List of User Publications

Tognini, P., Murakami, M., Liu, Y, Eckel-Mahan, K.L., Newman, J.C., Vardin, 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

Nguyen, H.X., Hooshmand, M.J., Saiwai, H., Maddox, J., Salehi, A., Lakatos, A., Nishi, R., Salazar, D., Uchida, N. and Anderson, A.J.  Systematic neutrophil depletion modulates the migration and fate of transplanted human neural stem cells to rescue functional repair.  (2017) The Journal of Neuroscience Aug 28 epub

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 signatuare 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 fo BRAF mutant melanomas.  (2017) PLOS Genetics July 28 epub

Abdelsayed, M.M., Ho, B.T., Vu, M.M.K., 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 Chemical Biology 12: 2149-2156

Roger, 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

Lim, R.G., Quan, C., Reyes-Ortiz, A.M., Lutz, S.E., Kedaigle, A.J., Gipson T.A., Wu, J., Vatine, G.D., Stocksdale, J., Casale, M.S., Svendsen, C.N.,  Fraenkel, E., Housman, D.E., Agalliu, D. and Thompson, L.M. Huntington's disease iPSC-derived brain microvascular endothelial cells reveal WNT-mediated angiogenic and blood-brain barrier deficits. (2017) Cell Reports 19: 1365 - 1377

Lim RG, Salazar LL, Wilton DK, King AR, Stocksdale JT, Sharifabad D, Lau AL, Stevens B, Reidling JC, Winokur ST, Casale MS, Thompson LM, Pardo M, Díaz-Barriga AG, Straccia M, Sanders P, Alberch J, Canals JM, Kaye JA, Dunlap M, Jo L, May H, Mount E, Anderson-Bergman C, Haston K, Finkbeiner S, Kedaigle AJ, Gipson TA, Yildirim F, Ng CW, Milani P, Housman DE, Fraenkel E, Allen ND, Kemp PJ, Atwal RS, Biagioli M, Gusella JF, MacDonald ME, Akimov SS, Arbez N, Stewart J, Ross CA, Mattis VB, Tom CM, Ornelas L, Sahabian A, Lenaeus L, Mandefro B, Sareen D, Svendsen CN. Developmental alterations in Huntington's disease neural cells and pharmacological rescue in cells and mice.  (2017)  Nature Neuroscience March 20 Epub

Charney, R.M., Forouzmand, E., Cho, J.S., Cheung, J., Paraiso, K.D., Yasuoka, Y., Takashi, S., 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

Chen, C.-F., Ruiz-Vega, R., Vasudeva, P., Espitia, F., Krasieva, 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

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.  NRSR-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilence.  (2017)  Molecular Psychiatry 00: 1-10

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

Taylor, P.H., Cinquin, A. and Cinquin, O.  Quantificaiton 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

Butts, C.T., Bierma, J.C. and Martin, R.W. Novel proteases from the genome of the carnivorous plant Drosera capensis:  Structural 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 Epub

Zeng, W., Jiang, 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  August 26 Epub

Ho, M-M., Manughian-Peter, A., Spivia, W.R., Taylor, A. and Fraser, D.A.  Macrophage molecular signaling and inflammatory responses during injestion of atherogenic lipoproteins are modulated by complement protein C1q. (2016) Atherosclerosis 253: 38-46

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

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 in Drosophila 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 in Saccharomyces 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.,, 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.

Grimaldi, B., Bellet, M. M., Katada, S., Astarita, G., Hirayama, J., Amin, R. H., Granneman, J. G., Piomelli, D., Leff, T. and Sassone-Corsi. P.  PER2 controls lipid metabolism by direct regulation of PPAR. Cell Metabolism (2010) 12: 508-20.

Daily KM, Rigor PM, Christley SE, Xie X, Baldi PF, Data Structures and Compression Algorithms for High-Throughput Sequencing Technologies. BMC Bioinformatics (2010) 11: 514-26.

