Michael Wendl

2023

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clinical Proteomic Tumor Analysis Consortium, Jan 9 2023, In: Cancer Cell. 41, 1, p. 139-163.e17

Research output: Contribution to journal › Article › peer-review

Open Access

2022

Pollock: fishing for cell states

Storrs, E. P., Zhou, D. C., Wendl, M. C., Wyczalkowski, M. A., Karpova, A., Wang, L. B., Li, Y., Southard-Smith, A., Jayasinghe, R. G., Yao, L., Liu, R., Wu, Y., Terekhanova, N. V., Zhu, H., Herndon, J. M., Puram, S., Chen, F., Gillanders, W. E., Fields, R. C. & Ding, L., 2022, In: Bioinformatics Advances. 2, 1, vbac028.

Research output: Contribution to journal › Article › peer-review

Open Access

Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer

Cui Zhou, D., Jayasinghe, R. G., Chen, S., Herndon, J. M., Iglesia, M. D., Navale, P., Wendl, M. C., Caravan, W., Sato, K., Storrs, E., Mo, C. K., Liu, J., Southard-Smith, A. N., Wu, Y., Naser Al Deen, N., Baer, J. M., Fulton, R. S., Wyczalkowski, M. A., Liu, R., Fronick, C. C., & 46 othersFulton, L. A., Shinkle, A., Thammavong, L., Zhu, H., Sun, H., Wang, L. B., Li, Y., Zuo, C., McMichael, J. F., Davies, S. R., Appelbaum, E. L., Robbins, K. J., Chasnoff, S. E., Yang, X., Reeb, A. N., Oh, C., Serasanambati, M., Lal, P., Varghese, R., Mashl, J. R., Ponce, J., Terekhanova, N. V., Yao, L., Wang, F., Chen, L., Schnaubelt, M., Lu, R. J. H., Schwarz, J. K., Puram, S. V., Kim, A. H., Song, S. K., Shoghi, K. I., Lau, K. S., Ju, T., Chen, K., Chatterjee, D., Hawkins, W. G., Zhang, H., Achilefu, S., Chheda, M. G., Oh, S. T., Gillanders, W. E., Chen, F., DeNardo, D. G., Fields, R. C. & Ding, L., Sep 2022, In: Nature Genetics. 54, 9, p. 1390-1405 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

2021

AeQTL: eQTL analysis using region-based aggregation of rare genomic variants

Dong, G., Wendl, M. C., Zhang, B., Ding, L. & Huang, K. L., 2021, In: Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 26, p. 172-183 12 p.

Research output: Contribution to journal › Article › peer-review

Co-evolution of tumor and immune cells during progression of multiple myeloma

Liu, R., Gao, Q., Foltz, S. M., Fowles, J. S., Yao, L., Wang, J. T., Cao, S., Sun, H., Wendl, M. C., Sethuraman, S., Weerasinghe, A., Rettig, M. P., Storrs, E. P., Yoon, C. J., Wyczalkowski, M. A., McMichael, J. F., Kohnen, D. R., King, J., Goldsmith, S. R., O’Neal, J., & 9 othersFulton, R. S., Fronick, C. C., Ley, T. J., Jayasinghe, R. G., Fiala, M. A., Oh, S. T., DiPersio, J. F., Vij, R. & Ding, L., Dec 1 2021, In: Nature communications. 12, 1, 2559.

Research output: Contribution to journal › Article › peer-review

Open Access

28 Scopus citations

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment

The NCI PDXNet Consortium, Dec 1 2021, In: Nature communications. 12, 1, 5086.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

PDXNET Consortium & EurOPDX Consortium, Jan 2021, In: Nature Genetics. 53, 1, p. 86-99 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

71 Scopus citations

MSIsensor-ct: Microsatellite instability detection using cfDNA sequencing data

Han, X., Zhang, S., Zhou, D. C., Wang, D., He, X., Yuan, D., Li, R., He, J., Duan, X., Wendl, M. C., Ding, L. & Niu, B., Sep 1 2021, In: Briefings in Bioinformatics. 22, 5, bbaa402.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Proteogenomic and metabolomic characterization of human glioblastoma

Clinical Proteomic Tumor Analysis Consortium, Apr 12 2021, In: Cancer Cell. 39, 4, p. 509-528.e20

Research output: Contribution to journal › Article › peer-review

Open Access

133 Scopus citations

Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma

Clinical Proteomic Tumor Analysis Consortium, Mar 8 2021, In: Cancer Cell. 39, 3, p. 361-379.e16

Research output: Contribution to journal › Article › peer-review

Open Access

100 Scopus citations

Spatially interacting phosphorylation sites and mutations in cancer

Huang, K. L., Scott, A. D., Zhou, D. C., Wang, L. B., Weerasinghe, A., Elmas, A., Liu, R., Wu, Y., Wendl, M. C., Wyczalkowski, M. A., Baral, J., Sengupta, S., Lai, C. W., Ruggles, K., Payne, S. H., Raphael, B., Fenyö, D., Chen, K., Mills, G. & Ding, L., Dec 1 2021, In: Nature communications. 12, 1, 2313.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

2020

Discovery of driver non-coding splice-site-creating mutations in cancer

Cao, S., Zhou, D. C., Oh, C., Jayasinghe, R. G., Zhao, Y., Yoon, C. J., Wyczalkowski, M. A., Bailey, M. H., Tsou, T., Gao, Q., Malone, A., Reynolds, S., Shmulevich, I., Wendl, M. C., Chen, F. & Ding, L., Dec 1 2020, In: Nature communications. 11, 1, 5573.

