• 5082 Citations
20042019

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2019

Chemotherapy-induced distal enhancers drive transcriptional programs to maintain the chemoresistant state in ovarian cancer

Shang, S., Yang, J., Jazaeri, A. A., Duval, A. J., Tufan, T., Fischer, N. L., Benamar, M., Guessous, F., Lee, I., Campbell, R. M., Ebert, P. J., Abbas, T., Landen, C. N., Difeo, A., Scacheri, P. C. & Adli, M., Sep 15 2019, In : Cancer Research. 79, 18, p. 4599-4611 13 p.

Research output: Contribution to journalArticle

3 Scopus citations

Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells

Kuscu, C., Mammeadov, R., Czikora, A., Unlu, H., Tufan, T., Fischer, N. L., Arslan, S., Bekiranov, S., Kanemaki, M. & Adli, M., Jan 4 2019, In : Journal of Molecular Biology. 431, 1, p. 111-121 11 p.

Research output: Contribution to journalArticle

Open Access
5 Scopus citations
2018

CRISPR knockout screening identifies combinatorial drug targets in pancreatic cancer and models cellular drug response

Szlachta, K., Kuscu, C., Tufan, T., Adair, S. J., Shang, S., Michaels, A. D., Mullen, M. G., Fischer, N. L., Yang, J., Liu, L., Trivedi, P., Stelow, E. B., Stukenberg, P. T., Parsons, J. T., Bauer, T. W. & Adli, M., Dec 1 2018, In : Nature communications. 9, 1, 4275.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations

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, B. M. & Adli, M., Nov 7 2018, In : Genome biology. 19, 1, 190.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Super-enhancers maintain renin-expressing cell identity and memory to preserve multi-system homeostasis

Martinez, M. F., Medrano, S., Brown, E. A., Tufan, T., Shang, S., Bertoncello, N., Guessoum, O., Adli, M., Belyea, B. C., Sequeira-Lopez, M. L. S. & Gomez, R. A., Nov 1 2018, In : Journal of Clinical Investigation. 128, 11, p. 4787-4803 17 p.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

Transgenerational effects of bisphenol a on gene expression and DNA methylation of imprinted genes in brain

Drobná, Z., Henriksen, A. D., Wolstenholme, J. T., Montiel, C., Lambeth, P. S., Shang, S., Harris, E. P., Zhou, C., Flaws, J. A., Adli, M. & Rissman, E. F., Jan 1 2018, In : Endocrinology. 159, 1, p. 132-144 13 p.

Research output: Contribution to journalArticle

Open Access
36 Scopus citations
2017

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., Jun 29 2017, In : Nature Methods. 14, 7, p. 710-712 3 p.

Research output: Contribution to journalArticle

98 Scopus citations

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., Mar 14 2017, In : Nature communications. 8, 14725.

Research output: Contribution to journalArticle

Open Access
76 Scopus citations
2016

Evolution of Osteocrin as an activity-regulated factor in the primate brain

Ataman, B., Boulting, G. L., Harmin, D. A., Yang, M. G., Baker-Salisbury, M., Yap, E. L., Malik, A. N., Mei, K., Rubin, A. A., Spiegel, I., Durresi, E., Sharma, N., Hu, L. S., Pletikos, M., Griffith, E. C., Partlow, J. N., Stevens, C. R., Adli, M., Chahrour, M., Sestan, N. & 4 others, Walsh, C. A., Berezovskii, V. K., Livingstone, M. S. & Greenberg, M. E., Nov 9 2016, In : Nature. 539, 7628, p. 242-247 6 p.

Research output: Contribution to journalArticle

46 Scopus citations

Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers

Illendula, A., Gilmour, J., Grembecka, J., Tirumala, V. S. S., Boulton, A., Kuntimaddi, A., Schmidt, C., Wang, L., Pulikkan, J. A., Zong, H., Parlak, M., Kuscu, C., Pickin, A., Zhou, Y., Gao, Y., Mishra, L., Adli, M., Castilla, L. H., Rajewski, R. A., Janes, K. A. & 3 others, Guzman, M. L., Bonifer, C. & Bushweller, J. H., Jun 1 2016, In : EBioMedicine. 8, p. 117-131 15 p.

Research output: Contribution to journalArticle

Open Access
35 Scopus citations
2015

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

Singh, R., Kuscu, C., Quinlan, A., Qi, Y. & Adli, M., 2015, In : Nucleic acids research. 43, 18, e118.

