Faculty Highlighted Publications

(Listed in chronological order)

Sixt BS, Bastidas RJ, Finethy R, Baxter RM, Carpenter VK, Kroemer G, Coers J, Valdivia RH. The Chlamydia trachomatis Inclusion Membrane Protein CpoS Counteracts STING-Mediated Cellular Surveillance and Suicide Programs. Cell Host Microbe. 2017 Jan 11;21(1):113-121. doi: 10.1016/j.chom.2016.12.002. Epub 2016 Dec 29.[EPub

Gokhale NS, Horner SM.RNA modifications go viral. PLoS Pathog. 2017 Mar 9;13(3):e1006188. doi: 10.1371/journal.ppat.1006188. eCollection 2017 Mar. No abstract available. PMID:28278189

Bisogno LS, Keene JD. RNA regulons in cancer and inflammation. Curr Opin Genet
Dev. 2017 Nov 22;48:97-103. doi: 10.1016/j.gde.2017.11.004. [Epub ahead of print]
Review. PubMed PMID: 29175729.

Bisogno LS, Keene JD. Analysis of post-transcriptional regulation during
cancer progression using a donor-derived isogenic model of tumorigenesis.
Methods. 2017 Aug 15;126:193-200. doi: 10.1016/j.ymeth.2017.05.012. Epub 2017 May
19. PubMed PMID: 28529064.

Nicholson CO, Friedersdorf M, Keene JD. Quantifying RNA binding sites
transcriptome-wide using DO-RIP-seq. RNA. 2017 Jan;23(1):32-46. Epub 2016 Oct 14.
PubMed PMID: 27742911; PubMed Central PMCID: PMC5159647.

Nicholson CO, Friedersdorf MB, Bisogno LS, Keene JD. DO-RIP-seq to quantify
RNA binding sites transcriptome-wide. Methods. 2017 Apr 15;118-119:16-23. doi:
10.1016/j.ymeth.2016.11.004. Epub 2016 Nov 10. PubMed PMID: 27840290; PubMed
Central PMCID: PMC5411286.

  1. Balenga N, Azimzadeh P, Hogue JA, Staats PN, Shi Y, Koh J, Dressman H, Olson JA Jr. Orphan Adhesion GPCR GPR64/ADGRG2 is overexpressed in parathyroid tumors and attenuates calcium-sensing receptor-mediated signaling.  J Bone Miner Res. 2017 32:654-666.  PMID 27760455

JD Silverman, A Washburne, S Mukherjee, LA David. A phylogenetic transform enhances analysis of compositional microbiota data. eLife, 10.7554/eLife.21887, Feb 2017. [link]

Heaton BE, Kennedy EM, Dumm RE, Harding AT, Sacco MT, Sachs D, Heaton NS. A CRISPR Activation Screen Identifies a Pan-avian Influenza Virus Inhibitory Host Factor.  Cell Reports. 2017 20(7): p1503-1512.  DOI: http://dx.doi.org/10.1016/j.celrep.2017.07.060  PMID: 28813663

Heaton NS. Revisiting the concept of a cytopathic viral infection. PLoS Pathogens. 2017 13(7): e1006409. https://doi.org/10.1371/journal.ppat.1006409. PMID: 28727844

Harding AT, Heaton BE, Dumm RE, Heaton NS. Rationally Designed Influenza Virus Vaccines That Are Antigenically Stable during Growth in Eggs. mBio. 2017 June 6, Vol. 8 no.3 e00669-17 doi: 10.1128/mBio.00669-17. PMID: 28588131

Eudailey J., Dennis M., Parker M., Phillips B., Huffman T., Bay C., Hudgens M., Wiseman R., Pollara J., Fouda G.G., Ferrari G., Pickup D., Kozlowski P., Van Rompay K., De Paris K., and Permar S. Maternal HIV-1 Env vaccination for systemic and breast milk immunity to prevent oral SHIV acquisition in infant macaques (2017) In press, mSphere.

Phillips B., Fouda G.G., Eudailey J., Pollara J., Curtis A.D. 2nd, Kunz E., Dennis M.,
Shen X., Bay C., Hudgens M., Pickup D., Alam S.M., Ardeshir A., Kozlowski P.A., Van Rompay
K.K.A., Ferrari G., Moody M.A., Permar S., De Paris K. (2017) Impact of Poxvirus Vector
Priming, Protein Coadministration, and Vaccine Intervals on HIV gp120
Vaccine-Elicited Antibody Magnitude and Function in Infant Macaques. Clin. Vaccine
Immunol. 2017 Oct 5;24(10). pii: e00231-17. doi: 10.1128/CVI.00231-17. PMCID: PMC5629672.

Sloan R, Huang SN, Pommier Y, Jinks-Robertson S.Effects of camptothecin or TOP1 overexpression on genetic stability in Saccharomyces cerevisiae. DNA Repair (Amst). 2017 Nov;59:69-75. doi: 10.1016/j.dnarep.2017.09.004. Epub 2017 Sep 18.

Guo X, Hum YF, Lehner K, Jinks-Robertson S.Regulation of hetDNA Length during Mitotic Double-Strand Break Repair in Yeast. Mol Cell. 2017 Aug 17;67(4):539-549.e4. doi: 10.1016/j.molcel.2017.07.009. Epub 2017 Aug 3. PMID:

Hum YF, Jinks-Robertson S.Mitotic Gene Conversion Tracts Associated with Repair of a Defined Double-Strand Break in Saccharomyces cerevisiae. Genetics. 2017 Sep;207(1):115-128. doi: 10.1534/genetics.117.300057. Epub 2017 Jul 25. PMID:

Kim N, Jinks-Robertson S.The Top1 paradox: Friend and foe of the eukaryotic genome.
DNA Repair (Amst). 2017 Aug;56:33-41. doi: 10.1016/j.dnarep.2017.06.005. Epub 2017 Jun 9. Review.

