• 10704 Citations
  • 24 h-Index
20102019

Research output per year

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Research Output

  • 10704 Citations
  • 24 h-Index
  • 51 Article
  • 2 Comment/debate
  • 2 Review article
  • 1 Letter
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Article
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

5049 Scopus citations
2012

A Likelihood-Based Framework for Variant Calling and De Novo Mutation Detection in Families

Li, B., Chen, W., Zhan, X., Busonero, F., Sanna, S., Sidore, C., Cucca, F., Kang, H. M. & Abecasis, G. R., Oct 2012, In : PLoS Genetics. 8, 10, e1002944.

Research output: Contribution to journalArticle

51 Scopus citations
2013

Accurate Local-Ancestry Inference in Exome-Sequenced Admixed Individuals via Off-Target Sequence Reads

Hu, Y., Willer, C., Zhan, X., Kang, H. M. & Abecasis, G. R., Nov 7 2013, In : American Journal of Human Genetics. 93, 5, p. 891-899 9 p.

Research output: Contribution to journalArticle

12 Scopus citations

Genotype imputation reference panel selection using maximal phylogenetic diversity

Zhang, P., Zhan, X., Rosenberg, N. A. & Zöllner, S., Oct 2013, In : Genetics. 195, 2, p. 319-330 12 p.

Research output: Contribution to journalArticle

10 Scopus citations

Identification of a rare coding variant in complement 3 associated with age-related macular degeneration

Zhan, X., Larson, D. E., Wang, C., Koboldt, D. C., Sergeev, Y. V., Fulton, R. S., Fulton, L. L., Fronick, C. C., Branham, K. E., Bragg-Gresham, J., Jun, G., Hu, Y., Kang, H. M., Liu, D., Othman, M., Brooks, M., Ratnapriya, R., Boleda, A., Grassmann, F., Von Strachwitz, C. & 40 others, Olson, L. M., Buitendijk, G. H. S., Hofman, A., Van Duijn, C. M., Cipriani, V., Moore, A. T., Shahid, H., Jiang, Y., Conley, Y. P., Morgan, D. J., Kim, I. K., Johnson, M. P., Cantsilieris, S., Richardson, A. J., Guymer, R. H., Luo, H., Ouyang, H., Licht, C., Pluthero, F. G., Zhang, M. M., Zhang, K., Baird, P. N., Blangero, J., Klein, M. L., Farrer, L. A., DeAngelis, M. M., Weeks, D. E., Gorin, M. B., Yates, J. R. W., Klaver, C. C. W., Pericak-Vance, M. A., Haines, J. L., Weber, B. H. F., Wilson, R. K., Heckenlively, J. R., Chew, E. Y., Stambolian, D., Mardis, E. R., Swaroop, A. & Abecasis, G. R., Nov 2013, In : Nature Genetics. 45, 11, p. 1375-1381 7 p.

Research output: Contribution to journalArticle

97 Scopus citations

QPLOT: A quality assessment tool for next generation sequencing data

Li, B., Zhan, X., Wing, M. K., Anderson, P., Kang, H. M. & Abecasis, G. R., 2013, In : BioMed Research International. 2013, 865181.

Research output: Contribution to journalArticle

10 Scopus citations
2014

A Bayesian framework for de novo mutation calling in parents-offspring trios

Wei, Q., Zhan, X., Zhong, X., Liu, Y., Han, Y., Chen, W. & Li, B., Nov 5 2014, In : Bioinformatics. 31, 9, p. 1375-1381 7 p.

Research output: Contribution to journalArticle

25 Scopus citations

A generalized genetic random field method for the genetic association analysis of sequencing data

Li, M., He, Z., Zhang, M., Zhan, X., Wei, C., Elston, R. C. & Lu, Q., 2014, In : Genetic Epidemiology. 38, 3, p. 242-253 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis

Chen, R., Wei, Q., Zhan, X., Zhong, X., Sutcliffe, J. S., Cox, N. J., Cook, E. H., Li, C., Chen, W. & Li, B., Nov 5 2014, In : Bioinformatics. 31, 9, p. 1452-1459 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Ancestry estimation and control of population stratification for sequence-based association studies

Wang, C., Zhan, X., Bragg-Gresham, J., Kang, H. M., Stambolian, D., Chew, E. Y., Branham, K. E., Heckenlively, J., Fulton, R., Wilson, R. K., Mardis, E. R., Lin, X., Swaroop, A., Zöllner, S. & Abecasis, G. R., 2014, In : Nature Genetics. 46, 4, p. 409-415 7 p.

