Publications

Publications 

2022
  1. Tip60 acetylation of histone H3K4 temporally controls chromosome passenger complex localization.
    Niedzialkowska E, Liu L, Kuscu C, Mayo Z, Minor W, Strahl BD, Adli M, Stukenberg PT.
    Molecular Biology of Cell, 2022 Aug 1;33(9):br15. doi: 10.1091/mbc.E21-06-0283.
    PMID: 35653296
  1. ISL2 is a putative tumor suppressor whose epigenetic silencing reprograms the metabolism of pancreatic cancer.
    Ozturk H, Cingoz H, Tufan T, Yang J, Adair SJ, Tummala KS, Kuscu C, Kinali M, Comertpay G, Nagdas S, Goudreau BJ, Luleyap HU, Bingul Y, Ware TB, Hwang WL, Hsu KL, Kashatus DF, Ting DT, Chandel NS, Bardeesy N, Bauer TW, Adli M.
    Developmental Cell. 2022 Jun 6;57(11):1331-1346.e9. doi: 10.1016/j.devcel.2022.04.014.
    PMID: 35508175

  2. FOXK2 promotes ovarian cancer stemness by regulating the unfolded protein response pathway.
    Zhang Y, Wang Y, Zhao G, Tanner EJ, Adli M, Matei D.
    Journal of Clinical Investigation. 2022 May 16;132(10):e151591. doi: 10.1172/JCI151591.
    PMID: 35349489

  3. Evolutionary Biology and Gene Editing of Cat Allergen, Fel d 1.
    Brackett NF, Davis BW, Adli M, Pomés A, Chapman MD.
    CRISPR Journal, 2022 Apr;5(2):213-223. doi: 10.1089/crispr.2021.0101.
    PMID: 35343817


2021
  1. A Functional Variant on 9p21.3 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B AS1.
    Ali MW, Patro CPK, Devall M, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lai RK, Casey G.
    Human Mutation, 2021 Oct;42(10):1208-1214. doi: 10.1002/humu.24244. Epub 2021 Jun 29.
    PMID: 34153138

  2. Adenomyosis pathogenesis: insights from next-generation sequencing.
    Bulun SE, Yildiz S, Adli M, Wei JJ.
    Human Reproduction Update, 2021 Oct 18;27(6):1086-1097. doi: 10.1093/humupd/dmab017.
    PMID: 34131719

  3. A functional variant on 20q13.33 related to glioma risk alters enhancer activity and modulates expression of multiple genes.
    Ali MW, Patro CPK, Zhu JJ, Dampier CH, Plummer SJ, Kuscu C, Adli M, Lau C, Lai RK, Casey G.
    Human Mutation, 2021 Jan;42(1):77-88. doi: 10.1002/humu.24134.
    PMID: 33169458

2020
    1. Targeted CRISPR screening identifies PRMT5 as synthetic lethality combinatorial target with gemcitabine in pancreatic cancer cells.
      Wei X, Yang J, Adair SJ, Ozturk H, Kuscu C, Lee KY, Kane WJ, O’Hara PE, Liu D, Demirlenk YM, Habieb AH, Yilmaz E, Dutta A, Bauer TW, Adli M.
      Proceeding of National Academy of Sciences, U S A. 2020 Nov 10;117(45):28068-28079. doi: 10.1073/pnas.2009899117.
      PMID: 33097661

    2. Ethical Considerations in Therapeutic Clinical Trials Involving Novel Human Germline-Editing Technology.
      Brokowski C, Adli M.
      CRISPR Journal. 2020 Feb;3(1):18-26. doi: 10.1089/crispr.2019.0051.
      PMID: 32091258

    2019
    1. Mapping and Making Sense of Noncoding Mutations in the Genome.
      Yang J, Adli M.
      Cancer Research, 2019 Sep 1;79(17):4309-4314. doi: 10.1158/0008-5472.CAN-19-0905.
      PMID: 31387922 Review.

