Zhiping Weng

According to our database1, Zhiping Weng authored at least 37 papers between 2001 and 2021.

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Bibliography

2021
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides.
Bioinform., 2021

2020
Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.
Bioinform., 2020

LogoJS: a Javascript package for creating sequence logos and embedding them in web applications.
Bioinform., 2020

2018
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans.
Nucleic Acids Res., 2018

2017
Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.
BMC Bioinform., 2017

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection.
Bioinform., 2017

2016
Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data.
Briefings Bioinform., 2016

The prediction of human splicing branchpoints by multi-label learning.
Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015
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., 2015

2014
Computational Design of the Affinity and Specificity of a Therapeutic T Cell Receptor.
PLoS Comput. Biol., 2014

Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes.
BMC Bioinform., 2014

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers.
Bioinform., 2014

Evaluating template-based and template-free protein-protein complex structure prediction.
Briefings Bioinform., 2014

2013
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.
Nucleic Acids Res., 2013

Session Introduction.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Gene set enrichment analysis: performance evaluation and usage guidelines.
Briefings Bioinform., 2012

2011
ACT: aggregation and correlation toolbox for analyses of genome tracks.
Bioinform., 2011

2010
Predicting Nucleosome Positioning Using Multiple Evidence Tracks.
Proceedings of the Research in Computational Molecular Biology, 2010

2005
Preface.
J. Comput. Sci. Technol., 2005

Transcriptional Regulatory Networks Activated by PI3K and ERK Transduced Growth Signals in Human Glioblastoma Cells.
J. Comput. Sci. Technol., 2005

M-ZDOCK: a grid-based approach for C<sub>n</sub> symmetric multimer docking.
Bioinform., 2005

Less is more: towards an optimal universal description of protein folds.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

Genome-wide decoding of hierarchical modular structure of transcriptional regulation by <i>cis</i>-element and expression clustering.
Proceedings of the ECCB/JBI'05 Proceedings, Fourth European Conference on Computational Biology/Sixth Meeting of the Spanish Bioinformatics Network (Jornadas de BioInformática), Palacio de Congresos, Madrid, Spain, September 28, 2005

2004
SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation.
Nucleic Acids Res., 2004

CARRIE web service: automated transcriptional regulatory network inference and interactive analysis.
Nucleic Acids Res., 2004

PromoSer: improvements to the algorithm, visualization and accessibility.
Nucleic Acids Res., 2004

MotifViz: an analysis and visualization tool for motif discovery.
Nucleic Acids Res., 2004

CisML: an XML-based format for sequence motif detection software.
Bioinform., 2004

Limited agreement among three global gene expression methods highlights the requirement for non-global validation.
Bioinform., 2004

2003
Managing Biological Sequence and Protein Structure Data.
OMICS, 2003

PromoSer: a large-scale mammalian promoter and transcription start site identification service.
Nucleic Acids Res., 2003

Cluster-Buster: finding dense clusters of motifs in DNA sequences.
Nucleic Acids Res., 2003

SeqVISTA: a graphical tool for sequence feature visualization and comparison.
BMC Bioinform., 2003

Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules.
Bioinform., 2003

2002
HugeIndex: a database with visualization tools for high-density oligonucleotide array data from normal human tissues.
Nucleic Acids Res., 2002

2001
Detection of cis -element clusters in higher eukaryotic DNA.
Bioinform., 2001


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