Jie Zhang

  • 802 Citations
  • 17 h-Index
20012019

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Publications

  • 802 Citations
  • 17 h-Index
  • 42 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
8 Scopus citations

Correlation analysis of histopathology and proteogenomics data for breast cancer

Zhan, X., Cheng, J., Huang, Z., Han, Z., Helm, B., Liu, X., Zhang, J., Wang, T. F., Ni, D. & Huang, K., Jan 1 2019, In : Molecular and Cellular Proteomics. 18, 8, p. S37-S51

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Gene co-expression networks restructured gene fusion in rhabdomyosarcoma cancers

Helm, B. R., Zhan, X., Pandya, P. H., Murray, M. E., Pollok, K. E., Renbarger, J. L., Ferguson, M. J., Han, Z., Ni, D., Zhang, J. & Huang, K., Sep 2019, In : Genes. 10, 9, 665.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

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

Integration of molecular features with clinical information for predicting outcomes for neuroblastoma patients

Han, Y., Ye, X., Wang, C., Liu, Y., Zhang, S., Feng, W., Huang, K. & Zhang, J., Aug 23 2019, In : Biology Direct. 14, 1, 16.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

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
2 Scopus citations

LAmbDA: Label ambiguous domain adaptation dataset integration reduces batch effects and improves subtype detection

Johnson, T. S., Wang, T., Huang, Z., Yu, C. Y., Wu, Y., Han, Y., Zhang, Y., Huang, K., Zhang, J. & Berger, B., Nov 1 2019, In : Bioinformatics. 35, 22, p. 4696-4706 11 p.

Research output: Contribution to journalArticle

3 Scopus citations

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., 2019, In : Frontiers in Genetics. 10, MAR, 166.

Research output: Contribution to journalArticle

Open Access
9 Scopus citations
2018

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

2 Scopus citations

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
4 Scopus citations

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

4 Scopus citations
2017

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

6 Scopus citations

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

4 Scopus citations

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

17 Scopus citations
17 Scopus citations
2016

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

7 Scopus citations

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

11 Scopus citations

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

7 Scopus citations

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

6 Scopus citations

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 2016, In : PloS one. 11, 11, e0165962.

Research output: Contribution to journalArticle

22 Scopus citations
2013

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

29 Scopus citations

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

22 Scopus citations

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., 2013, In : International Journal of Computational Biology and Drug Design. 6, 1-2, p. 60-71 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

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

9 Scopus citations

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 2013, In : PLoS computational biology. 9, 11, e1003326.

Research output: Contribution to journalArticle

120 Scopus citations
2012

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 2012, In : Nucleic acids research. 40, 20, p. 10172-10186 15 p.

Research output: Contribution to journalArticle

43 Scopus citations

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 2012, In : Nucleic acids research. 40, 20, p. 10187-10202 16 p.

Research output: Contribution to journalArticle

6 Scopus citations

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

Zhang, J., Parvin, J. & Huang, K., 2012, In : Unknown Journal. 13 Suppl 8

Research output: Contribution to journalArticle

Open Access
18 Scopus citations

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 2012, In : PLoS computational biology. 8, 8, e1002656.

Research output: Contribution to journalArticle

50 Scopus citations
2011

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., 2011, In : PloS one. 6, 6, e20560.

Research output: Contribution to journalArticle

12 Scopus citations
2010

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

24 Scopus citations

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

8 Scopus citations

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

40 Scopus citations
2008

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

30 Scopus citations
2007

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

25 Scopus citations
2005

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

51 Scopus citations
2004

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

19 Scopus citations
33 Scopus citations

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

3 Scopus citations
2002

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

25 Scopus citations

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

54 Scopus citations
2001

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

27 Scopus citations