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus citations

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 82-93 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

1058 Scopus citations

Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma

Clinical Proteomic Tumor Analysis Consortium, Jul 9 2020, In: Cell. 182, 1, p. 200-225.e35

Research output: Contribution to journal › Article › peer-review

Open Access

209 Scopus citations

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

MC3 Working Group, PCAWG novel somatic mutation calling methods working group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4748.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

Sex differences in oncogenic mutational processes

PCAWG Tumour Subtypes and Clinical Translation & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 4330.

Research output: Contribution to journal › Article › peer-review

Open Access

33 Scopus citations

2019

Integrated transcriptomic–genomic tool Texomer profiles cancer tissues

Wang, F., Zhang, S., Kim, T. B., Lin, Y. Y., Iqbal, R., Wang, Z., Mohanty, V., Sircar, K., Karam, J. A., Wendl, M. C., Meric-Bernstam, F., Weinstein, J. N., Ding, L., Mills, G. B. & Chen, K., May 1 2019, In: Nature Methods. 16, 5, p. 401-404 4 p.

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Regulated phosphosignaling associated with breast cancer subtypes and druggability

Huang, K. L., Wu, Y., Primeau, T., Wang, Y. T., Gao, Y., McMichael, J. F., Scott, A. D., Cao, S., Wendl, M. C., Johnson, K. J., Ruggles, K., Held, J., Payne, S. H., Davies, S., Dar, A., Kinsinger, C. R., Mesri, M., Rodriguez, H., Ellis, M. J., Reid Townsend, R., & 6 othersChen, F., Fenyö, D., Li, S., Liu, T., Carr, S. A. & Ding, L., 2019, In: Molecular and Cellular Proteomics. 18, 8, p. 1630-1650 21 p.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

2018

Comprehensive Characterization of Cancer Driver Genes and Mutations

The MC3 Working Group & The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 371-385.e18

Research output: Contribution to journal › Article › peer-review

Open Access

952 Scopus citations

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

The Fusion Analysis Working Group & The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 227-238.e3

Research output: Contribution to journal › Article › peer-review

Open Access

279 Scopus citations

Integrative omics analyses broaden treatment targets in human cancer

Sengupta, S., Sun, S. Q., Huang, K. L., Oh, C., Bailey, M. H., Varghese, R., Wyczalkowski, M. A., Ning, J., Tripathi, P., McMichael, J. F., Johnson, K. J., Kandoth, C., Welch, J., Ma, C., Wendl, M. C., Payne, S. H., Fenyö, D., Townsend, R. R., Dipersio, J. F., Chen, F., & 1 othersDing, L., Jul 27 2018, In: Genome medicine. 10, 1, 60.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Pathogenic Germline Variants in 10,389 Adult Cancers

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 355-370.e14

Research output: Contribution to journal › Article › peer-review

Open Access

403 Scopus citations

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

The Cancer Genome Atlas Research Network, Apr 5 2018, In: Cell. 173, 2, p. 305-320.e10

Research output: Contribution to journal › Article › peer-review

Open Access

178 Scopus citations

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

The Cancer Genome Atlas Research Network, Apr 3 2018, In: Cell Reports. 23, 1, p. 270-281.e3

Research output: Contribution to journal › Article › peer-review

Open Access

136 Scopus citations

2017

BreakPoint Surveyor: A pipeline for structural variant visualization

Wyczalkowski, M. A., Wylie, K. M., Cao, S., Mclellan, M. D., Flynn, J., Huang, M., Ye, K., Fan, X., Chen, K., Wendl, M. C. & Ding, L., Oct 1 2017, In: Bioinformatics. 33, 19, p. 3121-3122 2 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Huang, K. L., Li, S., Mertins, P., Cao, S., Gunawardena, H. P., Ruggles, K. V., Mani, D. R., Clauser, K. R., Tanioka, M., Usary, J., Kavuri, S. M., Xie, L., Yoon, C., Qiao, J. W., Wrobel, J., Wyczalkowski, M. A., Erdmann-Gilmore, P., Snider, J. E., Hoog, J., Singh, P., & 25 othersNiu, B., Guo, Z., Sun, S. Q., Sanati, S., Kawaler, E., Wang, X., Scott, A., Ye, K., McLellan, M. D., Wendl, M. C., Malovannaya, A., Held, J. M., Gillette, M. A., Fenyö, D., Kinsinger, C. R., Mesri, M., Rodriguez, H., Davies, S. R., Perou, C. M., Ma, C., Townsend, R. R., Chen, X., Carr, S. A., Ellis, M. J. & Ding, L., Apr 25 2017, In: Nature communications. 8, p. 15479 1 p., 15479.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

GenomeVIP: A cloud platform for genomic variant discovery and interpretation

Mashl, R. J., Scott, A. D., Huang, K. L., Wyczalkowski, M. A., Yoon, C. J., Niu, B., DeNardo, E., Yellapantula, V. D., Handsaker, R. E., Chen, K., Koboldt, D. C., Ye, K., Fenyö, D., Raphael, B. J., Wendl, M. C. & Ding, L., Aug 2017, In: Genome research. 27, 8, p. 1450-1459 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus citations

Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Huang, K. L., Li, S., Mertins, P., Cao, S., Gunawardena, H. P., Ruggles, K. V., Mani, D. R., Clauser, K. R., Tanioka, M., Usary, J., Kavuri, S. M., Xie, L., Yoon, C., Qiao, J. W., Wrobel, J., Wyczalkowski, M. A., Erdmann-Gilmore, P., Snider, J. E., Hoog, J., Singh, P., & 25 othersNiu, B., Guo, Z., Sun, S. Q., Sanati, S., Kawaler, E., Wang, X., Scott, A., Ye, K., McLellan, M. D., Wendl, M. C., Malovannaya, A., Held, J. M., Gillette, M. A., Fenyö, D., Kinsinger, C. R., Mesri, M., Rodriguez, H., Davies, S. R., Perou, C. M., Ma, C., Reid Townsend, R., Chen, X., Carr, S. A., Ellis, M. J. & Ding, L., Mar 28 2017, In: Nature communications. 8, 14864.

