Publications

  • 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,

  • G-DAug: Generative Data Augmentation for Commonsense Reasoning,
    Yang, Y., Malaviya, C., Fernandez, J., Swayamdipta, W., Le Bras, R., Wang, J.-P. , Bhagavatula, C., Choi, Y. and Downey, D., Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing, 2020, p1008-1025

  • 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

  • Mobilizable antibiotic resistance genes are present in dust microbial communities
    Maamar, S.B., Glawe, A.J., Brown, T.K., Hellgeth, N., Hu, J., Wang, J.-P.,Huttenhower, C. and Hartmann, E.M., PLoS Pathog., 2020, 16(1): e1008211. https://doi.org/10.1371/journal.ppat.1008211.

  • Using Large Corpus N-gram Statistics to Improve Recurrent Neural Language Models,
    Yang,Y., Wang, J.-P., Downey, D., Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, (Volume 1: Long and Short Papers), , 2019, NAACL,3268-3273, Minneapolis, Minnesota.

  • 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

  • An Integrative Classification Model for Multiple Sclerosis Lesion Detection in Multimodal MRI
    Zhang, F., Wang, J.-P., Jiang, W. Statistics and Its Interface, 2019, 12(2).

  • Extracting Commonsense Properties from Embeddings with Limited Human Guidance
    Yang,Y., Birnbaum, L., Wang, J.-P., Downey, D. . Proceedings of the 56th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers) ,2018, Association for Computational Linguistics, 644--649, Melbourne, Australia

  • 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 Bayesian probit model with spatially varying coefficients for brain decoding using fMRI data
    Zhang, F., Jiang, W.,Wong, P.W., Wang, J.-P., Statistics in Medicine, 2016,10.1002/sim.6999.

  • Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory,
    D'Urso, A ., Yoh-hei Takahashi, Y.-H., Xiong, B., Marone, J., Coukos, R., Randise-Hinchliff, C., Wang, J.-P., Shilatifard, A., and Brickner, J.H eLife, 2016,10.7554/eLife.16691.

  • Involvement of PARP-1 in the regulation of alternative splicing
    Elena, M., Maiorano, J., Zhang, Q., Convertini, P., Stamm, S., Wang, J.-P., and Yvonne N. Fondufe-Mittendorf Cell Discovery, 15046(2016).

  • Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells,
    Sebeson,A., Xi, L., Zhang, Q.,Sigmund, A., Wang, J.-P., Widom, J. and Wang, X. PLoS ONE, 2015,DOI: 10.1371/journal.pone.0127214.

  • Integrative network analysis of TCGA data for ovarian cancer,
    Zhang, Q., Burdette, J.E., Wang, J.-P., BMC Systems Biology, 2014, 8:1338.

  • Decoding multiple sound categories in the human temporal cortex using high resolution fMRI,
    Zhang, F., Wang, J.-P., Kim, J., Parrish, T., Wong, P.C.M. PLoS ONE, 2015, 10(2):e0117303.

  • Histone Methyltransferase MMSET/NSD2 Alters EZH2 Binding and Reprograms the Myeloma Epigenome through Global and Focal Changes in H3K36 and H3K27 Methylation,
    Popovic, R., Martinez-Garcia, E., Giannopoulou, E., Zhang, Q., Ezponda, T., Shah, M.Y., Zheng, Y., Will, C.M., Small, E.C., Hua, Y., Bulic, M., Jiang, Y., Carrara, M., Calogero, R.A., Kath, W.L., Kelleher, N.L., Wang, J.-P., Elemento, O. and Licht, J.D., PLoS Genetics 2014,10(9):e1004566,DOI: 10.1371/journal.pgen.1004566 .

  • Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity,
    Small, E.C., Xi, L., Wang, J.-P., Widom, J., and Licht, J.D., PNAS 2014,111(24):E2462-71,doi: 10.1073/pnas.1400517111.

  • The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo,
    Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, E.D., Codomo, C.A., Brogaard, K., Widom, J., Wang, J.-P., Henikoff, J.G., eLife 2014, 3:e01861.

