• 22711 Citations
  • 30 h-Index
20002020

Research output per year

If you made any changes in Pure these will be visible here soon.

Publications

2020

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 journalArticle

2 Scopus citations

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

International 22q11.2DS Brain and Behavior Consortium, Jan 1 2020, (Accepted/In press) In : Molecular Psychiatry.

Research output: Contribution to journalArticle

3 Scopus citations
2019

SIRT6 Is Responsible for More Efficient DNA Double-Strand Break Repair in Long-Lived Species

Tian, X., Firsanov, D., Zhang, Z., Cheng, Y., Luo, L., Tombline, G., Tan, R., Simon, M., Henderson, S., Steffan, J., Goldfarb, A., Tam, J., Zheng, K., Cornwell, A., Johnson, A., Yang, J. N., Mao, Z., Manta, B., Dang, W., Zhang, Z. & 8 others, Vijg, J., Wolfe, A., Moody, K., Kennedy, B. K., Bohmann, D., Gladyshev, V. N., Seluanov, A. & Gorbunova, V., Apr 18 2019, In : Cell. 177, 3, p. 622-638.e22

Research output: Contribution to journalArticle

21 Scopus citations

The nutritional environment determines which and how intestinal stem cells contribute to homeostasis and tumorigenesis

Li, W., Zimmerman, S. E., Peregrina, K., Houston, M., Mayoral, J., Zhang, J., Maqbool, S., Zhang, Z., Cai, Y., Ye, K. & Augenlicht, L. H., Aug 22 2019, In : Carcinogenesis. 40, 8, p. 937-946 10 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations
2018

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 journalArticle

3 Scopus citations

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 journalArticle

1 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 journalArticle

10 Scopus citations

PGA: Post-GWAS analysis for disease gene identification

Lin, J. R., Jaroslawicz, D., Cai, Y., Zhang, Q., Wang, Z. & Zhang, Z. D., May 15 2018, In : Bioinformatics. 34, 10, p. 1786-1788 3 p.

Research output: Contribution to journalArticle

1 Scopus citations

Variance of IQ is partially dependent on deletion type among 1,427 22q11.2 deletion syndrome subjects

the International 22q11.2 Brain and Behavior Consortium, Oct 1 2018, In : American Journal of Medical Genetics, Part A. 176, 10, p. 2172-2181 10 p.

Research output: Contribution to journalArticle

1 Scopus citations
2017

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 journalArticle

3 Scopus citations

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 1 2017, In : PLoS Genetics. 13, 12, e1007142.

Research output: Contribution to journalArticle

3 Scopus citations

Nested Inversion Polymorphisms Predispose Chromosome 22q11.2 to Meiotic Rearrangements

International 22q11.2 Brain and Behavior Consortium, Oct 5 2017, In : American Journal of Human Genetics. 101, 4, p. 616-622 7 p.

Research output: Contribution to journalArticle

4 Scopus citations

Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes

Johnson, S. C., Gonzalez, B., Zhang, Q., Milholland, B., Zhang, Z. & Suh, Y., Jan 1 2017, In : Human Genetics. 136, 1, p. 55-65 11 p.

Research output: Contribution to journalArticle

5 Scopus citations

Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model

Cai, Y., Nogales-Cadenas, R., Zhang, Q., Lin, J. R., Zhang, W., O'Brien, K., Montagna, C. & Zhang, Z. D., Feb 17 2017, In : BMC Genomics. 18, 1, 185.

Research output: Contribution to journalArticle

11 Scopus citations

Translation fidelity coevolves with longevity

Ke, Z., Mallik, P., Johnson, A. B., Luna, F., Nevo, E., Zhang, Z. D., Gladyshev, V. N., Seluanov, A. & Gorbunova, V., Oct 2017, In : Aging cell. 16, 5, p. 988-993 6 p.

Research output: Contribution to journalArticle

21 Scopus citations
2016

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 journalArticle

23 Scopus citations

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 1 2016, In : Genetics. 204, 4, p. 1587-1600 14 p.

Research output: Contribution to journalArticle

15 Scopus citations

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.

Research output: Contribution to journalArticle

12 Scopus citations

Prioritization of schizophrenia risk genes by a network-regularized logistic regression method

Zhang, W., Lin, J. R., Nogales-Cadenas, R., Zhang, Q., Cai, Y. & Zhang, Z. D., 2016, Bioinformatics and Biomedical Engineering - 4th International Conference, IWBBIO 2016, Proceedings. Springer Verlag, Vol. 9656. p. 434-445 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9656).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sensitivity of primary fibroblasts in culture to atmospheric oxygen does not correlate with species lifespan

Patrick, A., Seluanov, M., Hwang, C., Tam, J., Khan, T., Morgenstern, A., Wiener, L., Vazquez, J. M., Zafar, H., Wen, R., Muratkalyeva, M., Doerig, K., Zagorulya, M., Cole, L., Catalano, S., Lobo Ladd, A. A. B., Coppi, A. A., Coskun, Y., Tian, X., Ablaeva, J. & 6 others, Nevo, E., Gladyshev, V. N., Zhang, Z., Vijg, J., Seluanov, A. & Gorbunova, V., 2016, In : Aging. 8, 5, p. 841-847 7 p.

