Publications

Trainees are underlined; * junior authors with equal contribution;  †senior authors with equal contribution

2024

  1. Zhu C, Tong T, Farrell JJ, Martin ER, Bush WS, Pericak-Vance MA, Wang L, Schellenberg GD, Haines JL, Lunetta KL, Farrer LA†, Zhang X†. MitoH3: Mitochondrial Haplogroup and Homoplasmic/Heteroplasmic Variant Calling Pipeline for Alzheimer’s Disease Sequencing Project. JAD Reports. (In press)
  2. Wang Y*, Huang J*, Ang TFA, Zhu Y, Tao Q, Mez J, Alosco M, Denis G, Belkina A, Gurnani A, Ross M, Gong B, Han J, Lunetta KL, Stern TD, Au R, Farrer LA, Zhang X†, Qiu W†. The Association between Circulating CD34+CD133+ Endothelial Progenitor Cells and Reduced Risk of Alzheimer’s Disease in the Framingham Heart Study. Exploration of Medicine. (In press)
  3. Rehman H, Ang TFA, Tao Q, Espenilla AL, Zhang X†, Qiu W†. Comparison of commonly measured plasma and cerebrospinal fluid proteins and their significance for the characterization of cognitive impairment status. Journal of Alzheimer’s Disease. 2024;97(2):621-633. PMID: 38143358

2023

  1. O’Neill N, Stein TD, Hu J, Rehman H, Campbell JD, Yajima M, Zhang X†, Farrer LA†. Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. BMC Bioinformatics. 2023 Sep 19;24(1):349. PMID: 37726653
  2. Puri S*, Hu J*, Sun Z, Lin M, Stern TD, Farrer LA, Wolozin B†, Zhang X†. Identification of circRNAs Linked to Alzheimer’s Disease and Related Dementias. Alzheimer’s & Dementia. 2023 Feb 16.  PMID: 36795937. (* equal contribution)
  3. Tao Q, Zhang C, Mercier G, Akhter-Khan S, Ang TFA, Zhang Z, Taylor A, Killiany R, Goldstein L, Alosco M, Mez J, Au R, Zhang X, Farrer LA, Qiu W. Identification of an APOE ε4-specific blood-based molecular pathway for Alzheimer’s Disease Risk. Alzheimers Dement (Amst). 2023 Oct 16;15(4):e12490.  PMID: 37854772

2022

  1. Huang J, Tao Q, Ang TFA, Farrell J, Zhu C, Wang Y, Stern TD, Lunetta KL, Massaro J, Mez J, Au R, Farrer LA, Qiu W†, Zhang X†. The impact of increasing levels of blood C-reactive protein on the inflammatory loci SPI1 and CD33 in Alzheimer’s disease. Transl Psychiatry. 2022 Dec 22;12(1):523. PMID: 36550123
  2. Huang J, Stern TD, Wang Y, Ang TFA, Tao Q, Lunetta KL, Massaro J, Akhter-Khan SC, Mez J, Au R, Farrer LA, Zhang X†, Qiu W†. Blood levels of MCP-1 modulate the genetic risks of Alzheimer’s disease mediated by HLA-DRB1 and APOE for Alzheimer’s disease. Alzheimer’s & Dementia. 2022 Nov 17. PMID: 36396603.
  3. Tao Q*, Akhter-Khan SC*, Ang TFA, DeCarli C, Alosco ML, Mez J, Killiany R, Devine S, Rokach A, Itchapurapu IS, Zhang X, Lunetta KL, Steffens DC, Farrer LA, Greve DN, Au R, Qiu W. Different loneliness types, cognitive function, and brain structure in midlife: Findings from the Framingham Heart Study. (EclinicalMedicine. 2022 Sep 6;53:101643, (* equal contribution) PMID: 36105871
  4. Chung J, Das A, Sun X, Sobreira DR, Leung YY, Iguarta C, Mozaffari S, Chou YF, Thiagalingam S, Mez J, Zhang X, Jun GR, Kunkle B, Martin ER, Pericak-Vance MA, Mayeux R, Haines JL, Schellenberg GD, No. brega MA, Lunetta KL, Pinto JM, Wang LS, Ober C, Farrer LA. Genome-wide association and multi-omics studies identify MGMT as a novel risk gene for Alzheimer’s disease among women. Alzheimer’s & Dementia. 2022 Jun 30;10.1002/alz.12719. PMID: 35770850
  5. Olayinka OA, O’Neill NK, Farrer LA, Wang G, Zhang X. Molecular Quantitative Trait Locus Mapping in Human Complex Diseases. Current Protocols. 2022 May;2(5):e426. PMID: 35587224
  6. Bellenguez C, Küçükali F, Iris Jansen I, …, the European Alzheimer’s Disease BioBank (EADB) consortium, …, Zhang X, …, Hiltunen M, Sleegers K, Schellenberg GD, van Duijn CM, Sims R, van der Flier WM, Ruiz A, Ramirez A, Lambert JC. New insights into the genetic etiology of Alzheimer’s disease and related dementia. Nat Genet. 2022 Apr;54(4):412-436. PMID: 35379992
  7. Zhang X†, Tong T, Andrew C, Ang TFA, Tao Q, Auerbach S, Devine S, Qiu W, Mez J, Massaro J, Lunetta KL, Au R and Farrer LA. Midlife lipid and glucose levels are associated with Alzheimer’s disease. Alzheimer’s & Dementia. 2022, Mar 23. PMID: 35319157 (†Corresponding author)

