EXPANDER – an integrative program suite for microarray data analysis
- R. Shamir, A. Maron-Katz, R. Elkon
- BiologyBMC Bioinformatics
- 21 September 2005
BackgroundGene expression microarrays are a prominent experimental tool in functional genomics which has opened the opportunity for gaining global, systems-level understanding of transcriptional…
Transcription factor and microRNA motif discovery: the Amadeus platform and a compendium of metazoan target sets.
- Chaim Linhart, Y. Halperin, R. Shamir
- BiologyGenome Research
- 1 July 2008
Amadeus is developed, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks, and demonstrates that by searching for motifs based on their genome-wide localization or chromosomal distributions, Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.
Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells.
- R. Elkon, Chaim Linhart, R. Sharan, R. Shamir, Y. Shiloh
- BiologyGenome Research
- 1 May 2003
Using human genomic sequences, models for binding sites of known transcription factors, and gene expression data, it is demonstrated that the reverse engineering approach, which infers regulatory mechanisms from gene expression patterns, can reveal transcriptional networks in human cells.
Expander: from expression microarrays to networks and functions
- I. Ulitsky, A. Maron-Katz, R. Shamir
- Biology, Computer ScienceNature Protocols
- 1 February 2010
The microarray analysis described in this protocol starts with importing the data into Expander 5.0 and is followed by normalization and filtering, followed by clustering and network-based analyses, which identify the gene groups identified and are tested for enrichment in function, co-regulation or co-location.
The Degenerate Primer Design Problem
- Chaim Linhart, R. Shamir
- MathematicsIntelligent Systems in Molecular Biology
- 1 July 2002
It is proved that various simplified versions of the problem of designing a pair of primers with prescribed degeneracy that math a maximum number of given input sequences are hard, show the polynomiality of some restricted cases, and develop approximation algorithms for one variant.
Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis
- R. Elkon, S. Rashi-Elkeles, Y. Shiloh
- BiologyGenome Biology
- 13 April 2005
The results demonstrate that the combined experimental strategy of expression arrays and RNAi is indeed a powerful method for the dissection of complex transcriptional networks, and that computational promoter analysis can provide a strong complementary means for assessing the accuracy of this dissection.
PAKDD Data Mining Competition 2009: New Ways of Using Known Methods
- Chaim Linhart, G. Harari, Sharon Abramovich, Altina Buchris
- Computer SciencePAKDD Workshops
- 27 April 2009
The novelty of this approach is the integration of existing models, namely feeding the results of KNN as an input variable to the logistic regression, and re-coding categorical variables as numerical values that represent each category's statistical impact on the target label.
The Degenerate Primer Design Problem: Theory and Applications
- Chaim Linhart, R. Shamir
- MathematicsJ. Comput. Biol.
- 9 May 2005
It is proved that various simplified versions of the problem of designing a pair of primers with prescribed degeneracy that match a maximum number of given input sequences are hard, the polynomiality of some restricted cases is shown, and approximation algorithms for one variant are developed.
Faster pattern matching with character classes using prime number encoding
- Chaim Linhart, R. Shamir
- Computer ScienceJournal of computer and system sciences (Print)
- 1 May 2009
The canine olfactory subgenome.
- T. Olender, Tania Fuchs, D. Lancet
- BiologyGenomics
- 1 March 2004
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