Cho JE, Jinks-Robertson S.Ribonucleotides and Transcription-Associated Mutagenesis in Yeast.
J Mol Biol. 2017 Oct 27;429(21):3156-3167. doi: 10.1016/j.jmb.2016.08.005. Epub 2016 Aug 7. Review. PMID:

Larsen PA*, Harris RA*, Liu Y, Murali SC, Campbell CR, Brown AD, Sullivan BA, Shelton J, Brown SJ, Raveendran M, Dudchencko O, Machol I, Lieberman E, Muzny DM, Gibbs RA, Yoder AD, Rogers J, Worley KC (2017) Hybrid de novo assembly and centromere characterization of the gray mouse lemur (Microcebus murinus). BMC Biology, 15:110. (*joint first authors) https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0439-6

McNulty SM, Sullivan LL, Sullivan BA (2017) Human centromeres produce chromosome-specific and array-specific alpha satellite transcripts that are complexed with CENP-A and CENP-C. Dev Cell, 42:226-240. https://www.ncbi.nlm.nih.gov/pubmed/28787590

Johnson WL*, Yewdell WT*, Bell JC, McNulty SM, Duda Z, O’Neill RJ, Sullivan BA, Straight AF (2017) RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife, 6:e25299. (*joint first authors) https://elifesciences.org/articles/25299

McFadden MJ, Gokhale NS, Horner SM.Protect this house: cytosolic sensing of viruses. Curr Opin Virol. 2017 Feb;22:36-43. doi: 10.1016/j.coviro.2016.11.012. Epub 2016 Dec 9. Review.PMID:27951430

Gokhale NS, Horner SM.Knotty Zika Virus Blocks Exonuclease to Produce Subgenomic Flaviviral RNAs.Cell Host Microbe. 2017 Jan 11;21(1):1-2. doi: 10.1016/j.chom.2016.12.013.PMID:28081439

Vazquez C, Beachboard DC, Horner SM.Methods to Visualize MAVS Subcellular Localization.Methods Mol Biol. 2017;1656:131-142. doi: 10.1007/978-1-4939-7237-1_7.PMID:28808966

  1. Himburg HA, Sasine J, Yan X, Kan J, Dressman H, Chute JP. A molecular profile of the endothelial cell response to ionizing radiation. Radiation Research. 2016 186:141-52. PMID 27387861

Price AM, Dai J, Bazot Q, Patel L, Nikitin PA, Djavadian R, Winter PS, Salinas CA, Barry AP, Wood KC, Johannsen EC, Letai A, Allday MJ, Luftig MA. Elife. Epstein-Barr virus ensures B cell survival by uniquely modulating apoptosis at early and late times after infection. 2017 Apr 20;6. pii: e22509. doi: 10.7554/eLife.22509.

Kennedy, Edward M., Bogerd, Hal P., Kornepati, Anand V.R., Kang, Dong, Ghoshal, Delta, Marshall, Joy B., Poling, Brigid C., Tsai, Kevin, Gokhale, Nandan S., Horner, Stacy M. and Cullen, Bryan R. (2016). Posttranscriptional m6A Editing of HIV-1 mRNAs Enhances Viral Gene Expression. Cell Host and Microbe, 19: 675-685

Kennedy, Edward M. and Cullen, Bryan R. (2017) Gene Editing: A New Tool for Viral Disease. Annual Review of Medicine, 68: 401-411.

Kennedy, Edward M., Kornepati, Anand V., Bogerd, Hal P. and Cullen, Bryan R. (2017) Partial reconstitution of the RNAi response in human cells using Drosophila gene products. RNA, 23: 153-160.

Bogerd, Hal P., Kennedy, Edward M., Whisnant, Adam W. and Cullen, Bryan R. (2017) Induced packaging of cellular microRNAs into HIV-1 virions can inhibit infectivity. mBio, 8: e02125-16.

Kennedy, Edward M., Courtney, David G., Tsai, Kevin and Cullen, Bryan R. (2017) Viral epitranscriptomics. Journal of Virology, 91: e02263-16.

Poling, Brigid C., Tsai, Kevin, Kang, Dong, Ren, Linda, Kennedy, Edward M. and Cullen, Bryan R. (2017) A lentiviral vector bearing a reverse intron demonstrates superior expression of both proteins and microRNAs. RNA Biology. 1-10. doi:10.1080/15476286.2017.1334755.

Courtney, David G., Kennedy, Edward M., Dumm, Rebekah E., Bogerd, Hal P., Tsai, Kevin, Heaton, Nicholas S. and Cullen, Bryan R. (2017) Epitranscriptomic enhancement of influenza A virus gene expression and replication. Cell Host & Microbe, 22: 377-386.e5.

Cullen, Bryan R. (2017) RNA interference in mammals: The virus strikes back. Immunity, 46: 970-972.

Poling, Brigid C., Price, Alexander M., Luftig, Micah A. and Cullen, Bryan R. (2017). The Epstein-Barr virus miR-BHRF1 microRNAs regulate viral gene expression in cis. Virology, 512: 113-123.

Heaton, Nicholas S. and Cullen, Bryan R. (2017). Viruses hijack a long noncoding RNA. Nature, in press

Piro, AS., Hernandez, D., Luoma, S., Feeley, EM., Finethy, R., Yirga, A., Frickel, EM., Lesser, CF., Coers, J. Detection of cytosolic Shigelle flexneri via a C-terminal triple-ariginine motif of GBP1 inhibits actin-based motility. mBio 2017 Dec 12;8(6) pii: e01979-17. PMID: 29233899

Feeley, EM.*, Pilla-Moffett, D.*, Zwack, EE., Piro, AS., Finethy, R., Kolb, JP, Martinez, J., Brodsky, IE., Coers, J. Galectin-3 directs antimicrobial Guanylate Binding Proteins to vacuoles furnished with bacterial secretion systems. (*Authors contributed equally to this study). Proc Natl Acad Sci U.S.A. 2017 Feb 28;114(9):E1698-E1706 PMID: 28193861

Finethy, R., Luoma, S., Orench-Rivera, N., Feeley, EM., Haldar, AK., Yamaoto, Y., Kanneganti, TD., Kuehn, MJ., Coers, J. Inflammasome activation by bacterial outer membrane vesicles requires guanylate binding proteins. mBio 2017 Oct 3;8(5). pii: e01188-17. PMID: 28974614

Zhang K, Xue-Chang W, Zheng D-Q, Petes TD Effects of temperature on the meiotic recombination landscape of the yeast Saccharomyces cerevisiae. mBio 2017, in press.

McGinty RJ, Rubinstein RG, Neil AJ, Dominska M, Kiktev D, Petes TD, Mirkin SM. Nanopore sequencing of complex genomic rearrangements in yeast reveals mechanisms of repeat-mediated double-strand break repair. Genome Res. 2017 Nov 7. doi: 10.1101/gr.228148.117. PMID: 29113982 [EPub]

Yin Y, Dominska M, Yim E, Petes TD. High-resolution mapping of heteroduplex DNA formed during UV-induced and spontaneous mitotic recombination events in yeast. Elife. 2017 Jul 17;6. pii: e28069. doi: 10.7554/eLife.28069. PMID: 28714850 [EPub]

Zhao Y, Dominska M, Petrova A, Bagshaw H, Kokoska RJ, Petes TD. Properties of Mitotic and Meiotic Recombination in the Tandemly-Repeated CUP1 Gene Cluster in the Yeast Saccharomyces cerevisiae. Genetics. 2017 Jun;206(2):785-800. doi: 10.1534/genetics.117.201285. Epub 2017 Apr 4. PMID: 28381587 [EPub]

