Designing Specific Oligonucleotide Probes for the Entire S. cerevisiae Transcriptome. - Doron Lipson; Peter Webb; Zohar Yakhini (WABI, 2002)

Joint Analysis of DNA Copy Numbers and Gene Expression Levels. - Doron Lipson; Amir Ben-Dor; Elinor Dehan; Zohar Yakhini (WABI, 2004)

Efficient Calculation of Interval Scores for DNA Copy Number Data Analysis. - Doron Lipson; Yonatan Aumann; Amir Ben-Dor; Nathan Linial; Zohar Yakhini (RECOMB, 2005)

Framework for Identifying Common Aberrations in DNA Copy Number Data. - Amir Ben-Dor; Doron Lipson; Anya Tsalenko; Mark Reimers; Lars O. Baumbusch; Michael T. Barrett; John N. Weinstein; Anne-Lise Børresen-Dale; Zohar Yakhini (RECOMB, 2007)

Optimization of probe coverage for high-resolution oligonucleotide aCGH. - Doron Lipson; Zohar Yakhini; Yonatan Aumann (Bioinform., 2007)

Discovering Motifs in Ranked Lists of DNA Sequences. - Eran Eden; Doron Lipson; Sivan Yogev; Zohar Yakhini (PLoS Comput. Biol., 2007)

Computational aspects of DNA copy number measurement. - Doron Lipson (2007)

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. - Eran Eden; Roy Navon; Israel Steinfeld; Doron Lipson; Zohar Yakhini (BMC Bioinform., 2009)

Methods for Allocating Ambiguous Short-reads. - Doron Lipson; Terence P. Speed; Margaret Taub (Commun. Inf. Syst., 2010)

Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families. - Eldar Giladi; John Healy; Gene Myers; Chris Hart; Philipp Kapranov; Doron Lipson; Steve Roels; Edward C. Thayer; Stan Letovsky (J. Comput. Biol., 2010)

A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal. - James X. Sun; Yuting He; Eric Sanford; Meagan Montesion; Garrett M. Frampton; Stéphane Vignot; Jean-Charles Soria; Jeffrey S. Ross; Vincent A. Miller; Philip J. Stephens; Doron Lipson; Roman Yelensky (PLoS Comput. Biol., 2018)