Contact information:

University of Miami,

Department of Human Genetics,

1501 NW 10th Ave,

Office: BRB 709A

Lab: BRB 742F,

Locator code: C227,

Miami, FL 33136

Office phone: (305) 243-7333

Lab Phone: (305) 243-2237

  1.      Adelman ER, Huang HT, Roisman A, Olsson A, Colaprico A, Qin T, Lindsley RC, Bejar R, Salomonis N, Grimes HL, Figueroa ME. Aging Human Hematopoietic Stem Cells Manifest Profound Epigenetic Reprogramming of Enhancers That May Predispose to Leukemia. Cancer Discov. 2019 May 13;. doi: 10.1158/2159-8290.CD-18-1474. [Epub ahead of print] PubMed PMID: 31085557.     

  2. Beke A, Laplane L, Riviere J, Yang Q, Torres-Martin M, Dayris T, Rameau P, Saada V, Bilhou-Nabera C, Hurtado A, Lordier L, Vainchenker W, Figueroa ME, Droin N, Solary E. Multilayer intraclonal heterogeneity in chronic myelomonocytic leukemia. Haematologica. 2019 May 2;. doi: 10.3324/haematol.2018.208488. [Epub ahead of print] PubMed PMID: 31048357.

  3. Fernandez AGL, Crescenzi B, Pierini V, Di Battista V, Barba G, Pellanera F, Di Giacomo D, Roti G, Piazza R, Adelman ER, Figueroa ME, Mecucci C. A distinct epigenetic program underlies the 1;7 translocation in myelodysplastic syndromes. Leukemia. 2019 Mar 28;. doi: 10.1038/s41375-019-0433-9. [Epub ahead of print] PubMed PMID: 30923319.

  4. Núñez FJ, Mendez FM, Kadiyala P, Alghamri MS, Savelieff MG, Garcia-Fabiani MB, Haase S, Koschmann C, Calinescu AA, Kamran N, Saxena M, Patel R, Carney S, Guo MZ, Edwards M, Ljungman M, Qin T, Sartor MA, Tagett R, Venneti S, Brosnan-Cashman J, Meeker A, Gorbunova V, Zhao L, Kremer DM, Zhang L, Lyssiotis CA, Jones L, Herting CJ, Ross JL, Hambardzumyan D, Hervey-Jumper S, Figueroa ME, Lowenstein PR, Castro MG. IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response. Sci Transl Med. 2019 Feb 13;11(479). doi: 10.1126/scitranslmed.aaq1427. PubMed PMID: 30760578; PubMed Central PMCID: PMC6400220.

  5. Dominguez PM, Ghamlouch H, Rosikiewicz W, Kumar P, Béguelin W, Fontán L, Rivas MA, Pawlikowska P, Armand M, Mouly E, Torres-Martin M, Doane AS, Calvo Fernandez MT, Durant M, Della-Valle V, Teater M, Cimmino L, Droin N, Tadros S, Motanagh S, Shih AH, Rubin MA, Tam W, Aifantis I, Levine RL, Elemento O, Inghirami G, Green MR, Figueroa ME, Bernard OA, Aoufouchi S, Li S, Shaknovich R, Melnick AM. TET2 Deficiency Causes Germinal Center Hyperplasia, Impairs Plasma Cell Differentiation, and Promotes B-cell Lymphomagenesis. Cancer Discov. 2018 Dec;8(12):1632-1653. doi: 10.1158/2159-8290.CD-18-0657. Epub 2018 Oct 1. PubMed PMID: 30274972; PubMed Central PMCID: PMC6279514.

  6. Chan HL, Beckedorff F, Zhang Y, Garcia-Huidobro J, Jiang H, Colaprico A, Bilbao D, Figueroa ME, LaCava J, Shiekhattar R, Morey L. Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms. Nat Commun. 2018 Aug 23;9(1):3377. doi: 10.1038/s41467-018-05728-x. PubMed PMID: 30139998; PubMed Central PMCID: PMC6107513.

  7. Jin X, Qin T, Zhao M, Bailey N, Liu L, Yang K, Ng V, Higashimoto T, Coolon R, Ney G, Figueroa ME, Li Q. Oncogenic N-Ras and Tet2 haploinsufficiency collaborate to dysregulate hematopoietic stem and progenitor cells. Blood Adv. 2018 Jun 12;2(11):1259-1271. doi: 10.1182/bloodadvances.2018017400. PubMed PMID: 29866713; PubMed Central PMCID: PMC5998937.