Research output: Contribution to journalArticle

5 Scopus citations

Systems-level analysis of human aging genes shed new light on mechanisms of aging

Zhang, Q., Nogales-Cadenas, R., Lin, J. R., Zhang, W., Cai, Y., Vijg, J. & Zhang, Z. D., 2016, In : Human Molecular Genetics. 25, 14, p. 2934-2947 14 p.

Research output: Contribution to journalArticle

16 Scopus citations
2015

Comparative analysis of genome maintenance genes in naked mole rat, mouse, and human

Macrae, S. L., Zhang, Q., Lemetre, C., Seim, I., Calder, R. 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 journalArticle

28 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., Jan 1 2015, In : Aging. 7, 12, p. 1171-1184 14 p.

Research output: Contribution to journalArticle

60 Scopus citations

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.

Research output: Contribution to journalArticle

38 Scopus citations

RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships

Nadel, J., Athanasiadou, R., Lemetre, C., Wijetunga, N. A., Ó Broin, P., Sato, H., Zhang, Z., Jeddeloh, J., Montagna, C., Golden, A., Seoighe, C. & Greally, J. M., Nov 16 2015, In : Epigenetics and Chromatin. 8, 1, 40.

Research output: Contribution to journalArticle

54 Scopus citations

Whole-Genome Sequencing and Integrative Genomic Analysis Approach on Two 22q11.2 Deletion Syndrome Family Trios for Genotype to Phenotype Correlations

Chung, J. H., Cai, J., Suskin, B. G., Zhang, Z., Coleman, K. & Morrow, B. E., Aug 1 2015, In : Human Mutation. 36, 8, p. 797-807 11 p.

Research output: Contribution to journalArticle

10 Scopus citations
2014

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 article

102 Scopus citations

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.

Research output: Contribution to journalArticle

56 Scopus citations
2013

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

Lemetre, C. & Zhang, Z. D., Sep 20 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

1 Scopus citations
2 Scopus citations

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.

Research output: Contribution to journalArticle

70 Scopus citations

SubNet: A Java application for subnetwork extraction

Zhang, Q. & Zhang, Z. D., Jan 1 2013, In : Bioinformatics. 29, 19, p. 2509-2511 3 p.

Research output: Contribution to journalArticle

12 Scopus citations

The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes

Montgomery, S. B., Goode, D. L., Kvikstad, E., Albers, C. A., Zhang, Z. D., Mu, X. J., Ananda, G., Howie, B., Karczewski, K. J., Smith, K. S., Anaya, V., Richardson, R., Davis, J., MacArthur, D. G., Sidow, A., Duret, L., Gerstein, M., Makova, K. D., Marchini, J., McVean, G. & 1 others, Lunter, G., May 1 2013, In : Genome research. 23, 5, p. 749-761 13 p.

Research output: Contribution to journalArticle

111 Scopus citations
2012

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 journalArticle

7970 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 journalArticle

720 Scopus citations

The Einstein Genome Gateway using WASP - A high throughput multi-layered life sciences portal for XSEDE

Golden, A., McLellan, A. S., Dubin, R. A., Jing, Q., Broin, P. Ó., Moskowitz, D., Zhang, Z., Suzuki, M., Hargitai, J., Calder, R. B. & Greally, J. M., Jan 1 2012, HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences. IOS Press, p. 182-191 10 p. (Studies in Health Technology and Informatics; vol. 175).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2011

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 1 2011, In : Bioinformatics. 27, 8, p. 1152-1154 3 p., btr092.

Research output: Contribution to journalArticle

26 Scopus citations

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.

