Publications by GMB Students

Publications on which a GMB student was first or co-first author (indicated by *) are listed below (past five years only).
All GMB student authors are highlighted.

2022

• S.M. Brotman, C.K. Raulerson, S. Vadlamudi, K.W. Currin, Q. Shen, V.A. Parsons, A.K. Iyengar, T.S. Roman, T.S. Furey, J. Kuusisto, F.S. Collins, M. Boehnke, M. Laakso, P. Pajukanta, and K.L. Mohlke (2022). Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits. Am J Hum Genet 109: 66-80. doi: 10.1016/j.ajhg.2021.11.019.
• J.N. Diehl, P.S. Hibshman, I. Ozkan-Dagliyan, C.M. Goodwin, S.V. Howard, A.D. Cox, and C.J. Der (2022). Targeting the ERK mitogen-activated protein kinase cascade for the treatment of KRAS-mutant pancreatic cancer. Adv Cancer Res 153: 101-130. doi: 10.1016/bs.acr.2021.07.008.
• C.A. Schmidt, L.Y. Min, M.H. McVay, J.D. Giusto, J.C. Brown, H.R. Salzler, and A.G. Matera (2022). Mutations in Drosophila tRNA processing factors cause phenotypes similar to Pontocerebellar Hypoplasia. Biol Open doi: 10.1242/bio.058928.
• A. Tovar, W.L. Crouse, G.J. Smith, J.M. Thomas, B.P. Keith, K.M. McFadden, T.P. Moran, T.S. Furey, and S.N.P. Kelada (2022). Integrative analysis reveals mouse strain-dependent responses to acute ozone exposure associated with airway macrophage transcriptional activity. Am J Physiol Lung Cell Mol Physiol 322: L33-L49. doi: 10.1152/ajplung.00237.2021.

2021

• J. Carvajal-Garcia, K.N. Crown, D.A. Ramsden, and J. Sekelsky (2021). DNA polymerase theta suppresses mitotic crossing over. PLoS Genet 17: e1009267. doi: 10.1371/journal.pgen.1009267.
• T. Hatkevich, D.E. Miller, C.A. Turcotte, M.C. Miller, and J. Sekelsky (2021). A pathway for error-free non-homologous end joining of resected meiotic double-strand breaks. Nucleic Acids Res 49: 879-890. doi: 10.1093/nar/gkaa1205.
• L.P. Havlik, A. Das, M. Mietzsch, D.K. Oh, J. Ark, R. McKenna, M. Agbandje-McKenna, and A. Asokan (2021). Receptor Switching in Newly Evolved Adeno-associated Viruses. J Virol 95: e0058721. doi: 10.1128/JVI.00587-21.
• R.M. Meganck, J. Liu, A.E. Hale, K.E. Simon, M.M. Fanous, H.A. Vincent, J.E. Wilusz, N.J. Moorman, W.F. Marzluff, and A. Asokan (2021). Engineering highly efficient backsplicing and translation of synthetic circRNAs. Mol Ther Nucleic Acids 23: 821-834. doi: 10.1016/j.omtn.2021.01.003.
• M.J. Niederhuber and D.J. McKay (2021). Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. Curr Opin Insect Sci 43: 21-28. doi: 10.1016/j.cois.2020.08.007.
• S.L. Nystrom and D.J. McKay (2021). Memes: A motif analysis environment in R using tools from the MEME Suite. PLoS Comput Biol 17: e1008991. doi: 10.1371/journal.pcbi.1008991.
• N.M. Pazhayam, C.A. Turcotte, and J. Sekelsky (2021). Meiotic Crossover Patterning. Front Cell Dev Biol 9: 681123. doi: 10.3389/fcell.2021.681123.
• J.M. Potter-Birriel, G.B. Gonsalvez, and W.F. Marzluff (2021). A region of SLBP outside the mRNA-processing domain is essential for deposition of histone mRNA into the Drosophila egg. J Cell Sci 134: doi: 10.1242/jcs.251728.
• N.L. Rittenhouse, Z.M. Carico, Y.F. Liu, H.C. Stefan, N.L. Arruda, J. Zhou, and J.M. Dowen (2021). Functional impact of cancer-associated cohesin variants on gene expression and cellular identity. Genetics 217: doi: 10.1093/genetics/iyab025.
• R. Rivera-Soto, Y. Yu, D.P. Dittmer, and B. Damania (2021). Combined Inhibition of Akt and mTOR Is Effective Against Non-Hodgkin Lymphomas. Front Oncol 11: 670275. doi: 10.3389/fonc.2021.670275.
• J.D. Sanford, J. Yang, J. Han, L.A. Tollini, A. Jin, and Y. Zhang (2021). MDMX is essential for the regulation of p53 protein levels in the absence of a functional MDM2 C-terminal tail. BMC Mol Cell Biol 22: 46. doi: 10.1186/s12860-021-00385-3.
• M.J. Slaughter, E.K. Shanle, A. Khan, K.F. Chua, T. Hong, L.D. Boxer, C.D. Allis, S.Z. Josefowicz, B.A. Garcia, S.B. Rothbart, B.D. Strahl, and I.J. Davis (2021). HDAC inhibition results in widespread alteration of the histone acetylation landscape and BRD4 targeting to gene bodies. Cell Rep 34: 108638. doi: 10.1016/j.celrep.2020.108638.
• H.J. Wiedner and J. Giudice (2021). It’s not just a phase: function and characteristics of RNA-binding proteins in phase separation. Nat Struct Mol Biol 28: 465-473. doi: 10.1038/s41594-021-00601-w.

