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Items: 1 to 20 of 22


Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation.

Zhou J, Ma J, Chen Y, Cheng C, Bao B, Peng J, Sejnowski TJ, Dixon JR, Ecker JR.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14011-14018. doi: 10.1073/pnas.1901423116. Epub 2019 Jun 24.


DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies.

Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T.

Cell Syst. 2019 Mar 27;8(3):267-273.e3. doi: 10.1016/j.cels.2019.02.003. Epub 2019 Mar 13.


Classifying tumors by supervised network propagation.

Zhang W, Ma J, Ideker T.

Bioinformatics. 2019 Jul;35(14):2528. doi: 10.1093/bioinformatics/bty1072. Epub 2019 Feb 4. No abstract available.


Typing tumors using pathways selected by somatic evolution.

Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T.

Nat Commun. 2018 Oct 8;9(1):4159. doi: 10.1038/s41467-018-06464-y.


Classifying tumors by supervised network propagation.

Zhang W, Ma J, Ideker T.

Bioinformatics. 2018 Jul 1;34(13):i484-i493. doi: 10.1093/bioinformatics/bty247. Erratum in: Bioinformatics. 2019 Feb 4;35(14):2528.


Visible Machine Learning for Biomedicine.

Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T.

Cell. 2018 Jun 14;173(7):1562-1565. doi: 10.1016/j.cell.2018.05.056.


Using deep learning to model the hierarchical structure and function of a cell.

Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T.

Nat Methods. 2018 Apr;15(4):290-298. doi: 10.1038/nmeth.4627. Epub 2018 Mar 5.


Annotating gene sets by mining large literature collections with protein networks.

Wang S, Ma J, Yu MK, Zheng F, Huang EW, Han J, Peng J, Ideker T.

Pac Symp Biocomput. 2018;23:602-613.


DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields.

Shao M, Ma J, Wang S.

Bioinformatics. 2017 Jul 15;33(14):i267-i273. doi: 10.1093/bioinformatics/btx267.


AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields.

Wang S, Ma J, Xu J.

Bioinformatics. 2016 Sep 1;32(17):i672-i679. doi: 10.1093/bioinformatics/btw446.


ModuleAlign: module-based global alignment of protein-protein interaction networks.

Hashemifar S, Ma J, Naveed H, Canzar S, Xu J.

Bioinformatics. 2016 Sep 1;32(17):i658-i664. doi: 10.1093/bioinformatics/btw447.


Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

Wang S, Peng J, Ma J, Xu J.

Sci Rep. 2016 Jan 11;6:18962. doi: 10.1038/srep18962.


Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning.

Ma J, Wang S, Wang Z, Xu J.

Bioinformatics. 2015 Nov 1;31(21):3506-13. doi: 10.1093/bioinformatics/btv472. Epub 2015 Aug 14.


DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields.

Wang S, Weng S, Ma J, Tang Q.

Int J Mol Sci. 2015 Jul 29;16(8):17315-30. doi: 10.3390/ijms160817315.


An integrative computational approach for prioritization of genomic variants.

Dubchak I, Balasubramanian S, Wang S, Cem M, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC.

PLoS One. 2014 Dec 15;9(12):e114903. doi: 10.1371/journal.pone.0114903. eCollection 2014. Erratum in: PLoS One. 2015;10(4):e0124700. Meyden, Cem [corrected to Meydan, Cem].


MRFalign: protein homology detection through alignment of Markov random fields.

Ma J, Wang S, Wang Z, Xu J.

PLoS Comput Biol. 2014 Mar 27;10(3):e1003500. doi: 10.1371/journal.pcbi.1003500. eCollection 2014 Mar.


Algorithms, applications, and challenges of protein structure alignment.

Ma J, Wang S.

Adv Protein Chem Struct Biol. 2014;94:121-75. doi: 10.1016/B978-0-12-800168-4.00005-6.


RaptorX server: a resource for template-based protein structure modeling.

Källberg M, Margaryan G, Wang S, Ma J, Xu J.

Methods Mol Biol. 2014;1137:17-27. doi: 10.1007/978-1-4939-0366-5_2.


Protein threading using context-specific alignment potential.

Ma J, Wang S, Zhao F, Xu J.

Bioinformatics. 2013 Jul 1;29(13):i257-65. doi: 10.1093/bioinformatics/btt210.

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