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)

Modeling dependencies in protein-DNA binding sites. - Yoseph Barash; Gal Elidan; Nir Friedman; Tommy Kaplan (RECOMB, 2003)

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

CIS: compound importance sampling method for protein-DNA binding site p-value estimation. - Yoseph Barash; Gal Elidan; Tommy Kaplan; Nir Friedman (Bioinform., 2005)

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

Nucleosome positioning from tiling microarray data. - Moran Yassour; Tommy Kaplan; Ariel Jaimovich; Nir Friedman (ISMB, 2008)

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

From DNA sequence to chromatin dynamics : computational analysis of transcriptional regulation (Computational analysis of transcriptional regulation.; ניתוח חישובי של בקרת שעתוק.; מרצף הדנ"א ועד דינמיקה של כרומטין.). - Tommy Kaplan (2008)