Research output: Contribution to journal › Article › peer-review

Open Access

88 Scopus citations

2016

Divergent viral presentation among human tumors and adjacent normal tissues

Cao, S., Wendl, M. C., Wyczalkowski, M. A., Wylie, K., Ye, K., Jayasinghe, R., Xie, M., Wu, S., Niu, B., Grubb, R., Johnson, K. J., Gay, H., Chen, K., Rader, J. S., Dipersio, J. F., Chen, F. & Ding, L., Jun 24 2016, In: Scientific reports. 6, 28294.

Research output: Contribution to journal › Article › peer-review

Open Access

50 Scopus citations

Protein-structure-guided discovery of functional mutations across 19 cancer types

Niu, B., Scott, A. D., Sengupta, S., Bailey, M. H., Batra, P., Ning, J., Wyczalkowski, M. A., Liang, W. W., Zhang, Q., McLellan, M. D., Sun, S. Q., Tripathi, P., Lou, C., Ye, K., Jay Mashl, R., Wallis, J., Wendl, M. C., Chen, F. & Ding, L., Aug 1 2016, In: Nature Genetics. 48, 8, p. 827-837 11 p.

Research output: Contribution to journal › Article › peer-review

89 Scopus citations

Systematic discovery of complex insertions and deletions in human cancers

Ye, K., Wang, J., Jayasinghe, R., Lameijer, E. W., McMichael, J. F., Ning, J., McLellan, M. D., Xie, M., Cao, S., Yellapantula, V., Huang, K. L., Scott, A., Foltz, S., Niu, B., Johnson, K. J., Moed, M., Slagboom, P. E., Chen, F., Wendl, M. C. & Ding, L., Jan 1 2016, In: Nature medicine. 22, 1, p. 97-104 8 p.

Research output: Contribution to journal › Article › peer-review

73 Scopus citations

Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases

Hoadley, K. A., Siegel, M. B., Kanchi, K. L., Miller, C. A., Ding, L., Zhao, W., He, X., Parker, J. S., Wendl, M. C., Fulton, R. S., Demeter, R. T., Wilson, R. K., Carey, L. A., Perou, C. M. & Mardis, E. R., Dec 2016, In: PLoS medicine. 13, 12, e1002174.

Research output: Contribution to journal › Article › peer-review

Open Access

71 Scopus citations

2015

Characteristics of de novo structural changes in the human genome

Genome of the Netherlands Consortium, Jun 1 2015, In: Genome research. 25, 6, p. 792-801 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

88 Scopus citations

Optimizing Cancer Genome Sequencing and Analysis

Griffith, M., Miller, C. A., Griffith, O. L., Krysiak, K., Skidmore, Z. L., Ramu, A., Walker, J. R., Dang, H. X., Trani, L., Larson, D. E., Demeter, R. T., Wendl, M. C., McMichael, J. F., Austin, R. E., Magrini, V., McGrath, S. D., Ly, A., Kulkarni, S., Cordes, M. G., Fronick, C. C., & 7 othersFulton, R. S., Maher, C. A., Ding, L., Klco, J. M., Mardis, E. R., Ley, T. J. & Wilson, R. K., Sep 23 2015, In: Cell Systems. 1, 3, p. 210-223 14 p., 35.

Research output: Contribution to journal › Article › peer-review

Open Access

131 Scopus citations

Patterns and functional implications of rare germline variants across 12 cancer types

Lu, C., Xie, M., Wendl, M. C., Wang, J., McLellan, M. D., Leiserson, M. D. M., Huang, K. L., Wyczalkowski, M. A., Jayasinghe, R., Banerjee, T., Ning, J., Tripathi, P., Zhang, Q., Niu, B., Ye, K., Schmidt, H. K., Fulton, R. S., McMichael, J. F., Batra, P., Kandoth, C., & 23 othersBharadwaj, M., Koboldt, D. C., Miller, C. A., Kanchi, K. L., Eldred, J. M., Larson, D. E., Welch, J. S., You, M., Ozenberger, B. A., Govindan, R., Walter, M. J., Ellis, M. J., Mardis, E. R., Graubert, T. A., Dipersio, J. F., Ley, T. J., Wilson, R. K., Goodfellow, P. J., Raphael, B. J., Chen, F., Johnson, K. J., Parvin, J. D. & Ding, L., Dec 22 2015, In: Nature communications. 6, 10086.

Research output: Contribution to journal › Article › peer-review

Open Access

182 Scopus citations

2014

Age-related mutations associated with clonal hematopoietic expansion and malignancies

Xie, M., Lu, C., Wang, J., McLellan, M. D., Johnson, K. J., Wendl, M. C., McMichael, J. F., Schmidt, H. K., Yellapantula, V., Miller, C. A., Ozenberger, B. A., Welch, J. S., Link, D. C., Walter, M. J., Mardis, E. R., Dipersio, J. F., Chen, F., Wilson, R. K., Ley, T. J. & Ding, L., Dec 1 2014, In: Nature medicine. 20, 12, p. 1472-1478 7 p.