Research output: Contribution to journalArticle

38 Scopus citations

Improved Ancestry Estimation for both Genotyping and Sequencing Data using Projection Procrustes Analysis and Genotype Imputation

Wang, C., Zhan, X., Liang, L., Abecasis, G. R. & Lin, X., Nov 15 2014, (Accepted/In press) In : American Journal of Human Genetics.

Research output: Contribution to journalArticle

31 Scopus citations

In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes

Vrieze, S. I., Malone, S. M., Vaidyanathan, U., Kwong, A., Kang, H. M., Zhan, X., Flickinger, M., Irons, D., Jun, G., Locke, A. E., Pistis, G., Porcu, E., Levy, S., Myers, R. M., Oetting, W., Mcgue, M., Abecasis, G. & Iacono, W. G., Dec 1 2014, In : Psychophysiology. 51, 12, p. 1309-1320 12 p.

Research output: Contribution to journalArticle

20 Scopus citations

Meta-analysis of gene-level tests for rare variant association

Liu, D. J., Peloso, G. M., Zhan, X., Holmen, O. L., Zawistowski, M., Feng, S., Nikpay, M., Auer, P. L., Goel, A., Zhang, H., Peters, U., Farrall, M., Orho-Melander, M., Kooperberg, C., Mcpherson, R., Watkins, H., Willer, C. J., Hveem, K., Melander, O., Kathiresan, S. & 1 others, Abecasis, G. R., 2014, In : Nature Genetics. 46, 2, p. 200-204 5 p.

Research output: Contribution to journalArticle

106 Scopus citations

Modeling and testing for joint association using a genetic random field model

He, Z., Zhang, M., Zhan, X. & Lu, Q., Sep 1 2014, In : Biometrics. 70, 3, p. 471-479 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration

Ratnapriya, R., Zhan, X., Fariss, R. N., Branham, K. E., Zipprer, D., Chakarova, C. F., Sergeev, Y. V., Campos, M. M., Othman, M., Friedman, J. S., Maminishkis, A., Waseem, N. H., Brooks, M., Rajasimha, H. K., Edwards, A. O., Lotery, A., Klein, B. E., Truitt, B. J., Li, B., Schaumberg, D. A. & 47 others, Morgan, D. J., Morrison, M. A., Souied, E., Tsironi, E. E., Grassmann, F., Fishman, G. A., Silvestri, G., Scholl, H. P. N., Kim, I. K., Ramke, J., Tuo, J., Merriam, J. E., Merriam, J. C., Park, K. H., Olson, L. M., Farrer, L. A., Johnson, M. P., Peachey, N. S., Lathrop, M., Baron, R. V., Igo, R. P., Klein, R., Hagstrom, S. A., Kamatani, Y., Martin, T. M., Jiang, Y., Conley, Y., Sahel, J. A., Zack, D. J., Chan, C. C., Pericak-Vance, M. A., Jacobson, S. G., Gorin, M. B., Klein, M. L., Allikmets, R., Iyengar, S. K., Weber, B. H., Haines, J. L., Léveillard, T., Deangelis, M. M., Stambolian, D., Weeks, D. E., Bhattacharya, S. S., Chew, E. Y., Heckenlively, J. R., Abecasis, G. R. & Swaroop, A., Nov 1 2014, In : Human Molecular Genetics. 23, 21, p. 5827-5837 11 p.

Research output: Contribution to journalArticle

26 Scopus citations

RAREMETAL: Fast and powerful meta-analysis for rare variants

Feng, S., Liu, D., Zhan, X., Wing, M. K. & Abecasis, G. R., Apr 2 2014, In : Bioinformatics. 30, 19, p. 2828-2829 2 p.

Research output: Contribution to journalArticle

50 Scopus citations
2015

Activation of HIF-1α and LL-37 by commensal bacteria inhibits Candida albicans colonization

Fan, D., Coughlin, L. A., Neubauer, M. M., Kim, J., Kim, M. S., Zhan, X., Simms-Waldrip, T. R., Xie, Y., Hooper, L. V. & Koh, A., Jun 8 2015, In : Nature Medicine. 21, 7, p. 808-814 7 p.

