• Source: Scopus
  • Calculated based on no. of publications stored in Pure and citations from Scopus
1996 …2022

Research activity per year

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Search results

  • 2013

    Common genetic variants regulating ADD3 gene expression alter biliary atresia risk

    Cheng, G., Tang, C. S. M., Wong, E. H. M., Cheng, W. W. C., So, M. T., Miao, X., Zhang, R., Cui, L., Liu, X., Ngan, E. S. W., Lui, V. C. H., Chung, P. H. Y., Chan, I. H. Y., Liu, J., Zhong, W., Xia, H., Yu, J., Qiu, X., Wu, X. Z., Wang, B. & 13 others, Dong, X., Tou, J., Huang, L., Yi, B., Ren, H., Chan, E. K. W., Ye, K., O'Reilly, P. F., Wong, K. K. Y., Sham, P. C., Cherny, S. S., Tam, P. K. H. & Garcia-Barceló, M. M., Dec 2013, In: Journal of Hepatology. 59, 6, p. 1285-1291 7 p.

    Research output: Contribution to journalArticlepeer-review

    54 Scopus citations
  • 2012

    An integrated map of genetic variation from 1,092 human genomes

    Altshuler, D. M., Durbin, R. M., Abecasis, G. R., 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., Marth, G. T. & 371 others, McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Li, Z., Liu, X., Lu, Y., Ma, X., Su, Z., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Zhou, Y., Gupta, N., Clarke, L., Leinonen, R., Smith, R. E., 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., Fulton, R., Weinstock, G. M., 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., Auton, A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Coin, L. J. M., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Qin, N., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zhang, F., Zheng, H., Zhu, H., Garrison, E. P., Kural, D., Lee, W. P., Fung Leong, W., Ward, A. N., Wu, J., Zhang, M., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., Von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., McCarroll, S. A., Nemesh, J. C., Poplin, R. E., Schaffner, S. F., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Cheol Kim, K., Rausch, T., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Gottipati, S., Keinan, A., Rodriguez-Flores, J. L., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Bauer, M., Keira Cheetham, R., Cox, T., Eberle, M., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Squire, K., Xiao, C., Sebat, J., Bafna, V., Ye, K., Burchard, E. G., Hernandez, R. D., Gignoux, C. R., Haussler, D., Katzman, S. J., James Kent, W., Howie, B., Ruiz-Linares, A., Dermitzakis, E. T., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Min Kang, H., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Jun, G., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Kate Trost, M., Awadalla, P., Hodgkinson, A., Lunter, G., Marchini, J. L., Myers, S., Churchhouse, C., Delaneau, O., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Oleksyk, T. K., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Tyler-Smith, C., Albers, C. A., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Li, H., Scally, A., Walter, K., Xue, Y., Zhang, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Habegger, L., Harmanci, A. O., Jin, M., Khurana, E., Jasmine Mu, X., Sisu, C., Degenhardt, J., Stütz, A. M., Keira Cheetham, R., Church, D., Michaelson, J. J., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Mu, X. J., Fowler, G., Hale, W., Kalra, D., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Vaughan, B., Ananiev, V., Belaia, Z., Beloslyudtsev, D., Bouk, N., Chen, C., 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., Barnes, K. C., Beiswanger, C., Cai, H., Cao, H., Gharani, N., Henn, B., Jones, D., Kaye, J. S., Kent, A., Kerasidou, A., Mathias, R., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Tian, Z., Tishkoff, S., Toji, L. H., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ming, C. Z., Yang, G., Jia You, C., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Guyer, M. S., Peterson, J. L. & Lacroute, P., Nov 1 2012, In: Nature. 491, 7422, p. 56-65 10 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    5473 Scopus citations
  • De Novo Gene Disruptions in Children on the Autistic Spectrum

    Iossifov, I., Ronemus, M., Levy, D., Wang, Z., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y. H., Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K. & 15 others, Ghiban, E., Kramer, M., Parla, J., Demeter, R., Fulton, L. L., Fulton, R. S., Magrini, V. J., Ye, K., Darnell, J. C., Darnell, R. B., Mardis, E. R., Wilson, R. K., Schatz, M. C., McCombie, R. W. & Wigler, M., Apr 26 2012, In: Neuron. 74, 2, p. 285-299 15 p.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    984 Scopus citations
  • Design and statistical analysis of pooled next generation sequencing for rare variants

    Wang, T., Lin, C. Y., Zhang, Y., Wen, R. & Ye, K., 2012, In: Journal of Probability and Statistics. 524724.

