Bing Zhang, Ph.D.

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Publications

The following timeline graph is generated from all co-authored publications.

1. Integrative Omics Analysis Reveals Post-Transcriptionally Enhanced Protective Host Response in Colorectal Cancers with Microsatellite Instability. Liu Q, Zhang B (2016) J Proteome Res 15(3): 766-76
   › Primary publication · 26680540 (PubMed) · PMC4782175 (PubMed Central)
2. proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data. Wang X, Slebos RJ, Chambers MC, Tabb DL, Liebler DC, Zhang B (2016) Mol Cell Proteomics 15(3): 1164-75
   › Primary publication · 26657539 (PubMed) · PMC4813696 (PubMed Central)
3. Global gene expression profiling reveals a suppressed immune response pathway associated with 3q amplification in squamous carcinoma of the lung. Qian J, Zou Y, Wang J, Zhang B, Massion PP (2015) Genom Data : 272-4
   › Primary publication · 26484266 (PubMed) · PMC4583673 (PubMed Central)
4. Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL (2015) J Proteome Res 14(12): 5318-26
   › Primary publication · 26483142 (PubMed)
5. Calcium/magnesium intake ratio, but not magnesium intake, interacts with genetic polymorphism in relation to colorectal neoplasia in a two-phase study. Zhu X, Shrubsole MJ, Ness RM, Hibler EA, Cai Q, Long J, Chen Z, Li G, Jiang M, Hou L, Kabagambe EK, Zhang B, Smalley WE, Edwards TL, Giovannucci EL, Zheng W, Dai Q (2016) Mol Carcinog 55(10): 1449-57
   › Primary publication · 26333203 (PubMed) · PMC4775445 (PubMed Central)
6. Biogenesis, delivery, and function of extracellular RNA. Patton JG, Franklin JL, Weaver AM, Vickers K, Zhang B, Coffey RJ, Ansel KM, Blelloch R, Goga A, Huang B, L'Etoille N, Raffai RL, Lai CP, Krichevsky AM, Mateescu B, Greiner VJ, Hunter C, Voinnet O, McManus MT (2015) J Extracell Vesicles : 27494
   › Primary publication · 26320939 (PubMed) · PMC4553266 (PubMed Central)
7. Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics. Hu Z, Scott HS, Qin G, Zheng G, Chu X, Xie L, Adelson DL, Oftedal BE, Venugopal P, Babic M, Hahn CN, Zhang B, Wang X, Li N, Wei C (2015) Sci Rep : 10940
   › Primary publication · 26156868 (PubMed) · PMC4496727 (PubMed Central)
8. KRAS-dependent sorting of miRNA to exosomes. Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG (2015) Elife : e07197
   › Primary publication · 26132860 (PubMed) · PMC4510696 (PubMed Central)
9. Activation of the Endogenous Renin-Angiotensin-Aldosterone System or Aldosterone Administration Increases Urinary Exosomal Sodium Channel Excretion. Qi Y, Wang X, Rose KL, MacDonald WH, Zhang B, Schey KL, Luther JM (2016) J Am Soc Nephrol 27(2): 646-56
   › Primary publication · 26113616 (PubMed) · PMC4731116 (PubMed Central)
10. Proteomic analysis of colon and rectal carcinoma using standard and customized databases. Slebos RJ, Wang X, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC (2015) Sci Data : 150022
    › Primary publication · 26110064 (PubMed) · PMC4477697 (PubMed Central)
11. Linking patient outcome to high throughput protein expression data identifies novel regulators of colorectal adenocarcinoma aggressiveness. French CL, Ye F, Revetta F, Zhang B, Coffey RJ, Washington MK, Deane NG, Beauchamp RD, Weaver AM (2015) F1000Res : 99
    › Primary publication · 26097693 (PubMed) · PMC4457132 (PubMed Central)
12. Identification of HPV integration and gene mutation in HeLa cell line by integrated analysis of RNA-Seq and MS/MS data. Sun H, Chen C, Lian B, Zhang M, Wang X, Zhang B, Li Y, Yang P, Xie L (2015) J Proteome Res 14(4): 1678-86
    › Primary publication · 25698088 (PubMed)
13. Empowering biologists with multi-omics data: colorectal cancer as a paradigm. Zhu J, Shi Z, Wang J, Zhang B (2015) Bioinformatics 31(9): 1436-43
    › Primary publication · 25527095 (PubMed) · PMC4410657 (PubMed Central)
14. Nuclear factor of activated T-cell activity is associated with metastatic capacity in colon cancer. Tripathi MK, Deane NG, Zhu J, An H, Mima S, Wang X, Padmanabhan S, Shi Z, Prodduturi N, Ciombor KK, Chen X, Washington MK, Zhang B, Beauchamp RD (2014) Cancer Res 74(23): 6947-57
    › Primary publication · 25320007 (PubMed) · PMC4252979 (PubMed Central)
15. Leveraging the complementary nature of RNA-Seq and shotgun proteomics data. Wang X, Liu Q, Zhang B (2014) Proteomics 14(23-24): 2676-87
    › Primary publication · 25266668 (PubMed) · PMC4270470 (PubMed Central)
16. Calcium intake and ion transporter genetic polymorphisms interact in human colorectal neoplasia risk in a 2-phase study. Zhu X, Liang J, Shrubsole MJ, Ness RM, Cai Q, Long J, Chen Z, Li G, Wiese D, Zhang B, Smalley WE, Edwards TL, Giovannucci E, Zheng W, Dai Q (2014) J Nutr 144(11): 1734-41
