Jiping Wang

  • 2220 Citations
20042023
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Research Output 2004 2019

2019

An integrative classification model for multiple sclerosis lesion detection in multimodal MRI

(Zoe) Zhang, F., Wang, J. & Jiang, W., Jan 1 2019, In : Statistics and its Interface. 12, 2, p. 193-202 10 p.

Research output: Contribution to journalArticle

Multiple Sclerosis
Magnetic resonance
Magnetic resonance imaging
Textures
Neuroimaging

DegNorm: Normalization of generalized transcript degradation improves accuracy in RNA-seq analysis

Xiong, B., Yang, Y., Fineis, F. R. & Wang, J., Apr 16 2019, In : Genome biology. 20, 1, 75.

Research output: Contribution to journalReview article

Open Access
RNA
degradation
Genes
gene
RNA Stability
2018

Extracting commonsense properties from embeddings with limited human guidance

Yang, Y., Birnbaum, L. A., Wang, J. & Downey, D. C., Jan 1 2018, ACL 2018 - 56th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference (Short Papers). Association for Computational Linguistics (ACL), p. 644-649 6 p. (ACL 2018 - 56th Annual Meeting of the Association for Computational Linguistics, Proceedings of the Conference (Long Papers); vol. 2).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Intelligent systems
Experiments
Problem-Based Learning
2017
5 Citations (Scopus)

Genome-wide Mapping of the Nucleosome Landscape by Micrococcal Nuclease and Chemical Mapping

Voong, L. N., Xi, L., Wang, J. & Wang, X., Aug 1 2017, In : Trends in Genetics. 33, 8, p. 495-507 13 p.

Research output: Contribution to journalReview article

Micrococcal Nuclease
Nucleosomes
Chromosome Mapping
Genome
DNA
2016
2 Citations (Scopus)

A Bayesian probit model with spatially varying coefficients for brain decoding using fMRI data

Zhang, F., Jiang, W., Wong, P. & Wang, J., Oct 30 2016, In : Statistics in Medicine. 35, 24, p. 4380-4397 18 p.

Research output: Contribution to journalArticle

Probit Model
Varying Coefficients
Functional Magnetic Resonance Imaging
Bayesian Model
Decoding
47 Citations (Scopus)

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

Voong, L. N., Xi, L., Sebeson, A. C., Xiong, B., Wang, J. & Wang, X., Dec 1 2016, In : Cell. 167, 6, p. 1555-1570.e15

Research output: Contribution to journalArticle

Nucleosomes
Stem cells
Genes
Transcription
Mouse Embryonic Stem Cells
18 Citations (Scopus)

Involvement of PARP1 in the regulation of alternative splicing

Matveeva, E., Maiorano, J., Zhang, Q., Eteleeb, A. M., Convertini, P., Chen, J., Infantino, V., Stamm, S., Wang, J., Rouchka, E. C. & Fondufe-Mittendorf, Y. N., Feb 16 2016, In : Cell Discovery. 2, 15046.

Research output: Contribution to journalArticle

Poly(ADP-ribose) Polymerases
Alternative Splicing
Chromatin
Genes
Histone Code
35 Citations (Scopus)

Set1/COMPASS and mediator are repurposed to promote epigenetic transcriptional memory

D’Urso, A., Takahashi, Y., Xiong, B., Marone, J., Coukos, R., Randise-Hinchliff, C., Wang, J., Shilatifard, A. & Brickner, J. H., Jun 23 2016, In : eLife. 5, JUN2016, e16691.

Research output: Contribution to journalArticle

Epigenomics
Data storage equipment
RNA Polymerase II
Yeasts
Yeast
2015
6 Citations (Scopus)

Decoding multiple sound categories in the human temporal cortex using high resolution fMRI

Zhang, F., Wang, J., Kim, J., Parrish, T. B. & Wong, P. C. M., Feb 18 2015, In : PLoS One. 10, 2, e0117303.

Research output: Contribution to journalArticle

Temporal Lobe
Decoding
cortex
Magnetic Resonance Imaging
Acoustic waves
5 Citations (Scopus)

Differential nucleosome occupancies across Oct4-Sox2 binding sites in murine embryonic stem cells

Sebeson, A., Xi, L., Zhang, Q., Sigmund, A., Wang, J., Widom, J. & Wang, X., May 18 2015, In : PLoS One. 10, 5, e0127214.