    Research output: Contribution to journalArticlepeer-review

    Open Access
    4 Scopus citations
  • 21 Scopus citations
  • Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens

    Kotorashvili, A., Ramnauth, A., Liu, C., Lin, J., Ye, K., Kim, R., Hazan, R., Rohan, T., Fineberg, S. & Loudig, O., Apr 13 2012, In: PloS one. 7, 4, e34683.

    Research output: Contribution to journalArticlepeer-review

    51 Scopus citations
  • Gene Size Matters

    Mirina, A., Atzmon, G., Ye, K. & Bergman, A., Nov 9 2012, In: PloS one. 7, 11, e49093.

    Research output: Contribution to journalArticlepeer-review

    17 Scopus citations
  • Genotype copy number variations using Gaussian mixture models: Theory and algorithms

    Lin, C. Y., Lo, Y. & Ye, K. Q., Sep 2012, In: Statistical Applications in Genetics and Molecular Biology. 11, 5, 5.

    Research output: Contribution to journalArticlepeer-review

    2 Scopus citations
  • Reducing system noise in copy number data using principal components of self-self hybridizations

    Lee, Y. H., Ronemus, M., Kendall, J., Lakshmi, B., Leotta, A., Levy, D., Esposito, D., Grubor, V., Ye, K., Wigler, M. & Yamroma, B., Jan 17 2012, In: Proceedings of the National Academy of Sciences of the United States of America. 109, 3, p. E103-E110

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations
  • 2011

    Detecting multiple causal rare variants in exome sequence data

    Ye, K. Q. & Engelman, C. D., 2011, In: Genetic Epidemiology. 35, SUPPL. 1, p. S18-S21

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples

    Wang, T., Pradhan, K., Ye, K., Wong, L. J. & Rohan, T. E., 2011, In: Frontiers in Genetics. 2, AUG, Article 51.

    Research output: Contribution to journalArticlepeer-review

    10 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 journalArticlepeer-review

    787 Scopus citations
  • Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders

    Levy, D., Ronemus, M., Yamrom, B., Lee, Y. H., Leotta, A., Kendall, J., Marks, S., Lakshmi, B., Pai, D., Ye, K., Buja, A., Krieger, A., Yoon, S., Troge, J., Rodgers, L., Iossifov, I. & Wigler, M., Jun 9 2011, In: Neuron. 70, 5, p. 886-897 12 p.

    Research output: Contribution to journalArticlepeer-review

    500 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 journalArticlepeer-review

    Open Access
    5750 Scopus citations
  • Genome-wide analysis of DNA binding and transcriptional regulation by the mammalian Doublesex homolog DMRT1 in the juvenile testis

    Murphy, M. W., Sarver, A. L., Rice, D., Hatzi, K., Ye, K., Melnick, A., Heckert, L. L., Zarkower, D. & Bardwell, V. J., Jul 27 2010, In: Proceedings of the National Academy of Sciences of the United States of America. 107, 30, p. 13360-13365 6 p.

    Research output: Contribution to journalArticlepeer-review

    71 Scopus citations
  • Resequencing of pooled DNA for detecting disease associations with rare variants

    Wang, T., Lin, C. Y., Rohan, T. E. & Ye, K., Jul 2010, In: Genetic Epidemiology. 34, 5, p. 492-501 10 p.

    Research output: Contribution to journalArticlepeer-review

    21 Scopus citations
  • 2009

    A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped

    Wang, T., Ho, G., Ye, K., Strickler, H. & Elston, R. C., 2009, In: Genetic Epidemiology. 33, 1, p. 6-15 10 p.

    Research output: Contribution to journalArticlepeer-review

    37 Scopus citations
  • High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

    Hodges, E., Smith, A. D., Kendall, J., Xuan, Z., Ravi, K., Rooks, M., Zhang, M. Q., Ye, K., Bhattacharjee, A., Brizuela, L., McCombie, W. R., Wigler, M., Hannon, G. J. & Hicks, J. B., Sep 2009, In: Genome research. 19, 9, p. 1593-1605 13 p.