Wang Y, Xia XQ, Jia Z, Sawyers A, Yao H, Wang-Rodriquez J, Mercola D, McClelland M. In silico estimates of tissue components in surgical samples based on expression profiling data Cancer Res. (2010)  Aug 15;70(16):6448-55. Epub 2010 Jul 27.

Liu Q, Lin KK, Andersen B, Smyth P, Ihler A. Estimating replicate time shifts using Gaussian process regression Bioinformatics. (2010) Mar 15;26(6):770-6. Epub 2010 Feb 9.

Geyfman M, Andersen B.  Clock genes, hair growth and aging  Aging (Albany NY).  (2010) Mar 31;2(3):122-8.

Zhao F, Edwards R, Dizon D, Afrasiabi K, Mastroianni JR, Geyfman M, Ouellette AJ, Andersen B, Lipkin SM. Disruption of Paneth and goblet cell homeostasis and increased endoplasmic reticulum stress in Agr2-/- mice.   Dev Biol. (2010) Feb 15;338(2):270-9. Epub 2009 Dec 16.

Potkin SG, Macciardi F, Guffanti G, Wang Q, Turner JA, Lakatos A, Miles MF, Lander A, Vawter MP, Xie X. Identifying gene regulatory networks in schizophrenia  Neuroimage. (2010) Jun 22.

Swamidass SJ, Azencott CA, Daily KM, Baldi PF. A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinformatics (2010) 26: 1348-56.

Sikandar SS, Pate KT, Dizon D, Edwards RA, Waterman ML, Lipkin SM, Anderson SA: NOTCH signaling is required for formation and self-renewal of tumor-initiating cells and for repression of secretory cell differentiation in colon cancer. Cancer Res (2010) 70, 1469-78.

Molina DM, Pal S, Kayala MA, Teng A, Kim PJ, Baldi PF, Felgner PL, Liang X. Identification of immunodominant antigens of Chlamydia trachomatis using proteome microarrays. Vaccine (2010) 28, 3014-24.

Mochon AB, Ye J, Kayala MA, Wingard JR, Clancy CJ, Nguyen MH, Felgner PL, Baldi PF, Liu H: Serological profiling of a Candida albicans protein microarray reveals permanent host-pathogen interplay and stage-specific responses during candidemia. PLoS Pathog  (2010) 6, e1000827.

Liu Q, Lin KK, Andersen B, Smyth PJ, Ihler AT. Estimating replicate time shifts using Gaussian process regression. Bioinformatics (2010) 26, 770-6.

Leng D, Burk CR, Nakajima-Sasaki R, Kayala MA, Atluri VL, Pablo J, Unal B, Ficht TA, Gotuzzo E, Saito M, Morrow WJ, Liang X, Baldi PF, Gilman RH, Vinetz JM, Tsolis RM, Felgner PL, Liang L. Large scale immune profiling of infected humans and goats reveals differential recognition of Brucella melitensis antigens. PLoS Negl Trop Dis (2010) 4, e673.

Kim YK, Kwon YJ. Separation and recovery of nucleic acids with improved biological activity by acid-degradable polyacrylamide gel electrophoresis. Electrophoresis (2010) 31, 1656-61.

Garner CP. A statistical method for scanning the genome for regions with rare disease alleles. Genet Epidemiol (2010) 34, 386-95.

Crompton PD, Kayala MA, Traore B, Kayentao K, Ongoiba A, Weiss GE, Molina DM, Burk CR, Waisberg M, Jasinskas A, Tan X, Doumbo S, Doumtabe D, Kone Y, Narum DL, Liang X, Doumbo OK, Miller LH, Doolan DL, Baldi PF, Felgner PL, Pierce SK: A prospective analysis of the Ab response to Plasmodium falciparum before and after a malaria season by protein microarray. Proc Natl Acad Sci U S A (2010) 107, 6958-63.

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