Publications

  • Yamamoto, C.M., Oakes, M.L., Murakami, T., Muto, M.G., Berkowitz, R.S. and Ng, S-W.  Comparison of benign peritoneal fluid- and ovarian cancer ascites-derived extracelluar vesicle RNA biomarkers.  (2018) Journal of Ovarian Research 11:20-29

  • Sierra, R.A., Hoverter, N.P., Ramirez, R.N., Vuong, L.M., Mortazavi, A., Merrill, B.J., Waterman, M.L. and Donovan, P.J.  TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency.  (2018) Development January 18 Epub

  • Zhu, Y., Wang, X., Forouzmand, E., Jeong, J., Qiao, F., Sowd, G.A., Engelman, A.N., Xie, X., Hertel, K.J. and Shi, Y.  Molecular mechanisms for CFlm-mediated regulation of mRNA alternative polyadenylation.  (2018) Molecular Cell 69: 62-74

  • Chakraborty, M., VanKuren, N.W., Zhao, R., Zhang, X., Kalsow, S. and Emerson, J.J.  Hidden genetic variation shapes the structure of functional elements in Drosophila.  (2018) Nature Genetics 50: 20-25

  • Baldwin-Brown, J.G., Weeks, S.C. and Long, A.D.  A new standard for crustacean genomes:  the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome.  (2018) Genome Biology & Evolution 10(1): 143-156

  • Hernandez, M.X., Jiang, S., Cole, T.A., Chu, S-H., Fonseca, M.I., Fang, M.J., Hohsfield, L.A., Torres, M.D., Green, K.N., Wetsel, R.A., Mortazavi, A., and Tenner, A.J.  Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss (2017) Molecular Neurodegeneration 12: 66-85

  • Chakraborty, M., VanKuren, N.W., Zhao, R, Zhang, X., Kalsow, S., Emerson, J.J. Hidden genetic variation shapes the structure of functional elements in Drosophila.  (2017) Nature Genetics December 18 Epub

  • Moser, B.A., Steinhardt, R.C. and Esser-Kahn, A.P.  Surface coating of nanoparticles reduces background inflammatory activity while increasing particle uptake and delivery.  (2017) ACS Biomaterial Science Engineering 3(2);  206-213

  • Zhou, Y., Massonnet, M., Sanjak, J.S., Cantu, D. and Gaut, B.S.  Evolutionary genomics of grape (Vitus vinifera ssp. vinifera) domestication. (2017)  Proceedings of the National Academy of Sciences 114(44):  11715-11720

  • Herndon Klein, R., Hu, W., Kashgari, G., Lin, Z., Nguyen, T., Doan, M. and Andersen, B.  Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation.  (2017)  Journal of Biological Chemistry 292(46):  18937-18950

  • Gonzalez-Gonzalez, A., Hug, S.M., Rodriguez-Verdugo, A., Patel, J.S. and Gaut, B.S.  Adaptive mutations in RNA polymerase and the transcriptional terminator Rho have similar effects on Escherichia coli gene expression.  (2017)  Molecular Biological Evolution 34(11):  2839-2855

  • Macias-Munoz, A., McCulloch, K.J. and Briscoe, A.D. Copy number variation and expression analysis reveals a non-orthologous pinta gene family member involved in butterfly vision. (2017) Genome Biology and Evolution November 9 Epub

  • Tognini, P., Murakami, M., Liu, Y., Eckel-Mahan, K.L., Newman, J.C., Verdin, E., Baldi, P. and Sassone-Corsi, P.  Distinct circadian signatures in liver and gut clocks revealed by ketogenic diet. (2017) Cell Metabolism 26: 523-538

  • Orozco-Solis, R., Montellier, E., Aguilar-Arnal, L., Sato, S., Vawter, M.P., Bunney, B.G., Bunney, W.E. and Sassone-Corsi, P.  A circadian genomic signature common to ketamine and sleep deprivation in the anterior cingulate cortex.  (2017) Biological Psychiatry 82:351-360

