Zhengdong Zhang, Ph.D.

  • Source: Scopus
  • Calculated based on no. of publications stored in Pure and citations from Scopus
20002021

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Search results

  • A brief introduction to tiling microarrays: Principles, concepts, and applications

    Lemetre, C. & Zhang, Z. D., 2013, Tiling Arrays: Methods and Protocols. Lee, T-L. & Luk, A. C. S. (eds.). p. 3-19 17 p. (Methods in Molecular Biology; vol. 1067).

    Research output: Chapter in Book/Report/Conference proceedingChapter

    2 Scopus citations
  • ACT: Aggregation and correlation toolbox for analyses of genome tracks

    Jee, J., Rozowsky, J., Yip, K. Y., Lochovsky, L., Bjornson, R., Zhong, G., Zhang, Z., Fu, Y., Wang, J., Weng, Z. & Gerstein, M., Apr 2011, In: Bioinformatics. 27, 8, p. 1152-1154 3 p., btr092.

    Research output: Contribution to journalArticlepeer-review

    27 Scopus citations
  • A map of human genome variation from population-scale sequencing

    Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., Collins, F. S., De La Vega, F. M., Donnelly, P., Egholm, M., Flicek, P., Gabriel, S. B., Gibbs, R. A., Knoppers, B. M., Lander, E. S., Lehrach, H., Mardis, E. R., McVean, G. A., Nickerson, D. A., Peltonen, L. & 348 others, Schafer, A. J., Sherry, S. T., Wang, J., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Wang, S. J., Li, J., Jian, M., Li, G., Li, R., Liang, H., Tian, G., Wang, B., Wang, J., Wang, W., Yang, H., Zhang, X., Zheng, H., Ambrogio, L., Bloom, T., Cibulskis, K., Fennell, T. J., Jaffe, D. B., Shefler, E., Sougnez, C. L., Bentley, I. D. R., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., Mc Kernan, K. J., Costa, G. L., Ichikawa, J. K., Lee, C. C., Sudbrak, R., Borodina, T. A., Dahl, A., Davydov, A. N., Marquardt, P., Mertes, F., Nietfeld, W., Rosenstiel, P., Schreiber, S., Soldatov, A. V., Timmermann, B., Tolzmann, M., Affourtit, J., Ashworth, D., Attiya, S., Bachorski, M., Buglione, E., Burke, A., Caprio, A., Celone, C., Clark, S., Conners, D., Desany, B., Gu, L., Guccione, L., Kao, K., Kebbel, A., Knowlton, J., Labrecque, M., McDade, L., Mealmaker, C., Minderman, M., Nawrocki, A., Niazi, F., Pareja, K., Ramenani, R., Riches, D., Song, W., Turcotte, C., Wang, S., Dooling, D., Fulton, L., Fulton, R., Weinstock, G., Burton, J., Carter, D. M., Churcher, C., Coffey, A., Cox, A., Palotie, A., Quail, M., Skelly, T., Stalker, J., Swerdlow, H. P., Turner, D., De Witte, A., Giles, S., Bainbridge, M., Challis, D., Sabo, A., Yu, F., Yu, J., Fang, X., Guo, X., Li, Y., Luo, R., Tai, S., Wu, H., Zheng, H., Zheng, X., Zhou, Y., Marth, G. T., Garrison, E. P., Huang, W., Indap, A., Kural, D., Lee, W. P., Leong, W. F., Quinlan, A. R., Stewart, C., Stromberg, M. P., Ward, A. N., Wu, J., Lee, C., Mills, R. E., Shi, X., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., Handsaker, R. E., Hanna, M., Hartl, C., Kernytsky, A. M., Korn, J. M., Li, H., Maguire, J. R., McKenna, A., Nemesh, J. C., Philippakis, A. A., Poplin, R. E., Price, A., Rivas, M. A., Sabeti, P. C., Schaffner, S. F., Shlyakhter, I. A., Cooper, D. N., Ball, E. V., Mort, M., Phillips, A. D., Stenson, P. D., Sebat, J., Makarov, V., Ye, K., Yoon, S. C., Bustamante, C. D., Boyko, A., Degenhardt, J., Gravel, S., Gutenkunst, R. N., Kaganovich, M., Keinan, A., Lacroute, P., Ma, X., Reynolds, A., Clarke, L., Cunningham, F., Herrero, J., Keenen, S., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Smith, R. E., Zalunin, V., Korbel, J. O., Stütz, A. M., Humphray, I. S., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Ye, K., Fu, Y., Hyland, F. C. L., Manning, J. M., Stephen, F. M., Peckham, H. E., Sakarya, O., Sun, Y. A., Tsung, E. F., Mark, A. B., Konkel, M. K., Walker, J. A., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H. M., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Gil, A. M., Auton, A. J., Iqbal, Z., Lunter, G., Marchini, J. L., Moutsianas, L., Myers, S., Tumian, A., Knight, J., Winer, R., Craig, D. W., Beckstrom-Sternberg, S. M., Christoforides, A., Kurdoglu, A. A., Pearson, J. V., Sinari, S. A., Tembe, W. D., Haussler, D., Hinrichs, A. S., Katzman, S. J., Kern, A., Kuhn, R. M., Przeworski, M., Hernandez, R. D., Howie, B., Kelley, J. L., Melton, S. C., Li, Y., Anderson, P., Blackwell, T., Chen, W., Cookson, W. O., Ding, J., Kang, H. M., Lathrop, M., Liang, L., Moffatt, M. F., Scheet, P., Sidore, C., Snyder, M., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Eichler, E. E., Aksay, G., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Kidd, J. M., CenkSahinalp, S., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Albers, C. A., Ayub, Q., Balasubramaniam, S., Barrett, J. C., Chen, Y., Conrad, D. F., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Matt, E. H., Jin, H., Jostins, L., Keane, T. M., Quang Le, S., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Chris Tyler-Smith, T-S., Walter, K., Zhang, Y., Gerstein, M. B., Snyder, M., Abyzov, A., Balasubramanian, S., Bjornson, R., Grubert, F., Habegger, L., Haraksingh, R., Khurana, E., Lam, H. Y. K., Leng, J., Mu, X. J., Urban, A. E., Zhang, Z., McCarroll, S. A., Zheng-Bradley, X., Batzer, M. A., Hurles, M. E., Du, J., Jee, J., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Coffey, A., Scott, C., Tyler-Smith, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Felsenfeld, A. L., McEwen, J. E., Abdallah, A., Juenger, C. R., Clemm, N. C., Duncanson, A., Green, E. D., Guyer, M. S. & Peterson, J. L., Oct 28 2010, In: Nature. 467, 7319, p. 1061-1073 13 p.