2020

• K. Rehain Bell, M.E. Werner, A. Doshi, D.B. Cortes, A. Sattler, T. Vuong-Brender, M. Labouesse, and A.S. Maddox (2020). Novel cytokinetic ring components drive negative feedback in cortical contractility. Mol Biol Cell 31: 1623-1636. doi: 10.1091/mbc.E20-05-0304.
• G. Broussard and B. Damania (2020). Regulation of KSHV Latency and Lytic Reactivation. Viruses 12: doi: 10.3390/v12091034.
• G. Broussard and B. Damania (2019). KSHV: Immune modulation and immunotherapy. Front Immunol 10: 3084. doi: 10.3389/fimmu.2019.03084.
• J. Carvajal-Garcia, J.E. Cho, P. Carvajal-Garcia, W. Feng, R.D. Wood, J. Sekelsky, G.P. Gupta, S.A. Roberts, and D.A. Ramsden (2020). Mechanistic basis for microhomology identification and genome scarring by polymerase theta. Proc Natl Acad Sci U S A 117: 8476-8485. doi: 10.1073/pnas.1921791117.
• J. Carvajal-Garcia, E.R. Gales, D.A. Ramsden, and J. Sekelsky (2020). The Drosophila melanogaster ortholog of RFWD3 functions independently of RAD51 during DNA repair. G3 (Bethesda) 10: 999-1004. doi: 10.1534/g3.119.400903.
• M. Cheng, X. Yu, K. Lu, L. Xie, L. Wang, F. Meng, X. Han, X. Chen, J. Liu, Y. Xiong, and J. Jin (2020). Discovery of potent and selective epidermal growth factor receptor (EGFR) bifunctional small-molecule degraders. J Med Chem 63: 1216-1232. doi: 10.1021/acs.jmedchem.9b01566.
• A.M. Chiarella, K.V. Butler, B.E. Gryder, D. Lu, T.A. Wang, X. Yu, S. Pomella, J. Khan, J. Jin, and N.A. Hathaway (2020). Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery. Nat Biotechnol 38: 50-55. doi: 10.1038/s41587-019-0296-7.
• T.A. Dinh R. Sritharan, F.D. Smith, A.B. Francisco, R.K. Ma, R.P. Bunaciu, M. Kanke, C.G. Danko, A.P. Massa, J.D. Scott, and P. Sethupathy (2020). Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal candidate oncogenic pathways and therapeutic vulnerabilities. Cell Rep 31: 107509. doi: 10.1016/j.celrep.2020.03.073.
• L.P. Havlik, K.E. Simon, J.K. Smith, K.A. Klinc, L.V. Tse, D.K. Oh, M.M. Fanous, R.M. Meganck, M. Mietzsch, J. Kleinschmidt, M. Agbandje-McKenna, and A. Asokan (2020). Coevolution of Adeno-associated Virus Capsid Antigenicity and Tropism through a Structure-Guided Approach. J Virol 94: doi: 10.1128/JVI.00976-20.
• C. Hodgens, N. Chang, G.E. Schaller, and J.J. Kieber (2020). Mutagenomics: A Rapid, High-Throughput Method to Identify Causative Mutations from a Genetic Screen. Plant Physiol 184: 1658-1673. doi: 10.1104/pp.20.00609.
• M. Justice, Z.M. Carico, H.C. Stefan, and J.M. Dowen (2020). A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity. Cell Rep 31: 107503. doi: 10.1016/j.celrep.2020.03.067.
• L.T. Laudermilk, A. Tovar, A.K. Homstad, J.M. Thomas, K.M. McFadden, M.K. Tune, D.O. Cowley, J.R. Mock, F. Ideraabdullah, and S.N.P. Kelada (2020). Baseline and innate immune response characterization of a Zfp30 knockout mouse strain. Mamm Genome 31: 205-214. doi: 10.1007/s00335-020-09847-z.
• V.J. Madigan, G.E. Berry, T.O. Tyson, D. Nardone-White, J. Ark, Z.C. Elmore, G. Murlidharan, H.A. Vincent, and A. Asokan (2020). The Golgi Calcium ATPase Pump Plays an Essential Role in Adeno-associated Virus Trafficking and Transduction. J Virol 94: doi: 10.1128/JVI.01604-20.
• B.L. Mouery, L. Mei, and J.G. Cook (2020). Programming pluripotent stem cells: Can’t teach an old cell new DNA replication tricks. J Cell Biol 219: doi: 10.1083/jcb.202008014.
• M.J. Niederhuber and D.J. McKay (2020). Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. Curr Opin Insect Sci 43: 21-28. doi: 10.1016/j.cois.2020.08.007.
• S.L. Nystrom, M.J. Niederhuber, and D.J. McKay (2020). Expression of E93 provides an instructive cue to control dynamic enhancer activity and chromatin accessibility during development. Development doi: 10.1242/dev.181909.
• R. Rivera-Soto, N.J. Dissinger, and B. Damania (2020). Kaposi’s Sarcoma-associated herpesvirus viral interleukin-6 signaling upregulates integrin beta3 levels and is dependent on STAT3. J Virol 94: doi: 10.1128/JVI.01384-19.
• K.N. Schaefer, M. Pronobis, C.E. Williams, S. Zhang, L. Bauer, D. Goldfarb, F. Yan, M.B. Major, and M. Peifer (2020). Wnt Regulation: Exploring Axin-Disheveled interactions and defining mechanisms by which the SCF E3 ubiquitin ligase is recruited to the destruction complex. Mol Biol Cell mbcE19110647. doi: 10.1091/mbc.E19-11-0647.
• C.A. Schmidt and A.G. Matera (2020). tRNA introns: Presence, processing, and purpose. Wiley Interdiscip Rev RNA 11: e1583. doi: 10.1002/wrna.1583.
• A. Tovar, G.J. Smith, J.M. Thomas, W.L. Crouse, J.R. Harkema, and S.N.P. Kelada (2020). Transcriptional profiling of the murine airway response to acute ozone exposure. Toxicol Sci 173: 114-130. doi: 10.1093/toxsci/kfz219.

