLINICAL CANCER RESEARCH 11 (16): 5793-5801 AUG 15 2005 

Wu Y, Halverson G, Basir Z, et al.
Aberrant methylation at HOXA10 may be responsible for its aberrant expression in the endometrium of patients with endometriosis 
AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY 193 (2): 371-380 AUG 2005 

Rouchka EC, Khalyfa A, Cooper NGF
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays 
BMC BIOINFORMATICS 6: Art. No. 175 JUL 13 2005 

Park CW, Kren BT, Largaespada DA, et al.
DNA methylation of Sleeping Beauty with transposition into the mouse genome 
GENES TO CELLS 10 (8): 763-776 AUG 2005 

Fujimoto A, Mitalipov SM, Clepper LL, et al.
Development of a monkey model for the study of primate genomic imprinting 
MOLECULAR HUMAN REPRODUCTION 11 (5-6): 413-422 MAY-JUN 2005 

Enokida H, Shiina H, Urakami S, et al.
Ethnic group-related differences in CpG hypermethylation of the GSTP1 gene promoter among African-American, Caucasian and Asian patients with prostate cancer 
INTERNATIONAL JOURNAL OF CANCER 116 (2): 174-181 AUG 20 2005 

Horak P, Pils D, Haller G, et al.
Contribution of epigenetic silencing of tumor necrosis factor-related apoptosis inducing ligand receptor 1 (DR4) to TRAIL resistance and ovarian cancer 
MOLECULAR CANCER RESEARCH 3 (6): 335-343 JUN 2005 

Iwamoto K, Bundo M, Yamada K, et al.
DNA methylation status of SOX10 correlates with its downregulation and oligodendrocyte dysfunction in schizophrenia 
JOURNAL OF NEUROSCIENCE 25 (22): 5376-5381 JUN 1 2005 

Tchurikov NA
Molecular mechanisms of epigenetics 
BIOCHEMISTRY-MOSCOW 70 (4): 406-423 APR 2005 

Gan YH, Shen YH, Wang J, et al.
Role of histone deacetylation in cell-specific expression of endothelial nitric-oxide synthase 
JOURNAL OF BIOLOGICAL CHEMISTRY 280 (16): 16467-16475 APR 22 2005 

Keen JC, Garrett-Mayer E, Petit C, et al.
Epigenetic regulation of protein phosphatase 2A (PP2A), lymphotactin (XCL1) and estrogen receptor alpha (ER) expression in human breast cancer cells 
CANCER BIOLOGY & THERAPY 3 (12): 1304-1312 DEC 2004 

Yang WC, Bancroft L, Augenlicht LH
Methylation in the p21(WAF1/cip1) promoter of Apc(+/-), p21(+/-) mice and lack of response to sulindac 
ONCOGENE 24 (12): 2104-2109 MAR 17 2005 

Liu ZJ, Lu X, Zhang Y, et al.
Downregulated mRNA expression of ASPP and the hypermethylation of the 5 '-untranslated region in cancer cell lines retaining wild-type p53 
FEBS LETTERS 579 (7): 1587-1590 MAR 14 2005 

Song F, Smith JF, Kimura MT, et al.
Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression 
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 102 (9): 3336-3341 MAR 1 2005 

Deb-Rinker P, Ly D, Jezierski A, et al.
Sequential DNA methylation of the Nanog and Oct-4 upstream regions in human NT2 cells during neuronal differentiation 
JOURNAL OF BIOLOGICAL CHEMISTRY 280 (8): 6257-6260 FEB 25 2005 

Ogishima T, Shiina H, Breault JE, et al.
Increased heparanase expression is caused by promoter hypomethylation and up-regulation of transcriptional factor early growth response-1 in human prostate cancer 
CLINICAL CANCER RESEARCH 11 (3): 1028-1036 FEB 1 2005 

Derks S, Lentjes MHFM, Hellebrekers DMEI, et al.
Methylation-specific PCR unraveled 
CELLULAR ONCOLOGY 26 (5-6): 291-299 2004 