    Research output: Contribution to journalArticlepeer-review

    5666 Scopus citations
  • Analysis of nuclear receptor pseudogenes in vertebrates: How the silent tell their stories

    Zhang, Z. D., Cayting, P., Weinstock, G. & Gerstein, M., Jan 2008, In: Molecular Biology and Evolution. 25, 1, p. 131-143 13 p.

    Research output: Contribution to journalArticlepeer-review

    21 Scopus citations
  • An integrated encyclopedia of DNA elements in the human genome

    Principal investigators (steering committee), Boise State University and University of North Carolina at Chapel Hill Proteomics groups (data production and analysis), Broad Institute Group (data production and analysis), Cold Spring Harbor University of Geneva Center for Genomic Regulation Barcelona RIKEN Sanger Institute University of Lausanne GenomeInstitute of Singapore group (data production and analysis), Data coordination center at UC Santa Cruz (production data coordination), Duke University EBI University of Texas Austin University of North Carolina-Chapel Hill group (data production and analysis), Genome Institute of Singapore group (data production and analysis), HudsonAlpha Institute Caltech UC Irvine Stanford group (data production and analysis), Lawrence Berkeley National Laboratory group (targeted experimental validation), NHGRI groups (data production and analysis), Sanger Institute Washington University Yale University Center for Genomic Regulation Barcelona UCSC MIT University of Lausanne CNIO group (data production and analysis), Stanford-Yale Harvard University of Massachusetts Medical School University of Southern California/UC Davis group (data production and analysis), University of Albany SUNY group (data production and analysis), University of Chicago Stanford group (data production and analysis), University of Heidelberg group (targeted experimental validation), University of Massachusetts Medical School Bioinformatics group (data production and analysis), University of Washington University of Massachusetts Medical Center group (data production and analysis), Data Analysis Center (data analysis), The ENCODE Project Consortium, Data production leads (data production) & 3 others, Lead analysts (data analysis), Writing group & NHGRI project management (scientific management), Sep 6 2012, In: Nature. 489, 7414, p. 57-74 18 p.

