Jie Zhang
Jie Zhang
Medical & Molecular Genetics, School of Medicine, Indiana University
Verified email at - Homepage
Cited by
Cited by
Practical guidelines for the comprehensive analysis of ChIP-seq data
T Bailey, P Krajewski, I Ladunga, C Lefebvre, Q Li, T Liu, P Madrigal, ...
PLoS computational biology 9 (11), e1003326, 2013
MOGONET integrates multi-omics data using graph convolutional networks allowing patient classification and biomarker identification
T Wang, W Shao, Z Huang, H Tang, J Zhang, Z Ding, K Huang
Nature communications 12 (1), 3445, 2021
SALMON: survival analysis learning with multi-omics neural networks on breast cancer
Z Huang, X Zhan, S Xiang, TS Johnson, B Helm, CY Yu, J Zhang, ...
Frontiers in genetics 10, 166, 2019
Integrative analysis of histopathological images and genomic data predicts clear cell renal cell carcinoma prognosis
J Cheng, J Zhang, Y Han, X Wang, X Ye, Y Meng, A Parwani, Z Han, ...
Cancer research 77 (21), e91-e100, 2017
BERMUDA: a novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes
T Wang, TS Johnson, W Shao, Z Lu, BR Helm, J Zhang, K Huang
Genome biology 20, 1-15, 2019
Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site
I Belevich, VB Borisov, J Zhang, K Yang, AA Konstantinov, RB Gennis, ...
Proceedings of the National Academy of Sciences 102 (10), 3657-3662, 2005
Weighted frequent gene co-expression network mining to identify genes involved in genome stability
J Zhang, K Lu, Y Xiang, M Islam, S Kotian, Z Kais, C Lee, M Arora, H Liu, ...
Public Library of Science 8 (8), e1002656, 2012
Interactions between Heme d and Heme b595 in Quinol Oxidase bd from Escherichia coli: A Photoselection Study Using Femtosecond Spectroscopy
VB Borisov, U Liebl, F Rappaport, JL Martin, J Zhang, RB Gennis, ...
Biochemistry 41 (5), 1654-1662, 2002
Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes
H Liu, J Zhang, GF Heine, M Arora, H Gulcin Ozer, R Onti-Srinivasan, ...
Nucleic acids research 40 (20), 10172-10186, 2012
Deep-learning–based characterization of tumor-infiltrating lymphocytes in breast cancers from histopathology images and multiomics data
Z Lu, S Xu, W Shao, Y Wu, J Zhang, Z Han, Q Feng, K Huang
JCO clinical cancer informatics 4, 480-490, 2020
Deep learning-based cancer survival prognosis from RNA-seq data: approaches and evaluations
Z Huang, TS Johnson, Z Han, B Helm, S Cao, C Zhang, P Salama, ...
BMC medical genomics 13, 1-12, 2020
Analysis of BRCA1 variants in double‐strand break repair by homologous recombination and single‐strand annealing
WI Towler, J Zhang, DJR Ransburgh, AE Toland, C Ishioka, N Chiba, ...
Human mutation 34 (3), 439-445, 2013
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia
J Zhang, Y Xiang, L Ding, K Keen-Circle, TB Borlawsky, HG Ozer, R Jin, ...
BMC bioinformatics 11, 1-9, 2010
Integrative analysis of pathological images and multi-dimensional genomic data for early-stage cancer prognosis
W Shao, Z Han, J Cheng, L Cheng, T Wang, L Sun, Z Lu, J Zhang, ...
IEEE transactions on medical imaging 39 (1), 99-110, 2019
Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11. 2 translocation renal cell carcinoma
J Cheng, Z Han, R Mehra, W Shao, M Cheng, Q Feng, D Ni, K Huang, ...
Nature communications 11 (1), 1778, 2020
Visceral adipose microRNA 223 is upregulated in human and murine obesity and modulates the inflammatory phenotype of macrophages
JA Deiuliis, R Syed, D Duggineni, J Rutsky, P Rengasamy, J Zhang, ...
PloS one 11 (11), e0165962, 2016
Strong Excitonic Interactions in the Oxygen-Reducing Site of bd-Type Oxidase:  The Fe-to-Fe Distance between Hemes d and b595 is 10
AM Arutyunyan, VB Borisov, VI Novoderezhkin, J Ghaim, J Zhang, ...
Biochemistry 47 (6), 1752-1759, 2008
Pan-cancer analysis of frequent DNA co-methylation patterns reveals consistent epigenetic landscape changes in multiple cancers
J Zhang, K Huang
Bmc Genomics 18, 1-14, 2017
Multi-task multi-modal learning for joint diagnosis and prognosis of human cancers
W Shao, T Wang, L Sun, T Dong, Z Han, Z Huang, J Zhang, D Zhang, ...
Medical image analysis 65, 101795, 2020
Normalized imqcm: An algorithm for detecting weak quasi-cliques in weighted graph with applications in gene co-expression module discovery in cancers
J Zhang, K Huang
Cancer informatics 13, CIN. S14021, 2014
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