The Short Time-series Expression Miner (STEM) (2008)
The Short Time-series Expression Miner (STEM) is a Java application with a graphical user interface (GUI) designed for the analysis of short time-series gene expression microarray data. The software...
Supplementary Methods for: Combining Static and (2008)
Time Series Data, Itamar Simon, Siegfried Zahava, Jason Ernst, Ziv Bar-joseph
problem: max YC P (Y i |Y C ) such that C M i dt = 1 (1) Here we are looking for a curve C with W (C) = M i , such that the observed values for i (Y i ) are a noisy sample of the values used for...
Supplementary Results For: Combining Static and (2008)
Time Series Data, Itamar Simon, Siegfried Zahava, Jason Ernst, Ziv Bar-joseph
this paper, this is not always the case and so we believe that it is better to first use Checksum and only afterwards, when it is determined that the temporal profiles are accurate, to normalize the...
John C. Dumer, Timothy P. Hanratty, John Yen, Dwi Widyantoro, Jason Ernst, T. J. Rogers
Today’s modern battlespace can generally be defined as any and all aspects of the region of time and space surrounding a battle. Most see dominating the battlespace through digitization as the key...
STEM: a tool for the analysis of short time series gene expression data (2006)
Abstract Background Time series microarray experiments are widely used to study dynamical biological processes. Due to the cost of microarray experiments, and also in some cases the limited...
Edoardo Maria Airoldi, David Blei, Deepay Chakrabarti, Taeryon Choi, Donato Michele Cifarelli, ...
with designated emphasis in
Jason Ernst, Gerard J. Nau, Ziv Bar-joseph
Vol. 21 Suppl. 1 2005, pages i159–i168 doi:10.1093/bioinformatics/bti1022
Clustering Short Time Series Gene Expression Data (2005)
Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph
Motivation: Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These...
Clustering short time series gene expression data (2005)
Ernst, Jason, Nau, Gerard J., Bar-Joseph, Ziv
Motivation: Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These...
Reconstructing dynamic regulatory maps
Ernst, Jason, Vainas, Oded, Harbison, Christopher T, Simon, Itamar, Bar-Joseph, Ziv
Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein–DNA interactions that allows the specific regulation...
A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli
Ernst, Jason, Beg, Qasim K., Kay, Krin A., Balázsi, Gábor, Oltvai, Zoltán N., Bar-Joseph, Ziv
While Escherichia coli has one of the most comprehensive datasets of experimentally verified transcriptional regulatory interactions of any organism, it is still far from complete. This presents a...
Impact of the solvent capacity constraint on E. coli metabolism
Vazquez, Alexei, Beg, Qasim K, DeMenezes, Marcio A, Ernst, Jason, Bar-Joseph, Ziv, Barabási, Albert-László, ...
IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability
Ernst, Jason, Ghanem, Louis, Bar-Joseph, Ziv, McNamara, Michael, Brown, Jason, Steinman, Richard A.
The growth factor interleukin-3 (IL-3) promotes the survival and growth of multipotent hematopoietic progenitors and stimulates myelopoiesis. It has also been reported to oppose terminal...