Publications

2019

  1. A Probabilistic Multi-Omics Data Matching Method for Detecting Sample Errors in Integrative Analysis, Lee, E., Yoo, S., Wang, W., Tu, Z., and Zhu, J.*, Gigascience, 8 (2019).
  2. Viral Integration Drives Multifocal Hcc During the Occult Hbv Infection, Chen, X. P., Long, X., Jia, W. L., Wu, H. J., Zhao, J., Liang, H. F., Laurence, A., Zhu, J., Dong, D., Chen, Y., Lin, L., Xia, Y. D., Li, W. Y., Li, G. B., Zhao, Z. K., Wu, K., Hou, Y., Yu, J. J., Xiao, W., Wang, G. P., Zhu, P. C., Chen, W., Bai, M. Z., Jian, Y. X., Kristiansen, K., and Chen, Q.,  J Exp Clin Cancer Res, 38 (2019), 261.
  3. Prostate Cancer in World Trade Center Responders Demonstrates Evidence of an Inflammatory Cascade, Gong, Y., Wang, L., Yu, H., Alpert, N., Cohen, M. D., Prophete, C., Horton, L., Sisco, M., Park, S. H., Lee, H. W., Zelikoff, J., Chen, L. C., Suarez-Farinas, M., Donovan, M. J., Aaronson, S. A., Galsky, M., Zhu, J., Taioli, E., and Oh, W. K., Mol Cancer Res (2019).
  4. Fibroblast Growth Factor Receptor 3 Alterations and Response to Pd-1/Pd-L1 Blockade in Patients with Metastatic Urothelial Cancer, Wang, L., Gong, Y., Saci, A., Szabo, P. M., Martini, A., Necchi, A., Siefker-Radtke, A., Pal, S., Plimack, E. R., Sfakianos, J. P., Bhardwaj, N., Horowitz, A., Farkas, A. M., Mulholland, D., Fischer, B. S., Oh, W. K., Sharma, P., Zhu, J.*, and Galsky, M. D.*,  Eur Urol (2019).
  5. Detecting Virus-Specific Effects on Post-Infection Temporal Gene Expression, Chen, Q., and Zhu, J*., BMC Bioinformatics,20 (2019), 129
  6. Gut Microbiota Density Influences Host Physiology and Is Shaped by Host and Microbial Factors, Contijoch, E. J., Britton, G. J., Yang, C., Mogno, I., Li, Z., Ng, R., Llewellyn, S. R., Hira, S., Johnson, C., Rabinowitz, K. M., Barkan, R., Dotan, I., Hirten, R. P., Fu, S. C., Luo, Y., Yang, N., Luong, T., Labrias, P. R., Lira, S., Peter, I., Grinspan, A., Clemente, J. C., Kosoy, R., Kim-Schulze, S., Qin, X., Castillo, A., Hurley, A., Atreja, A., Rogers, J., Fasihuddin, F., Saliaj, M., Nolan, A., Reyes-Mercedes, P., Rodriguez, C., Aly, S., Santa-Cruz, K., Peters, L., Suarez-Farinas, M., Huang, R., Hao, K.,Zhu, J., Zhang, B., Losic, B., Irizar, H., Song, W. M., Di Narzo, A., Wang, W., Cohen, B. L., DiMaio, C., Greenwald, D., Itzkowitz, S., Lucas, A., Marion, J., Maser, E., Ungaro, R., Naymagon, S., Novak, J., Shah, B., Ullman, T., Rubin, P., George, J., Legnani, P., Telesco, S. E., Friedman, J. R., Brodmerkel, C., Plevy, S., Cho, J. H., Colombel, J. F., Schadt, E. E., Argmann, C., Dubinsky, M., Kasarskis, A., Sands, B., and Faith, J. J., Elife, 8 (2019).
  7. The Polarity Protein Scrib Limits Atherosclerosis Development in Mice.  Schurmann, C., Dienst, F. L., Palfi, K., Vasconez, A. E., Oo, J. A., Wang, S., Buchmann, G. K., Offermanns, S., van de Sluis, B., Leisegang, M. S., Gunther, S., Humbert, P. O., Lee, E., Zhu, J., Weigert, A., Mathoor, P., Wittig, I., Kruse, C., and Brandes, R. P.,  Cardiovasc Res (2019).