  • Ruiz, R., Jahid, S., Harris, M., Marzese, D.M., Espitia, F., Vasudeva, P., Chen, C-F., de Feraudy, S., Wu, J., Gillen, D.L., Krasieva, T.B., Tromberg, B.J., Pavan, W.J., Hoon, D.S. and Ganesan, A.K. The RhoJ-BAD signaling network:  An Achilles’ heel for BRAF mutant melanomas.  PLOS Genetics July 28 Epub

  • Abdelsayed, M.M., Ho, B.T., Vu, M.K.M., Polanco, J., Spitale, R.C. and Luptak, A.  Multiplex aptamer discovery through Apta-Seq and its application to ATP aptamers derived from Human-Genomic SELEX.  (2017) ACS June 19 Epub

  •  Rogers, R.L., Shao, L. and Thornton, K.R. Tandem duplications lead to novel expression patterns through exon shuffling in Drosophila yakuba.  (2017) PLOS Genetics May 22 Epub

  • Herndon Klein, R., Lin, Z., Hopkin, A. S., Gordon, W., Tsoi, L.C., Liang, Y., Gudjonsson, J.E. and Andersen, B.  (2017)  GRHL3 binding and enhancers rearrange as epidermal keratinocytes transistion between functional states.  (2017) PLOS Genetics April 26 Epub

  • Chen, C-F., Ruiz-Vega, R., Vasudeva, P., Espitia, F., Krasiava, T.B., de Ferauly. S., Tromberg, B.J., Huang, S., Garner, C.P., Wu, J., Hoon, D.S. and Ganesan, A.K. ATR mutations promote the growth of melanoma tumors by modulating the immune microenvironment.  (2017)  Cell Reports 18: 2331-2342

  • Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Shuji, T., Taira, M., Blitz, I.L., Xie, X. and Cho, K.W.Y.  Foxh1 occupies cis-regulatory modules prior to dynamic transcription factor interactions controlling the mesendoderm gene program.  (2017)  Developmental Cell 40: 595-607

  • Lim, R., Salazar, L.I, Stocksdale, J.T., Lau, AlI., Reidling, J.C., Winokur, S.T., Casale, M.S., Thompson, L.M. and HD IPSC Consortium. Developmental alterations in Huntington’s disease neural cells and pharmacological rescue in cells and mice.  (2017)  Nature Neuroscience 20(5): 648-660

  • de Moraes, M.H., Desai, P., Porwolilk, S., Canals, R., Perez, D.R., Chu, W., McClelland, M. and Teplitski, M.  Salmonella persistence in tomatoes requires a distinct set of metabolic functions identified by transposon insertion sequencing.  (2017) Applied and Environmental Microbiology 83(5): e03028-16

  •  Singh-Taylor, A., Molet, J., Jiang, S., Korosi, A., Bolton, J.L., Noam, Y., Simeone, K., Cope, J., Chen, Y., Mortazavi, A. and Baram, T.Z.  NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience.  (2017) Molecular Psychiatry Jan 11 Epub

  • Unhelkar, M.H., Duong, V.T., Enendu, K.N., Kelly J.E., Tahir, S., Butts, C.T. and Martin, R.W.  Structure prediction and network analysis of chitinases from the Cape sundew, Drosera capensis (2017) Biochem Biophysis Acta 1861(3): 636-643

  • Clifton, B.D., Librado, P., Yeh, S-D., Solares, E.S., Real, D.A., Jayasekera, S.U., Zhang, W., Shi, M, Park, R.D., Magie, R.D., Ma, H-C., Xia, X-Q., Marco, A., Rozas, J. and Ranz, J.M. Rapid functional and sequence differentiation  of a tandemly repeated species-specific multigene family in Drosophila. (2016) Molecular Biology & Evolution 34(1): 51-65

  • Taylor, P.H., Cinquin, A. and Cinquin, O.  Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq. (2016) Genome Research 26: 1600-1611

  • Movassi, M., Orabb, T.L., Busch, A., Yao, O., Reynolds, D.J. and Shi, Y.  Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns.  (2016)  RNA BIOLOGY 13(7): 645-655

  • Butts, C., Bierma, J.C. and Martin, R.W.  Novel proteases from the genome of the carnivorous plant Drosera capensis:  structure prediction and comparative analysis. (2016)  Proteins. 84: 1517-1533.