2019

• B.H. Albright, K.E. Simon, M. Pillai, G.W. Devlin, and A. Asokan (2019). Modulation of sialic acid dependence influences the central nervous system transduction profile of adeno-associated viruses. J Virol 93: doi: 10.1128/JVI.00332-19.
• A. Arceci, T. Bonacci, X. Wang, K. Stewart, J.S. Damrauer, K.A. Hoadley, and M.J. Emanuele (2019). FOXM1 deubiquitination by USP21 regulates cell cycle progression and paclitaxel sensitivity in basal-like breast cancer. Cell Rep 26: 3076-3086 e6. doi: 10.1016/j.celrep.2019.02.054.
• R.L. Armstrong and R.J. Duronio (2019). Phasing in heterochromatin during development. Genes Dev 33: 379-381. doi: 10.1101/gad.324731.119.
• R.L. Armstrong, T.J.R. Penke, S.K. Chao, G.M. Gentile, B.D. Strahl, A.G. Matera, D.J. McKay, and R.J. Duronio (2019). H3K9 promotes under-replication of pericentromeric heterochromatin in Drosophila salivary gland polytene chromosomes. Genes (Basel) 10: doi: 10.3390/genes10020093.
• S.H. Azam, A. Porrello, E.B. Harrison, P.L. Leslie, X. Liu, T.A. Waugh, A. Belanger, L.S. Mangala, G. Lopez-Berestein, H.L. Wilson, J.V. McCann, W.Y. Kim, A.K. Sood, J. Liu, A.C. Dudley, and C.V. Pecot (2019). Quaking orchestrates a post-transcriptional regulatory network of endothelial cell cycle progression critical to angiogenesis and metastasis. Oncogene doi: 10.1038/s41388-019-0786-6.
• G. Broussard and B. Damania (2019). KSHV: Immune Modulation and Immunotherapy. Front Immunol 10: 3084. doi: 10.3389/fimmu.2019.03084.
• A.R. Coffey, M. Kanke, T.L. Smallwood, J. Albright, W. Pitman, R.Z. Gharaibeh, K. Hua, E. Gertz, S.B. Biddinger, R.E. Temel, D. Pomp, P. Sethupathy, and B.J. Bennett (2019). microRNA-146a association with the cardiometabolic disease risk factor TMAO. Physiol Genomics doi: 10.1152/physiolgenomics.00079.2018.
• T.A. Dinh, M.L. Jewell, M. Kanke, A. Francisco, R. Sritharan, R.E. Turnham, S. Lee, E.R. Kastenhuber, E. Wauthier, C.D. Guy, R.S. Yeung, S.W. Lowe, L.M. Reid, J.D. Scott, A.M. Diehl, and P. Sethupathy (2019). MicroRNA-375 suppresses the growth and invasion of fibrolamellar carcinoma. Cell Mol Gastroenterol Hepatol 7: 803-817. doi: 10.1016/j.jcmgh.2019.01.008.
• M.L. Engle, J.N. Monk, C.M. Jania, J.R. Martin, J.C. Gomez, H. Dang, J.S. Parker, and C.M. Doerschuk (2019). Dynamic changes in lung responses after single and repeated exposures to cigarette smoke in mice. PLoS One 14: e0212866. doi: 10.1371/journal.pone.0212866.
• M. Hartmann, K.P. Kohl, J. Sekelsky, and T. Hatkevich (2019). Meiotic MCM proteins promote and inhibit crossovers during meiotic recombination. Genetics doi: 10.1534/genetics.119.302221.
• M. Hartmann, J. Umbanhowar, and J. Sekelsky (2019). Centromere-proximal meiotic crossovers in Drosophila melanogaster are suppressed by both highly repetitive heterochromatin and proximity to the centromere. Genetics 213: 113-125. doi: 10.1534/genetics.119.302509.
• T. Hatkevich, V. Boudreau, T. Rubin, P.S. Maddox, J.R. Huynh, and J. Sekelsky (2019). Centromeric SMC1 promotes centromere clustering and stabilizes meiotic homolog pairing. PLoS Genet 15: e1008412. doi: 10.1371/journal.pgen.1008412.
• E.R. Hinkle, H.J. Wiedner, A.J. Black, and J. Giudice (2019). RNA processing in skeletal muscle biology and disease. Transcription 10: 1-20. doi: 10.1080/21541264.2018.1558677.
• V.J. Madigan, T.O. Tyson, J.A. Yuziuk, M. Pillai, S. Moller-Tank, and A. Asokan (2019). A CRISPR screen identifies the cell polarity determinant Crumbs 3 as an adeno-associated virus restriction factor in hepatocytes. J Virol 93: doi: 10.1128/JVI.00943-19.
• V.J. Madigan, J.A. Yuziuk, A.M. Chiarella, T.O. Tyson, R.M. Meganck, Z.C. Elmore, L.V. Tse, N.A. Hathaway, and A. Asokan (2019). Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription. PLoS Pathog 15: e1007988. doi: 10.1371/journal.ppat.1007988.
• K.Z. Perez-Vale and M. Peifer (2020). Orchestrating morphogenesis: building the body plan by cell shape changes and movements. Development 147: doi: 10.1242/dev.191049.
• R. Rivera-Soto and B. Damania (2019). Modulation of angiogenic processes by the human gammaherpesviruses, Epstein-Barr Virus and Kaposi’s Sarcoma-Associated Herpesvirus. Front Microbiol 10: 1544. doi: 10.3389/fmicb.2019.01544.
• K.N. Schaefer and M. Peifer (2019). Wnt/Beta-catenin signaling regulation and a role for biomolecular condensates. Dev Cell 48: 429-444. doi: 10.1016/j.devcel.2019.01.025.
• M.D. Schertzer, K.C.A. Braceros, J. Starmer, R.E. Cherney, D.M. Lee, G. Salazar, M. Justice, S.R. Bischoff, D.O. Cowley, P. Ariel, M.J. Zylka, J.M. Dowen, T. Magnuson, and J.M. Calabrese (2019). lncRNA-induced spread of Polycomb controlled by genome architecture, RNA abundance, and CpG island DNA. Mol Cell 75: 523-537 e10. doi: 10.1016/j.molcel.2019.05.028.
• M.D. Schertzer, M.M. Murvin, and J.M. Calabrese (2020). Using RNA Sequencing and Spike-in RNAs to Measure Intracellular Abundance of lncRNAs and mRNAs. Bio Protoc 10: doi: 10.21769/bioprotoc.3772.
• M.D. Schertzer, E. Thulson, K.C.A. Braceros, D.M. Lee, E.R. Hinkle, R.M. Murphy, S.O. Kim, E.C.M. Vitucci, and J.M. Calabrese (2019). A piggyBac-based toolkit for inducible genome editing in mammalian cells. RNA 25: 1047-1058. doi: 10.1261/rna.068932.118.
• C.A. Schmidt, J.D. Giusto, A. Bao, A.K. Hopper, and A.G. Matera (2019). Molecular determinants of metazoan tricRNA biogenesis. Nucleic Acids Res doi: 10.1093/nar/gkz311.
• C.E. Trincot, W. Xu, H. Zhang, M.R. Kulikauskas, T.G. Caranasos, B.C. Jensen, A. Sabine, T.V. Petrova, and K.M. Caron (2019). Adrenomedullin induces cardiac lymphangiogenesis after myocardial infarction and regulates cardiac edema via connexin 43. Circ Res 124: 101-113. doi: 10.1161/CIRCRESAHA.118.313835.
• R. Watkins-Schulz, P. Tiet, M.D. Gallovic, R.D. Junkins, C. Batty, E.M. Bachelder, K.M. Ainslie, and J.P.Y. Ting (2019). A microparticle platform for STING-targeted immunotherapy enhances natural killer cell- and CD8(+) T cell-mediated anti-tumor immunity. Biomaterials 205: 94-105. doi: 10.1016/j.biomaterials.2019.03.011.
• A.O.B. Whitlock, R.B.R. Azevedo, and C.L. Burch (2019). Population structure promotes the evolution of costly sex in artificial gene networks. Evolution 73: 1089-1100. doi: 10.1111/evo.13733.

