Informative priors based on transcription factor structural class improve de novo motif discovery. - Leelavati Narlikar; Raluca Gordân; Uwe Ohler; Alexander J. Hartemink (ISMB (Supplement of Bioinformatics), 2006)

Nucleosome Occupancy Information Improves de novo Motif Discovery. - Leelavati Narlikar; Raluca Gordân; Alexander J. Hartemink (RECOMB, 2007)

A Nucleosome-Guided Map of Transcription Factor Binding Sites in Yeast. - Leelavati Narlikar; Raluca Gordân; Alexander J. Hartemink (PLoS Comput. Biol., 2007)

Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. - Raluca Gordân; Alexander J. Hartemink (Pacific Symposium on Biocomputing, 2008)

A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. - Raluca Gordân; Leelavati Narlikar; Alexander J. Hartemink (RECOMB, 2008)

Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. - Raluca Gordân; Alexander J. Hartemink; Martha L. Bulyk (RECOMB, 2010)

Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans. - Raluca Gordân; Saumyadipta Pyne; Martha L. Bulyk (Pacific Symposium on Biocomputing, 2012)

Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors. - Alina Munteanu; Raluca Gordân (RECOMB, 2013)

Stability selection for regression-based models of transcription factor-DNA binding specificity. - Fantine Mordelet; John Horton; Alexander J. Hartemink; Barbara E. Engelhardt; Raluca Gordân (Bioinform., 2013)

COUGER - co-factors associated with uniquely-bound genomic regions. - Alina Munteanu; Uwe Ohler; Raluca Gordân (Nucleic Acids Res., 2014)

NAR Breakthrough Article: TFBSshape: a motif database for DNA shape features of transcription factor binding sites. - Lin Yang; Tianyin Zhou; Iris Dror; Anthony Mathelier; Wyeth W. Wasserman; Raluca Gordân; Remo Rohs (Nucleic Acids Res., 2014)

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes. - Ariel Afek; Hila Cohen; Shiran Barber-Zucker; Raluca Gordân; David B. Lukatsky (PLoS Comput. Biol., 2015)

Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. - Jingkang Zhao; Dongshunyi Li; Jungkyun Seo; Andrew S. Allen; Raluca Gordân (RECOMB, 2017)

QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants. - Vincentius Martin; Jingkang Zhao; Ariel Afek; Zachery Mielko; Raluca Gordân (Nucleic Acids Res., 2019)

Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer. - Jingkang Zhao; Vincentius Martin; Raluca Gordân (RECOMB, 2022)