2018

  1. EMT- and Stroma-Related Gene Expression and Resistance to Pd-1 Blockade in Urothelial Cancer, Wang, L., Saci, A., Szabo, P. M., Chasalow, S. D., Castillo-Martin, M., Domingo-Domenech, J., Siefker-Radtke, A., Sharma, P., Sfakianos, J. P., Gong, Y., Dominguez-Andres, A., Oh, W. K., Mulholland, D., Azrilevich, A., Hu, L., Cordon-Cardo, C., Salmon, H., Bhardwaj, N., Zhu, J.*, and Galsky, M. D.*,  Nat Commun, 9 (2018), 3503.
  2. Temporal Genetic Association and Temporal Genetic Causality Methods for Dissecting Complex Networks, Lin, L., Chen, Q., Hirsch, J. P., Yoo, S., Yeung, K., Bumgarner, R. E., Tu, Z., Schadt, E. E., and Zhu, J.*, , Nat Commun, 9 (2018), 3980.
  3. Identification of Micror-106b as a Prognostic Biomarker of P53-Like Bladder Cancers by ActMiR,  Lee, E., Collazo-Lorduy, A., Castillo-Martin, M., Gong, Y., Wang, L., Oh, W. K., Galsky, M. D., Cordon-Cardo, C., and Zhu, J.* Oncogene (2018)
    Press coverage by News Medical & Life Sciences,  Health Imaging, Fierce Biotech, Biotech Daily.
  4. Comparison of Glioblastoma (Gbm) Molecular Classification Methods,  Lee, E., Yong, R. L., Paddison, P., and Zhu, J.*,  Semin Cancer Biol (2018).
  5. Oxidized Phospholipids Regulate Amino Acid Metabolism through Mthfd2 to Facilitate Nucleotide Release in Endothelial Cells, Hitzel, J., Lee, E., Zhang, Y., Bibli, S. I., Li, X., Zukunft, S., Pfluger, B., Hu, J., Schurmann, C., Vasconez, A. E., Oo, J. A., Kratzer, A., Kumar, S., Rezende, F., Josipovic, I., Thomas, D., Giral, H., Schreiber, Y., Geisslinger, G., Fork, C., Yang, X., Sigala, F., Romanoski, C. E., Kroll, J., Jo, H., Landmesser, U., Lusis, A. J., Namgaladze, D., Fleming, I., Leisegang, M. S., Zhu, J.*, and Brandes, R. P.*,  Nat Commun, 9 (2018), 2292.   ***  Press coverage by Drug Target Review, Medical Xpress, Science Codex, Dotemirates, News Medical.
  6. A New Method for Constructing Tumor Specific Gene Co-Expression Networks Based on Samples with Tumor Purity Heterogeneity, Petralia, F., Wang, L., Peng, J., Yan, A., Zhu, J., and Wang, P.,  Bioinformatics, 34 (2018), i528-i36.
  7. Oncogenic Role of Sfrp2 in P53-Mutant Osteosarcoma Development Via Autocrine and Paracrine Mechanism, Kim, H., Yoo, S., Zhou, R., Xu, A., Bernitz, J. M., Yuan, Y., Gomes, A. M., Daniel, M. G., Su, J., Demicco, E. G., Zhu, J., Moore, K. A., Lee, D. F., Lemischka, I. R., and Schaniel, C.,  Proc Natl Acad Sci U S A (2018).
  8. Treatment-Associated Tp53 DNA-Binding Domain Missense Mutations in the Pathogenesis of Secondary Gliosarcoma, Pain, M., Wang, H., Lee, E., Strahl, M., Hamou, W., Sebra, R., Zhu, J., and Yong, R. L.,  Oncotarget, 9 (2018), 2603-21.


2017

  1. A Pilot Systematic Genomic Comparison of Recurrence Risks of Hepatitis B Virus-associated Hepatocellular Carcinoma with low and high degree of liver fibrosis,Yoo, S., Wang, W., Wang, Q., Fiel, MI., Lee, E., Hiotis, SP., and Zhu, J.*BMC Medicine  15 (2017), 214.
  2. Mir-500a-5p Regulates Oxidative Stress Response Genes in Breast Cancer and Predicts Cancer Survival, Degli Esposti, D., Aushev, V. N., Lee, E., Cros, M. P., Zhu, J., Herceg, Z., Chen, J., and Hernandez-Vargas, H., Sci Rep, 7 (2017), 15966.
  3. Novel predictors of breast cancer survival derived from miRNA activity analysis, Aushev, V., Lee, E., Zhu, J., Gopalakrishnan, K., Li, Q., Teitelbaum, S., Wetmur, J., Esposti, DD., Hernandez-Vargas, , Herceg, Z., Parada, H., Santella, R.,  Gammon, M., and Chen, J.  Clinical Cancer Res. (2017).
  4. Sensitivity to Bub1b Inhibition Defines an Alternative Classification of Glioblastoma, Lee, E., Pain, M., Wang, H., Herman, J. A., Toledo, C. M., DeLuca, J. G., Yong, R. L., Paddison, P., and Zhu, J.*, Cancer Res, 77 (2017), 5518-29.
  5. A Functional Genomics Predictive Network Model Identifies Regulators of Inflammatory Bowel Disease, Peters, L. A., Perrigoue, J., Mortha, A., Iuga, A., Song, W. M., Neiman, E. M., Llewellyn, S. R., Di Narzo, A., Kidd, B. A., Telesco, S. E., Zhao, Y., Stojmirovic, A., Sendecki, J., Shameer, K., Miotto, R., Losic, B., Shah, H., Lee, E., Wang, M., Faith, J. J., Kasarskis, A., Brodmerkel, C., Curran, M., Das, A., Friedman, J. R., Fukui, Y., Humphrey, M. B., Iritani, B. M., Sibinga, N., Tarrant, T. K., Argmann, C., Hao, K., Roussos, P., Zhu, J., Zhang, B., Dobrin, R., Mayer, L. F., and Schadt, E. E. , Nat Genet, 49 (2017), 1437-49.
  6. Multiscale Network Modeling of Oligodendrocytes Reveals Molecular Components of Myelin Dysregulation in Alzheimer’s Disease, McKenzie, A. T., Moyon, S., Wang, M., Katsyv, I., Song, W. M., Zhou, X., Dammer, E. B., Duong, D. M., Aaker, J., Zhao, Y., Beckmann, N., Wang, P., Zhu, J., Lah, J. J., Seyfried, N. T., Levey, A. I., Katsel, P., Haroutunian, V., Schadt, E. E., Popko, B., Casaccia, P., and Zhang, B., Mol Neurodegener, 12 (2017), 82.
  7. DNA Methylation Alters Transcriptional Rates of Differentially Expressed Genes and Contributes to Pathophysiology in Mice Fed a High Fat Diet, Zhang, P., Chu, T., Dedousis, N., Mantell, B. S., Sipula, I., Li, L., Bunce, K. D., Shaw, P. A., Katz, L. S., Zhu, J., Argmann, C., O’Doherty, R. M., Peters, D. G., and Scott, D. K., Mol Metab, 6 (2017), 327-39.
  8. Detect Differentially Methylated Regions Using Non-Homogeneous Hidden Markov Model for Methylation Array Data, Shen, L., Zhu, J., Robert Li, S. Y., and Fan, X.,, Bioinformatics (2017).
  9. Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy Pollak, J., Rai, K. G., Funk, C. C., Arora, S., Lee, E., Zhu, J., Price, N. D., Paddison, P. J., Ramirez, J. M., and Rostomily, R. C., PLoS One, 12 (2017), e0172884


