Ma J - Search Results

1

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. Zhou J, et al. Among authors: ma j. Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14011-14018. doi: 10.1073/pnas.1901423116. Epub 2019 Jun 24. Proc Natl Acad Sci U S A. 2019. PMID: 31235599 Free PMC article.

2

A conditional neural fields model for protein threading.

Ma J, Peng J, Wang S, Xu J. Ma J, et al. Bioinformatics. 2012 Jun 15;28(12):i59-66. doi: 10.1093/bioinformatics/bts213. Bioinformatics. 2012. PMID: 22689779 Free PMC article.

3

Protein structure alignment beyond spatial proximity.

Wang S, Ma J, Peng J, Xu J. Wang S, et al. Among authors: ma j. Sci Rep. 2013;3:1448. doi: 10.1038/srep01448. Sci Rep. 2013. PMID: 23486213 Free PMC article.

4

Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields.

Wang S, Peng J, Ma J, Xu J. Wang S, et al. Among authors: ma j. Sci Rep. 2016 Jan 11;6:18962. doi: 10.1038/srep18962. Sci Rep. 2016. PMID: 26752681 Free PMC article.

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. Wang S, et al. Among authors: ma j. Pac Symp Biocomput. 2018;23:602-613. Pac Symp Biocomput. 2018. PMID: 29218918 Free PMC article.

6

Typing tumors using pathways selected by somatic evolution.

Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Wang S, et al. Among authors: ma j. Nat Commun. 2018 Oct 8;9(1):4159. doi: 10.1038/s41467-018-06464-y. Nat Commun. 2018. PMID: 30297789 Free PMC article.

7

Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients.

Ma J, Fong SH, Luo Y, Bakkenist CJ, Shen JP, Mourragui S, Wessels LFA, Hafner M, Sharan R, Peng J, Ideker T. Ma J, et al. Nat Cancer. 2021 Feb;2(2):233-244. doi: 10.1038/s43018-020-00169-2. Epub 2021 Jan 25. Nat Cancer. 2021. PMID: 34223192 Free PMC article.

8

Deep learning guided optimization of human antibody against SARS-CoV-2 variants with broad neutralization.

Shan S, Luo S, Yang Z, Hong J, Su Y, Ding F, Fu L, Li C, Chen P, Ma J, Shi X, Zhang Q, Berger B, Zhang L, Peng J. Shan S, et al. Among authors: ma j. Proc Natl Acad Sci U S A. 2022 Mar 15;119(11):e2122954119. doi: 10.1073/pnas.2122954119. Epub 2022 Mar 1. Proc Natl Acad Sci U S A. 2022. PMID: 35238654 Free PMC article.

9

Boosting single-cell gene regulatory network reconstruction via bulk-cell transcriptomic data.

Shu H, Ding F, Zhou J, Xue Y, Zhao D, Zeng J, Ma J. Shu H, et al. Among authors: ma j. Brief Bioinform. 2022 Sep 20;23(5):bbac389. doi: 10.1093/bib/bbac389. Brief Bioinform. 2022. PMID: 36070863

10

Modeling gene regulatory networks using neural network architectures.

Shu H, Zhou J, Lian Q, Li H, Zhao D, Zeng J, Ma J. Shu H, et al. Among authors: ma j. Nat Comput Sci. 2021 Jul;1(7):491-501. doi: 10.1038/s43588-021-00099-8. Epub 2021 Jul 22. Nat Comput Sci. 2021. PMID: 38217125

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