Cancer Epigenetics

The Laird Laboratory’s goal is to develop a detailed understanding of the molecular basis of human disease, with a particular emphasis on the role of epigenetics in cancer. Cancer often is considered to have a primarily genetic basis, with contributions from germline variations in risk and somatically acquired mutations, rearrangements, and copy number alterations. However, it is clear that non-genetic mechanisms can exert a powerful influence on cellular phenotype, as evidenced by the marked diversity of cell types within the human body, virtually all of which contain an identical genetic code. This is accomplished by differential gene expression controlled by tissue-specific transcription factors and variations in chromatin packaging and modification, which provides stable phenotypic states governed by epigenetic — not genetic — mechanisms. It seems intrinsically likely that an opportunistic disease such as cancer would take advantage of such a potent mediator of cellular phenotype. The Laird Laboratory is dedicated to understanding how epigenetic mechanisms contribute to the origins of cancer and how to translate this knowledge into more effective cancer prevention, detection, treatment, and monitoring.

One of the best-understood epigenetic marks is the covalent modification of DNA as 5-methylcytosine in CpG dinucleotides. The Laird team uses a multidisciplinary approach to understand the role of DNA methylation in cancer, relying in part on technology developed by Dr. Laird and colleagues, mechanistic studies in model organisms and cell culture, clinical and translational collaborations, genome scale and bioinformatic analyses, and epidemiological studies. In recent years, the Laird team has participated in the generation and analysis of high-dimensional epigenetic data sets, including the production of all epigenomic data for The Cancer Genome Atlas (TCGA) and the application of next-generation sequencing technology to single-base-pair resolution, whole-genome DNA methylation analysis. The lab leverages this epigenomic data for translational applications and hypothesis testing in animal models. A major focus of the Laird Laboratory is to develop mouse models for investigating epigenetic mechanisms and drivers of cancer, and to develop novel strategies for single-cell epigenomic analysis.

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  • 121 peer-reviewed papers published in 2023
  • 62 peer-reviewed papers published in high-impact journals in 2023
  • 55 clinical trials launched to date

Peter W. Laird, Ph.D.

Professor, Department of Epigenetics; Peter and Emajean Cook Endowed Chair in Epigenetics

Areas of Expertise

Cancer epigenomics, experimental models of cancer epigenetics, epigenetic characterization of technology, epigenomic bioinformatics, clinical and translational epigenetics


Dr. Laird earned his B.S. and M.S. from the University of Leiden and earned his Ph.D. in 1988 from the University of Amsterdam with Dr. Piet Borst. He completed postdoctoral training in the laboratory of Dr. Anton Berns at the Netherlands Cancer Institute and with Dr. Rudolf Jaenisch at the Whitehead Institute for Biomedical Research. Dr. Laird was a faculty member at the University of Southern California (USC) from 1996 to 2014, where he served as professor of surgery, biochemistry and molecular biology; as Skirball-Kenis Professor of Cancer Research; as a program leader in epigenetics and regulation for the Norris Comprehensive Cancer Center; and as director of the USC Epigenome Center. Dr. Laird joined VAI as a professor in September 2014.

For a full list of Dr. Laird’s publications, please visit PubMed.

Zhou W, Johnson BK, Morrison J, Beddows I, Eapen J, Katsman E, Semwal A, Habib W, Heo L, Laird PW, Berman B, Triche T, Shen H. 2024. BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studiesNuc Acids Res 52(6):e32.

Piras IS, Brokaw D, Kong Y, Weisenberger DJ, Krate J, Delvaux E, Mahurkar S, Blattler A, Siegmund KD, Sue L, Serrano GE, Beach TG, Laird PW, Huentelman MJ, Coleman PD. 2023. Integrated DNA methylation/rna profiling in middle temporal gyrus of Alzheimer’s disease. Cell Mol Neurobiol 43(5):2289–2307.

Miller AL, Perurena N, Gardner A, Hinoue T, Loi P, Laird PW, Cichowski K. 2023. DAP2IP is a bifunctional tumor suppressor that regulates wildtype RAS and inflammatory cascades in KRAS mutant colon cancerCancer Res 83(11):1800–1814.

Laird PW. 2022. How epigenomics broke the mold: An interview with Peter W. Laird. Epigenomics. 14(6):303–308.

