Group Leader

R. David Hawkins, Ph.D.

Research Area and Interests

Epigenomics includes histone tail modifications, DNA methylation and noncoding RNAs. These factors are closely linked to transcriptional regulation, and provide unique signatures of cellular identity. The epigenome exhibits remarkable cellular specificities and likely critical in defining unique cell populations such stem cells.
Using next-generation sequencing and computational technologies, we are investigating how the epigenome

  • plays a role in pluri- and multi-potency of stem cells.
  • provides insight into transcriptional regulation
  • establishes unique signatures of cellular differentiation


  • Kalyan Pasumarthy
  • Cristina Valensisi

Recent Publications

Heintzman ND†, Hon G†, Hawkins RD†, Kheradpour P, Ching KA, Stuart RK, Harp LF, Ching CW, Liu H, Zhang X, Green RD, Crawford GE, Kellis M, and Ren B. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression.  Nature 459: 108-112.

Lister R†, Pelizzola M†, Dowen RH, Hawkins RD, Hon GC, Tonti-Filippini J, Nery JR, Lee LK, Edsall LE, Antosiewicz-Bourget J, Ruotti V, Elwell A, Hernandez A, Stewart R, Millar AH, Thomson JA, Ren B, Ecker JR. (2009) Human DNA methylomes at single-base resolution reveal widespread cell-specific epigenetic signatures. Nature 462: 315-322.

Hawkins RD†, Hon GC †, Lee LK, Ngo Q, Lister R, Pelizzola M, Kuan S, Edsall LE, Ye Z, Espinoza C, Antosiewicz-Bourget J, Agarwahl S, Shen L, Ruotti V, Wang W, Stewart R, Thomson JA, Ecker JR, Ren B. (2010) Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6: 279-491.

Hawkins RD†, Hon GC†, Ren B. (2010) Next-Generation Genomics: An Integrative Approach. Nature Reviews Genetics 11(7); 476-486.

Elo LL†, Järvenpää H†, Tuomela S†, Raghav S†, Ahlfors H, Laurila K, Gupta B, Lund RJ, Tahvanainen J, Hawkins RD, Oresic M, Lähdesmäki H, Rasool O, Rao KV, Aittokallio T, Lahesmaa R. (2010) Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming. Immunity 32: 852-862.

Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28(10), 852-862

Egelhofer TA†, Minoda A†, Klugman S†, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel, S, Gorchakov, AA, Gu T, Kharchenko PV, Kuan, S, Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC, Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SCR, Kuroda MI, Pirrotta V, Ren B, Strome S, Park PJ^, Karpen G^, Hawkins RD^, and Lieb JD^ (2010) Assessment of histone-modification antibody quality. Nature Structural & Molecular Biology. Accepted.  ^Co-corresponding Authors.
†Equal contribution of work