    2. Chemotherapy-Induced Distal Enhancers Drive Transcriptional Programs to Maintain the Chemoresistant State in Ovarian Cancer.
      Shang S, Yang J, Jazaeri AA, Duval AJ, Tufan T, Lopes Fischer N, Benamar M, Guessous F, Lee I, Campbell RM, Ebert PJ, Abbas T, Landen CN, Difeo A, Scacheri PC, Adli M.
      Cancer Research, 2019 Sep 15;79(18):4599-4611. doi: 10.1158/0008-5472.CAN-19-0215.
      PMID: 31358529

    3. The Biology and Application Areas of CRISPR Technologies.
      Adli M.
      Journal of Molecular Biology, 2019 Jan 4;431(1):1-2. doi: 10.1016/j.jmb.2018.11.012.
      PMID: 30447221

    4. Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells.
      Kuscu C, Mammadov R, Czikora A, Unlu H, Tufan T, Fischer NL, Arslan S, Bekiranov S, Kanemaki M, Adli M.
      Journal of Molecular Biology, 2019 Jan 4;431(1):111-121. doi: 10.1016/j.jmb.2018.08.001.
      PMID: 30098338

    5. CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool.
      Brokowski C, Adli M.
      Journal of Molecular Biology, 2019 Jan 4;431(1):88-101. doi: 10.1016/j.jmb.2018.05.044.
      PMID: 29885329

    2018
    1. Recurrent mutations at estrogen receptor binding sites alter chromatin topology and distal gene expression in breast cancer.
      Yang J, Wei X, Tufan T, Kuscu C, Unlu H, Farooq S, Demirtas E, Paschal BM, Adli M.
      Genome Biology, 2018 Nov 7;19(1):190. doi: 10.1186/s13059-018-1572-4.
      PMID: 30404658

    2. CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response.
      Szlachta K, Kuscu C, Tufan T, Adair SJ, Shang S, Michaels AD, Mullen MG, Fischer NL, Yang J, Liu L, Trivedi P, Stelow EB, Stukenberg PT, Parsons JT, Bauer TW, Adli M.
      Nature Commutations, 2018 Oct 15;9(1):4275. doi: 10.1038/s41467-018-06676-2.
      PMID: 30323222

    3. Super-enhancers maintain renin-expressing cell identity and memory to preserve multi-system homeostasis.
      Martinez MF, Medrano S, Brown EA, Tufan T, Shang S, Bertoncello N, Guessoum O, Adli M, Belyea BC, Sequeira-Lopez MLS, Gomez RA.
      Journal of Clinical Investigations, 2018 Nov 1;128(11):4787-4803. doi: 10.1172/JCI121361.
      PMID: 30130256

    4. The CRISPR tool kit for genome editing and beyond.
      Adli M. Nature Communications, 2018 May 15;9(1):1911. doi: 10.1038/s41467-018-04252-2.
      PMID: 29765029


    5. Transgenerational Effects of Bisphenol A on Gene Expression and DNA Methylation of Imprinted Genes in Brain.
      Drobná Z, Henriksen AD, Wolstenholme JT, Montiel C, Lambeth PS, Shang S, Harris EP, Zhou C, Flaws JA, Adli M, Rissman EF. Endocrinology. 2018 Jan 1;159(1):132-144. doi: 10.1210/en.2017-00730.
      PMID: 29165653
    2017
    1. CRISPR-STOP: gene silencing through base-editing-induced nonsense mutations.
      Kuscu C, Parlak M, Tufan T, Yang J, Szlachta K, Wei X, Mammadov R, Adli M.
      Nature Methods, 2017 Jul;14(7):710-712. doi: 10.1038/nmeth.4327.
      PMID: 28581493

    2. 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.
      PMID: 28290446

    2016
    1. 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.
      PMID: 27898061 No abstract available.

    2. 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.
      PMID: 27830782

    3. Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers.
      Illendula A, Gilmour J, Grembecka J, Tirumala VSS, 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;8:117-131. doi: 10.1016/j.ebiom.2016.04.032.
      PMID: 27428424

    2015
    1. Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection.
      Anderson CJ, Clark DE, Adli M, Kendall MM.
      PLoS Pathogen, 2015 Nov 13;11(11):e1005278. doi: 10.1371/journal.ppat.1005278.
      PMID: 26565973

    2. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction.
      Singh R, Kuscu C, Quinlan A, Qi Y, Adli M.
      Nucleic Acids Research, 2015 Oct 15;43(18):e118. doi: 10.1093/nar/gkv575.
      PMID: 26032770

    3. 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.
      PMID: 25921540

    4. Correction: 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 Apr 10;11(4):e1005161. doi: 10.1371/journal.pgen.1005161.
      PMID: 25860022

    5. Integrative analysis of 111 reference human epigenomes.
      Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.
      Nature, 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.
      PMID: 25693563

    6. 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. doi: 10.1371/journal.pgen.1005001.
      PMID: 25658338

