Zhiping Weng

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