  • Magnan, C., Yu, J., Chang, I., Jahn, E., Kanomata, Y., Wu, J., Zeller, M., Oakes, M., Baldi, P. and Sandmeyer, S.  Sequence assembly of Yarrowia lipolytica strain W29/CLIB89 shows transposable element diversity. (2016) PLOS one Sept 7, 2016

  • Zeng, W., Jian, S., Kong, X., El-Ali, N., Ball, A.R.Jr., Ma, C.I-H., Hashimoto, N., Yokomori, K. and Mortazavi, A.  Single nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. (2016) Nucleic Acids Research 44(21): e158-173

  • Chakraborty, M., Baldwin-Brown, J.G., Long, A.D. and Emerson, J.J.  Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage.  (2016)  Nucleic Acids Research Jul 25 Epub

  • Butts, C.T., Zhang, X., Kelly, J.E., Roskamp, K.W., Unhelkar, M.H., Freites, J.A., Tahir, S. and Martin, R.  Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis. (2016) Computational and Structural Biotechnology Journal 14: 271-282.

  • Herndon Klein, R., Stephens, D.N., Ho, H., Chen, J.K., Salmans, M.L., Wang, W., Yu, Z. and Andersen, B.  Cofactors of LIM domains associate with estrogen receptor alpha to regulate the expression of noncoding RNA H19 and corneal epithelial progenitor cell function. (2016) Journal of Biological Chemistry Apr 29 Epub

  • Masri, S., Papagiannakopoulos, T., Kinochi, K., Liu, Y., Cervantes, M., Baldi, P., Jacks, T. and Sassone-Corsi, P. Lung adenocarcinoma distally rewires hepatic circadian homeostasis. (2016) Cell 165: 896-909

  • Marsh, S.E., Abud, E.M., Lakatos, A., Karimzadeh, A., Yeung, S.T., Davtyan, H., Fote, G.M., Lau, L., Weinger, J.G., Lane, T.E., Inlay, M.A., Poon, W.W. and Blurton-Jones, M. The adaptive immune system restrains Alzheimer’s disease pathogenesis by modulating microglial function. (2016) Proc Natl Academy of Science Feb 16 Epub

  • Spangenberg, E.E., Lee, R.J., Najafi, A.R., Rice, R.A., Elmore, M.R.P., Blurton-Jones, M., West, B.L. and Green, K.N. Eliminating microglia in Alzheimer’s mice prevents neuronal loss without modulating amyloid-B pathology. (2016) Brain Feb 26 Epub

  • Schneider, K., Valdez, J., Nguyen, J., Vawter, M., Galke, B., Kurtz, T.W. and Chan, J.Y. Increased energy expenditure, UCP1 expression and resistance to diet-induced obesity in mice lacking nuclear factor-erythroid-2 related transcription factor-2 (Nrf2). (2016) Journal of Biological Chemistry  Feb 3 Epub

  • Elhadad, D., Desai, P., Grassl, G.A., McClelland, M., Rahav and Gal-Mor, O. Differences in host cell invassion and SPI-1 expression between Salmonella enterica serovar Paratyphi A and the non-Typhoidal serovar Typhimurium. (2016) Infection and Immunity Feb 8 Epub

  • Barbour, A.G., Multiple and diverse vsp and vlp sequences in Boreelia miaymotoi, a hard tick-borne zoontoic pathogen. PLos One (2016) 11(1):  e0146283

  • Paterson, E.K., Fielder, T.J., MacGregor, G.R., Ito, S., Wakamatsu, K., Gillen, D.L., Eby, V., Boissy, R.E. and Ganesan, A.K.  Tyrosinase depletion prevents the maturation of melansomes in the mouse hair follicle.  PLos One (2016) 10(11):  e0143702

  • Tom, J.K., Dotsey, E.Y., Wong, H.Y., Stutts, L. Moore, T., Davies, D.H., Felgner, P.L. and Esser-Kahn, A.P.  Modulation of innate immune responses via covalently linked TLR agaonists. (2016) ACS Oct 28 Epub

