Zhou JL, Guruvaryurappan K, Chen HV, Chen AR, McVicker G (2023) Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and without epistatic-like interactions BioRxiv.
Preprint

Zhou JL, de Guglielmo G, Ho AJ, Kallupi M, Pokhrel N, Li H, Chitre AS, Munro D, Mohammadi P, Carrette LLG, George O, Palmer AA, McVicker G*, Telese F* (2023) Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. Nature Neuroscience
Journal

Chen HV*, Lorenzini MH*, Lavalle SN*, Sajeev K, Fonseca A, Fiaux PC, Sen A, Luthra I, Ho AJ, Chen AR, Guruvayurappan K, O’Connor C, McVicker G (2023). Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases. American Journal of Human Genetics.
Journal

Xu Z*, Lee DS*, Chandran S, Le VT, Bump R, Yasis J, Dallarda S, Marcotte S, Clock B, Haghani N, Cho CY, Akdemir K, Tyndale S, Futreal PA, McVicker G, Wahl GM, Dixon JR. (2022) Structural variants drive context-dependent oncogene activation in cancer. Nature.
Journal

Chen PB, Fiaux PC, Zhang K, Li B, Kubo N, Jiang S, Hu R, Rooholfada E, Wu S, Wang M, Wang W, McVicker G, Mischel P, Ren B. (2022) Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. Cell Reports.
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Sen A, Huo Y, Elster J, Zage PE, McVicker G (2022). Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma Genome Biology.
Journal

Sen A*, Prager BC*, Zhong C, Park D, Zhu Z, Gimple RC, Wu Q, Bernatchez JA, Beck S, Clark AE, Siqueira-Neto JL, Rich JN, McVicker G (2022) Leveraging Allele-Specific Expression for Therapeutic Response Gene Discovery in Glioblastoma. Cancer Research.
Journal

Massarat AR, Sen A, Jaureguy J, Tyndale ST, Fu Y, Erikson G, McVicker G (2021) Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq. Nucleic Acids Research.
Journal

Fiaux PC, Chen HV, Chen PB, Chen AR, McVicker G (2020) Discovering functional sequences with RELICS, an analysis method for CRISPR screens. PLOS Computational Biology.
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Nott A*, Holtman IR*, Coufal NG*, Schlachetzki JCM, Yu M, Hu R, Han CZ, Pena M, Xiao J, Wu Y, Keulen Z, Pasillas MP, O’Connor C, Nickl CK, Schafer ST, Shen Z, Rissman RA, Brewer JB, Gosselin D, Gonda DD, Levy ML, Rosenfeld MG, McVicker G, Gage FH, Ren B, Glass CK. (2019) Brain cell type-specific enhancer-promoter interactome maps and disease risk association. Science.
Journal

Schmiedel BJ, Singh D,1 Madrigal A, Valdovino-Gonzalez AG, White BM,1 Zapardiel-Gonzalo Jose, Ha B, Altay G, Greenbaum JA, McVicker G, Seumois G, Rao A, Kronenberg M, Peters B, Vijayanand P. (2018) Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. Cell.
Journal PubMed Central

Martin RL, Maiorano J, Beitel GJ, Marko JF, McVicker G, Fondufe-Mittendorf YN. (2017) A comparison of nucleosome organization in Drosophila cell lines. PLOS One.
Journal

van de Geijn B*, McVicker G*, Gilad Y, Pritchard JK (2015) WASP: allele-specific software for robust discovery of molecular quantitative trait loci. Nature Methods.
Journal PubMed Central

Banovich NE*, Lan X*, McVicker G, van de Geijn B, Degner JF, Blischak JD, Roux J, Pritchard JK, Gilad Y. (2014). Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. PLOS Genetics, 10(9):e1004663.
Journal PubMed Central

Nalabothula N*, McVicker G*, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN (2014) The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics,15:92.
Journal PubMed Central

McVicker G*, van de Geijn B*, Degner JF, Cain CE, Banovich NE, Lewellen N, Myrthil M, Gilad Y, Pritchard JK (2013). Identification of genetic variants that affect histone modification in human cells. Science, 342(6159):747-9.
Journal PubMed Central

Gaffney DJ*, McVicker G*, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK (2012). Controls of nucleosome positioning in the human genome. PLOS Genetics, 8(11):e1003036.
Journal PubMed Central

D’Souza CA et al. [one of 41 authors] (2011) Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio, 2(1):e00342-10.
Journal PubMed Central

George RD, McVicker G, Diederich R, Ng SB, MacKenzie AP, Swanson WJ, Shendure J, Thomas JH (2011). Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. Genome Research, 14(5):929-33.
Journal PubMed Central

McVicker G, Green P (2010). Genomic signatures of germline gene expression. Genome Research, 20(11):1503-11.
Journal PubMed Central

McVicker G, Gordon D, Davis C, Green P (2009). Widespread genomic signatures of natural selection in hominid evolution. PLOS Genetics, 5(5):e1000471.
Journal PubMed Central

Hubbard T et al. [one of 55 authors] (2005). Ensembl 2005. Nucleic Acids Research, 33:D447-53.
Journal PubMed Central

Stabenau A, McVicker G, Melsopp C, Proctor G, Clamp M, Birney E (2004). The Ensembl Core Software Libraries. Genome Research, 14(5):929-33.
Journal PubMed Central

Birney E et al. [one of 48 authors] (2004). An overview of Ensembl. Genome Research, 14(5):925-8.
Journal PubMed Central

Birney E et al. [one of 48 authors] (2004). Ensembl 2004. Nucleic Acids Research, 32:D468-70.
Journal PubMed Central

Shah S, McVicker G, Mackworth A, Rogic S, Ouellette BFF (2003) GeneComber: Combining outputs of gene prediction programs for improved results. Bioinformatics, 19(10): 1296-7
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