Lorenzini, M.H., Balderson, B., Sajeev, K., Ho, A.J., McVicker, G. Joint single-cell profiling of Cas9 edits and transcriptomes reveals widespread off-target events and effects on gene expression. (2025) bioRxiv. DOI: 10.1101/2025.02.07.636966

Balderson, B., Tule, S., Okino, M.L., Rieger, W.J., Corban, S., Jaureguy, J., Palpant, N., Gaulton, K.J., Bodén, M., McVicker, G. Comprehensive molecular impact mapping of common and rare variants at GWAS loci. (2025) bioRxiv. DOI: 10.1101/2025.06.05.658079

Arthur, T.D., Nguyen, J.P., Henson, B.A., D'Antonio-Chronowska, A., Jaureguy, J., Silva, N., , Panopoulos, A.D., Izpisua Belmonte, J.C., D'Antonio, M., McVicker, G., Frazer, K.A. Multiomic QTL mapping reveals phenotypic complexity of GWAS loci and prioritizes putative causal variants. (2025) Zellgenom.:100775 DOI: 10.1016/j.xgen.2025.100775

Laub, D., Ho, A., Jaureguy, J., Klie, A., Salem, R.M., McVicker, G., Carter, H. GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics. (2025) bioRxiv. DOI: 10.1101/2025.01.15.633240

Zhou, J.L., Guruvayurappan, K., Toneyan, S., Chen, H.V., Chen, A.R., Koo, P., McVicker, G. Analysis of single-cell CRISPR perturbations indicates that enhancers predominantly act multiplicatively. (2024) Zellgenom.:100672 DOI: 10.1016/j.xgen.2024.100672

Arthur, T.D., Nguyen, J.P., D'Antonio-Chronowska, A., Jaureguy, J., Silva, N., Henson, B., , Panopoulos, A.D., Belmonte, J.C.I., D'Antonio, M., McVicker, G., Frazer, K.A. Multi-omic QTL mapping in early developmental tissues reveals phenotypic and temporal complexity of regulatory variants underlying GWAS loci. (2024) bioRxiv. DOI: 10.1101/2024.04.10.588874

Zhou, J.L., de Guglielmo, G., Ho, A.J., Kallupi, M., Pokhrel, N., Li, H.R., Chitre, A.S., Munro, D., Mohammadi, P., Carrette, L.L.G., George, O., Palmer, A.A., McVicker, G., Telese, F. Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in gene amygdala GABAergic inhibition. (2023) Nature Neuroscience. DOI: 10.1038/s41593-023-01452-y

Zhou, J., Guruvayurappan, K., Chen, H.V., Chen, A.R., McVicker, G. Genome-wide analysis of CRISPR perturbations indicates that enhancers act multiplicatively and without epistatic-like interactions. (2023) bioRxiv. DOI: 10.1101/2023.04.26.538501

Chen, H.V., Lorenzini, M.H., Lavalle, S.N., Sajeev, K., Fonseca, A., Fiaux, P.C., Sen, A., Luthra, I., Ho, A.J., Chen, A.R., Guruvayurappan, K., O'Connor, C., McVicker, G. Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases. (2023) American Journal of Human Genetics. DOI: 10.1016/j.ajhg.2023.03.008

Xu, Z., Lee, D.S., Chandran, S., Le, V.T., Bump, R., Yasis, J., Dallarda, S., Marcotte, S., Clock, B., Haghani, N., Cho, C.Y., Akdemir, K.C., Tyndale, S., Futreal, P.A., McVicker, G., Wahl, G.M., Dixon, J.R. Structural variants drive context-dependent oncogene activation in cancer. (2022) Natur. DOI: 10.1038/s41586-022-05504-4

Chen, P.B., Fiaux, P.C., Zhang, K., Li, B., Kubo, N., Jiang, S., Hu, R., Rooholfada, E., Wu, S., Wang, M., Wang, W., McVicker, G., Mischel, P.S., Ren, B. Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation. (2022) Cell Reports. 41(6):111630. DOI: 10.1016/j.celrep.2022.111630

Sen, A., Huo, Y., Elster, J., Zage, P.E., McVicker, G. Allele-specific expression reveals genes with recurrent cis-regulatory alterations in high-risk neuroblastoma. (2022) Genome Biology. 23(1):71. DOI: 10.1186/s13059-022-02640-y