    Research output: Contribution to journalArticlepeer-review

    9860 Scopus citations
  • A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: Systematically incorporating validated biological knowledge

    Du, J., Rozowsky, J. S., Korbel, J. O., Zhang, Z. D., Royce, T. E., Schultz, M. H., Snyder, M. & Gerstein, M., Dec 15 2006, In: Bioinformatics. 22, 24, p. 3016-3024 9 p.

    Research output: Contribution to journalArticlepeer-review

    29 Scopus citations
  • A systematic survey of loss-of-function variants in human protein-coding genes

    MacArthur, D. G., Balasubramanian, S., Frankish, A., Huang, N., Morris, J., Walter, K., Jostins, L., Habegger, L., Pickrell, J. K., Montgomery, S. B., Albers, C. A., Zhang, Z. D., Conrad, D. F., Lunter, G., Zheng, H., Ayub, Q., DePristo, M. A., Banks, E., Hu, M., Handsaker, R. E. & 31 others, Rosenfeld, J. A., Fromer, M., Jin, M., Mu, X. J., Khurana, E., Ye, K., Kay, M., Saunders, G. I., Suner, M. M., Hunt, T., Barnes, I. H. A., Amid, C., Carvalho-Silva, D. R., Bignell, A. H., Snow, C., Yngvadottir, B., Bumpstead, S., Cooper, D. N., Xue, Y., Romero, I. G., Wang, J., Li, Y., Gibbs, R. A., McCarroll, S. A., Dermitzakis, E. T., Pritchard, J. K., Barrett, J. C., Harrow, J., Hurles, M. E., Gerstein, M. B. & Tyler-Smith, C., Feb 17 2012, In: Science. 335, 6070, p. 823-828 6 p.

    Research output: Contribution to journalArticlepeer-review

    805 Scopus citations
  • Beaver and Naked Mole Rat Genomes Reveal Common Paths to Longevity

    Zhou, X., Dou, Q., Fan, G., Zhang, Q., Sanderford, M., Kaya, A., Johnson, J., Karlsson, E. K., Tian, X., Mikhalchenko, A., Kumar, S., Seluanov, A., Zhang, Z. D., Gorbunova, V., Liu, X. & Gladyshev, V. N., Jul 28 2020, In: Cell Reports. 32, 4, 107949.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    7 Scopus citations
  • Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity

    Ma, S., Upneja, A., Galecki, A., Tsai, Y. M., Burant, C. F., Raskind, S., Zhang, Q., Zhang, Z. D., Seluanov, A., Gorbunova, V., Clish, C. B., Miller, R. A. & Gladyshev, V. N., Nov 22 2016, In: eLife. 5, NOVEMBER2016, e19130.

    Research output: Contribution to journalArticlepeer-review

    44 Scopus citations
  • Common 5S rRNA variants are likely to be accepted in many sequence contexts

    Zhang, Z., D'Souza, L. M., Lee, Y. H. & Fox, G. E., Jan 1 2003, In: Journal of Molecular Evolution. 56, 1, p. 69-76 8 p.

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human

    Macrae, S. L., Zhang, Q., Lemetre, C., Seim, I., Calder, B., Hoeijmakers, J., Suh, Y., Gladyshev, V. N., Seluanov, A., Gorbunova, V., Vijg, J. & Zhang, Z. D., Apr 1 2015, In: Aging cell. 14, 2, p. 288-291 4 p.

    Research output: Contribution to journalArticlepeer-review

    40 Scopus citations
  • Comparative genetics of longevity and cancer: Insights from long-lived rodents

    Gorbunova, V., Seluanov, A., Zhang, Z., Gladyshev, V. N. & Vijg, J., Aug 2014, In: Nature Reviews Genetics. 15, 8, p. 531-540 10 p.

    Research output: Contribution to journalReview articlepeer-review

    128 Scopus citations
  • Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects

    International 22q11.2 Brain and Behavior Consortium, Jan 2 2020, In: American Journal of Human Genetics. 106, 1, p. 26-40 15 p.