  • Begum, A.N., Guoynes, C., Cho, J., Hao, J., Lutfy, K. and Hong, Y. Rapid generation of sub-type, region-specific neurons and neural networks from human pluripotent stem cell-derived neurospheres. (2015) Stem Cell Research 15: 731-741

  • Mesak, F., Tatarenkov, A. and Avise, J.C.  Transcriptomics of diapause in an isogenic self-fertilizing vertebrate.  BMC Genomics (2015) 16: 989-1000

  • Agrawal, S., Ganguly, S., Hajian, P., Cao, J-N, Agrawal, A. PDGF upregulates CLEC-2 to induce T regulatory cells. Oncotarget (2015) 6(30): 28621-28632

  • Macias-Munoz, A., Smith, G., Monteiro, A. and Briscoe, A.  Transcriptome-wide differential gene expression in Bicyclus anynana butterflies:  Female vision-related genes are more plastic.  Molecular Biology and Evolution (2015) Sept 14 Epub

  • Lane, S., Di Lena, P., Tormanen, K., Baldi, P. and Liu, H.  Function and regulation of Cph2 in Candida albicans.  Eukaryotic Cell (2015)  Sept 4 Epub

  • Elhadad, D., Desai, P., Rahav, G., McClelland, M., and Gal-Mor, O.  Flagellin is required for host cell invasion and normal Salmonella pathogenicity island I expression by Salmonella enterica serovar paratyphi A.  Infection and Immunity (2015) 83(9): 3355-3368

  • Rahmatpanah, F.B., Jia, Z., Chen, X., Char, J.E., Men, B., Franke, A-C., Jones, F.E., McClelland, M., and Mercola. D. A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors. Oncotarget (2015) 6(2): 1286-1301

  • Salehi, F., Baronio, R., Idrogo-Lam, R., Vu, H., Hall, L.V., Kaiser, P. and Lathrop, R.H. CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generational sequencing. (2015) PLOS 10(2): e0116877

  • Hoverter, N.P., Zeller, M.D., McQuade, M.M., Garibaldi, A., Busch, A., Selwan, E.M., Hertel, K.J., Baldi, P. and Waterman, M. The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.  Nucleic Acids Research (2014) 42(9): 13615-13632

  • Chiu, W.T., Le, R.C., Blitz, I.L., Fish, M.B., Li, Y., Biesinger, J., Xie, X. and Cho, K.W. Genome-wide view of TGFB/Foxh1 regulation of the early mesendoderm program. Development (2014) Oct 30 Epub

  • Gordon, M.W., Zeller, M.D., Klein, R.H., Swindell, W.R., Ho, H., Espetia, F., Gudionsson, J.E., Baldi, P.F. and Andersen, B.  A GRHL3-regulated repair pathway suppresses immune-mediated epidermal hyperplasia.  J. Clin. Invest (2014) Oct 27 Epub

  • Rogers, R.L., Shao, L., Sanjak, J.S., Andolfatto, P. and Thornton, K.R.  Revised annotations, sex-biased expression and lineage-specific genes in the Drosophila melanogaster group.  G3 (Bethesda) (2014) Oct 1 Epub

  • Rogers, R.L., Cridland, J.M., Shao, L., Hu, T.T., Andolfatto, P. and Thornton, K.R.  Landscape of standing variation for tandem duplications inDrosophila yakuba and Drosophila simulans.  Mol. Biol. Evol. (2014) 31(7): 1750-1766.

  • Smith, G., Macias-Munoz, A. and Briscoe, A.D. Genome sequence of a novel Iflavirus from mRNA sequencing of the butterfly Heliconius erato.  Genome Announcements (2014) 2(1):  e00398-14.

  • Diez, C.M., Meca, E., Tenaillon, M.I., and Gaut, B.S. Three groups of transposable elements with contrasting copy number dynamics and host responses in the Maize (Zea mays ssp. mays) genome.  PLOS Genetics (2014) 10(4):  e1004298.

