Daniel J. Weisenberger
Daniel J. Weisenberger
Assistant Professor
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Department of Biochemistry & Molecular Biology
University of Southern California
USA

Education

1996-1999 Graduate Research Assistant Wayne State University, Department of Chemistry, Detroit, Michigan
2000-2003 Post-doctoral Fellow University of Southern California, USC/Norris Comprehensive Cancer Center, Los Angeles, CA
2003-2006 Research Associate University of Southern California, USC/Norris Comprehensive Cancer Center, Los Angeles, CA

 

Biography

Daniel J. Weisenberger,  is an Assistant Professor of Research Biochemistry & Molecular Biology. School, Keck School of Medicine of USC. Department Department of Biochemistry and Molecular Biology. He published many papers in National and International Journals.

Research Interest

DNA methylation, epigenetics, genomics, gene regulation, chromatin

 

Professional Activities:

1996 The Esther and Stanley Kirschner Award for Excellence as a Teaching,
Assistant in General Chemistry, Wayne State University, Detroit, MI
1999 Awarded Best Oral Presentation, 1st Annual Chemistry Department
Graduate Student Symposium, Wayne State University, Detroit, MI
2000-2002 Awarded a T32 NIH-sponsored post-doctoral training grant position.

 

Publications

  1. Daniel J. Weisenberger and Louis J. Romano, "Cytosine Methylation in a CpG Sequence Leads to Enhanced Reactivity with Benzo[a]pyrene That Correlates With a Structural Change" (1999) J Biol Chem 274:23948- 23955.
  2. Mihaela Velicescu, Daniel J. Weisenberger, Felicidad A. Gonzales, Carvell T. Nguyen, and Peter A. Jones, "Cell Division is Required for de novo Methylation of CpG Islands in bladder cancer cells" (2002) Cancer Res 62:2378-2384.
  3. Daniel J. Weisenberger, Mihaela Velicescu, Miguel Angel Preciado, Felicidad A. Gonzales, Gangning Liang, and Peter A. Jones, "Identification and characterization of alternatively spliced variants of DNA methyltransferase 3a in mammalian cells" (2002) Gene 298:91-99.
  4. Carvell T. Nguyen, Daniel J. Weisenberger, Mihaela Velicescu, Felicidad Gonzales, Joy C.Y. Lin, Gangning Liang and Peter A. Jones, "Histone H3 lysine 9 methylation in human cancer cells" (2002) Cancer Res 62:6456-6461.
  5. Jonathan C. Cheng, Daniel J. Weisenberger, Felicidad A. Gonzales, Gangning Liang, Guo-Liang Xu, Ye-Guang Hu, Victor E. Marquez, and Peter A. Jones, “Continuous zebularine treatment effectively sustains demethylation in human bladder cancer cells” (2004) Mol Cell Biol 24:1270-1278.
  6. Daniel J. Weisenberger, Mihaela Velicescu, Jonathan C. Cheng, Gangning Liang, Felicidad A. Gonzales and Peter A. Jones, “Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation” (2004) Mol Cancer Res 2:62-72.
  7. Gangning Liang, Joy Lin Vivian Wei, Christine Yoo, Jonathan C. Cheng, Carvell T. Nguyen, Daniel J. Weisenberger, Gerda Egger, Daiya Takai, Felicidad A. Gonzales, and Peter A. Jones, "Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome" (2004) Proc Natl Acad Sci USA 101:7357-736.
  8. M.G. Friedrich, M.I. Toma, A. Hellstern, K. Pantel, D.J. Weisenberger, J. Noldus and H. Huland, “Comparison of multitarget fluorescence in situ hybridization in urine with other noninvasive tests for detecting bladder cancer,” (2003) BJU Int. 92:911-914.
  9. Jonathan C. Cheng, Christine B. Yoo, Daniel J. Weisenberger, Jody Chuang, Chandra Wozniak, Gangning Liang, Victor E. Marquez, Sheldon Greer, Torben F. Orntoft, Thomas Thykjaer and Peter A. Jones “Preferential Response of Cancer Cells to Zebularine” (2004) Cancer Cell 6:151-158.
