Jie Zhang

  • 697 Citations
  • 16 h-Index
20012019
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Publications 2001 2019

  • 697 Citations
  • 16 h-Index
  • 38 Article
  • 4 Conference contribution
  • 1 Comment/debate
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Article
2019

BERMUDA: A novel deep transfer learning method for single-cell RNA sequencing batch correction reveals hidden high-resolution cellular subtypes

Wang, T., Johnson, T. S., Shao, W., Lu, Z., Helm, B. R., Zhang, J. & Huang, K., Aug 12 2019, In : Genome Biology. 20, 1, 165.

Research output: Contribution to journalArticle

Open Access
RNA Sequence Analysis
RNA
learning
sequence analysis
cells

Generalized gene co-expression analysis via subspace clustering using low-rank representation

Wang, T., Zhang, J. & Huang, K., May 1 2019, In : BMC Bioinformatics. 20, 196.

Research output: Contribution to journalArticle

Open Access
Subspace Clustering
Cluster Analysis
Genes
Gene
Gene Expression
1 Citation (Scopus)

Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients' survival time

Han, Y., Ye, X., Cheng, J., Zhang, S., Feng, W., Han, Z., Zhang, J. & Huang, K., Feb 13 2019, In : Biology Direct. 14, 1, 4.

Research output: Contribution to journalArticle

Open Access
Gene Regulatory Networks
Survival Time
Neuroblastoma
Gene expression
Gene Expression
1 Citation (Scopus)

Salmon: Survival analysis learning with multi-omics neural networks on breast cancer

Huang, Z., Zhan, X., Xiang, S., Johnson, T. S., Helm, B., Yu, C. Y., Zhang, J., Salama, P., Rizkalla, M., Han, Z. & Huang, K., Jan 1 2019, In : Frontiers in Genetics. 10, MAR, 166.

Research output: Contribution to journalArticle

Open Access
Salmon
Survival Analysis
Learning
Breast Neoplasms
Gene Expression
2018
1 Citation (Scopus)

Chromatin-associated APC regulates gene expression in collaboration with canonical WNT signaling and AP-1

Hankey, W., Chen, Z., Bergman, M. J., Fernandez, M. O., Hancioglu, B., Lan, X., Jegga, A. G., Zhang, J., Jin, V. X., Aronow, B. J., Wang, Q. & Groden, J., Jul 27 2018, In : Oncotarget. 9, 58, p. 31214-31230 17 p.

Research output: Contribution to journalArticle

APC Genes
Transcription Factor AP-1
Chromatin
Gene Expression
Adenoma
2 Citations (Scopus)

Condition-specific gene co-expression network mining identifies key pathways and regulators in the brain tissue of Alzheimer's disease patients

Xiang, S., Huang, Z., Wang, T., Han, Z., Yu, C. Y., Ni, D., Huang, K. & Zhang, J., Dec 31 2018, In : BMC Medical Genomics. 11, 115.

Research output: Contribution to journalArticle

Open Access
Alzheimer Disease
Gene Expression
Brain
Transcription Factors
Virus Diseases
3 Citations (Scopus)

Mutational mechanisms that activate wnt signaling and predict outcomes in colorectal cancer patients

Hankey, W., McIlhatton, M. A., Ebede, K., Kennedy, B., Hancioglu, B., Zhang, J., Brock, G. N., Huang, K. & Groden, J., Feb 1 2018, In : Cancer Research. 78, 3, p. 617-630 14 p.

Research output: Contribution to journalArticle

Colorectal Neoplasms
Adenoma
Mutation
Colon
Gene Expression
2017
4 Citations (Scopus)

Classification of Indeterminate Melanocytic Lesions by MicroRNA Profiling

Latchana, N., del Campo, S. E. M., Grignol, V. P., Clark, J. R., Albert, S. P., Zhang, J., Wei, L., Aldrink, J. H., Nicol, K. K., Ranalli, M. A., Peters, S. B., Gru, A., Trihka, P., Payne, P. R. O., Howard, J. H. & Carson, W. E., Feb 1 2017, In : Annals of Surgical Oncology. 24, 2, p. 347-354 8 p.

Research output: Contribution to journalArticle

MicroRNAs
Neoplasms
Epithelioid and Spindle Cell Nevus
Unnecessary Procedures
Nevus
4 Citations (Scopus)

Functional Virtual Flow Cytometry: A Visual Analytic Approach for Characterizing Single-Cell Gene Expression Patterns

Han, Z., Johnson, T., Zhang, J., Zhang, X. & Huang, K., Jan 1 2017, In : BioMed Research International. 2017, 3035481.