    Research output: Contribution to journalArticlepeer-review

    181 Scopus citations
  • Model-robust supersaturated and partially supersaturated designs

    Jones, B. A., Li, W., Nachtsheim, C. J. & Ye, K. Q., Jan 2009, In: Journal of Statistical Planning and Inference. 139, 1, p. 45-53 9 p.

    Research output: Contribution to journalArticlepeer-review

    14 Scopus citations
  • Sensitive and accurate detection of copy number variants using read depth of coverage

    Yoon, S., Xuan, Z., Makarov, V., Ye, K. & Sebat, J., Sep 2009, In: Genome research. 19, 9, p. 1586-1592 7 p.

    Research output: Contribution to journalArticlepeer-review

    430 Scopus citations
  • The BCL6 transcriptional program features repression of multiple oncogenes in primary B cells and is deregulated in DLBCL

    Ci, W., Polo, J. M., Cerchietti, L., Shaknovich, R., Wang, L., Shao, N. Y., Ye, K., Farinha, P., Horsman, D. E., Gascoyne, R. D., Elemento, O. & Melnick, A., 2009, In: Blood. 113, 22, p. 5536-5548 13 p.

    Research output: Contribution to journalArticlepeer-review

    164 Scopus citations
  • 2008

    An integrative genomic and epigenomic approach for the study of transcriptional regulation

    Figueroa, M. E., Reimers, M., Thompson, R. F., Ye, K., Li, Y., Selzer, R. R., Fridriksson, J., Paietta, E., Wiernik, P., Green, R. D., Greally, J. M. & Melnick, A., Mar 26 2008, In: PloS one. 3, 3, e1882.

    Research output: Contribution to journalArticlepeer-review

    76 Scopus citations
  • Computing power and sample size for case-control association studies with copy number polymorphism: Application of mixture-based likelihood ratio test

    Kim, W., Gordon, D., Sebat, J., Ye, K. Q. & Finch, S. J., Oct 22 2008, In: PloS one. 3, 10, e3475.

    Research output: Contribution to journalArticlepeer-review

    13 Scopus citations
  • Meta-analysis of microarray studies reveals a novel hematopoietic progenitor cell signature and demonstrates feasibility of inter-platform data integration

    Sohal, D., Yeatts, A., Ye, K., Pellagatti, A., Zhou, L., Pahanish, P., Mo, Y., Bhagat, T., Mariadason, J., Boultwood, J., Melnick, A., Greally, J. & Verma, A., Aug 13 2008, In: PloS one. 3, 8, e2965.

    Research output: Contribution to journalArticlepeer-review

    22 Scopus citations
  • 2007

    A unified genetic theory for sporadic and inherited autism

    Zhao, X., Leotta, A., Kustanovich, V., Lajonchere, C., Geschwind, D. H., Law, K., Law, P., Qiu, S., Lord, C., Sebat, J., Ye, K. & Wigler, M., Jul 31 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 31, p. 12831-12836 6 p.

    Research output: Contribution to journalArticlepeer-review

    233 Scopus citations
  • Buffering mechanisms in aging: A systems approach toward uncovering the genetic component of aging

    Bergman, A., Atzmon, G., Ye, K., MacCarthy, T. & Barzilai, N., Aug 2007, In: PLoS Computational Biology. 3, 8, p. 1648-1656 9 p.

    Research output: Contribution to journalArticlepeer-review

    98 Scopus citations
  • Model discrimination-another perspective on model-robust designs

    Jones, B. A., Li, W., Nachtsheim, C. J. & Ye, K. Q., May 1 2007, In: Journal of Statistical Planning and Inference. 137, 5, p. 1576-1583 8 p.

    Research output: Contribution to journalArticlepeer-review

    19 Scopus citations
  • Positive association of schizophrenia to JARID2 gene

    Pedrosa, E., Ye, K., Nolan, K. A., Morrell, L., Okun, J. M., Persky, A. D., Saito, T. & Lachman, H. M., Jan 5 2007, In: American Journal of Medical Genetics, Part B: Neuropsychiatric Genetics. 144, 1, p. 45-51 7 p.