  10. Martin G. Friedrich, Daniel J. Weisenberger, Jonathan C. Cheng, Shahin Chandrasoma, Kimberly D. Siegmund, Mark L. Gonzalgo, Marieta I. Toma, Hartwig Huland, Christine Yoo, Yvonne C. Tsai, Peter W. Nichols, Bernard H. Bochner, Peter A. Jones and Gangning Liang, “Detection of Methylated Apoptosis-Associated Genes in Urine Sediments of Bladder Cancer Patients” (2004) Clin Cancer Res 10:7457-7465.
  11. Karen Woodson, Daniel J. Weisenberger, Mihaela Campan, Peter W. Laird, Joseph Tangrea, Arthur Schatzkin and Elaine Lanza, “Gene-Specific Methylation and Subsequent Risk of Colorectal Adenomas Among Participants of the Polyp Prevention Trial” (2005) Cancer Epidemiol Biomarkers Prev 14:1219-1223.
  12. Martin G. Friedrich, Shahin Chandrasoma, Kimberly D. Siegmund, Daniel J. Weisenberger, Jonathan C. Cheng, Marieta I. Toma, Hartwig Huland, Peter A. Jones, and Gangning Liang, “Prognostic Relevance of Methylation Markers in Patients With Non-muscle Invasive Bladder Carcinoma,” (2005) Eur J Cancer 41:2769-2778.
  13. Merhnaz Fatemi, Martha M. Pao, Shinwu Jeong, Einev N. Gal-Yam, Gerda Egger, Daniel J. Weisenberger and Peter A. Jones, “Footprinting of mammalian promoters: use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level,” (2005) Nucleic Acids Res 33:e176.
  14. Daniel J. Weisenberger, Mihaela Campan, Tiffany I. Long, Myungjin Kim, Christian Woods, Emerich Fiala, Melanie Ehrlich and Peter W. Laird, “Analysis of Repetitive Element DNA Methylation by MethyLight,” (2005) Nucleic Acids Res 33:6823-6836.
  15. Shuji Ogino, Mami Cantor, Takako Kawasaki, Mohan Brahmandam, Gregory Kirkner, Daniel J. Weisenberger, Mihaela Campan, Peter W. Laird, Massimo Loda and Charles S. Fuchs, “CpG island methylator phenotype (CIMP) of colorectal cancer is best characterized by quantitative DNA methylation analysis and prospective cohort studies,” (2006) Gut 55:1000-1006.
  16. Melanie Ehrlich, Christian B. Woods, Mimi C. Yu, Louis Dubeau, Fan Yang, Mihaela Campan, Daniel J. Weisenberger, Tiffany I. Long, Byungwoo Youn, Emerich S. Fiala and Peter W. Laird, “Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors,” (2006) Oncogene 25:2636-2645.
  17. Shuji Ogino, Takako Kawasaki, Mohan Brahmandam, Mimi Cantor, Gregory J.Kirkner, Donna Spiegelman, G. Mike Makrigiorgos, Daniel J. Weisenberger, Peter W. Laird, Massimo Loda and Charles S. Fuchs, “Precision and Performance Characteristics of Bisulfite Conversion and Real-Time PCR (MethyLight) for Quantitative DNA Methylation Analysis,” (2006) J Mol Diagn 8:209-217.
  18. Daniel J. Weisenberger, Kimberly D. Siegmund, Mihaela Campan, Joanne Young, Tiffany I. Long, Mark A. Faasse, Gyeong Hoon Kang, Martin Widschwendter, Deborah Weener, Daniel Buchanan, Hoey Koh, Lisa Simms, Melissa Barker, Barbara Leggett, Joan Levine, Myungjin Kim, Amy J. French, Stephen N. Thibodeau, Jeremy Jass, Robert Haile and Peter W. Laird, “CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer,” (2006) Nat Genet 38:787-793.
  19. Martin Widschwendter, Heidi Fiegl, Daniel Egle, Elisabeth Mueller- Holzner, Gilbert Spizzo, Christian Marth, Daniel J. Weisenberger, Mihaela Campan, Joanne Young, Ian Jacobs and Peter W. Laird, “Epigenetic Stem Cell Signature in Cancer,” (2007) Nat Genet 39:157-158.
  20. Kimberly D. Siegmund, Caroline M. Connor, Mihaela Campan, Tiffany I. Long, Daniel J. Weisenberger, Detlev Biniskiewicz, Rudolf Jaenisch, Peter W. Laird and Schahram Akbarian, “DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons,” (2007) PLoS ONE 2:e895.
