Peer-reviewed Publications

  1. Zhu J* & Adli M*#, Zou J, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, Cowan C, Meissner A, Epstein CB, Shoresh N and Bernstein BE#
    Genome-wide chromatin state transitions associated with developmental and environmental cues
    *Equally contributed
    #corresponding author
    Cell (Accepted, in press, Nov 2012 )
    Please click to access our human epigenome resource paper

  2. T.W. Yu, M.H. Chahrour, M.E. Coulter, S. Jiralerspong, K. Okamura-Ikeda, B. Ataman, D.A. Harmin, Adli M, A.N. Malik, A. D'Gama, K. Schmitz-Abe, E. Lim, S.J. Sanders, G.H. Mochida, J.N. Partlow, C.M. Sunu, J.M. Felie, J. Rodriguez, J. Ware, R.M. Joseph, R.S. Hill, B.Y. Kwan, M. Al-Saffar, N.M. Mukaddes, A. Hashmi, S. Balkhy, G.G. Gascon, F.M. Hisama, E. LeClair, A. Poduri, O. Oner, S. Al-Saad, T. Ben-Omran, L. Al-Gazali, V. Eapen, C.R. Stevens, L. Rappaport, S.B. Gabriel, K. Markianos, M.W. State, M.E. Greenberg, H. Taniguchi, N.E. Braverman, E.M. Morrow, C.A. Walsh.
    Using whole exome sequencing to identify inherited causes of autism
    Neuron (Accepted, in press, Nov 2012
    Cancer Cell Cover image
  3. Abdel-Wahab O*, Adli M*, LaFave L*, Gao J, Hricik T, Shih AH, Pandey A, Patel JP, Chung YR, Koche R, Perna F, Zhao X, Taylor JE, Park CY, Carroll M, Melnick A, Nimer SD, Jaffe JD, Aifantis I, Bernstein BE, Levine RL.
    ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2- Mediated Gene Repression
    *Equally contributed
    ** Cover article in Cancer Cell
    Cancer Cell, Aug 2012.

  4. Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F, Saunders LM, Mullally A, Abdel Wahab O, Leung L, Weinstein A, Marubayashi S, Goel A, Gonen M, Estrov Z, Ebert BL, Chiosis G, Nimer SD, Bernstein BE, Verstovsek S, Levine RL.
    Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy
    Nature, Jul 22, 2012.

  5. Adli M* & Bernstein BE*.
    Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.
    * Co-corresponding author
    Nature Protocols, Sept, 2011.

  6. Chapman M, Lawrence M, Keats J, Cibulskis K, Sougnez C, Schinzel C, Harview CL, Brunet J, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR.
    Initial genome sequencing and analysis of multiple myeloma
    Nature, Mar, 2011.

  7. Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A.
    Reprogramming factor expression initiates widespread targeted chromatin remodeling
    Cell Stem Cell, Jan, 2011.

    8. Nature methods Cover image
  8. Adli M, Zhu J & Bernstein BE.
    Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors
    Nature Methods , Aug, 2010.
    *Highlighted in News & Views: Nature Methods 7, 597-600 (2010).
    *Our article was one of the featured methods advertised on the cover.

  9. Adli M, Merkhofer E, Cogswell P & Baldwin AS.
    IKKalpha and IKKbeta each function to regulate NF-kappaB activation in the TNF-induced/canonical pathway
    PloS One , Feb, 2010.

  10. Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.
    Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
    Nature Methods , feb, 2010.

  11. Ku M, Koche R P, Rheinbay E, Mendenhall E M, Endoh M, Mikkelsen T S, Presser A, Nusbaum C, Chi AS, Adli M, Kasif S, Xie X, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE.
    Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains
    PloS Genetics , Oct, 2008.

  12. Dan HC, Adli M, Baldwin, AS.
    Regulation of mammalian target of rapamycin activity in PTEN-inactive prostate cancer cells by I kappa B kinase alpha
    Cancer Research , Jul, 2007.

  13. Adli M & Baldwin AS.
    IKK-i/IKKepsilon controls constitutive, cancer cell-associated NF-kappaB activity via regulation of Ser-536 p65/RelA phosphorylation
    Journal of Biological Chemistry , Sept, 2006.

  14. Kutuk O, Adli M, Poli G, Basaga H.
    Resveratrol protects against 4-HNE induced oxidative stress and apoptosis in Swiss 3T3 fibroblasts
    Bio Factors , 2004.

    Manuscripts in Submission or in Review

  1. Abdelwahab O*, Gao J*, Adli M* et al.
    Conditional Deletion of Asxl1 Results in Myelodysplasia
    * Equally contributed
    Nature Medicine , in submission.

    Patents
  1. Adli M, Mikkelsen T, Bernstein BE. Methods for preparing high throughput sequencing libraries from scarce amount of DNA. Patent #: USA, 12/699,508

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