  8. Santini V, Allione B, Zini G, Gioia D, Lunghi M, Poloni A, Cilloni D, Sanna A, Masiera E, Ceccarelli M, Abdel-Wahab O, Terenzi A, Angelucci E, Finelli C, Onida F, Pelizzari A, Ferrero D, Saglio G, Figueroa M, Levis A. A phase II, multicentre trial of decitabine in higher-risk chronic myelomonocytic leukemia. Leukemia. 2018 Feb;32(2):413-418. doi: 10.1038/leu.2017.186. Epub 2017 Jun 13. PubMed PMID: 28607470; PubMed Central PMCID: PMC5808077.

  9. Kramer AC, Kothari A, Wilson WC, Celik H, Nikitas J, Mallaney C, Ostrander EL, Eultgen E, Martens A, Valentine MC, Young AL, Druley TE, Figueroa ME, Zhang B, Challen GA. Dnmt3a regulates T-cell development and suppresses T-ALL transformation. Leukemia. 2017 Nov;31(11):2479-2490. doi: 10.1038/leu.2017.89. Epub 2017 Mar 21. PubMed PMID: 28321121; PubMed Central PMCID: PMC5636646.

  10. Cimmino L, Dolgalev I, Wang Y, Yoshimi A, Martin GH, Wang J, Ng V, Xia B, Witkowski MT, Mitchell-Flack M, Grillo I, Bakogianni S, Ndiaye-Lobry D, Martín MT, Guillamot M, Banh RS, Xu M, Figueroa ME, Dickins RA, Abdel-Wahab O, Park CY, Tsirigos A, Neel BG, Aifantis I. Restoration of TET2 Function Blocks Aberrant Self-Renewal and Leukemia Progression. Cell. 2017 Sep 7;170(6):1079-1095.e20. doi: 10.1016/j.cell.2017.07.032. Epub 2017 Aug 17. PubMed PMID: 28823558; PubMed Central PMCID: PMC5755977.

  11. Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov. 2017 Aug;7(8):868-883. doi: 10.1158/2159-8290.CD-16-1032. Epub 2017 Apr 13. PubMed PMID: 28408400; PubMed Central PMCID: PMC5540802.

  12. Ho TT, Warr MR, Adelman ER, Lansinger OM, Flach J, Verovskaya EV, Figueroa ME, Passegué E. Autophagy maintains the metabolism and function of young and old stem cells. Nature. 2017 Mar 9;543(7644):205-210. doi: 10.1038/nature21388. Epub 2017 Mar 1. PubMed PMID: 28241143; PubMed Central PMCID: PMC5344718.

  13. Luskin MR, Gimotty PA, Smith C, Loren AW, Figueroa ME, Harrison J, Sun Z, Tallman MS, Paietta EM, Litzow MR, Melnick AM, Levine RL, Fernandez HF, Luger SM, Carroll M, Master SR, Wertheim GB. A clinical measure of DNA methylation predicts outcome in de novo acute myeloid leukemia. JCI Insight. 2016 Jun 16;1(9). doi: 10.1172/jci.insight.87323. PubMed PMID: 27446991; PubMed Central PMCID: PMC4951094.

  14. Rampal R, Figueroa ME. Wilms tumor 1 mutations in the pathogenesis of acute myeloid leukemia. Haematologica. 2016 Jun;101(6):672-9. doi: 10.3324/haematol.2015.141796. Review. PubMed PMID: 27252512; PubMed Central PMCID: PMC5013955.

  15. Meyer SE, Qin T, Muench DE, Masuda K, Venkatasubramanian M, Orr E, Suarez L, Gore SD, Delwel R, Paietta E, Tallman MS, Fernandez H, Melnick A, Le Beau MM, Kogan S, Salomonis N, Figueroa ME, Grimes HL. DNMT3A Haploinsufficiency Transforms FLT3ITD Myeloproliferative Disease into a Rapid, Spontaneous, and Fully Penetrant Acute Myeloid Leukemia. Cancer Discov. 2016 May;6(5):501-15. doi: 10.1158/2159-8290.CD-16-0008. Epub 2016 Mar 25. PubMed PMID: 27016502; PubMed Central PMCID: PMC4861898.

  16. Merlevede J, Droin N, Qin T, Meldi K, Yoshida K, Morabito M, Chautard E, Auboeuf D, Fenaux P, Braun T, Itzykson R, de Botton S, Quesnel B, Commes T, Jourdan E, Vainchenker W, Bernard O, Pata-Merci N, Solier S, Gayevskiy V, Dinger ME, Cowley MJ, Selimoglu-Buet D, Meyer V, Artiguenave F, Deleuze JF, Preudhomme C, Stratton MR, Alexandrov LB, Padron E, Ogawa S, Koscielny S, Figueroa M, Solary E. Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents. Nat Commun. 2016 Feb 24;7:10767. doi: 10.1038/ncomms10767. PubMed PMID: 26908133; PubMed Central PMCID: PMC4770084.

