Criteria for best paper, 2008

First three were agreed upon as MOST IMPORTANT halfway through course

 

  1. Flow of arguments—one experiment leads to the next
  2. Design of experiments good—controls complete, leads to significant questions, addresses those questions.
  3. Interpretation fair to data—state if only possible conclusion or if other possibilities exist (ideally, complete work to point where only one explanation possible)
  4. Clear figures
  5. Good transitions
  6. Thorough materials and methods—to understand what they did
  7. Easily understandable intro (with significance of experiment)
  8. Readability (interesting topic)
  9. Originality—breakthrough experiment
  10. Design is streamlined/elegant/creative

 

 

Paper nominees (sorted by presenter)

 

Brad

Yen et al., p93 Latchman, on the stability of tubulin mRNA

Cai, S, Han, H-J, and Kohwi-Shigematsu, T.  Tissue-specific nuclear architecture and gene expression regulated by SATB1.  Nature Genetics 34:42-51 (2003).

Hanahan** paper, p 173 Latchman, on pancreatic tumorigenesis in transgenic mice caused by an enhancer being attached to an oncogene.

Takahashi, K, Tanabe, K, Ohnuki, M, Narita,M, Ichisaka, T, Tomoda, K, and Yamanaka, S.  Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors.  Cell 131: 1-12 (Nov, 2007)

 

Eleanor

Martinez-Garcia et al., Direct targeting of light signals to a promoter element-bound transcription factor.  Science 288:859-891 (2000). 

 

Jessica

Bourc'his**, D, Xu, GL, Lin, CS, Bollman, B, Bestor, T, Dnmt3L and the establishment of maternal genomic imprints.  Science 294:2536-2539 (2001).

Kadonaga et al., p 201 Latchman, on the functional analysis of the Sp1 transcription factor.

 

Paul

Knight and Bass, A role for the RNAse III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans.  Science 293:2269-2271 (2001).  

Linhart**, H, Lin, H, Yamada, Y, Moran, E, Steine, E, Goldhale, S, Lo, G, Cantu, E, Ehrich, M, He, T, Meissner, A, and Jaenisch, R  Dnmt3b promotes tumorigenesis in vivo by gene-specific de novo methylation and transcriptional silencing.  Gene & Devel. 21:3110-3122 (2007).

Lee, **Jeannie T. Evidence that homologus X-chromosome pairing requires transcription and CTCF protein.  Nature Genetics 29(11):1390-1396

Muse*, G, Gilchrist D, Nechaev, S, Shah, R, Parker, J, Grisson, S, Zeitlinger, J, Adelman, K.  RNA Polymerase is poised for activation across the genome.  Nature 39:1507-1511 (2007).