Research output: Contribution to journalArticle

Flow cytometry
Gene expression
Flow Cytometry
Genes
Workflow
6 Citations (Scopus)

Integrative analysis of histopathological images and genomic data predicts clear cell renal cell carcinoma prognosis

Cheng, J., Zhang, J., Han, Y., Wang, X., Ye, X., Meng, Y., Parwani, A., Han, Z., Feng, Q. & Huang, K., Nov 1 2017, In : Cancer Research. 77, 21, p. e91-e100

Research output: Contribution to journalArticle

Renal Cell Carcinoma
Neoplasms
Genomics
Survival
Workflow
15 Citations (Scopus)
DNA Methylation
Epigenomics
Neoplasms
Methylation
Gene Silencing
2016
7 Citations (Scopus)

A matrix rank based concordance index for evaluating and detecting conditional specific co-expressed gene modules

Han, Z., Zhang, J., Sun, G., Liu, G. & Huang, K., Aug 22 2016, In : BMC Genomics. 17, 519.

Research output: Contribution to journalArticle

Gene Regulatory Networks
Gene Expression
Gene Fusion
Computational Biology
Genes
11 Citations (Scopus)

Exome-wide single-base substitutions in tissues and derived cell lines of the constitutive Fhit knockout mouse

Paisie, C. A., Schrock, M. S., Karras, J. R., Zhang, J., Miuma, S., Ouda, I. M., Waters, C. E., Saldivar, J. C., Druck, T. & Huebner, K., Apr 1 2016, In : Cancer Science. 107, 4, p. 528-535 8 p.

Research output: Contribution to journalArticle

Exome
Knockout Mice
Cell Line
Mutation
Genome
7 Citations (Scopus)

Fhit loss-associated initiation and progression of neoplasia in vitro

Karras, J. R., Schrock, M. S., Batar, B., Zhang, J., La Perle, K., Druck, T. & Huebner, K., Nov 1 2016, In : Cancer Science. 107, 11, p. 1590-1598 9 p.

Research output: Contribution to journalArticle

Cell Line
Neoplastic Processes
Neoplasms
Proteins
Gene Rearrangement
5 Citations (Scopus)

Integrative analysis of somatic mutations and transcriptomic data to functionally stratify breast cancer patients

Zhang, J., Abrams, Z., Parvin, J. D. & Huang, K., Aug 22 2016, In : BMC Genomics. 17, 513.

Research output: Contribution to journalArticle

Breast Neoplasms
Mutation
Biomarkers
Transcriptome
Genes
16 Citations (Scopus)

Visceral adipose MicroRNA 223 is upregulated in human and murine obesity and modulates the inflammatory phenotype of macrophages

Deiuliis, J. A., Syed, R., Duggineni, D., Rutsky, J., Rengasamy, P., Zhang, J., Huang, K., Needleman, B., Mikami, D., Perry, K., Hazey, J. & Rajagopalan, S., Nov 1 2016, In : PLoS One. 11, 11, e0165962.

Research output: Contribution to journalArticle

Macrophages
Toll-Like Receptor 4
MicroRNAs
microRNA
macrophages
2013
28 Citations (Scopus)

Analysis of BRCA1 Variants in Double-Strand Break Repair by Homologous Recombination and Single-Strand Annealing

Towler, W. I., Zhang, J., Ransburgh, D. J. R., Toland, A. E., Ishioka, C., Chiba, N. & Parvin, J. D., Mar 1 2013, In : Human Mutation. 34, 3, p. 439-445 7 p.

Research output: Contribution to journalArticle

Recombinational DNA Repair
Genetic Recombination
DNA Repair
BRCA1 Gene
Genetic Counseling
22 Citations (Scopus)

Fhit deficiency-induced global genome instability promotes mutation and clonal expansion

Miuma, S., Saldivar, J. C., Karras, J. R., Waters, C. E., Paisie, C. A., Wang, Y., Jin, V., Sun, J., Druck, T., Zhang, J. & Huebner, K., Nov 14 2013, In : PLoS One. 8, 11, e80730.

Research output: Contribution to journalArticle

Genomic Instability
Fibroblasts
Genes
mutation
Mutation
5 Citations (Scopus)

Gene co-expression analysis predicts genetic aberration loci associated with colon cancer metastasis

Zhang, J., Ni, S., Xiang, Y., Parvin, J. D., Yang, Y., Zhou, Y. & Huang, K., Mar 5 2013, In : International Journal of Computational Biology and Drug Design. 6, 1-2, p. 60-71 12 p.