  17. Prebet T, Sun Z, Ketterling RP, Zeidan A, Greenberg P, Herman J, Juckett M, Smith MR, Malick L, Paietta E, Czader M, Figueroa M, Gabrilove J, Erba HP, Tallman MS, Litzow M, Gore SD. Azacitidine with or without Entinostat for the treatment of therapy-related myeloid neoplasm: further results of the E1905 North American Leukemia Intergroup study. Br J Haematol. 2016 Feb;172(3):384-91. doi: 10.1111/bjh.13832. Epub 2015 Nov 18. PubMed PMID: 26577691; PubMed Central PMCID: PMC4794257.

  18. Meldi KM, Figueroa ME. Cytosine modifications in myeloid malignancies. Pharmacol Ther. 2015 Aug;152:42-53. doi: 10.1016/j.pharmthera.2015.05.002. Epub 2015 May 5. Review. PubMed PMID: 25956466.

  19. Gaillard C, Tokuyasu TA, Rosen G, Sotzen J, Vitaliano-Prunier A, Roy R, Passegué E, de Thé H, Figueroa ME, Kogan SC. Transcription and methylation analyses of preleukemic promyelocytes indicate a dual role for PML/RARA in leukemia initiation. Haematologica. 2015 Aug;100(8):1064-75. doi: 10.3324/haematol.2014.123018. Epub 2015 Jun 18. PubMed PMID: 26088929; PubMed Central PMCID: PMC5004423.

  20. Amabile G, Di Ruscio A, Müller F, Welner RS, Yang H, Ebralidze AK, Zhang H, Levantini E, Qi L, Martinelli G, Brummelkamp T, Le Beau MM, Figueroa ME, Bock C, Tenen DG. Dissecting the role of aberrant DNA methylation in human leukaemia. Nat Commun. 2015 May 22;6:7091. doi: 10.1038/ncomms8091. PubMed PMID: 25997600; PubMed Central PMCID: PMC4443494.

  21. Meldi K, Qin T, Buchi F, Droin N, Sotzen J, Micol JB, Selimoglu-Buet D, Masala E, Allione B, Gioia D, Poloni A, Lunghi M, Solary E, Abdel-Wahab O, Santini V, Figueroa ME. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia. J Clin Invest. 2015 May;125(5):1857-72. doi: 10.1172/JCI78752. Epub 2015 Mar 30. PubMed PMID: 25822018; PubMed Central PMCID: PMC4611703.

  22. Park SM, Gönen M, Vu L, Minuesa G, Tivnan P, Barlowe TS, Taggart J, Lu Y, Deering RP, Hacohen N, Figueroa ME, Paietta E, Fernandez HF, Tallman MS, Melnick A, Levine R, Leslie C, Lengner CJ, Kharas MG. Musashi2 sustains the mixed-lineage leukemia-driven stem cell regulatory program. J Clin Invest. 2015 Mar 2;125(3):1286-98. doi: 10.1172/JCI78440. Epub 2015 Feb 9. PubMed PMID: 25664853; PubMed Central PMCID: PMC4362230.

  23. Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM. Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. J Vis Exp. 2015 Feb 24;(96):e52246. doi: 10.3791/52246. PubMed PMID: 25742437; PubMed Central PMCID: PMC4354670.

  24. Wertheim GB, Smith C, Luskin M, Rager A, Figueroa ME, Carroll M, Master SR. Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP. Clin Chem. 2015 Jan;61(1):249-58. doi: 10.1373/clinchem.2014.229781. Epub 2014 Oct 27. PubMed PMID: 25348669; PubMed Central PMCID: PMC4384518.

  25. Gölzenleuchter M, Kanwar R, Zaibak M, Al Saiegh F, Hartung T, Klukas J, Smalley RL, Cunningham JM, Figueroa ME, Schroth GP, Therneau TM, Banck MS, Beutler AS. Plasticity of DNA methylation in a nerve injury model of pain. Epigenetics. 2015;10(3):200-12. doi: 10.1080/15592294.2015.1006493. PubMed PMID: 25621511; PubMed Central PMCID: PMC4622653.

  26. Meldi KM, Figueroa ME. Epigenetic deregulation in myeloid malignancies. Transl Res. 2015 Jan;165(1):102-14. doi: 10.1016/j.trsl.2014.04.012. Epub 2014 Apr 24. Review. PubMed PMID: 24813528.