  21. Gyeong-Hoon Kang, Sun Lee, Nam-Yun Cho, Tasha Gandamihardja, Tiffany I. Long, Daniel J. Weisenberger, Mihaela Campan and Peter W. Laird, “DNA methylation profiles of gastric carcinoma characterized by quantitative DNA methylation analysis,” (2008) Lab Invest 88:161-170.
  22. BL Pike, TC Greiner, X Wang, DD Weisenburger, YH Hsu, G Renaud, TG Wolfsberg, M Kim, DJ Weisenberger, KD Siegmund, W Ye, S Groshen, R Mehrian-Shai, J Delabie, WC Chan, PW Laird and JG Hacia, “DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status,” (2008) Leukemia 22:1035-1043.
  23. Paul P. Anglim, Janice S. Galler, Michael N. Koss, Jeffrey A. Hagen, Sally Turla, Mihaela Campan, Daniel J. Weisenberger, Peter W. Laird, Kimberly D. Siegmund and Ite Laird-Offringa “DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update“ (2008) Mol Cancer 7:62.
  24. Daniel J. Weisenberger, Binh N. Trinh, Mihaela Campan, Shikhar Sharma, Tiffany I. Long, Suchitra Ananthnarayan, Gangning Liang, Francisco J. Esteva, Gabriel N. Hortobagyi, Frank McCormick, Peter A. Jones and Peter W. Laird, “DNA methylation analysis by digital bisulfite sequencing and digital MethyLight,” (2008) Nucleic Acids Res 36:4689- 4698.
  25. Cancer Genome Atlas Research Network: Roger McLendon, Allan Friedman,….,Raju Kucherlapati, Peter W. Laird, Leslie Cope, James G. Herman, Daniel J. Weisenberger, Fei Pan, David Van Den Berg, Leander Van Neste, Yi Joo Me, Kornel E. Schuebel, Stephen B. Baylin,….Jane Peterson and Elizabeth Thomson, “Comprehensive genomic characterization defines human glioblastoma genes and core pathways,” (2008) Nature 455:1061-1068.
  26. Jenny N. Poynter, Kimberly D. Siegmund, Daniel J. Weisenberger, Tiffany I. Long, Stephen N. Thibodeau, Noralene Lindor, Joanne Young, Mark A. Jenkins, John L. Hopper, John A. Baron, Dan Buchanan, Graham Casey, A. Joan Levine, Loic Le Marchand, Steven Gallinger, Bharati Bapat, John D. Potter, Polly A. Newcomb, Robert W. Haile, Peter W. Laird for the Colon Cancer Family Registry Investigators, “Molecular characterization of MSI-H colorectal cancer by MLH1 promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening,” (2008) Cancer Epidemiol Biomarkers Prev 17:3208- 3215.
  27. Mihaela Campan, Daniel J. Weisenberger, Binh N.Trinh and Peter W. Laird, “MethyLight” (2009) Methods Mol Biol 507:325-337.
  28. Kyoung-Jin Sohn, Hyeran Jang, Mihaela Campan, Daniel J. Weisenberger, Jeffrey Dickhout, Yi-Cheng Wang, Robert C. Cho, Zoe Yates, Mark Lucock, En-Pei Chiang, Richard C. Austin, Sang-Woon Choi, Peter W. Laird and Young-In Kim, “The methylenetetrahydrofolate reductase C677T mutation induces cell-specific changes in genomic DNA methylation and uracil misincorporation: A possible molecular basis for the site-specific cancer risk modification,” (2009) Int J Cancer 124:1999-2005.
  29. Benjamin P. Berman, Daniel J. Weisenberger and Peter W. Laird, “Locking in on the human methylome,” (2009) Nat Biotechnol 27:341-342.
  30. Marco M. Boks, Eske M. Derks, Daniel J. Weisenberger, Erik Strengman, Esther Janson, Iris E. Sommer, Rene S. Kahn and Roel A. Ophoff, “The relationship of DNA methylation with age, gender and genotype in twins and healthy controls.” (2009) PLoS ONE 4:e6767.
  31. Hyang-Min Byun, Kimberly D. Siegmund, Fei Pan, Daniel J. Weisenberger, Gary Kanel, Peter W. Laird and Allen S. Yang, “Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns,” (2009) Hum Mol Genet 24:4808-4817.
  32. Toshinori Hinoue, Daniel J. Weisenberger, Fei Pan, Mihaela Campan, Myungjin Kim, Joanne Young, Vicki L. Whitehall, Barbara A. Leggett and Peter W. Laird, “Analysis of the association between CIMP and BRAF(V600E) in colorectal cancer by DNA methylation profiling,” (2009) PLoS ONE 4:e8357.