  • Salmans, M.L., Zhengquan Y., Watanabe, K., Cam, E., Sun, P., Smyth, P., Dai, X. and Andersen, B.  The co-factor of LIM domains (CLIM/LDB/NLI) maintains basal mammary epithelial stem cells and promotes breast tumorigenesis.  PLOS Genetics (2014) 10: e1004520

  • Pate, K.T., Stringari, C., Sprowl-Tania, S., Wang,  K., TeSiaa, T., Hoverter, N.P., McQuade, M.M., Garner, C., Digman, M.A., Teitell, M.A., Edwards, R.A., Gratton, E., and Waterman, M.L.  Wnt signaling directs a metabolic program of glycolysis and angiogenesis in colon cancer. EMBO (2014) May 13 Epub

  • Allison, S.D., Lu, L., Kent, A.G., Martiny, A.C.  Extracellular enzyme production and cheating in Pseudomonas fluorescens depend on diffusion rates. Frontiers in Microbiology (2014) 5: 169.

  • Berlemont, R., Allison, S.D., Weihe, C., Lu, Y., Brodie, E.L., Martiny, J.B.H., Martiny, A.C. Cellulolytic potential under environmental changes in microbial communities from grassland litter.  Frontiers in Microbiology (2014) 5: 639.

  • Watanabe, K., Villarreal-Ponce, A., Sun, P., Salmans, M.L., Fallahi, M., Andersen, B. and Dai,X.  Mammary morphogenesis and regeneration require the inhibition of EMT at terminal end buds by Ovol2 transcription repressor.  Developmental Cell (2014) 29: 59-74.

  • Lee, B., Villarreal-Ponce, A., Fallahi, M., Ovadia, J., Sun, P., Yu, Q-C., Ito, S., Sinha, S., Nie, Q. and Dai, X.  Transcriptional mechanisms link epithelial plasticity to adhesion and differentiation of epidermal progenitor cells. Developmental Cell (2014) 29: 47-58.

  • Burke, M., King, E.G., Shahrestani, P., Rose, M.R. and Long, A.D.  Genome-wide association study of extreme longevity in Drosophila melanogaster. Genome Biology and Evolution (2014) 6(1): 1-11.

  • Salazar, L., Kashiwada, T., Krejci, P., Meyer, A.N., Casale, M., Hallowell, M., Wilcox, W.R., Donoghue, D.J. and Thompson, L.M.  Fibroblast growth factor receptor 3 interacts with and activates TGFB-activated kinase 1 tyrosine phosphorylation and NFkB signaling in multiple myeloma and bladder cancer. PLOS One (2014) 9: e86470

  • Barbour, A.G. and Campeau Miller, S. Genome sequence of Borrelia parkeri, an agent of enzootic relapsing fever in western North America. Genome Announc (2014) 2(1): e00018

  • Eckel-Mahan, K.L., Patel, V.R., de Mateo, S., Orozco-Solis, R., Ceglia, N.J., Sahar, B., Dilag-Penilla, S.A., Dyar, K.A., Baldi, P. and Sassone-Corsi, P. Reprogramming of the circadian clock by nutritional challenge.  Cell (2013) 155: 1464-1478

  • Aguilar-Arnal, L., Hakim, O., Patel, V.R., Baldi, P., Hager, G.L. and Sassone-Corsi, P. Cycles in spatial and temporal chromosomal organization driven by the circadian clock. Nature Structural and Molecular Biology (2013) 20: 1206-1213.

  • Stephens, D.N., Herndon-Klein, R., Salmons, M.L., Gordon, W., Ho, H. and Andersen, B. The Ets transcription factor EHF as a regulatory of cornea epithelial cell identity.  Journal of Biological Chemistry (2013) 288: 34304-34324

  • Briscoe, A.D., Macias-Munoz, A., Koszak, K.M., Walters, J.R., Yuan, F., Jamie, G.A., Martin, S.H., Dasmahapatra, K.K., Ferguson, L.C., Mallet, J., Jacquin-Joly, E. and Jiggins, C.D. Female behaviour drives expression and evolution of gustatory receptors in butterflies.  PLOS Genetics (2013) 9(7): e1003620

