• 2407 Citations
20042020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

2020

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. & Hartmann, E. M., 2020, In : PLoS pathogens. 16, 1, e1008211.

Research output: Contribution to journalArticle

Open Access
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

1 Scopus citations

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

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

Research output: Contribution to journalReview article

Open Access
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

3 Scopus citations
2017

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

8 Scopus citations
2016

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

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

Research output: Contribution to journalArticle

2 Scopus citations

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

62 Scopus citations

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

21 Scopus citations

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

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

Research output: Contribution to journalArticle

45 Scopus citations
2015

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

9 Scopus citations

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. & Wang, X., May 18 2015, In : PloS one. 10, 5, e0127214.

Research output: Contribution to journalArticle

5 Scopus citations
2014

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

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

Research output: Contribution to journalArticle

4 Scopus citations

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

7 Scopus citations

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

Research output: Contribution to journalArticle

85 Scopus citations

Integrative network analysis of TCGA data for ovarian cancer

Zhang, Q., Burdette, J. E. & Wang, J. P., Dec 31 2014, (Accepted/In press) In : BMC systems biology. p. 1-18 18 p.

Research output: Contribution to journalArticle

43 Scopus citations

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

60 Scopus citations

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., Apr 15 2014, In : eLife. 2014, 3

Research output: Contribution to journalArticle

45 Scopus citations

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

2013

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, J. N., Santangelo, T. J. & Fondufe-Mittendorf, Y. N., Jun 10 2013, In : BMC Genomics. 14, 1, 391.

Research output: Contribution to journalArticle

19 Scopus citations

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. & Wang, J. P., 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

55 Scopus citations

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., Aug 1 2013, In : PLoS pathogens. 9, 8, e1003579.

Research output: Contribution to journalArticle

48 Scopus citations

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. & Pipkin, M. E., Apr 1 2013, In : Nucleic acids research. 41, 7, p. e87

Research output: Contribution to journalArticle

14 Scopus citations

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 2013, In : Nucleic acids research. 41, 5, p. 2857-2868 12 p.

Research output: Contribution to journalArticle

14 Scopus citations

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

7 Scopus citations
2012

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

Brogaard, K. R., Xi, L., Wang, J. P. & Widom, J., 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

16 Scopus citations

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

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

Research output: Contribution to journalArticle

241 Scopus citations

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

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

Research output: Contribution to journalArticle

28 Scopus citations

NuCMap: R package for chemical mapping of nucleosome positioning

Wang, J., 2012

Research output: Non-textual formSoftware

2011

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

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

Research output: Contribution to journalArticle

11 Scopus citations

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

37 Scopus citations

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

23 Scopus citations

Predicting nucleosome positioning using a duration Hidden Markov Model

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

Research output: Contribution to journalArticle

79 Scopus citations
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

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

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

Research output: Contribution to journalArticle

8 Scopus citations
2008

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

14 Scopus citations

Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae

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

Research output: Contribution to journalArticle

53 Scopus citations
2007
6 Scopus citations

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

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

Research output: Contribution to journalArticle

83 Scopus citations
2006

A genomic code for nucleosome positioning

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

Research output: Contribution to journalArticle

1084 Scopus citations
2005

A penalized nonparametric maximum likelihood approach to species richness estimation

Wang, J. P. Z. & 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

58 Scopus citations

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. & de Pamphilis, C. W., Dec 13 2005, In : BMC bioinformatics. 6, 300.

Research output: Contribution to journalArticle

23 Scopus citations

Improved alignment of nucleosome DNA sequences using a mixture model.

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

Research output: Contribution to journalArticle

27 Scopus citations
2004

EST clustering error evaluation and correction

Wang, J. P. Z., 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

59 Scopus citations