203,192 interactions from Chip-seq/chip studies

153,920 interactions from logof followed by microarrays

1,037 protein protein interactions

693,552 miRNA target interactions

661 Putative pluripotency genes determined by RNAi screens

7,044 Undifferentiated and differentiating ESC specific proteins

16,881 histone modifications determined by Chip-seq/chip

4,012 Undifferentiated and differentiating ESC specific phosphoproteins from phosphoproteomics

9 genome-wide mRNA expression profile summaries

3,136 miRNA expression entries

14,105 time course expression entries from J1 #1

17,022 time course expression entries from J1 #2

14,105 time course expression entries from R1 #1

17,022 time course expression entries from R1 #2

14,668 time course expression entries from V6.5 #1

17,022 time course expression entries from V6.5 #2

14,698 time-course expression entries of shRNAi #1

18,265 time-course expression entries of shRNAi #2

Self-organizing circuitry and emergent computation in mouse embryonic stem cells.
Halley JD, Smith-Miles K, Winkler DA, Kalkan T, Huang S, Smith A. in Stem Cell Research (2011)

Wdr5 Mediates Self-Renewal and Reprogramming via the Embryonic Stem Cell Core Transcriptional Network.
Yen-Sin Ang, Su-Yi Tsai, Dung-Fang Lee, Jonathan Monk, Jie Su, Kajan Ratnakumar, et al. in Cell (2011)

SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells.
Huilei Xu, Ihor R Lemischka, Avi Ma'ayan in BMC systems biology (2010)

GATE: software for the analysis and visualization of high-dimensional time series expression data.
Ben D MacArthur, Alexander Lachmann, Ihor R Lemischka, Avi Ma'ayan in Bioinformatics (2010)

Systems-level dynamic analyses of fate change in murine embryonic stem cells.
Rong Lu, Florian Markowetz, Richard D Unwin, Jeffrey T Leek, Edoardo M Airoldi, Ben D MacArthur, et al. in Nature (2009)

Systems biology of stem cell fate and cellular reprogramming.
Ben D MacArthur, Avi Ma'ayan, Ihor R Lemischka in Nat Rev Mol Cell Biol (2009)

Embryonic stem cells (ESCs) are derived from the inner-cell-mass of a blastocyst and can be maintained indefinitely in culture as well as differentiate into all adult cell types. In order to harness the translational biomedical potential of ESCs, we need to characterize the molecular regulatory networks responsible for controlling pluripotency, self-renewal as well as commitment and differentiation into specific lineages. To aid in this challenge, we constructed a mamalian embryonic stem cell specific database called ESCAPE (Embryonic Stem Cell Atlas from Pluripotency Evidence), by collecting and integrating data reporting results from various published studies that profiled human and mouse ESCs including: protein-DNA binding interactions extracted from ChIP-seq/chip experiments, gene regulatory interactions from loss/gain-of-function studies followed by genome-wide mRNA expression profiling, protein interactions from nine immunoprecipitation followed by mass-spectrometry proteomics studies, a list of potential pluripotency regulators from five RNA interference screens, ESC-specific proteins and phosphoproteins with specified phosphosites from proteomics and phosphoproteomics studies, time-course genome-wide mRNA microarray datasets from differentiating mouse ESCs, and nine histone modification status genome-wide studies. Additionally, we constructed a miRNA-target table consolidated from four public miRNA databases. The ESCAPE database facilitates data integration of various types of interactions from high-throughput technologies as well as from manually curated small-scale studies.

Scientists Produce Eye Structures from Human Blood-Derived Stem Cells
Scientists from the University of Wisconsin (Madison) have made early retina structures containing proliferating neuroretinal progenitor cells using induced pluripotent stem (iPS) cells derived from human blood.
Read more at http://www.sciencedaily.com/releases/ 2012/03/120313185232.htm

Embryonic stem cell trials for macular degeneration: a preliminary report
Researchers at the UCLA medical center have begun clincal trials for a macular degeneration treatment derived from embryonic stem cells. Two women had cells implanted in their retinas last July and both patients have seen meaningful changes in their vision. This marks the first case of human embryonic stem cell transplantation into human patients.
Check out the findings published in the Lancet or read the NYTimes article.

New database could speed up drug discovery
A new database and software, called ChIP Enrichment Analysis, or ChEA, is set to revolutionize how researchers identify drug targets and biomarkers. Until ChEA was developed, no centralized database integrated results from, for instance, ChIP-seq and ChIP-chip experiments (these are used to identify how "transcription factor" proteins might regulate all genes in humans and mice). Now this new computational method should help streamline how scientists analyze these gene expression experiments.
Read more at http://news.cnet.com/8301-27083_3-20016583-247.html