Identification of common motifs in unaligned DNA sequences: application to Escherichia coli Lrp regulon. - Y. M. Fraenkel; Y. Mandel; D. Friedberg; Hanah Margalit (Comput. Appl. Biosci., 1995)

Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold. - Iddo Friedberg; Tommy Kaplan; Hanah Margalit (ISMB, 2000)

A Structure-Based Approach for Prediction of Protein Binding Sites in Gene-Upstream Regions. - Yael Mandel-Gutfreund; A. Baron; Hanah Margalit (Pacific Symposium on Biocomputing, 2001)

Markovian domain fingerprinting: statistical segmentation of protein sequences. - Gill Bejerano; Yevgeny Seldin; Hanah Margalit; Naftali Tishby (Bioinform., 2001)

PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. - Ruti Hershberg; Gill Bejerano; Alberto Santos-Zavaleta; Hanah Margalit (Nucleic Acids Res., 2001)

PeCoP: automatic determination of persistently conserved positions in protein families. - Iddo Friedberg; Hanah Margalit (Bioinform., 2002)

IntAct: an open source molecular interaction database. - Henning Hermjakob; Luisa Montecchi-Palazzi; Chris Lewington; Sugath Mudali; Samuel Kerrien; Sandra E. Orchard; Martin Vingron; Bernd Roechert; Peter Roepstorff; Alfonso Valencia; Hanah Margalit; John Armstrong; et al. (Nucleic Acids Res., 2004)

Towards an Integrated Protein-Protein Interaction Network. - Ariel Jaimovich; Gal Elidan; Hanah Margalit; Nir Friedman (RECOMB, 2005)

Predicting Transcription Factor Binding Sites Using Structural Knowledge. - Tommy Kaplan; Nir Friedman; Hanah Margalit (RECOMB, 2005)

Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge. - Tommy Kaplan; Nir Friedman; Hanah Margalit (PLoS Comput. Biol., 2005)

Towards an Integrated Protein-Protein Interaction Network: A Relational Markov Network Approach. - Ariel Jaimovich; Gal Elidan; Hanah Margalit; Nir Friedman (J. Comput. Biol., 2006)

A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval. - Naomi Habib; Tommy Kaplan; Hanah Margalit; Nir Friedman (PLoS Comput. Biol., 2008)

Preferential use of protein domain pairs as interaction mediators: order and transitivity. - Zohar Itzhaki; Eyal Akiva; Hanah Margalit (Bioinform., 2010)

Modularity and directionality in genetic interaction maps. - Ariel Jaimovich; Ruty Rinott; Maya Schuldiner; Hanah Margalit; Nir Friedman (Bioinform., 2010)

A wide repertoire of miRNA binding sites: prediction and functional implications. - Naama Elefant; Yael Altuvia; Hanah Margalit (Bioinform., 2011)

RepTar: a database of predicted cellular targets of host and viral miRNAs. - Naama Elefant; Amnon Berger; Harel Shein; Matan Hofree; Hanah Margalit; Yael Altuvia (Nucleic Acids Res., 2011)

A Dynamic View of Domain-Motif Interactions. - Eyal Akiva; Gilgi Friedlander; Zohar Itzhaki; Hanah Margalit (PLoS Comput. Biol., 2012)