2016

  1. Constructing Bayesian Networks by Integrating Gene Expression and Copy Number Data Identifies Nlgn4y as a Novel Regulator of Prostate Cancer Progression,  Gong, Y., Wang, L., Chippada-Venkata, U., Dai, X., Oh, W. K., and Zhu, J.*,  Oncotarget (2016).
  2. Disease-Specific Classification Using Deconvoluted Whole Blood Gene Expression,   Wang, L., Oh, W. K., and Zhu, J.*, Sci Rep, 6 (2016), 32976.
  3. Discover the Network Mechanisms Underlying the Connections between Aging and Age-Related Diseases, Yang, J., Huang, T., Song, W. M., Petralia, F., Mobbs, C. V., Zhang, B., Zhao, Y., Schadt, E. E., Zhu, J., and Tu, Z., Sci Rep, 6 (2016), 32566.
  4. Impact of Non-Neoplastic Vs Intratumoural Hepatitis B Viral DNA and Replication on Hepatocellular Carcinoma Recurrence, Wang, Q., Lin, L., Yoo, S., Wang, W., Blank, S., Fiel, M. I., Kadri, H., Luan, W., Warren, L., Zhu, J.*, and Hiotis, S. P.*, Br J Cancer, 115 (2016), 841-7.
  5. Meditation and Vacation Effects Have an Impact on Disease-Associated Molecular Phenotypes, Epel, E. S., Puterman, E., Lin, J., Blackburn, E. H., Lum, P. Y., Beckmann, N. D., Zhu, J., Lee, E., Gilbert, A., Rissman, R. A., Tanzi, R. E., and Schadt, E. E., Transl Psychiatry, 6 (2016), e880.
  6. Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia, Fromer, M., Roussos, P., Sieberts, S. K., Johnson, J. S., Kavanagh, D. H., Perumal, T. M., Ruderfer, D. M., Oh, E. C., Topol, A., Shah, H. R., Klei, L. L., Kramer, R., Pinto, D., Gumus, Z. H., Cicek, A. E., Dang, K. K., Browne, A., Lu, C., Xie, L., Readhead, B., Stahl, E. A., Xiao, J., Parvizi, M., Hamamsy, T., Fullard, J. F., Wang, Y. C., Mahajan, M. C., Derry, J. M., Dudley, J. T., Hemby, S. E., Logsdon, B. A., Talbot, K., Raj, T., Bennett, D. A., De Jager, P. L., Zhu, J., Zhang, B., Sullivan, P. F., Chess, A., Purcell, S. M., Shinobu, L. A., Mangravite, L. M., Toyoshiba, H., Gur, R. E., Hahn, C. G., Lewis, D. A., Haroutunian, V., Peters, M. A., Lipska, B. K., Buxbaum, J. D., Schadt, E. E., Hirai, K., Roeder, K., Brennand, K. J., Katsanis, N., Domenici, E., Devlin, B., and Sklar, P., Nat Neurosci (2016).
  7. Eprs Is a Critical Regulator of Cell Proliferation and Estrogen Signaling in Er+ Breast Cancer, Katsyv, I., Wang, M., Song, W. M., Zhou, X., Zhao, Y., Park, S., Zhu, J., Zhang, B., and Irie, H. Y., Oncotarget (2016).
  8. Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders, Meng, Q., Ying, Z., Noble, E., Zhao, Y., Agrawal, R., Mikhail, A., Zhuang, Y., Tyagi, E., Zhang, Q., Lee, J. H., Morselli, M., Orozco, L., Guo, W., Kilts, T. M., Zhu, J., Zhang, B., Pellegrini, M., Xiao, X., Young, M. F., Gomez-Pinilla, F., and Yang, X., EBioMedicine, 7 (2016), 157-66.