  • High Density Nucleosome Occupancy Map of Human Chromosome 9p21-22 Reveals Chromatin Organization of the Type I Interferon Gene Cluster,
    Freaney, J., Zhang, Q., Yigit, E., Kim, R., Widom, J., Wang, J.-P., Horvath, C., Journal of Interferon & Cytokine Research, 2014,34(9):676-85

  • 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

  • Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions
    McCallum, K.J. and Wang, J.-P., Biostatistics, 2013, Jul;14(3):600-11. doi: 10.1093/biostatistics/kxt003

  • Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection
    Marques, J.T., Wang, J.-P., Wang, X., de Oliveira, K.P.V., Gao, C., Aguiar, E.R.G.R. Jafari,N., Carthew, R.W., PLoS Pathog 2013, 9(8): e1003579. doi:10.1371/journal.ppat.1003579

  • Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs
    Nalabothula,N., Xi,L., Bhattacharyya,S., Widom,J., Wang, J.-P., Reeve,NJ, Santangelo, JT, Fondufe-Mittendorf, NY, BMC Genomics 2013, 14:391 PDF

  • High-resolution nucleosome mapping of targeted regions using BAC-based enrichment
    Yigit, E., Zhang, Q., Xi, L., Grilley, D., Widom, J., Wang, J.-P., Rao, A. and Pipkin, M.E. Nucleic Acids Res. 2013;doi: 10.1093/nar/gkt081 PDF;Supplementary materials

  • Nucleosome mapping across the CFTR locus identifies novel regulatory factors
    Yigit, E., Bischof, J.M., Zhang, Z., Ott, C.J., Kerschner, J.L., Leir, S.H., Buitrago-Delgado, E., Zhang, Q., Wang, J.P., Widom, J., Harris, A. Nucleic Acids Res. 2013;doi: 10.1093/nar/gks1462 PDF

  • A chemical approach to mapping nucleosomes at base pair resolution
    Brogaard, K., Xi, L., Wang, J.-P., and Widom, J., Methods Enzymol. 2012;513:315-34

  • 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

  • Large-scale Cortical Network Properties Predict Future Sound-to-Word Learning Success
    Sheppard, J.P., Wang, J.-P. and Wong, P.C.M., Journal of Cognitive Neuroscience, 2012, 24(5), 1087-1103, PDF
  • SPECIES: An R package for Species Richness Estimation
    Wang, J.P., Journal of Statistical Software, 2011, 40(9),1-15 PDF

  • An Empirical Bayes Based Approach forMethylation Differentiation at the Single Nucleotide Resolution
    McCallum, K., Jiang, W. and Wang, J.-P., International Journal of Mathematics and Computer Science, 2010, 5(2) 87-100 PDF

  • Large-scale Cortical Functional Organization and Speech Perception across the Lifespan
    Sheppard, J.P., Wang, J.-P.,Wong, P.C.M., PLoS ONE, 2010, 6(1):e16510.doi:10.1371/journal.pone.0016510 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

  • Estimation in Capture-Recapture models when covariates are subject to measurement errors and missing data
    Xi, L, Watson, R., Wang, J.-P. and Yip, P.S.F,The Canadian Journal of Statistics 2009, 37:645–658 PDF

  • A flexible Statistical Model for Chromatin Sequences
    Wang, J.-P. and Xi, L., In Frontiers of Biostatistics and Bioinformatics, Ma, S., Wang, Y. (eds). University of Science and Technology of China Press, 2009, Anhui, P.R. China

  • 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

  • An exponential partial prior for improving NPMLestimation for mixtures
    Wang, J.-P.,  and Lindsay, B.G., Statistical Methodology, 2008,5:30-45 PDF

  • Meta-analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
    Keegan, K., Pradhan, S. Wang, J.-P. and Allada, R., PLoS Computational Biology , 2007, 3(11) e208, PDF

  • Some optimization results and a VDM/ECM algorithm for penalized and constrained nonparametric maximum likelihood estimation for mixtures
    Wang, J.-P. , Computational Statistics and Data Analysis , 2007, 51:2946-2957 PDF

  • 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

  • Improved alignment of nucleosome DNA sequences using a mixture model
    Wang, J.-P. Z.     and Widom, J. , Nucleic Acids Research, 2005 , 33(21):6743-6755 2005, PDF Supplementary and codes

  • 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

  • Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries
    Wang, J.-P. Z.    , Lindsay, B.G., Cui, L., Wall, P.K., Marion, J., Zhang, J. and W., dePamphilis, C., BMC Bioinformatics, 2005,6:300 PDF Supplementary and software

  • EST Clustering Error Evaluation and Correction
    Wang, J.-P. Z.    , Lindsay, B.G., Leebens-Mack, J. , Cui, L., Wall, P.K., Miller, W.C. and W., dePamphilis, C., Bioinformatics, 2004, 20(17):2973-2984  PDF  Supplementary and software