2021

  1. Zhang X†, van Rooij J, Wakabayashi Y, Hwang SH, Yang Y, Ghanbari M, Bos D, BIOS Consortium, Levy D, Johnson AD, van Meurs J, Kavousi M, Zhu J, O’Donnell CJ†. Genome-Wide Transcriptome Study using Deep RNA Sequencing for Myocardial Infarction and Coronary Artery Calcification. BMC Med Genomics. 2021 Feb 10; 14(1):45. PMID: 33568140 (†Co-corresponding authors)
  2. Patel D, Zhang X, Farrell JJ, Lunetta KL, Farrer LA. Set-Based Rare Variant Expression Quantitative Trait Loci Associated with Alzheimer Disease in Human Blood and Brain. Genes (Basel). 2021 Mar 15;12(3):419. PMID: 33804025
  3. Patel D, Zhang X, Farrell JJ, Chung J, Stein TD, Lunetta KL, and Farrer LA. Cell-type specific expression quantitative trait loci associated with Alzheimer disease in blood and brain tissue. Transl Psychiatry. 2021 Apr 27;11(1):250. PMID: 33907181
  4. Zhang X†, Farrell JJ, Tong T, Hu J, Zhu C, Alzheimer’s Disease Sequencing Project, Wang L, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Lunetta KL, Farrer LA. Association of Mitochondrial Variants and Haplogroups Identified by Whole Exome Sequencing with Alzheimer Disease. Alzheimer’s & Dementia. 2021 Jun 20. PMID: 34152079 (†Corresponding author)
  5. Tao Q, Ang TFA, Akhter-Khan SC, Itchapurapu IS, Killiany R, Zhang X, Kowall N, Budson AE, Turk KW, Goldstein L, Mez J, Alosco ML, Qiu W. Impact of C-reactive protein on cognition and the Alzheimer’s disease biomarkers in homozygous APOE &[epsilon]4 carriers. Neurology, 2021 Jul 15;97(12): e1243-e1252. PMID: 34266923
  6. Zhang Z, Na H, Gan Q, Tao Q, Alekseyev Y, Hu J, Yan Z, Yang J, Tian H, Zhu E, Li Q, Rajab IM, Blusztajn JK, Wolozin B, Emili A, Zhang X, Stein T, Potempa LA, Qiu W. Monomeric C-reactive protein via endothelial CD31 for neurovascular inflammation in an ApoE genotype dependent pattern: a risk factor for Alzheimer’s disease? Aging Cell. 2021 Oct 23; e13501. PMID: 34687487
  7. Castaneda AB, Petty LE, Scholz M, Jansen R, Weiss S, Zhang X, …, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Subclinical Working Group, Hofman A, Franco OH, Penninx BWJH, Prokisch H, Völzke H, Loeffler M, O’Donnell CJ, Below JE, Dehghan A, de Vries PS. Associations of carotid intima media thickness with gene expression in whole blood and genetically predicted gene expression across 48 tissues. Hum Mol Genet. 2021 Nov 12:ddab236. PMID: 34788810