    Research output: Contribution to journalArticlepeer-review

    26 Scopus citations
  • Strong association of de novo copy number mutations with autism

    Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., Leotta, A., Pai, D., Zhang, R., Lee, Y. H., Hicks, J., Spence, S. J., Lee, A. T., Puura, K., Lehtimäki, T., Ledbetter, D. & 12 others, Gregersen, P. K., Bregman, J., Sutcliffe, J. S., Jobanputra, V., Chung, W., Warburton, D., King, M. C., Skuse, D., Geschwind, D. H., Gilliam, T. C., Ye, K. & Wigler, M., Apr 20 2007, In: Science. 316, 5823, p. 445-449 5 p.

    Research output: Contribution to journalArticlepeer-review

    2039 Scopus citations
  • Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas

    Polo, J. M., Juszczynski, P., Monti, S., Cerchietti, L., Ye, K., Greally, J. M., Shipp, M. & Melnick, A., Feb 27 2007, In: Proceedings of the National Academy of Sciences of the United States of America. 104, 9, p. 3207-3212 6 p.

    Research output: Contribution to journalArticlepeer-review

    106 Scopus citations
  • 2006

    Analysis of polymorphisms in AT-rich domains of neuregulin 1 gene in schizophrenia

    Lachman, H. M., Pedrosa, E., Nolan, K. A., Glass, M., Ye, K. & Saito, T., Jan 5 2006, In: American Journal of Medical Genetics - Neuropsychiatric Genetics. 141 B, 1, p. 102-109 8 p.

    Research output: Contribution to journalArticlepeer-review

    34 Scopus citations
  • Comparative isoschizomer profiling of cytosine methylation: The HELP assay

    Khulan, B., Thompson, R. F., Ye, K., Fazzari, M. J., Suzuki, M., Stasiek, E., Figueroa, M. E., Glass, J. L., Chen, Q., Montagna, C., Hatchwell, E., Selzer, R. R., Richmond, T. A., Green, R. D., Melnick, A. & Greally, J. M., 2006, In: Genome research. 16, 8, p. 1046-1055 10 p.

    Research output: Contribution to journalArticlepeer-review

    332 Scopus citations
  • Novel patterns of genome rearrangement and their association with survival in breast cancer

    Hicks, J., Krasnitz, A., Lakshmi, B., Navin, N. E., Riggs, M., Leibu, E., Esposito, D., Alexander, J., Troge, J., Grubor, V., Yoon, S., Wigler, M., Ye, K., Børresen-Dale, A. L., Naume, B., Schlicting, E., Norton, L., Hägerström, T., Skoog, L., Auer, G. & 3 others, Månér, S., Lundin, P. & Zetterberg, A., Dec 2006, In: Genome research. 16, 12, p. 1465-1479 15 p.

    Research output: Contribution to journalArticlepeer-review

    264 Scopus citations
  • Variable selection for Gaussian process models in computer experiments

    Linkletter, C., Bingham, D., Hengartner, N., Higdon, D. & Ye, K. Q., Nov 2006, Technometrics, 48, 4, p. 478-490 13 p.

    Research output: Contribution to specialist publicationArticle

    91 Scopus citations
  • 2005

    A Bayesian approach for applying Haseman-Elston methods

    Yoon, S., Suh, Y. J., Mendell, N. R. & Ye, K. Q., Dec 30 2005, In: BMC genetics. 6, SUPPL.1, S39.

    Research output: Contribution to journalArticlepeer-review

    3 Scopus citations
  • A gene-model-free method for linkage analysis of a disease-related-trait based on analysis of proband/sibling pairs

    Sung, H., Finch, S. J., Ye, K. Q. & Mendell, N. R., Dec 30 2005, In: BMC genetics. 6, SUPPL.1, S47.

    Research output: Contribution to journalArticlepeer-review

    2 Scopus citations
  • Mechanical modulation of molecular signals which regulate anabolic and catabolic activity in bone tissue

    Judex, S., Zhong, N., Squire, M. E., Ye, K., Donahue, L. R., Hadjiargyrou, M. & Rubin, C. T., Apr 1 2005, In: Journal of Cellular Biochemistry. 94, 5, p. 982-994 13 p.

    Research output: Contribution to journalArticlepeer-review

    52 Scopus citations
  • Power for complex trait genetic association

    Gordon, D., De La Vega, F. M., Finch, S. J. & Ye, K. Q., Sep 2005, In: Clinical Neuroscience Research. 5, 1 SPEC. ISS., p. 31-35 5 p.