Research output: Contribution to journal › Article › peer-review

1202 Scopus citations

Clonal architectures and driver mutations in metastatic melanomas

Ding, L., Kim, M., Kanchi, K. L., Dees, N. D., Lu, C., Griffith, M., Fenstermacher, D., Sung, H., Miller, C. A., Goetz, B., Wendl, M. C., Griffith, O., Cornelius, L. A., Linette, G. P., McMichael, J. F., Sondak, V. K., Fields, R. C., Ley, T. J., Mulé, J. J., Wilson, R. K., & 1 othersWeber, J. S., Nov 13 2014, In: PloS one. 9, 11, e111153.

Research output: Contribution to journal › Article › peer-review

Open Access

58 Scopus citations

Comprehensive molecular profiling of lung adenocarcinoma: The cancer genome atlas research network

Collisson, E. A., Campbell, J. D., Brooks, A. N., Berger, A. H., Lee, W., Chmielecki, J., Beer, D. G., Cope, L., Creighton, C. J., Danilova, L., Ding, L., Getz, G., Hammerman, P. S., Hayes, D. N., Hernandez, B., Herman, J. G., Heymach, J. V., Jurisica, I., Kucherlapati, R., Kwiatkowski, D., & 290 othersLadanyi, M., Robertson, G., Schultz, N., Shen, R., Sinha, R., Sougnez, C., Tsao, M. S., Travis, W. D., Weinstein, J. N., Wigle, D. A., Wilkerson, M. D., Chu, A., Cherniack, A. D., Hadjipanayis, A., Rosenberg, M., Weisenberger, D. J., Laird, P. W., Radenbaugh, A., Ma, S., Stuart, J. M., Byers, L. A., Baylin, S. B., Govindan, R., Meyerson, M., Gabriel, S. B., Cibulskis, K., Kim, J., Stewart, C., Lichtenstein, L., Lander, E. S., Lawrence, M. S., Getz, E., Fulton, R., Fulton, L. L., McLellan, M. D., Wilson, R. K., Ye, K., Fronick, C. C., Maher, C. A., Miller, C. A., Wendl, M. C., Cabanski, C., Mardis, E., Wheeler, D., Balasundaram, M., Butterfield, Y. S. N., Carlsen, R., Chuah, E., Dhalla, N., Guin, R., Hirst, C., Lee, D., Li, H. I., Mayo, M., Moore, R. A., Mungall, A. J., Schein, J. E., Sipahimalani, P., Tam, A., Varhol, R., Robertson, A. G., Wye, N., Thiessen, N., Holt, R. A., Jones, S. J. M., Marra, M. A., Imielinski, M., Onofrio, R. C., Hodis, E., Zack, T., Helman, E., Pedamallu, C. S., Mesirov, J., Saksena, G., Schumacher, S. E., Carter, S. L., Garraway, L., Beroukhim, R., Lee, S., Mahadeshwar, H. S., Pantazi, A., Protopopov, A., Ren, X., Seth, S., Song, X., Tang, J., Yang, L., Zhang, J., Chen, P. C., Parfenov, M., Xu, A. W., Santoso, N., Chin, L., Park, P. J., Hoadley, K. A., Auman, J. T., Meng, S., Shi, Y., Buda, E., Waring, S., Veluvolu, U., Tan, D., Mieczkowski, P. A., Jones, C. D., Simons, J. V., Soloway, M. G., Bodenheimer, T., Jefferys, S. R., Roach, J., Hoyle, A. P., Wu, J., Balu, S., Singh, D., Prins, J. F., Marron, J. S., Parker, J. S., Perou, C. M., Liu, J., Maglinte, D. T., Lai, P. H., Bootwalla, M. S., Van Den Berg, D. J., Triche, T., Cho, J., DiCara, D., Heiman, D., Lin, P., Mallard, W., Voet, D., Zhang, H., Zou, L., Noble, M. S., Gehlenborg, N., Thorvaldsdottir, H., Nazaire, M. D., Robinson, J., Aksoy, B. A., Ciriello, G., Taylor, B. S., Dresdner, G., Gao, J., Gross, B., Seshan, V. E., Reva, B., Sumer, S. O., Weinhold, N., Sander, C., Ng, S., Zhu, J., Benz, C. C., Yau, C., Haussler, D., Spellman, P. T., Kimes, P. K., Broom, B. M., Wang, J., Lu, Y., Ng, P. K. S., Diao, L., Liu, W., Amos, C. I., Akbani, R., Mills, G. B., Curley, E., Paulauskis, J., Lau, K., Morris, S., Shelton, T., Mallery, D., Gardner, J., Penny, R., Saller, C., Tarvin, K., Richards, W. G., Cerfolio, R., Bryant, A., Raymond, D. P., Pennell, N. A., Farver, C., Czerwinski, C., Huelsenbeck-Dill, L., Iacocca, M., Petrelli, N., Rabeno, B., Brown, J., Bauer, T., Dolzhanskiy, C. O., Potapova, O., Rotin, D., Voronina, O., Nemirovich-Danchenko, E., Fedosenko, K. V., Gal, A., Behera, M., Ramalingam, S. S., Sica, G., Flieder, D., Boyd, J., Weaver, J. E., Kohl, B., Thinh, D. H. Q., Sandusky, G., Juhl, H., Duhig, E., Illei, P., Gabrielson, E., Shin, J., Lee, B., Rogers, K., Trusty, D., Brock, M. V., Williamson, C., Burks, E., Rieger-Christ, K., Holway, A., Sullivan, T., Asiedu, M. K., Kosari, F., Rekhtman, N., Zakowski, M., Rusch, V. W., Zippile, P., Suh, J., Pass, H., Goparaju, C., Owusu-Sarpong, Y., Bartlett, J. M. S., Kodeeswaran, S., Parfitt, J., Sekhon, H., Albert, M., Eckman, J., Myers, J. B., Morrison, C., Gaudioso, C., Borgia, J. A., Bonomi, P., Pool, M., Liptay, M. J., Moiseenko, F., Zaytseva, I., Dienemann, H., Meister, M., Schnabel, P. A., Muley, T. R., Peifer, M., Gomez-Fernandez, C., Herbert, L., Egea, S., Huang, M., Thorne, L. B., Boice, L., Salazar, A. H., Funkhouser, W. K., Rathmell, W. K., Dhir, R., Yousem, S. A., Dacic, S., Schneider, F., Siegfried, J. M., Hajek, R., Watson, M. A., McDonald, S., Meyers, B., Clarke, B., Yang, I. A., Fong, K. M., Hunter, L., Windsor, M., Bowman, R. V., Peters, S., Letovanec, I., Khan, K. Z., Jensen, M. A., Snyder, E. E., Srinivasan, D., Kahn, A. B., Baboud, J., Pot, D. A., Shaw, K. R. M., Sheth, M., Davidsen, T., Demchok, J. A., Yang, L., Wang, Z., Tarnuzzer, R., Zenklusen, J. C., Ozenberger, B. A., Sofia, H. J. & Cheney, R., 2014, In: Nature. 511, 7511, p. 543-550 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3553 Scopus citations