Research output: Contribution to journalArticle

nucleosomes
Nucleosomes
embryonic stem cells
Embryonic Stem Cells
Stem cells
2014
3 Citations (Scopus)

A Locally Convoluted Cluster Model for Nucleosome Positioning Signals in Chemical Maps

Xi, L., Brogaard, K., Zhang, Q., Lindsay, B., Widom, J. & Wang, J., Jan 1 2014, In : Journal of the American Statistical Association. 109, 505, p. 48-62 15 p.

Research output: Contribution to journalArticle

Positioning
Cell
Deconvolution
Quantification
Packing
5 Citations (Scopus)

High-density nucleosome occupancy map of human chromosome 9p21-22 reveals chromatin organization of the type I interferon gene cluster

Freaney, J. E., Zhang, Q., Yigit, E., Kim, R., Widom, J., Wang, J. & Horvath, C. M., Sep 1 2014, In : Journal of Interferon and Cytokine Research. 34, 9, p. 676-685 10 p.

Research output: Contribution to journalArticle

Chromosomes, Human, Pair 22
Interferon Type I
Nucleosomes
Human Chromosomes
Multigene Family
73 Citations (Scopus)

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. G., Zhang, Q., 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., Elemento, O. & Licht, J. D., Sep 1 2014, In : PLoS genetics. 10, 9

Research output: Contribution to journalArticle

myeloma
methyltransferases
methylation
histones
Histones
25 Citations (Scopus)

Integrative network analysis of TCGA data for ovarian cancer

Zhang, Q., Burdette, J. E. & Wang, J., Jan 1 2014, In : BMC systems biology. 8, 1 p.

Research output: Contribution to journalArticle

Ovarian Cancer
Atlases
Atlas
Network Analysis
Electric network analysis
51 Citations (Scopus)

Single-cell nucleosome mapping reveals the molecular basis of gene expression heterogeneity

Small, E. C., Xi, L., Wang, J., Widom, J. & Licht, J. D., Jan 1 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 24

Research output: Contribution to journalArticle

Nucleosomes
Gene Expression
Chromatin
Poly dA-dT
Mutation
42 Citations (Scopus)

The budding yeast centromere DNA element II wraps a stable Cse4 hemisome in either orientation in vivo

Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T. D., Codomo, C. A., Brogaard, K., Widom, J., Wang, J. & Henikoff, J. G., Apr 15 2014, In : eLife. 2014, 3

Research output: Contribution to journalArticle

Saccharomycetales
Nucleosomes
Centromere
Yeast
DNA

The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo

Henikoff, S., Ramachandran, S., Krassovsky, K., Bryson, T. D., Codomo, C. A., Brogaard, K., Widom, J., Wang, J. P. & Henikoff, J. G., Jan 1 2014, In : eLife. 3, p. e01861

Research output: Contribution to journalArticle

Saccharomycetales
Nucleosomes
Centromere
Yeast
DNA
2013
17 Citations (Scopus)

Archaeal nucleosome positioning in vivo and in vitro is directed by primary sequence motifs

Nalabothula, N., Xi, L., Bhattacharyya, S., Widom, J., Wang, J., Reeve, J. N., Santangelo, T. J. & Fondufe-Mittendorf, Y. N., Jun 10 2013, In : BMC Genomics. 14, 1, 391.

Research output: Contribution to journalArticle

Nucleosomes
Histones
Eukaryota
DNA
Archaea
52 Citations (Scopus)

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. A., Widom, J. & Wang, J., Dec 10 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 50, p. 20158-20163 6 p.

Research output: Contribution to journalArticle

Schizosaccharomyces
Nucleosomes
Transcription Initiation Site
Saccharomyces cerevisiae
DNA
45 Citations (Scopus)

Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection

Marques, J. T., Wang, J., Wang, X., de Oliveira, K. P. V., Gao, C., Aguiar, E. R. G. R., Jafari, N. & Carthew, R. W., Aug 1 2013, In : PLoS Pathogens. 9, 8, e1003579.