  33. Andrew E. Teschendorff, Usha Menon, Aleksandra Gentry-Maharaj, Susan J. Ramus, Daniel J. Weisenberger, Hui Shen, Mihaela Campan, Houtan Noushmehr, Christopher G. Bell, A. Peter Maxwell, David A. Savage, Elisabeth Mueller-Holzner, Christian Marth, Gabrijela Kocjan, Simon A. Gayther, Allison Jones, Stephan Beck, Wolfgang Wagner, Peter W. Laird, Ian J. Jacobs and Martin Widschwendter, “Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer,” (2010) Genome Res 20:440-446.
  34. Houtan Noushmehr, Daniel J. Weisenberger, Kristin Diefes, Heidi S. Phillips, Kanan Pujara, Benjamin P. Berman, Fei Pan, Christoper E. Pelloski, Erik P. Sulman, Krishna P. Bhat, Roel G. Verhaak, Katherine A. Hoadley, D. Neil Hayes, Charles M. Perou, Heather K. Schmidt, Li Ding, Richard K. Wilson, David Van Den Berg, Hui Shen, Henrik Bengtsson, Pierre Neuvial, Leslie M. Cope, Jonathan Buckley, James G. Herman, Stephen B. Baylin, Peter W. Laird, Ken Aldape and The Cancer Genome Atlas Research Network, “Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma,” Cancer Cell (2010) 17:510-522.
  35. David Limsui, Robert A. Vierkant, Lori S. Tillmans, Alice H. Wang, Daniel J. Weisenberger, Peter W. Laird, Charles F. Lynch, Kristin E. Anderson, Amy J. French, Robert W. Haile, Lisa J. Harnack, John D. Potter,Susan L. Slager, Thomas C. Smyrk, Stephen N. Thibodeau, James R. Cerhan, Paul J. Limburg, “Cigarette smoking and colorectal cancer risk by molecularly defined subtypes,” J Natl Cancer Inst (2010) 102:1012-1022.
  36. Erika M. Wolff, Yoshitomo Chihara, Fei Pan, Daniel J. Weisenberger, Kimberly D. Siegmund, Kokichi Sugano, Kiyotaka Kawashima, Peter W. Laird, Peter A. Jones and Gangning Liang, “Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue,” (2010) Cancer Res 70:8169-8178.
  37. Kandeleria Rumilla, Karen V. Schowalter, Noralene M. Lindor, Brittany C. Thomas, Kara A. Mensink, Steven Gallinger, Spring Holter, Polly A. Newcomb, John D. Potter, Mark A. Jenkins, John L. Hopper, Tiffany I. Long, Daniel J. Weisenberger, Robert W. Haile, Graham Casey, Peter W. Laird, Loic Le Marchand and Stephen N. Thibodeau, “Frequency of Deletions of EPCAM (TACSTD1) in MSH2-associated Lynch Syndrome Cases, (2011) J Mol Diag 13:93-99.
  38. Toshinori Hinuoe, Daniel J. Weisenberger, Christopher C.P. Lange, Hui Shen, Hyang-Min Byun, David Van Den Berg, Simeen Malik, Fei Pan, Houtan Noushmehr, Cornelis M. van Dijk, Rob A.E.M. Tollenaar and Peter W. Laird, “Genome-scale analysis of aberrant DNA methylation in colorectal cancer,” (2012) Genome Res 22:271-282.
  39. The Cancer Genome Atlas Research Network: Bell D, …Laird PW, Cope L, Herman JG, Shen H, Weisenberger DJ, Noushmehr, H, Pan, F, Triche Jr., T, …, ”Integrated genomic analyses of ovarian carcinoma,” (2011) Nature 474:609-615.
  40. Cyril Rakovski, Daniel J. Weisenberger, Paul Marjoram, Peter W. Laird and Kimberly D. Siegmund, “Modeling measurement error in tumor characterization studies,” (2011) BMC Bioinformatics 12:284. 9
  41. Anthony A. Razzak, Amy S. Oxentenko, Robert A. Vierkant, Lori S. Tillmans, Alice H. Wang, Daniel J. Weisenberger, Peter W. Laird, Charles F. Lynch, Kristin E. Anderson, Amy J. French, Robert W. Haile, Lisa J. Harnack, Susan L. Slager, Thomas C. Smyrk, Stephen N. Thibodeau and Paul J. Limburg, “Alcohol intake and colorectal cancer risk by molecularly defined subtypes in a prospective study of older women”, (2011) Cancer Prev Res 4:2035-2043.