    Research output: Contribution to journalArticlepeer-review

    20 Scopus citations
  • Cyclin C regulates adipogenesis by stimulating transcriptional activity of CCAAT/enhancer-binding protein α

    Song, Z., Xiaoli, A. M., Zhang, Q., Zhang, Y., Yang, E. S. T., Wang, S. E., Chang, R., Zhang, Z. D., Yang, G., Strich, R., Pessin, J. E. & Yang, F., May 26 2017, In: Journal of Biological Chemistry. 292, 21, p. 8918-8932 15 p.

    Research output: Contribution to journalArticlepeer-review

    6 Scopus citations
  • Database of non-canonical base pairs found in known RNA structures

    Nagaswamy, U., Voss, N., Zhang, Z. & Fox, G. E., Jan 1 2000, In: Nucleic acids research. 28, 1, p. 375-376 2 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    87 Scopus citations
  • Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer’s disease, providing new insights into its disease mechanisms

    Wang, Z., Zhang, Q., Lin, J. R., Jabalameli, M. R., Mitra, J., Nguyen, N. & Zhang, Z. D., Dec 2021, In: Scientific reports. 11, 1, 20511.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Detection of copy number variation from array intensity and sequencing read depth using a stepwise Bayesian model

    Zhang, Z. D. & Gerstein, M. B., Oct 31 2010, In: BMC bioinformatics. 11, 539.

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations
  • Divergence of transcription factor binding sites across related yeast species

    Borneman, A. R., Gianoulis, T. A., Zhang, Z. D., Yu, H., Rozowsky, J., Seringhaus, M. R., Lu, Y. W., Gerstein, M. & Snyder, M., Aug 10 2007, In: Science. 317, 5839, p. 815-819 5 p.

    Research output: Contribution to journalArticlepeer-review

    278 Scopus citations
  • DNA repair in species with extreme lifespan differences

    MacRae, S. L., Croken, M. M. K., Calder, R. B., Aliper, A., Milholland, B., White, R. R., Zhavoronkov, A., Gladyshev, V. N., Seluanov, A., Gorbunova, V., Zhang, Z. D. & Vijg, J., 2015, In: Aging. 7, 12, p. 1171-1184 14 p.

    Research output: Contribution to journalArticlepeer-review

    91 Scopus citations
  • EBNA1 regulates cellular gene expression by binding cellular promoters

    Canaan, A., Haviv, I., Urban, A. E., Schulz, V. P., Hartman, S., Zhang, Z., Palejev, D., Deisseroth, A. B., Lacy, J., Snyder, M., Gerstein, M. & Weissman, S. M., Dec 19 2009, In: Proceedings of the National Academy of Sciences of the United States of America. 106, 52, p. 22421-22426 6 p.

    Research output: Contribution to journalArticlepeer-review

    68 Scopus citations
  • Ectopic cervical thymi and no thymic involution until midlife in naked mole rats

    Emmrich, S., Tolibzoda Zakusilo, F., Trapp, A., Zhou, X., Zhang, Q., Irving, E. M., Drage, M. G., Zhang, Z., Gladyshev, V. N., Seluanov, A. & Gorbunova, V., Oct 2021, In: Aging cell. 20, 10, e13477.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Enhancer release and retargeting activates disease-susceptibility genes

    Oh, S., Shao, J., Mitra, J., Xiong, F., D’Antonio, M., Wang, R., Garcia-Bassets, I., Ma, Q., Zhu, X., Lee, J. H., Nair, S. J., Yang, F., Ohgi, K., Frazer, K. A., Zhang, Z. D., Li, W. & Rosenfeld, M. G., Jul 29 2021, In: Nature. 595, 7869, p. 735-740 6 p.

    Research output: Contribution to journalArticlepeer-review

    2 Scopus citations
  • Epigenetic alterations to Polycomb targets precede malignant transition in a mouse model of breast cancer

    Cai, Y., Lin, J. R., Zhang, Q., O'Brien, K., Montagna, C. & Zhang, Z. D., Dec 1 2018, In: Scientific reports. 8, 1, 5535.