Research output: Contribution to journalArticle

Virus Diseases
Small Interfering RNA
RNA Viruses
Viral RNA
Drosophila
13 Citations (Scopus)

High-resolution nucleosome mapping of targeted regions using BAC-based enrichment

Yigit, E., Zhang, Q., Xi, L., Grilley, D., Widom, J., Wang, J., Rao, A. & Pipkin, M. E., Apr 1 2013, In : Nucleic acids research. 41, 7

Research output: Contribution to journalArticle

Nucleosomes
Genome
T-Lymphocytes
Bacterial Artificial Chromosomes
Chromatin
14 Citations (Scopus)

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. Z., Widom, J. & Harris, A., Mar 1 2013, In : Nucleic acids research. 41, 5, p. 2857-2868 12 p.

Research output: Contribution to journalArticle

Cystic Fibrosis Transmembrane Conductance Regulator
Nucleosomes
Trans-Activators
Binding Sites
Transcription Factors
6 Citations (Scopus)

Quantifying copy number variations using a hidden Markov model with inhomogeneous emission distributions

Mccallum, K. J. & Wang, J., Jul 1 2013, In : Biostatistics. 14, 3, p. 600-611 12 p.

Research output: Contribution to journalArticle

Markov Model
Sequencing
Negative Binomial
Regression
Genetic Variation
2012
14 Citations (Scopus)

A chemical approach to mapping nucleosomes at base pair resolution in yeast

Brogaard, K. R., Xi, L., Wang, J. & Widom, J., Jan 1 2012, Methods in Enzymology. Academic Press Inc., p. 315-334 20 p. (Methods in Enzymology; vol. 513).

Research output: Chapter in Book/Report/Conference proceedingChapter

Nucleosomes
Base Pairing
Yeast
Yeasts
Genes
216 Citations (Scopus)

A map of nucleosome positions in yeast at base-pair resolution

Brogaard, K., Xi, L., Wang, J. & Widom, J., Jun 28 2012, In : Nature. 486, 7404, p. 496-501 6 p.

Research output: Contribution to journalArticle

Nucleosomes
Base Pairing
Yeasts
Histone Code
DNA-Directed RNA Polymerases
23 Citations (Scopus)

Large-scale cortical network properties predict future sound-to-word learning success

Sheppard, J. P., Wang, J. & Wong, P. C. M., May 1 2012, In : Journal of Cognitive Neuroscience. 24, 5, p. 1087-1103 17 p.

Research output: Contribution to journalArticle

learning success
Aptitude
Language
Learning
Brain

NuCMap: R package for chemical mapping of nucleosome positioning

Wang, J., 2012

Research output: Non-textual formSoftware

positioning
software
chemical
2011
10 Citations (Scopus)

Large-scale cortical functional organization and speech perception across the lifespan

Sheppard, J. P., Wang, J. & Wong, P. C. M., Feb 9 2011, In : PloS one. 6, 1, e16510.

Research output: Contribution to journalArticle

Speech Perception
Efficiency
Atrophy
Brain
Magnetic Resonance Imaging
34 Citations (Scopus)

SPECIES: An r package for species richness estimation

Wang, J., Jan 1 2011, In : Journal of Statistical Software. 40, 9, p. 1-15 15 p.

Research output: Contribution to journalArticle

Species Richness
Nonparametric Maximum Likelihood Estimation
Semiparametric Methods
Wrapper
Maximum likelihood estimation
Software
22 Citations (Scopus)

Estimating species richness by a poisson-compound gamma model

Wang, J., Sep 1 2010, In : Biometrika. 97, 3, p. 727-740 14 p.

Research output: Contribution to journalArticle

Species Richness
Compound Poisson
Shape Parameter
Least-Squares Analysis
Nonparametric Maximum Likelihood
Nucleosomes
Software
Genome
73 Citations (Scopus)

Predicting nucleosome positioning using a duration Hidden Markov Model

Xi, L., Fondufe-Mittendorf, Y., Xia, L., Flatow, J., Widom, J. & Wang, J., Jun 24 2010, In : BMC bioinformatics. 11, 346.