  42. David Limsui, Robert A. Vierkant, Lori S. Tillmans, Alice H. Wang, Daniel J. Weisenberger, Peter W. Laird, Charles F. Lynch, Kristin E. Anderson, Amy J. French, Robert W. Haile, Lisa J. Harnack, John D. Potter, Susan L. Slager, Thomas C. Smyrk, Stephen N. Thibodeau, James R. Cerhan and Paul J. Limburg, “Postmenopausal hormone therapy and colorectal cancer risk by molecularly defined subtypes among older women”, (2011) Gut doi:10.1136/gutjnl-2011-300719.
  43. Xinhui Wang, Gyeong Hoon Kang, Mihaela Campan, Daniel J. Weisenberger, Tiffany I. Long, Wendy Cozen, Leslie Bernstein, Anna H. Wu, Kimberly D. Siegmund, Darryl Shibata and Peter W. Laird, “Epigenetics subgroups of esophageal and gastric adenocarcinoma with differential GATA5 DNA methylation associated with clinical and lifestyle factors”, (2011) PLoS ONE 6:e25985.
  44. The International Stem Cell Initiative, Amps K, Andrews PW, Anyfantis G, Armstrong L, Avery S, Baharvand H, Baker J, Baker D, Munoz MB, Beil S, Benvenisty N, Ben-Yosef D, Biancotti JC, Bosman A, Brena RM, Brison D, Caisander G, Camarasa MV, Chen J, Chiao E, Choi YM, Choo AB, Collins D, Colman A, Crook JM, Daley GQ, Dalton A, De Sousa PA, Denning C, Downie J, Dvorak P, Montgomery KD, Feki A, Ford A, Fox V, Fraga AM, Frumkin T, Ge L, Gokhale PJ, Golan-Lev T, Gourabi H, Gropp M, Guangxiu L, Hampl A, Harron K, Healy L, Herath W, Holm F, Hovatta O, Hyllner J, Inamdar MS, Irwanto AK, Ishii T, Jaconi M, Jin Y, Kimber S, Kiselev S, Knowles BB, Kopper O, Kukharenko V, Kuliev A, Lagarkova MA, Laird PW, Lako M, Laslett AL, Lavon N, Lee DR, Lee JE, Li C, Lim LS, Ludwig TE, Ma Y, Maltby E, Mateizel I, Mayshar Y, Mileikovsky M, Minger SL, Miyazaki T, Moon SY, Moore H, Mummery C, Nagy A, Nakatsuji N, Narwani K, Oh SK, Oh SK, Olson C, Otonkoski T, Pan F, Park IH, Pells S, Pera MF, Pereira LV, Qi O, Raj GS, Reubinoff B, Robins A, Robson P, Rossant J, Salekdeh GH, Schulz TC, Sermon K, Mohamed JS, Shen H, Sherrer E, Sidhu K, Sivarajah S, Skottman H, Spits C, Stacey GN, Strehl R, Strelchenko N, Suemori H, Sun B, Suuronen R, Takahashi K, Tuuri T, Venu P, Verlinsky Y, Oostwaard DW, Weisenberger DJ, Wu Y, Yamanaka S, Young L and Zhou Q “Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage”, (2011) Nat Biotechnol 29:1132- 1144.10
  45. Benjamin P. Berman, Daniel J. Weisenberger, Joseph F. Aman, Toshinori Hinoue, Zachary Ramjan, Yaping Liu, Houtan Noushmehr, Christopher C.P. Lange, Corneils M. van Dijk, Rob A.E.M. Tollenaar, David Van Den Berg and Peter W. Laird, “Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains”, (2011) Nat Genet 44:40-46.
  46. A. Joan Levine, Aung Ko Win, Daniel D. Buchanan, Mark A. Jenkins, John Baron, Joanne P. Young, Tiffany I. Long, Daniel J. Weisenberger, Peter W. Laird, Rebecca L. McCall, David J. Duggan, and Robert W. Haile, “Cancer risks for the relatives of colorectal cancer cases with a methylated MLH1 promoter region: data from the Colorectal Cancer Family Registry”, (2012) Cancer Prev Res 5:328-335.
  47. Lenora W.M. Loo, Iona Cheng, Maarit Tiirikainen, Annette Lum-Jones, Ann Seifried, Lucas M. Dunklee, James M. Church, Robert Gryfe, Daniel J. Weisenberger, Robert W. Haile, Steven Gallinger, David J. Duggan, Stephen N. Thibodeau, Graham Casey, Loic Le Marchand, “cis- Expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue,” (2012) PLoS ONE 7:e30477.
  48. Hariharan Easwaran, Sarah E. Johnstone, Leander Van Neste, Joyce Ohm, Tim Mosbruger, Qiuju Wang, Martin J. Aryee, Patrick Joyce, Nita Ahuja, Dan Weisenberger, Eric Collisson, Jingchun Zhu, Srinivasan Yegnasubramanian, William Matsui and Stephen B. Baylin, “A DNA hypermethylation module for the stem/progenitor cell signature of cancer,” (2012) Genome Res 22:837-849.