  • Takumo, S. and Gaut, B.  Gene body methylation is conserved between plant orthologs and is of evolutionary consequence. Proc. Natl. Acad. Sci. (2013) 110(5): 1797-1802

  • Liu, P., Chernyshov, A., Najdi, T., Fu, Y., Dickerson, J., Sandmeyer, S. and Jarboe, L.  Membrane stress caused by octanoic acid inSaccharomyces cerevisiae Appl. Microbiol Biotechnol. (2013) 97: 3239-3251

  • Pedram, A., Razandi, M., O’Mahony, F., Harvey, H., Harvey, B.J. and Levin, E.R. Estrogen reduces lipid content in the liver exclusively from membrane receptor signalling. Science Signalling (2013) 6(276): ra36

  • Gu, B., Watanabe, K., Sun, P., Fallahi, M. and Dai, X.  Chromatin effector Pygo2 mediates Wnt-Notch crosstalk to suppress luminal/alveolar potential of mammary stem and basal cells.  Cell Stem Cell (2013) 13:48-61

  • Vogel-Ciernia, A., Matheos, D.P., Barrett, R.M., Kramar, E.A., Azzawi, S., Chen, Y., Magnan, C.N., Zeller, M., Sylvain, A., Haettig, J., Jia, Y., Tran, A., Dang, R., Post, R.J., Chabrier, M., Babayan, A.H., Wu, J.I., Crabtree, G.R., Baldi, P., Baram, T.Z., Lynch, G., and Wood, M.A. The neuron-specific chromatin regulatory subunti BAF53b is necessary for synaptic plasticity and memory. Nature Neuroscience (2013) 16(5): 552-563

  • Lee, B., Geyfman, M., Andersen, B. and Dai, X.  Analysis of gene expression in skin using laser capture microdissection.  Methods Mol. Biol. (2013) 989:  109-117.

  • Hu, T.T., Eisen, M.B., Thornton, K.R. and Andolfatto, P.  A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.  Genome Research (2013) 23(1): 89-98

  • Gordon, W., Galitovskiy, V., Edwards, R., Andersen, B. and Grando, S.A.  The tobacco carcinogen nitrosamine induces a differential gene expression response in tumour susceptible A/J and resistant C3H mouse lungs.  European Journal of Cancer (2013) 49: 725-733.

  • Laquer, V.T., Hevezi, P.A., Albrecht, H., Chen, T.S., Zlotnik, A., and Kelly, K.M., Microarray analysis of port wine stains before and after pulsed dye laser treatment. Lasers in Surgery and Medicine (2013) 45: 67-75

  • Benoit, M.E., Hernandez, M.X., Dinh, M.L., Benavente, F., Vasquez, O. and Tenner, A.J.  C1q-induced LRP1B and GPR6 proteins expressed early in alzheimer disease mouse models, are essential for the C1q-mediated protection against amyloid-B neurotoxicity.  J. Biological Chemistry (2013) 288(1):  654-665.

  • Yang, J., Gu, P., Menges, S. and Klassen, H. Quantitative changes in gene transcription during induction of differentiation in porcine neural progenitor cells.  Molecular Vision (2012) 18:  1484-1504.

  • Benoit, M.E., Clarke, E.V., Morgado, P., Fraser, D.A. and Tenner, A.J.  Complement protein C1q directs macrophage polarization and limits inflammasome activity during the uptake of apoptotic cells.  J. Immunology (2012) 188(11): 5682-5693.

  • Hoverter, N.P., Ting, J.-H., Sundaresh, S., Baldi, P. and Waterman, M.L. A WNT/p21 circuit directed by the C-Clamp, a sequence-specific DNA binding domain in TCFs. Mol. and Cellular Biol.  (2012) 32(18): 3648-3862

  • Cribbs, D.H., Berchtold, N.C., Perreau, V., Coleman, P.D., Rogers, J., Tenner, A.J., and Cotman, C.W.  Extensive innate immune gene activation accompanies brain aging, increasing vulnerability to cognitive decline and neurodegeneration:  a microarray study.  J. of Neuroinflammation (2012) 9: 179-197.