Mitchell C, Silver DL. Enhancing our brains: Genomic mechanisms underlying cortical evolution. Invited review article. Semin Cell Dev Biol. Aug 29. pii: S1084-9521(17)30235-5. 2017 [EPub]

Lennox, AL, Mao, H, and Silver, DL. RNA on the brain: emerging layers of post-transcriptional regulation in cerebral cortex development. Wiley Interdisciplinary Reviews Developmental Biology. Aug 24 online. 2017 Invited review article.[EPub]

MGM publications 1Pilaz, L-J. and Silver, DL. Moving messages in the developing brain: Emerging roles for mRNA transport and local translation in neural stem cells. FEBs Letters. June; 591 (11): 1526-2539. 2017 Invited review article.[EPub]



Miller, EE+, Kobayashi, GS+, Musso, CM, Allen, M, Ishiy, FAA, Caires Junior, LC, Guimarães, ESG, Griesi-Oliveira, K, Zechi-Ceide, RM, Richieri-Costa, A, Bertola, DR, Passos-Bueno, MR*, Silver, DL*. EIF4A3 deficient human iPSCs and mouse models demonstrate neural crest defects that underlie Richieri-Costa-Pereira Syndrome. Human Molecular Genetics. June 15; 26 (12): 2177-2191. 2017, *co-corresponding authors, + co-first authors [EPub]

Mao, H, Brown, H, and Silver, DL. Mouse models of Casc3 reveal developmental functions distinct from other components of the exon junction complex. RNA. Jan;23(1):23-31. 2017[EPub]

Carpenter V1, Chen YS1, Dolat L1, Valdivia RH1.The Effector TepP Mediates Recruitment and Activation of Phosphoinositide 3-Kinase on Early Chlamydia trachomatis Vacuoles. mSphere. 2017 Jul 19;2(4). pii: e00207-17. doi: 10.1128/mSphere.00207-17. eCollection 2017 Jul-Aug.[EPub]

Reddy A, Zhang J, Davis NS, Moffitt AB, Love CL, Waldrop A, Leppa S, Pasanen A, Meriranta L, Karjalainen-Lindsberg ML, Nørgaard P, Pedersen M, Gang AO, Høgdall E, Heavican TB, Lone W, Iqbal J, Qin Q, Li G, Kim SY, Healy J, Richards KL, Fedoriw Y, Bernal-Mizrachi L, Koff JL, Staton AD, Flowers CR, Paltiel O, Goldschmidt N, Calaminici M, Clear A, Gribben J, Nguyen E, Czader MB, Ondrejka SL, Collie A, Hsi ED, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Choi WWL, Evens AM, Pilichowska M, Sengar M, Reddy N, Li S, Chadburn A, Gordon LI, Jaffe ES, Levy S, Rempel R, Tzeng T, Happ LE, Dave T, Rajagopalan D, Datta J, Dunson DB, Dave SS. Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma. Cell. 2017 Oct 5;171(2):481-494. PMID: 28985567.[EPub]

Subramanian S, Gottschalk WK, Kim SY, Roses AD, Chiba-Falek O. The effects of PPARγ on the regulation of the TOMM40-APOE-C1 genes cluster. Biochim Biophys Acta. 2017 Mar;1863(3):810-816. PMID: 28065845.[EPub]

Davison, J.M., Lickwar, C.R., Song, L., Breton, G., Crawford, G.E., and Rawls, J.F. (2017) Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome Research 27(7): 1195-1206. [EPub] [News Release]

Lickwar, C.R., Camp, J.G., Weiser, M., Kingsley, D.M., Furey, T.S., Sheikh, S.Z., and Rawls, J.F. (2017) Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells. PLoS Biology 15(8):e2002054 [EPub] [News Release]

McClung JM, McCord TJ, Ryan TE, Schmidt CA, Green TD, Southerland KW, Reinardy JL, Mueller SB, Venkatraman TN, Lascola CD, Keum S, Marchuk DA, Spangenburg EE, Dokun A, Annex BH, Kontos CD. BAG3 (Bcl-2-Associated Athanogene-3) Coding Variant in Mice Determines Susceptibility to Ischemic Limb Muscle Myopathy by Directing Autophagy.Circulation. 2017 Jul 18;136(3):281-296. doi: 10.1161/CIRCULATIONAHA.116.024873. Epub 2017 Apr 25. [EPub]

Billmyre RB, Clancey SA, Heitman J. Natural mismatch repair mutations mediate phenotypic diversity and drug resistance in Cryptococcus deuterogattii. eLife. 2017 Sep 26;6. pii: e28802. doi: 10.7554/eLife.28802.[EPub]

Sun S, Yadav V, Billmyre RB, Cuomo CA, Nowrousian M, Wang L, Souciet JL, Boekhout T, Porcel B, Wincker P, Granek JA, Sanyal K, Heitman J. Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination. PLoS Biol. 2017 Aug 11;15(8):e2002527. doi: 10.1371/journal.pbio.2002527. eCollection 2017 Aug.[EPub]

Chow EW, Clancey SA, Billmyre RB, Averette AF, Granek JA, Mieczkowski P, Cardenas ME, Heitman J. Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. PLoS Genet. 2017 Apr 4;13(4):e1006667. doi: 10.1371/journal.pgen.1006667. eCollection 2017 Apr. [EPub]

Calo S, Nicolás FE, Lee SC, Vila A, Cervantes M, Torres-Martinez S, Ruiz-Vazquez RM, Cardenas ME, Heitman J. A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides. PLoS Genet. 2017 Mar 24;13(3):e1006686. doi: 10.1371/journal.pgen.1006686. eCollection 2017 Mar. [EPub]

 Sharma R, Ishimaru Y, Davison I, Ikegami K, Chien MS, You H, Chi Q, Kubota M, Yohda M, Ehlers M, Matsunami H.Olfactory receptor accessory proteins play crucial roles in receptor function and gene choice.Elife. 2017 Mar 6;6. pii: e21895. doi: 10.7554/eLife.21895.[EPub]

Pilaz, L-J, Lennox, A.L., Rouanet, J.P., and Silver, DL. Dynamic mRNA transport and local translation in radial glial progenitors of the developing brain. Current Biology. Dec 19;26(24):3383-3392. 2016 (Featured in accompanying Preview article in same issue by Ehses et al. and in F1000Prime).[EPub]

Haldar, AK., Piro, AS., Finethy, R., Espenschied, ST., Brown, HE., Giebel, AM., Frickel, E-A., Nelson, DE., Coers, J. Chlamydia trachomatis is resistant to inclusion ubiquitination and associated host defense in IFNgamma-primed human cells. mBio 2016. Dec 13;7(6). pii: e01417-16. PMID: 27965446

Aldrup-MacDonald ME*, Kuo ME*, Sullivan LL*, Chew K, Sullivan BA (2016) Genomic variation within alpha satellite DNA influences centromere location on human chromosomes with metastable epialleles. Genome Res 26:1301-1311. (*joint first authors)
press release: https://www.eurekalert.org/pub_releases/2016-08/du-vi083016.php
radio spot: http://www.wfdd.org/story/predictive-power-junk-your-genome-0.

