Reducing negativity artifacts in emission tomography: post-processing filtered backprojection solutions. - Finbarr O'Sullivan; Yudianto Pawitan; David R. Haynor (IEEE Trans. Medical Imaging, 1993)

Data-dependent bandwidth selection for emission computed tomography reconstruction. - Yudi Pawitan; Finbarr O'Sullivan (IEEE Trans. Medical Imaging, 1993)

ProSpect: An R Package for Analyzing SELDI Measurements Identifying Protein Biomarkers. - Andreas Quandt; Alexander Ploner; Chuen Seng Tan; Janne Lehtiö; Yudi Pawitan (CompLife, 2005)

False discovery rate, sensitivity and sample size for microarray studies. - Yudi Pawitan; Stefan Michiels; Serge Koscielny; Arief Gusnanto; Alexander Ploner (Bioinform., 2005)

Bias in the estimation of false discovery rate in microarray studies. - Yudi Pawitan; Karuturi R. Krishna Murthy; Stefan Michiels; Alexander Ploner (Bioinform., 2005)

Correlation test to assess low-level processing of high-density oligonucleotide microarray data. - Alexander Ploner; Lance D. Miller; Per Hall; Jonas Bergh; Yudi Pawitan (BMC Bioinform., 2005)

Non-Gaussian smoothing of low-count transmission scans for PET whole-body studies. - Yudi Pawitan; Valentino Bettinardi; M. Teras (IEEE Trans. Medical Imaging, 2005)

Estimation of false discovery proportion under general dependence. - Yudi Pawitan; Stefano Calza; Alexander Ploner (Bioinform., 2006)

Multidimensional local false discovery rate for microarray studies. - Alexander Ploner; Stefano Calza; Arief Gusnanto; Yudi Pawitan (Bioinform., 2006)

Finding regions of significance in SELDI measurements for identifying protein biomarkers. - Chuen Seng Tan; Alexander Ploner; Andreas Quandt; Janne Lehtiö; Yudi Pawitan (Bioinform., 2006)

Robust smooth segmentation approach for array CGH data analysis. - Jian Huang 005; Arief Gusnanto; Kathleen O'Sullivan; Johan Staaf; Åke Borg; Yudi Pawitan (Bioinform., 2007)

Detecting differential expression in microarray data: comparison of optimal procedures. - Elena Perelman; Alexander Ploner; Stefano Calza; Yudi Pawitan (BMC Bioinform., 2007)

Unequal group variances in microarray data analyses. - Meaza Demissie; Barbara Mascialino; Stefano Calza; Yudi Pawitan (Bioinform., 2008)

Normalization of oligonucleotide arrays based on the least-variant set of genes. - Stefano Calza; Davide Valentini; Yudi Pawitan (BMC Bioinform., 2008)

Correlating gene and protein expression data using Correlated Factor Analysis. - Chuen Seng Tan; Agus Salim; Alexander Ploner; Janne Lehtiö; Kee Seng Chia; Yudi Pawitan (BMC Bioinform., 2009)

Super-sparse principal component analyses for high-throughput genomic data. - Donghwan Lee 001; Woojoo Lee; Youngjo Lee 001; Yudi Pawitan (BMC Bioinform., 2010)

Identification of recurrent regions of copy-number variants across multiple individuals. - Teo Shu Mei; Agus Salim; Stefano Calza; Ku Chee Seng; Kee Seng Chia; Yudi Pawitan (BMC Bioinform., 2010)

Multi-platform segmentation for joint detection of copy number variants. - Teo Shu Mei; Yudi Pawitan; Vikrant Kumar; Anbupalam Thalamuthu; Mark Seielstad; Kee Seng Chia; Agus Salim (Bioinform., 2011)

Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. - Arief Gusnanto; Henry M. Wood; Yudi Pawitan; Pamela Rabbitts; Stefano Berri (Bioinform., 2012)

Statistical challenges associated with detecting copy number variations with next-generation sequencing. - Teo Shu Mei; Yudi Pawitan; Ku Chee Seng; Kee Seng Chia; Agus Salim (Bioinform., 2012)

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks. - Andrey Alexeyenko; Woojoo Lee; Maria Pernemalm; Justin Guegan; Philippe Dessen; Vladimir Lazar; Janne Lehtiö; Yudi Pawitan (BMC Bioinform., 2012)

Partial least squares and logistic regression random-effects estimates for gene selection in supervised classification of gene expression data. - Arief Gusnanto; Alexander Ploner; Farag Shuweihdi; Yudi Pawitan (J. Biomed. Informatics, 2013)

Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. - Chen Suo; Stefano Calza; Agus Salim; Yudi Pawitan (Bioinform., 2014)

Rediscovery rate estimation for assessing the validation of significant findings in high-throughput studies. - Andrea Ganna; Donghwan Lee 001; Erik Ingelsson; Yudi Pawitan (Briefings Bioinform., 2015)

Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival. - Chen Suo; Olga Hrydziuszko; Donghwan Lee 001; Setia Pramana; Dhany Saputra; Himanshu Joshi; Stefano Calza; Yudi Pawitan (Bioinform., 2015)

A random-effect model approach for group variable selection. - Sangin Lee; Yudi Pawitan; Youngjo Lee 001 (Comput. Stat. Data Anal., 2015)

Beta-Poisson model for single-cell RNA-seq data analyses. - Trung-Nghia Vu; Quin F. Wills; Krishna R. Kalari; Nifang Niu; Liewei Wang; Mattias Rantalainen; Yudi Pawitan (Bioinform., 2016)

Isoform-level gene expression patterns in single-cell RNA-sequencing data. - Trung-Nghia Vu; Quin F. Wills; Krishna R. Kalari; Nifang Niu; Liewei Wang; Yudi Pawitan; Mattias Rantalainen (Bioinform., 2018)

Sparse pathway-based prediction models for high-throughput molecular data. - Sangin Lee; Youngjo Lee 001; Yudi Pawitan (Comput. Stat. Data Anal., 2018)

Cell-level somatic mutation detection from single-cell RNA sequencing. - Trung-Nghia Vu; Ha-Nam Nguyen; Stefano Calza; Krishna R. Kalari; Liewei Wang; Yudi Pawitan (Bioinform., 2019)

Alternating EM algorithm for a bilinear model in isoform quantification from RNA-seq data. - Wenjiang Deng; Tian Mou; Krishna R. Kalari; Nifang Niu; Liewei Wang; Yudi Pawitan; Trung-Nghia Vu (Bioinform., 2020)

Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. - Dat Thanh Nguyen; Quang Thinh Trac; Thi-Hau Nguyen; Ha-Nam Nguyen; Nir Ohad; Yudi Pawitan; Trung-Nghia Vu (BMC Bioinform., 2021)

Isoform-level quantification for single-cell RNA sequencing. - Lu Pan; Huy Q. Dinh; Yudi Pawitan; Trung-Nghia Vu (Bioinform., 2022)

Confidence in the Reasoning of Large Language Models. - Yudi Pawitan; Chris Holmes (CoRR, 2024)