The National Research Council Ranks Stanford CSB #1
The National Research Council released the Data-Based Assessment of Research-Doctorate Programs on September 28, 2010. The report consists of a descriptive volume, and a comprehensive data table in Excel containing data on characteristics and ranges of rankings for over 5000 programs in 62 fields at 212 institutions.

Out of 116 pharmacology-related programs, Stanford University was rated #1 by one overall metric (S-rankings), and was one of nine tightly-clustered schools at the top by the other overall metric (R-rankings). Stanford’s greatest strength was seen to be in the area of research activity.

Every 10-15 years the National Research Council rates PhD programs in the US. They recently published this year's results, which were based on information collected in 2006-2007. The factors that weighed into the ratings included students' GRE scores, faculty pubs and impact factors, median time to degree, and the presence or absence of various program-related resources and requirements (e.g. an active grad students association and formal ethics training, which Stanford has, and formal writing instruction, which Stanford does not have).

The last time around (1995) Stanford was ranked #27.

S-rankings

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Check out some of our department’s latest research:

Mol Cell. 2012 Jan 27.
A Two-Dimensional ERK-AKT Signaling Code for an NGF-Triggered Cell-Fate Decision.
Jia-yun Chen, Jerry R. Lin, Karlene A. Cimprich, Tobias Meyer

Differentiation versus proliferation decisions are often triggered by growth factor-activated signaling.  It was not clear how individual cells integrate complex signaling responses to make all-or-none cell-fate decisions. In the study published on Jan. 27 in Molecular Cell, Chen et al. identified a two dimensional phospho-ERK(pERK)-phospho-AKT(pAKT) response map with a curved boundary that separates differentiating from proliferating cells. The individual cell decisions are guided by their relative strengths of ERK and AKT activity, and the homeostatic balance of cell-fate decisions are actively maintained by a PI3K-regulated Ras GAP, which places the population close to the decision boundary.

Read more at: http://www.ncbi.nlm.nih.gov/pubmed/22206868

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Cell. 2011 Nov 11;147(4):934-46.
A mechanism for the evolution of phosphorylation sites
 Samuel M. Pearlman, Zach Serber, James E. Ferrell, Jr.

Using a comparative genomics approach, Pearlman et al. show that the technique of substituting negatively charged amino acids to mimic phosphorylated serine, threonine and tyrosine sites in proteins has been employed by nature in reverse, evolving phosphorylation sites from glutamate and aspartate residues. The evolution of phosphorylation sites from glutamate and aspartate provides a rationale for why phosphorylation sometimes activates proteins, and helps explain the origins of this important and complex process.

Read more at: http://www.ncbi.nlm.nih.gov/pubmed/22078888

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Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14485-90.
Parallel adaptive feedback enhances reliability of the Ca2+ signaling system.
Ellen Abell*, Robert Ahrends*, Samuel Bandara, Byung Ouk Park, and Mary N. Teruel
*equal contribution

“This paper highlights the simple, though very complex, issue of how cells transmit signals correctly despite the large cell-to-cell variations in the concentrations of individual signaling proteins. In particular, the authors focus their attention on the ubiquitous and fundamental calcium signaling system, which mediates extracellular signals. They put forward the intriguing suggestion that parallel feedback loops are one way in which cells can produce robust signals despite variation in protein expression levels……[Their] hypothesis is demonstrated using convincing approaches like quantitative modeling, RNA interference and targeted selective reaction monitoring (SRM) mass spectrometry….. The discovery of these multiple parallel adaptive feedbacks can be compared in terms of importance to the observation that intracellular signals are compartmentalized to achieve specificity. ” Reviews from the Faculty of 1000

(http://f1000.com/13395960#eval14866088), designated as “exceptional and a must read.”

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Sci Transl Med. 2011 Nov2;3(107):107ra111
ALDH2 activator inhibits increased myocardial infarction injury by nitroglycerin tolerance. Lihan Sun, Julio C. Ferreira, and Daria Mochly-Rosen

Continuous dose of nitroglycerin increases severity of heart attacks, study shows. When given for hours as a continuous dose, the heart medication nitroglycerin backfires — increasing the severity of subsequent heart attacks. “Basically it’s a cautionary tale,” said professor of chemical and systems biology Daria Mochly-Rosen, PhD, senior author of the study. “Here is a practice in medicine used for over 100 years. Nitroglycerin is so old that a proper clinical trial has never been formally done. Our study says it’s time for cardiologists to examine the value of nitroglycerin treatment that extends for hours at a time.”

 Read more at: http://med.stanford.edu/ism/2011/november/nitro.html

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Congratulations to the departmental retreat prize winners!

Winner of best talk by a CSB postdoctoral fellow:
Julie Sollier (Cimprich Lab)
“RNA metabolism and genome stability”

Winner of best talk by a CSB graduate student:
Lin Gan (Meyer Lab)
“The Amino Acid Sensing System”

Winner of best poster by a CSB postdoctoral fellow:
Sayumi Yamazoe (Chen Lab)
“Next-generation caged morpholinos”

Winner of best poster by a CSB graduate student:
Jia-Yun Chen (Meyer Lab)
"A Two-dimensional ERK-AKT Signaling Code for an NGF-Triggered Cell-Fate Decision."

Winners of the Most Initiative Prize  for outstanding talk given by a non-CSB postdoc or grad student:

• Kyle Kovary (Teruel Lab)
  “Using SRM mass spectrometry to identify nuclear states in adipocytes that correspond to metabolic disease”

• Julie Saiki (SPARK program and Dept. of Music)
  “Development of a botanical as a treatment for inflammatory bowel disease (ulcerative colitis)”