  27. Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, Li Y, Ahn J, Abdel-Wahab O, Shih A, Lu C, Ward PS, Tsai JJ, Hricik T, Tosello V, Tallman JE, Zhao X, Daniels D, Dai Q, Ciminio L, Aifantis I, He C, Fuks F, Tallman MS, Ferrando A, Nimer S, Paietta E, Thompson CB, Licht JD, Mason CE, Godley LA, Melnick A, Figueroa ME, Levine RL. DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. Cell Rep. 2014 Dec 11;9(5):1841-1855. doi: 10.1016/j.celrep.2014.11.004. Epub 2014 Dec 4. PubMed PMID: 25482556; PubMed Central PMCID: PMC4267494.

  28. Park Y, Figueroa ME, Rozek LS, Sartor MA. MethylSig: a whole genome DNA methylation analysis pipeline. Bioinformatics. 2014 Sep 1;30(17):2414-22. doi: 10.1093/bioinformatics/btu339. Epub 2014 May 16. PubMed PMID: 24836530; PubMed Central PMCID: PMC4147891.

  29. Collins C, Wang J, Miao H, Bronstein J, Nawer H, Xu T, Figueroa M, Muntean AG, Hess JL. C/EBPα is an essential collaborator in Hoxa9/Meis1-mediated leukemogenesis. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9899-904. doi: 10.1073/pnas.1402238111. Epub 2014 Jun 23. PubMed PMID: 24958854; PubMed Central PMCID: PMC4103350.

  30. Taskesen E, Havermans M, van Lom K, Sanders MA, van Norden Y, Bindels E, Hoogenboezem R, Reinders MJ, Figueroa ME, Valk PJ, Löwenberg B, Melnick A, Delwel R. Two splice-factor mutant leukemia subgroups uncovered at the boundaries of MDS and AML using combined gene expression and DNA-methylation profiling. Blood. 2014 May 22;123(21):3327-35. doi: 10.1182/blood-2013-07-512855. Epub 2014 Mar 25. PubMed PMID: 24668493.

  31. Prebet T, Sun Z, Figueroa ME, Ketterling R, Melnick A, Greenberg PL, Herman J, Juckett M, Smith MR, Malick L, Paietta E, Czader M, Litzow M, Gabrilove J, Erba HP, Gore SD, Tallman MS. Prolonged administration of azacitidine with or without entinostat for myelodysplastic syndrome and acute myeloid leukemia with myelodysplasia-related changes: results of the US Leukemia Intergroup trial E1905. J Clin Oncol. 2014 Apr 20;32(12):1242-8. doi: 10.1200/JCO.2013.50.3102. Epub 2014 Mar 24. PubMed PMID: 24663049; PubMed Central PMCID: PMC3986386.

  32. Wertheim GB, Smith C, Figueroa ME, Kalos M, Bagg A, Carroll M, Master SR. Microsphere-based multiplex analysis of DNA methylation in acute myeloid leukemia. J Mol Diagn. 2014 Mar;16(2):207-15. doi: 10.1016/j.jmoldx.2013.10.010. Epub 2013 Dec 25. PubMed PMID: 24373919; PubMed Central PMCID: PMC3937537.

  33. Slamova L, Starkova J, Fronkova E, Zaliova M, Reznickova L, van Delft FW, Vodickova E, Volejnikova J, Zemanova Z, Polgarova K, Cario G, Figueroa M, Kalina T, Fiser K, Bourquin JP, Bornhauser B, Dworzak M, Zuna J, Trka J, Stary J, Hrusak O, Mejstrikova E. CD2-positive B-cell precursor acute lymphoblastic leukemia with an early switch to the monocytic lineage. Leukemia. 2014 Mar;28(3):609-20. doi: 10.1038/leu.2013.354. Epub 2013 Nov 25. PubMed PMID: 24270736.

  34. Vu LP, Perna F, Wang L, Voza F, Figueroa ME, Tempst P, Erdjument-Bromage H, Gao R, Chen S, Paietta E, Deblasio T, Melnick A, Liu Y, Zhao X, Nimer SD. PRMT4 blocks myeloid differentiation by assembling a methyl-RUNX1-dependent repressor complex. Cell Rep. 2013 Dec 26;5(6):1625-38. doi: 10.1016/j.celrep.2013.11.025. Epub 2013 Dec 12. PubMed PMID: 24332853; PubMed Central PMCID: PMC4073674.

  35. Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG. DNMT1-interacting RNAs block gene-specific DNA methylation. Nature. 2013 Nov 21;503(7476):371-6. doi: 10.1038/nature12598. Epub 2013 Oct 9. PubMed PMID: 24107992; PubMed Central PMCID: PMC3870304.

