Ji‑Ping Wang

Ji‑Ping Wang

Professor of Statistics & Data Science, Adjunct Professor of Molecular BioSciences

Faculty at NSF‑Simons National Institute for Theory & Mathematics in Biology, Northwestern University

Research Interests

Bioinformatics and computational biology; Nucleosome mapping and positioning prediction; Epigenetics; Species number and population size estimation; Mixture models and computing algorithms

Some Bioinformatic Tools We Developed

DNAcycP2

DNAcycP2 is an improved version of previously released DNAcycP for DNA cyclizability or bendability prediction trained based on loop-seq data after removing biotin bias using a newly developed data augmentation approach.

BoostMEC

BoostMEC is a boosting tree based approach, utilizing LightGBM for the prediction of wild-type CRISPR-Cas9 editing efficiency.

GitHub

NuPoP

NuPoP is an R package for Nucleosome Positioning Prediction based on DNA sequence. The model is trained based on in vivo chemical map or Mnase map of nucelosomes.

SPECIES

SPECIES is an R package that implements various popular methods in species richness estimation.

CRAN
GitHub

RiboDiPA

RiboDiPA is a bioinformatics pipeline developed for differential pattern analysis of Ribo-seq footprint data.

DegNorm

DegNorm is a bioinformatics pipeline to correct for bias due to the heterogeneous patterns of transcript degradation in RNA-seq data.

Selected Publications

DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation
Kendall, B., Jin, C., Li, K., Ruan, F., Wang, X.A., and Wang, J.-P., Nucleic Acids Research , 2025, 53, gkaf145, download Python package , R package

BNLSDeconv: an efficient cell-type deconvolution method for spatial transcriptomics data
Chen, Y., Ruan, F. and Wang, J.-P., Bioinformatics, 2025,41(1).https://doi.org/10.1093/bioinformatics/btae747

BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models
Zarate, O.A., Yang, Y., Wang, X. Wang, J.-P. BMC Bioinformatics, 23, 446 (2022). https://doi.org/10.1186/s12859-022-04998-z
Python package download

DNAcycP: a deep learning tool for DNA cyclizability prediction
Li, K., Caroll,M.,Vafabakhsh, R., Wang, X., Wang, J.-P. Nucleic Acids Research, 2022, https://doi.org/10.1093/nar/gkac162
Python package download: GitHub, Run DNA bendabilty/cyclizabilty prediction in real time web server,

RiboDiPA: A novel tool for differential pattern analysis in Ribo-seq data
Li, K., Hope, M., Wang, X., Wang, J.-P. Nucleic Acids Research, 2020,48(21), doi:10.1093/nar/gkaa1049

DegNorm: normalization of generalized transcript degradation improves accuracy in RNA-seq analysis
Xiong, B., Yang, Y., Fineis, F. Wang, J.-P., Genome Biology, 2019, 20:75.
DegNorm python package at Github

Genome-wide mapping of the nucleosome landscape by micrococcal nuclease and chemical mapping
Voong,L. N., Xi, L., Wang, J.-P., Wang, X. . Trends in Genetics, 2017,33(8),495-507 DOI: http://dx.doi.org/10.1016/.tig.2017.05.007.

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping
Voong,L. N., Xi, L., Sebeson, A.C., Xiong, B., Wang, J.-P., Wang, X. . Cell, 2016, 167(6),1555-1570.e15, DOI: http://dx.doi.org/10.1016/j.cell.2016.10.049. highlighted in Nature Reviews Molecular Cell Biology

A locally convoluted cluster model for nucleosome positioning signals in chemical map
Xi, L., Brogaard,K., Zhang, Q., Lindsay, B.G., Widom, and Wang, J.-P., Journal of American Statistical Association , 2014, 109(505) 48-62, DOI:10.1080/01621459.2013.862169

Chemical map of Schizosaccharomyces pombe reveals species-specific features in nucleosome positioning
Moyle-Heyrman, G., Zaichuk, T., Xi, L., Zhang, Q., Uhlenbeck, O.C., Holmgren, R., Widom, J. and Wang, J.-P., PNAS 2013,110(50),20158-20163 pdf; Supplementary materials

A Map of Nucleosome Positions in Yeast at base-pair resolution
Brogaard, K., Xi, L., Wang, J.-P., and Widom, J., Nature, 2012, 486: 496–501.
Online Supplementary Methods; Other supplementary materials

SPECIES: An R package for Species Richness Estimation
Wang, J.P., Journal of Statistical Software, 2011, 40(9),1-15 PDF

Predicting nucleosome positioning using a duration Hidden Markov Model
Xi ,L., Fondufe-Mittendorf , Y.,Xia, L., Flatow,J., Widom ,J. and Wang, J.-P.,
BMC Bioinformatics , 2010, doi:10.1186/1471-2105-11-346, PDF, NuPoP software Bioconductor download

A Poisson-compound Gamma model for species richness estimation
Wang, J.-P. , Biometrika, 2010, 97(3): 727-740, suppplemental materials SPECIES_V1.0 R package

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae
Wang, J.-P., Fondufe-Mittendorf,Y., Xi, L., Tsai, G.,Segal, E. and Widom, J., PLoS Computational Biology, 2008, 4(9) e1000175 PDF, Supplementary and codes

A genomic code for nucleosome positioning
Segal, E., Fondufe-Mittendorf,Y., Chen,L., Thåström, A., Field, Y., Moore, I.K., Wang, J.-P.Z. and Widom,J., Nature, 2006, 442(7104):772-778

A penalized nonparametric maximum likelilhood approach to species richness estimation
Wang, J.-P. Z. and Lindsay, B. G., Journal of American Statistical Association, 2005,100(471):942-959. PDF