Research output: Contribution to journalArticle

46 Scopus citations

Mapping copy number variation by population-scale genome sequencing

Mills, R. E., Walter, K., Stewart, C., Handsaker, R. E., Chen, K., Alkan, C., Abyzov, A., Yoon, S. C., Ye, K., Cheetham, R. K., Chinwalla, A., Conrad, D. F., Fu, Y., Grubert, F., Hajirasouliha, I., Hormozdiari, F., Iakoucheva, L. M., Iqbal, Z., Kang, S., Kidd, J. M. & 353 others, Konkel, M. K., Korn, J., Khurana, E., Kural, D., Lam, H. Y. K., Leng, J., Li, R., Li, Y., Lin, C. Y., Luo, R., Mu, X. J., Nemesh, J., Peckham, H. E., Rausch, T., Scally, A., Shi, X., Stromberg, M. P., Sütz, A. M., Urban, A. E., Walker, J. A., Wu, J., Zhang, Y., Zhang, Z. D., Batzer, M. A., Ding, L., Marth, G. T., McVean, G., Sebat, J., Snyder, M., Wang, J., Ye, K., Eichler, E. E., Gerstein, M. B., Hurles, M. E., Lee, C., McCarroll, S. A., Korbel, J. O., Collins, F. S., Altshuler, D. L., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., Clark, A. G., 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., Schafer, A. J., Sherry, S. T., Wilson, R. K., Deiros, D., Metzker, M., Muzny, D., Reid, J., Wheeler, D., Li, J., Jian, M., Li, G., Liang, H., Tian, G., Wang, B., 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., Gormley, N., Humphray, S., Kingsbury, Z., Koko-Gonzales, P., Stone, J., McKernan, 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., Tai, S., Wu, H., Zheng, X., Zhou, Y., Garrison, E. P., Huang, W., Indap, A., Lee, W. P., Leong, W. F., Quinlan, A. R., Ward, A. N., Daly, M. J., DePristo, M. A., Ball, A. D., Banks, E., Browning, B. L., Garimella, K. V., Grossman, S. R., 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., Makarov, V., 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., Zheng-Bradley, X., Stütz, A. M., Bauer, M., Cox, T., Eberle, M., James, T., Kahn, S., Murray, L., Hyland, F. C., Manning, J. M., McLaughlin, S. F., Sakarya, O., Sun, Y. A., Tsung, E. F., Albrecht, M. W., Amstislavskiy, V. S., Herwig, R., Parkhomchuk, D. V., Agarwala, R., Khouri, H., Morgulis, A. O., Paschall, J. E., Phan, L. D., Rotmistrovsky, K. E., Sanders, R. D., Shumway, M. F., Xiao, C., Auton, A., 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., 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., Zhan, X., Zöllner, S., Awadalla, P., Casals, F., Idaghdour, Y., Keebler, J., Stone, E. A., Zilversmit, M., Jorde, L., Xing, J., Aksay, G., Sahinalp, S. C., Sudmant, P. H., 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., Danecek, P., Dermitzakis, E. T., Hu, M., Huang, N., Jin, H., Jostins, L., Keane, T. M., Le, S. Q., Lindsay, S., Long, Q., MacArthur, D. G., Montgomery, S. B., Parts, L., Tyler-Smith, C., Balasubramanian, S., Bjornson, R., Du, J., Habegger, L., Haraksingh, R., Jee, J., Lam, H. Y., Jeng, J., Zhang, Z., Bank, E., Yoon, S., Kidd, J., Coafra, C., Dinh, H., Kovar, C., Lee, S., Nazareth, L., Wilkinson, J., Khouri, H. M., Scott, C., Gharani, N., Kaye, J. S., Kent, A., Li, T., McGuire, A. L., Ossorio, P. N., Rotimi, C. N., Su, Y., Toji, L. H., Brooks, L. D., 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., Feb 3 2011, In : Nature. 470, 7332, p. 59-65 7 p.

Research output: Contribution to journalArticle

711 Scopus citations
2010

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., 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 journalArticle

5144 Scopus citations

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 journalArticle

5 Scopus citations

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

Zhang, Z. D., Frankish, A., Hunt, T., Harrow, J. & Gerstein, M., Mar 8 2010, In : Genome biology. 11, 3, r26.

Research output: Contribution to journalArticle

95 Scopus citations
2009

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 journalArticle

61 Scopus citations

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 1 2009, In : PLoS Computational Biology. 5, 7, e1000432.

Research output: Contribution to journalArticle

10 Scopus citations

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

Rozowsky, J., Euskirchen, G., Auerbach, R. K., Zhang, Z. D., Gibson, T., Bjornson, R., Carriero, N., Snyder, M. & Gerstein, M. B., Jan 25 2009, In : Nature biotechnology. 27, 1, p. 66-75 10 p.

Research output: Contribution to journalArticle

402 Scopus citations

PEMer: A computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

Korbel, J. O., Abyzov, A., Mu, X. J., Carriero, N., Cayting, P., Zhang, Z., Snyder, M. & Gerstein, M. B., Feb 23 2009, In : Genome biology. 10, 2, R23.

Research output: Contribution to journalArticle

179 Scopus citations

Rapid in vivo exploration of a 5S rRNA neutral network

Zhang, Z. D., Nayar, M., Ammons, D., Rampersad, J. & Fox, G. E., Feb 1 2009, In : Journal of Microbiological Methods. 76, 2, p. 181-187 7 p.

Research output: Contribution to journalArticle

3 Scopus citations
2008

Analysis of nuclear receptor pseudogenes in vertebrates: How the silent tell their stories

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

Research output: Contribution to journalArticle

19 Scopus citations

Modeling ChIP sequencing in silico with applications

Zhang, Z. D., Rozowsky, J., Snyder, M., Chang, J. & Gerstein, M., Aug 1 2008, In : PLoS Computational Biology. 4, 8, e1000158.

Research output: Contribution to journalArticle

48 Scopus citations