    2019

    1. Patel D, Mez J, Vardarajan BN, Staley L, Chung J, Zhang X, Farrell JJ, Rynkiewicz MJ, Cannon-Albright LA, Teerlink CC, Stevens J, Corcoran C, Gonzalez Murcia JD, Lopez OL, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg G, Kauwe JSK, Lunetta KL, Farrer LA; Alzheimer’s Disease Sequencing Project. Association of Rare Coding Mutations with Alzheimer Disease and Other Dementias among Adults of European Ancestry. JAMA Netw Open. 2019 Mar 1;2(3):e191350, PMID: 30924900
    2. Ma Y, Jun GR, Chung J, Zhang X, Kunkle BW, Naj AC, White CC, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Farrer LA, Lunetta KL. CpG-related SNPs in the MS4A region have a dose-dependent effect on risk of late-onset Alzheimer disease. Aging Cell. 2019 May 29; e12964. PMID: 31144443.
    3. Ma Y, Jun GR, Zhang X, Chung J, Naj AC, Chen Y, Bellenguez C, Hamilton-Nelson K, Martin ER, Kunkle BW, Bis JC, Debette S, DeStefano AL, Fornage M, Nicolas G, van Duijn C, Bennett DA, De Jager PL, Mayeux R, Haines JL, Pericak-Vance MA, Seshadri S, Lambert JC, Schellenberg GD, Lunetta KL, Farrer LA. Analysis of Whole-Exome Sequencing Data for Alzheimer Disease Stratified by APOE Genotype. JAMA Neurol. 2019 Jun 10. PMID: 31180460.
    4. Malhotra, A.C. Mauer, X. Guo, J. Yao, X. Zhang, F. Wunderer, A.V. Smith, Q. Wong, S. Pechlivanis, S. Hwang, J. Wang, …, D.B. Bloch#, W. S. Post#,, and C.J. O’Donnell#,, for the CHARGE Extracoronary Calcium Working Group. HDAC9 is implicated in Atherosclerotic Aortic Calcification and Affects Vascular Smooth Muscle Cell Phenotype. Nat Genet. 2019 Nov;51(11):1580-1587. doi: 10.1038/s41588-019-0514-8. PMID: 31659325
    5. Guo C*, Zhao Z*, Chen D., He S., Sun N., Li Z., Liu J., Zhang D., Zhang J., Li J., Zhang M., Zhang X†, Fan Z†. Detection of clinically relevant genetic variants in Chinese patients with nanophthalmos by trio-based whole-genome sequencing study. Investigative Ophthalmology & Visual Science. July 2019, Vol.60, 2904-2913. doi:10.1167/iovs.18-26275, PMID: 31266062
    6. Zhu H, Tao Q, Ang TFA, Massaro J, Gan Q, Salim S, Zhu RY, Kolachalama VB, Zhang X, Devine S, Auerbach SH, DeCarli C, Au R, Qiu WQ. Association of Plasma Amylin Concentration with Alzheimer Disease and Brain Structure in Older Adults. JAMA Netw Open. 2019 Aug 2;2(8):e199826. PMID: 31433485
    7. Choi KY, Lee JJ, Gunasekaran T, …, Zhang X, Zhu C, …, Farrer LA, Lee KH, Neuroimaging Initative AD. APOE Promoter Polymorphism-219T/G is an Effect Modifier of the Influence of APOE ε4 on Alzheimer’s Disease Risk in a Multiracial Sample. Journal of Clinical Medicine. 2019 Aug 16;8(8). pii: E1236. PMID: 31426376