Ross JE, Woodlief KS, Sullivan BA (2016) Inheritance of the CENP-A chromatin domain is spatially and temporally constrained at human centromeres. Epigenetics Chromatin 9:20.

Smola MJ, Christy TW, Inoue K, Nicholson CO, Friedersdorf M, Keene JD, Lee DM,
Calabrese JM, Weeks KM. SHAPE reveals transcript-wide interactions, complex
structural domains, and protein interactions across the Xist lncRNA in living
cells. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10322-7. doi:
10.1073/pnas.1600008113. Epub 2016 Aug 30. PubMed PMID: 27578869; PubMed Central
PMCID: PMC5027438.

Wetzel-Strong SE, Detter MR, Marchuk DA. The pathobiology of vascular malformations: insights from human and model organism genetics. J Pathol. 2017 Jan;241(2):281-293. doi: 10.1002/path.4844. Epub 2016 Dec 4. Review. PMID: 27859310 [EPub]

Roko-Rasin, M, and Silver, D. The crossroads of RNA regulation and function in neurodevelopment. Int J Dev Neurosci. Dec;55:101. 2016. Invited review article.[EPub]

McMahon, JJ, Miller, EE, and Silver, DL. The exon junction complex in neural development and neurodevelopmental disease. International Journal of Developmental Neuroscience. 2016 Dec;55:117-123. 2016 Invited review article.[EPub]

Mao, H, McMahon, JJ, Tsai, Y-H., Wang, Z, and Silver, DL. Haploinsufficiency for core exon junction complex components disrupts neurogenesis and causes p53-mediated microcephaly. PLoS Genetics. Sept. 12.; 12(9): e1006282. 2016 (Featured in radio interview)[EPub]


Silver, DL. Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex. Bioessays. Feb;38(2)162-71. 2016 Invited review article.[Abstract]

Zheng DQ, Zhang K, Wu XC, Mieczkowski PA, Petes TD. Global analysis of genomic instability caused by DNA replication stress in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8114-E8121. Epub 2016 Nov 28. PMID: 27911848 [EPub]

Singh, SK, Stogsdill, JA, Pulimood, N, Dingsdale, H, Kim YH, Pilaz, LJ, Kim, IH, Manhaes, AC, Rodrigues-Junior, WS, Pamukcu, A, Enustun, E, Ertuz, Z, Scheiffele, P, Soderling, S, Silver, DL, Li, R, Medina, AJ, and Eroglu, C. Astrocytes Assemble Thalamocortical Synapses by Bridging Neurexin-1α and Neuroligin-1 via Hevin. Cell. Jan 14; 164 (1-2): 183-96. 2016 [EPub]

Pilaz, LJ, McMahon, JJ, Miller, EE, Lennox, AL, Suzuki, A, Salmon, E, Silver, DL, Prolonged mitosis of neural progenitors alters cell fate in the developing brain. Neuron. Jan 6; 89(1):83-99. 2016 (Featured in F1000Prime).[EPub]

Cronan MR1, Beerman RW1, Rosenberg AF1, Saelens JW1, Johnson MG2, Oehlers SH1, Sisk DM1, Jurcic Smith KL3, Medvitz NA4, Miller SE4, Trinh LA5, Fraser SE5, Madden JF4, Turner J6, Stout JE2, Lee S3, Tobin DM7.Macrophage Epithelial Reprogramming Underlies Mycobacterial Granuloma Formation and Promotes Infection.Immunity. 2016 Oct 18;45(4):861-876. doi: 10.1016/j.immuni.2016.09.014. [EPub]

Andersen SL, Zhang A, Dominska M, Moriel-Carretero M, Herrera-Moyano E, Aguilera A, Petes TD. High-Resolution Mapping of Homologous Recombination Events in rad3 Hyper-Recombination Mutants in Yeast. PLoS Genet. 2016 Mar 11;12(3):e1005938. doi: 10.1371/journal.pgen.1005938. eCollection 2016 Mar.PMID: 26968037 [EPub]

Feretzaki M, Billmyre RB, Clancey SA, Wang X, Heitman Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAiSilencing Componenets in the Cryptococcus Pathogenic Species Complex.  J.PLoS Genet. 2016 Mar 4 12(3):e1005868. doi: 10.1371/journal.pgen.1005868. eCollection 2016 Mar. [EPub]

Shi C, Shenkar R, Zeineddine HA, Girard R, Fam MD, Austin C, Moore T, Lightle R, Zhang L, Wu M, Cao Y, Gunel M, Louvi A, Rorrer A, Gallione C, Marchuk DA, Awad IA. B-Cell Depletion Reduces the Maturation of Cerebral Cavernous Malformations in Murine Models.J Neuroimmune Pharmacol. 2016 Jun;11(2):369-77. doi: 10.1007/s11481-016-9670-0. Epub 2016 Apr 16. PMID: 27086141

Sullivan LL, Maloney KA, Towers AJ, Gregory SG, Sullivan BA (2016) Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res 24(4):451-466.

Girard R, Zeineddine HA, Orsbon C, Tan H, Moore T, Hobson N, Shenkar R, Lightle R, Shi C, Fam MD, Cao Y, Shen L, Neander AI, Rorrer A, Gallione C, Tang AT, Kahn ML, Marchuk DA, Luo ZX, Awad IA. Micro-computed tomography in murine models of cerebral cavernous malformations as a paradigm for brain disease. J Neurosci Methods. 2016 Sep 15;271:14-24. doi: 10.1016/j.jneumeth.2016.06.021. Epub 2016 Jun 23. PMID: 27345427 [EPub]

 Bae S, Mueller O, Wong S, Rawls JF, Valdivia RH

Genomic sequencing-based mutational enrichment analysis identifies motility genes in a genetically intractable gut microbe.Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14127-14132. Epub 2016 Nov 23. [EPub]

Zhou T, Chien MS, Kaleem S, Matsunami H Single cell transcriptome analysis of mouse carotid body glomus cells.J Physiol. 2016 Aug 1;594(15):4225-51. doi: 10.1113/JP271936. Epub 2016 Apr 13.[EPub]

McFadden K, Hafez AY, Kishton R, Messinger JE, Nikitin PA, Rathmell JC, Luftig MA (2016) Metabolic stress is a barrier to Epstein-Barr virus mediated B-cell immortalization. Proc Natl Acad Sci U S A 113:E782-90. [Article]