2018

• R.L. Armstrong*, T.J.R. Penke*, B.D. Strahl, A.G. Matera, D.J. McKay, D.M. MacAlpine, and R.J. Duronio (2018). Chromatin conformation and transcriptional activity are permissive regulators of DNA replication initiation in Drosophila. Genome Res 28: 1688-1700. doi: 10.1101/gr.239913.118.
• S.H. Azam, M. Smith, V. Somasundaram, and C.V. Pecot (2018). Incorporating pericytes into an endothelial cell bead sprouting assay. J Vis Exp doi: 10.3791/57309.
• M.M. Brady, S. McMahan, and J. Sekelsky (2018). Loss of Drosophila Mei-41/ATR alters meiotic crossover patterning. Genetics 208: 579-588. doi: 10.1534/genetics.117.300634.
• S.E. Brnich, E.A. Rivera-Munoz, and J.S. Berg (2018). Quantifying the potential of functional evidence to reclassify variants of uncertain significance in the categorical and Bayesian interpretation frameworks. Hum Mutat 39: 1531-1541. doi: 10.1002/humu.23609.
• M.E. Cannon and K.L. Mohlke (2018). Deciphering the emerging complexities of molecular mechanisms at GWAS Loci. Am J Hum Genet 103: 637-653. doi: 10.1016/j.ajhg.2018.10.001.
• A.M. Chiarella, A.L. Quimby, M. Mehrab-Mohseni, B. Velasco, S.K. Kasoji, I.J. Davis, P.A. Dayton, N.A. Hathaway, and S.G. Pattenden (2018). Cavitation enhancement increases the efficiency and consistency of chromatin fragmentation from fixed cells for downstream quantitative applications. Biochemistry 57: 2756-2761. doi: 10.1021/acs.biochem.8b00075.
• A.M. Chiarella, T.A. Wang, K.V. Butler, J. Jin, and N.A. Hathaway (2018). Repressing gene transcription by redirecting cellular machinery with chemical epigenetic modifiers. J Vis Exp doi: 10.3791/58222.
• K.M. Gray, K.A. Kaifer, D. Baillat, Y. Wen, T.R. Bonacci, A.D. Ebert, A.C. Raimer, A.M. Spring, S.T. Have, J.J. Glascock, K. Gupta, G.D. Van Duyne, M.J. Emanuele, A.I. Lamond, E.J. Wagner, C.L. Lorson, and A.G. Matera (2018). Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCF(Slmb) degron. Mol Biol Cell 29: 96-110. doi: 10.1091/mbc.E17-11-0627.
• L.T. Laudermilk, J.M. Thomas, and S.N. Kelada (2018). Differential regulation of Zfp30 expression in murine airway epithelia through altered binding of ZFP148 to rs51434084. G3 (Bethesda) 8: 687-693. doi: 10.1534/g3.117.300507.
• J. Lawrimore, A. Doshi, B. Friedman, E. Yeh, and K. Bloom (2018). Geometric partitioning of cohesin and condensin is a consequence of chromatin loops. Mol Biol Cell 29: 2737-2750. doi: 10.1091/mbc.E18-02-0131.
• R.C. McMullan, M.T. Ferris, T.A. Bell, V.D. Menachery, R.S. Baric, K. Hua, D. Pomp, A.E. Smith-Ryan, and F. Pardo-Manuel de Villena (2018). CC002/Unc females are mouse models of exercise-induced paradoxical fat response. Physiol Rep 6: e13716. doi: 10.14814/phy2.13716.
• M.P. Meers, K. Adelman, R.J. Duronio, B.D. Strahl, D.J. McKay, and A.G. Matera (2018). Transcription start site profiling uncovers divergent transcription and enhancer-associated RNAs in Drosophila melanogaster. BMC Genomics 19: 157. doi: 10.1186/s12864-018-4510-7.
• M.P. Meers, M. Leatham-Jensen, T.J.R. Penke, D.J. McKay, R.J. Duronio, and A.G. Matera (2018). An animal model for genetic analysis of mMulti-gene families: Cloning and transgenesis of large tandemly repeated histone gene clusters. Methods Mol Biol 1832: 309-325. doi: 10.1007/978-1-4939-8663-7_17.