  9. Functional Characterization of DNA Methylation in the Oligodendrocyte Lineage, Moyon, S., Huynh, J. L., Dutta, D., Zhang, F., Ma, D., Yoo, S., Lawrence, R., Wegner, M., John, G. R., Emery, B., Lubetzki, C., Franklin, R. J., Fan, G., Zhu, J., Dupree, J. L., and Casaccia, P., Cell Rep (2016).
  10. Development and Clinical Application of an Integrative Genomic Approach to Personalized Cancer Therapy, Uzilov, A. V., Ding, W., Fink, M. Y., Antipin, Y., Brohl, A. S., Davis, C., Lau, C. Y., Pandya, C., Shah, H., Kasai, Y., Powell, J., Micchelli, M., Castellanos, R., Zhang, Z., Linderman, M., Kinoshita, Y., Zweig, M., Raustad, K., Cheung, K., Castillo, D., Wooten, M., Bourzgui, I., Newman, L. C., Deikus, G., Mathew, B., Zhu, J., Glicksberg, B. S., Moe, A. S., Liao, J., Edelmann, L., Dudley, J. T., Maki, R. G., Kasarskis, A., Holcombe, R. F., Mahajan, M., Hao, K., Reva, B., Longtine, J., Starcevic, D., Sebra, R., Donovan, M. J., Li, S., Schadt, E. E., and Chen, R., Genome Med , 8 (2016), 62.
  11. Urachal Carcinoma Shares Genomic Alterations with Colorectal Carcinoma and May Respond to Epidermal Growth Factor Inhibition,   Collazo-Lorduy, A., Castillo-Martin, M., Wang, L., Patel, V., Iyer, G., Jordan, E., Al-Ahmadie, H., Leonard, I., Oh, W. K., Zhu, J., McBride, R. B., Cordon-Cardo, C., Solit, D. B., Sfakianos, J. P., and Galsky, M. D.,  Eur Urol (2016).
  12. A 2-Gene Panel Derived from Prostate Cancer-Enhanced Transcripts in Whole Blood Is Prognostic for Survival and Predicts Treatment Benefit in Metastatic Castration-Resistant Prostate Cancer,   Heck, M. M., Thalgott, M., Schmid, S. C., Oh, W. K., Gong, Y., Wang, L., Zhu, J., Seitz, A. K., Porst, D., Hoppner, M., Retz, M., Gschwend, J. E., and Nawroth, R., Prostate (2016).
  13. Inter-Tissue Coexpression Network Analysis Reveals Dpp4 as an Important Gene in Heart to Blood Communication,   Long, Q., Argmann, C., Houten, S. M., Huang, T., Peng, S., Zhao, Y., Tu, Z., The GTEx Consortium, Zhu, J.*,Genome Med, 8 (2016), 15.
  14. Variants in Trim22 That Affect Nod2 Signaling Are Associated with Very Early Onset Inflammatory Bowel Disease , Li, Q., Lee, C. H., Peters, L. A., Mastropaolo, L. A., Thoeni, C., Elkadri, A., Schwerd, T., Zhu, J., Zhang, B., Zhao, Y., Hao, K., Dinarzo, A., Hoffman, G., Kidd, B. A., Murchie, R., Al Adham, Z., Guo, C., Kotlarz, D., Cutz, E., Walters, T. D., Shouval, D. S., Curran, M., Dobrin, R., Brodmerkel, C., Snapper, S. B., Klein, C., Brumell, J. H., Hu, M., Nanan, R., Snanter-Nanan, B., Wong, M., Le Deist, F., Haddad, E., Roifman, C. M., Deslandres, C., Griffiths, A. M., Gaskin, K. J., Uhlig, H. H., Schadt, E. E., and Muise, A. M.,  Gastroenterology (2016).
  15. A Next Generation Multiscale View of Inborn Errors of Metabolism, Argmann, C. A., Houten, S. M., Zhu, J., and Schadt, E. E.,  Cell Metab, 23 (2016), 13-26.