Research output: Contribution to journalArticle

102 Scopus citations

A global reference for human genetic variation

Auton, A., Abecasis, G. R., Altshuler, D. M., Durbin, R. M., Bentley, D. R., Chakravarti, A., Clark, A. G., Donnelly, P., Eichler, E. E., Flicek, P., Gabriel, S. B., Gibbs, R. A., Green, E. D., Hurles, M. E., Knoppers, B. M., Korbel, J. O., Lander, E. S., Lee, C., Lehrach, H., Mardis, E. R. & 457 others, Marth, G. T., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Boerwinkle, E., Doddapaneni, H., Han, Y., Korchina, V., Kovar, C., Lee, S., Muzny, D., Reid, J. G., Zhu, Y., Chang, Y., Feng, Q., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Lan, T., Li, G., Li, J., Li, Y., Liu, S., Liu, X., Lu, Y., Ma, X., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Xu, X., Yin, Y., Zhang, D., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Gupta, N., Gharani, N., Toji, L. H., Gerry, N. P., Resch, A. M., Barker, J., Clarke, L., Gil, L., Hunt, S. E., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Thormann, A., Toneva, I., Vaughan, B., Zheng-Bradley, X., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Fulton, L., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., Church, D., Cohen, R., Cook, C., Garner, J., Hefferon, T., Kimelman, M., Liu, C., Lopez, J., Meric, P., O'Sullivan, C., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Campbell, C. L., Kong, Y., Marcketta, A., Yu, F., Antunes, L., Bainbridge, M., Sabo, A., Huang, Z., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Alkan, C., Dal, E., Kahveci, F., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Stromberg, M., Ward, A. N., Wu, J., Zhang, M., Daly, M. J., DePristo, M. A., Handsaker, R. E., Banks, E., Bhatia, G., Del Angel, G., Genovese, G., Li, H., Kashin, S., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Yoon, S. C., Lihm, J., Makarov, V., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Rausch, T., Fritz, M. H., Stütz, A. M., Beal, K., Datta, A., Herrero, J., Ritchie, G. R. S., Zerbino, D., Sabeti, P. C., Shlyakhter, I., Schaffner, S. F., Vitti, J., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Cheetham, R. K., Cox, A., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Kenny, E. E., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Ding, L., Koboldt, D. C., Larson, D., Ye, K., Gravel, S., Swaroop, A., Chew, E., Lappalainen, T., Erlich, Y., Gymrek, M., Willems, T. F., Simpson, J. T., Shriver, M. D., Rosenfeld, J. A., Bustamante, C. D., Montgomery, S. B., De La Vega, F. M., Byrnes, J. K., Carroll, A. W., DeGorter, M. K., Lacroute, P., Maples, B. K., Martin, A. R., Moreno-Estrada, A., Shringarpure, S. S., Zakharia, F., Halperin, E., Baran, Y., Cerveira, E., Hwang, J., Malhotra, A., Plewczynski, D., Radew, K., Romanovitch, M., Zhang, C., Hyland, F. C. L., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Antaki, D., Gujral, M., Noor, A., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., Kent, W. J., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Devine, S. E., Kang, H. M., Kidd, J. M., Blackwell, T., Caron, S., Chen, W., Emery, S., Fritsche, L., Fuchsberger, C., Jun, G., Li, B., Lyons, R., Scheller, C., Sidore, C., Song, S., Sliwerska, E., Taliun, D., Tan, A., Welch, R., Wing, M. K., Zhan, X., Awadalla, P., Hodgkinson, A., Li, Y., Shi, X., Quitadamo, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Kretzschmar, W., Iqbal, Z., Mathieson, I., Menelaou, A., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Browning, S. R., Hormozdiari, F., Sudmant, P. H., Khurana, E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Colonna, V., Jostins, L., Walter, K., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Lee, D., Liu, J., Mu, X. J., Zhang, J., Zhang, Y., Hartl, C., Shakir, K., Degenhardt, J., Meiers, S., Raeder, B., Casale, F. P., Stegle, O., Lameijer, E. W., Hall, I., Bafna, V., Michaelson, J., Gardner, E. J., Mills, R. E., Dayama, G., Chen, K., Fan, X., Chong, Z., Chen, T., Chaisson, M. J., Huddleston, J., Malig, M., Nelson, B. J., Parrish, N. F., Blackburne, B., Lindsay, S. J., Ning, Z., Zhang, Y., Lam, H., Sisu, C., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Yu, J., Li, W., Habegger, L., Yu, H., Cunningham, F., Dunham, I., Lage, K., Jespersen, J. B., Horn, H., Kim, D., Desalle, R., Narechania, A., Sayres, M. A. W., Mendez, F. L., Poznik, G. D., Underhill, P. A., Mittelman, D., Banerjee, R., Cerezo, M., Fitzgerald, T. W., Louzada, S., Massaia, A., Yang, F., Kalra, D., Hale, W., Dan, X., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Cai, Z., Gao, Y., Chu, J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Mathias, R. A., Hennis, A., Watson, H., McKenzie, C., Qadri, F., LaRocque, R., Deng, X., Asogun, D., Folarin, O., Happi, C., Omoniwa, O., Stremlau, M., Tariyal, R., Jallow, M., Joof, F. S., Corrah, T., Rockett, K., Kwiatkowski, D., Kooner, J., Hien, T. T., Dunstan, S. J., ThuyHang, N., Fonnie, R., Garry, R., Kanneh, L., Moses, L., Schieffelin, J., Grant, D. S., Gallo, C., Poletti, G., Saleheen, D., Rasheed, A., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Vaydylevich, Y., Duncanson, A., Dunn, M. & Schloss, J. A., Sep 30 2015, In : Nature. 526, 7571, p. 68-74 7 p.