Roh W, Geffen Y, Cha H, Miller M, Anand S, Kim J, Heiman DI, Gainor JF, Laird PW, Cherniak AD, Ock C-Y, Lee SH, Getz G. 2022. High-resolution profiling of lung adenocarcinoma identifies expression subtypes with specific biomarkers and clinically relevant vulnerabilities. Cancer Res 82(21):3917–3931.

Garcia-Recio et al., Hinoue T#, Wheeler GL#, Kelly BJ#, Garrido-Castro AC# … Lee AV*, Balko JM*, Hoadley KA*, Laird PW*, Mardis AR*, King TA*, AURORA US Network, Perou CM*. 2022. Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis. Nat Can 4:128–147.
* These authors jointly supervised this work
# These authors contributed equally

Endicott JL, Nolte PA, Shen H, Laird PW. 2022. Cell division drives DNA methylation loss in late-replicating domains in primary human cellsNat Comm 13:6659.

Chambwe N, Sayaman RW, Hu D, Huntsman, The Cancer Genome Atlas Network*, Kemal A, Caesar-Johnson S, Zenklusen JC, Ziv E, Beroukim R, Cherniack AD. 2022. Analysis of germline-driven ancestry-associated gene expression in cancers. STAR Protoc 3(3).
*Dr. Laird is a member of The Cancer Genome Atlas Network

Zhou W, Hinoue T, Barnes B, Mitchell O, Iqbal W, Lee SM, Foy KK, Lee KH, Moyer EJ, VanderArk A, Koeman JM, Ding W, Kalkat M, Spix NJ, Eagleson B, Pospisilik JA, Szabó PE, Bartolomei M, Vander Schaaf NA, Kang L, Wiseman AK, Jones PA, Krawczyk CM, Adams M, Porecha R, Chen BH, Shen H, Laird PW. 2022. DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse. Cell Genom 2(7):100144.

*Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, . . ., Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, CGAR Network, Meyerson M, Govindan R,  Imielinski M. 2021. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathwayCell Rep 34(5):108707.

*Conley BA … Shen H, Laird PW, Esteller M, Miller V, Johnson A, Edmondson EF, Goiordano TJ, Kim B, Ivy SP. 2021. The Exceptional Responders Initiative: feasibility of a National Cancer Institute pilot studyJ Natl Cancer Inst 113(1):27–37.

*Wheeler DA … Laird PW … Conley BA, Ivy SP, Staudt LM. 2021. Molecular features of cancers exhibiting exceptional responses to treatmentCan Cell 39(1):38–53.e37.

Carrot-Zhang J, Han S, Zhou W, Damrauer JS, Kemal A, Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R. 2021. Analytical protocol to identify local ancestry-associated molecular features in cancerSTAR Protoc 2(4):100766.
Dr. Laird is a member of the Cancer Genome Atlas Analysis Network 

Carrot-Zhang J, … Laird PW… Cancer Genome Atlas Research Network, Cherniack AD, Beroukhim R. 2020. Comprehensive analysis of genetic ancestry and its molecular correlates in cancerCan Cell 37(5):639–654.e636.

Coyne GOS, … Laird PW, Ferry-Galow KV, Kinders RJ, Parchment RE, Doroshow JH, Chen AP. 2020. Phase I trial of TRC102 (methoxyamine HCl) in combination with temozolomide in patients with relapsed solid tumors and lymphomas. Oncotarget 11(44):3959–3971.

Haider S, Tyekucheva S, Prandi S, Fox NS, Ahn J, Xu AW, Pantazi A, Park PJ, Laird PW, Sander C, Wang W, Demichelis F, Loda M, Boutros PC and CGAR Network. 2020. Systematic assessment of tumor purity and its clinical implicationsJCO Precision Oncol 4:995–1005.

Gao GF, … Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tamuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Genomic Data Analysis Network, Liang H, Noble MS. 2019. Before and after: comparison of legacy and harmonized TCGA Genomic Data Commons’ dataCell Sys 9(1):24–34.e10.

Liang W, Zhao Y, Huang W, Gao Y, Xu W, Tao J, Yang M, Li L, Ping W, Shen H, Fu X, Chen Z, Laird PW, Cai X, Fan JB, He J. 2019. Non-invasive diagnosis of early-stage lung cancer using high-throughput targeted DNA methylation sequencing of circulating tumor DNA (ctDNA)Theranostics 9(7):2056–2070.