• R.M. Meganck, E.K. Borchardt, R.M. Castellanos Rivera, M.L. Scalabrino, J.E. Wilusz, W.F. Marzluff, and A. Asokan (2018). Tissue-dependent expression and translation of circular RNAs with recombinant AAV vectors in vivo. Mol Ther Nucleic Acids 13: 89-98. doi: 10.1016/j.omtn.2018.08.008.
• J.H. Meserve and R.J. Duronio (2018). Fate mapping during regeneration: Cells that undergo compensatory proliferation in damaged Drosophila eye imaginal discs differentiate into multiple retinal accessory cell types. Dev Biol 444: 43-49. doi: 10.1016/j.ydbio.2018.10.011.
• T.J.R. PenkeT, D.J. McKay, B.D. Strahl, A.G. Matera, and R.J. Duronio (2018). Functional redundancy of variant and canonical histone H3 lysine 9 modification in Drosophila. Genetics 208: 229-244. doi: 10.1534/genetics.117.300480.
• K.Z. Perez-Vale and M. Peifer (2018). Modulating apical-basal polarity by building and deconstructing a Yurt. J Cell Biol 217: 3772-3773. doi: 10.1083/jcb.201810059.
• P.N. Pozo, J.P. Matson, Y. Cole, K.M. Kedziora, G.D. Grant, B. Temple, and J.G. Cook (2018). Cdt1 variants reveal unanticipated aspects of interactions with Cyclin/CDK and MCM important for normal genome replication. Mol Biol Cell mbcE18040242. doi: 10.1091/mbc.E18-04-0242.
• J.S. Runge, J.R. Raab, and T. Magnuson (2018). Identification of Two distinct classes of the human INO80 complex genome-wide. G3 (Bethesda) 8: 1095-1102. doi: 10.1534/g3.117.300504.
• K.N. Schaefer, T.T. Bonello, S. Zhang, C.E. Williams, D.M. Roberts, D.J. McKay, and M. Peifer (2018). Supramolecular assembly of the beta-catenin destruction complex and the effect of Wnt signaling on its localization, molecular size, and activity in vivo. PLoS Genet 14: e1007339. doi: 10.1371/journal.pgen.1007339.
• M.B. Siegel, X. He, K.A. Hoadley, A. Hoyle, J.B. Pearce, A.L. Garrett, S. Kumar, V.J. Moylan, C.M. Brady, A.E. Van Swearingen, D. Marron, G.P. Gupta, L.B. Thorne, N. Kieran, C. Livasy, E.R. Mardis, J.S. Parker, M. Chen, C.K. Anders, L.A. Carey, and C.M. Perou (2018). Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. J Clin Invest 128: 1371-1383. doi: 10.1172/JCI96153.
• M.J. Slaughter, E.K. Shanle, A.W. McFadden, E.S. Hollis, L.E. Suttle, B.D. Strahl, and I.J. Davis (2018). PBRM1 bromodomains variably influence nucleosome interactions and cellular function. J Biol Chem 293: 13592-13603. doi: 10.1074/jbc.RA118.003381.
• L. Smith and P. Maddox (2018). Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles. Cytoskeleton (Hoboken) doi: 10.1002/cm.21493.
• M. Tegowski and A. Baldwin (2018). Noncanonical NF-kappaB in cancer. Biomedicines 6: doi: 10.3390/biomedicines6020066.
• M. Tegowski, C. Fan, and A.S. Baldwin (2018). Thioridazine inhibits self-renewal in breast cancer cells via DRD2-dependent STAT3 inhibition, but induces a G1 arrest independent of DRD2. J Biol Chem 293: 15977-15990. doi: 10.1074/jbc.RA118.003719.
• C.M. Wilczewski, A.J. Hepperla, T. Shimbo, L. Wasson, Z.L. Robbe, I.J. Davis, P.A. Wade, and F.L. Conlon (2018). CHD4 and the NuRD complex directly control cardiac sarcomere formation. Proc Natl Acad Sci U S A 115: 6727-6732. doi: 10.1073/pnas.1722219115.
• L.A. Wylie, K.P. Mouillesseaux, D.C. Chong, and V.L. Bautch (2018). Developmental SMAD6 loss leads to blood vessel hemorrhage and disrupted endothelial cell junctions. Dev Biol 442: 199-209. doi: 10.1016/j.ydbio.2018.07.027.