Tusnady GE, Simon I, Varadi A, et al.
BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes 
NUCLEIC ACIDS RESEARCH 33 (1): Art. No. e9 2005 

Marshall OJ
PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR 
BIOINFORMATICS 20 (15): 2471-2472 OCT 12 2004 

Park CW, Chen ZY, Kren BT, et al.
Double-stranded siRNA targeted to the huntingtin gene does not induce DNA methylation 
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 323 (1): 275-280 OCT 8 2004 

Krona C, Ejeskar K, Caren H, et al.
A novel 1p36.2 located gene, APITD1, with tumour-suppressive properties and a putative p53-binding domain, shows low expression in neuroblastoma tumours 
BRITISH JOURNAL OF CANCER 91 (6): 1119-1130 SEP 13 2004 

De Preter K, Vandesompele J, Hoebeeck J, et al.
No evidence for involvement of SDHD in neuroblastoma pathogenesis 
BMC CANCER 4: Art. No. 55 AUG 24 2004 

Li LC, Shiina H, Deguchi M, et al.
Age-dependent methylation of ESR1 gene in prostate cancer 
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 321 (2): 455-461 AUG 20 2004 

Thomas CP, Loftus RW, Liu KZ
AVP-induced VIT32 gene expression in collecting duct cells occurs via trans-activation of a CRE in the 5 '-flanking region of the VIT32 gene 
AMERICAN JOURNAL OF PHYSIOLOGY-RENAL PHYSIOLOGY 287 (3): F460-F468 SEP 2004 

Hoek K, Rimm DL, Williams KR, et al.
Expression profiling reveals novel pathways in the transformation of melanocytes to melanomas 
CANCER RESEARCH 64 (15): 5270-5282 AUG 1 2004 

Saleem A, Dutta J, Malegaonkar D, et al.
The topoisomerase I- and p53-binding protein topors is differentially expressed in normal and malignant human tissues and may function as a tumor suppressor 
ONCOGENE 23 (31): 5293-5300 JUL 8 2004 

Kalisz S, Purugganan MD
Epialleles via DNA methylation: consequences for plant evolution 
TRENDS IN ECOLOGY & EVOLUTION 19 (6): 309-314 JUN 2004 

Boyd VL, Zon G
Bisulfite conversion of genomic DNA for methylation analysis: protocol simplification with higher recovery applicable to limited samples and increased throughput 
ANALYTICAL BIOCHEMISTRY 326 (2): 278-280 MAR 15 2004 

Wolff L, Garin MT, Koller R, et al.
Hypermethylation of the Ink4b locus in murine myeloid leukemia and increased susceptibility to leukemia in p15(Ink4b)-defficient mice 
ONCOGENE 22 (58): 9265-9274 DEC 18 2003 

Shteper PJ, Zcharia E, Ashhab Y, et al.
Role of promoter methylation in regulation of the mammalian heparanase gene 
ONCOGENE 22 (49): 7737-7749 OCT 30 2003 

Wang GL, Wei LN, Loh HH
Transcriptional regulation of mouse delta-opioid receptor gene by CpG methylation - Involvement of Sp3 and A methyl-CpG-binding protein, MBD2, in transcriptional repression of mouse delta-opioid receptor gene in Neuro2A cells 
JOURNAL OF BIOLOGICAL CHEMISTRY 278 (42): 40550-40556 OCT 17 2003 

Sasaki M, Anast J, Bassett W, et al.
Bisulfite conversion-specific and methylation-specific PCR: a sensitive technique for accurate evaluation of CpG methylation 
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 309 (2): 305-309 SEP 19 2003 

Dahl C, Guldberg P
DNA methylation analysis techniques 
BIOGERONTOLOGY 4 (4): 233-250 2003 

Laird PW
The power and the promise of DNA methylation markers 
NATURE REVIEWS CANCER 3 (4): 253-266 APR 2003