Meng L, Mulcahy B, Cook SJ, Neubauer M, Wan A, Jin Y, Yan D. The cell death pathway regulates synapse elimination through cleavage of celsolin in Caenorhabditis elegans neurons. Cell Rep, 11:1737-48.  2015. PMCID: PMC4481169. [EPub]

Haldar, AK., Finethy, R., Piro, AS., Feeley, EM., Pilla-Moffett, D., Foltz, C., Komatsu, M., Frickel, EM., Coers, J. Ubiquitin systems mark pathogen-containing vacuoles for host defense by Guanylate Binding Proteins. Proc Natl Acad Sci U.S.A. 2015 Oct 13;112(41):E5628-37. PMID: 26417105

Finethy, R., Jorgensen, I., Haldar, AK., de Zoete, MR., Flavell, RA., Yamamoto, M., Nagarajan, UM., Miao, EA., Coers, J. Guanylate Binding Proteins enable rapid activation of canonical and noncanonical inflammasomes in Chlamydia-infected macrophages. Infection and Immunity 2015 Dec; 83(12):4740-9. PMID: 26416908

Kang D, Skalsky RL, Cullen BR. EBV BART microRNAs target multiple pro-apoptotic cellular genes to promote epithelial cell survival. PLoS Pathogens11, e1004979, 2015. [Epub]

Blackinton JG, Keene JD. Functional coordination and HuR-mediated regulation
of mRNA stability during T cell activation. Nucleic Acids Res. 2016 Jan
8;44(1):426-36. doi: 10.1093/nar/gkv1066. Epub 2015 Oct 20. PubMed PMID:
26490963; PubMed Central PMCID: PMC4705648.

Jiang Y, Gong NN, Hu XS, Ni MJ, Pasi R, Matsunami H.Molecular profiling of activated olfactory neurons identifies odorant receptors for odors in vivo.Nat Neurosci. 2015 Oct;18(10):1446-54. doi: 10.1038/nn.4104. Epub 2015 Aug 31. [EPub]

Kokes M. Dunn JD, Granek JA, Nguyen BD, Barker JR, Valdivia RH, Bastidas RJ. Integrating chemical mutagenesis and whole-genome sequencing as a platform for forward and reverse genetic analysis of Chlamydia. Cell Host Microbe. 2015. [Epub]

Oehlers SH, Cronan MR, Thomas MI, Okuda KS, Walton EM, Beerman RW, Crosier PS,     Tobin DM. Interception of host angiogenic signalling limits mycobacterial growth. Nature 517: 612-15, 2015. [Epub]

MGM Publications 2Minchin JN, Dahlman I, Harvey CJ, Mejhert N, Singh MK, Epstein JA, Arner P, Torres-Vázquez J and Rawls JF. Plexin D1 determines body fat distribution by regulating the type V collagen microenvironment in viseceral adipose tissue. Proc Natl Acad Sci USA 112(14): 4363-8. 22015, 2015. [Epub] Featured on  cover.



MGM Publications 3Mao H, Pilaz LJ, McMahon J, Golzio C, Wu D, Shi L, Katsanis N and Silver DL Rbm8a haploinsufficiency disrupts embryonic cortical development resulting in microcephaly. Journal of Neuroscience. May 6; 35(18): 7003-7018, 2015. [Epub] Featured on cover.



Strope PK, Skelly DA, Kozmin SG, Mahadevan G, Stone EA, Magwene PM, Dietrich FS, McCusker JH. The 100-genomes strains, an S. cerevisiae resource that illuminates its natural phenotypic and genotypic variation and emergence as an opportunistic pathogen. Genome Res. 2015 May;25(5):762-74. Doi: 10.1101/gr.185538.114. [Epub]

Jiang Y, Li YR, Tian H, Ma M, Matsunami H. Muscarinic acetylcholine receptor M3   modulates odorant receptor activity via inhibition of β-arrestin-2 recruitment. Nat Commun. 2015 Mar 24;6:6448. doi: 10.1038/ncomms7448. PubMed PMID: 25800153; PubMed Central PMCID: PMC4372811. [Epub]

Shenkar R, Shi C, Rebeiz T, Stockton RA, McDonald DA, Mikati AG, Zhang L, Austin C, Akers AL, Gallione CJ, Rorrer A, Gunel M, Min W, De Souza JM, Lee C, Marchuk DA, Awad IA. Exceptional aggressiveness of cerebral cavernous malformation disease associated with PDCD10 mutations. Genet Med. 2015 Mar;17(3):188-196. doi: 10.1038/gim.2014.97. Epub 2014 Aug 14. PMID: 25122144 [EPub]

Moon SL, Blackinton JG, Anderson JR, Dozier MK, Dodd BJ, Keene JD, Wilusz CJ,
Bradrick SS, Wilusz J. XRN1 stalling in the 5′ UTR of Hepatitis C virus and
Bovine Viral Diarrhea virus is associated with dysregulated host mRNA stability.
PLoS Pathog. 2015 Mar 6;11(3):e1004708. doi: 10.1371/journal.ppat.1004708.
eCollection 2015 Mar. PubMed PMID: 25747802; PubMed Central PMCID: PMC4352041.

Boyd JL, Skove SL, Rouanet JP, Pilaz L-J, Bepler T, Gordân R, Wray GA, and Silver DL. Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Current Biology. Mar 16; 25 (6) 772-9, 2015. [Epub]

Dokun AO, Chen L, Okutsu M, Farber CR, Hazarika S, Jones WS, Craig D, Marchuk DA, Lye RJ, Shah SH, Annex BH. ADAM12: a genetic modifier of preclinical peripheral arterial disease. Am J Physiol Heart Circ Physiol. 2015 Sep;309(5):H790-803. doi: 10.1152/ajpheart.00803.2014. Epub 2015 Jul 10. PMID: 26163448 [EPub]

Bogerd, H.P., Skalsky, R.L., Kennedy, E.M., Furuse, Y., Whisnant, A.W., Flores, O., Schultz, K.L., Putnam, N., Barrows, N.J., Sherry, B., Scholle, F., Garcia-Blanco, M.A., Griffin, D.E., and Cullen, B.R. (2014) Replication of many human viruses is refractory to inhibition by endogenous cellular microRNAs. J Virol, 88:8065-8076. [Abstract]

Shen F, Degos V, Chu PL, Han Z, Westbroek EM, Choi EJ, Marchuk D, Kim H, Lawton MT, Maze M, Young WL, Su H. Endoglin deficiency impairs stroke recovery. Stroke. 2014 Jul;45(7):2101-6. doi: 10.1161/STROKEAHA.114.005115. Epub 2014 May 29. PMID: 24876084 [EPub]