Research output: Contribution to journalArticle

Nucleosomes
Hidden Markov models
Markov Model
Positioning
Genes
2009

A flexible Statistical Model for Chromatin Sequences

Wang, J. & Xi, L., 2009, Frontiers of Biostatistics and Bioinformatics. Anhui, P.R., China: University of Science and Technology, China Press

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Citations (Scopus)

Estimation in capture-recapture models when covariates are subject to measurement errors and missing data

Xi, L., Watson, R., Wang, J. & Yip, P. S. F., Dec 1 2009, In : Canadian Journal of Statistics. 37, 4, p. 645-658 14 p.

Research output: Contribution to journalArticle

Capture-recapture
Estimating Equation
Missing Data
Measurement Error
Covariates
2008
14 Citations (Scopus)

An exponential partial prior for improving nonparametric maximum likelihood estimation in mixture models

Wang, J. & Lindsay, B. G., Jan 1 2008, In : Statistical Methodology. 5, 1, p. 30-45 16 p.

Research output: Contribution to journalArticle

Nonparametric Maximum Likelihood Estimation
Mixture Model
Binomial Mixture
Plug-in Estimator
Empirical Bayes Estimation
48 Citations (Scopus)

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae

Wang, J., Fondufe-Mittendorf, Y., Xi, L., Tsai, G. F., Segal, E. & Widom, J., Sep 1 2008, In : PLoS Computational Biology. 4, 9, e1000175.

Research output: Contribution to journalArticle

Saccharomyces Cerevisiae
Yeast
Saccharomyces cerevisiae
DNA
nucleosomes
2007
6 Citations (Scopus)
Nonparametric Maximum Likelihood Estimation
Military electronic countermeasures
Specification languages
Maximum likelihood estimation
Mixture Model
77 Citations (Scopus)

Meta-analysis of Drosophila circadian microarray studies identifies a novel set of rhythmically expressed genes

Keegan, K. P., Pradhan, S., Wang, J. & Allada, R., Nov 1 2007, In : PLoS Computational Biology. 3, 11, p. 2087-2110 24 p.

Research output: Contribution to journalArticle

Drosophilidae
meta-analysis
Microarrays
Microarray
Drosophila
2006
1051 Citations (Scopus)

A genomic code for nucleosome positioning

Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thåström, A., Field, Y., Moore, I. K., Wang, J. & Widom, J., Aug 17 2006, In : Nature. 442, 7104, p. 772-778 7 p.

Research output: Contribution to journalArticle

Nucleosomes
Genome
DNA
DNA-Binding Proteins
Transcription Factors
2005
55 Citations (Scopus)

A penalized nonparametric maximum likelihood approach to species richness estimation

Wang, J. & Lindsay, B. G., Sep 1 2005, In : Journal of the American Statistical Association. 100, 471, p. 942-959 18 p.

Research output: Contribution to journalReview article

Species Richness
Nonparametric Maximum Likelihood
Nonparametric Maximum Likelihood Estimator
Likelihood
Conditional Likelihood
23 Citations (Scopus)

Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries

Wang, J., Lindsay, B. G., Cui, L., Wall, P. K., Marion, J., Zhang, J. & de Pamphilis, C. W., Dec 13 2005, In : BMC Bioinformatics. 6, 300.

Research output: Contribution to journalArticle

Expressed Sequence Tags
Sequencing
Libraries
Overlap
Genes
25 Citations (Scopus)

Improved alignment of nucleosome DNA sequences using a mixture model.

Wang, J. P. Z. & Widom, J., Jan 1 2005, In : Nucleic acids research. 33, 21, p. 6743-6755 13 p.

Research output: Contribution to journalArticle

Nucleosomes
Periodicity
Sequence Alignment
DNA
Fourier Analysis
2004
58 Citations (Scopus)

EST clustering error evaluation and correction

Wang, J., Lindsay, B. G., Leebens-Mack, J., Cui, L., Wall, K., Miller, W. C. & dePamphilis, C. W., Nov 22 2004, In : Bioinformatics. 20, 17, p. 2973-2984 12 p.

Research output: Contribution to journalArticle

Expressed Sequence Tags
Cluster Analysis
Clustering
Type I error
Evaluation