Zhiping Weng

Publication Activity (10 Years)

Years Active: 2001-2023
Publications (10 Years): 10

Top Topics

Saccharomyces Cerevisiae

Protein Complexes

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Publications

Hufeng Zhou, Theodore Arapoglou, Xihao Li, Zilin Li, Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E. Blue, Steven Buyske, Nancy J. Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Cox Matise, Anthony Philippakis, Heidi L. Rehm, Heidi J. Sofia, Grace Snyder, Zhiping Weng, Benjamin M. Neale, Shamil R. Sunyaev, Xihong Lin
FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res. 51 (D1) (2023)
Henry E. Pratt, Gregory R. Andrews, Nishigandha Phalke, Jack D. Huey, Michael J. Purcaro, Arjan van der Velde, Jill Moore, Zhiping Weng
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Res. 50 (D1) (2022)
Tyler Borrman, Brian G. Pierce, Thom Vreven, Brian M. Baker, Zhiping Weng
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinform. 36 (22-23) (2021)
Henry Pratt, Zhiping Weng
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. Bioinform. 36 (11) (2020)
Sweta Vangaveti, Thom Vreven, Yang Zhang, Zhiping Weng
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinform. 36 (3) (2020)
Wei-Sheng Wu, Wei-Che Huang, Jordan S. Brown, Donglei Zhang, Xiaoyan Song, Hao Chen, Shikui Tu, Zhiping Weng, Heng-Chi Lee
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. BMC Bioinform. 18 (S-13) (2017)
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
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. Bioinform. 33 (12) (2017)
Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, Zhiping Weng
The prediction of human splicing branchpoints by multi-label learning. BIBM (2016)
Junko Tsuji, Zhiping Weng
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. Briefings Bioinform. 17 (6) (2016)
Bo W. Han, Wei Wang, Phillip D. Zamore, Zhiping Weng
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. Bioinform. 31 (4) (2015)
Thom Vreven, Howook Hwang, Brian G. Pierce, Zhiping Weng
Evaluating template-based and template-free protein-protein complex structure prediction. Briefings Bioinform. 15 (2) (2014)
Brian G. Pierce, Kevin Wiehe, Howook Hwang, Bong-Hyun Kim, Thom Vreven, Zhiping Weng
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinform. 30 (12) (2014)
Brian G. Pierce, Thom Vreven, Zhiping Weng
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. BMC Bioinform. 15 (2014)
Brian G. Pierce, Lance M. Hellman, Moushumi Hossain, Nishant K. Singh, Craig W. Vander Kooi, Zhiping Weng, Brian M. Baker
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. PLoS Comput. Biol. 10 (2) (2014)
Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. BCB (2013)
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, Zhiping Weng
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41 (Database-Issue) (2013)
Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng
Session Introduction. Pacific Symposium on Biocomputing (2013)
Jui-Hung Hung, Tun-Hsiang Yang, Zhenjun Hu, Zhiping Weng, Charles DeLisi
Gene set enrichment analysis: performance evaluation and usage guidelines. Briefings Bioinform. 13 (3) (2012)
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
ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinform. 27 (8) (2011)
Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble
Predicting Nucleosome Positioning Using Multiple Evidence Tracks. RECOMB (2010)
Joseph D. Szustakowski, Simon Kasif, Zhiping Weng
Less is more: towards an optimal universal description of protein folds. ECCB/JBI (2005)
Dmitriy Leyfer, Zhiping Weng
-element and expression clustering. ECCB/JBI (2005)
Brian G. Pierce, Weiwei Tong, Zhiping Weng
symmetric multimer docking. Bioinform. 21 (8) (2005)
Ying Xu, Liming Cai, Zhiping Weng
Preface. J. Comput. Sci. Technol. 20 (4) (2005)
Peter M. Haverty, Zhiping Weng, Ulla Hansen
Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells. J. Comput. Sci. Technol. 20 (4) (2005)
Peter M. Haverty, Zhiping Weng
CisML: an XML-based format for sequence motif detection software. Bioinform. 20 (11) (2004)
Zhenjun Hu, Yutao Fu, Anason S. Halees, Szymon M. Kielbasa, Zhiping Weng
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Peter M. Haverty, Martin C. Frith, Zhiping Weng
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen, Zhiping Weng
Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinform. 20 (18) (2004)
Yutao Fu, Martin C. Frith, Peter M. Haverty, Zhiping Weng
MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Anason S. Halees, Zhiping Weng
PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Zhenjun Hu, Martin C. Frith, Tianhua Niu, Zhiping Weng
SeqVISTA: a graphical tool for sequence feature visualization and comparison. BMC Bioinform. 4 (2003)
Björn Peters, Weiwei Tong, John Sidney, Alessandro Sette, Zhiping Weng
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Bioinform. 19 (14) (2003)
Anason S. Halees, Dmitriy Leyfer, Zhiping Weng
PromoSer: a large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 31 (13) (2003)
Zhiping Weng
Managing Biological Sequence and Protein Structure Data. OMICS 7 (1) (2003)
Martin C. Frith, Michael C. Li, Zhiping Weng
Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31 (13) (2003)
Peter M. Haverty, Zhiping Weng, Nathan L. Best, Kenneth R. Auerbach, Li-Li Hsiao, Roderick V. Jensen, Steven R. Gullans
HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues. Nucleic Acids Res. 30 (1) (2002)
Martin C. Frith, Ulla Hansen, Zhiping Weng
Detection of cis -element clusters in higher eukaryotic DNA. Bioinform. 17 (10) (2001)