AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. - Ramana V. Davuluri; Hao Sun 001; Saranyan K. Palaniswamy; Nicole Matthews; Carlos Molina; Mike Kurtz; Erich Grotewold (BMC Bioinform., 2003)

Java-based application framework for visualization of gene regulatory region annotations. - Hao Sun 001; Ramana V. Davuluri (Bioinform., 2004)

HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development. - Twyla T. Pohar; Hao Sun 001; Ramana V. Davuluri (Nucleic Acids Res., 2004)

OMGProm: a database of orthologous mammalian gene promoters. - Saranyan K. Palaniswamy; Victor X. Jin; Hao Sun 001; Ramana V. Davuluri (Bioinform., 2005)

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data. - Hao Sun 001; Saranyan K. Palaniswamy; Twyla T. Pohar; Victor X. Jin; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 2006)

Methy-Pipe: An integrated bioinformatics data analysis pipeline for whole genome methylome analysis. - Peiyong Jiang; Xiaoxi Sun; Eric Z. Chen; Kun Sun 003; Rossa W. K. Chiu; Yuk Ming Dennis Lo; Hao Sun 001 (BIBM Workshops, 2010)

Genome-wide identification of TF-miRNA regulatory networks in myogenesis. - Leina Lu; Liang Zhou; Eric Z. Chen; Kun Sun 003; Peiyong Jiang; Susie Su; Lijun Wang; Hao Sun 001; Huating Wang (BIBM Workshops, 2011)

Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. - Hao Sun 001; Jiejun Wu; Priyankara Wikramasinghe; Sharmistha Pal; Ravi Gupta; Anirban Bhattacharyya; Francisco J. Agosto-Perez; Louise C. Showe; Tim Hui-Ming Huang; Ramana V. Davuluri (Nucleic Acids Res., 2011)

FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. - Peiyong Jiang; K. C. Allen Chan; Gary J. W. Liao; Yama W. L. Zheng; Tak Y. Leung; Rossa W. K. Chiu; Yuk Ming Dennis Lo; Hao Sun 001 (Bioinform., 2012)

YY1TargetDB: an integral information resource for Yin Yang 1 target loci. - Andy M. Guo; Kun Sun 003; Xiaoxi Su; Huating Wang; Hao Sun 001 (Database J. Biol. Databases Curation, 2013)

Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. - Xiaofeng Song; Minghao Wang; Yi-Ping Phoebe Chen; Huating Wang; Ping Han; Hao Sun 001 (Comput. Biol. Medicine, 2013)

The Online Diagnosis System for sanger sequencing based genetic testing. - Kun Sun 003; Yuet-Ping Yuen; Huating Wang; Hao Sun 001 (BigComp, 2014)

BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data. - Kun Sun 003; Fiona F. M. Lun; Peiyong Jiang; Hao Sun 001 (Bioinform., 2017)

GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. - Kun Sun 003; Jiguang Wang; Huating Wang; Hao Sun 001 (Bioinform., 2018)

lncFunTK: a toolkit for functional annotation of long noncoding RNAs. - Jiajian Zhou; Yile Huang; Yingzhe Ding; Jie Yuan; Huating Wang; Hao Sun 001 (Bioinform., 2018)

SKmDB: an integrated database of next generation sequencing information in skeletal muscle. - Jie Yuan; Jiajian Zhou; Huating Wang; Hao Sun 001 (Bioinform., 2019)

RNA binding proteins (RBPs) regulate lncRNA nuclear retention. - Yile Huang; Yulong Qiao; Yu Zhao; Yingzhe Ding; Jie Yuan; Jiajian Zhou; Huating Wang; Hao Sun 001 (BIBM, 2020)

Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit. - Kun Sun 003; Lishi Li; Li Ma; Yu Zhao; Lin Deng; Huating Wang; Hao Sun 001 (Patterns, 2020)

Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. - Yile Huang; Yulong Qiao; Yu Zhao; Yuying Li; Jie Yuan; Jiajian Zhou; Hao Sun 001; Huating Wang (Briefings Bioinform., 2021)

NAMS webserver: coding potential assessment and functional annotation of plant transcripts. - Kun Sun 003; Huating Wang; Hao Sun 001 (Briefings Bioinform., 2021)

GENESO: A Framework for Pan-Cancer Classification and Marker Gene Discovery by Symmetrical Occlusion Method Using Deep Learning. - Xing Zhao 008; Huating Wang; Hao Sun 001 (ICBBS, 2023)

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing. - Yusen Lin; Yongjun Zhang; Hang Sun; Hang Jiang; Xing Zhao 008; Xiaojuan Teng; Jingxia Lin; Bowen Shu; Hao Sun 001; Yuhui Liao; Jiajian Zhou (Briefings Bioinform., 2024)

Occlusion enhanced pan-cancer classification via deep learning. - Xing Zhao 008; Zigui Chen; Huating Wang; Hao Sun 001 (BMC Bioinform., 2024)