Research output: Contribution to journalArticle

3853 Scopus citations

Erratum: Prediction of human population responses to toxic compounds by a collaborative competition (Nature Biotechnology (2015) 33 (933-940))

Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R., Norman, T., Kellen, M., Menden, M. P., Yang, J., Zhan, X., Zhong, R., Xiao, G., Xia, M., Abdo, N., Kosyk, O., Friend, S., Dearry, A., Simeonov, A., Tice, R. R. & 5 others, Rusyn, I., Wright, F. A., Stolovitzky, G., Xie, Y. & Saez-Rodriguez, J., Oct 8 2015, In : Nature Biotechnology. 33, 10, p. 1109 1 p.

Research output: Contribution to journalArticle

Leveraging Identity-by-Descent for Accurate Genotype Inference in Family Sequencing Data

Li, B., Wei, Q., Zhan, X., Zhong, X., Chen, W., Li, C. & Haines, J., Jul 1 2015, In : PLoS Genetics. 11, 6, e1005271.

Research output: Contribution to journalArticle

2 Scopus citations

Prediction of human population responses to toxic compounds by a collaborative competition

Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R., Norman, T., Kellen, M., Menden, M. P., Yang, J., Zhan, X., Zhong, R., Xiao, G., Xia, M., Abdo, N., Kosyk, O., Friend, S., Dearry, A., Simeonov, A., Tice, R. R. & 5 others, Rusyn, I., Wright, F. A., Stolovitzky, G., Xie, Y. & Xie, Y., Sep 10 2015, In : Nature Biotechnology. 33, 9, p. 933-940 8 p.

Research output: Contribution to journalArticle

52 Scopus citations

Real-time resolution of point mutations that cause phenovariance in mice

Wang, T., Zhan, X., Bua, C. H., Lyona, S., Pratta, D., Hildebrand, S., Choi, J. H., Zhang, Z., Zeng, M., Wang, K. W., Turer, E. E., Chen, Z., Zhang Ph.D., D-W., Yue, T., Wang, Y., Shi, H-X., Wang, J., Sun, L., SoRelle, J., McAlpine, W. & 28 others, Hutchins, N., Zhan, X., Fin, M., Gobert, R., Quan, J., Kreutzer, M., Arnett, S., Hawkins, K., Leach, A., Tate, C., Daniel, C., Reyna, C., Prince, L., Davis, S., Purrington, J., Bearden, R., Weatherly, J., White, D., Russell, J. L., Sun, Q., Tang, M., Li, X., Scott, L., Moresco, E. M. Y., McInerney, G. M., Karlsson Hedestam, G. B., Xie, Y. & Beutler, B. A., Feb 3 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 5, p. E440-E449

Research output: Contribution to journalArticle

30 Scopus citations

SEQMINER: An R-Package to Facilitate the Functional Interpretation of Sequence-Based Associations

Zhan, X. & Liu, D. J., Dec 1 2015, In : Genetic Epidemiology. 39, 8, p. 619-623 5 p.