2015

  1. Genome-Wide Crispr-Cas9 Screens Reveal Loss of Redundancy between Pkmyt1 and Wee1 in Glioblastoma Stem-Like Cells, Toledo, C. M., Ding, Y., Hoellerbauer, P., Davis, R. J., Basom, R., Girard, E. J., Lee, E., Corrin, P., Hart, T., Bolouri, H., Davison, J., Zhang, Q., Hardcastle, J., Aronow, B. J., Plaisier, C. L., Baliga, N. S., Moffat, J., Lin, Q., Li, X. N., Nam, D. H., Lee, J., Pollard, S. M., Zhu, J., Delrow, J. J., Clurman, B. E., Olson, J. M., and Paddison, P. J., Cell Rep,13 (2015), 2425-39
  2. Targeting the Sin3a-Pf1 Interaction Inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer, Bansal, N., Petrie, K., Christova, R., Chung, C. Y., Leibovitch, B. A., Howell, L., Gil, V., Sbirkov, Y., Lee, E., Wexler, J., Ariztia, E. V., Sharma, R., Zhu, J., Bernstein, E., Zhou, M. M., Zelent, A., Farias, E., and Waxman, S., Oncotarget, 6 (2015), 34087-105.
  3. Synchronized Age-Related Gene Expression Changes across Multiple Tissues in Human and the Link to Complex Diseases, Yang, J., Huang, T., Petralia, F., Long, Q., Zhang, B., Argmann, C., Zhao, Y., Mobbs, C. V., Schadt, E. E., Zhu, J., Tu, Z., and The GTEx Consortium,  Sci Rep, 5 (2015), 15145
  4. Inferred Mirna Activity Identifies Mirna-Mediated Regulatory Networks Underlying Multiple Cancers, Lee, E., Ito, K., Zhao, Y., Schadt, E. E., Irie, H. Y., and Zhu, J.*,  Bioinformatics (2015).
  5. A Robust Blood Gene Expression-Based Prognostic Model for Castration-Resistant Prostate Cancer, Wang, L., Gong, Y., Chippada-Venkata, U., Heck, M. M., Retz, M., Nawroth, R., Galsky, M., Tsao, C. K., Schadt, E., de Bono, J., Olmos, D., Zhu, J.*, and Oh, W. K.*,  BMC Med, 13 (2015), 201.
  6. Characterization of Genetic Networks Associated with Alzheimer’s Disease, Zhang, B., Tran, L., Emilsson, V., and Zhu, J., , Methods Mol Biol, 1303 (2016), 459-77.
  7. Human genomics.The Genotype-Tissue Expression (Gtex) Pilot Analysis: Multitissue Gene Regulation in Humans, The GTEx Consortium , Science, 348 (2015), 648-60.
  8. Integrative Network Analysis Reveals Molecular Mechanisms of Blood Pressure Regulation, Huan, T., Meng, Q., Saleh, M. A., Norlander, A. E., Joehanes, R., Zhu, J., Chen, B. H., Zhang, B., Johnson, A. D., Ying, S., Courchesne, P., Raghavachari, N., Wang, R., Liu, P., O’Donnell, C. J., Vasan, R., Munson, P. J., Madhur, M. S., Harrison, D. G., Yang, X., and Levy, D.,  Mol Syst Biol, 11 (2015), 799
  9. Kras as a Predictor of Poor Prognosis and Benefit from Postoperative FOLFOX Chemotherapy in Patients with Stage II and III Colorectal Cancer,  Deng, Y., Wang, L., Tan, S., Kim, G. P., Dou, R., Chen, D., Cai, Y., Fu, X., Zhu, J., and Wang, J.,  Mol Oncol (2015)
  10. Molecular Portraits of Epithelial, Mesenchymal and Hybrid States in Lung Adenocarcinoma and Their Relevance to Survival, Schliekelman, M. J., Taguchi, A., Zhu, J., Dai, X., Rodriguez, J., Celiktas, M., Zhang, Q., Chin, A., Wong, C. H., Wang, H., McFerrin, L., Selamat, S. A., Yang, C., Kroh, E. M., Garg, K. S., Behrens, C., Gazdar, A. F., Laird-Offringa, I. A., Tewari, M., Wistuba, II, Thiery, J. P., and Hanash, S. M.,  Cancer Res (2015).
  11. A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits, Zhu, J*,  Chen, C, Yang, B, Guo, Y, Ai, H,  Ren, J,  Peng, Z, Tu, Z, Yang, X, Meng, Q, Friend, S, and Huang, L,  BMC Genomics (2015) 16:88 DOI 10.1186/s12864-015-1240-y
  12. Integrative Analysis of DNA Methylation and Gene Expression Data Identifies Epas1 as a Key Regulator of COPD, Yoo, S., Takikawa, S., Geraghty, P., Argmann, C., Campbell, J., Lin, L., Huang, T., Tu, Z., Feronjy, R., Spira, A., Schadt, E. E., Powell, C. A., and Zhu, J*, PLoS Genet, 11 (2015), e1004898


2014

  1. MODMatcher: Multi-Omics Data Matcher for Integrative Genomic Analysis,Yoo, S., Huang, T., Campbell, J. D., Lee, E., Tu, Z., Geraci, M. W., Powell, C. A., Schadt, E. E., Spira, A., and Zhu, J.*, ”, PLoS Comput Biol, 10 (2014), e1003790.
  2. Common Dysregulation Network in the Human Prefrontal Cortex Underlies Two Neurodegenerative Diseases, Narayanan, M., Huynh, J. L., Wang, K., Yang, X., Yoo, S., McElwee, J., Zhang, B., Zhang, C., Lamb, J. R., Xie, T., Suver, C., Molony, C., Melquist, S., Johnson, A. D., Fan, G., Stone, D. J., Schadt, E. E., Casaccia, P., Emilsson, V., and Zhu, J.*, Mol Syst Biol, 10 (2014), 743.
  3. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease, Makinen, V. P., Civelek, M., Meng, Q., Zhang, B., Zhu, J., Levian, C., Huan, T., Segre, A. V., Ghosh, S., Vivar, J., Nikpay, M., Stewart, A. F., Nelson, C. P., Willenborg, C., Erdmann, J., Blakenberg, S., O’Donnell, C. J., Marz, W., Laaksonen, R., Epstein, S. E., Kathiresan, S., Shah, S. H., Hazen, S. L., Reilly, M. P., Lusis, A. J., Samani, N. J., Schunkert, H., Quertermous, T., McPherson, R., Yang, X., and Assimes, T. L., PLoS Genet, 10 (2014), e1004502.
  4. Biomarkers for Bladder Cancer Management: Present and Future, Ye, F., Wang, L., Castillo-Martin, M., McBride, R., Galsky, M. D., Zhu, J., Boffetta, P., Zhang, D. Y., and Cordon-Cardo, C.,  Am J Clin Exp Urol, 2 (2014), 1-14.
  5. Epigenome-Wide Differences in Pathology-Free Regions of Multiple Sclerosis-Affected Brains, Huynh, J. L., Garg, P., Thin, T. H., Yoo, S., Dutta, R., Trapp, B. D., Haroutunian, V., Zhu, J., Donovan, M. J., Sharp, A. J., and Casaccia, P.,Nat Neurosci, 17 (2014), 121-30.