  • The Heliconius Genome Consortium, Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.  Nature (2012) 487(7405):  94-98.

  • Geyfman, M., Kumar, V., Liu, Q., Ruiz, R., Gordon, W., Espitia, F., Cam, E., Millar, S.E., Smyth, P., Ihler, A., Takahashi, J.S. and Andersen, B., Brain and muscle Arnt-like protein-1 (BMAL1) controls circadian cell proliferation and susceptibility to UVB-induced DNA damage in the epidermis.  Proc. Natl. Acad. Sci. (2012) 109(29): 11758-11763.

  • Smith, M., Flodman, P.L., Gargus, J.J., Simon, M.T., Verrell, K., Haas, R., Reinger, G.E., Naviaux, R., Osann, K., Spence, M.A. and Wallace, D.C., Mitochondrial and ion channel gene alterations in autism.  Biochemica et Biophysica Acta (2012) Apr [Eub ahead of print]

  • Kayala, M.A. and Baldi, P., Cyber-T web server:  differential analysis of high-throughput data.  Nucleic Acids Research (2012) May 16 [Epub ahead of print]

  • Mackay, T., Richards, S., Stone, E.A., Brabadilla, A., et.al., The Drosophila melanogaster genetic reference panel.  Nature (2012) 482: 173-178

  • Garrigan, D., Kingan, S.B., Geneva, A.J., Andolfatto, P., Clark, A.G., Thornton, K.R. and Presgraves, D.C.  Genome sequencing reveals complex speciation in the Drosophila simulans clade.  Genome Research (2012) Apr 13 [Epub ahead of print]

  • Tenaillon, O., Rodriquez-Verdugo, A., Gaut, R.L., McDonald, P., Bennett, A.F., Long, A.D. and Gaut, B.S., The molecular diversity of adaptive convergence. Science (2012) 335(6067): 457-461

  • Muto, A., Calof, A., Lander, A., and Schilling, T.  Multifactorial origins of heart and gut defects in nipbl-deficient Zebrafish, a model of Cornelia de Lange Syndrome.  PLos Biol. (2011) 9(10): e1001181

  • Bhandari, A., Salmans, M., Gordon, W., and Anderson, B. Transcriptional regulation of epidermal barrier formation. Methods Mol. Biol. (2011) 763: 51-71.

  • Lee, C., Lee, C., Hu, T., Nguyen, J., Zhang, J., Martin, M., Vawter, M., Huang, E., and Chan, J.  Loss of nuclear factor E2-related factor 1 in the brain leads to dysregulation of proteasome gene expression and neurodegeneration.  Proc. Natl. Acad. Sci. (2011)  108(20): 8408-8413.

  • Jia, Z., Wang, Y., Sawyers, A., Yao, H., Rahmatpanah, F., Xia, X-Q., Xu, Q., Pio, R., Turan, T., Koziol, J., Goodison, S., Carpenter, P., Wang-Rodgriguez, J., Simoneau, A., Meyskens, F., Sutton, M., Lernhardt, W., Beach, T., Monforte, J., McClelland, M. and Mercola, D.,  Diagnosis of Prostate Cancer using Differentially Expressed Genes in Stroma.  Cancer Research (2011) 71(7): 2476-2487.

  • Im, S-S., Yousef, L., Biaschitz, C., Liu, J.Z., Edwards, R.A., Young, S.G., Raffatellu, M. and Osborne, T.F.  Linking lipid metabolism to the innate immune response in macrophages through sterol regulatory element binding protein 1-a.  Cell Metabolism (2011) May 4 13:  540-549.

  • Garner, C. Confounded by sequencing depth in association studies of rare alleles. Genet. EpidemIol. (2011) 35(4): 261-268

  • Benoit, M.E. and Tenner, J.J.  Complement protein C1q-mediated neuroprotection is correlated with regulation of neuronal gene and miRNA expression.  J. Neuroscience (2011) 31(9):  3459-3469

  • Katada, S. and Sassone-Corsi, P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nature Struct. Mol. Biol. (2010) 11: 1414-21.

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