2017

• B.H. Albright, C.M. Storey, G. Murlidharan, R.M. Castellanos Rivera, G.E. Berry, V.J. Madigan, and A. Asokan (2017). Mapping the structural determinants required for AAVrh.10 transport across the blood-brain barrier. Mol Ther doi: 10.1016/j.ymthe.2017.10.017.
• R. Beck, M. Styblo, and P. Sethupathy (2017). Arsenic exposure and Type 2 diabetes: microRNAs as mechanistic links? Curr Diab Rep 17: 18. doi: 10.1007/s11892-017-0845-8.
• S.P. Bellendir*, D.J. Rognstad*, L.P. Morris, G. Zapotoczny, W.G. Walton, M.R. Redinbo, D.A. Ramsden, J. Sekelsky, and D.A. Erie (2017). Substrate preference of Gen endonucleases highlights the importance of branched structures as DNA damage repair intermediates. Nucleic Acids Res 45: 5333-5348. doi: 10.1093/nar/gkx214.
• R.L. Bigler, J.W. Kamande, R. Dumitru, M. Niedringhaus, and A.M. Taylor (2017). Messenger RNAs localized to distal projections of human stem cell derived neurons. Sci Rep 7: 611. doi: 10.1038/s41598-017-00676-w.
• E.K. Borchardt, R.M. Meganck, H.A. Vincent, C.B. Ball, S.B.V. Ramos, N.J. Moorman, W.F. Marzluff, and A. Asokan (2017). Inducing circular RNA formation using the CRISPR endoribonuclease Csy4. RNA 23: 619-627. doi: 10.1261/rna.056838.116.
• D.C. Chong, Z. Yu, H.E. Brighton, J.E. Bear, and V.L. Bautch (2017). Tortuous microvessels contribute to wound healing via sprouting angiogenesis. Arterioscler Thromb Vasc Biol 37: 1903-1912. doi: 10.1161/ATVBAHA.117.309993.
• A.R. Coffey, T.L. Smallwood, J. Albright, K. Hua, M. Kanke, D. Pomp, B.J. Bennett, and P. Sethupathy (2017). Systems genetics identifies a co-regulated module of liver microRNAs associated with plasma LDL cholesterol in murine diet-induced dyslipidemia. Physiol Genomics 49: 618-629. doi: 10.1152/physiolgenomics.00050.2017.
• M.P. Conlin, D.A. Reid, G.W. Small, H.H. Chang, G. Watanabe, M.R. Lieber, D.A. Ramsden, and E. Rothenberg (2017). DNA ligase IV guides end-processing choice during nonhomologous end joining. Cell Rep 20: 2810-2819. doi: 10.1016/j.celrep.2017.08.091.
• T.A. Dinh, E.C. Vitucci, E. Wauthier, R.P. Graham, W.A. Pitman, T. Oikawa, M. Chen, G.O. Silva, K.G. Greene, M.S. Torbenson, L.M. Reid, and P. Sethupathy (2017). Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma. Sci Rep 7: 44653. doi: 10.1038/srep44653.
• L.J. Donoghue, A. Livraghi-Butrico, K.M. McFadden, J.M. Thomas, G. Chen, B.R. Grubb, W.K. O’Neal, R.C. Boucher, and S.N.P. Kelada (2017). Identification of trans protein QTL for secreted airway mucins in mice and a causal role for Bpifb1. Genetics 207: 801-812. doi: 10.1534/genetics.117.300211.
• J.K. Durand and A.S. Baldwin (2017). Targeting IKK and NF-kappaB for therapy. Adv Protein Chem Struct Biol 107: 77-115. doi: 10.1016/bs.apcsb.2016.11.006.
• A. Emery, S. Zhou, E. Pollom, and R. Swanstrom (2017). Characterizing HIV-1 splicing by using next-generation sequencing. J Virol 91: doi: 10.1128/JVI.02515-16.
• C.C. Fahey and I.J. Davis (2017). SETting the stage for cancer development: SETD2 and the consequences of lost methylation. Cold Spring Harb Perspect Med 7: doi: 10.1101/cshperspect.a026468.
• L. Freeman, H. Guo, C.N. David, W.J. Brickey, S. Jha, and J.P. Ting (2017). NLR members NLRC4 and NLRP3 mediate sterile inflammasome activation in microglia and astrocytes. J Exp Med 214: 1351-1370. doi: 10.1084/jem.20150237.
• M.A. Hartmann and J. Sekelsky (2017). The absence of crossovers on chromosome 4 in Drosophila melanogaster: Imperfection or interesting exception? Fly (Austin) 11: 253-259. doi: 10.1080/19336934.2017.1321181.
• T. Hatkevich and J. Sekelsky (2017). Bloom syndrome helicase in meiosis: Pro-crossover functions of an anti-crossover protein. Bioessays 39: doi: 10.1002/bies.201700073.
• T. Hatkevich*, K.P. Kohl*, S. McMahan, M.A. Hartmann, A.M. Williams, and J. Sekelsky (2017). Bloom Syndrome Helicase Promotes Meiotic Crossover Patterning and Homolog Disjunction. Curr Biol 27: 96-102. doi: 10.1016/j.cub.2016.10.055.
• C. Hodgens, Z.L. Nimchuk, and J.J. Kieber (2017). indCAPS: A tool for designing screening primers for CRISPR/Cas9 mutagenesis events. PLoS One 12: e0188406. doi: 10.1371/journal.pone.0188406.
• J.K. Holsclaw and J. Sekelsky (2017). Annealing of Complementary DNA Sequences During Double-Strand Break Repair in Drosophila Is Mediated by the Ortholog of SMARCAL1. Genetics 206: 467-480. doi: 10.1534/genetics.117.200238.
• D.M. Irvin, R.S. McNeill, R.E. Bash, and C.R. Miller (2017). Intrinsic Astrocyte Heterogeneity Influences Tumor Growth in Glioma Mouse Models. Brain Pathol 27: 36-50. doi: 10.1111/bpa.12348.