  49. The Cancer Genome Atlas Research Network: Donna N. Muzny, Matthew N. Bainbridge, … Toshinori Hinoue, Daniel J. Weisenberger, Dennis T. Maglinte, … ”Comprehensive molecular characterization of human colon and rectal cancer,” (2012) Nature 487:330-337.
  50. The Cancer Genome Atlas Research Network: Peter S. Hammerman, Michael S. Lawrence, … Leslie Cope, Ludmila Danilova, Daniel J. Weisenberger, Dennis T. Maglinte, …”Comprehensive genomic characterization of squamous cell lung cancers,” (2012) Nature 489:519- 525.
  51. The Cancer Genome Atlas Research Network: Daniel C. Koboldt, Robert S. Fulton, … Simeen Malik, Swapna Mahurkar, Hui Shen, Daniel J.Weisenberger, Timothy Triche Jr., … “Comprehensive molecular portraits of human breast tumors,” (2012) Nature 490:61-70.
  52. Anthony A. Razzak, Amy S. Oxentenko, Robert A. Vierkant, Lori S. Tilmans, Alice H. Wang, Daniel J. Weisenberger, Peter W. Laird, Charles F. Lynch, Kristin E. Anderson, Amy J. French, Robert W. Haile, Lisa J. Harnack, John D. Potter, Susan L. Slagel, Thomas C. Smyrk, Stephen N. Thibodeau, James R. Cerhan and Paul J. Limburg PJ, “Associations between intake of folate and related micronutrients with molecularly defined colorectal cancer risks in the Iowa Women’s Health Study,” (2012) Nutr Cancer 64:899-910.
  53. Christopher P.E. Lange, Mihaela Campan, Toshinori Hinoue, Roderick F. Schmitz, Andrea E. van der Meulen-de Jong, Hilde Slingerland, Peter J.M.J. Kok, Cornelis M. van Dijk, Daniel J. Weisenberger, Hui Shen, Robert A.E.M Tollenaar and Peter W. Laird, “Genome-scale discovery of DNA-Methylation biomarkers for blood-based detection of colorectal cancer,” (2012) PLoS ONE 7:e50266.
  54. Lenora W.M. Woo, Maarit Tiirikainen, Iona Cheng, Annette Lum-Jones, Ann Seifreid, James M. Church, Robert Gryfe, Daniel J. Weisenberger, Noralene M. Lindor, Steven Gallinger, Robert W. Haile, David J. Duggan, Stephen N. Thibodeau, Graham Casey, and Loic LeMarchand, “Integrated analysis of genome-wide copy number alterations and gene expression in microsatellite stable, CpG island methyator phenotype-negative colon cancer,” (2013) Genes Chrom Cancer 52:450-466.
  55. Fan Gao, Lingling Shi, Jonathan Russin, Liyun Zeng, Xiao Chang, Shuhan He, Thomas C. Chen, Steven L. Giannotta, Daniel J. Weisenberger, Gabriel Zada, William J. Mack and Kai Wang, “DNA methylation in the malignant transformation of meningiomas,” (2013) PLoS ONE 8:e54114.
  56. Arkadiusz Gertych, Hin Ho Oh, Koija A. Wawrowsky, Daniel J. Weisenberger and Jian Tajbakhsh, “3-D DNA methylation profiles correlate with cytotoxicity levels in prostate and liver cancer cell models,” (2013) BMC Pharmacology and Toxicology 14:11.
  57. Timothy J. Triche, Jr., Daniel J. Weisenberger, David Van Den Berg, Peter W. Laird and Kimberly D. Siegmund, “Low-level processing of Illumina Infinium DNA methylation BeadArrays,” (2013) Nucleic Acids Res 41:e90.
  58. The Cancer Genome Atlas Research Network, Timothy J. Ley, …. Phillip H. Lai, Hui Shen, David J. Van Den Berg, Daniel J. Weisenberger, …. and Richard K. Wilson, “Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia,” (2013) N Engl J Med 368:2059-2074.
  59. The Cancer Genome Atlas Research Network, Cyriac Kandoth, Nicolas Schultz, …. Moiz S. Bootwalla, Phillip H. Lai, Timothy J. Triche, Jr., David 12 J Van Den Berg, Daniel J. Weisenberger, Peter W. Laird, … Bradley A. Ozenberger and Heidi J. Sofia, “Integrated gemomic characterization of endometrial carcinoma,” (2013) Nature 497:67-73.