Research output: Contribution to journalArticle

15 Scopus citations
2016

A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

Fritsche, L. G., Igl, W., Bailey, J. N. C., Grassmann, F., Sengupta, S., Bragg-Gresham, J. L., Burdon, K. P., Hebbring, S. J., Wen, C., Gorski, M., Kim, I. K., Cho, D., Zack, D., Souied, E., Scholl, H. P. N., Bala, E., ELee, K., Hunter, D. J., Sardell, R. J., Mitchell, P. & 142 others, Merriam, J. E., Cipriani, V., Hoffman, J. D., Schick, T., Lechanteur, Y. T. E., Guymer, R. H., Johnson, M. P., Jiang, Y., Stanton, C. M., Buitendijk, G. H. S., Zhan, X., Kwong, A. M., Boleda, A., Brooks, M., Gieser, L., Ratnapriya, R., Branham, K. E., Foerster, J. R., Heckenlively, J. R., Othman, M. I., Vote, B. J., Liang, H. H., Souzeau, E., McAllister, I. L., Isaacs, T., Hall, J., Lake, S., Mackey, D. A., Constable, I. J., Craig, J. E., Kitchner, T. E., Yang, Z., Su, Z., Luo, H., Chen, D., Ouyang, H., Flagg, K., Lin, D., Mao, G., Ferreyra, H., Stark, K., Von Strachwitz, C. N., Wolf, A., Brandl, C., Rudolph, G., Olden, M., Morrison, M. A., Morgan, D. J., Schu, M., Ahn, J., Silvestri, G., Tsironi, E. E., Park, K. H., Farrer, L. A., Orlin, A., Brucker, A., Li, M., Curcio, C. A., Mohand-Sa'd, S., Sahel, J. A., Audo, I., Benchaboune, M., Cree, A. J., Rennie, C. A., Goverdhan, S. V., Grunin, M., Hagbi-Levi, S., Campochiaro, P., Katsanis, N., Holz, F. G., Blond, F., Blanché, H., Deleuze, J. F. O., Igo, R. P., Truitt, B., Peachey, N. S., Meuer, S. M., Myers, C. E., Moore, E. L., Klein, R., Hauser, M. A., Postel, E. A., Courtenay, M. D., Schwartz, S. G., Kovach, J. L., Scott, W. K., Liew, G., Tan, A. G., Gopinath, B., Merriam, J. C., Smith, R. T., Khan, J. C., Shahid, H., Moore, A. T., McGrath, J. A., Laux, R., Brantley, M. A., Agarwal, A., Ersoy, L., Caramoy, A., Langmann, T., Saksens, N. T. M., Jong, E. K., Hoyng, C. B., Cain, M. S., Richardson, A. J., Martin, T. M., Blangero, J., Weeks, D. E., Dhillon, B., Van Duijn, C. M., Doheny, K. F., Romm, J., Klaver, C. C. W., Hayward, C., Gorin, M. B., Klein, M. L., Baird, P. N., Den Hollander, A. I., Fauser, S., WYates, J. R., Allikmets, R., Wang, J. J., Schaumberg, D. A., Klein, B. E. K., Hagstrom, S. A., Chowers, I., Lotery, A. J., Léveillard, T., Zhang, K., Brilliant, M. H., Hewitt, A. W., Swaroop, A., Chew, E. Y., Pericak-Vance, M. A., DeAngelis, M., Stambolian, D., Haines, J. L., Iyengar, S. K., Weber, B. H. F., Abecasis, G. R. & Heid, I. M., Feb 1 2016, In : Nature Genetics. 48, 2, p. 134-143 10 p.

Research output: Contribution to journalArticle

361 Scopus citations

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

The Rheumatoid Arthritis Challenge Consortium & Tang, H., Aug 23 2016, In : Nature Communications. 7, 12460.

Research output: Contribution to journalArticle

40 Scopus citations

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Allen, G. I., Amoroso, N., Anghel, C., Balagurusamy, V., Bare, C. J., Beaton, D., Bellotti, R., Bennett, D. A., Boehme, K. L., Boutros, P. C., Caberlotto, L., Caloian, C., Campbell, F., Chaibub Neto, E., Chang, Y. C., Chen, B., Chen, C. Y., Chien, T. Y., Clark, T., Das, S. & 81 others, Davatzikos, C., Deng, J., Dillenberger, D., Dobson, R. J. B., Dong, Q., Doshi, J., Duma, D., Errico, R., Erus, G., Everett, E., Fardo, D. W., Friend, S. H., Fröhlich, H., Gan, J., St George-Hyslop, P., Ghosh, S. S., Glaab, E., Green, R. C., Guan, Y., Hong, M. Y., Huang, C., Hwang, J., Ibrahim, J., Inglese, P., Iyappan, A., Jiang, Q., Katsumata, Y., Kauwe, J. S. K., Klein, A., Kong, D., Krause, R., Lalonde, E., Lauria, M., Lee, E., Lin, X., Liu, Z., Livingstone, J., Logsdon, B. A., Lovestone, S., Ma, T. W., Malhotra, A., Mangravite, L. M., Maxwell, T. J., Merrill, E., Nagorski, J., Namasivayam, A., Narayan, M., Naz, M., Newhouse, S. J., Norman, T. C., Nurtdinov, R. N., Oyang, Y. J., Pawitan, Y., Peng, S., Peters, M. A., Piccolo, S. R., Praveen, P., Priami, C., Sabelnykova, V. Y., Senger, P., Shen, X., Simmons, A., Sotiras, A., Stolovitzky, G., Tangaro, S., Tateo, A., Tung, Y. A., Tustison, N. J., Varol, E., Vradenburg, G., Weiner, M. W., Xiao, G., Xie, L., Xie, Y., Xu, J., Yang, H., Zhan, X., Zhou, Y., Zhu, F., Zhu, H. & Zhu, S., Jun 1 2016, In : Alzheimer's and Dementia. 12, 6, p. 645-653 9 p.