• S.L. McDaniel, A.J. Hepperla, J. Huang, R. Dronamraju, A.T. Adams, V.G. Kulkarni, I.J. Davis, and B.D. Strahl (2017). H3K36 methylation regulates nutrient stress response in Saccharomyces cerevisiae by enforcing transcriptional fidelity. Cell Rep 19: 2371-2382. doi: 10.1016/j.celrep.2017.05.057.
• S.L. McDaniel and B.D. Strahl (2017). Shaping the cellular landscape with Set2/SETD2 methylation. Cell Mol Life Sci doi: 10.1007/s00018-017-2517-x.
• M.P. Meers, T. Henriques, C.A. Lavender, D.J. McKay, B.D. Strahl, R.J. Duronio, K. Adelman, and A.G. Matera (2017). Histone gene replacement reveals a post-transcriptional role for H3K36 in maintaining metazoan transcriptome fidelity. Elife 6: doi: 10.7554/eLife.23249.
• J.H. Meserve and R.J. Duronio (2017). A population of G2-arrested cells are selected as sensory organ precursors for the interommatidial bristles of the Drosophila eye. Dev Biol 430: 374-384. doi: 10.1016/j.ydbio.2017.06.023.
• .E. NesmithJ, J.C. Chappell, J.G. Cluceru, and V.L. Bautch (2017). Blood vessel anastomosis is spatially regulated by Flt1 during angiogenesis. Development 144: 889-896. doi: 10.1242/dev.145672.
• J.J. Noto, C.A. Schmidt, and A.G. Matera (2017). Engineering and expressing circular RNAs via tRNA splicing. RNA Biol 1-7. doi: 10.1080/15476286.2017.1317911.
• C.M. Parobek, J.B. Parr, N.F. Brazeau, C. Lon, S. Chaorattanakawee, P. Gosi, E.J. Barnett, L.D. Norris, S.R. Meshnick, M.D. Spring, C.A. Lanteri, J.A. Bailey, D.L. Saunders, J.T. Lin, and J.J. Juliano (2017). Partner-drug resistance and population substructuring of artemisinin-resistant Plasmodium falciparum in Cambodia. Genome Biol Evol 9: 1673-1686. doi: 10.1093/gbe/evx126.
• C.M. Parobek, F.I. Archer, M.E. DePrenger-Levin, S.M. Hoban, L. Liggins, and A.E. Strand (2017). skelesim: an extensible, general framework for population genetic simulation in R. Mol Ecol Resour 17: 101-109. doi: 10.1111/1755-0998.12607.
• B.C. Peck, A.T. Mah, W.A. Pitman, S. Ding, P.K. Lund, and P. Sethupathy (2017). Functional Transcriptomics in Diverse Intestinal Epithelial Cell Types Reveals Robust MicroRNA Sensitivity in Intestinal Stem Cells to Microbial Status. J Biol Chem 292: 2586-2600. doi: 10.1074/jbc.M116.770099.
• M.I. Pronobis, N. Deuitch, V. Posham, Y. Mimori-Kiyosue, and M. Peifer (2017). Reconstituting regulation of the canonical Wnt pathway by engineering a minimal beta-catenin destruction machine. Mol Biol Cell 28: 41-53. doi: 10.1091/mbc.E16-07-0557.
• A.C. Raimer, K.M. Gray, and A.G. Matera (2017). SMN – A chaperone for nuclear RNP social occasions? RNA Biol 14: 701-711. doi: 10.1080/15476286.2016.1236168.
• K. Rehain-Bell, A. Love, M.E. Werner, I. MacLeod, J.R. Yates, 3rd, and A.S. Maddox (2017). A Sterile 20 Family Kinase and Its Co-factor CCM-3 Regulate Contractile Ring Proteins on Germline Intercellular Bridges. Curr Biol 27: 860-867. doi: 10.1016/j.cub.2017.01.058.
• S.W. Renner, L.M. Walker, L.J. Forsberg, J.Z. Sexton, and J.E. Brenman (2017). Carbonic anhydrase III (Car3) is not required for fatty acid synthesis and does not protect against high-fat diet induced obesity in mice. PLoS One 12: e0176502. doi: 10.1371/journal.pone.0176502.
• T.S. Roman, M.E. Cannon, S. Vadlamudi, M.L. Buchkovich, B.N. Wolford, R.P. Welch, M.A. Morken, G.J. Kwon, A. Varshney, R. Kursawe, Y. Wu, A.U. Jackson, P. National Institutes of Health Intramural Sequencing Center Comparative Sequencing, M.R. Erdos, J. Kuusisto, M. Laakso, L.J. Scott, M. Boehnke, F.S. Collins, S.C.J. Parker, M.L. Stitzel, and K.L. Mohlke (2017). A Type 2 Diabetes-Associated Functional Regulatory Variant in a Pancreatic Islet Enhancer at the ADCY5 Locus. Diabetes 66: 2521-2530. doi: 10.2337/db17-0464.
• L. Smith and P.S. Maddox (2017). Reading the centromere epigenetic mark. Dev Cell 42: 110-112. doi: 10.1016/j.devcel.2017.07.011.
• N.R. Tackmann and Y. Zhang (2017). Mouse modelling of the MDM2/MDMX-p53 signalling axis. J Mol Cell Biol 9: 34-44. doi: 10.1093/jmcb/mjx006.
• C.M. Uyehara*, S.L. Nystrom*, M.J. Niederhuber, M. Leatham-Jensen, Y. Ma, L.A. Buttitta, and D.J. McKay (2017). Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev doi: 10.1101/gad.298182.117.
• M. Vitucci*, D.M. Irvin*, R.S. McNeill, R.S. Schmid, J.M. Simon, H.D. Dhruv, M.B. Siegel, A.M. Werneke, R.E. Bash, S. Kim, M.E. Berens, and C.R. Miller (2017). Genomic profiles of low-grade murine gliomas evolve during progression to glioblastoma. Neuro Oncol doi: 10.1093/neuonc/nox050.
• G. Zapotoczny and J. Sekelsky (2017). Human Cell Assays for Synthesis-Dependent Strand Annealing and Crossing over During Double-Strand Break Repair. G3 (Bethesda) 7: 1191-1199. doi: 10.1534/g3.116.037390.

