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Journal covers that displayed or presented our research articles

2017

  • CRISPR-STOP: Gene silencing through base editer-induced nonsense mutations
    Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, Mammadov R, Adli M.
    Nature Methods. 2017 June

  • Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9.
    Qin P, Parlak M, Kuscu C, Bandaria J, Mir M, Szlachta K, Singh R, Darzacq X, Yildiz A, Adli M.
    Nature Communications. 2017 Mar 14;8:14725. doi: 10.1038/ncomms14725.

  • 2016

  • CRISPR-Cas9-AID base editor is a powerful gain-of-function screening tool.
    Kuscu C, Adli M.
    Nature Methods. 2016 Nov 29;13(12):983-984. doi: 10.1038/nmeth.4076

  • Evolution of Osteocrin as an activity-regulated factor in the primate brain.
    Ataman B, Boulting GL, Harmin DA, Yang MG, Baker-Salisbury M, Yap EL, Malik AN, Mei K, Rubin AA, Spiegel I, Durresi E, Sharma N, Hu LS, Pletikos M, Griffith EC, Partlow JN, Stevens CR, Adli M, Chahrour M, Sestan N, Walsh CA, Berezovskii VK, Livingstone MS, Greenberg ME.
    Nature. 2016 Nov 10;539(7628):242-247. doi: 10.1038/nature20111.

  • Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers.
    Illendula A, Gilmour J, Grembecka J, Tirumala VS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH.
    Ebiomedicine. 2016 Jun;8:117-31. doi: 10.1016/j.ebiom.2016.04.032.

  • 2015

  • Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection.
    Anderson CJ, Clark DE, Adli M, Kendall MM.
    PLoS Pathogen. 2015 Dec;11(12):e1005365.

  • Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.
    Singh R, Kuscu C, Quinlan A, Qi Y, Adli M.
    Nucleic Acid Research. 2015 Jun 1. pii: gkv575.

  • Degree of Recruitment of DOT1L to MLL-AF9 Defines Level of H3K79 Di- and Tri-methylation on Target Genes and Transformation Potential.
    Kuntimaddi A, Achille NJ, Thorpe J, Lokken AA, Singh R, Hemenway CS, Adli M, Zeleznik-Le NJ, Bushweller JH
    Cell Reports. 2015 May 5;11(5):808-20. doi: 10.1016/j.celrep.2015.04.004.

  • Integrative analysis of 111 reference human epigenomes.
    Roadmap Epigenomics Consortium
    Nature. 2015 Feb 19;518(7539):317-30.

  • Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells.
    Qin F, Song Z, Babiceanu M, Song Y, Facemire L, Singh R, Adli M, Li H.
    PloS Genetics. 2015 Feb 6;11(2):e1005001.

  • Epigenetic States of Nephron Progenitors and Epithelial Differentiation.
    Adli M, Parlak M, Li Y, El-Dahr S.
    J Cell Biochem. 22015 Jan 5. doi: 10.1002/jcb.25048

  • 2014

  • Synaptic, transcriptional and chromatin genes disrupted in autism.
    Poultney CS, Samocha K, Kou Y, Liu L, Walker S, Singh T, Klei L, Kosmicki J, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Crawford EL, Crooks L, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Jimenez Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Wang LS, Weiss LA, Jeremy Willsey A, Yu TW, Yuen RK; DDD Study; Homozygosity Mapping Collaborative for Autism; UK10K Consortium; Autism Sequencing Consortium, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Roeder K.
    Nature. 2014 Nov 13;515(7526):209-15

  • Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease.
    Kuscu C, Arslan S, Singh R, Thorpe J, Adli M.
    Nature Biotechnology. 2014 Jul;32(7):677-83


    Commented on in
    More specific CRISPR editing
    Nature Methods. 2014 Jul;11(7):712.

  • Transgenerational epigenetic inheritance: focus on endocrine disrupting compounds.
    Rissman EF, Adli M.
    Endocrinology. 2014 Aug;155(8):2770-80.

  • 2013

  • Deletion of Asxl1 Results in Myelodysplasia and Severe Developmental Defects in Vivo.
    Abdel-Wahab O*, Gao j*, Adli M*, Dey A, Trimarchi T, Rock Chung RY, Kuscu C, Hricik T, Lobry ND, La Fave L, Koche R, Shih AH, Guryanova OA, Pandey S, Shin Y, Bhatt PK, Monette S, Taylor JE, Zhao X, Jaffe JD, Dixit V, Park CY, Bernstein BE, Aifantis I, and Levine RL.
    *Equally contributed
    Journal of Experimental Medicine. 2013 Nov 18;210(12):2641-59.

  • Cancer Cell Cover image
  • Using whole exome sequencing to identify inherited causes of autism.
    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.
    #Cover Article
    Neuron. 2013 Jan 23;77(2):259-73.

  • Cancer Cell Cover image
  • Genome-wide chromatin state transitions associated with developmental and environmental cues.
    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#
    #Corresponding Author
    *Equally Contributed
    ***Selected as "Best papers of 2013" by Cell Press.
    Cell. 2013 Jan 31;152(3):642-54.

  • 2012

    Cancer Cell Cover image
  • ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2- Mediated Gene Repression.
    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.
    *Equally Contributed
    #Cover Article
    Cancer Cell. 2012 Aug 14;22(2):180-93.

  • Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy.
    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.
    Nature. 2012 Sep 6;489(7414):155-9

  • 2011

  • Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.
    Adli M* & Bernstein BE*.
    * Corresponding Author
    Nature Protocols. 2011 Sep 29;6(10):1656-68

  • Initial genome sequencing and analysis of multiple myeloma.
    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.
    Nature. 2011 Mar 24;471(7339):467-72.

  • Reprogramming factor expression initiates widespread targeted chromatin remodeling.
    Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A.
    Cell Stem Cell. 2011 Jan 7;8(1):96-105

  • 2010

    Nature methods Cover image
  • Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors.
    Adli M, Zhu J & Bernstein BE.
    Nature Methods. 2010 Aug;7(8):615-8

  • IKKalpha and IKKbeta each function to regulate NF-kappaB activation in the TNF-induced/canonical pathway.
    Adli M, Merkhofer E, Cogswell P & Baldwin AS.
    PloS One. 2010 Feb 25;5(2):e9428.

  • Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.
    Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE.
    Nature Methods. 2010 Aug;7(8):615-8.

  • 2008 and before

  • Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
    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.
    PloS Genetics. 2008 Oct;4(10):e1000242.

  • Regulation of mammalian target of rapamycin activity in PTEN-inactive prostate cancer cells by I kappa B kinase alpha.
    Dan HC, Adli M, Baldwin, AS.
    Cancer Research. 2007 Jul 1;67(13):6263-9

  • IKK-i/IKKepsilon controls constitutive, cancer cell-associated NF-kappaB activity via regulation of Ser-536 p65/RelA phosphorylation.
    Adli M & Baldwin AS.
    Journal of Biological Chemistry. 2006 Sep 15;281(37):26976-84

  • Resveratrol protects against 4-HNE induced oxidative stress and apoptosis in Swiss 3T3 fibroblasts.
    Kutuk O, Adli M, Poli G, Basaga H.
    BioFactors.2004;20(1):1-10.

  • 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