Research output: Contribution to journalArticle

43 Scopus citations

FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies

Kim, J., Kim, M. S., Koh, A., Xie, Y. & Zhan, X., Oct 10 2016, In : BMC Bioinformatics. 17, 1, 420.

Research output: Contribution to journalArticle

22 Scopus citations

RVTESTS: An efficient and comprehensive tool for rare variant association analysis using sequence data

Zhan, X., Hu, Y., Li, B., Abecasis, G. R. & Liu, D. J., May 1 2016, In : Bioinformatics. 32, 9, p. 1423-1426 4 p.

Research output: Contribution to journalArticle

74 Scopus citations

Understanding taxi travel patterns

Cai, H., Zhan, X., Zhu, J., Jia, X., Chiu, A. S. F. & Xu, M., Sep 1 2016, In : Physica A: Statistical Mechanics and its Applications. 457, p. 590-597 8 p.

Research output: Contribution to journalArticle

34 Scopus citations
2017

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gönen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 105 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Afsari, B., Airola, A., Aittokallio, T., Bivol, A., Boehm, J. S., Bunte, K., Carlin, D., Chang, Y. C., Chen, T., Chong, Z., Chopra, S., Cowley, G. S., Deran, A., Ellrott, K., Elmarakeby, H., Fertig, E. J., Gonçalves, E., Gönen, M., Gong, P., Gopalacharyulu, P., Graim, K., Guan, Y., Hafemeister, C., Hahn, W. C., Heath, L., Hoff, B., Howell, S., Jaiswal, A., Karasuyama, M., Kaski, S., Kędziorski, Ł., Khan, S. A., Khemka, N., King, E. K., Lauria, M., Liu, M., Machado, D., Mamitsuka, H., Marbach, D., Margolin, A. A., Xiao, G., Menden, M. P., Migacz, S., Newton, Y., Ng, S., Nie, Z., Norman, T. C., Pahikkala, T., Paull, E., Praveen, P., Priami, C., Rizzetto, S., Rocha, M., Root, D. E., Rudd, C., Rudnicki, W. R., Saez-Rodriguez, J., Sokolov, A., Song, L., Stolovitzky, G., Stuart, J. M., Sun, D., Szalai, B., Tang, H., Tang, J., Tsherniak, A., Uzunangelov, V., Vazquez, F., Wang, T., Wang, D., Weir, B. A., Wennerberg, K., Wu, L. Y., Xiao, G., Xie, Y., Ye, J., Ye, Y., Zhan, X., Zhou, W., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C. & Margolin, A. A., Nov 22 2017, In : Cell Systems. 5, 5, p. 485-497.e3

Research output: Contribution to journalArticle

5 Scopus citations
3 Scopus citations

Antibiotic-Induced Depletion of Anti-inflammatory Clostridia Is Associated with the Development of Graft-versus-Host Disease in Pediatric Stem Cell Transplantation Patients

Simms-Waldrip, T. R., Sunkersett, G., Coughlin, L. A., Savani, M. R., Arana, C., Kim, J., Kim, M., Zhan, X., Greenberg, D. E., Xie, Y., Davies, S. M. & Koh, A., May 1 2017, In : Biology of Blood and Marrow Transplantation. 23, 5, p. 820-829 10 p.

Research output: Contribution to journalArticle

36 Scopus citations

Creatine maintains intestinal homeostasis and protects against colitis

Turer, E. E., McAlpine, W., Wang, K. W., Lu, T., Li, X., Tang, M., Zhan, X., Wang, T., Zhan, X., Bu, C. H., Murray, A. R. & Beutler, B. A., Feb 14 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1273-E1281

Research output: Contribution to journalArticle

16 Scopus citations

Genetic pleiotropy between age-related macular degeneration and 16 complex diseases and traits

International AMD Genomics Consortium (IAMDGC), Mar 27 2017, In : Genome Medicine. 9, 1, 29.