2016

• G.E. Berry and A. Asokan (2016). Chemical modulation of endocytic sorting augments adeno-associated viral transduction. J Biol Chem 291: 939-47.
• G.E. Berry and A. Asokan (2016). Cellular transduction mechanisms of adeno-associated viral vectors. Curr Opin Virol 21: 54-60.
• L.C. Freeman and J.P. Ting (2016). The pathogenic role of the inflammasome in neurodegenerative diseases. J Neurochem 136 Suppl 1: 29-38.
• Y. Gao*, E. Mutter-Rottmayer*, A.M. Greenwalt*, D. Goldfarb, F. Yan, Y. Yang, R.C. Martinez-Chacin, K.H. Pearce, S. Tateishi, M.B. Major, and C. Vaziri (2016). A neomorphic cancer cell-specific role of MAGE-A4 in trans-lesion synthesis. Nat Commun 7: 12105.
• N.C. Gomez, A.J. Hepperla, R. Dumitru, J.M. Simon, F. Fang, and I.J. Davis (2016). Widespread chromatin accessibility at repetitive elements links stem cells with human cancer. Cell Rep 17: 1607-1620.
• K.E. Hacker*, C.C. Fahey*, S.A. Shinsky*, Y.J. Chiang*, J.V. DiFiore*, D.K. Jha, A.H. Vo, J.A. Shavit, I.J. Davis, B.D. Strahl, and W.K. Rathmell (2016). Structure/function analysis of recurrent mutations in SETD2 protein reveals a critical and conserved role for a SET domain residue in maintaining protein stability and histone H3 Lys-36 trimethylation. J Biol Chem 291: 21283-21295.
• T.K. Hayes, N.F. Neel, C. Hu, P. Gautam, M. Chenard, B. Long, M. Aziz, M. Kassner, K.L. Bryant, M. Pierobon, R. Marayati, S. Kher, S.D. George, M. Xu, A. Wang-Gillam, A.A. Samatar, A. Maitra, K. Wennerberg, E.F. Petricoin, 3rd, H.H. Yin, B. Nelkin, A.D. Cox, J.J. Yeh, and C.J. Der (2016). Long-term ERK inhibition in KRAS-mutant pancreatic cancer is associated with MYC degradation and senescence-like growth suppression. Cancer Cell 29: 75-89.
• M.D. Iglesia, J.S. Parker, K.A. Hoadley, J.S. Serody, C.M. Perou, and B.G. Vincent (2016). Genomic analysis of immune cell infiltrates across 11 tumor types. J Natl Cancer Inst 108:
• M.R. Irvin, D.M. Rotroff, S. Aslibekyan, D. Zhi, B. Hidalgo, A. Motsinger-Reif, S. Marvel, V. Srinivasasainagendra, S.A. Claas, J.B. Buse, R.J. Straka, J.M. Ordovas, I.B. Borecki, X. Guo, I.Y. Chen, J.I. Rotter, M.J. Wagner, and D.K. Arnett (2016). A genome-wide study of lipid response to fenofibrate in Caucasians: a combined analysis of the GOLDN and ACCORD studies. Pharmacogenet Genomics 26: 324-33.
• P.L. Leslie and Y. Zhang (2016). MDM2 oligomers: antagonizers of the guardian of the genome. Oncogene
• V.J. Madigan and A. Asokan (2016). Engineering AAV receptor footprints for gene therapy. Curr Opin Virol 18: 89-96.
• X. Meng*, N.R. Tackmann*, S. Liu, J. Yang, J. Dong, C. Wu, A.D. Cox, and Y. Zhang (2016). RPL23 links oncogenic RAS signaling to p53-mediated tumor suppression. Cancer Res 76: 5030-9.
• C.J. Miller and D.R. Matute (2016). The effect of temperature on Drosophila hybrid fitness. G3 (Bethesda)
• C.J. Miller and D.R. Matute (2016). Evolutionary genetics: reuse, recycle, converge. Curr Biol 26: R838-40.
• G. Murlidharan, A. Crowther, R.A. Reardon, J. Song, and A. Asokan (2016). Glymphatic fluid transport controls paravascular clearance of AAV vectors from the brain. JCI Insight 1: e88034.
• G. Murlidharan, K. Sakamoto, L. Rao, T. Corriher, D. Wang, G. Gao, P. Sullivan, and A. Asokan (2016). CNS-restricted transduction and CRISPR/Cas9-mediated gene deletion with an engineered AAV vector. Mol Ther Nucleic Acids 5: e338.
• C.M. Parobek, J.T. Lin, D.L. Saunders, E.J. Barnett, C. Lon, C.A. Lanteri, S. Balasubramanian, N. Brazeau, D.K. DeConti, D.L. Garba, S.R. Meshnick, M.D. Spring, C.M. Chuor, J.A. Bailey, and J.J. Juliano (2016). Selective sweep suggests transcriptional regulation may underlie Plasmodium vivax resilience to malaria control measures in Cambodia. Proc Natl Acad Sci U S A 113: E8096-E8105.
• B.C. Peck, J. Sincavage, S. Feinstein, A.T. Mah, J.G. Simmons, P.K. Lund, and P. Sethupathy (2016). miR-30 family controls proliferation and differentiation of intestinal epithelial cell models by directing a broad gene expression program that includes SOX9 and the ubiquitin ligase pathway. J Biol Chem
• T.J. Penke, D.J. McKay, B.D. Strahl, A.G. Matera, and R.J. Duronio (2016). Direct interrogation of the role of H3K9 in metazoan heterochromatin function. Genes Dev 30: 1866-80.
• P.N. Pozo and J.G. Cook (2016). Regulation and function of Cdt1; A key factor in cell proliferation and genome stability. Genes (Basel) 8: doi: 10.3390/genes8010002.
• M.I. Pronobis, N. Deuitch, and M. Peifer (2016). The Miraprep: A protocol that uses a miniprep kit and provides maxiprep yields. PLoS One 11: e0160509.
• N.E. Romero, S.W. Matson, and J. Sekelsky (2016). Biochemical activities and genetic functions of the Drosophila melanogaster Fancm helicase in DNA repair. Genetics 204: 531-541.
• J.S. Runge, J.R. Raab, and T. Magnuson (2016). Epigenetic regulation by ATP-dependent chromatin-remodeling enzymes: SNF-ing out crosstalk. Curr Top Dev Biol 117: 1-13.
• C.A. Schmidt, J.J. Noto, G.S. Filonov, and A.G. Matera (2016). A method for expressing and imaging abundant, stable, circular RNAs in vivo using tRNA splicing. Methods Enzymol 572: 215-36.
• D.W. Serber, J.S. Runge, D.U. Menon, and T. Magnuson (2016). The Mouse INO80 chromatin-remodeling complex is an essential meiotic factor for spermatogenesis. Biol Reprod 94: 8.
• L.C. Tsao, H. Guo, J. Jeffrey, J.A. Hoxie, and L. Su (2016). CCR5 interaction with HIV-1 Env contributes to Env-induced depletion of CD4 T cells in vitro and in vivo. Retrovirology 13: 22.
• L. Waldron, J.D. Steimle, T.M. Greco, N.C. Gomez, K.M. Dorr, J. Kweon, B. Temple, X.H. Yang, C.M. Wilczewski, I.J. Davis, I.M. Cristea, I.P. Moskowitz, and F.L. Conlon (2016). The cardiac TBX5 interactome reveals a chromatin remodeling network essential for cardiac septation. Dev Cell 36: 262-75.
• A.O. Whitlock, K.M. Peck, R.B. Azevedo, and C.L. Burch (2016). An evolving genetic architecture interacts with Hill-Robertson interference to determine the benefit of sex. Genetics 203: 923-36.
• D.W. Wyatt, W. Feng, M.P. Conlin, M.J. Yousefzadeh, S.A. Roberts, P. Mieczkowski, R.D. Wood, G.P. Gupta, and D.A. Ramsden (2016). Essential roles for polymerase theta-mediated end joining in the repair of chromosome breaks. Mol Cell 63: 662-73.