    7. Epigenetic States of nephron progenitors and epithelial differentiation.
      Adli M, Parlak M, Li Y, El-Dahr SS.
      Journal of Cellular Biochemistry, 2015 Jun;116(6):893-902. doi: 10.1002/jcb.25048.
      PMID: 25560433

    2014
    1. Synaptic, transcriptional and chromatin genes disrupted in autism.
      De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei 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, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK; DDD Study; Homozygosity Mapping Collaborative for Autism; UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD.
      Nature, 2014 Nov 13;515(7526):209-15. doi: 10.1038/nature13772.
      PMID: 25363760

    2. Minireview: transgenerational epigenetic inheritance: focus on endocrine disrupting compounds.
      Rissman EF, Adli M.
      Endocrinology, 2014 Aug;155(8):2770-80. doi: 10.1210/en.2014-1123.
      PMID: 24885575

    3. 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. doi: 10.1038/nbt.2916.
      PMID: 24837660

    2013
    1. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo.
      Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung YR, Kuscu C, Hricik T, Ndiaye-Lobry D, Lafave LM, Koche R, Shih AH, Guryanova OA, Kim E, Li S, Pandey S, Shin JY, Telis L, Liu J, Bhatt PK, Monette S, Zhao X, Mason CE, Park CY, Bernstein BE, Aifantis I, Levine RL.
      Journal of Experimental Medicine, 2013 Nov 18;210(12):2641-59. doi: 10.1084/jem.20131141.
      PMID: 24218140

    2. Using whole-exome sequencing to identify inherited causes of autism.
      Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin DA, Adli M, Malik AN, D’Gama AM, Lim ET, Sanders SJ, Mochida GH, Partlow JN, Sunu CM, Felie JM, Rodriguez J, Nasir RH, Ware J, Joseph RM, Hill RS, Kwan BY, Al-Saffar M, Mukaddes NM, Hashmi A, Balkhy S, Gascon GG, Hisama FM, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi SA, Bastaki L, Ben-Omran T, Teebi AS, Al-Gazali L, Eapen V, Stevens CR, Rappaport L, Gabriel SB, Markianos K, State MW, Greenberg ME, Taniguchi H, Braverman NE, Morrow EM, Walsh CA.
      Neuron, 2013 Jan 23;77(2):259-73. doi: 10.1016/j.neuron.2012.11.002.
      PMID: 23352163

    3. Genome-wide chromatin state transitions associated with developmental and environmental cues.
      Zhu J, Adli M#, Zou JY, 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 CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE#.
      Cell, 2013 Jan 31;152(3):642-54. doi: 10.1016/j.cell.2012.12.033.
      PMID: 23333102
      *Co-first, #Co-correspondence

    2012
    1. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.
      Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, Pandey S, 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.
      Cancer Cell, 2012 Aug 14;22(2):180-93. doi: 10.1016/j.ccr.2012.06.032.
      PMID: 22897849

    2. 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, Gönen M, Estrov Z, Ebert BL, Chiosis G, Nimer SD, Bernstein BE, Verstovsek S, Levine RL.
      Nature, 2012 Sep 6;489(7414):155-9. doi: 10.1038/nature11303.
      PMID: 22820254
    2011
    1. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.
      Adli M, Bernstein BE.
      Nature Protocols, 2011 Sep 29;6(10):1656-68. doi: 10.1038/nprot.2011.402.
      PMID: 21959244

    2. Initial genome sequencing and analysis of multiple myeloma.
      Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, 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. doi: 10.1038/nature09837.
      PMID: 21430775

    3. 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. doi: 10.1016/j.stem.2010.12.001.
      PMID: 21211784
    2010
    1. 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. doi: 10.1038/nmeth.1478.
      PMID: 20622861

    2. 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. doi: 10.1371/journal.pone.0009428.
      PMID: 20195534

    3. 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 Jan;7(1):47-9. doi: 10.1038/nmeth.1404.
      PMID: 19946276

    2008
    1. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
      Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE.
      PLoS Genetics, 2008 Oct;4(10):e1000242. doi: 10.1371/journal.pgen.1000242.
      PMID: 18974828
    2007
    1. 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. doi: 10.1158/0008-5472.CAN-07-1232.
      PMID: 17616684
    2006
    1. 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. doi:
      10.1074/jbc.M603133200.
      PMID: 16840782

    2004
    1. 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. doi: 10.1002/biof.5520200101.
      PMID: 15096656