Recent Faculty Publications

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Justin Blau	Mazzoni EO, Desplan C, Blau J. Circadian pacemaker neurons transmit and modulate visual information to control a rapid behavioral response. Neuron. 2005 Jan 20;45(2):293-300. Collins B, Mazzoni EO, Stanewsky R, Blau J. Drosophila CRYPTOCHROME is a circadian transcriptional repressor. Curr Biol. 2006 Mar 7;16(5):441-9.
Suse Broyde	Wang L, Broyde S. A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). Nucleic Acids Res. 2006 Feb 1;34(3):785-95. Print 2006. Perlow-Poehnelt RA, Likhterov I, Wang L, Scicchitano DA, Geacintov NE, Broyde S. Increased flexibility enhances misincorporation: Temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase. J Biol Chem. 2006 Nov 6
Gloria Coruzzi	Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD. Cell-specific nitrogen responses mediate developmental plasticity. Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8. Epub 2008 Jan 7. Gutiérrez RA, Lejay LV, Dean A, Chiaromonte F, Shasha DE, Coruzzi GM. Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis. Genome Biol. 2007;8(1):R7. Gutierrez RA, Shasha DE, Coruzzi GM. Systems biology for the virtual plant. Plant Physiol. 2005 Jun;138(2):550-4. Review.
Claude Desplan	Wernet MF, Labhart T, Baumann F, Mazzoni EO, Pichaud F, Desplan C. Homothorax switches function of Drosophila photoreceptors from color to polarized light sensors. Cell. 2003 Oct 31;115(3):267-79. Mazzoni EO, Desplan C, Blau J. Circadian pacemaker neurons transmit and modulate visual information to control a rapid behavioral response. Neuron. 2005 Jan 20;45(2):293-300. Mikeladze-Dvali T, Wernet MF, Pistillo D, Mazzoni EO, Teleman AA, Chen YW, Cohen S, Desplan C. The growth regulators warts/lats and melted interact in a bistable loop to specify opposite fates in Drosophila R8 photoreceptors. Cell. 2005 Sep 9;122(5):775-87. Lynch JA, Brent AE, Leaf DS, Pultz MA, Desplan C. Localized maternal orthodenticle patterns anterior and posterior in the long germ wasp Nasonia. Nature. 2006 Feb 9;439(7077):728-32. Wernet MF, Mazzoni EO, Celik A, Duncan DM, Duncan I, Desplan C. Stochastic spineless expression creates the retinal mosaic for colour vision. Nature. 2006 Mar 9;440(7081):174-80.
Patrick Eichenberger	Wang ST, Setlow B, Conlon EM, Lyon JL, Imamura D, Sato T, Setlow P, Losick R, Eichenberger P. The forespore line of gene expression in Bacillus subtilis. J Mol Biol. 2006 Apr 21;358(1):16-37. Epub 2006 Feb 8.
David Fitch	Del Rio-Albrechtsen T, Kiontke K, Chiou SY, Fitch DH. Novel gain-of-function alleles demonstrate a role for the heterochronic gene lin-41 in C. elegans male tail tip morphogenesis. Dev Biol. 2006 Sep 1;297(1):74-86. Epub 2006 May 6. Kiontke K, Gavin NP, Raynes Y, Roehrig C, Piano F, Fitch DH. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9003-8. Epub 2004 Jun 7. Kiontke K, Fitch D.H.A. The Phylogenetic relationships of Caenorhabditis and other rhabditids. WormBook. 2005 Aug 11;:1-11.
Kristin Gunsalus	Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol. 2006 Mar 7;16(5):460-71. Epub 2006 Feb 2. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature. 2005 Aug 11;436(7052):861-5. Sonnichsen B, Koski LB, Walsh A, Marschall P, Neumann B, Brehm M, Alleaume AM, Artelt J, Bettencourt P, Cassin E, Hewitson M, Holz C, Khan M, Lazik S, Martin C, Nitzsche B, Ruer M, Stamford J, Winzi M, Heinkel R, Roder M, Finell J, Hantsch H, Jones SJ, Jones M, Piano F, Gunsalus KC, Oegema K, Gonczy P, Coulson A, Hyman AA, Echeverri CJ. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature. 2005 Mar 24;434(7032):462-9. Fernandez AG, Gunsalus KC, Huang J, Chuang LS, Ying N, Liang HL, Tang C, Schetter AJ, Zegar C, Rual JF, Hill DE, Reinke V, Vidal M, Piano F. New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res. 2005 Feb;15(2):250-9.
