Section of Computational Biology

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  • 2023

    Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials

    Peehl, D. M., Badea, C. T., Chenevert, T. L., Daldrup-Link, H. E., Ding, L., Dobrolecki, L. E., Houghton, A. M. G., Kinahan, P. E., Kurhanewicz, J., Lewis, M. T., Li, S., Luker, G. D., Ma, C. X., Manning, H. C., Mowery, Y. M., O’Dwyer, P. J., Pautler, R. G., Rosen, M. A., Roudi, R., Ross, B. D., & 5 othersShoghi, K. I., Sriram, R., Talpaz, M., Wahl, R. L. & Zhou, R., Apr 2023, In: Tomography (Ann Arbor, Mich.). 9, 2, p. 657-680 24 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    2 Scopus citations
  • Proteogenomic data and resources for pan-cancer analysis

    Clinical Proteomic Tumor Analysis Consortium, Aug 14 2023, In: Cancer Cell. 41, 8, p. 1397-1406 10 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    7 Scopus citations
  • 2022

    Cancer proteogenomics: current impact and future prospects

    Mani, D. R., Krug, K., Zhang, B., Satpathy, S., Clauser, K. R., Ding, L., Ellis, M., Gillette, M. A. & Carr, S. A., May 2022, In: Nature Reviews Cancer. 22, 5, p. 298-313 16 p.

    Research output: Contribution to journalReview articlepeer-review

    61 Scopus citations
  • 2021

    Moving pan-cancer studies from basic research toward the clinic

    Chen, F., Wendl, M. C., Wyczalkowski, M. A., Bailey, M. H., Li, Y. & Ding, L., Sep 2021, In: Nature Cancer. 2, 9, p. 879-890 12 p.

    Research output: Contribution to journalReview articlepeer-review

    33 Scopus citations
  • RNA splicing and immune-checkpoint inhibition

    Ding, L. & Odunsi, K., Nov 4 2021, In: New England Journal of Medicine. 385, 19, p. 1807-1809 3 p.

    Research output: Contribution to journalReview articlepeer-review

    3 Scopus citations
  • 2020

    The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

    Human Tumor Atlas Network, Apr 16 2020, In: Cell. 181, 2, p. 236-249 14 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    231 Scopus citations
  • Tumor-on-a-chip platform to interrogate the role of macrophages in tumor progression

    Bi, Y., Shirure, V. S., Liu, R., Cunningham, C., Ding, L., Meacham, J. M., Goedegebuure, S. P., George, S. C. & Fields, R. C., Sep 1 2020, In: Integrative Biology. 12, 9, p. 221-232 12 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    35 Scopus citations
  • 2015

    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 othersMarth, 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 journalReview articlepeer-review

    Open Access
    9902 Scopus citations
  • 2014

    Expanding the computational toolbox for mining cancer genomes

    Ding, L., Wendl, M. C., McMichael, J. F. & Raphael, B. J., Aug 2014, In: Nature Reviews Genetics. 15, 8, p. 556-570 15 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    142 Scopus citations
  • 2013

    Advances for studying clonal evolution in cancer

    Ding, L., Raphael, B. J., Chen, F. & Wendl, M. C., Nov 1 2013, In: Cancer Letters. 340, 2, p. 212-219 8 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    55 Scopus citations
  • Computational approaches to identify functional genetic variants in cancer genomes

    Gonzalez-Perez, A., Mustonen, V., Reva, B., Ritchie, G. R. S., Creixell, P., Karchin, R., Vazquez, M., Fink, J. L., Kassahn, K. S., Pearson, J. V., Bader, G. D., Boutros, P. C., Muthuswamy, L., Ouellette, B. F. F., Reimand, J., Linding, R., Shibata, T., Valencia, A., Butler, A., Dronov, S., & 8 othersFlicek, P., Shannon, N. B., Carter, H., Li, D., Sander, C., Stuart, J. M., Stein, L. D. & Lopez-Bigas, N., Aug 2013, In: Nature Methods. 10, 8, p. 723-729 7 p.

    Research output: Contribution to journalReview articlepeer-review

    132 Scopus citations
  • 2012

    Computational models for mechanics of morphogenesis

    Wyczalkowski, M. A., Chen, Z., Filas, B. A., Varner, V. D. & Taber, L. A., Jun 2012, In: Birth Defects Research Part C - Embryo Today: Reviews. 96, 2, p. 132-152 21 p.

    Research output: Contribution to journalReview articlepeer-review

    77 Scopus citations
  • The pediatric cancer genome project

    Downing, J. R., Wilson, R. K., Zhang, J., Mardis, E. R., Pui, C. H., Ding, L., Ley, T. J. & Evans, W. E., Jun 2012, In: Nature Genetics. 44, 6, p. 619-622 4 p.

    Research output: Contribution to journalReview articlepeer-review

    267 Scopus citations
  • 2010

    Challenges of sequencing human genomes

    Koboldt, D. C., Ding, L., Mardis, E. R. & Wilson, R. K., Sep 20 2010, In: Briefings in Bioinformatics. 11, 5, p. 484-498 15 p., bbq016.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    116 Scopus citations
  • 2006

    A general coverage theory for shotgun DNA sequencing

    Wendl, M. C., Jul 2006, In: Journal of Computational Biology. 13, 6, p. 1177-1196 20 p.

    Research output: Contribution to journalReview articlepeer-review

    14 Scopus citations
  • 2002

    Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing

    Wendl, M. C. & Waterston, R. H., Dec 1 2002, In: Genome research. 12, 12, p. 1943-1949 7 p.

    Research output: Contribution to journalReview articlepeer-review

    Open Access
    23 Scopus citations
  • 2001

    Automated processing of raw DNA sequence data: A software framework for practically "hands-off" analysis and handling of DNA data

    Wendl, M. C., Korf, I., Chinwalla, A. T. & Hillier, L. W., 2001, In: IEEE Engineering in Medicine and Biology Magazine. 20, 4, p. 41-48 8 p.

    Research output: Contribution to journalReview articlepeer-review

    1 Scopus citations