    Research output: Contribution to journalArticlepeer-review

    6 Scopus citations
  • Erratum: SubNet: A Java application for subnetwork extraction (Bioinformatics (2013) 29:19 (2509-2511) doi: 10.1093/bioinformatics/btt430)

    Lemetre, C., Zhang, Q. & Zhang, Z. D., Nov 15 2013, In: Bioinformatics. 29, 22, p. 2958 1 p.

    Research output: Contribution to journalComment/debatepeer-review

    2 Scopus citations
  • Finishing the euchromatic sequence of the human genome

    International Human Genome Sequencing Consortium, Oct 21 2004, In: Nature. 431, 7011, p. 931-945 15 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    3299 Scopus citations
  • Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

    International 22q11.2DS Brain and Behavior Consortium, Aug 2021, In: Molecular Psychiatry. 26, 8, p. 4496-4510 15 p.

    Research output: Contribution to journalArticlepeer-review

    23 Scopus citations
  • Genetic signature of human longevity in PKC and NF-κB signaling

    Ryu, S., Han, J., Norden-Krichmar, T. M., Zhang, Q., Lee, S., Zhang, Z., Atzmon, G., Niedernhofer, L. J., Robbins, P. D., Barzilai, N., Schork, N. J. & Suh, Y., Jul 2021, In: Aging cell. 20, 7, e13362.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    1 Scopus citations
  • Genetics of extreme human longevity to guide drug discovery for healthy ageing

    Zhang, Z. D., Milman, S., Lin, J. R., Wierbowski, S., Yu, H., Barzilai, N., Gorbunova, V., Ladiges, W. C., Niedernhofer, L. J., Suh, Y., Robbins, P. D. & Vijg, J., Aug 1 2020, In: Nature Metabolism. 2, 8, p. 663-672 10 p.

    Research output: Contribution to journalReview articlepeer-review

    10 Scopus citations
  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution

    Gibbs, R. A., Weinstock, G. M., Metzker, M. L., Muzny, D. M., Sodergren, E. J., Scherer, S., Scott, G., Steffen, D., Worley, K. C., Burch, P. E., Okwuonu, G., Hines, S., Lewis, L., Deramo, C., Delgado, O., Dugan-Rocha, S., Miner, G., Morgan, M., Hawes, A., Gill, R. & 214 others, Holt, R. A., Adams, M. D., Amanatides, P. G., Baden-Tillson, H., Barnstead, M., Chin, S., Evans, C. A., Ferriera, S., Fosler, C., Glodek, A., Gu, Z., Jennings, D., Kraft, C. L., Nguyen, T., Pfannkoch, C. M., Sitter, C., Sutton, G. G., Venter, J. C., Woodage, T., Smith, D., Lee, H. M., Gustafson, E., Cahill, P., Kana, A., Doucette-Stamm, L., Weinstock, K., Fechtel, K., Weiss, R. B., Dunn, D. M., Green, E. D., Blakesley, R. W., Bouffard, G. G., de Jong, P. J., Osoegawa, K., Zhu, B., Marra, M., Schein, J., Bosdet, I., Fjell, C., Jones, S., Krzywinski, M., Mathewson, C., Siddiqui, A., Wye, N., McPherson, J., Zhao, S., Fraser, C. M., Shetty, J., Shatsman, S., Geer, K., Chen, Y., Abramzon, S., Nierman, W. C., Weinstock, G. M., Havlak, P. H., Chen, R., Durbin, K. J., Egan, A., Ren, Y., Song, X. Z., Li, B., Liu, Y., Qin, X., Cawley, S., Weinstock, G. M., Worley, K. C., Cooney, A. J., D'Souza, L. M., Martin, K., Wu, J. Q., Gonzalez-Garay, M. L., Jackson, A. R., Kalafus, K. J., McLeod, M. P., Milosavljevic, A., Virk, D., Volkov, A., Wheeler, D. A., Zhang, Z., Bailey, J. A., Eichler, E. E., Tuzun, E., Birney, E., Mongin, E., Ureta-Vidal, A., Woodwark, C., Zdobnov, E., Bork, P., Suyama, M., Torrents, D., Alexandersson, M., Trask, B. J., Young, J. M., Smith, D., Huang, H., Fechtel, K., Wang, H., Xing, H., Weinstock, K., Daniels, S., Gietzen, D., Schmidt, J., Stevens, K., Vitt, U., Wingrove, J., Camara, F., Albà, M. M., Abril, J. F., Guigo, R., Smit, A., Dubchak, I., Rubin, E. M., Couronne, O., Poliakov, A., Hübner, N., Ganten, D., Goesele, C., Hummel, O., Kreitler, T., Lee, Y. A., Monti, J., Schulz, H., Zimdahl, H., Himmelbauer, H., Lehrach, H., Jacob, H. J., Bromberg, S., Gullings-Handley, J., Jensen-Seaman, M. I., Kwitek, A. E., Lazar, J., Pasko, D., Tonellato, P. J., Twigger, S., Ponting, C. P., Duarte, J. M., Rice, S., Goodstadt, L., Beatson, S. A., Emes, R. D., Winter, E. E., Webber, C., Brandt, P., Nyakatura, G., Adetobi, M., Chiaromonte, F., Elnitski, L., Eswara, P., Hardison, R. C., Hou, M., Kolbe, D., Makova, K., Miller, W., Nekrutenko, A., Riemer, C., Schwartz, S., Taylor, J., Yang, S., Zhang, Y., Lindpaintner, K., Andrews, T. D., Caccamo, M., Clamp, M., Clarke, L., Curwen, V., Durbin, R., Eyras, E., Searle, S. M., Cooper, G. M., Batzoglou, S., Brudno, M., Sidow, A., Stone, E. A., Venter, J. C., Payseur, B. A., Bourque, G., López-Otín, C., Puente, X. S., Chakrabarti, K., Chatterji, S., Dewey, C., Pachter, L., Bray, N., Yap, V. B., Caspi, A., Tesler, S. D. G., Pevzner, P. A., Haussler, S. C. D., Roskin, K. M., Baertsch, R., Clawson, H., Furey, T. S., Hinrichs, A. S., Karolchik, D., Kent, W. J., Rosenbloom, K. R., Trumbower, H., Weirauch, M., Cooper, D. N., Stenson, P. D., Ma, B., Brent, M., Arumugam, M., Shteynberg, D., Copley, R. R., Taylor, M. S., Riethman, H., Mudunuri, U., Peterson, J., Guyer, M., Felsenfeld, A., Old, S., Mockrin, S. & Collins, F., Apr 1 2004, In: Nature. 428, 6982, p. 493-520 28 p.