Research output: Contribution to journalArticle

Genetic Loci
Aberrations
Colonic Neoplasms
Genes
Neoplasm Metastasis
6 Citations (Scopus)

Mining the tissue-tissue gene co-expression network for tumor microenvironment study and biomarker prediction

Xiang, Y., Zhang, J. & Huang, K., Jan 1 2013, In : BMC Genomics. 14, S4.

Research output: Contribution to journalArticle

Tumor Microenvironment
Tumor Biomarkers
Gene Expression
Breast Neoplasms
Neoplasms
97 Citations (Scopus)

Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data

Bailey, T., Krajewski, P., Ladunga, I., Lefebvre, C., Li, Q., Liu, T., Madrigal, P., Taslim, C. & Zhang, J., Nov 1 2013, In : PLoS Computational Biology. 9, 11, e1003326.

Research output: Contribution to journalArticle

Encyclopedias
DNA
Chip
Workflow
Guidelines
2012
42 Citations (Scopus)

Chromatin modification by SUMO-1 stimulates the promoters of translation machinery genes

Liu, H. W., Zhang, J., Heine, G. F., Arora, M., Gulcin Ozer, H., Onti-Srinivasan, R., Huang, K. & Parvin, J. D., Nov 1 2012, In : Nucleic Acids Research. 40, 20, p. 10172-10186 15 p.

Research output: Contribution to journalArticle

Ubiquitin
Chromatin
Genes
Sumoylation
Ribosome Subunits
4 Citations (Scopus)

Promoters active in interphase are bookmarked during mitosis by ubiquitination

Arora, M., Zhang, J., Heine, G. F., Ozer, G., Liu, H. W., Huang, K. & Parvin, J. D., Nov 1 2012, In : Nucleic Acids Research. 40, 20, p. 10187-10202 16 p.

Research output: Contribution to journalArticle

Ubiquitination
Interphase
Mitosis
Chromatin
Histone Code
16 Citations (Scopus)

Redistribution of H3K4me2 on neural tissue specific genes during mouse brain development.

Zhang, J., Parvin, J. & Huang, K., Dec 1 2012, In : BMC Genomics. 13 Suppl 8, S5.

Research output: Contribution to journalArticle

Brain
Genes
Embryonic Stem Cells
Cell Differentiation
Body Regions
48 Citations (Scopus)

Weighted Frequent Gene Co-expression Network Mining to Identify Genes Involved in Genome Stability

Zhang, J., Lu, K., Xiang, Y., Islam, M., Kotian, S., Kais, Z., Lee, C., Arora, M., Liu, H. W., Parvin, J. D. & Huang, K., Aug 1 2012, In : PLoS Computational Biology. 8, 8, e1002656.

Research output: Contribution to journalArticle

Genomic Instability
Mining
cancer
Genome
genome
2011
12 Citations (Scopus)

Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: Translational systems approach to modeling human parturition

Li, R., Ackerman, W. E., Summerfield, T. L., Yu, L., Gulati, P., Zhang, J., Huang, K., Romero, R. & Kniss, D. A., Jun 9 2011, In : PLoS One. 6, 6, e20560.

Research output: Contribution to journalArticle

amnion
Amnion
Gene Regulatory Networks
Systems Analysis
Extraembryonic Membranes
2010
22 Citations (Scopus)

Heme-heme and heme-ligand interactions in the di-heme oxygen-reducing site of cytochrome bd from Escherichia coli revealed by nanosecond absorption spectroscopy

Rappaport, F., Zhang, J., Vos, M. H., Gennis, R. B. & Borisov, V. B., Sep 1 2010, In : Biochimica et Biophysica Acta - Bioenergetics. 1797, 9, p. 1657-1664 8 p.

Research output: Contribution to journalArticle

Carbon Monoxide
Cytochromes
Heme
Absorption spectroscopy
Escherichia coli
7 Citations (Scopus)

Multi-dimensional discovery of biomarker and phenotype complexes

Payne, P. R. O., Huang, K., Keen-Circle, K., Kundu, A., Zhang, J. & Borlawsky, T. B., Oct 28 2010, In : BMC Bioinformatics. 11, SUPPL. 9, S3.

Research output: Contribution to journalArticle

Biomarkers
Phenotype
Granularity
Literature
Genes
38 Citations (Scopus)

Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia

Zhang, J., Xiang, Y., Ding, L., Keen-Circle, K., Borlawsky, T. B., Ozer, H. G., Jin, R., Payne, P. & Huang, K., Oct 28 2010, In : BMC Bioinformatics. 11, SUPPL. 9, S5.

Research output: Contribution to journalArticle

Leukemia
Biomarkers
Network Analysis
B-Cell Chronic Lymphocytic Leukemia
Electric network analysis
2008
28 Citations (Scopus)

Strong excitonic interactions in the oxygen-reducing site of bd-type oxidase: The Fe-to-Fe distance between hemes d and b595 is 10 Å

Arutyunyan, A. M., Borisov, V. B., Novoderezhkin, V. I., Ghaim, J., Zhang, J., Gennis, R. B. & Konstantinov, A. A., Feb 12 2008, In : Biochemistry. 47, 6, p. 1752-1759 8 p.

Research output: Contribution to journalArticle

Oxidoreductases
Dithionite
Oxygen
Circular Dichroism
Cytochromes
2007
23 Citations (Scopus)

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

Yang, K., Zhang, J., Vakkasoglu, A. S., Hielscher, R., Osborne, J. P., Hemp, J., Miyoshi, H., Hellwig, P. & Gennis, R. B., Mar 20 2007, In : Biochemistry. 46, 11, p. 3270-3278 9 p.

Research output: Contribution to journalArticle

Cytochromes
Escherichia coli
Protons
Glutamic Acid
Catalytic Domain
2005
46 Citations (Scopus)

Time-resolved electrometric and optical studies on cytochrome bd suggest a mechanism of electron-proton coupling in the di-heme active site

Belevich, I., Borisov, V. B., Zhang, J., Yang, K., Konstantinov, A. A., Gennis, R. B. & Verkhovsky, M. I., Mar 8 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 10, p. 3657-3662 6 p.

Research output: Contribution to journalArticle

Cytochromes
Heme
Protons
Catalytic Domain
Electrons
2004
17 Citations (Scopus)

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

Zhang, J., Hellwig, P., Osborne, J. P. & Gennis, R. B., Dec 24 2004, In : Journal of Biological Chemistry. 279, 52, p. 53980-53987 8 p.

Research output: Contribution to journalArticle

Cytochromes
Heme
Escherichia coli
Arginine
Oxidoreductases
33 Citations (Scopus)
Gene Fusion
Escherichia coli
Catalytic Domain
Oxidoreductases
Fusion reactions
3 Citations (Scopus)

Proton NMR study of the heme environment in bacterial quinol oxidases

Zhang, J., Osborne, J. P., Gennis, R. B. & Wang, X., Jan 15 2004, In : Archives of Biochemistry and Biophysics. 421, 2, p. 186-191 6 p.

Research output: Contribution to journalArticle

Heme
Protons
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Cyanides
2002
25 Citations (Scopus)

FTIR spectroscopic evidence for the involvement of an acidic residue in quinone binding in cytochrome bd from Escherichia coli

Zhang, J., Oettmeier, W., Gennis, R. B. & Hellwig, P., Apr 9 2002, In : Biochemistry. 41, 14, p. 4612-4617 6 p.

Research output: Contribution to journalArticle

Fourier Transform Infrared Spectroscopy
Cytochromes
Escherichia coli
Binding Sites
Oxidation-Reduction
52 Citations (Scopus)

Interactions between heme d and heme b595 in quinol oxidase bd from Escherichia coli: A photoselection study using femtosecond spectroscopy

Borisov, V. B., Liebl, U., Rappaport, F., Martin, J. L., Zhang, J., Gennis, R. B., Konstantinov, A. A. & Vos, M. H., Feb 5 2002, In : Biochemistry. 41, 5, p. 1654-1662 9 p.

Research output: Contribution to journalArticle

Carbon Monoxide
Escherichia coli
Spectrum Analysis
Spectroscopy
Cytochromes
2001
26 Citations (Scopus)

Site-directed mutation of the highly conserved region near the Q-loop of the cytochrome bd quinol oxidase from Escherichia coli specifically perturbs heme b595

Zhang, J., Hellwig, P., Osborne, J. P., Huang, H. W., Moënne-Loccoz, P., Konstantinov, A. A. & Gennis, R. B., Jul 24 2001, In : Biochemistry. 40, 29, p. 8548-8556 9 p.

Research output: Contribution to journalArticle

Cytochromes
Heme
Escherichia coli
Mutation
Prosthetics