  60. N. Jewel Samadder, Robert A. Vierkant, Lori S. Tillmans, Alice H. Wang, Daniel J. Weisenberger, Peter W. Laird, Charles F. Lynch, Kristin E. Anderson, Amy J. French, Robert W. Haile, John D. Potter, Susan L. Slager, Thomas C. Smyrk, Stephen N. Thibodeau, James R. Cerhan and Paul J. Limburg, “Associations between colorectal cancer molecular markers and pathways with clinicopathologic features in older women,” (2013) Gastroenterology 145:348-356.
  61. The Cancer Genome Atlas Research Network, Chad J. Creighton, Margaret Morgan, … Peter Park, Hui Shen, Timothy J. Triche, Jr., Daniel J. Weisenberger, Phillip H. Lai, … Bradley A. Ozenberger and Heidi J. Sofia, “Comprehensive molecular characterization of clear cell renal carcinoma,” (2013) Nature 499:43-49.
  62. In-Seon Choi, Kevin Yu, Jayoung Kim, Erika De Guzman, Daniel J. Weisenberger, Shirley Oghamian, Hee Ju Kim, Kyung Hwa Lee, Cindy Carroll, Binh N. Trinh, Myungjin Kim, Sahar Houshdaran, Peter W. Laird, Peter A. Jones, David A. Warburton, Gangning Liang and Chester J. Koh, “Alterations in deoxyribonucleic acid (DNA) methylation patterns of Calca, Timp3, Mmp2 and Igfr2 are associated with chronic cystitis in a cyclophosphamide-induced mouse model,” (2013) Urology 82:253.e9- 253.e15.
  63. The Cancer Genome Atlas Research Network, John N. Weinstein, Eric A. Collisson, … Toshinori Hinoue, Peter W. Laird, Suhn K. Rhie, Hui Shen, Timothy J. Triche, Jr., Daniel J. Weisenberger, Scott L. Carter, … Teresia Kling and Jose Sanchez, “The Cancer Genome Atlas pan-cancer analysis project,” (2013) Nat Genet 45:1113-1120.
  64. Cameron W. Brennan, Roel G. Verhaak, Aaron McKenna, … Greg Foltz, Jerome Lyers, Daniel J. Weisenberger, Robert Penny, … Gad Getz, Lynda Chin and TCGA Research Network, “The somatic genomic landscape of glioblastoma,” (2013) Cell 155:462-477.
  65. John Wrangle, Wei Wang, Alexander Koch, Hariharan Easwaran, Helai P. Mohammad, Frank Vendetti, Wim VanCriekings, Timothy DeMeyer, Zhenqzong Du, Princy Parsana, Kristen Rogers, Ray-Whay Yen, Cynthia Zanhow, Janis M. Taube, Julie R. Brahmer, Scott S. Tykodi, Keith Easton, Richard D. Carvajal, Peter A. Jones, Peter W. Laird, Daniel J. Weisenberger, Salina Tsai, Rosalyn A. Juergens, Suzanne L. Topalian, Charles M. Rudin, Malcolm V. Brock, Drew Pardoll and Stephen B. Baylin, 13 “Alterations of immune response of non-small cell lung cancer with azacytidine,” (2013) Oncotarget 4:11.
  66. Xiao Chang, Lingling Shi, Fan Gao, Jonathan Russin, Kiyun Zeng, Shuhan He, Thomas C. Chen, Steven L. Gianotta, Daniel J. Weisenberger, Gabriel Zada, Kai Wang and William J. Mack, “Genomic and transcriptome analysis revealing and oncogenic functional module in meningiomas,” (2013) Neurosurg Focus 35:E3.
  67. Daniel J. Weisenberger, “Characterizing DNA methylation alterations from The Cancer Genome Atlas,” (2014) J Clin Invest 124:17-23.
  68. John N. Weinstein, Rehan Akbani, …, Phillip H. Lai, David J. Van Den Berg, Daniel J. Weisenberger, … , and The Cancer Genome Atlas Research Network, “Comprehensive molecular characterization of urothelial bladder carcinoma,” (2014) Nature 507:315-322.
  69. Chao Ling, Matthew Pease, Lingling Shi, Vasu Punj, Mark S. Shiroishi, Deborah Commins, Daniel J. Weisenberger, Kai Wang and Gabriel Zada, “A pilot genome-scale profiling of DNA methylation in sporadic pituitary macroadenomas: association with tumor invasion and histopathological subtypes,” (2014) PLoS ONE 9:e96178.