Chen YS, Bastidas RJ, Saka HA, Carpenter VK, Richards KL, Plano GV, Valdivia RH. The Chlamydia trachomatis type III secretion chaperone Slc1 engages multiple early effectors, including TepP, a tyrosine-phosphorylated protein required for the recruitment of CrkI-II to nascent inclusions and innate immune signaling. PLoS Pathog. 2014 Feb 20;10(2):e1003954. doi: 10.1371/journal.ppat.1003954. PMID:  24586162 [Epub]

Engström P, Krishnan KS, Ngyuen BD, Chorell E, Normark J, Silver J, Bastidas RJ, Welch MD, Hultgren SJ, Wolf-Watz H, Valdivia RH, Almqvist F, Bergström S. A 2-pyridone-amide inhibitor targets the glucose metabolism pathway of Chlamydia trachomatis. MBio. 2014 PMID: 25550323 [Epub]

Snavely EA, Kokes M, Dunn JD, Saka HA, Nguyen BD, Bastidas RJ, McCafferty DG, Valdivia RH. Reassessing the role of the secreted protease CPAF in Chlamydia trachomatis infection through genetic approaches. Pathog Dis. 2014 PMID: 24838663 [Epub]

Cai Y, Cao X, and Aballay A. Whole-animal chemical screen identifies colistin as a new immunomodulator that targets conserved pathways. mBio, Aug 12;5(4). pii: e01235-14. doi: 10.1128/mBio.01235-14, 2014. [Epub]

Head B. and Aballay, A. Recovery from an acute infection in C. elegans requires the GATA transcription factor ELT-2. PLOS Genetics, Oct 23. doi: 10.1371/journal.pgen.1004609, 2014. [Epub]  [News Release]

Billmyre RB, Croll D, Li W, Mieczkowski P, Carter DA, Cuomo CA, Kronstad JW, Heitman J. Highly recombinant VGII Cryptococcus gatti population develops clonal outbreak clusters through both sexual macroevolution and asecual mecroevolution. mBio. 2014 Jul 29;5(4):e01494-14. doi: 10.1128/mBio.01494-14. [Epub]

Springer DJ, Billmyre RB, Filler EE, Voelz K, Pursall R, Mieczkowski PA, Larsen RA, Dietrich FS, May RC, Filler SG, Heitman J. Cryptococcus gattii VGII isolates causing infections in HIV/AIDS patients in Southern California: identification of the local environment source as arboreal. PLoS Pathog. 2014 Aug 21;10(8):e1004285. doi: 10.1371/journal.ppat.1004285. eCollection 2014 Aug. [Epub]

Calo S, Shertz-Wall C, Lee SC, Bastidas RJ, Nicolás FE, Granek JA, Mieczkowski P, Torres-Martínez S, Ruiz-Vázquez RM, Cardenas ME, Heitman J. Antifungl drug resistance evoked via RNAi-dependent epimutations. Nature. 2014 Sep 25;513(7519):555-8. doi: 10.1038/nature13575. [Epub]

Stimpson KM, Sullivan LL, Kuo ME, Sullivan BA. Nucleolar Organization, Ribosomal DNA Array Stability, and Acrocentric Chromosome Integrity Are Linked to Telomere Function. PLoS ONE 9(3): e92432. doi: 10.1371/journal.pone.0092432. 2014. [Epub]

Bogerd HP, Whisnant AW, Kennedy EM, Flores O and Cullen BR. Derivation and characterization of Dicer- and microRNA-deficient human cells. RNA20, 923-937. 2014. [Epub]

Friedersdorf M. and Keene JD. Advancing Functional Utility of PAR-CLIP by Quantifying Background Binding to mRNAs and lncRNAs. Genome Biology 15:R2. 2014. [Epub]

Cullen, B.R. (2014) Replication of many human viruses is refractory to inhibition by endogenous cellular microRNAs. J Virol, 88:8065-8076. [Abstract]

Song, W., Dominska, M., Greenwell, P. W., and Petes, T. (2014) Genome-wide high-resolution mapping of chromosome fragile sites in Saccharomyces cerevisiaeProc Nat Acad Sci, U S A, 111:E2210-8. [Abstract]

Pilla, D., Hagar, J.A., Haldar, A.K., Mason, A.K., Ernst, R.K., Yamamoto M., Miao, E.A., and Coers, J. (2014) Guanylate binding proteins promote caspase-11-dependent pyroptosis in response to cytoplasmic LPS. Proc Natl Acad Sci U S A, 111:6046-51. [Abstract]

Janbon, G. et al., and Dietrich, F.S. (2014) Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLOS Genetics, 10:e1004261. [Abstract]

MGM Publications 4Camp, J.G., Frank, C.L., Lickwar, C.R., Guturu, H., Rube, T., Wenger, A.M., Chen, J. Bejerano, G., Crawford, G.E., and Rawls, J.F. (2014) Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape. Genome Res, Sep;24(9):1504-16 [Epub 2014 Jun 24]. [Abstract] Featured on the cover.



Mainland, J.D., Keller, A., Li, Y.R, Zhou, T., Snyder, L.L., Moberly, A.H., Adipietro, K.A., Liu, W.L.L., Zhuang, H., Zhan, S., Lee, S.S., Lin, A., and Matsunami, H. (2014) The missense of smell: functional variability in the human odorant receptor repertoire. Nat Neurosci [Epub 2013 Dec 8]. [Abstract]

Bastidas RJ, Elwell CA, Engel JN, Valdivia RH. Chlamydial intracellular survival strategies.Cold Spring Harb Perspect Med. 2013 May 1;3(5):a010256. doi: 10.1101/cshperspect.a010256. Review. PMID:  23637308 [Epub]

Barker JR, Koestler BJ, Carpenter VK, Burdette DL, Waters CM, Vance RE, Valdivia RH. STING-dependent recognition of cyclic di-AMP mediates type I interferon responses during Chlamydia trachomatis infection. MBio. 2013 Apr 30;4(3):e00018-13. doi: 10.1128/mBio.00018-13. PMID: 23631912. Free PMC Article [Epub]

Mitchel K, Lehner K. and Jinks-Robertson S.  Heteroduplex DNA position defines the roles of the Sgs1, Srs2 and Mph1 helicases in promoting distinct recombination outcomes.  PLoS Genet9,e1003340. 2013. [Epub]

Aksenova, A.Y., Greenwell, P. W., Dominska, M., Shishkin, A. A., Kim, J. C., Petes, T. D., and Mirkin, S. M. (2013) Genomerearrangements caused by interstitial telomeric sequences in yeast. Proc Nat Acad Sci, U S A, 110:19866-19871. [Abstract]

Haldar, A.K., Saka, H.A., Piro, A.S., Dunn, .JD., Henry, S.C., Taylor, G.A., Frickel, E.M., Valdivia, R.H., and Coers, J. (2013) IRG and GBP host resistance factors target aberrant, “non-self” vacuoles characterized by the missing of “self” IRGM proteins. PLOS Pathogens, 6:e1003414. [Abstract]