2013

  1.  Network-Based Differential Gene Expression Analysis Suggests Cell Cycle Related Genes Regulated by E2f1 Underlie the Molecular Difference between Smoker and Non-Smoker Lung Adenocarcinoma, Wu, C., Zhu, J.*, and Zhang, X., BMC Bioinformatics, 14 (2013), 365.
  2. Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease. Zhang, B., Gaiteri, C., Bodea, L. G., Wang, Z., McElwee, J., Podtelezhnikov, A. A., Zhang, C., Xie, T., Tran, L., Dobrin, R., Fluder, E., Clurman, B., Melquist, S., Narayanan, M., Suver, C., Shah, H., Mahajan, M., Gillis, T., Mysore, J., Macdonald, M. E., Lamb, J. R., Bennett, D. A., Molony, C., Stone, D. J., Gudnason, V., Myers, A. J., Schadt, E. E., Neumann, H.,Zhu, J., and Emilsson, V., Cell, 153 (2013), 707-20
  3. Modeling Causality for Pairs of Phenotypes in System Genetics. Neto, E. C., Broman, A. T., Keller, M. P., Attie, A. D., Zhang, B., Zhu, J., and Yandell, B. S. , Genetics, 193 (2013), 1003-13
  4. A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease. Huan, T., Zhang, B., Wang, Z., Joehanes, R., Zhu, J., Johnson, A. D., Ying, S., Munson, P. J., Raghavachari, N., Wang, R., Liu, P., Courchesne, P., Hwang, S. J., Assimes, T. L., McPherson, R., Samani, N. J., Schunkert, H., Meng, Q., Suver, C., O’Donnell, C. J., Derry, J., Yang, X., and Levy, D., Arterioscler Thromb Vasc Biol, 33 (2013), 1427-34
  5. An Ashkenazi Jewish Smn1 Haplotype Specific to Duplication Alleles Improves Pan-Ethnic Carrier Screening for Spinal Muscular Atrophy. Luo, M., Liu, L., Peter, I., Zhu, J., Scott, S. A., Zhao, G., Eversley, C., Kornreich, R., Desnick, R. J., and Edelmann, L.,  Genet Med (2013)


2012

  1. Integrative Analysis of a Cross-Loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets.  Tu Z, Keller MP, Zhang C, Rabaglia ME, Greenawalt DM, Yang X, Wang IM, Dai H, Bruss MD, Lum PY, Zhou Y-P, Kemp DM, Kendziorski C, Yandell BS, Attie AD, Schadt EE, Zhu J.*  PLoS Genet. 8(12):e1003107 (2012).
  2. 11 beta-HSD1 inhibition reduces atherosclerosis in mice by altering pro-inflammatory gene expression in the vasculature. Luo MJ, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, Plump A, Balkovec JM, Cheng K, Ding GJ, Kawka DW, Koo GC, Le Grand CB, Luo Q, Maletic MM, Malkowitz L, Shah K, Singer I, Waddell ST, Wu KK, Yuan J, Zhu J, Stepaniants S, Yang X, Lum PY, Wang IM. Physiol Genomics X Nov 20 (2012).
  3. Cancer-specific requirement for BUB1B/BubR1 in human brain tumor isolates and genetically transformed cells. Ding Y, Hubert CG, Herman J, Corrin P, Toledo CM, Skutt-Kakaria K, Vazquez J, Basom R, Zhang B, Risler JK, Pollard SM, Nam DH, Delrow JJ, Zhu J, Lee J, Deluca J, Olson JM, Paddison PJ.  Cancer Discovery Nov 15 (2012).
  4. Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. Wu C, Zhu J, Zhang X. BMC Bioinformatics. 2012 Jul 28;13(1):182
  5. Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics.Yang X, Zhang B, Zhu J.* Curr Drug Metab. 2012
  6. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY. BMC Syst Biol. 2012 Aug 16;6(1):101
  7. Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers. Wang IM, Zhang B, Yang X, Zhu J, Stepaniants S, Zhang C, Meng Q, Peters M, He Y, Ni C, Slipetz D, Crackower MA, Houshyar H, Tan CM, Asante-Appiah E, O’Neill G, Jane Luo M, Thieringer R, Yuan J, Chiu CS, Yee Lum P, Lamb J, Boie Y, Wilkinson HA, Schadt EE, Dai H, Roberts C. Mol Syst Biol. 2012 Jul 17;8:594
  8. Stitching together multiple data dimensions reveals interacting metabolomic and transcriptomic networks that modulate cell regulation. Zhu J*, Sova P, Xu Q, Dombek KM, Xu EY, Vu H, Tu Z, Brem RB, Bumgarner RE, Schadt EE. PLoS Biol. 2012;10(4):e1001301