Fabio Piano	Fernandez AG, Piano F. MEL-28 is downstream of the Ran cycle and is required for nuclear-envelope function and chromatin maintenance. Curr Biol. 2006 Sep 5;16(17):1757-63. Lall S, Grun D, Krek A, Chen K, Wang YL, Dewey CN, Sood P, Colombo T, Bray N, Macmenamin P, Kao HL, Gunsalus KC, Pachter L, Piano F, Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol. 2006 Mar 7;16(5):460-71. Epub 2006 Feb 2. Gunsalus KC, Ge H, Schetter AJ, Goldberg DS, Han JD, Hao T, Berriz GF, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature. 2005 Aug 11;436(7052):861-5.
Carol Reiss	Ireland DD, Reiss CS. Gene Expression Contributing to Recruitment of Circulating Cells in Response to Vesicular Stomatitis Virus Infection of the CNS Viral Immunol. 2006;19(3):536–545. Trottier MD Jr, Palian BM, Shoshkes Reiss C. VSV replication in neurons is inhibited by type I IFN at multiple stages of infection. Virology. 2005 Mar 15;333(2):215-25. Jingjun Yang, Derin Tugal and Carol Shoshkes Reiss The role of the proteasome–ubiquitin pathway in regulation of the IFN-γ mediated anti-VSV response in neurons Journal of Neuroimmunology, Volume 181, Issues 1-2, December 2006, Pages 34-45
Christine Rushlow	Xu M, Kirov N, Rushlow C. Peak levels of BMP in the Drosophila embryo control target genes by a feed-forward mechanism. Development. 2005 Apr;132(7):1637-47. Epub 2005 Feb 23. Lin MC, Park J, Kirov N, Rushlow C. Threshold response of C15 to the Dpp gradient in Drosophila is established by the cumulative effect of Smad and Zen activators and negative cues. Development. 2006 Dec;133(24):4805-13. Epub 2006 Nov 8.
David Scicchitano	Scicchitano DA, Olesnicky EC, Dimitri A. Transcription and DNA adducts: what happens when the message gets cut off? DNA Repair (Amst). 2004 Dec 2;3(12):1537-48. Review. Schinecker TM, Perlow RA, Broyde S, Geacintov NE, Scicchitano DA. Human RNA polymerase II is partially blocked by DNA adducts derived from tumorigenic benzo[c]phenanthrene diol epoxides: relating biological consequences to conformational preferences. Nucleic Acids Res. 2003 Oct 15;31(20):6004-15. Plosky B, Samson L, Engelward BP, Gold B, Schlaen B, Millas T, Magnotti M, Schor J, Scicchitano DA. Base excision repair and nucleotide excision repair contribute to the removal of N-methylpurines from active genes. DNA Repair (Amst). 2002 Aug 6;1(8):683-96. Perlow RA, Likhterov I, Scicchitano DA., Geacintov NE, Broyde S The Spacious Active Site of a Y-Family DNA Polymerase Facilitates Promiscuous Nucleotide Incorporation Opposite a Bulky Carcinogen-DNA Adduct: ELUCIDATING THE STRUCTURE-FUNCTION RELATIONSHIP THROUGH EXPERIMENTAL AND COMPUTATIONAL APPROACHES J. Biol. Chem., Aug 2004; 279: 36951 - 36961 Scicchitano DA. Transcription past DNA adducts derived from polycyclic aromatic hydrocarbons. Mutat Res. 2005 Sep 4;577(1-2):146-54. Review.
Mark Siegal	Siegal ML, Promislow DE, Bergman A. Functional and evolutionary inference in gene networks: does topology matter? Genetica. 2006 Aug 8 Siegal ML, Baker BS. Functional conservation and divergence of intersex, a gene required for female differentiation in Drosophila melanogaster. Dev Genes Evol. 2005 Jan;215(1):1-12. Epub 2004 Nov 12. Bergman A, Siegal ML. Evolutionary capacitance as a general feature of complex gene networks. Nature. 2003 Jul 31;424(6948):549-52.
Stephen Small	Yucel G, Small S. Morphogens: precise outputs from a variable gradient. Curr Biol. 2006 Jan 10;16(1):R29-31. Oberstein A, Pare A, Kaplan L, Small S. Site-specific transgenesis by Cre-mediated recombination in Drosophila. Nat Methods. 2005 Aug;2(8):583-5. Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, Papatsenko D, Small S. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc Natl Acad Sci U S A. 2005 Apr 5;102(14):4960-5. Epub 2005 Mar 25.
Daniel Tranchina	Hamer RD, Nicholas SC, Tranchina D, Lamb TD, Jarvinen JL. Toward a unified model of vertebrate rod phototransduction. Vis Neurosci. 2005 Jul-Aug;22(4):417-36. Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 2006 Sep;4(10):e309.