Fakultät für Informatik
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Technische Universität München
Lehrstuhl für Effiziente Algorithmen
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Physical Module Networks: An integrative approach for reconstructing transcription regulation
Noa Novershtern
,
Aviv Regev
,
Nir Friedman
Bioinformatics
27
(13), 2011, pp. 177-185
An integrative clustering and modeling algorithm for dynamical gene expression data
Julia Sivriver
,
Naomi Habib
,
Nir Friedman
Bioinformatics
27
(13), 2011, pp. 392-400
Modularity and directionality in genetic interaction maps
Ariel Jaimovich
,
Ruty Rinott
,
Maya Schuldiner
,
Hanah Margalit
,
Nir Friedman
Bioinformatics
26
(12), 2010, pp. 228-236
Identifying novel constrained elements by exploiting biased substitution patterns
Manuel Garber
,
Mitchell Guttman
,
Michele Clamp
,
Michael C. Zody
,
Nir Friedman
,
Xiaohui Xie
Bioinformatics
25
(12), 2009, pp. 54-62
Nucleosome positioning from tiling microarray data
Moran Yassour
,
Tommy Kaplan
,
Ariel Jaimovich
,
Nir Friedman
Bioinformatics
24
(13), 2008, pp. 139-146
Phylogeny reconstruction: Increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates
Matan Ninio
,
Eyal Privman
,
Tal Pupko
,
Nir Friedman
Bioinformatics
23
(2), 2007, pp. 136-141
Automatic genome-wide reconstruction of phylogenetic gene trees
Ilan Wapinski
,
Avi Pfeffer
,
Nir Friedman
,
Aviv Regev
Bioinformatics
23
(13), 2007, pp. 549-558
Towards an integrated protein-protein interaction network
Ariel Jaimovich
,
Gal Elidan
,
Hanah Margalit
,
Nir Friedman
LNCS/LNBI
3500
, 2005, pp. 14-30
Predicting transcription factor binding sites using structural knowledge
Tommy Kaplan
,
Nir Friedman
,
Hanah Margalit
LNCS/LNBI
3500
, 2005, pp. 522-537
A Gamma mixture model better accounts for among site rate heterogeneity
Itay Mayrose
,
Nir Friedman
,
Tal Pupko
Bioinformatics
21
(S2), 2005, pp. 151-158
Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays
Yoseph Barash
,
Elinor Dehan
,
Meir Krupsky
,
Wilbur Franklin
,
Marc Geraci
,
Nir Friedman
,
Naftali Kaminski
Bioinformatics
20
(6), 2004, pp. 839-846
Modeling dependencies in protein-DNA binding sites
Yoseph Barash
,
Gal Elidan
,
Nir Friedman
,
Tommy Kaplan
Technical Report (2003-45), 2003
Modeling dependencies in protein-DNA binding sites
Yoseph Barash
,
Gal Elidan
,
Nir Friedman
,
Tommy Kaplan
Proceedings of the 7th Annual International Conference on Research in Computational Molecular Biology, RECOMB'2003 (Berlin, Germany, April 10-13, 2003)
, 2003, pp. 28-37
The information bottleneck expectation maximization algorithm
Gal Elidan
,
Nir Friedman
Technical Report (2003-39), 2003
Probabilistic models for identifying regulation networks
Nir Friedman
Bioinformatics
19
(S2), 2003, pp. 57-57
Learning module networks
Eran Segal
,
Dana Pe'er
,
Aviv Regev
,
Daphne Koller
,
Nir Friedman
Technical Report (2003-14), 2003
Module networks: Discovering regulatory modules and their condition specific regulators from gene expression data
Eran Segal
,
Aviv Regev
,
Dana Pe'er
,
Micha Shapira
,
David Botstein
,
Daphne Koller
,
Nir Friedman
Technical Report (2003-15), 2003
Context-specific Bayesian clustering for gene expression data
Yoseph Barash
,
Nir Friedman
Technical Report (2002-5), 2002
Overabundance analysis and class discovery in gene expression data
A. Ben-Dor
,
Nir Friedman
,
Z. Yakhini
Technical Report (2002-50), 2002
Data perturbation for escaping local maxima in learning
Gal Elidan
,
Matan Ninio
,
Nir Friedman
Technical Report (2002-54), 2002
Being Bayesian about network structure: A Bayesian approach to structure discovery in Bayesian networks
Nir Friedman
,
Daphne Koller
Technical Report (2002-8), 2002
A structural EM algorithm for phylogenetic inference
Nir Friedman
,
Matan Ninio
,
Itsik Pe'er
,
Tal Pupko
Technical Report (2002-6), 2002
Inferring subnetworks from perturbed expression profiles
Dana Pe'er
,
Aviv Regev
,
Gal Elidan
,
Nir Friedman
Technical Report (2002-9), 2002
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
Tal Pupko
,
Itsik Pe'er
,
Masami Hasegawa
,
Dan Graur
,
Nir Friedman
Bioinformatics
18
(8), 2002, pp. 1116-1123
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites
Tal Pupko
,
Itsik Pe'er
,
Masami Hasegawa
,
Dan Graur
,
Nir Friedman
Technical Report (2002-7), 2002
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