Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. - Quansong Ruan; Debojyoti Dutta; Michael S. Schwalbach; Joshua A. Steele; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2006)

A dynamic programming algorithm for binning microbial community profiles. - Quansong Ruan; Joshua A. Steele; Michael S. Schwalbach; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2006)

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates. - Li C. Xia; Joshua A. Steele; Jacob A. Cram; Zoe G. Cardon; Sheri L. Simmons; Joseph J. Vallino; Jed A. Fuhrman; Fengzhu Sun (BMC Syst. Biol., 2011)

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data. - Li C. Xia; Dongmei Ai; Jacob A. Cram; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2013)

Statistical significance approximation in local trend analysis of high-throughput time-series data using the theory of Markov chains. - Li C. Xia; Dongmei Ai; Jacob A. Cram; Xiaoyi Liang; Jed A. Fuhrman; Fengzhu Sun (BMC Bioinform., 2015)

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge. - Yang Young Lu; Ting Chen 006; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2017)

Prediction of virus-host infectious association by supervised learning methods. - Mengge Zhang; Lianping Yang; Jie Ren 006; Nathan A. Ahlgren; Jed A. Fuhrman; Fengzhu Sun (BMC Bioinform., 2017)

CAFE: aCcelerated Alignment-FrEe sequence analysis. - Yang Young Lu; Kujin Tang; Jie Ren 006; Jed A. Fuhrman; Michael S. Waterman; Fengzhu Sun (Nucleic Acids Res., 2017)

Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. - Ziye Wang; Ying Wang; Jed A. Fuhrman; Fengzhu Sun; Shanfeng Zhu (Briefings Bioinform., 2020)

Identifying viruses from metagenomic data using deep learning. - Jie Ren 006; Kai Song; Chao Deng; Nathan A. Ahlgren; Jed A. Fuhrman; Yi Li; Xiaohui Xie; Ryan Poplin; Fengzhu Sun (Quant. Biol., 2020)

Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. - Ziye Wang; Ying Wang; Jed A. Fuhrman; Fengzhu Sun; Shanfeng Zhu (Briefings Bioinform., 2021)

Phage-bacterial contig association prediction with a convolutional neural network. - Tianqi Tang 004; Shengwei Hou; Jed A. Fuhrman; Fengzhu Sun (Bioinform., 2022)

Normalizing Metagenomic Hi-C Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression. - Yuxuan Du; Sarah M. Laperriere; Jed A. Fuhrman; Fengzhu Sun (J. Comput. Biol., 2022)

DeepLINK-T: deep learning inference for time series data using knockoffs and LSTM. - Wenxuan Zuo; Zifan Zhu; Yuxuan Du; Yi-Chun Yeh; Jed A. Fuhrman; Jinchi Lv; Yingying Fan; Fengzhu Sun (CoRR, 2024)