  36. Kuo HP, Wang Z, Lee DF, Iwasaki M, Duque-Afonso J, Wong SH, Lin CH, Figueroa ME, Su J, Lemischka IR, Cleary ML. Epigenetic roles of MLL oncoproteins are dependent on NF-κB. Cancer Cell. 2013 Oct 14;24(4):423-37. doi: 10.1016/j.ccr.2013.08.019. Epub 2013 Sep 19. PubMed PMID: 24054986; PubMed Central PMCID: PMC3816582.

  37. Malinge S, Chlon T, Doré LC, Ketterling RP, Tallman MS, Paietta E, Gamis AS, Taub JW, Chou ST, Weiss MJ, Crispino JD, Figueroa ME. Development of acute megakaryoblastic leukemia in Down syndrome is associated with sequential epigenetic changes. Blood. 2013 Oct 3;122(14):e33-43. doi: 10.1182/blood-2013-05-503011. Epub 2013 Aug 26. PubMed PMID: 23980066; PubMed Central PMCID: PMC3790517.

  38. Figueroa ME, Chen SC, Andersson AK, Phillips LA, Li Y, Sotzen J, Kundu M, Downing JR, Melnick A, Mullighan CG. Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia. J Clin Invest. 2013 Jul;123(7):3099-111. doi: 10.1172/JCI66203. Epub 2013 Jun 10. PubMed PMID: 23921123; PubMed Central PMCID: PMC3696550.

  39. Will B, Vogler TO, Bartholdy B, Garrett-Bakelman F, Mayer J, Barreyro L, Pandolfi A, Todorova TI, Okoye-Okafor UC, Stanley RF, Bhagat TD, Verma A, Figueroa ME, Melnick A, Roth M, Steidl U. Satb1 regulates the self-renewal of hematopoietic stem cells by promoting quiescence and repressing differentiation commitment. Nat Immunol. 2013 May;14(5):437-45. doi: 10.1038/ni.2572. Epub 2013 Apr 7. PubMed PMID: 23563689; PubMed Central PMCID: PMC3633104.

  40. Krivtsov AV, Figueroa ME, Sinha AU, Stubbs MC, Feng Z, Valk PJ, Delwel R, Döhner K, Bullinger L, Kung AL, Melnick AM, Armstrong SA. Cell of origin determines clinically relevant subtypes of MLL-rearranged AML. Leukemia. 2013 Apr;27(4):852-60. doi: 10.1038/leu.2012.363. Epub 2012 Dec 13. PubMed PMID: 23235717; PubMed Central PMCID: PMC4693300.

  41. Kannan S, Sutphin RM, Hall MG, Golfman LS, Fang W, Nolo RM, Akers LJ, Hammitt RA, McMurray JS, Kornblau SM, Melnick AM, Figueroa ME, Zweidler-McKay PA. Notch activation inhibits AML growth and survival: a potential therapeutic approach. J Exp Med. 2013 Feb 11;210(2):321-37. doi: 10.1084/jem.20121527. Epub 2013 Jan 28. PubMed PMID: 23359069; PubMed Central PMCID: PMC3570106.

  42. Figueroa ME. Understanding and utilizing new molecular genetics in MDS. Clin Adv Hematol Oncol. 2013 Feb;11(2):106-8. PubMed PMID: 23598913.

  43. Polo JM, Anderssen E, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S, Hochedlinger K. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell. 2012 Dec 21;151(7):1617-32. doi: 10.1016/j.cell.2012.11.039. PubMed PMID: 23260147; PubMed Central PMCID: PMC3608203.

  44. Alberich-Jordà M, Wouters B, Balastik M, Shapiro-Koss C, Zhang H, Di Ruscio A, Radomska HS, Ebralidze AK, Amabile G, Ye M, Zhang J, Lowers I, Avellino R, Melnick A, Figueroa ME, Valk PJ, Delwel R, Tenen DG. C/EBPγ deregulation results in differentiation arrest in acute myeloid leukemia. J Clin Invest. 2012 Dec;122(12):4490-504. doi: 10.1172/JCI65102. Epub 2012 Nov 19. PubMed PMID: 23160200; PubMed Central PMCID: PMC3533560.

  45. Busque L, Patel JP, Figueroa ME, Vasanthakumar A, Provost S, Hamilou Z, Mollica L, Li J, Viale A, Heguy A, Hassimi M, Socci N, Bhatt PK, Gonen M, Mason CE, Melnick A, Godley LA, Brennan CW, Abdel-Wahab O, Levine RL. Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis. Nat Genet. 2012 Nov;44(11):1179-81. doi: 10.1038/ng.2413. Epub 2012 Sep 23. PubMed PMID: 23001125; PubMed Central PMCID: PMC3483435.