    Research output: Contribution to journalArticlepeer-review

    1599 Scopus citations
  • Genomic analysis of the nuclear receptor family: New insights into structure, regulation, and evolution from the rat genome

    Zhang, Z., Burch, P. E., Cooney, A. J., Lanz, R. B., Pereira, F. A., Wu, J., Gibbs, R. A., Weinstock, G. & Wheeler, D. A., Apr 2004, In: Genome research. 14, 4, p. 580-590 11 p.

    Research output: Contribution to journalArticlepeer-review

    162 Scopus citations
  • Genomic expansion of Aldh1a1 protects beavers against high metabolic aldehydes from lipid oxidation

    Zhang, Q., Tombline, G., Ablaeva, J., Zhang, L., Zhou, X., Smith, Z., Zhao, Y., Xiaoli, A. M., Wang, Z., Lin, J. R., Jabalameli, M. R., Mitra, J., Nguyen, N., Vijg, J., Seluanov, A., Gladyshev, V. N., Gorbunova, V. & Zhang, Z. D., Nov 9 2021, In: Cell Reports. 37, 6, 109965.

    Research output: Contribution to journalArticlepeer-review

    Open Access
  • Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung

    Dong, X., Shi, M., Lee, M., Toro, R., Gravina, S., Han, W., Yasuda, S., Wang, T., Zhang, Z., Vijg, J., Suh, Y. & Spivack, S. D., Mar 4 2018, In: Epigenetics. 13, 3, p. 264-274 11 p.

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • HEDD: Human Enhancer Disease Database

    Wang, Z., Zhang, Q., Zhang, W., Lin, J. R., Cai, Y., Mitra, J. & Zhang, Z. D., Jan 1 2018, In: Nucleic acids research. 46, D1, p. D113-D120

    Research output: Contribution to journalArticlepeer-review

    19 Scopus citations
  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

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  • Identification and analysis of unitary pseudogenes: Historic and contemporary gene losses in humans and other primates

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  • Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset

    Zhang, Z., Willson, R. C. & Fox, G. E., 2002, In: Bioinformatics. 18, 2, p. 244-250 7 p.