Lynn BCD, Bodelon C, Pfeiffer RM, Yang HP, Yang H, Lee M, Laird PW, Campan M, Weisenberger DJ, Murphy J, Sampson JN, Browne EP, Anderton DL, Sherman ME, Arcaro KF, Gierach GL. 2019. Differences in genome-wide DNA methylation profiles in breast milk by race and lactation duration. Cancer Prev Res 12(11): 781–790.

Vander Schaaf NA, Oghamian S, Park JA, Kang L, Laird PW, Lee KH. 2019. In vivo application of the REMOTE-control system for the manipulation of endogenous gene expressionJ Visualized Exp145.

Hoadley KA, Yau C, Hinoue T…Laird PW. 2018. Cell-of-origin patterns molecular classification of 10,000 tumors from 33 types of cancerCell 173(2):291–304.
*One of three theme papers for the 
PanCancer Atlas

Sanchez-Vega F, Mina M, Armenia J…Zhou W, Shen H, Laird PW…Schultz N. 2018. Oncogenic signaling pathways in The Cancer Genome Atlas. Cell 173(2):321–337.
*One of three theme papers for the PanCancer Atlas

Malta TM, Sokolov A…Laird PW, Noushmehr H, Wizernowicz M. 2018. Machine learning identifies stemness features associated with oncogenic dedifferentiationCell 173(2):338–354.

Liu Y, Sethi NS, Hinoue T, Schneider BG…Thorsson V, Bass AJ, Laird PW. 2018. Comparative molecular analysis of gastrointestinal adenocarcinomasCan Cell 33(4):721–735.

Berger AC, Korkut A, Kanchi RS…Fan H, Shen H…Akbani R. 2018. A comprehensive pan-cancer molecular study of gynecological and breast cancers. Can Cell 33(4):690–705.

Knijnenburg T, Wang L, Zimmerman MT, Chambwe N…Fan H, Shen H…Laird PW…Wang C. 2018. Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome AtlasCell Rep 23(1):239–254.

Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C…Shen H…Laird PW…Waes CV. 2018. Genomic, pathway network, and immunologic features distinguishing squamous carcinomasCell Rep 23(1):194–212.

Ricketts CJ…Fan H…Shen H…Laird PW…Spellman P, Rathmell K, Linehan WM. 2018. Comprehensive molecular characterization of renal cell carcinoma. Cell Rep 23(1):313–326.

Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. 2018. DNA methylation loss in late-replicating domains is linked to mitotic cell divisionNat Gen 50:591–602.

The Cancer Genome Atlas Research Network. 2017. Comprehensive and integrative genomic characterization of hepatocellular carcinomaCell 169(7):1327–1341.

Farshidfar F…The Cancer Genome Atlas Research Network…Laird PW…Andersen JB, Bardeesy N, Roberts LR, Kwong LN. 2017. Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profilesCell Rep 18(11):2780–2794.

Cherniack AD, Shen H…Laird PW…The Cancer Genome Atlas Research Network..Akbani R, Levine DA. 2017. Integrated molecular characterization of uterine carcinomaCan Cell 31(3):411–423.

The Cancer Genome Atlas Research Network. 2017. Integrated genomic characterization of oesophageal carcinomaNature 541:169–175.

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. 2015. Comprehensive molecular portraits of invasive lobular breast cancerCell 163(2):506–519.
*Laird PW is one of 126 collaborators.

Cancer Genome Atlas Network. 2015. Genomic classification of cutaneous melanomaCell 161(7):1681–1696

Kim H, Zheng S, Amini SA, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. 2015. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolutionGenome Res 25(3): 316–327.

Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. 2015. Inferring regulatory element landscapes and transcription factor networks from cancer methylomesGenome Biol 16:105.

Kim SE, Hinoue T, Kim MS, Sohn KJ, Cho RC, Cole PD, Weisenberger DJ, Laird PW, Kim YI. 2015. γ-Glutamyl hydrolase modulation significantly influences global and gene-specific DNA methylation and gene expression in human colon and breast cancer cellsGenes Nutr 10(1):444.