Research output: Contribution to journalArticle

Open Access
92 Scopus citations

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, N. J., Thorpe, J., Lokken, A. A., Singh, R., Hemenway, C. S., Adli, M., Zeleznik-Le, N. J. & Bushweller, J. H., 2015, In : Cell reports. 11, 5, p. 808-820 13 p.

Research output: Contribution to journalArticle

Open Access
52 Scopus citations

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., 2015, In : PLoS genetics. 11, 2, p. 1-19 19 p., e1005001.

Research output: Contribution to journalArticle

Open Access
46 Scopus citations

Epigenetic states of nephron progenitors and epithelial differentiation

Adli, M., Parlak, M., Li, Y. & El-Dahr, S. S., Jun 1 2015, In : Journal of Cellular Biochemistry. 116, 6, p. 893-902 10 p.

Research output: Contribution to journalArticle

7 Scopus citations

Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection

Anderson, C. J., Clark, D. E., Adli, M. & Kendall, M. M., Nov 1 2015, In : PLoS pathogens. 11, 11, e1005278.

Research output: Contribution to journalArticle

Open Access
37 Scopus citations
2014

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease

Kuscu, C., Arslan, S., Singh, R., Thorpe, J. & Adli, M., Jul 2014, In : Nature biotechnology. 32, 7, p. 677-683 7 p.

Research output: Contribution to journalArticle

431 Scopus citations
2013

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo

Abdel-Wahab, O., Gao, J., Adli, M., Dey, A., Trimarchi, T., Chung, Y. R., Kuscu, C., Hricik, T., Ndiaye-Lobry, D., LaFave, L. M., Koche, R., Shih, A. H., Guryanova, O. A., Kim, E., Li, S., Pandey, S., Shin, J. Y., Telis, L., Liu, J., Bhatt, P. K. & 7 others, Monette, S., Zhao, X., Mason, C. E., Park, C. Y., Bernstein, B. E., Aifantis, I. & Levine, R. L., Nov 2013, In : Journal of Experimental Medicine. 210, 12, p. 2641-2659 19 p.

Research output: Contribution to journalArticle

Open Access
177 Scopus citations

Genome-wide chromatin state transitions associated with developmental and environmental cues

Zhu, J., Adli, M., Zou, J. Y., Verstappen, G., Coyne, M., Zhang, X., Durham, T., Miri, M., Deshpande, V., De Jager, P. L., Bennett, D. A., Houmard, J. A., Muoio, D. M., Onder, T. T., Camahort, R., Cowan, C. A., Meissner, A., Epstein, C. B., Shoresh, N. & Bernstein, B. E., Jan 31 2013, In : Cell. 152, 3, p. 642-654 13 p.

Research output: Contribution to journalArticle

Open Access
336 Scopus citations

Using Whole-Exome Sequencing to Identify Inherited Causes of Autism

Yu, T. W., Chahrour, M. H., Coulter, M. E., Jiralerspong, S., Okamura-Ikeda, K., Ataman, B., Schmitz-Abe, K., Harmin, D. A., Adli, M., Malik, A. N., D'Gama, A. M., Lim, E. T., Sanders, S. J., Mochida, G. H., Partlow, J. N., Sunu, C. M., Felie, J. M., Rodriguez, J., Nasir, R. H., Ware, J. & 29 others, Joseph, R. M., Hill, R. S., Kwan, B. Y., Al-Saffar, M., Mukaddes, N. M., Hashmi, A., Balkhy, S., Gascon, G. G., Hisama, F. M., LeClair, E., Poduri, A., Oner, O., Al-Saad, S., Al-Awadi, S. A., Bastaki, L., Ben-Omran, T., Teebi, A. S., Al-Gazali, L., Eapen, V., Stevens, C. R., Rappaport, L., Gabriel, S. B., Markianos, K., State, M. W., Greenberg, M. E., Taniguchi, H., Braverman, N. E., Morrow, E. M. & Walsh, C. A., Jan 23 2013, In : Neuron. 77, 2, p. 259-273 15 p.

Research output: Contribution to journalArticle

Open Access
259 Scopus citations
2012

ASXL1 Mutations Promote Myeloid Transformation through Loss of PRC2-Mediated Gene Repression

Abdel-Wahab, O., Adli, M., LaFave, L. M., Gao, J., Hricik, T., Shih, A. H., Pandey, S., Patel, J. P., Chung, Y. R., Koche, R., Perna, F., Zhao, X., Taylor, J. E., Park, C. Y., Carroll, M., Melnick, A., Nimer, S. D., Jaffe, J. D., Aifantis, I., Bernstein, B. E. & 1 others, Levine, R. L., Aug 14 2012, In : Cancer Cell. 22, 2, p. 180-193 14 p.

Research output: Contribution to journalArticle

Open Access
328 Scopus citations

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, L. M., Mullally, A., Abdel-Wahab, O., Leung, L., Weinstein, A., Marubayashi, S., Goel, A., Gonen, M., Estrov, Z., Ebert, B. L., Chiosis, G., Nimer, S. D., Bernstein, B. E. & 2 others, Verstovsek, S. & Levine, R. L., Sep 6 2012, In : Nature. 489, 7414, p. 155-159 5 p.

Research output: Contribution to journalArticle

213 Scopus citations
2011

Initial genome sequencing and analysis of multiple myeloma

Chapman, M. A., Lawrence, M. S., Keats, J. J., Cibulskis, K., Sougnez, C., Schinzel, A. C., Harview, C. L., Brunet, J. P., Ahmann, G. J., Adli, M., Anderson, K. C., Ardlie, K. G., Auclair, D., Baker, A., Bergsagel, P. L., Bernstein, B. E., Drier, Y., Fonseca, R., Gabriel, S. B., Hofmeister, C. C. & 30 others, Jagannath, S., Jakubowiak, A. J., Krishnan, A., Levy, J., Liefeld, T., Lonial, S., Mahan, S., Mfuko, B., Monti, S., Perkins, L. M., Onofrio, R., Pugh, T. J., Rajkumar, S. V., Ramos, A. H., Siegel, D. S., Sivachenko, A., Stewart, A. K., Trudel, S., Vij, R., Voet, D., Winckler, W., Zimmerman, T., Carpten, J., Trent, J., Hahn, W. C., Garraway, L. A., Meyerson, M., Lander, E. S., Getz, G. & Golub, T. R., Mar 24 2011, In : Nature. 471, 7339, p. 467-472 6 p.

Research output: Contribution to journalArticle

Open Access
972 Scopus citations

Reprogramming factor expression initiates widespread targeted chromatin remodeling

Koche, R. P., Smith, Z. D., Adli, M., Gu, H., Ku, M., Gnirke, A., Bernstein, B. E. & Meissner, A., Jan 7 2011, In : Cell stem cell. 8, 1, p. 96-105 10 p.

Research output: Contribution to journalArticle

Open Access
253 Scopus citations

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

Adli, M. & Bernstein, B. E., Oct 1 2011, In : Nature Protocols. 6, 10, p. 1656-1668 13 p.

Research output: Contribution to journalArticle

127 Scopus citations
2010

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

Adli, M., Zhu, J. & Bernstein, B. E., Aug 1 2010, In : Nature Methods. 7, 8, p. 615-618 4 p.

Research output: Contribution to journalArticle

124 Scopus citations

IKKα and IKKβ each function to regulate NF-κB activation in the TNF-induced/canonical pathway

Adli, M., Merkhofer, E., Cogswell, P. & Baldwin, A. S., Feb 25 2010, In : PloS one. 5, 2, e9428.

Research output: Contribution to journalArticle

Open Access
62 Scopus citations
2008

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., Xie, X., Chi, A. S., Adli, M., Kasif, S., Ptaszek, L. M., Cowan, C. A., Lander, E. S., Koseki, H. & Bernstein, B. E., Oct 2008, In : PLoS genetics. 4, 10, e1000242.

Research output: Contribution to journalArticle

Open Access
683 Scopus citations
2007

Regulation of mammalian target of rapamycin activity in PTEN-inactive prostate cancer cells by IκB kinase α

Dan, H. C., Adli, M. & Baldwin, A. S., Jul 1 2007, In : Cancer Research. 67, 13, p. 6263-6269 7 p.

Research output: Contribution to journalArticle

Open Access
53 Scopus citations
2006

IKK-i/IKKε controls constitutive, cancer cell-associated NF-κB activity via regulation of Ser-536 p65/RelA phosphorylation

Adli, M. & Baldwin, A. S., Sep 15 2006, In : Journal of Biological Chemistry. 281, 37, p. 26976-26984 9 p.

Research output: Contribution to journalArticle

Open Access
111 Scopus citations
2004

Resveratrol protects against 4-HNE induced oxidative stress and apoptosis in Swiss 3T3 fibroblasts

Kutuk, O., Adli, M., Poli, G. & Basaga, H., Jan 1 2004, In : BioFactors. 20, 1, p. 1-10 10 p.

Research output: Contribution to journalArticle

30 Scopus citations