Jie Zhang
Jie Zhang
Medical & Molecular Genetics, School of Medicine, Indiana University
Verified email at iu.edu - Homepage
Title
Cited by
Cited by
Year
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 Comput Biol 9 (11), e1003326, 2013
2712013
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, ...
PLoS Comput Biol 8 (8), e1002656, 2012
752012
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
732002
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
712005
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
622012
Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia
J Zhang, Y Xiang, L Ding, TB Borlawsky, HG Ozer, R Jin, P Payne, ...
BMC bioinformatics 11 (S9), S5, 2010
522010
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
512013
Gene fusions with β-lactamase show that subunit I of the cytochrome bd quinol oxidase from E. coli has nine transmembrane helices with the O2 reactive site near the periplasmic†…
J Zhang, B Barquera, RB Gennis
FEBS letters 561 (1-3), 58-62, 2004
452004
Strong Excitonic Interactions in the Oxygen-Reducing Site of bd-Type Oxidase:  The Fe-to-Fe Distance between Hemes d and b595 is 10 Ň
AM Arutyunyan, VB Borisov, VI Novoderezhkin, J Ghaim, J Zhang, ...
Biochemistry 47 (6), 1752-1759, 2008
432008
FTIR Spectroscopic Evidence for the Involvement of an Acidic Residue in Quinone Binding in Cytochrome bd from Escherichia coli
J Zhang, W Oettmeier, RB Gennis, P Hellwig
Biochemistry 41 (14), 4612-4617, 2002
402002
Glutamate 107 in Subunit I of the Cytochrome bd Quinol Oxidase from Escherichia coli Is Protonated and near the Heme d/Heme b595 Binuclear Center
K Yang, J Zhang, AS Vakkasoglu, R Hielscher, JP Osborne, J Hemp, ...
Biochemistry 46 (11), 3270-3278, 2007
372007
Site-directed mutation of the highly conserved region near the Q-loop of the cytochrome bd quinol oxidase from Escherichia coli specifically perturbs heme b 595
J Zhang, P Hellwig, JP Osborne, H Huang, P MoŽnne-Loccoz, ...
Biochemistry 40 (29), 8548-8556, 2001
362001
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
352017
Heme–heme and heme–ligand interactions in the di-heme oxygen-reducing site of cytochrome bd from Escherichia coli revealed by nanosecond absorption spectroscopy
F Rappaport, J Zhang, MH Vos, RB Gennis, VB Borisov
Biochimica et Biophysica Acta (BBA)-Bioenergetics 1797 (9), 1657-1664, 2010
312010
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
302019
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), 1-14, 2017
302017
Fhit deficiency-induced global genome instability promotes mutation and clonal expansion
S Miuma, JC Saldivar, JR Karras, CE Waters, CA Paisie, Y Wang, V Jin, ...
PLoS One 8 (11), e80730, 2013
302013
Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development
J Zhang, J Parvin, K Huang
Bmc Genomics 13 (8), 1-10, 2012
302012
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
282016
Arginine 391 in subunit I of the cytochrome bd quinol oxidase from Escherichia coli stabilizes the reduced form of the hemes and is essential for quinol oxidase activity
J Zhang, P Hellwig, JP Osborne, RB Gennis
Journal of Biological Chemistry 279 (52), 53980-53987, 2004
262004
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