Weisenberger DJ, Levine AJ, Long TI, Buchanan DD, Walters R, Clendenning M, Rosty C, Joshi AD, Stern MC, Le Marchand L, Lindor NM, Daftary D, Gallinger S, Selander T, Bapat B, Newcomb PA, Campbell PT, Casey G, Ahnen DJ, Baron JA, Haile RW, Hopper JL, Young JP, Laird PW, Siegmund KD; for the Colon Cancer Family Registry. 2015. Association of the colorectal CpG island methylator phenotype with molecular features, risk factors, and family historyCancer Epidemiol Biomarkers Prev 24(3):512–519.

Cancer Genome Atlas Network. 2015. Comprehensive genomic characterization of head and neck squamous cell carcinomasNature 517(7536):576–582.
*Laird PW is one of 348 co-authors

Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RG. 2015. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolutionGenome Res 25(3):316–327.

Phipps AI, Limburg PJ, Baron JA, Burnett-Hartman AN, Weisenberger DJ, Laird PW, Sinicrope FA, Rosty C, Buchanan DD, Potter JD, Newcomb PA. 2014. Association between molecular subtypes of colorectal cancer and patient survivalGastroenterology 148(1):77–87.

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network*. 2014. Characterization of HPV and host genome interactions in primary head and neck cancersProc Natl Acad Sci USA 111(43):15544–15549.       
*Laird PW is included among 340 collaborators

Cancer Genome Atlas Network*. 2014. Integrated genomic characterization of papillary thyroid carcinomaCell 159(3):676–690.      
*Laird PW is one of 243 co-authors

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of gastric adenocarcinomaNature 513(7517):202–209.
*Laird PW was one of three co-chairs for this project and was one of 315 co-authors as well as a member of the writing team and analysis working group.

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC,  Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ; Cancer Genome Atlas Research Network. 2014. The somatic genomic landscape of chromophobe renal cell carcinomaCancer Cell 26(3):319–330.

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van’t Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. 2014. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of originCell 158(4):929–944.

Cancer Genome Atlas Network. 2014. Comprehensive molecular profiling of lung adenocarcinomaNature 511(7511):543–550.
*Laird PW is one of 383 co-authors and member of the writing team and analysis working group

Knijnenburg TA, Ramsey SA, Berman BP, Kennedy KA, Smit AF, Wessels LF, Laird PW, Aderem A, Shmulevich I. 2014. Multiscale representation of genomic signals.  Nat Methods 11:689–694.

Wang X, Laird PW, Hinoue T, Groshen S, Siegmund KD. 2014. Non-specific filtering of beta-distributed dataBMC Bioinformatics 15:199.

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of urothelial bladder carcinomaNature 507: 315-322.
*Laird PW is one of 366 co-authors and member of the writing team and analysis working group

Kim TM, Laird PW, Park PJ. 2013. The landscape of microsatellite instability in colorectal and endometrial cancer genomesCell 155(4):858–868.

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O’Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network. 2013. The somatic genomic landscape of glioblastomaCell 155(2):462–477.

Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W, Treviño V, Shen H, Laird PW, Levine DA, Carter SL, Getz G, Stemke-Hale K, Mills GB, Verhaak RG. 2013. Inferring tumour purity and stromal and immune cell admixture from expression dataNat Commun 4:2612.

Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, Lawrence MS, Zhang CZ, Wala J, Mermel CH, Sougnez C, Gabriel SB, Hernandez B, Shen H, Laird PW, Getz G, Meyerson M, Beroukhim R. 2013. Pan-cancer patterns of somatic copy number alteration. Nat Genet 45(10):1134–1140.    PubMed

Cancer Genome Atlas Research Network; Genome Characterization Center, Chang K, Creighton CJ,…, Hinoue T, Laird PW, Rhie SK, Shen H,…, Sander C, Stuart JM. 2013. The Cancer Genome Atlas pan-cancer analysis projectNat Genet 45(10):1113–1120.

Cancer Genome Atlas Network*. 2013. Comprehensive molecular characterization of clear cell renal cell carcinomaNature 499(7456):43–49.
*Laird PW is one of 346 co-authors and member of the writing team and analysis working group

Cancer Genome Atlas Research Network*. 2013. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemiaN Engl J Med 368(22):2059–2074.    PubMed
*Laird PW is one of 139 co-authors

Shen H, Laird PW. 2013. Interplay between the cancer genome and epigenomeCell 153(1):38-55.

Shen H, Fridley BL, Song H,…, Australian Ovarian Cancer Study Group; Australian Cancer Study,…, Laird PW, Goode EL, Leigh Pearce C. 2013. Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancerNat Commun 4:1628.