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences

Colonna, V., Ayub, Q., Chen, Y., Pagani, L., Luisi, P., Pybus, M., Garrison, E., Xue, Y., Tyler-Smith, C., Abecasis, G. R., Auton, A., Brooks, L. D., Depristo, M. A., Durbin, R. M., Handsaker, R. E., Kang, H. M., Marth, G. T., McVean, G., Altshuler, D. M., Durbin, R. M., & 685 othersAbecasis, 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., McVean, G. A., Nickerson, D. A., Schmidt, J. P., Sherry, S. T., Wang, J., Wilson, R. K., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Wang, J., 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., Lander, E. S., Altshuler, D. M., Gabriel, S. B., Gupta, N., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Lehrach, H., Sudbrak, R., Albrecht, M. W., Amstislavskiy, V. S., Borodina, T. A., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Sherry, S. T., McVean, G. A., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Durbin, R. M., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Auton, A., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Wang, Y., Yu, J., Wang, J., Coin, L. J., Fang, L., Guo, X., Jin, X., Li, G., Li, Q., Li, Y., 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., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Daly, M. J., Depristo, M. A., Altshuler, D. M., Banks, E., Bhatia, G., Carneiro, M. O., Del Angel, G., Gabriel, S. B., Genovese, G., Gupta, N., Handsaker, R. E., Hartl, C., Lander, E. S., 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., Kim, K. C., Korbel, J. O., Rausch, T., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Smith, R. E., Zheng-Bradley, X., Clark, A. G., 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., Bentley, D. R., Barnes, B., Bauer, M., Cheetham, R., Cox, T., Eberle, M., Humphray, S., Kahn, S., Murray, L., Peden, J., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Macarthur, D. G., Lek, M., Sudbrak, R., Amstislavskiy, V. S., Herwig, R., Shriver, M. D., Bustamante, C. D., Byrnes, J. K., De La Vega, F. M., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., 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., Sherry, S. T., Xiao, C., Sebat, J., Bafna, V., 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., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Anderson, P., Angius, A., Bigham, A., Blackwell, T., Busonero, F., Cucca, F., Fuchsberger, C., Jones, C., Li, Y., Lyons, R., Maschio, A., Porcu, E., Reinier, F., Sanna, S., Schlessinger, D., Sidore, C., Tan, A., Trost, M. K., Awadalla, P., Hodgkinson, A., Lunter, G., McVean, G. A., 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., Mardis, E. R., Chen, K., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Durbin, R. M., Hurles, M. E., Tyler-Smith, C., Albers, C. A., Ayub, Q., Balasubramaniam, S., Chen, Y., Coffey, A. J., Colonna, V., Danecek, P., Huang, N., Jostins, L., Keane, T. M., Li, H., McCarthy, S., Scally, A., Stalker, J., 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., Mu, X. J., Sisu, C., Li, Y., Luo, R., Zhu, H., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Shi, X., von Grotthuss, M., Zhang, C., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Ward, A. N., Wu, J., Zhang, M., McCarroll, S. A., Altshuler, D. M., Banks, E., Del Angel, G., Genovese, G., Handsaker, R. E., Hartl, C., Nemesh, J. C., Shakir, K., Yoon, S. C., Lihm, J., Makarov, V., Degenhardt, J., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Korbel, J. O., Rausch, T., Stütz, A. M., Bentley, D. R., Barnes, B., Cheetham, R., Eberle, M., Humphray, S., Kahn, S., Murray, L., Shaw, R., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., Lacroute, P., Craig, D. W., Homer, N., Church, D., Xiao, C., Sebat, J., Bafna, V., Michaelson, J. J., Ye, K., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Lunter, G., McVean, G. A., Iqbal, Z., Witherspoon, D., Xing, J., Eichler, E. E., Alkan, C., Hajirasouliha, I., Hormozdiari, F., Ko, A., Sudmant, P. H., Chen, K., Chinwalla, A., Ding, L., McLellan, M. D., Wallis, J. W., Hurles, M. E., Blackburne, B., Li, H., Lindsay, S. J., Ning, Z., Scally, A., Walter, K., Zhang, Y., Gerstein, M. B., Abyzov, A., Chen, J., Clarke, D., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Kovar, C., Lewis, L., Lu, J., Muzny, D., Nagaswamy, U., Reid, J., Sabo, A., Yu, J., Guo, X., Li, Y., Wu, R., Marth, G. T., Garrison, E. P., Leong, W. F., Ward, A. N., Del