Feature Selection for Classification with Proteomic Data of Mixed Quality. - Elena Marchiori; Niels H. H. Heegaard; Connie R. Jimenez; Mikkel West-Nielsen (CIBCB, 2005)

Robust SVM-Based Biomarker Selection with Noisy Mass Spectrometric Proteomic Data. - Elena Marchiori; Connie R. Jimenez; Mikkel West-Nielsen; Niels H. H. Heegaard (EvoWorkshops, 2006)

Robust Peak Detection and Alignment of nanoLC-FT Mass Spectrometry Data. - Marius C. Codrea; Connie R. Jimenez; Sander R. Piersma; Jaap Heringa; Elena Marchiori (EvoBIO, 2007)

Tools for computational processing of LC-MS datasets: A user's perspective. - Marius C. Codrea; Connie R. Jimenez; Jaap Heringa; Elena Marchiori (Comput. Methods Programs Biomed., 2007)

OplAnalyzer: A Toolbox for MALDI-TOF Mass Spectrometry Data Analysis. - Thang V. Pham; Connie R. Jimenez (MDA, 2008)

On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. - Thang V. Pham; Sander R. Piersma; Marc Warmoes; Connie R. Jimenez (Bioinform., 2010)

An accurate paired sample test for count data. - Thang V. Pham; Connie R. Jimenez (Bioinform., 2012)

Simulated linear test applied to quantitative proteomics. - Thang V. Pham; Connie R. Jimenez (Bioinform., 2016)

iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics. - Thang Viet Pham; Alex A. Henneman; Connie R. Jimenez (Bioinform., 2020)

DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins. - Zhangzhi Xue; Tiansheng Zhu; Fangfei Zhang; Cheng Zhang; Nan Xiang; Liujia Qian; Xiao Yi; Yaoting Sun; Wei Liu; Xue Cai; Linyan Wang; Xizhe Dai; et al. (Patterns, 2023)

msproteomics sitereport: reporting DIA-MS phosphoproteomics experiments at site level with ease. - Thang V. Pham; Alex A. Henneman; Nam X. Truong; Connie R. Jimenez (Bioinform., 2024)