Triche TJ Jr, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD. 2013. Low-level processing of Illumina Infinium DNA Methylation BeadArraysNucleic Acids Res 41(7):e90.

Lange CP, Campan M, Hinoue T, Schmitz RF, van der Meulen-de Jong AE, Slingerland H, Kok PJ, van Dijk CM, Weisenberger DJ, Shen H, Tollenaar RA, Laird PW. 2012. Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancerPLoS One 7(11):e50266.

Cancer Genome Atlas Network*. 2012. Comprehensive molecular portraits of human breast tumoursNature 490(7418):61–70.
*Laird PW is one of 357 co-authors

Cancer Genome Atlas Network. 2012. Comprehensive genomic characterization of squamous cell lung cancersNature 489(7417):519–525.
*Laird PW is one of 412 co-authors

Cancer Genome Atlas Network. 2012. Comprehensive molecular characterization of human colon and rectal cancerNature 487(7407):330–337.
*Laird PW is one of 326 co-authors

Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, Laird PW, Onofrio RC, Winckler W, Weir BA, Beroukhim R, Pellman D, Levine DA, Lander ES, Meyerson M, Getz G. 2012. Absolute quantification of somatic DNA alterations in human cancerNat Biotechnol 30(5):413–421.

Shen H, Laird PW. 2012. In epigenetic therapy, less is moreCell Stem Cell 10(4):353–354.

Hinoue T, Weisenberger DJ, Lange CPE, Shen H, Byun HM, Van Den Berg D, Malik S, Pan F, Noushmehr H, van Dijk CM, Tollenaar RAEM, and Laird PW. 2012. Genome-scale analysis of aberrant DNA methylation in colorectal cancerGenome Res 22(2):271–282.

Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, Van Den Berg D, Laird PW. 2011. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domainsNat Genet 44(1):40-46.
*Cited in Genome Biology (Vol 12, 137) as one of the most important papers published in 2011

Cancer Genome Atlas Research Network*. 2011. Integrated genomic analyses of ovarian carcinoma. Nature 474(7353):609–615.
*Laird PW is one of 297 co-authors; also listed among co-authors who contributed substantively to the writing of the manuscript
**Cited more than 700 times (ISI)

Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW*, Aldape K*, The Cancer Genome Atlas Research Network. 2010. Identification of a CpG island methylator phenotype that defines a distinct subgroup of gliomaCancer Cell 17(5):510–522.
*Corresponding author, equal contribution
**Cancer Cell Preview: Wright KD, Gilbertson JD. 2010. To infinium, and beyond! Cancer Cell 17(5):419–420.
**Faculty of 1000 Citation “Must Read”
**Listed as “Hot Paper” by ISI**Listed as “Highly Cited Paper in the Past Decade” by ISI
**Listed among Top Five Papers for Cancer Cell 10th Anniversary

Laird PW. 2010. Principles and challenges of genomewide DNA methylation analysisNat Rev Genet 11(3):191–203.
*Listed as “Highly Cited Paper in the Past Decade” by ISI

Cancer Genome Atlas Research Network*. 2008. Comprehensive genomic characterization defines human glioblastoma genes and core pathwaysNature 455(7216):1061–1068.
Laird PW is one of 231 co-authors
**Listed as “Highly Cited Paper in the Past Decade” by ISI
**Cited more than 1,600 times (ISI)

Weisenberger DJ, Trinh BN, Campan M, Sharma S, Long TI, Ananthnarayan S, Liang G, Esteva FJ, Hortobagyi GN, McCormick F, Jones PA, Laird PW. 2008. DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLightNucleic Acids Res 36(14):4689–4698.

Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, Marth C, Weisenberger DJ, Campan M, Young J, Jacobs I, Laird PW. 2007. Epigenetic stem cell signature in cancerNat Genet 39(2):157–158.
*Highlighted in Research Highlights: Nature Reviews Genetics 8, 90-91, 2007
*Faculty of 1000 Citation
*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited more than 500 times (ISI)

Sodir NM, Chen X, Park R, Nickel AE, Conti PS, Moats R, Bading JR, Shibata D, Laird PW. 2006. Smad3 deficiency promotes tumorigenesis in the distal colon of ApcMin/+ miceCancer Res 66(1):8430–8438.

