Detection of cis -element clusters in higher eukaryotic DNA. - Martin C. Frith; Ulla Hansen; Zhiping Weng (Bioinform., 2001)

HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. - Peter M. Haverty; Zhiping Weng; Nathan L. Best; Kenneth R. Auerbach; Li-Li Hsiao; Roderick V. Jensen; Steven R. Gullans (Nucleic Acids Res., 2002)

Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. - Björn Peters; Weiwei Tong; John Sidney; Alessandro Sette; Zhiping Weng (Bioinform., 2003)

SeqVISTA: a graphical tool for sequence feature visualization and comparison. - Zhenjun Hu; Martin C. Frith; Tianhua Niu; Zhiping Weng (BMC Bioinform., 2003)

Cluster-Buster: finding dense clusters of motifs in DNA sequences. - Martin C. Frith; Michael C. Li; Zhiping Weng (Nucleic Acids Res., 2003)

PromoSer: a large-scale mammalian promoter and transcription start site identification service. - Anason S. Halees; Dmitriy Leyfer; Zhiping Weng (Nucleic Acids Res., 2003)

Managing Biological Sequence and Protein Structure Data. - Zhiping Weng (OMICS, 2003)

Limited agreement among three global gene expression methods highlights the requirement for non-global validation. - Peter M. Haverty; Li-Li Hsiao; Steven R. Gullans; Ulla Hansen; Zhiping Weng (Bioinform., 2004)

CisML: an XML-based format for sequence motif detection software. - Peter M. Haverty; Zhiping Weng (Bioinform., 2004)

MotifViz: an analysis and visualization tool for motif discovery. - Yutao Fu; Martin C. Frith; Peter M. Haverty; Zhiping Weng (Nucleic Acids Res., 2004)

PromoSer: improvements to the algorithm, visualization and accessibility. - Anason S. Halees; Zhiping Weng (Nucleic Acids Res., 2004)

CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. - Peter M. Haverty; Martin C. Frith; Zhiping Weng (Nucleic Acids Res., 2004)

SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. - Zhenjun Hu; Yutao Fu; Anason S. Halees; Szymon M. Kielbasa; Zhiping Weng (Nucleic Acids Res., 2004)

Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. - Dmitriy Leyfer; Zhiping Weng (ECCB/JBI, 2005)

Less is more: towards an optimal universal description of protein folds. - Joseph D. Szustakowski; Simon Kasif; Zhiping Weng (ECCB/JBI, 2005)

M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. - Brian G. Pierce; Weiwei Tong; Zhiping Weng (Bioinform., 2005)

Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells. - Peter M. Haverty; Zhiping Weng; Ulla Hansen (J. Comput. Sci. Technol., 2005)

Preface. - Ying Xu 001; Liming Cai; Zhiping Weng (J. Comput. Sci. Technol., 2005)

Predicting Nucleosome Positioning Using Multiple Evidence Tracks. - Sheila M. Reynolds; Zhiping Weng; Jeff A. Bilmes; William Stafford Noble (RECOMB, 2010)

ACT: aggregation and correlation toolbox for analyses of genome tracks. - Justin Jee; Joel S. Rozowsky; Kevin Y. Yip; Lucas Lochovsky; Robert D. Bjornson; Guoneng Zhong; Zhengdong D. Zhang; Yutao Fu; Jie Wang; Zhiping Weng; Mark Gerstein (Bioinform., 2011)

Gene set enrichment analysis: performance evaluation and usage guidelines. - Jui-Hung Hung; Tun-Hsiang Yang; Zhenjun Hu; Zhiping Weng; Charles DeLisi (Briefings Bioinform., 2012)

Unsupervised pattern discovery in human chromatin structure through genomic segmentation. - Michael M. Hoffman; Orion J. Buske; Jie Wang; Zhiping Weng; Jeff A. Bilmes; William Stafford Noble (BCB, 2013)

Session Introduction. - Alexander J. Hartemink; Manolis Kellis; William Stafford Noble; Zhiping Weng (Pacific Symposium on Biocomputing, 2013)

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. - Jie Wang; Jiali Zhuang; Sowmya Iyer; Xin-Ying Lin; Melissa C. Greven; Bong-Hyun Kim; Jill Moore; Brian G. Pierce; Xianjun Dong; Daniel Virgil; Ewan Birney; Jui-Hung Hung; et al. (Nucleic Acids Res., 2013)

Evaluating template-based and template-free protein-protein complex structure prediction. - Thom Vreven; Howook Hwang; Brian G. Pierce; Zhiping Weng (Briefings Bioinform., 2014)

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. - Brian G. Pierce; Kevin Wiehe; Howook Hwang; Bong-Hyun Kim; Thom Vreven; Zhiping Weng (Bioinform., 2014)

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. - Brian G. Pierce; Thom Vreven; Zhiping Weng (BMC Bioinform., 2014)

Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. - Brian G. Pierce; Lance M. Hellman; Moushumi Hossain; Nishant K. Singh; Craig W. Vander Kooi; Zhiping Weng; Brian M. Baker (PLoS Comput. Biol., 2014)

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. - Bo W. Han; Wei Wang; Phillip D. Zamore; Zhiping Weng (Bioinform., 2015)

The prediction of human splicing branchpoints by multi-label learning. - Wen Zhang 008; Xiaopeng Zhu; Yu Fu; Junko Tsuji; Zhiping Weng (BIBM, 2016)

Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. - Junko Tsuji; Zhiping Weng (Briefings Bioinform., 2016)

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. - Iain H. Moal; Didier Barradas-Bautista; Brian Jiménez-García; Mieczyslaw Torchala; Arjan van der Velde; Thom Vreven; Zhiping Weng; Paul A. Bates; Juan Fernández-Recio (Bioinform., 2017)

Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. - Wen Zhang 008; Xiaopeng Zhu; Yu Fu; Junko Tsuji; Zhiping Weng (BMC Bioinform., 2017)

pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. - Wei-Sheng Wu; Wei-Che Huang; Jordan S. Brown; Donglei Zhang; Xiaoyan Song; Hao Chen; Shikui Tu; Zhiping Weng; Heng-Chi Lee (Nucleic Acids Res., 2018)

LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. - Henry E. Pratt; Zhiping Weng (Bioinform., 2020)

Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. - Sweta Vangaveti; Thom Vreven; Yang Zhang 040; Zhiping Weng (Bioinform., 2020)

High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. - Tyler Borrman; Brian G. Pierce; Thom Vreven; Brian M. Baker; Zhiping Weng (Bioinform., 2021)

Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. - Henry E. Pratt; Gregory R. Andrews; Nishigandha Phalke; Jack D. Huey; Michael J. Purcaro; Arjan van der Velde; Jill Moore; Zhiping Weng (Nucleic Acids Res., 2022)

FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. - Hufeng Zhou; Theodore Arapoglou; Xihao Li; Zilin Li; Xiuwen Zheng 001; Jill Moore; Abhijith Asok; Sushant Kumar; Elizabeth E. Blue; Steven Buyske; Nancy J. Cox; Adam Felsenfeld; et al. (Nucleic Acids Res., 2023)