    2018

    1. Hwang S, Onuma O, Massaro JM, Zhang X, Fu Y, Hoffmann U, Fox CS, O’Donnell CJ. Maintenance of Ideal Cardiovascular Health and Coronary Artery Calcium Progression in Low-Risk Men and Women in the Framingham Heart Study. Circulation:Cardiovascular Imaging, 2018;11:e006209. PMID: 29305347
    2. Chung J., Zhang X., Allen M., Wang X., Ma Y., Beecham G., Montine TJ., Younkin SG., Dickson DW., Golde TE., Price ND., Ertekin-Taner N., Lunetta KL., Mez J., Alzheimer’s Disease Genetics Consortium, Mayeux R., Haines J., Pericak-Vance M., Schellenberg G., Jun G., Farrer LA. Genome-wide Pleiotropy Analysis of Neuropathological Traits Related to Alzheimer Disease. Alzheimer’s Research & Therapy, 2018;10:22. PMID: 29458411
    3. Zhang X, Frame AA, Williams JS, Wainford RD. GNAI2 polymorphic variance associates with salt sensitivity of blood pressure in the Genetic Epidemiology Network of Salt Sensitivity Study. Physiol Genomics. 2018 Sep 1;50(9):724-725. PMID: 29906209
    4. Bis JC*, Jian X*, Kunkle BW*, Chen Y*, Hamilton-Nelson KL, …, Zhang X; Alzheimer’s Disease Sequencing Project, Bellenguez C, Lambert JC, Kurki MI, Palotie A, Daly M, Boerwinkle E, Lunetta KL, Destefano AL, Dupuis J, Martin ER, Schellenberg GD, Seshadri S, Naj A**, Fornage M**, Farrer LA**. Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry. 2018 Aug 14. PMID: 30108311
    5. Cox JW*, Patel D*, Chung J., Lent S., Fisher V., Pitsillides A., Farrer L., Zhang X. An Efficient Analytic Approach in Genome-wide Identification of DNA Methylation Quantitative Trait Loci Response to Fenofibrate Treatment. BMC Proceedings. 2018 Volume 12 (Suppl 9) :44. PMID: 30275893 PMCID: PMC6157188 .
    6. Abdolmaleky HM, Gower AC, Wong CK, Cox JW, Zhang X, Thiagalingam A, Shafa R, Sivaraman V, Zhou JR, Thiagalingam S. Aberrant transcriptomes and DNA methylomes define pathways that drive pathogenesis and loss of brain laterality/asymmetry in schizophrenia and bipolar disorder. Am J Med Genet B Neuropsychiatr Genet. 2019 Mar;180(2):138-149. PMID: 30468562
    7. Zhang X., Zhu C, Beecham G, Vardarajan BN, Ma Y, Lancour D, Farrell JJ, Chung J; Alzheimer’s Disease Sequencing Project, Mayeux R, Haines JL, Schellenberg GD, Pericak-Vance MA, Lunetta KL, Farrer L. A rare missense variant of CASP7 is associated with familial late-onset Alzheimer’s disease. Alzheimers Dement. 2019 Mar;15(3):441-452. PMID: 30503768
    8. Franceschini N, Giambartolomei C, de Vries PS, Finan C, Bis JC, …, Zhang X, Guo X, Saba Y; MEGASTROKE Consortium, Dehghan A, Seldenrijk A, Morrison AC, Hamsten A, Psaty BM, van Duijn CM, Lawlor DA, Mook-Kanamori DO, Bowden DW, Schmidt H, Wilson JF, Wilson JG, Rotter JI, Wardlaw JM, Deanfield J, Halcox J, Lyytikäinen LP, Loeffler M, Evans MK, Debette S, Humphries SE, Völker U, Gudnason V, Hingorani AD, Björkegren JLM, Casas JP, O’Donnell CJ. GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes. Nat Commun. 2018 Dec 3;9(1):5141. PMID: 30510157
    9. Tao Q, Ang TFA, DeCarli C, Auerbach SH, Devine S, Stein TD, Zhang X, Massaro J, Au R, Qiu WQ. Association of Chronic Low-grade Inflammation with Risk of Alzheimer Disease in ApoE4 Carriers. JAMA Netw Open. 2018 Oct 5;1(6):e183597. PMID: 30646251

        2017

        1. R. Warren, J.F. O’Sullivan, M. Friesen1, C.E. Becker, X. Zhang, Y. Wakabayashi, J.E. Morningstar, X. Shi, J. Choi, F. Xia, D.T. Peters, M.H.C. Florido, J. Shay, K. Musunuru, S. Kathiresan, L. Daheron, J. Zhu, R.E. Gerszten, R. Deo, V. Ramachandran, C. J. O’Donnell, and C.A. Cowan. Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease. Cell Stem Cell. 2017 Apr 6;20(4):547-557. PMID: 28388431
        2. Joehanes, R*., Zhang, X*., Huan, T., Yao, C., Ying, S., …, C.J. O’Donnell, P. J. Munson, D. Levy. Integrated Genome-wide Analysis of Expression Quantitative Trait Loci Identifies Putative Disease-Related Genes and Pathways. Genome Biology 2017 Jan 25;18(1):16. PMID: 28122634 (* equal contribution)
        3. Chung J., Wang X., Maruyama T., Ma Y., Zhang X., Mez J., Sherva R., Takeyama H., The Alzheimer’s Disease Neuroimaging Initiative*, Lunetta K.L., Farrer L.A., and Jun G.R. Genome-Wide Association Study of Alzheimer Disease Endophenotypes at Preclinical and MCI Stages. Alzheimers Dement. 2017 Dec 20. pii: S1552-5260(17)33842-6. PMID: 29274321