Weisenberger DJ, Siegmund KD, Campan M, Young J, Long TI, Faasse MA, Kang GH, Widschwendter M, Weener D, Buchanan D, Koh H, Simms L, Barker M, Leggett B, Levine J, Kim M, French AJ, Thibodeau SN, Jass J, Haile R, Laird PW. 2006. CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancerNat Genet 38(7):787–793.
*Highlighted in News and Views: Schuebel et al. Nature Genetics 38,706-708, 2006
*Selected Summary in Gastroenterology 132, 1184-1195, 2007
*Listed as “Highly Cited Paper in the Past Decade” by ISI

Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E, Ehrlich M, Laird PW. 2005. Analysis of repetitive element DNA methylation by MethyLightNucleic Acids Res 33(21):6823–6836.
*Selected as “Recent Hot Paper” by Nucleic Acids Research*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited More Than 700 Times (ISI)

Laird PW. 2003. The power and the promise of DNA methylation markersNat Rev Cancer 3(4):253–266.
*Highlighted in “Nature Reviews Focus on DNA methylation”
*Listed as “Highly Cited Paper in the Past Decade” by ISI
*Cited More Than 700 Times (ISI)

Eads CA, Nickel AE, Laird PW. 2002. Complete genetic suppression of polyp formation and reduction in CpG-island hypermethylation in Apc (Min/+) Dnmt1-hypomorphic miceCancer Res 62(5):1296–1299.

Eads CA, Danenberg KD, Kawakami K, Saltz LB, Blake C, Shibata D, Danenberg PV, Laird PW. 2000. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 28(8):E32.
*Cited more than 500 times (ISI)

Jones PA, Laird PW. 1999. Cancer epigenetics comes of ageNat Genet 21(2):163–167.
*Listed until 2010 as the highest cited paper of all Nature Genetics papers in the past decade among ISI “Highly Cited Papers”
*Cited more than 1,600 times (ISI)

Xiong Z, Laird PW. 1997. COBRA – A sensitive and quantitative DNA methylation assayNucleic Acids Res 25(12):2532–2534.
*Cited more than 700 times (ISI)

Laird PW*, Jackson-Grusby L*, Fazeli A*, Dickinson SL, Jung WE, Li E, Weinberg RA, Jaenisch R. 1995. Suppression of intestinal neoplasia by DNA hypomethylationCell 81(2):197–205.    PubMed
*Equal contribution
**Cited in “Milestones in Cancer” in Nature, April 2006 (Milestone 19)**Cited more than 500 times (ISI)

Laird PW, Zijderveld A, Linders K, Rudnicki MA, Jaenisch R, Berns A. 1991. Simplified mammalian DNA isolation procedureNucleic Acids Res 19(15):4293.
*Cited more than 1,100 times (ISI)

Sadie Blaszczyk

Student Intern, Department of Epigenetics

Emily Eugster, M.S.

Senior Research Technician, Department of Epigenetics

Kelly Foy, B.S.

Laboratory Manager, Department of Epigenetics

Toshinori Hinoue, Ph.D.

Bioinformatics Scientist, Department of Epigenetics

Manpreet Kalkat, Ph.D.

Research Scientist, Department of Epigenetics

Liang Kang, A.S.

Senior Research Technician, Department of Epigenetics

Hsiao-Yun Yeh (Christy) Milliron, Ph.D.

Research Scientist, Department of Epigenetics

Paula Nolte, B.S.

Research Technician, Department of Epigenetics

Amy Nuffesse

Senior Administrative Assistant II, Department of Epigenetics

Jae Min (Jamie) Park

Ph.D. Candidate, VAI Graduate School

Nathan Spix

M.D.-Ph.D. Student

Thesis: Deep molecular characterization of DNA methylation in human colorectal cancer

Lab Alumni

Jamie Endicott, Ph.D.

Van Andel Institute Graduate School Student

Walid Abi Habib, Ph.D.

Postdoctoral Fellow

Emily Jung, B.S.

Research Technician

Bethany Khol, B.S.

Assistant Research Technician

Kwang-Ho Lee, Ph.D.

Senior Research Scientist

Owen Mitchell, B.S.

Assistant Research Technician

Nicole Vander Schaaf, Ph.D.

Van Andel Institute Graduate School Student

Elysa Wolf, B.S.

Assistant Research Technician

Zhouwei Zhang, B.S.

Assistant Research Technician