Research output: Contribution to journalArticle

25 Scopus citations

IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice

Choi, J. H., Wang, K. W., Zhang Ph.D., D-W., Zhan, X., Wang, T., Bu, C. H., Behrendt, C. L., Zeng, M., Wang, Y., Misawa, T., Li, X., Tang, M., Zhan, X., Scott, L., Hildebrand, S., Murray, A. R., Moresco, E. M. Y., Hooper, L. V. & Beutler, B. A., Feb 14 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1196-E1204

Research output: Contribution to journalArticle

17 Scopus citations

Meta-analysis approaches to combine multiple gene set enrichment studies

Lu, W., Wang, X., Zhan, X. & Gazdar, A. F., 2017, (Accepted/In press) In : Statistics in Medicine.

Research output: Contribution to journalArticle

2 Scopus citations

Rare and low-frequency coding variants alter human adult height

MAGIC Investigators, The EPIC-InterAct Consortium, EPIC-CVD Consortium, CHD Exome+ Consortium, ExomeBP Consortium, T2D-Genes Consortium, GoT2D Genes Consortium, Global Lipids Genetics Consortium & ReproGen Consortium, Feb 9 2017, In : Nature. 542, 7640, p. 186-190 5 p.

Research output: Contribution to journalArticle

194 Scopus citations

Recombinant haplotypes narrow the ARMS2/HTRA1 association signal for age-related macular degeneration

International AMD Genomics Consortium (IAMDGC), Feb 1 2017, In : Genetics. 205, 2, p. 919-924 6 p.

Research output: Contribution to journalArticle

24 Scopus citations

Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework

Li, M., Li, J., Li, M. J., Pan, Z., Hsu, J. S., Liu, D. J., Zhan, X., Junwen, W., Youqiang, S. & Sham, P. C., May 19 2017, In : Nucleic Acids Research. 45, 9, e75.

Research output: Contribution to journalArticle

10 Scopus citations

Severe Gut Microbiota Dysbiosis Is Associated with Poor Growth in Patients with Short Bowel Syndrome

Piper, H. G., Fan, D., Coughlin, L. A., Ho, E. X., McDaniel, M. M., Channabasappa, N., Kim, J., Kim, M., Zhan, X., Xie, Y. & Koh, A., Sep 1 2017, In : Journal of Parenteral and Enteral Nutrition. 41, 7, p. 1202-1212 11 p.

Research output: Contribution to journalArticle

23 Scopus citations
2018

Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors

Wang, Y., Cao, L., Lee, C. Y., Matsuo, T., Wu, K., Asher, G., Tang, L., Saitoh, T., Russell, J. L., Klewe-Nebenius, D., Wang, L., Soya, S., Hasegawa, E., Chérasse, Y., Zhou, J., Li, Y., Wang, T., Zhan, X., Miyoshi, C., Irukayama, Y. & 13 others, Cao, J., Meeks, J., Gautron, L., Wang, Z., Sakurai, K., Funato, H., Sakurai, T., Yanagisawa, M., Nagase, H., Kobayakawa, R., Kobayakawa, K., Beutler, B. A. & Liu, Q., Dec 1 2018, In : Nature Communications. 9, 1, 4324.

Research output: Contribution to journalArticle

4 Scopus citations

Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes

Jiang, Y., Chen, S., McGuire, D., Chen, F., Liu, M., Iacono, W. G., Hewitt, J. K., Hokanson, J. E., Krauter, K., Laakso, M., Li, K. W., Lutz, S. M., McGue, M., Pandit, A., Zajac, G. J. M., Boehnke, M., Abecasis, G. R., Vrieze, S. I., Zhan, X., Jiang, B. & 1 others, Liu, D. J., Jul 1 2018, In : PLoS Genetics. 14, 7, e1007452.