2011

  1. Construction of regulatory networks using expression time-series data of a genotyped population. Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE.  Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19436-41
  2. Inferring causal genomic alterations in breast cancer using gene expression data. Tran LM, Zhang B, Zhang Z, Zhang C, Xie T, Lamb JR, Dai H, Schadt EE, Zhu J. BMC Syst Biol. 2011 Aug 1;5:121
  3. Predictive genes in adjacent normal tissue are preferentially altered by sCNV during tumorigenesis in liver cancer and may rate limiting. Lamb JR, Zhang C, Xie T, Wang K, Zhang B, Hao K, Chudin E, Fraser HB, Millstein J, Ferguson M, Suver C, Ivanovska I, Scott M, Philippar U, Bansal D, Zhang Z, Burchard J, Smith R, Greenawalt D, Cleary M, Derry J, Loboda A, Watters J, Poon RT, Fan ST, Yeung C, Lee NP, Guinney J, Molony C, Emilsson V, Buser-Doepner C, Zhu J, Friend S, Mao M, Shaw PM, Dai H, Luk JM, Schadt EE.  PLoS One. 2011;6(7):e20090. Epub 2011 Jul 5
  4. A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort. Greenawalt DM, Dobrin R, Chudin E, Hatoum IJ, Suver C, Beaulaurier J, Zhang B, Castro V, Zhu J, Sieberts SK, Wang S, Molony C, Heymsfield SB, Kemp DM, Reitman ML, Lum PY, Schadt EE, Kaplan LM.  Genome Res. 2011 Jul;21(7):1008-16
  5. Forkhead transcription factor foxq1 promotes epithelial-mesenchymal transition and breast cancer metastasis. Zhang H, Meng F, Liu G, Zhang B, Zhu J, Wu F, Ethier SP, Miller F, Wu G.  Cancer Res. 2011 Feb 15;71(4):1292-301
  6. Bayesian models for detecting epistatic interactions from genetic data. Zhang Y, Jiang B, Zhu J, Liu JS.  Ann Hum Genet. 2011 Jan;75(1):183-93


2010

  1. An integrative multi-network and multi-classifier approach to predict genetic interactions. Pandey G, Zhang B, Chang AN, Myers CL, Zhu J, Kumar V, Schadt EE. PLoS Comput Biol. 2010 Sep 9;6(9).
  2. Identification and validation of genes affecting aortic lesions in mice. Yang X, Peterson L, Thieringer R, Deignan JL, Wang X, Zhu J, Wang S, Zhong H, Stepaniants S, Beaulaurier J, Wang IM, Rosa R, Cumiskey AM, Luo JM, Luo Q, Shah K, Xiao J, Nickle D, Plump A, Schadt EE, Lusis AJ, Lum PY. J Clin Invest. 2010 Jul;120(7):2414-22
  3. Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver. Yang X, Zhang B, Molony C, Chudin E, Hao K, Zhu J, Gaedigk A, Suver C, Zhong H, Leeder JS, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich RG, Slatter JG, Schadt EE, Kasarskis A, Lum PY. Genome Res. 2010 Aug;20(8):1020-36
  4. Simultaneous clustering of multiple gene expression and physical interaction datasets. Narayanan M, Vetta A, Schadt EE, Zhu J. PLoS Comput Biol. 2010 Apr 15;6(4):e1000742
  5. Characterizing dynamic changes in the human blood transcriptional network. Zhu J, Chen Y, Leonardson AS, Wang K, Lamb JR, Emilsson V, Schadt EE.PLoS Comput Biol. 2010 Feb 12;6(2):e1000671
  6. A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. Zhang W, Zhu J, Schadt EE, Liu JS. PLoS Comput Biol. 2010 Jan 15;6(1):e1000642
  7. The effect of food intake on gene expression in human peripheral blood. Leonardson AS, Zhu J, Chen Y, Wang K, Lamb JR, Reitman M, Emilsson V, Schadt EE. Hum Mol Genet. 2010 Jan 1;19(1):159-69


2009

  1. Meta-analysis of inter-species liver co-expression networks elucidates traits associated with common human diseases. Wang K, Narayanan M, Zhong H, Tompa M, Schadt EE, Zhu J. PLoS Comput Biol. 2009 Dec;5(12):e1000616
  2. Ppargamma2 is a key driver of longevity in the mouse. Argmann C, Dobrin R, Heikkinen S, Auburtin A, Pouilly L, Cock TA, Koutnikova H, Zhu J, Schadt EE, Auwerx J. PLoS Genet. 2009 Dec;5(12):e1000752
  3. Disentangling molecular relationships with a causal inference test. Millstein J, Zhang B, Zhu J, Schadt EE. BMC Genet. 2009 May 27;10:23
  4. Multi-tissue coexpression networks reveal unexpected subnetworks associated with disease. Dobrin R, Zhu J, Molony C, Argman C, Parrish ML, Carlson S, Allan MF, Pomp D, Schadt EE. Genome Biol. 2009;10(5):R55
  5. Advances in systems biology are enhancing our understanding of disease and moving us closer to novel disease treatments. Schadt EE, Zhang B, Zhu J. Genetica. 2009 Jun;136(2):259-69
  6. Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks. Yang X, Deignan JL, Qi H, Zhu J, Qian S, Zhong J, Torosyan G, Majid S, Falkard B, Kleinhanz RR, Karlsson J, Castellani LW, Mumick S, Wang K, Xie T, Coon M, Zhang C, Estrada-Smith D, Farber CR, Wang SS, van Nas A, Ghazalpour A, Zhang B, Macneil DJ, Lamb JR, Dipple KM, Reitman ML, Mehrabian M, Lum PY, Schadt EE, Lusis AJ, Drake TA. Nat Genet. 2009 Apr;41(4):415-23
  7. Integrating siRNA and protein-protein interaction data to identify an expanded insulin signaling network. Tu Z, Argmann C, Wong KK, Mitnaul LJ, Edwards S, Sach IC, Zhu J, Schadt EE. Genome Res. 2009 Jun;19(6):1057-67.