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  • Identification of genomic indels and structural variations using split reads

    Zhang, Z. D., Du, J., Lam, H., Abyzov, A., Urban, A. E., Snyder, M. & Gerstein, M., Jul 25 2011, In: BMC Genomics. 12, 375.

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  • Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways

    Sun, S., White, R. R., Fischer, K. E., Zhang, Z., Austad, S. N. & Vijg, J., Aug 1 2020, In: GeroScience. 42, 4, p. 1119-1132 14 p.

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  • INK4 locus of the tumor-resistant rodent, the naked mole rat, expresses a functional p15/p16 hybrid isoform

    Tian, X., Azpurua, J., Ke, Z., Augereau, A., Zhang, Z. D., Vijg, J., Gladyshev, V. N., Gorbunova, V. & Seluanov, A., Jan 27 2015, In: Proceedings of the National Academy of Sciences of the United States of America. 112, 4, p. 1053-1058 6 p.

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  • Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

    Trinklein, N. D., Karaöz, U., Wu, J., Halees, A., Aldred, S. F., Collins, P. J., Zheng, D., Zhang, Z. D., Gerstein, M. B., Snyder, M., Myers, R. M. & Weng, Z., Jun 2007, In: Genome research. 17, 6, p. 720-731 12 p.

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  • Integrated post-GWAS analysis sheds new light on the disease mechanisms of schizophrenia

    Lin, J. R., Cai, Y., Zhang, Q., Zhang, W., Nogales-Cadenas, R. & Zhang, Z. D., Dec 2016, In: Genetics. 204, 4, p. 1587-1600 14 p.

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  • Integrated rare variant-based risk gene prioritization in disease case-control sequencing studies

    Lin, J. R., Zhang, Q., Cai, Y., Morrow, B. E. & Zhang, Z. D., Dec 2017, In: PLoS genetics. 13, 12, e1007142.

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  • Integrating sequencing technologies in personal genomics: Optimal low cost reconstruction of structural variants

    Du, J., Bjornson, R. D., Zhang, Z. D., Kong, Y., Snyder, M. & Gerstein, M. B., Jul 2009, In: PLoS Computational Biology. 5, 7, e1000432.

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  • Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

    Euskirchen, G. M., Rozowsky, J. S., Wei, C. L., Wah, H. L., Zhang, Z. D., Hartman, S., Emanuelsson, O., Stolc, V., Weissman, S., Gerstein, M. B., Ruan, Y. & Snyder, M., Jun 2007, In: Genome research. 17, 6, p. 898-909 12 p.

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  • Microbial identification by mass cataloging

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  • MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice

    Nogales-Cadenas, R., Cai, Y., Lin, J. R., Zhang, Q., Zhang, W., Montagna, C. & Zhang, Z. D., Jul 22 2016, In: Breast Cancer Research. 18, 1, 75.

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  • Modeling ChIP sequencing in silico with applications

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  • Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder

    Berko, E. R., Suzuki, M., Beren, F., Lemetre, C., Alaimo, C. M., Calder, R. B., Ballaban-Gil, K., Gounder, B., Kampf, K., Kirschen, J., Maqbool, S. B., Momin, Z., Reynolds, D. M., Russo, N., Shulman, L., Stasiek, E., Tozour, J., Valicenti-McDermott, M., Wang, S., Abrahams, B. S. & 9 others, Hargitai, J., Inbar, D., Zhang, Z., Buxbaum, J. D., Molholm, S., Foxe, J. J., Marion, R. W., Auton, A. & Greally, J. M., May 2014, In: PLoS genetics. 10, 5, e1004402.

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  • Naked mole-rat has increased translational fidelity compared with the mouse, as well as a unique 28S ribosomal RNA cleavage

    Azpurua, J., Ke, Z., Chen, I. X., Zhang, Q., Ermolenko, D. N., Zhang, Z. D., Gorbunova, V. & Seluanov, A., Oct 22 2013, In: Proceedings of the National Academy of Sciences of the United States of America. 110, 43, p. 17350-17355 6 p.

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