Sen, A., Prager, B.C., Zhong, C., Park, D., Zhu, Z., Gimple, R.C., Wu, Q., Bernatchez, J.A., Beck, S., Clark, A.E., Siqueira-Neto, J.L., Rich, J.N., McVicker, G. Leveraging Allele-Specific Expression for Therapeutic Response Gene Discovery in Glioblastoma. (2021) Cancer Research. DOI: 10.1158/0008-5472.CAN-21-0810

Massarat, A.R., Sen, A., Jaureguy, J., Tyndale, S.T., Fu, Y., Erikson, G., McVicker, G. Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq. (2021) Nucleic Acids Research. DOI: 10.1093/nar/gkab621

Fiaux, P.C., Chen, H.V., Chen, P.B., Chen, A.R., McVicker, G. Discovering functional sequences with RELICS, an analysis method for CRISPR screens. (2020) PLOS Computational Biology. 16(9):e1008194. DOI: 10.1371/journal.pcbi.1008194

Nott, A., Holtman, I.R., Coufal, N.G., Schlachetzki, J.C.M., Yu, M., Hu, R., Han, C.Z., Pena, M., Xiao, J., Wu, Y., Keulen, Z., Pasillas, M.P., O'Connor, C., Nickl, C.K., Schafer, S.T., Shen, Z., Rissman, R.A., Brewer, J.B., Gosselin, D., Gonda, D.D., Levy, M.L., Rosenfeld, M.G., McVicker, G., Gage, F.H., Ren, B., Glass, C.K. Brain cell type-specific enhancer-promoter interactome maps and disease risk association. (2019) Wissenschaft. 366(6469):1134-1139. DOI: 10.1126/science.aay0793

Schmiedel, B.J., Singh, D., Madrigal, A., Valdovino-Gonzalez, A.G., White, B.M., Zapardiel-Gonzalo, J., Ha, B., Altay, G., Greenbaum, J.A., McVicker, G., Seumois, G., Rao, A., Kronenberg, M., Peters, B., Vijayanand, P. Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. (2018) Cell. DOI: 10.1016/j.cell.2018.10.022

Martin, R.L., Maiorano, J., Beitel, G.J., Marko, J.F., McVicker, G., Fondufe-Mittendorf, Y.N. A comparison of nucleosome organization in Drosophila cell lines. (2017) PLOS One. 12(6):e0178590. DOI: 10.1371/journal.pone.0178590

Elyashiv, E., Sattath, S., Hu, T.T., Strutsovsky, A., McVicker, G., Andolfatto, P., Coop, G., Sella, G. A Genomic Map of the Effects of Linked Selection in Drosophila. (2016) PLOS Genetics. 12(8):e1006130. DOI: 10.1371/journal.pgen.1006130

van de Geijn, B.*, McVicker, G.*, Gilad, Y., Pritchard, J.K. WASP: allele-specific software for robust molecular quantitative trait locus discovery. (2015) Nature Methods. 12(11):1061-1063. DOI: 10.1038/nmeth.3582

Banovich, N.E., Lan, X., McVicker, G., van de Geijn, B., Degner, J.F., Blischak, J.D., Roux, J., Pritchard, J.K., Gilad, Y. Methylation QTLs are associated with coordinated changes in transcription factor binding, histone modifications, and gene expression levels. (2014) PLOS Genetics. 10(9):e1004663. DOI: 10.1371/journal.pgen.1004663

Nalabothula, N.*, McVicker, G.*, Maiorano, J., Martin, R., Pritchard, J.K., Fondufe-Mittendorf, Y.N. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. (2014) BMC Genomics. 15:92. DOI: 10.1186/1471-2164-15-92

Raj, A., McVicker, G. The genome shows its sensitive side. (2014) Nature Methods. 11(1):39-40. DOI: 10.1038/nmeth.2770

McVicker, G.*, van de Geijn, B.*, Degner, J.F., Cain, C.E., Banovich, N.E., Raj, A., Lewellen, N., Myrthil, M., Gilad, Y., Pritchard, J.K. Identification of genetic variants that affect histone modifications in human cells. (2013) Wissenschaft. 342(6159):747-9. DOI: 10.1126/science.1242429

