Recommended Readings: Nicholas Ingolias, PH.D. Monday Jan 4, 2010

Faculty Candidate Seminar

Genome-wide Translational Profiling by Ribosome Footprinting

Nicholas Ingolia, PH.D. 

Postdoctoral Fellow, Dept. of Cellular and Molecular Pharmacology, University of California, San Francisco

January 4, 2010

4:00 p.m. Welch Hall, Level Two

Recommended Readings:

Morris DR.  2009.  Ribosomal footprints on a transcriptome landscape.   GENOME BIOLOGY  10(4):article Number: 215    

Bailey-Serres J., Sorenson R., Juntawong P.  2009.  Getting the message across: cytoplasmic ribonucleoprotein complexes.  TRENDS IN PLANT SCIENCE   14(8): 443-453    

Sanz E, Yang L, Su T, Morris DR, McKnight GS, Amieux PS.  2009.  Cell-type-specific isolation of ribosome-associated mRNA from complex tissues.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA     106(33): 13939-13944   

 Ingolia NT, Ghaemmaghami S, Newman JRS, et al.  2009.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling.   SCIENCE   324(5924): 218-223   

Baek D., Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP.  2008.  The impact of microRNAs on protein output.   NATURE   455(7209): 64-70  

Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs   NATURE     455(7209): 58-63    

Berezikov E., Cuppen E., Plasterk RHA.  2006.  Approaches to microRNA discovery.   NATURE GENETICS     38(suppl 6): S2-S7    

Arava Y, Boas FE, Brown PO, Herschlag D.  2005.  Dissecting eukaryotic translation and its control by ribosome density mappingNUCLEIC ACIDS RESEARCH  33(8): 2421-2432   

Recommended Readings: Claude Desplan, Ph.D.

Friday Lecture Series

Detection and Processing of Color Information in Drosophila

Claude Desplan, Ph.D.,

Professor, department of biology, and director, Center for Developmental Genetics,

New York University

December 18, 2009

3:45 p.m.-5:00 p.m. (Refreshments, 3:15 p.m., Abby Lounge)

Caspary Auditorium

Recommended Articles:

Mikeladze-Dvali, T., M. F. Wernet, D. Pistillo, E. O. Mazzoni, A. A. Teleman, Y. -W Chen, S. Cohen, and C. Desplan. 2005. The growth regulators warts/lats and melted interact in a bistable loop to specify opposite fates in drosophila R8 photoreceptors. Cell 122, (5): 775-787

Morante, J., and C. Desplan. 2008. The color-vision circuit in the medulla of drosophila. Current Biology 18, (8): 553-565

Sprecher, S. G., and C. Desplan. 2008. Switch of rhodopsin expression in terminally differentiated drosophila sensory neurons. Nature 454, (7203): 533-537

Wernet, M. F., E. O. Mazzoni, A. Çelik, D. M. Duncan, I. Duncan, and C. Desplan. 2006. Stochastic spineless expression creates the retinal mosaic for colour vision. Nature 440, (7081): 174-180

Yamaguchi, S., R. Wolf, C. Desplan, and M. Heisenberg. 2008. Motion vision is independent of color in drosophila. Proceedings of the National Academy of Sciences of the United States of America 105, (12): 4910-4915

Recommended Readings: George A. M. Cross Ph.D. Monday Dec. 14, 2009

Monday Lecture


Daring to be Different: Unusual Aspects of Gene

Transcription in Trypanosomes

George A. M. Cross Ph.D

André and Bella Meyer Professor
Laboratory of Molecular Parasitology

The Rockefeller University

Dec. 14, 2009

Welch Hall, Level Two  4 p.m.

Recommended Articles:

Figueiredo LM, Cross GAM, Janzen CJ .  2009.  Epigenetic regulation in African trypanosomes: a new kid on the block. NATURE REVIEWS. Microbiology.    7(7): 504-513    

Siegel TN, Hekstra DR, Kemp LE, et al.   2009.  Four histone variants mark the boundaries of polycistronic transcription units in Trypanosoma brucei .   GENES & DEVELOPMENT.   23(9): 1063-1076    

Talbert PB, Henikoff S. 2009.  Chromatin-based transcriptional punctuation . GENES & DEVELOPMENT    23(9): 1037-1041   

Ibrahim, B. Syed;  Kanneganti, Nalini;  Rieckhof, Gabrielle E.; Das, Anish;  Laurents, Douglas V.; Palenchar, Jennifer B.;  Bellofatto, Vivian;  Wah, David A.   2009.   Structure of the C-terminal domain of transcription factor IIB from Trypanosoma brucei. 2009.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA .   106 (32): 13242-13247   

Haenni S, Studer E, Burkard GS, et al. 2009.  Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma bruceiNUCLEIC ACIDS RESEARCH   37(15): 5007-5018   

Koumandou VL, Natesan SKA, Sergeenko T, et al.  2008.  The trypanosome transcriptome is remodelled during differentiation but displays limited responsiveness within life stages.   BMC GENOMICS    9: Article Number 298    

Das, A; Banday, M; Bellofatto, V.    2008.  RNA polymerase transcription machinery in trypanosomes Eukaryotic Cell.   7:429-434

Siegel, TN; Tan, KS; Cross, GAM.  2005.  Systematic study of sequence motifs for RNA trasn-splicing in Trypanosoma brucei.  Molecular and Cellular Biology.  25:9586-9594