Angel, G., Depristo, M. A., Gabriel, S. B., Gupta, N., Hartl, C., Poplin, R. E., Clark, A. G., Rodriguez-Flores, J. L., Flicek, P., Clarke, L., Smith, R. E., Zheng-Bradley, X., Macarthur, D. G., Bustamante, C. D., Gravel, S., Craig, D. W., Christoforides, A., Homer, N., Izatt, T., Sherry, S. T., Xiao, C., Dermitzakis, E., Abecasis, G. R., Kang, H. M., McVean, G. A., Mardis, E. R., Dooling, D., Fulton, L., Fulton, R., Koboldt, D. C., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Gerstein, M. B., Balasubramanian, S., Habegger, L., Garrison, E. P., Gibbs, R. A., Bainbridge, M., Muzny, D., Yu, F., Yu, J., Del Angel, G., Handsaker, R. E., Makarov, V., Rodriguez-Flores, J. L., Jin, H., Kim, W., Kim, K. C., Flicek, P., Beal, K., Clarke, L., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R., Zheng-Bradley, X., Tabrizi, S., Macarthur, D. G., Lek, M., Bustamante, C. D., De La Vega, F. M., Craig, D. W., Kurdoglu, A. A., Lappalainen, T., Rosenfeld, J. A., Michelson, L. P., Awadalla, P., Hodgkinson, A., McVean, G. A., Chen, K., Tyler-Smith, C., Chen, Y., Colonna, V., Frankish, A., Harrow, J., Xue, Y., Gerstein, M. B., Abyzov, A., Balasubramanian, S., Chen, J., Clarke, D., Fu, Y., Harmanci, A. O., Jin, M., Khurana, E., Mu, X. J., Sisu, C., Gibbs, R. A., Kovar, C., Kalra, D., Hale, W., Fowler, G., Muzny, D., Reid, J., Wang, J., Guo, X., Li, G., Li, Y., Zheng, X., Altshuler, D. M., Flicek, P., Clarke, L., Barker, J., Kelman, G., Kulesha, E., Leinonen, R., McLaren, W. M., Radhakrishnan, R., Roa, A., Smirnov, D., Smith, R. E., Streeter, I., Toneva, I., Vaughan, B., Zheng-Bradley, X., Bentley, D. R., Cox, T., Humphray, S., Kahn, S., Sudbrak, R., Albrecht, M. W., Lienhard, M., Craig, D. W., Izatt, T., Kurdoglu, A. A., Sherry, S. T., 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., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Xiao, C., Zhang, H., Haussler, D., Abecasis, G. R., McVean, G. A., Alkan, C., Ko, A., Dooling, D., Durbin, R. M., Balasubramaniam, S., Keane, T. M., McCarthy, S., Stalker, J., Chakravarti, A., Abecasis, G. R., Barnes, K. C., Beiswanger, C., Burchard, E., Bustamante, C. D., Cai, H., Cao, H., Durbin, R. M., Gharani, N., Gibbs, R. A., Gignoux, C. R., Gravel, S., Henn, B., Jones, D., Jorde, L., Kaye, J. S., Keinan, A., Kent, A., Kerasidou, A., Li, Y., Mathias, R., McVean, G., Moreno-Estrada, A., Ossorio, P. N., Parker, M., Reich, D., Rotimi, C. N., Royal, C. D., Sandoval, K., Su, Y., Sudbrak, R., Tian, Z., Timmermann, B., Tishkoff, S., Toji, L. H., Tyler-Smith, C., Via, M., Wang, Y., Yang, H., Yang, L., Zhu, J., Bodmer, W., Bedoya, G., Ruiz-Linares, A., Ming, C. Z., Yang, G., You, C. J., Peltonen, L., Garcia-Montero, A., Orfao, A., Dutil, J., Martinez-Cruzado, J. C., Oleksyk, T. K., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Duncanson, A., Dunn, M., Green, E. D., Guyer, M. S. & Peterson, J. L., Jun 30 2014, In: Genome biology. 15, 6, R88.

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51 Scopus citations

Integrated analysis of germline and somatic variants in ovarian cancer

Kanchi, K. L., Johnson, K. J., Lu, C., McLellan, M. D., Leiserson, M. D. M., Wendl, M. C., Zhang, Q., Koboldt, D. C., Xie, M., Kandoth, C., McMichael, J. F., Wyczalkowski, M. A., Larson, D. E., Schmidt, H. K., Miller, C. A., Fulton, R. S., Spellman, P. T., Mardis, E. R., Druley, T. E., Graubert, T. A., & 4 othersGoodfellow, P. J., Raphael, B. J., Wilson, R. K. & Ding, L., Jan 22 2014, In: Nature communications. 5, 3156.