  46. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012 Oct 3;13(10):R87. doi: 10.1186/gb-2012-13-10-r87. PubMed PMID: 23034086; PubMed Central PMCID: PMC3491415.

  47. Gönen M, Sun Z, Figueroa ME, Patel JP, Abdel-Wahab O, Racevskis J, Ketterling RP, Fernandez H, Rowe JM, Tallman MS, Melnick A, Levine RL, Paietta E. CD25 expression status improves prognostic risk classification in AML independent of established biomarkers: ECOG phase 3 trial, E1900. Blood. 2012 Sep 13;120(11):2297-306. doi: 10.1182/blood-2012-02-414425. Epub 2012 Aug 1. PubMed PMID: 22855599; PubMed Central PMCID: PMC3447784.

  48. Sasaki M, Knobbe CB, Munger JC, Lind EF, Brenner D, Brüstle A, Harris IS, Holmes R, Wakeham A, Haight J, You-Ten A, Li WY, Schalm S, Su SM, Virtanen C, Reifenberger G, Ohashi PS, Barber DL, Figueroa ME, Melnick A, Zúñiga-Pflücker JC, Mak TW. IDH1(R132H) mutation increases murine haematopoietic progenitors and alters epigenetics. Nature. 2012 Aug 30;488(7413):656-9. doi: 10.1038/nature11323. PubMed PMID: 22763442; PubMed Central PMCID: PMC4005896.

  49. Kawahara M, Pandolfi A, Bartholdy B, Barreyro L, Will B, Roth M, Okoye-Okafor UC, Todorova TI, Figueroa ME, Melnick A, Mitsiades CS, Steidl U. H2.0-like homeobox regulates early hematopoiesis and promotes acute myeloid leukemia. Cancer Cell. 2012 Aug 14;22(2):194-208. doi: 10.1016/j.ccr.2012.06.027. PubMed PMID: 22897850; PubMed Central PMCID: PMC3422691.

  50. Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781. doi: 10.1371/journal.pgen.1002781. Epub 2012 Jun 21. PubMed PMID: 22737091; PubMed Central PMCID: PMC3380828.

  51. Ribeiro AF, Pratcorona M, Erpelinck-Verschueren C, Rockova V, Sanders M, Abbas S, Figueroa ME, Zeilemaker A, Melnick A, Löwenberg B, Valk PJ, Delwel R. Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia. Blood. 2012 Jun 14;119(24):5824-31. doi: 10.1182/blood-2011-07-367961. Epub 2012 Apr 5. PubMed PMID: 22490330. 

  52. Pollyea DA, Kohrt HE, Gallegos L, Figueroa ME, Abdel-Wahab O, Zhang B, Bhattacharya S, Zehnder J, Liedtke M, Gotlib JR, Coutre S, Berube C, Melnick A, Levine R, Mitchell BS, Medeiros BC. Safety, efficacy and biological predictors of response to sequential azacitidine and lenalidomide for elderly patients with acute myeloid leukemia.Leukemia. 2012 May;26(5):893-901. doi: 10.1038/leu.2011.294. Epub 2011 Oct 28. PubMed PMID: 22033493. 

  53. Patel JP, Gönen M, Figueroa ME, Fernandez H, Sun Z, Racevskis J, Van Vlierberghe P, Dolgalev I, Thomas S, Aminova O, Huberman K, Cheng J, Viale A, Socci ND, Heguy A, Cherry A, Vance G, Higgins RR, Ketterling RP, Gallagher RE, Litzow M, van den Brink MR, Lazarus HM, Rowe JM, Luger S, Ferrando A, Paietta E, Tallman MS, Melnick A, Abdel-Wahab O, Levine RL. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med. 2012 Mar 22;366(12):1079-89. doi: 10.1056/NEJMoa1112304. Epub 2012 Mar 14. PubMed PMID: 22417203; PubMed Central PMCID: PMC3545649. 

  54. Lu C, Ward PS, Kapoor GS, Rohle D, Turcan S, Abdel-Wahab O, Edwards CR, Khanin R, Figueroa ME, Melnick A, Wellen KE, O'Rourke DM, Berger SL, Chan TA, Levine RL, Mellinghoff IK, Thompson CB. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature. 2012 Feb 15;483(7390):474-8. doi: 10.1038/nature10860. PubMed PMID: 22343901; PubMed Central PMCID: PMC3478770. 

  55. Abdel-Wahab O, Figueroa ME. Interpreting new molecular genetics in myelodysplastic syndromes. Hematology Am Soc Hematol Educ Program. 2012;2012:56-64. doi: 10.1182/asheducation-2012.1.56. Review. PubMed PMID: 23233561. 