Gaffney, D.J.*, McVicker, G.*, Pai, A.A., Fondufe-Mittendorf, Y.N., Lewellen, N., Michelini, K., Widom, J., Gilad, Y., Pritchard, J.K. Controls of nucleosome positioning in the human genome. (2012) PLOS Genetics. 8(11):e1003036. DOI: 10.1371/journal.pgen.1003036

George, R.D., McVicker, G., Diederich, R., Ng, S.B., MacKenzie, A.P., Swanson, W.J., Shendure, J., Thomas, J.H. Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection. (2011) Genome Research. 21(10):1686-1694. DOI: 10.1101/gr.121327.111

D'Souza, C.A., Kronstad, J.W., Taylor, G., Warren, R., Yuen, M., Hu, G., Jung, W.H., Sham, A., Kidd, S.E., Tangen, K., Lee, N., Zeilmaker, T., Sawkins, J., McVicker, G., Shah, S., Gnerre, S., Griggs, A., Zeng, Q., Bartlett, K., Li, W., Wang, X., Heitman, J., Stajich, J.E., Fraser, J.A., Meyer, W., Carter, D., Schein, J., Krzywinski, M., Kwon-Chung, K.J., Varma, A., Wang, J., Brunham, R., Fyfe, M., Ouellette, B.F., Siddiqui, A., Marra, M., Jones, S., Holt, R., Birren, B.W., Galagan, J.E., Cuomo, C.A. Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. (2011) MBio. 2(1):e00342-10. DOI: 10.1128/mBio.00342-10

McVicker, G., Green, P. Genomic signatures of germline gene expression. (2010) Genome Research. 20(11):1503-1511. DOI: 10.1101/gr.106666.110

McVicker, G., Gordon, D., Davis, C., Green, P. Widespread genomic signatures of natural selection in hominid evolution. (2009) PLOS Genetics. 5(5):e1000471. DOI: 10.1371/journal.pgen.1000471

Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez-Suarez, X.M., Gilbert, J., Hammond, M., Herrero, J., Hotz, H., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Kokocinsci, F., London, D., Longden, I., McVicker, G., Melsopp, C., Meidl, P., Potter, S., Proctor, G., Rae, M., Rios, D., Schuster, M., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Trevanion, S., Ureta-Vidal, A., Vogel, J., White, S., Woodwark, C., Birney, E. Ensembl 2005. (2005) Nucleic Acids Research. 33(Database i):D447-D453. DOI: 10.1093/nar/gki138

Stabenau, A., McVicker, G., Melsopp, C., Proctor, G., Clamp, M., Birney, E. The Ensembl core software libraries. (2004) Genome Research. 14(5):929-933. DOI: 10.1101/gr.1857204

Birney, E., Andrews, T.D., Bevan, P., Caccamo, M., Chen, Y., Clarke, L., Coates, G., Cuff, J., Curwen, V., Cutts, T., Down, T., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H.R., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, K.C., Cameron, G., Durbin, R., Cox, A., Hubbard, T., Clamp, M. An overview of Ensembl. (2004) Genome Research. 14(5):925-8. DOI: 10.1101/gr.1860604

Birney, E., Andrews, D., Bevan, P., Caccamo, M., Cameron, G., Chen, Y., Clarke, L., Coates, G., Cox, T., Cuff, J., Curwen, V., Cutts, T., Down, T., Durbin, R., Eyras, E., Fernandez-Suarez, X.M., Gane, P., Gibbins, B., Gilbert, J., Hammond, M., Hotz, H., Iyer, V., Kahari, A., Jekosch, K., Kasprzyk, A., Keefe, D., Keenan, S., Lehvaslaiho, H., McVicker, G., Melsopp, C., Meidl, P., Mongin, E., Pettett, R., Potter, S., Proctor, G., Rae, M., Searle, S., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Ureta-Vidal, A., Woodwark, C., Clamp, M., Hubbard, T. Ensembl 2004. (2004) Nucleic Acids Research. 32(Database i):D468-D470. DOI: 10.1093/nar/gkh038

Shah, S.P., McVicker, G.P., Mackworth, A.K., Rogic, S., Ouellette, B.F. GeneComber: combining outputs of gene prediction programs for improved results. (2003) Bioinformatics . 19(10):1296-1297.