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210 Scopus citations

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

Delaneau, O., Marchini, J., McVeanh, G. A., Donnelly, P., Lunter, G., Marchini, J. L., Myers, S., Gupta-Hinch, A., Iqbal, Z., Mathieson, I., Rimmer, A., Xifara, D. K., Kerasidou, A., Churchhouse, C., Altshuler, D. M., Gabriel, S. B., Lander, E. S., Gupta, N., Daly, M. J., DePristo, M. A., & 363 othersBanks, 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., Sabeti, P. C., Grossman, S. R., Tabrizi, S., Tariyal, R., Li, H., Reich, D., Durbin, R. M., Hurles, M. E., Balasubramaniam, S., Burton, J., Danecek, P., Keane, T. M., Kolb-Kokocinski, A., McCarthy, S., Stalker, J., Quail, M., Ayub, Q., Chen, Y., Coffey, A. J., Colonna, V., Huang, N., Jostins, L., Scally, A., Walter, K., Xue, Y., Zhang, Y., Blackburne, B., Lindsay, S. J., Ning, Z., Frankish, A., Harrow, J., Chris, T. S., Abecasis, G. R., Kang, H. M., Anderson, P., Blackwell, T., Busonero, F., Fuchsberger, C., Jun, G., Maschio, A., Porcu, E., Sidore, C., Tan, A., Trost, M. K., Bentley, D. R., Grocock, R., Humphray, S., James, T., Kingsbury, Z., Bauer, M., Cheetham, R. K., Cox, T., Eberle, M., Murray, L., Shaw, R., Chakravarti, A., Clark, A. G., Keinan, A., Rodriguez-Flores, J. L., De LaVega, F. M., Degenhardt, J., Eichler, E. E., Flicek, P., Clarke, L., Leinonen, R., Smith, R. E., Zheng-Bradley, X., Beal, K., Cunningham, F., Herrero, J., McLaren, W. M., Ritchie, G. R. S., Barker, J., Kelman, G., Kulesha, E., Radhakrishnan, R., Roa, A., Smirnov, D., Streeter, I., Toneva, I., Gibbs, R. A., Dinh, H., Kovar, C., Lee, S., Lewis, L., Muzny, D., Reid, J., Wang, M., Yu, F., Bainbridge, M., Challis, D., Evani, U. S., Lu, J., Nagaswamy, U., Sabo, A., Wang, Y., Yu, J., Fowler, G., Hale, W., Kalra, D., Green, E. D., Knoppers, B. M., Korbel, J. O., Rausch, T., Sttz, A. M., Lee, C., Griffin, L., Hsieh, C. H., Mills, R. E., Von Grotthuss, M., Zhang, C., Shi, X., Lehrach, H., Sudbrak, R., Amstislavskiy, V. S., Lienhard, M., Mertes, F., Sultan, M., Timmermann, B., Yaspo, M. L., Herwig, S. R., Mardis, E. R., Wilson, R. K., Fulton, L., Fulton, R., Weinstock, G. M., Chinwalla, A., Ding, L., Dooling, D., Koboldt, D. C., McLellan, M. D., Wallis, J. W., Wendl, M. C., Zhang, Q., Marth, G. T., Garrison, E. P., Kural, D., Lee, W. P., Leong, W. F., Ward, A. N., Wu, J., Zhang, M., Nickerson, D. A., Alkan, C., Hormozdiari, F., Ko, A., Sudmant, P. H., Schmidt, J. P., Davies, C. J., Gollub, J., Webster, T., Wong, B., Zhan, Y., Sherry, S. T., Xiao, C., Church, D., 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., Ostapchuk, Y., Phan, L., Ponomarov, S., Schneider, V., Shekhtman, E., Sirotkin, K., Slotta, D., Zhang, H., Wang, J., Fang, X., Guo, X., Jian, M., Jiang, H., Jin, X., Li, G., Li, J., Li, Y., Liu, X., Lu, Y., Ma, X., Tai, S., Tang, M., Wang, B., Wang, G., Wu, H., Wu, R., Yin, Y., Zhang, W., Zhao, J., Zhao, M., Zheng, X., Lachlan, H., Fang, L., Li, Q., Li, Z., Lin, H., Liu, B., Luo, R., Shao, H., Wang, B., Xie, Y., Ye, C., Yu, C., Zheng, H., Zhu, H., Cai, H., Cao, H., Su, Y., Tian, Z., Yang, H., Yang, L., Zhu, J., Cai, Z., Wang, J., Albrecht, M. W., Borodina, T. A., Auton, A., Yoon, S. C., Lihm, J., Makarov, V., Jin, H., Kim, W., Kim, K. C., Gottipati, S., Jones, D., Cooper, D. N., Ball, E. V., Stenson, P. D., Barnes, B., Kahn, S., Ye, K., Batzer, M. A., Konkel, M. K., Walker, J. A., MacArthur, D. G., Lek, M., Shriver, M. D., Bustamante, C. D., Gravel, S., Kenny, E. E., Kidd, J. M., Lacroute, P., Maples, B. K., Moreno-Estrada, A., Zakharia, F., Henn, B., Sandoval, K., Byrnes, J. K., Halperin, E., Baran, Y., Craig, D. W., Christoforides, A., Izatt, T., Kurdoglu, A. A., Sinari, S. A., Homer, N., Squire, K., Sebat, J., Bafna, V., 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., Lappalainen, T., Devine, S. E., Liu, X., Maroo, A., Tallon, L. J., Rosenfeld, J. A., Michelson, L. P., Angius, A., Cucca, F., Sanna, S., Bigham, A., Jones, C., Reinier, F., Li, Y., Lyons, R., Schlessinger, D., Awadalla, P., Hodgkinson, A., Oleksyk, T. K., Martinez-Cruzado, J. C., Fu, Y., Liu, X., Xiong, M., Jorde, L., Witherspoon, D., Xing, J., Browning, B. L., Hajirasouliha, I., Chen, K., Albers, C. A., Gerstein, M. B., Abyzov, A., Chen, J., Fu, Y., Habegger, L., Harmanci, A. O., Mu, X. J., Sisu, C., Balasubramanian, S., Jin, M., Khurana, E., Clarke, D., Michaelson, J. J., OSullivan, C., Barnes, K. C., Gharani, N., Toji, L. H., Gerry, N., Kaye, J. S., Kent, A., Mathias, R., Ossorio, P. N., Parker, M., Rotimi, C. N., Royal, C. D., Tishkoff, S., Via, M., Bodmer, W., Bedoya, G., Yang, G., You, C. J., Garcia-Montero, A., Orfao, A., Dutil, J., Brooks, L. D., Felsenfeld, A. L., McEwen, J. E., Clemm, N. C., Guyer, M. S., Peterson, J. L., Duncanson, A., Dunn, M. & Peltonen, L., Jun 13 2014, In: Nature communications. 5, 3934.