    Research output: Contribution to journalArticlepeer-review

    2 Scopus citations
  • Shock wave interactions in spherical and perturbed spherical geometries

    Dutta, S., George, E., Glimm, J., Grove, J. W., Jin, H., Lee, T., Li, X., Sharp, D. H., Ye, K., Yu, Y., Zhang, Y. & Zhao, M., Nov 30 2005, In: Nonlinear Analysis, Theory, Methods and Applications. 63, 5-7, p. 644-652 9 p.

    Research output: Contribution to journalArticlepeer-review

    4 Scopus citations
  • Statistical riemann problems and a composition law for errors in numerical solutions of shock physics problems

    Glimm, J., Grove, J. W., Kang, Y., Lee, T., Li, X., Sharp, D. H., Yu, Y., Ye, K. & Zhao, M., 2005, In: SIAM Journal on Scientific Computing. 26, 2, p. 666-697 32 p.

    Research output: Contribution to journalArticlepeer-review

    8 Scopus citations
  • Using mixture models to characterize disease-related traits

    Duan, T., Finch, S. J., Ye, K. Q., Chase, G. A. & Mendell, N. R., Dec 30 2005, In: BMC genetics. 6, SUPPL.1, S99.

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations
  • 2004

    A note on regular fractional factorial designs

    Ye, K. Q., Oct 1 2004, In: Statistica Sinica. 14, 4, p. 1069-1074 6 p.

    Research output: Contribution to journalArticlepeer-review

    16 Scopus citations
  • Blocked nonregular two-level factorial designs

    Cheng, S. W., Li, W. & Ye, K. Q., Aug 2004, Technometrics, 46, 3, p. 269-279 11 p.

    Research output: Contribution to specialist publicationArticle

    36 Scopus citations
  • Geometric isomorphism and minimum aberration for factorial designs with quantitative factors

    Cheng, S. W. & Ye, K. Q., Oct 2004, In: Annals of Statistics. 32, 5, p. 2168-2185 18 p.

    Research output: Contribution to journalArticlepeer-review

    87 Scopus citations
  • Large-scale copy number polymorphism in the human genome

    Sebat, J., Lakshmi, B., Troge, J., Alexander, J., Young, J., Lundin, P., Månér, S., Massa, H., Walker, M., Chi, M., Navin, N., Lucito, R., Healy, J., Hicks, J., Ye, K., Reiner, A., Gilliam, T. C., Trask, B., Patterson, N., Zetterberg, A. & 1 others, Wigler, M., Jul 23 2004, In: Science. 305, 5683, p. 525-528 4 p.

    Research output: Contribution to journalArticlepeer-review

    1929 Scopus citations
  • Sources of uncertainty and error in the simulation of flow in porous media

    Glimm, J., Hou, S., Lee, Y. H., Sharp, D. H. & Ye, K., 2004, In: Computational and Applied Mathematics. 23, 2-3, p. 109-120 12 p.

    Research output: Contribution to journalArticlepeer-review

    10 Scopus citations
  • 2003

    Adaptations of trabecular bone to low magnitude vibrations result in more uniform stress and strain under load

    Judex, S., Boyd, S., Quin, Y. X., Turner, S., Ye, K., Müller, R. & Rubin, C., 2003, In: Annals of Biomedical Engineering. 31, 1, p. 12-20 9 p.

    Research output: Contribution to journalArticlepeer-review

    90 Scopus citations
  • A method for evaluating the results of Bayesian model selection: Application to linkage analyses of attributes determined by two or more genes

    Suh, Y. J., Ye, K. Q. & Mendell, N. R., 2003, In: Human Heredity. 55, 2-3, p. 147-152 6 p.

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations
  • Data Mining and Computationally Intensive Methods: Summary of Group 7 Contributions to Genetic Analysis Workshop 13

    Costello, T. J., Falk, C. T. & Ye, K. Q., 2003, In: Genetic Epidemiology. 25, SUPPL. 1, p. S57-S63

    Research output: Contribution to journalArticlepeer-review

    5 Scopus citations
  • Indicator function and its application in two-level factorial designs

    Ye, K. Q., Jun 2003, In: Annals of Statistics. 31, 3, p. 984-994 11 p.

    Research output: Contribution to journalArticlepeer-review

    77 Scopus citations