    › Primary publication · 25165391 (PubMed) · PMC4195417 (PubMed Central)
17. Proteogenomic characterization of human colon and rectal cancer. Zhang B, Wang J, Wang X, Zhu J, Liu Q, Shi Z, Chambers MC, Zimmerman LJ, Shaddox KF, Kim S, Davies SR, Wang S, Wang P, Kinsinger CR, Rivers RC, Rodriguez H, Townsend RR, Ellis MJ, Carr SA, Tabb DL, Coffey RJ, Slebos RJ, Liebler DC, NCI CPTAC (2014) Nature 513(7518): 382-7
    › Primary publication · 25043054 (PubMed) · PMC4249766 (PubMed Central)
18. Integrating genomic, transcriptomic, and interactome data to improve Peptide and protein identification in shotgun proteomics. Wang X, Zhang B (2014) J Proteome Res 13(6): 2715-23
    › Primary publication · 24792918 (PubMed) · PMC4059263 (PubMed Central)
19. An open-source analytical platform for analysis of C. elegans swimming-induced paralysis. Hardaway JA, Wang J, Fleming PA, Fleming KA, Whitaker SM, Nackenoff A, Snarrenberg CL, Hardie SL, Zhang B, Blakely RD (2014) J Neurosci Methods : 58-62
    › Primary publication · 24792527 (PubMed) · PMC4179448 (PubMed Central)
20. Quantitative trait loci mapping and gene network analysis implicate protocadherin-15 as a determinant of brain serotonin transporter expression. Ye R, Carneiro AM, Han Q, Airey D, Sanders-Bush E, Zhang B, Lu L, Williams R, Blakely RD (2014) Genes Brain Behav 13(3): 261-75
    › Primary publication · 24405699 (PubMed) · PMC4436591 (PubMed Central)
21. Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis. Zhu J, Wang J, Shi Z, Franklin JL, Deane NG, Coffey RJ, Beauchamp RD, Zhang B (2013) PLoS One 8(11): e79282
    › Primary publication · 24260186 (PubMed) · PMC3829853 (PubMed Central)
22. Evaluation of heritable determinants of blood and brain serotonin homeostasis using recombinant inbred mice. Ye R, Carneiro AM, Airey D, Sanders-Bush E, Williams RW, Lu L, Wang J, Zhang B, Blakely RD (2014) Genes Brain Behav 13(3): 247-60
    › Primary publication · 24102824 (PubMed) · PMC3979832 (PubMed Central)
23. customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search. Wang X, Zhang B (2013) Bioinformatics 29(24): 3235-7
    › Primary publication · 24058055 (PubMed) · PMC3842753 (PubMed Central)
24. NetGestalt: integrating multidimensional omics data over biological networks. Shi Z, Wang J, Zhang B (2013) Nat Methods 10(7): 597-8
    › Primary publication · 23807191 (PubMed) · PMC3951100 (PubMed Central)
25. WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013. Wang J, Duncan D, Shi Z, Zhang B (2013) Nucleic Acids Res 41(Web Server issue): W77-83
    › Primary publication · 23703215 (PubMed) · PMC3692109 (PubMed Central)
26. Integrative omics analysis reveals the importance and scope of translational repression in microRNA-mediated regulation. Liu Q, Halvey PJ, Shyr Y, Slebos RJ, Liebler DC, Zhang B (2013) Mol Cell Proteomics 12(7): 1900-11
    › Primary publication · 23550052 (PubMed) · PMC3708174 (PubMed Central)
27. A network-based gene expression signature informs prognosis and treatment for colorectal cancer patients. Shi M, Beauchamp RD, Zhang B (2012) PLoS One 7(7): e41292
    › Primary publication · 22844451 (PubMed) · PMC3402487 (PubMed Central)
28. Protein identification using customized protein sequence databases derived from RNA-Seq data. Wang X, Slebos RJ, Wang D, Halvey PJ, Tabb DL, Liebler DC, Zhang B (2012) J Proteome Res 11(2): 1009-17
    › Primary publication · 22103967 (PubMed) · PMC3727138 (PubMed Central)
29. Semi-supervised learning improves gene expression-based prediction of cancer recurrence. Shi M, Zhang B (2011) Bioinformatics 27(21): 3017-23
    › Primary publication · 21893520 (PubMed) · PMC3198572 (PubMed Central)
30. Relating protein adduction to gene expression changes: a systems approach. Zhang B, Shi Z, Duncan DT, Prodduturi N, Marnett LJ, Liebler DC (2011) Mol Biosyst 7(7): 2118-27
    › Primary publication · 21594272 (PubMed) · PMC3659419 (PubMed Central)
31. A bioinformatics workflow for variant peptide detection in shotgun proteomics. Li J, Su Z, Ma ZQ, Slebos RJ, Halvey P, Tabb DL, Liebler DC, Pao W, Zhang B (2011) Mol Cell Proteomics 10(5): M110.006536
    › Primary publication · 21389108 (PubMed) · PMC3098595 (PubMed Central)
32. Network-assisted protein identification and data interpretation in shotgun proteomics. Li J, Zimmerman LJ, Park BH, Tabb DL, Liebler DC, Zhang B (2009) Mol Syst Biol : 303
    › Primary publication · 19690572 (PubMed) · PMC2736651 (PubMed Central)
33. Proteomic parsimony through bipartite graph analysis improves accuracy and transparency. Zhang B, Chambers MC, Tabb DL (2007) J Proteome Res 6(9): 3549-57
    › Primary publication · 17676885 (PubMed) · PMC2810678 (PubMed Central)

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