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252 Scopus citations

MSIsensor: Microsatellite instability detection using paired tumor-normal sequence data

Niu, B., Ye, K., Zhang, Q., Lu, C., Xie, M., McLellan, M. D., Wendl, M. C. & Ding, L., Apr 1 2014, In: Bioinformatics. 30, 7, p. 1015-1016 2 p.

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384 Scopus citations

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

The Cancer Genome Atlas Research Network, Aug 14 2014, In: Cell. 158, 4, p. 929-944 16 p.

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1005 Scopus citations

2013

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem

Wendl, M. C., Kota, K., Weinstock, G. M. & Mitreva, M., Nov 2013, In: Journal of Mathematical Biology. 67, 5, p. 1141-1161 21 p.

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21 Scopus citations

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia

Ley, T. J., Miller, C., Ding, L., Raphael, B. J., Mungall, A. J., Robertson, G., Hoadley, K., Triche, T. J., Laird, P. W., Baty, J. D., Fulton, L. L., Fulton, R., Heath, S. E., Kalicki-Veizer, J., Kandoth, C., Klco, J. M., Koboldt, D. C., Kanchi, K. L., Kulkarni, S., Lamprecht, T. L., & 119 othersLarson, D. E., Lin, G., Lu, C., McLellan, M. D., McMichael, J. F., Payton, J., Schmidt, H., Spencer, D. H., Tomasson, M. H., Wallis, J. W., Wartman, L. D., Watson, M. A., Welch, J., Wendl, M. C., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y., Chiu, R., Chu, A., Chuah, E., Chun, H. J., Corbett, R., Dhalla, N., Guin, R., He, A., Hirst, C., Hirst, M., Holt, R. A., Jones, S., Karsan, A., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, K., Parker, J., Pleasance, E., Plettner, P., Schein, J., Stoll, D., Swanson, L., Tam, A., Thiessen, N., Varhol, R., Wye, N., Zhao, Y., Gabriel, S., Getz, G., Sougnez, C., Zou, L., Leiserson, M. D. M., Vandin, F., Wu, H. T., Applebaum, F., Baylin, S. B., Akbani, R., Broom, B. M., Chen, K., Motter, T. C., Nguyen, K., Weinstein, J. N., Zhang, N., Ferguson, M. L., Adams, C., Black, A., Bowen, J., Gastier-Foster, J., Grossman, T., Lichtenberg, T., Wise, L., Davidsen, T., Demchok, J. A., Mills Shaw, K. R., Sheth, M., Sofia, H. J., Yang, L., Downing, J. R., Eley, G., Alonso, S., Ayala, B., Baboud, J., Backus, M., Barletta, S. P., Berton, D. L., Chu, A. L., Girshik, S., Jensen, M. A., Kahn, A., Kothiyal, P., Nicholls, M. C., Pihl, T. D., Pot, D. A., Raman, R., Sanbhadti, R. N., Snyder, E. E., Srinivasan, D., Walton, J., Wan, Y., Wang, Z., Issa, J. P. J., Beau, M. L., Carroll, M., Kantarjian, H., Kornblau, S., Bootwalla, M. S., Lai, P. H., Shen, H., Van Den Berg, D. J., Weisenberger, D. J., Link, D. C., Walter, M. J., Ozenberger, B. A., Mardis, E. R., Westervelt, P., Graubert, T. A., DiPersio, J. F. & Wilson, R. K., May 30 2013, In: New England Journal of Medicine. 368, 22, p. 2059-2074 16 p.

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3325 Scopus citations

Integrative annotation of variants from 1092 humans: Application to cancer genomics

1000 Genomes Project Consortium, Oct 4 2013, In: Science. 342, 6154, 1235587.

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272 Scopus citations

Mutational landscape and significance across 12 major cancer types

Kandoth, C., McLellan, M. D., Vandin, F., Ye, K., Niu, B., Lu, C., Xie, M., Zhang, Q., McMichael, J. F., Wyczalkowski, M. A., Leiserson, M. D. M., Miller, C. A., Welch, J. S., Walter, M. J., Wendl, M. C., Ley, T. J., Wilson, R. K., Raphael, B. J. & Ding, L., 2013, In: Nature. 502, 7471, p. 333-339 7 p.

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2943 Scopus citations

The cancer genome atlas pan-cancer analysis project

Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Sander, C., Stuart, J. M., Chang, K., Creighton, C. J., Davis, C., Donehower, L., Drummond, J., