An adaptive approach to wavelet filters design. - Nicola Neretti; Nathan Intrator (NNSP, 2002)

Image registration and mosaicing of noisy acoustic camera images. - Kio Kim; Nathan Intrator; Nicola Neretti (ICECS, 2004)

Adaptive pulse optimization for improved sonar range accuracy. - Nicola Neretti; Nathan Intrator; Leon N. Cooper (IEEE Signal Process. Lett., 2004)

Video Enhancement for Underwater Exploration Using Forward Looking Sonar. - Kio Kim; Nicola Neretti; Nathan Intrator (ACIVS, 2006)

Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation. - Nicola Neretti; Daniel Remondini; Marc Tatar; John M. Sedivy; Michela Pierini; Dawn Mazzatti; Jonathan Powell; Claudio Franceschi; Gastone C. Castellani (BMC Bioinform., 2007)

Networks from Gene Expression Time Series: Characterization of Correlation Patterns. - Daniel Remondini; Nicola Neretti; Claudio Franceschi; Paolo Tieri; John M. Sedivy; Luciano Milanesi; Gastone C. Castellani (Int. J. Bifurc. Chaos, 2007)

Reconstructing networks of pathways via significance analysis of their intersections. - Mirko Francesconi; Daniel Remondini; Nicola Neretti; John M. Sedivy; Leon N. Cooper; Ettore Verondini; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 2008)

MAP fusion method for superresolution of images with locally varying pixel quality. - Kio Kim; Nicola Neretti; Nathan Intrator (Int. J. Imaging Syst. Technol., 2008)

CORaL: Comparison of Ranked Lists for Analysis of Gene Expression Data. - Michael Antosh; David Fox; Leon N. Cooper; Nicola Neretti (J. Comput. Biol., 2013)

GINOM: A statistical framework for assessing interval overlap of multiple genomic features. - Darshan W. Bryner; Stephen Criscione; Andrew Leith; Quyen Huynh; Fred W. Huffer; Nicola Neretti (PLoS Comput. Biol., 2017)

Bayesian Estimation of Three-Dimensional Chromosomal Structure from Single-Cell Hi-C Data. - Michael Rosenthal; Darshan W. Bryner; Fred W. Huffer; Shane Evans; Anuj Srivastava; Nicola Neretti (J. Comput. Biol., 2019)

Representation of Chromosome Conformations Using a Shape Alphabet Across Modeling Methods. - Carlos Soto 002; Audrey Dalgarno; Darshan W. Bryner; Benjamin McLaughlin; Nicola Neretti; Anuj Srivastava (BIBM, 2021)

Toward a Three-Dimensional Chromosome Shape Alphabet. - Carlos Soto 002; Darshan W. Bryner; Nicola Neretti; Anuj Srivastava (J. Comput. Biol., 2021)

TADBay: A Bayesian Construction of Topologically Associated Domains. - Carlos Soto 002; Darshan W. Bryner; Audrey Dalgarno; Nicola Neretti; Anuj Srivastava (BIBM, 2022)