        2016

        1. M. Polfus, R.K. Khajuria, U.M. Schick, N. Pankratz, R. Pazoki, J.A. Brody, M.H. Chen, P.L. Auer, J.S. Floyd, J. Huang, L. Lange, F.J. van Rooij, R.A. Gibbs, G. Metcalf, D. Muzny, N. Veeraraghavan, K. Walter, L. Chen, L. Yanek, L.C. Becker, G.M. Peloso, A. Wakabayashi, M. Kals, A. Metspalu, T. Esko, K. Fox, R. Wallace, N. Franceshini, N. Matijevic, K.M. Rice, T.M. Bartz, L.P. Lyytikäinen, M. Kähönen, T. Lehtimäki, O.T. Raitakari, R. Li-Gao, D.O. Mook-Kanamori, G. Lettre, C.M. van Duijn, O.H. Franco, S.S. Rich, F. Rivadeneira, A. Hofman, A.G. Uitterlinden, J.G. Wilson, B.M. Psaty, N. Soranzo, A. Dehghan, E. Boerwinkle, X. Zhang, A.D. Johnson, C.J. O’Donnell, J.M. Johnsen, A.P. Reiner, S.K. Ganesh, V.G. Sankaran. Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis. American Journal Human Genetics. 2016 Aug 4;99(2):481-8. doi: 10.1016/j.ajhg.2016.06.016.  PMID: 27486782
        2. Pankratz, U.M. Schick, Y. Zhou, W. Zhou, …, X. Zhang, …. CHARGE Consortium Hematology Working Group. Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nature Genetics. 2016 Aug;48(8):867-76. doi: 10.1038/ng.3607. PMID: 27399967

        2015

        1. Huan, T., Liu, C., Joehanes, R., Zhang, X., Chen, B.H., Yao, C., Johnson, A. D., Munson, P. J., Courchesne, P., O’Donnell, C. J. & Levy, D. (2015). A Systematic Analysis of Heritability of the Whole Blood Transcriptome. Human Genetics. 134(3):343-58 PMCID: PMC4339826
        2. Yao, C., Chen, B.H., Joehanes, R., Zhang, X., Liu, C., Huan, T., Cupples, L.A., Meigs, J. B., Fox, C.S., Freedman, J.E., Courchesne, P., O’Donnell, C.J., Munson, P.J. & Levy, D. (2015). Integromic Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes. Circulation. 31(6):536-49. PMID: 25533967
        3. Zhang, X*., Joehanes, R*., Chen, B. H., Huan, T., Ying, S., Munson, P.J., Johnson, A.D., Levy, D., O’Donnell, C.J. (2015). Identification of common genetic variants controlling transcript isoform variation in human whole blood. Nature Genetics. 2015 Apr;47(4):345-52. PMID: 25685889 (* equal contribution)
        4. Huan, T., Rong, J., Liu, C., Zhang, X., Tanriverdi, K., Joehanes, R., Chen, B.H., Murabito, J.M., Yao, C., Courchesne, P., Munson, P. J., O’Donnell, C.J., Cox, N., Johnson, A.D., Larson, M. G., Levy, D., Freedman, J. E. (2015) Genome-wide Identification of microRNA expression quantitative trait loci. Nature Communication. 2015 Mar 20;6:6601.  PMCID: PMC4369777

