Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. - Yoseph Barash; Elinor Dehan; Meir Krupsky; Wilbur Franklin; Marc Geraci; Nir Friedman; Naftali Kaminski (Bioinform., 2004)

Comparison of normalization methods for CodeLink Bioarray data. - Wei Wu 023; Nilesh Dave; George C. Tseng; Thomas Richards; Eric P. Xing; Naftali Kaminski (BMC Bioinform., 2005)

A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies. - Naftali Kaminski; Ziv Bar-Joseph (J. Comput. Biol., 2007)

Alignment and classification of time series gene expression in clinical studies. - Tien-ho Lin; Naftali Kaminski; Ziv Bar-Joseph (ISMB, 2008)

Module-based prediction approach for robust inter-study predictions in microarray data. - Zhibao Mi; Kui Shen; Nan Song; Chunrong Cheng; Chi Song; Naftali Kaminski; George C. Tseng (Bioinform., 2010)

An R package suite for microarray meta-analysis in quality control, differentially expressed gene analysis and pathway enrichment detection. - Xingbin Wang; Dongwan D. Kang; Kui Shen; Chi Song; Shuya Lu; Lun-Ching Chang; Serena G. Liao; Zhiguang Huo; Shaowu Tang; Ying Ding; Naftali Kaminski; Etienne Sibille; et al. (Bioinform., 2012)

Novel Modeling of Combinatorial miRNA Targeting Identifies SNP with Potential Role in Bone Density. - Claudia Coronnello; Ryan J. Hartmaier; Arshi Arora; Luai Huleihel; Kusum V. Pandit; Abha S. Bais; Michael Butterworth; Naftali Kaminski; Gary D. Stormo; Steffi Oesterreich; Panayiotis V. Benos (PLoS Comput. Biol., 2012)

Missing value imputation in high-dimensional phenomic data: imputable or not, and how? - Serena G. Liao; Yan Lin; Dongwan D. Kang; Divay Chandra; Jessica Bon; Naftali Kaminski; Frank C. Sciurba; George C. Tseng (BMC Bioinform., 2014)

Bidirectional elastic image registration using B-spline affine transformation. - Suicheng Gu; Xin Meng; Frank C. Sciurba; Hongxia Ma; Joseph K. Leader; Naftali Kaminski; David Gur; Jiantao Pu (Comput. Medical Imaging Graph., 2014)

T-ReCS: Stable Selection of Dynamically Formed Groups of Features with Application to Prediction of Clinical Outcomes. - Grace T. Huang; Ioannis Tsamardinos; Vineet K. Raghu; Naftali Kaminski; Panayiotis V. Benos (Pacific Symposium on Biocomputing, 2015)

iDREM: Interactive visualization of dynamic regulatory networks. - Jun Ding; James S. Hagood; Namasivayam Ambalavanan; Naftali Kaminski; Ziv Bar-Joseph (PLoS Comput. Biol., 2018)

A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. - Hongyu Li; Biqing Zhu; Zhichao Xu; Taylor Adams; Naftali Kaminski; Hongyu Zhao 003 (BMC Bioinform., 2021)

CINS: Cell Interaction Network inference from Single cell expression data. - Ye Yuan; Carlos Cosme; Taylor Sterling Adams; Jonas Schupp; Koji Sakamoto; Nikos Xylourgidis; Matthew Ruffalo; Jiachen Li; Naftali Kaminski; Ziv Bar-Joseph (PLoS Comput. Biol., 2022)

A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy. - Wenxuan Deng; Bolun Li; Jiawei Wang; Wei Jiang 019; Xiting Yan; Ningshan Li; Milica Vukmirovic; Naftali Kaminski; Jing Wang 003; Hongyu Zhao 003 (Briefings Bioinform., 2023)

Comprehensive visualization of cell-cell interactions in single-cell and spatial transcriptomics with NICHES. - Micha Sam Brickman Raredon; Junchen Yang; Neeharika Kothapalli; Wesley Lewis; Naftali Kaminski; Laura E. Niklason; Yuval Kluger (Bioinform., 2023)

iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. - Yunqing Liu; Jiayi Zhao; Taylor Sterling Adams; Ningya Wang; Jonas Schupp; Weimiao Wu; John E. McDonough; Geoffrey Lowell Chupp; Naftali Kaminski; Zuoheng Wang; Xiting Yan (BMC Bioinform., 2023)

Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. - Yunqing Liu; Jiayi Zhao; Taylor Sterling Adams; Ningya Wang; Jonas Schupp; Weimiao Wu; John E. McDonough; Geoffrey Lowell Chupp; Naftali Kaminski; Zuoheng Wang; Xiting Yan (BMC Bioinform., 2023)

Predicting lung aging using scRNA-Seq data. - Qi Song; Alex Singh; John E. McDonough; Taylor Sterling Adams; Robin Vos; Ruben De Man; Greg Myers; Laurens J. Ceulemans; Bart M. Vanaudenaerde; Wim A. Wuyts; Xiting Yan; Jonas Schupp; et al. (PLoS Comput. Biol., 2024)