Mining gene functional networks to improve mass-spectrometry-based protein identification. - Smriti R. Ramakrishnan; Christine Vogel; Taejoon Kwon; Luiz O. F. Penalva; Edward M. Marcotte; Daniel P. Miranker (Bioinform., 2009)

Integrating shotgun proteomics and mRNA expression data to improve protein identification. - Smriti R. Ramakrishnan; Christine Vogel; John T. Prince; Rong Wang; Zhihua Li; Luiz O. F. Penalva; Margaret Myers; Edward M. Marcotte; Daniel P. Miranker (Bioinform., 2009)

Site identification in high-throughput RNA-protein interaction data. - Philip J. Uren; Emad Bahrami Samani; Suzanne C. Burns; Mei Qiao; Fedor V. Karginov; Emily Hodges; Gregory J. Hannon; Jeremy R. Sanford; Luiz O. F. Penalva; Andrew D. Smith (Bioinform., 2012)

A compendium of RNA-binding motifs for decoding gene regulation. - Debashish Ray; Hilal Kazan; Kate B. Cook; Matthew T. Weirauch; Hamed S. Najafabadi; Xiao Li; Serge Gueroussov; Mihai Albu; Hong Zheng; Ally Yang; Hong Na; Manuel Irimia; et al. (Nat., 2013)

Riborex: fast and flexible identification of differential translation from Ribo-seq data. - Wenzheng Li; Weili Wang; Philip J. Uren; Luiz O. F. Penalva; Andrew D. Smith (Bioinform., 2017)