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Publications

Laird Laboratory

Selected Publications

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

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

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 profiles. Cell Rep. 18(11):2780–2794.       Article

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

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

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 cancer. Cell 163(2):506–519  PubMed
*Laird PW is one of 126 collaborators.

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

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 evolution. Genome Res 25(3): 316–327.        PubMed

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

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 cells. Genes Nutr 10(1):444.   PubMed

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 history. Cancer Epidemiol Biomarkers Prev 24(3):512–519. PubMed

Cancer Genome Atlas Network. 2015. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517(7536):576–582.   PubMed 
*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 evolution. Genome Res 25(3):316–327.      PubMed

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 survival. Gastroenterology 148(1):77–87.       PubMed

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 cancers. Proc Natl Acad Sci USA 111(43):15544–15549.         PubMed
*
Laird PW is included among 340 collaborators

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

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513(7517):202–209.     PubMed
*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 carcinoma. Cancer Cell 26(3):319–330.    PubMed

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 origin. Cell 158(4):929–944.    PubMed

Cancer Genome Atlas Network. 2014. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511(7511):543–550.     PubMed
*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.    PubMed  

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

Cancer Genome Atlas Network*. 2014. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507: 315-322.    PubMed
*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 genomes. Cell 155(4):858–868.    PubMed

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 glioblastoma. Cell 155(2):462–477.    PubMed

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 data. Nat Commun 4:2612.    PubMed

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 project. Nat Genet 45(10):1113–1120.     PubMed

Cancer Genome Atlas Network*. 2013. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499(7456):43–49.     PubMed
*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 leukemia. N 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 epigenome. Cell 153(1):38-55.    PubMed

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 cancer. Nat Commun 4:1628.    PubMed

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

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 cancer. PLoS One 7(11):e50266.     PubMed

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

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

Cancer Genome Atlas Network. 2012. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330–337.    PubMed
*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 cancer. Nat Biotechnol 30(5):413–421.    PubMed

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

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 cancer. Genome Res 22(2):271–282.    PubMed

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 domains. Nat Genet 44(1):40-46.    PubMed
*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.    PubMed
*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 glioma. Cancer Cell 17(5):510–522.    PubMed
*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 analysis. Nat Rev Genet 11(3):191–203.    PubMed
*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 pathways. Nature 455(7216):1061–1068.    PubMed
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 MethyLight. Nucleic Acids Res 36(14):4689–4698.    PubMed

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 cancer. Nat Genet 39(2):157–158.    PubMed
*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/+ mice. Cancer Res 66(1):8430–8438.    PubMed

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 cancer. Nat Genet 38(7):787–793.    PubMed
*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 MethyLight. Nucleic Acids Res 33(21):6823–6836.    PubMed
*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 markers. Nat Rev Cancer 3(4):253–266.    PubMed
*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 mice. Cancer Res 62(5):1296–1299.    PubMed

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.    PubMed
*Cited more than 500 times (ISI)

Jones PA, Laird PW. 1999. Cancer epigenetics comes of age. Nat Genet 21(2):163–167.    PubMed
*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 assay. Nucleic Acids Res 25(12):2532–2534.    PubMed
*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 hypomethylation. Cell 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 procedure. Nucleic Acids Res 19(15):4293.    PubMed
*Cited more than 1,100 times (ISI)