  56. Shaknovich R, Cerchietti L, Tsikitas L, Kormaksson M, De S, Figueroa ME, Ballon G, Yang SN, Weinhold N, Reimers M, Clozel T, Luttrop K, Ekstrom TJ, Frank J, Vasanthakumar A, Godley LA, Michor F, Elemento O, Melnick A. DNA methyltransferase 1 and DNA methylation patterning contribute to germinal center B-cell differentiation. Blood. 2011 Sep 29;118(13):3559-69. doi: 10.1182/blood-2011-06-357996. Epub 2011 Aug 9. PubMed PMID: 21828137; PubMed Central PMCID: PMC3186332. 

  57. Moran-Crusio K, Reavie L, Shih A, Abdel-Wahab O, Ndiaye-Lobry D, Lobry C, Figueroa ME, Vasanthakumar A, Patel J, Zhao X, Perna F, Pandey S, Madzo J, Song C, Dai Q, He C, Ibrahim S, Beran M, Zavadil J, Nimer SD, Melnick A, Godley LA, Aifantis I, Levine RL. Tet2 loss leads to increased hematopoietic stem cell self-renewal and myeloid transformation. Cancer Cell. 2011 Jul 12;20(1):11-24. doi: 10.1016/j.ccr.2011.06.001. Epub 2011 Jun 30. PubMed PMID: 21723200; PubMed Central PMCID: PMC3194039. 

  58. Lugthart S, Figueroa ME, Bindels E, Skrabanek L, Valk PJ, Li Y, Meyer S, Erpelinck-Verschueren C, Greally J, Löwenberg B, Melnick A, Delwel R. Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1. Blood. 2011 Jan 6;117(1):234-41. doi: 10.1182/blood-2010-04-281337. Epub 2010 Sep 20. PubMed PMID: 20855866; PubMed Central PMCID: PMC3037746. 

  59. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Löwenberg B, Licht JD, Godley LA, Delwel R, Valk PJ, Thompson CB, Levine RL, Melnick A. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010 Dec 14;18(6):553-67. doi: 10.1016/j.ccr.2010.11.015. Epub 2010 Dec 9. PubMed PMID: 21130701; PubMed Central PMCID: PMC4105845. 

  60. Cerchietti LC, Hatzi K, Caldas-Lopes E, Yang SN, Figueroa ME, Morin RD, Hirst M, Mendez L, Shaknovich R, Cole PA, Bhalla K, Gascoyne RD, Marra M, Chiosis G, Melnick A. BCL6 repression of EP300 in human diffuse large B cell lymphoma cells provides a basis for rational combinatorial therapy. J Clin Invest. 2010 Dec 1;120(12):4569-82. doi: 10.1172/JCI42869. Epub 2010 Nov 1. PubMed PMID: 21041953; PubMed Central PMCID: PMC2993589. 

  61. Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, Tan KY, Apostolou E, Stadtfeld M, Li Y, Shioda T, Natesan S, Wagers AJ, Melnick A, Evans T, Hochedlinger K. Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol. 2010 Aug;28(8):848-55. doi: 10.1038/nbt.1667. Epub 2010 Jul 19. PubMed PMID: 20644536; PubMed Central PMCID: PMC3148605. 

  62. Shah MY, Vasanthakumar A, Barnes NY, Figueroa ME, Kamp A, Hendrick C, Ostler KR, Davis EM, Lin S, Anastasi J, Le Beau MM, Moskowitz IP, Melnick A, Pytel P, Godley LA.DNMT3B7, a truncated DNMT3B isoform expressed in human tumors, disrupts embryonic development and accelerates lymphomagenesis. Cancer Res. 2010 Jul 15;70(14):5840-50. doi: 10.1158/0008-5472.CAN-10-0847. Epub 2010 Jun 29. PubMed PMID: 20587527; PubMed Central PMCID: PMC2905468. 

  63. Schafer E, Irizarry R, Negi S, McIntyre E, Small D, Figueroa ME, Melnick A, Brown P.Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting. Blood. 2010 Jun 10;115(23):4798-809. doi: 10.1182/blood-2009-09-243634. Epub 2010 Mar 9. PubMed PMID: 20215641; PubMed Central PMCID: PMC2890186. 

  64. Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Löwenberg B, Delwel R, Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010 Jan 19;17(1):13-27. doi: 10.1016/j.ccr.2009.11.020. Epub 2010 Jan 7. PubMed PMID: 20060365; PubMed Central PMCID: PMC3008568. 

  65. Shaknovich R, Figueroa ME, Melnick A. HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes. Methods Mol Biol. 2010;632:191-201. doi: 10.1007/978-1-60761-663-4_12. PubMed PMID: 20217579. 