  70. Adam J. Bass, Vesteinn Thorsson, … , Toshinori Hinoue, Peter W. Laird, Hui Shen, Daniel J. Weisenberger, Moiz S. Bootwalla, Phillip H. Lai, … , and The Cancer Genome Atlas Research Network, “Comprehensive molecular characterization of gastric adenocarcinoma,” (2014) Nature doi:10.1038/nature13480.
  71. Eric A. Collisson, Barry S. Taylor, … , Daniel J. Weisenberger, Peter W. Laird, Dennis T. Maglinte, Phillip H. Lai, …, and The Cancer Genome Atlas Network, “Comprehensive molecular profiling of lung adenocarcinoma,” (2014) Nature 511, 543-550.
  72. Katherine A. Hoadley, Christina Yau, Denise M. Wolf, …, Eric A. Collison, The Cancer Genome Atlas Research Network (…, Nils Weinhold, Daniel J. Weisenberger, Michael C. Wendl,….), “Analysis of 12 cancer types reveals molecular classification within and across tissues of origin,” (2014) Cell 158:929-944.
  73. Caleb F. Davis, Christopher J. Ricketts, Min Wang, … , Ari Hakimi, The Cancer Genome Atlas Research Network (…, Charles M. Perou, Daniel J. Weisenberger, Moiz S. Bootwalla, …), Lynda Chin, … Richard A. Gibbs, W. Kimryn Rathmell and Chad J. Creighton, “The somatic genomic landscape of chromophobe renal cell carcinoma,” (2014) Cancer Cell 26:319-330. 14
  74. Amanda I. Phipps, Paul J. Limburg, John A. Baron, Andrea N. Burnett- Hartman, Daniel J. Weisenberger, Peter W. Laird, Frank A. Sinicrope, Christophe, Rosty, Daniel D. Buchanan, John D. Potter and Polly A. Newcomb, “Association between molecular subtypes of colorectal cancer and patient survival,” (2014) Gastroenterology 148:77-82.
  75. Michael Parfenov, Chandra Sekhar Pedamallu, …, Raju Kucherlapati and the Cancer Cenome Atlas Research Network (…, Timothy J. Triche, Jr., Daniel J. Weisenberger, David J. Van Den Berg, …), “Characterization of HPV and host genome interactions in primary head and neck cancers,” (2014) Proc Natl Acad Sci U.S.A. 111:15544-15549.
  76. The Cancer Genome Atlas Research Network: Nisha Agrawal, Rehan Akbani, …, John N. Weinstein, Daniel J. Weisenberger, David Wheeler, … , Erik Zmuda and Lihau Zou, “Integrated genomic characterization of papillary thyroid carcinoma,” (2014) Cell 159:676-690.
  77. Sung-Eun Kim, Toshinori Hinoue, Michael S. Kim, Kyoung-Jin Sohn, Robert C. Cho, Peter D. Cole, Daniel J. Weisenberger, Peter W. Laird and Young-In Kim, “γ-Glutamyl hydrolase modulation significantly increases global and gene-specific DNA methylation and gene expression in human colon and breast cancer cells,” (2015) Genes Nutr 10:444.
  78. Daniel J. Weisenberger, A. Joan Levine, Tiffany I. Long, Daniel D. Buchanan, Rhiannon Walters, Mark Clendenning, Christophe Rosty, Amit D. Joshi, Mariana C. Stern, Loic Le Marchand, Noralene M. Lindor, Darshana Daftary, Steven Gallinger, Teresa Selander, Bharati Bapat, Polly A. Newcomb, Peter T. Campbell, Graham Casey, Dennis J. Ahnen, John A. Baron, Robert W. Haile, John L. Hopper, Joanne P. Young, Peter W. Laird and Kimberly D. Siegmund for the Colon Cancer Family Registry, “Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family history,” (2015) Cancer Epidemiol Biomark Prev 24:512-519.
  79. The Cancer Genome Atlas Network, … Michael S. Lawrence, Carrie Sougnez, … , Timothy Triche, Jr., Daniel J. Weisenberger, David J. Van Den Berg, … , Michelle Pham and Wendell G. Yarbrough, “Comprehensive genomic characterization of head and neck squamous cell carcinomas,” (2015) Nature 517:576-582.
  80. The Cancer Genome Atlas Research Network, Daniel J. Brat, Roel G. Verhaak, …, Umadevi Veluvolu, Scot Waring, Daniel J. Weisenberger, Matthew D. Wilkerson, Tina Wong, … , Jonna L. Grimsby, Amie J. Radenbaugh and Jianan Zhang, “Comprehensive, integrative genomic

 

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