Ni, M.*, Feretzaki, M.*, Li, W., Floyd-Averette, A., Mieczkowski, P., Dietrich, F.S., and Heitman, J. (2013) Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformansPLOS Biology, 11: e1001653. [Abstract]

Nguyen BD, Valdivia RH. Virulence determinants in the obligate intracellular pathogen Chlamydia trachomatis revealed by forward genetic approaches. Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1263-8. doi: 10.1073/pnas.1117884109. Epub 2012 Jan 9.PMID:  22232666 [Epub]

Tobin DM, Roca FJ, Oh SF, McFarland R, Vickery TW, Ray JP, Ko DC, Zou Y, Bang ND, Chau TTH, Vary JC, Hawn TR, Dunstan SJ, Farrar JJ, Thwaites GE, King M-C, Serhan CN, Ramakrishnan L. Genotype-specific therapies can optimize the inflammatory response to mycobacterial infections. Cell148: 434-446. 2012. [Epub]

Skalsky RL, Corcoran DL, Gottwein E, Frank CL, Kang D, Hafner M, Nusbaum JD, Feederle R, Delecluse HJ, Luftig MA, Tuschl T, Ohler, Uwe, and Cullen BR. The viral and cellular microRNA targetome in lymphoblastoid cell lines. PLoS Pathogens8: e1002484. 2012. [Epub]

Adipietro, K.A., Mainland, J.D. and Matsunami, H. (2012) Functional evolution of mammalian odorant receptors. PloS Genetics 8,:e1002821. [Abstract]

Maloney, K.A., Sullivan, L.L., Matheny, J.E., Strome, E.D., Merrett, S.L., Ferris, A., Sullivan, B.A. (2012) Functional epialleles at an endogenous human centromere. Proc Natl Acad Sci U S A, 109(34):13704-13709. [Abstract]

Mukherjee N, Corcoran DL, Nusbaum J, Reid D, Georgiev S, Hafner M, Ascano Jr., M, Tuschl T, Ohler U. and Keene JD. Integrative regulatory mapping indicates that RNA-binding protein HuR (ELAVL1) couples pre-mRNA splicing and mRNA stability. Molecular Cell 43: 327-339. 2011. [Epub]

Gottwein E, Corcoran DL, Mukherjee N, Skalsky RL, Hafner M, Nusbaum JD, Shamulailatpam P, Love CL, Dave SS, Tuschl T, Ohler U and Cullen BR. Viral microRNA targetome of KSHV-infected primary effusion lymphoma cell lines. Cell Host & Microbe10, 515-526. 2011. [Epub]

Lippert MJ, Kim N, Cho JE, Larson RP, Schoenly NE, O’Shea SH. and Jinks-Robertson S.  Role for topoisomerase 1 in transcription-associated mutagenesis in yeast.  Proc. Natl. Acad. Sci. USA 108, 698-703. 2011. [Epub]

Dey, S. and Matsunami, H. (2011). Calreticulin chaperones regulate functional expression of V2R pheromone receptors. Proc Natl Acad Sci U S A, 108:16651-16656. (Direct submission) [Abstract]

Li, Y.R., and Matsunami, H. (2011). Activation state of the M3 muscarinic acetylcholine receptor modulates mammalian odorant receptor signaling. Sci Signal 4, ra1. [Abstract]

Kim, N., Huang, S.Y., Williams, J.S., Li, Y.C., Clark, A.B., Cho, J.E., Kunkel, T.A., Pommier, Y., and Jinks-Robertson, S. (2011) Mutagenic processing of ribonucleotides in DNA by yeast topoisomerase I. Science, 332:1561-1564. [Abstract]

Li, C.H., Cervantes, M., Springer, D.J., Boekhout, T., Ruiz-Vazquez, R.M., Torres-Martinez, S.R., Heitman, J., and Lee, S.C. (2011) Sporangiospore Size Dimorphism Is Linked to Virulence of Mucor circinelloidesPLoS Pathogens, 7, e1002086. [Abstract]

Chi, J.T., Thrall, D.E., Jiang, C., Snyder, S., Fels, D., Landon, C., McCall, L., Lan, L., Hauck, M., MacFall, J.R., Vigilanti, B.L., and Dewhirst, M.W. (2011).Comparison of genomics and functional imaging from canine sarcomas treated with thermoradiotherapy predicts therapeutic response and identifies combination therapeutics. Clinical Cancer Research 17, 2549-2560. [Abstract]

Sun, J., Singh, V., Kajino-Sakamoto, R., and Aballay, A. (2011) Neuronal GPCR controls innate immunity by regulating noncanonical unfolded protein response genes. Science 332, 729-732. [Abstract]

Goldstein, D.B. (2011).The importance of synthetic associations will only be resolved empirically. PLoS Biology 18, e1001008. [Abstract]

Tang, W., Dominska, M., Greenwell, P.W., Harvanek, Z., Lobachev, K.S., Kim, H.M., Narayanan, V., Mirkin, S.M., and Petes, T.D. (2011) Friedreich’s ataxia (GAA)n•(TTC)n repeats strongly stimulate mitotic crossovers in Saccharomyces cerevisaePLoS Genetics 13, e1001270. [Abstract]

Bogerd HP, Karnowski HW, Cai X, Shin J, Pohlers M and Cullen BR. A mammalian herpesvirus uses non-canonical expression and processing mechanisms to generate viral microRNAs. Molecular Cell37, 135-142. 2010. [Epub]

Cullen, B.R. (2010).Five questions about viruses and microRNAs. PLoS Pathogens 6, e1000787. [Abstract]

Mitchel, K., Zhang, H. Welz-Voegele, C., and Jinks-Robertson, S. (2010). Molecular structures of crossover and noncrossover intermediates during gap repair in yeast: implications for recombination. Molecular Cell 38, 211-222. [Abstract]

Stimpson, K.M., Son,g I.Y., Jauch, A., Holtgreve-Grez, H., Hayden, K.E., Bridger, J.M., and Sullivan, B.A. (2010) Telomere disruption results in non-random formation ofde novo dicentric chromosomes involving acrocentric human chromosomes. PLOS Genet, 6:e1001061. [Abstract]

Nikitin, P.A., Yan, C.M., Forte, E., Bocedi, A., Tourigny, J.P., White, R.E., Allday, M.J., Patel, A., Dave, S.S., Kim, W., Hu, K., Guo, J., Tainter, D., Rusyn, E., and Luftig, M.A. (2010) An ATM/Chk2-mediated DNA damage-responsive signaling pathway suppresses Epstein-Barr virus transformation of primary human B cells. Cell Host Microbe 16, 510-522.