2008

  1. Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Zhu J, Zhang B, Smith EN, Drees B, Brem RB, Kruglyak L, Bumgarner RE, Schadt EE. Nat Genet. 2008 Jul;40(7):854-61
  2. Mapping the genetic architecture of gene expression in human liver. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, GuhaThakurta D, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, Ulrich R. PLoS Biol. 2008 May 6;6(5):e107.
  3. A systems biology approach to drug discovery. Zhu J, Zhang B, Schadt EE. Adv Genet. 2008;60:603-35.
  4. Variations in DNA elucidate molecular networks that cause disease. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy MF, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE.  Nature. 2008 Mar 27;452(7186):429-35.
  5. Genetics of gene expression and its effect on disease. Emilsson V, Thorleifsson G, Zhang B, Leonardson AS, Zink F, Zhu J, Carlson S, Helgason A, Walters GB, Gunnarsdottir S, Mouy M, Steinthorsdottir V, Eiriksdottir GH, Bjornsdottir G, Reynisdottir I, Gudbjartsson D, Helgadottir A, Jonasdottir A, Jonasdottir A, Styrkarsdottir U, Gretarsdottir S, Magnusson KP, Stefansson H, Fossdal R, Kristjansson K, Gislason HG, Stefansson T, Leifsson BG, Thorsteinsdottir U, Lamb JR, Gulcher JR, Reitman ML, Kong A, Schadt EE, Stefansson K. Nature. 2008 Mar 27;452(7186):423-8.


2007

  1. Statistical power of phylo-HMM for evolutionarily conserved element detection. Fan X, Zhu J, Schadt EE, Liu JS.BMC Bioinformatics. 2007 Oct 5;8:374
  2. Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations. Zhu J, Wiener MC, Zhang C, Fridman A, Minch E, Lum PY, Sachs JR, Schadt EE. PLoS Comput Biol. 2007 Apr 13;3(4):e69


2006

  1. Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes. Lum PY, Chen Y, Zhu J, Lamb J, Melmed S, Wang S, Drake TA, Lusis AJ, Schadt EE. J Neurochem. 2006 Apr;97 Suppl 1:50-62


2005

  1. Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Cervino AC, Li G, Edwards S, Zhu J, Laurie C, Tokiwa G, Lum PY, Wang S, Castellani LW, Lusis AJ, Carlson S, Sachs AB, Schadt EE.Genomics. 2005 Nov;86(5):505-17
  2. An integrative genomics approach to infer causal associations between gene expression and disease. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D, Sieberts SK, Monks S, Reitman M, Zhang C, Lum PY, Leonardson A, Thieringer R, Metzger JM, Yang L, Castle J, Zhu H, Kash SF, Drake TA, Sachs A, Lusis AJ.Nat Genet. 2005 Jul;37(7):710-7.

2004

  1. An integrative genomics approach to the reconstruction of gene networks in segregating populations. Zhu J, Lum PY, Lamb J, GuhaThakurta D, Edwards SW, Thieringer R, Berger JP, Wu MS, Thompson J, Sachs AB, Schadt EE. Cytogenet Genome Res. 2004;105(2-4):363-74


Before 2000

  1. Database search based on Bayesian alignment. Zhu J, Luethy R, Lawrence CE.Proc Int Conf Intell Syst Mol Biol. 1999:297-305.
  2. Bayesian adaptive sequence alignment algorithms. Zhu J, Liu JS, Lawrence CE.Bioinformatics. 1998;14(1):25-39
  3. Bayesian adaptive alignment and inference. Zhu J, Liu J, Lawrence C.Proc Int Conf Intell Syst Mol Biol. 1997;5:358-68
  4. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. Zhu J, Penczek PA, Schroeder R, Frank J.J  Struct Biol. 1997 Apr;118(3):197-219.
  5. Three-dimensional reconstruction of the Escherichia coli 30 S ribosomal subunit in ice. Lata KR, Agrawal RK, Penczek P, Grassucci R, Zhu J, Frank J.J Mol Biol. 1996 Sep 13;262(1):43-52.
  6. A common-lines based method for determining orientations for N > 3 particle projections simultaneously. Penczek PA, Zhu J, Frank J.Ultramicroscopy. 1996 Jul;63(3-4):205-18.
  7. SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A.J Struct Biol. 1996 Jan-Feb;116(1):190-9.
  8. A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Frank J, Verschoor A, Li Y, Zhu J, Lata RK, Radermacher M, Penczek P, Grassucci R, Agrawal RK, Srivastava S.Biochem Cell Biol. 1995 Nov-Dec;73(11-12):757-65.
  9. A model of protein synthesis based on cryo-electron microscopy of the E. coli ribosome. Frank J, Zhu J, Penczek P, Li Y, Srivastava S, Verschoor A, Radermacher M, Grassucci R, Lata RK, Agrawal RK.Nature. 1995 Aug 3;376(6539):441-4