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Zhiping Weng
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2020 – today
- 2023
- [j33]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): 1300-1311 (2023) - 2022
- [j32]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): 141-149 (2022) - 2021
- [j31]Tyler Borrman, Brian G. Pierce
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides. Bioinform. 36(22-23): 5377-5385 (2021) - 2020
- [j30]Sweta Vangaveti
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction. Bioinform. 36(3): 751-757 (2020) - [j29]Henry E. Pratt, Zhiping Weng:
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications. Bioinform. 36(11): 3573-3575 (2020)
2010 – 2019
- 2018
- [j28]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): W43-W48 (2018) - 2017
- [j27]Iain H. Moal, Didier Barradas-Bautista
IRaPPA: information retrieval based integration of biophysical models for protein assembly selection. Bioinform. 33(12): 1806-1813 (2017) - [j26]Wen Zhang
Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods. BMC Bioinform. 18(S-13): 464:1-464:11 (2017) - 2016
- [j25]Junko Tsuji
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data. Briefings Bioinform. 17(6): 938-952 (2016) - [c6]Wen Zhang
The prediction of human splicing branchpoints by multi-label learning. BIBM 2016: 254-259 - 2015
- [j24]Bo W. Han
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): 593-595 (2015) - 2014
- [j23]Thom Vreven, Howook Hwang, Brian G. Pierce
Evaluating template-based and template-free protein-protein complex structure prediction. Briefings Bioinform. 15(2): 169-176 (2014) - [j22]Brian G. Pierce
ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers. Bioinform. 30(12): 1771-1773 (2014) - [j21]Brian G. Pierce
Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes. BMC Bioinform. 15: 319 (2014) - [j20]Brian G. Pierce
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor. PLoS Comput. Biol. 10(2) (2014) - 2013
- [j19]Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41(Database-Issue): 171-176 (2013) - [c5]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: 813 - [c4]Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng:
Session Introduction. Pacific Symposium on Biocomputing 2013: 65-68 - 2012
- [j18]Jui-Hung Hung
Gene set enrichment analysis: performance evaluation and usage guidelines. Briefings Bioinform. 13(3): 281-291 (2012) - 2011
- [j17]Justin Jee, Joel S. Rozowsky
ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinform. 27(8): 1152-1154 (2011) - 2010
- [c3]Sheila M. Reynolds, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble:
Predicting Nucleosome Positioning Using Multiple Evidence Tracks. RECOMB 2010: 441-455
2000 – 2009
- 2005
- [j16]Brian G. Pierce
M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinform. 21(8): 1472-1478 (2005) - [j15]Ying Xu, Liming Cai, Zhiping Weng:
Preface. J. Comput. Sci. Technol. 20(4): 433 (2005) - [j14]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): 439-445 (2005) - [c2]Joseph D. Szustakowski
Less is more: towards an optimal universal description of protein folds. ECCB/JBI 2005: 71 - [c1]Dmitriy Leyfer, Zhiping Weng:
Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. ECCB/JBI 2005: 203 - 2004
- [j13]Peter M. Haverty, Zhiping Weng:
CisML: an XML-based format for sequence motif detection software. Bioinform. 20(11): 1815-1817 (2004) - [j12]Peter M. Haverty, Li-Li Hsiao, Steven R. Gullans, Ulla Hansen
Limited agreement among three global gene expression methods highlights the requirement for non-global validation. Bioinform. 20(18): 3431-3441 (2004) - [j11]Anason S. Halees
PromoSer: improvements to the algorithm, visualization and accessibility. Nucleic Acids Res. 32(Web-Server-Issue): 191-194 (2004) - [j10]Peter M. Haverty, Martin C. Frith
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. Nucleic Acids Res. 32(Web-Server-Issue): 213-216 (2004) - [j9]Zhenjun Hu, Yutao Fu, Anason S. Halees
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation. Nucleic Acids Res. 32(Web-Server-Issue): 235-241 (2004) - [j8]Yutao Fu, Martin C. Frith
MotifViz: an analysis and visualization tool for motif discovery. Nucleic Acids Res. 32(Web-Server-Issue): 420-423 (2004) - 2003
- [j7]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): 1765-1772 (2003) - [j6]Zhenjun Hu, Martin C. Frith
SeqVISTA: a graphical tool for sequence feature visualization and comparison. BMC Bioinform. 4: 1 (2003) - [j5]Anason S. Halees
PromoSer: a large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res. 31(13): 3554-3559 (2003) - [j4]Martin C. Frith
Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31(13): 3666-3668 (2003) - [j3]Zhiping Weng:
Managing Biological Sequence and Protein Structure Data. OMICS 7(1): 25-26 (2003) - 2002
- [j2]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): 214-217 (2002) - 2001
- [j1]Martin C. Frith
Detection of cis -element clusters in higher eukaryotic DNA. Bioinform. 17(10): 878-889 (2001)
Coauthor Index
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