Pickup, D.J. (2010) Propelling progeny. Science 327, 787-788. [Abstract]

Lee, P.S. and Petes, T.D. (2010) From the Cover: mitotic gene conversion events induced in G1-synchronized yeast cells by gamma rays are similar to spontaneous conversion events. PNAS 107, 7383-7388. [Abstract]

Zhuang, H., Chien, M.S., and  Matsunami, H. (2009). Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. Proc Natl Acad Sci U S A 106, 21247-21251. (Direct submission). [Abstract] 

Saito, H., Chi, Q., Zhuang, H., Matsunami, H., and Mainland, J.D. (2009). Odor coding by a Mammalian receptor repertoire. Sci Signal 2, ra9. [Abstract]

Kim, N. and Jinks-Robertson, S. (2009). dUTP incorportation into genomic DNA is linked to transcription in yeast. Nature 459, 1150-1153. [Abstract]

Wheeler, F.C., Tang, H., Marks, O.A., Hadnott, T.N., Chu, P.L., Mao, L., Rockman, H.A., and Marchuk, D.A. (2009) Tnni3k modifies disease progression in murine models of cardiomyopathy. PLoS Genetics5, e1000647. [Abstract]

Bastidas, R.J., Heitman, J., and Cardenas, M.E. (2009). The protein kinase Tor1 regulates adhesin gene expression in Candida albicansPLoS Pathogens 5, e1000294. [Abstract]

Whitehead, K.J., Chan, A.C., Navankasattusas, S., Koh, W., London, N.R., Ling, J., Mayo, A.H., Drakos, S.G., Jones, C.A., Zhu, W., Marchuk, D.A., Davis, G.E., and Li, D.Y. (2009). The cerebral cavernous malformation signaling pathway promotes vascular inegrity via Rho GTPases. Nature Medicine15, 177-183. [Abstract]

Mukherjee, N., Lager, P.J., Friedersdorf, M.B., Thompson, M.A., and Keene, J.D. (2009). Coordinated post-transcriptional mRNA population dynamics during T-cell activation. Molecular Systems Biology5, 288-302. [Abstract]

Spaeth, K.E., Chen, Y.-S., and Valdivia, R.H. (2009). TheChlamydia type III secretion system C-ring engages a chaperone-effector protein complex. PLoS Pathogens 5, e10000579. [Abstract]

Kavanaugh, L.A. and Dietrich, F.S. (2009). Non-coding RNA prediction and verification in Saccharomyces cerevisiaePLoS Genetics 5, e1000321. [Abstract]

Umbach JL, Kramer MF, Jurak I, Karnowski HW, Coen DM and Cullen BR. MicroRNAs expressed by herpes simplex virus 1 during latent infection regulate viral mRNAs. Nature, 454, 780-783. 2008. [Epub]

Puria, R., Zurita-Martinez, S.A., and Cardenas, M.E. (2008). Nuclear translocation of Gln3 in response to nutrient signals requires Golgi-to-endosome trafficking in Saccharomyces cerevisiaePNAS 105, 7194-7199. [Abstract]

Tenor, J.L. and Aballay, A. (2008). A conserved toll-like receptor is required for Caenorhabditis elegansinnate immunity. EMBO reports 9, 103-109. [Abstract]

Haskins, K.A., Russell, J.F., Gaddis, N., Dressman, H.K., and Aballay, A. (2008). Unfolded protein response genes regulated by CED-1 are required for Caenorhabditis elegans innate immunity. Developmental Cell 15, 87-97. [Abstract]

Kumar, Y. and Valdivia, R.H. (2008). Actin and intermediate filaments stabilize the Chlamydia trachomatis vacuole by forming dynamic structural scaffolds. Cell Host & Microbe 4, 159-169. [Abstract]

Styer, K.L., Singh, V., Macosko, E., Steele, S.E., Bargmann, C.I., and Aballay, A. (2008). Innate immunity in Caenorhabditis elegans is regulated by neurons expressing NPR-1/GPCR. Science 322, 460-464. [Abstract]

Idnurm, A., Walton, F.J., Floyd, A., and Heitman, J. (2008). Identification of the sex genes in an early diverged fungus. Nature 451, 193-196. [Abstract]

Cocchiaro, J.L., Kumar, Y., Fischer, E.R., Hackstadt, T., and Valdivia, R.H. (2008). Cytoplasmic lipid droplets are translocated into the lumen of the Chlamydia trachomatisparasitophorous vacuole. PNAS105, 9379-9384. [Abstract]

Coers, J., Bernstein-Hanley, I., Grotsky, D., Parvanova, I., Howard, J.C., Taylor, G.A., Dietrich, W.F., and Starnbach, M.N. (2008). Chlamydia muridarum evades growth restriction by the IFN-{gamma}-inducible host resistance factor Irgb10. The Journal of Immunology 180, 6237-6245. [Abstract]

Keller, A., Zhuang, H., Chi, Q., Vosshall, L. B., and Matsunami, H. (2007). Genetic variation in a human odorant receptor alters odour perception. Nature, 2007 449, 468-472. [Abstract]

Ishimaru, Y., Inada, H., Kubota, M., Zhuang, H., Tominaga, M., and  Matsunami, H. (2006). Transient receptor potential family members PKD1L3 and PKD2L1 form a candidate sour taste receptor. Proc Natl Acad Sci U S A 103, 12569-12574. (Direct submission) [Abstract]

Singh, V. and Aballay, A. (2006). Heat-shock transcription factor (HSF)-1 pathway required for Caenorhabditis elegans immunity. PNAS 103, 13092-13097. [Abstract]

Kavanaugh, L.A., Fraser, J.A., and Dietrich, F.S. (2006). Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment. Molecular Biology and Evolution 23, 1879-1890. [Abstract]

Narayanan, V., Mieczkowski, P.A., Kim, H.M., Petes, T.D., and Lobachev, K.S. (2006). The pattern of gene amplification is determined by the chromosomal location of hairpin-capped breaks. Cell 125, 1283-1296. [Abstract]

Lam, A.L., Boivin, C.D., Bonney, C.F., Rudd, M.K., and Sullivan, B.A. (2006). Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA. PNAS 103, 4186-4191. [Abstract]

Fraser, J.A., Giles, S.S., Wenink, E.C., Geunes-Boyer, S.G., Wright, J.R., Diezmann, S., Allen, A., Stajich, J.E., Dietrich, F.S., Perfect, J.R., and Heitman, J. (2005). Same-sex mating and the origin of the Vancouver Island Cryptococcus gattii outbreak. Nature 437, 1360-1364. [Abstract]

Lin, X., Hull, C.M., and Heitman, J. (2005). Sexual reproduction between partners of the same mating type in Cryptococcus neoformansNature 434, 1017-1021. [Abstract]

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