  66. Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM, Carraway H, Licht JD, Gore SD, Melnick A. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. Blood. 2009 Oct 15;114(16):3448-58. doi: 10.1182/blood-2009-01-200519. Epub 2009 Aug 3. PubMed PMID: 19652201; PubMed Central PMCID: PMC2765680. 

  67. Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L, Green RD, Melnick A, Hatchwell E, Bouhassira EE, Verma A, Suzuki M, Greally JM. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 2009 Jul;37(12):3829-39. doi: 10.1093/nar/gkp260. Epub 2009 Apr 22. PubMed PMID: 19386619; PubMed Central PMCID: PMC2709560. 

  68. Figueroa ME, Wouters BJ, Skrabanek L, Glass J, Li Y, Erpelinck-Verschueren CA, Langerak AW, Löwenberg B, Fazzari M, Greally JM, Valk PJ, Melnick A, Delwel R.Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. Blood. 2009 Mar 19;113(12):2795-804. doi: 10.1182/blood-2008-08-172387. Epub 2009 Jan 23. PubMed PMID: 19168792; PubMed Central PMCID: PMC2945920. 

  69. Figueroa ME, Melnick A, Greally JM. Genome-wide determination of DNA methylation by Hpa II tiny fragment enrichment by ligation-mediated PCR (HELP) for the study of acute leukemias. Methods Mol Biol. 2009;538:395-407. doi: 10.1007/978-1-59745-418-6_20. PubMed PMID: 19277580. 

  70. Laurenzana A, Petruccelli LA, Pettersson F, Figueroa ME, Melnick A, Baldwin AS, Paoletti F, Miller WH Jr. Inhibition of DNA methyltransferase activates tumor necrosis factor alpha-induced monocytic differentiation in acute myeloid leukemia cells. Cancer Res.2009 Jan 1;69(1):55-64. doi: 10.1158/0008-5472.CAN-08-0245. PubMed PMID: 19117987. 

  71. Wilson AJ, Byun DS, Nasser S, Murray LB, Ayyanar K, Arango D, Figueroa M, Melnick A, Kao GD, Augenlicht LH, Mariadason JM. HDAC4 promotes growth of colon cancer cells via repression of p21. Mol Biol Cell. 2008 Oct;19(10):4062-75. doi: 10.1091/mbc.e08-02-0139. Epub 2008 Jul 16. PubMed PMID: 18632985; PubMed Central PMCID: PMC2555950. 

  72. Lopes EC, Valls E, Figueroa ME, Mazur A, Meng FG, Chiosis G, Laird PW, Schreiber-Agus N, Greally JM, Prokhortchouk E, Melnick A. Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines. Cancer Res.2008 Sep 15;68(18):7258-63. doi: 10.1158/0008-5472.CAN-08-0344. PubMed PMID: 18794111. 

  73. Figueroa ME, Reimers M, Thompson RF, Ye K, Li Y, Selzer RR, Fridriksson J, Paietta E, Wiernik P, Green RD, Greally JM, Melnick A. An integrative genomic and epigenomic approach for the study of transcriptional regulation. PLoS One. 2008 Mar 26;3(3):e1882. doi: 10.1371/journal.pone.0001882. PubMed PMID: 18365023; PubMed Central PMCID: PMC2266992. 

  74. McReynolds LJ, Gupta S, Figueroa ME, Mullins MC, Evans T. Smad1 and Smad5 differentially regulate embryonic hematopoiesis. Blood. 2007 Dec 1;110(12):3881-90. doi: 10.1182/blood-2007-04-085753. Epub 2007 Aug 29. PubMed PMID: 17761518; PubMed Central PMCID: PMC2200801. 

  75. Glass JL, Thompson RF, Khulan B, Figueroa ME, Olivier EN, Oakley EJ, Van Zant G, Bouhassira EE, Melnick A, Golden A, Fazzari MJ, Greally JM. CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res. 2007;35(20):6798-807. doi: 10.1093/nar/gkm489. Epub 2007 Oct 10. PubMed PMID: 17932072; PubMed Central PMCID: PMC2175314. 

  76. Khulan B, Thompson RF, Ye K, Fazzari MJ, Suzuki M, Stasiek E, Figueroa ME, Glass JL, Chen Q, Montagna C, Hatchwell E, Selzer RR, Richmond TA, Green RD, Melnick A, Greally JM. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006 Aug;16(8):1046-55. doi: 10.1101/gr.5273806. Epub 2006 Jun 29. PubMed PMID: 16809668; PubMed Central PMCID: PMC1524864.