        2014

        1. Zhang, X., Johnson, A.D. & O’Donnell, C.J. (2014). Genome-Wide Genetic Analysis of Expression for Genes Implicated in GWAS Studies for Atherosclerotic Cardiovascular Disease and Blood Phenotypes. Human Molecular Genetics. PMCID: PMC3900869
        2. Bis, J.C., White, C., Franceschini, N., Brody, J., Zhang, X., Muzny, D., Santibanez, J., Gibbs, R., Liu, X., Lin, H., Boerwinkle, E., Psaty, B., North, K., Cupples, A. & O’Donnell, C.J. (2014). Sequencing of Two Subclinical Atherosclerosis Candidate Regions in 3,669 Individuals: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study. Circulation: Cardivascular Genetics. 2014 Jun;7(3):359-64. PMCID: PMC4112104
        3. Zhang, X., Gierman, H.J., Levy, D., Plump, A., Dobrin, R., Goring, H.H., Curran, J. E, Johnson, M. P., Blangero, J., Kim, S. K., O’Donnell, C. J., Emilsson, V. & Johnson, A. D. (2014) Synthesis of 53 tissue and cell line expression QTL datasets reveals master eQTLs. BMC Genomics. PMCID: PMC4102726
        4. Gottlieb, D.J., Hek, K., Chen, T., Watson, N.F., Eiriksdottir, G., …, Zhang, X., …, Völzke, H., Mignot, E., Tiemeier, H. (2014). Novel loci associated with usual sleep duration: The CHARGE Consortium genomewide association study. Molecular Psychiatry. Dec 2. 2014.133. PMID: 25469926

        Before 2013

        1. Zhang, X. †, Lenburg, M. & Spira, A. (2013). Comparison of Nasal Epithelial Smoking-induced Gene Expression on Affymetrix Exon 1.0 and Gene 1.0 ST Arrays. The Scientific World Journal’s special issue of “Advances in Computational Genomics”, Volume 2013. PMCID: PMC3588192 (†Corresponding author)
        2. Quinton, L.J., Blahna, M.T., Jones MR, Allen E, Ferrari JD, Hilliard KL, Zhang, X, Sabharwal V, Algül H, Akira S, Schmid RM, Pelton SI, Spira A, Mizgerd JP. Hepatocyte-specific mutation of NF-kB RelA and STAT3 abrogates the acute phase response in mice. J Clin Invest. 2012 May;122(5):1758-63. PMCID: PMC3336975, PMID: 22466650
        3. Zhang, X†, Sebastiani, P., Liu, G., Schembri, F., Zhang, X., Dumas, Y., Langer, E., Alekseyev, Y., O’Connor, G., Brooks, D., Lenburg, M. & Spira, A†. (2010), Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiol Genomics. 41(1): 1–8. PMID: 19952278 PMCID:  PMC2841495 (†Co-corresponding authors)
        4. Yu, L., Coelho, J., Zhang, X., Fu, Y., Tillman, A., Karaoz, U., Fredholm, B.B., Weng, Z., Chen, J.F.. (2009), Uncovering multiple molecular targets for caffeine by a drug target validation strategy of combined A2A receptor knockouts and microarray profiling. Physiol Genomics. PMCID: PMC2685498
        5. Schembri, F., Sridhar, S., Perdomo, C., Gustafson, A.M., Zhang, X., Ergun, A., Lu, J., Liu, G., Zhang, X., Bowers, J., Sensinger, K., Collins, J., Brody, J., Getts, R., Lenburg, M. & Spira, A. (2009). MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A. 106(7):2319-24, PMCID: PMC2650144
        6. Zhang, X., Liu, G, Lenburg, M. & Spira, A. (2007) Comparison of Smoking-induced Gene Expression on Affymetrix Exon and 3’ based Expression Arrays. Genome Informatics.18:247-57, PMID: 18546492
        7. ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, …, Zhang X, …, Zhu B, de Jong PJ. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146):799-816. PMCID: PMC2212820

        Before 2004 (pursuing M.S. in Computer Science)

        1. Pei, J†. Zhang, X., Cho, M., Wang, H & Yu, P.S. (2003). MaPle: A Fast Algorithm for Maximal Pattern-based Clustering (Full paper). In Proceedings of the Third IEEE International Conference on Data Mining (ICDM’03), USA, DOI: 10.1109/ICDM.2003.1250928 (†supervisor & senior author)

            Textbook Chapters:

            1. Jian Pei, Xiaoling Zhang, Moonjung Cho, Haixun Wang, and Philip S.Yu. Data Mining for Business Applications (2009). (ISBN: 978-0-387-79419-8 e-ISBN: 978-0-387-79420-4)

            Chapter 3. On Mining Maximal Pattern-Based Clusters . . . . . . . . . . . . . . . . . . . . . 31-52