Research output: Contribution to journalArticle

5 Scopus citations

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

Turcot, V., Lu, Y., Highland, H. M., Schurmann, C., Justice, A. E., Fine, R. S., Bradfield, J. P., Esko, T., Giri, A., Graff, M., Guo, X., Hendricks, A. E., Karaderi, T., Lempradl, A., Locke, A. E., Mahajan, A., Marouli, E., Sivapalaratnam, S., Young, K. L., Alfred, T. & 380 others, Feitosa, M. F., Masca, N. G. D., Manning, A. K., Medina-Gomez, C., Mudgal, P., Ng, M. C. Y., Reiner, A. P., Vedantam, S., Willems, S. M., Winkler, T. W., Abecasis, G., Aben, K. K., Alam, D. S., Alharthi, S. E., Allison, M., Amouyel, P., Asselbergs, F. W., Auer, P. L., Balkau, B., Bang, L. E., Barroso, I., Bastarache, L., Benn, M., Bergmann, S., Bielak, L. F., Blüher, M., Boehnke, M., Boeing, H., Boerwinkle, E., Böger, C. A., Bork-Jensen, J., Bots, M. L., Bottinger, E. P., Bowden, D. W., Brandslund, I., Breen, G., Brilliant, M. H., Broer, L., Brumat, M., Burt, A. A., Butterworth, A. S., Campbell, P. T., Cappellani, S., Carey, D. J., Catamo, E., Caulfield, M. J., Chambers, J. C., Chasman, D. I., Chen, Y. D. 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H., Tönjes, A., Tromp, G., Trompet, S., Tsafantakis, E., Tuomilehto, J., Tybjaerg-Hansen, A., Tyrer, J. P., Uher, R., Uitterlinden, A. G., Uusitupa, M., Laan, S. W., Duijn, C. M., Leeuwen, N., Van Setten, J., Vanhala, M., Varbo, A., Varga, T. V., Varma, R., Velez Edwards, D. R., Vermeulen, S. H., Veronesi, G., Vestergaard, H., Vitart, V., Vogt, T. F., Völker, U., Vuckovic, D., Wagenknecht, L. E., Walker, M., Wallentin, L., Wang, F., Wang, C. A., Wang, S., Wang, Y., Ware, E. B., Wareham, N. J., Warren, H. R., Waterworth, D. M., Wessel, J., White, H. D., Willer, C. J., Wilson, J. G., Witte, D. R., Wood, A. R., Wu, Y., Yaghootkar, H., Yao, J., Yao, P., Yerges-Armstrong, L. M., Young, R., Zhan, X., Zhan, X., Zhang, W., Zhao, J. H., Zhao, W., Zhou, W., Zondervan, K. T., Rotter, J. I., Pospisilik, J. A., Rivadeneira, F., Borecki, I. B., Deloukas, P., Frayling, T. M., Lettre, G., North, K. E., Lindgren, C. M., Hirschhorn, J. N. & Loos, R. J. 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Research output: Contribution to journalArticle

79 Scopus citations
1 Scopus citations
2019

Assessment of circularized E7 RNA, GLUT1, and PD-L1 in anal squamous cell carcinoma

Chamseddin, B. H., Lee, E. E., Kim, J., Zhan, X., Yang, R., Murphy, K. M., Lewis, C., Hosler, G. A., Hammer, S. T. & Wang, R. C., Oct 1 2019, In : Oncotarget. 10, 57, p. 5958-5969 12 p.

Research output: Contribution to journalArticle

DEFOR: Depth- and frequency-based somatic copy number alteration detector

Zhang, H., Zhan, X., Brugarolas, J. & Xie, Y., Oct 1 2019, In : Bioinformatics. 35, 19, p. 3824-3825 2 p.

Research output: Contribution to journalArticle

Open Access

Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use

CHD Exome+ Consortium & Consortium for Genetics of Smoking Behaviour, Jun 1 2019, In : Biological Psychiatry. 85, 11, p. 946-955 10 p.

Research output: Contribution to journalArticle

6 Scopus citations

Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci

Understanding Society Scientific Group, EPIC-CVD, GSCAN, Consortium for Genetics of Smoking Behaviour, CHD Exome+ consortium, Jan 1 2019, (Accepted/In press) In : Molecular Psychiatry.

Research output: Contribution to journalArticle

3 Scopus citations

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution

T2D-Genes Consortium, The MAGIC Investigators, CHD Exome+ Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, InterAct & ReproGen Consortium, Mar 1 2019, In : Nature genetics. 51, 3, p. 452-469 18 p.

Research output: Contribution to journalArticle

12 Scopus citations

Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus

Zhao, J., Lee, E. E., Kim, J., Yang, R., Chamseddin, B., Ni, C., Gusho, E., Xie, Y., Chiang, C. M., Buszczak, M., Zhan, X., Laimins, L. & Wang, R. C., Dec 1 2019, In : Nature communications. 10, 1, 2300.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations