2017

  • Tyler E. Miller, Brian B. Liau, Lisa C. Wallace, Andrew R. Morton, Qi Xie, Deobrat Dixit, Daniel C. Factor, Leo J. Y. Kim, James J. Morrow, Qiulian Wu, Stephen C. Mack, Christopher G. Hubert, Shawn M. Gillespie, William A. Flavahan, Thomas Hoffmann, Rohit Thummalapalli, Michael T. Hemann, Patrick J. Paddison, Craig M. Horbinski, Johannes Zuber, Peter C. Scacheri, Bradley E. Bernstein, Paul J. Tesar & Jeremy N. Rich. (2017).

    Transcription elongation factors represent in vivo cancer dependencies in glioblastoma

    Nature (Epub ahead of print)
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  • Andrea J. Cohen, Alina Saiakhova, Olivia Corradin, Jennifer M. Luppino, Katreya Lovrenert, Cynthia F. Bartels, James J. Morrow, Stephen C. Mack, Gursimran Dhillon, Lydia Beard, Lois Myeroff, Matthew F. Kalady, Joseph Willis, James E. Bradner, Ruth A. Keri, Nathan A. Berger, Shondra M. Pruett-Miller, Sanford D. Markowitz & Peter C. Scacheri. (2017).

    Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

    Nat. Commun. 8, 14400 doi: 10.1038/ncomms14400 (Epub ahead of print)
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    2016

  • Olivia Corradin, Andrea J Cohen, Jennifer M Luppino, Ian M Bayles, Fredrick R Schumacher & Peter C Scacheri. (2016).

    Previous article NATURE GENETICS | ANALYSIS Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry

    Nature Genetics 48, 1313–1320 doi:10.1038/ng.3674
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  • Merry CR, McMahon S, Forrest ME, Bartels CF, Saiakhova A, Bartel CA, Scacheri PC, Thompson CL, Jackson MW, Harris LN, Khalil AM.. (2016).

    Transcriptome-wide identification of mRNAs and lincRNAs associated with trastuzumab-resistance in HER2-positive breast cancer.

    Oncotarget. (Epub ahead of print)
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    2015

  • Scacheri CA, Scacheri PC.. (2015).

    Mutations in the noncoding genome

    Curr Opin Pediatr.2015 Dec;27(6):659-64

  • Mack SC, Rich JN, Scacheri PC.. ().

    “PEAR-ing” Genomic and Epigenomic Analyses for Cancer Gene Discovery.

    Cancer Discov. 5(10):1018-20
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    2015

  • Vučićević D, Corradin O, Ntini E, Scacheri PC, Ørom UA. (2015).

    Long ncRNA expression associates with tissue-specific enhancers.

    Cell Cycle;14(2):253-60
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  • Bailey SD, Zhang X, Desai K, Aid M, Corradin O, Cowper-Sal Lari R, Akhtar-Zaidi B, Scacheri PC, Haibe-Kains B, Lupien M. ().

    ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters.

    Nat Commun;2:6186
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    2014

  • Corradin O, Scacheri PC. (2014).

    Enhancer variants: evaluating functions in common disease

    Genome Med;6:85
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  • Factor DC*, Corradin O*, Zentner GE, Saiakhova A, Song L, Chenoweth JG, McKay RD, Crawford GE, Scacheri PC**, Tesar PJ**. (*Co-first, **Co-senior). (2014).

    Epigenomic comparison reveals activation of “seed” enhancers during transition from naive to primed pluripotency.

    Cell Stem Cell
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  • Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal Lari R, Lupien M, Markowitz S, Scacheri PC. (2014).

    Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits.

    Genome Res;24(1):1-13
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    2013

  • Zentner GE, Balow SA, Scacheri PC. (2013).

    Genomic Characterization of the Mouse Ribosomal DNA Locus

    G3: Genes, Genomes, Genetics
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  • Balow SA, Pierce LX, Zentner GE, Conrad PA, Davis S, Sabaawy HE, McDermott BM, Scacheri PC. (2013).

    Knockdown of fbxl10/kdm2bb rescues chd7 morphant phenotype in a zebrafish model of CHARGE syndrome.

    Dev Biol;:
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    2012

  • Goodnough LH, Chang AT, Treloar C, Yang J, Scacheri PC, Atit RP. (2012).

    Twist1 mediates repression of chondrogenesis by β-catenin to promote cranial bone progenitor specification

    Development;139(23):4428-38
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  • Balasubramanian D, Akhtar-Zaidi B, Song L, Bartels CF, Veigl M, Beard L, Myeroff L, Guda K, Lutterbaugh J, Willis J, Crawford GE, Markowitz SD, Scacheri PC. (2012).

    H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites

    Genome Med;4(5):47
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  • Tie F, Banerjee R, Conrad PA, Scacheri PC, Harte PJ. (2012).

    Histone demethylase UTX and chromatin remodeler BRM bind directly to CBP and modulate acetylation of histone H3 lysine 27

    Mol Cell Biol;32(12):2323-34
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  • Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF, Willis J, Moore JH, Tesar PJ, Laframboise T, Markowitz S, Lupien M, Scacheri PC. (2012).

    Epigenomic enhancer profiling defines a signature of colon cancer

    Science;336(6082):736-9
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  • Tian C, Yu H, Yang B, Han F, Zheng Y, Bartels CF, Schelling D, Arnold JE, Scacheri PC, Zheng QY. (2012).

    Otitis media in a new mouse model for CHARGE syndrome with a deletion in the Chd7 gene

    PLoS One;7(4):e34944
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    2011

  • Najm FJ, Zaremba A, Caprariello AV, Nayak S, Freundt EC, Scacheri PC, Miller RH, Tesar PJ. (2011).

    Rapid and robust generation of functional oligodendrocyte progenitor cells from epiblast stem cells

    Nat Methods;8(11):957-62
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  • Zentner GE, Tesar PJ, Scacheri PC. (2011).

    Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

    Genome Res;:
    View Publication

  • Gabriel E. Zentner, Alina Saiakhova, Pavel Manaenkov, Mark D. Adams, Peter C. Scacheri. (2011).

    Integrative genomic analysis of human ribosomal DNA

    Nucleic Acids Research;doi: 10.1093

    2010

  • Bartels CF, Scacheri C, White L, Scacheri PC, Bale S. (2010).

    Mutations in the CHD7 Gene: The Experience of a Commercial Laboratory

    Genet Test Mol Biomarkers;14(6):881-91
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  • Tran TH, Jarrell A, Zentner GE, Welsh A, Brownell I, Scacheri PC, Atit R. (2010).

    Role of canonical Wnt signaling/{beta}-catenin via Dermo1 in cranial dermal cell development

    Development;:
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  • Zentner GE, Hurd EA, Schnetz MP, Handoko L, Wang C, Wang Z, Wei CL, Tesar PJ, Hatzoglou M, Martin DM, Scacheri PC. (2010).

    CHD7 functions in the nucleolus as a positive regulator of ribosomal RNA biogenesis

    Human Molecular Genetics;doi:10.1093

  • Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T, Tesar P, Wei CL, Scacheri PC. (2010).

    CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression

    PLoS Genet;6(7):e1001023
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  • Zentner GE, Layman WS, Martin DM, Scacheri PC. (2010).

    Molecular and phenotypic aspects of CHD7 mutation in CHARGE syndrome

    Am J Med Genet A;152A(3):674-686
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    2009

  • Balasubramanian D, Scacheri PC (2008). (2009).

    Functional studies of menin through genetic manipulation of the Men1 homolog in mice

    Adv Exp Med Biol;668:105-15
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  • Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, Zlobin A, Diaz MO, Scacheri PC, Harte PJ. (2009).

    CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing

    Development;136(18):3131-41
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  • Tao M, Scacheri PC, Marinis JM, Harhaj EW, Matesic LE, Abbott DW. (2009).

    ITCH K63-ubiquitinates the NOD2 binding protein, RIP2, to influence inflammatory signaling pathways

    Curr Biol;19(15):1255-63
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  • Schnetz MP, Bartels CF, Shastri K, Balasubramanian D, Zentner GE, Balaji R, Zhang X, Song L, Wang Z, Laframboise T, Crawford GE, Scacheri PC. (2009).

    Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

    Genome Res;:
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    2008

  • Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. (2008).

    Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

    Genome Res;18(3):393-403
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  • Zhang X, Guo C, Chen Y, Shulha HP, Schnetz MP, LaFramboise T, Bartels CF, Markowitz S, Weng Z, Scacheri PC, Wang Z. (2008).

    Epitope tagging of endogenous proteins for genome-wide ChIP-chip studies

    Nat Methods;5(2):163-5
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    2007

  • Agarwal SK, Impey S, McWeeney S, Scacheri PC, Collins FS, Goodman RH, Spiegel AM, Marx SJ. (2007).

    Distribution of menin-occupied regions in chromatin specifies a broad role of menin in transcriptional regulation

    Neoplasia;9(2):101-7
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    2006

  • Scacheri PC, Crawford GE, Davis S. (2006).

    Statistics for ChIP-chip and DNAse hypersensitivity experiments on NimbleGen arrays

    Methods Enzym.;411:270-82
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  • Crawford GE, Davis S,Scacheri PC,Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. (2006).

    DNase-chip: A high resolution method to identify DNaseI hypersensitive sites using tiled microarrays

    Nature Methods;3:503-9
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  • Scacheri PC, Davis S, Odom DT, Crawford GE, Perkins S, Halawi MJ, Agarwal SK, Marx SJ, Spiegel AM, Meltzer PS, Collins FS. (2006).

    Genome-wide analysis of menin binding provides insights into MEN1 tumorigenesis

    PLoS Genet.;2(4):e51
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    2005

  • Agarwal SK, Kennedy PA, Scacheri PC, Novotny EA, Hickman AB, Cerrato A, Rice TS, Moore JB, Rao S, Ji Y, Mateo C, Libutti SK, Oliver B, Chandrasekharappa SC, Burns AL, Collins FS, Spiegel AM, Marx SJ. (2005).

    Menin molecular interactions: insights into normal functions and tumorigenesis

    Horm Metab Res.;37(6):369-74
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    2004

  • Scacheri PC, Crabtree JS, Kennedy AL, Swain GP, Ward JM, Marx SJ, Spiegel AM, Collins FS. (2004).

    Homozygous loss of menin is well tolerated in liver, a tissue not affected in MEN1

    Mamm Genome.;15(11):872-7
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  • Scacheri PC, Kennedy AL, Chin K, Miller MT, Hodgson JG, Gray JW, Marx SJ, Spiegel AM, Collins FS. (2004).

    Pancreatic insulinomas in multiple endocrine neoplasia, type I knockout mice can develop in the absence of chromosome instability or microsatellite instability

    Cancer Res.;64(19):7039-44
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  • Agarwal SK, Lee Burns A, Sukhodolets KE, Kennedy PA, Obungu VH, Hickman AB, Mullendore ME, Whitten I, Skarulis MC, Simonds WF, Mateo C, Crabtree JS, Scacheri PC, Ji Y, Novotny EA, Garrett-Beal L, Ward JM, Libutti SK, Richard Alexander H, Cerrato A, Parisi MJ, Santa Anna-A S, Oliver B, Chandrasekharappa SC, Collins FS, Spiegel AM, Marx SJ. (2004).

    Molecular pathology of the MEN1 gene

    Ann N Y Acad Sci.;1014:189-98
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  • Scacheri PC, Rozenblatt-Rosen O, Caplen NJ, Wolfsberg TG, Umayam L, Lee JC, Hughes CM, Shanmugam KS, Bhattacharjee A, Meyerson M, Collins FS. (2004).

    Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells

    Proc Natl Acad Sci U S A.;101(7):1892-7
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    2003

  • Crabtree JS, Scacheri PC, Ward JM, McNally SR, Swain GP, Montagna C, Hager JH, Hanahan D, Edlund H, Magnuson MA, Garrett-Beal L, Burns AL, Ried T, Chandrasekharappa SC, Marx SJ, Spiegel AM, Collins FS. (2003).

    Of mice and MEN1: Insulinomas in a conditional mouse knockout

    Mol Cell Biol.;23(17):6075-85
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  • Yim SH, Ward JM, Dragan Y, Yamada A, Scacheri PC, Kimura S, Gonzalez FJ. (2003).

    Microarray analysis using amplified mRNA from laser capture microdissection of microscopic hepatocellular precancerous lesions and frozen hepatocellular carcinomas reveals unique and consistent gene e

    Toxicol Pathol.;31(3):295-303
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    2002

  • Scacheri PC, Gillanders EM, Subramony SH, Vedanarayanan V, Crowe CA, Thakore N, Bingler M, Hoffman EP. (2002).

    Novel mutations in collagen VI genes: expansion of the Bethlem myopathy phenotype

    Neurology.;58(4):593-602
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    2001

  • Scacheri PC, Crabtree JS, Novotny EA, Garrett-Beal L, Chen A, Edgemon KA, Marx SJ, Spiegel AM, Chandrasekharappa SC, Collins FS. (2001).

    Bidirectional transcriptional activity of PGK-neomycin and unexpected embryonic lethality in heterozygote chimeric knockout mice

    Genesis.;30(4):259-63
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  • Crabtree JS, Scacheri PC, Ward JM, Garrett-Beal L, Emmert-Buck MR, Edgemon KA, Lorang D, Libutti SK, Chandrasekharappa SC, Marx SJ, Spiegel AM, Collins FS. (2001).

    A mouse model of multiple endocrine neoplasia, type 1, develops multiple endocrine tumors

    Proc Natl Acad Sci U S A.;98(3):1118-23
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    2000

  • Scacheri PC, Hoffman EP, Fratkin JD, Semino-Mora C, Senchak A, Davis MR, Laing NG, Vedanarayanan V, Subramony SH. (2000).

    A novel ryanodine receptor gene mutation causing both cores and rods in congenital myopathy

    Neurology.;12;55(11):1689-96
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    1999

  • Scacheri PC, Garcia C, Hebert R, Hoffman EP. (1999).

    Unique PABP2 mutations in “Cajuns” suggest multiple founders of oculopharyngeal muscular dystrophy in populations with French ancestry

    Am J Med Genet.;86(5):477-81
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  • James SW, Bullock KA, Gygax SE, Kraynack BA, Matura RA, MacLeod JA, McNeal KK, Prasauckas KA, Scacheri PC, Shenefiel HL, Tobin HM, Wade SD. (1999).

    nimO, an Aspergillus gene related to budding yeast Dbf4, is required for DNA synthesis and mitotic checkpoint control

    J Cell Sci.;112 ( Pt 9):1313-24
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    1997

  • Garcia-Heras J, Martin JA, Witchel SF, Scacheri PC. (1997).

    De novo der(X)t(X;10)(q26;q21) with features of distal trisomy 10q: case report of paternal origin identified by late replication with BrdU and the human androgen receptor assay (HAR)

    J Med Genet;34: 242-245

  • Morrone A, Zammarchi E, Scacheri PC, Donati MA, Hoop RC, Servidei S, Galluzzi G, Hoffman EP. (1997).

    Asymptomatic dystrophinopathy

    Am J Med Genet.;69(3):261-7
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    1996

  • Hoffman EP, Pegoraro E, Scacheri PC, Burns RG, Taber JW, Weiss L, Spiro A, and Blattner P. (1996).

    Genetic counseling of isolated carriers of Duchenne muscular dystrophy

    Am J Med Genet;63: 573-580

    1995

  • James SW, Mirabito PM, Scacheri PC, Morris NR. (1995).

    The Aspergillus nidulans bimE (blocked-in-mitosis) gene encodes multiple cell cycle functions involved in mitotic checkpoint control and mitosis

    J Cell Sci.;108 ( Pt 11):3485-99
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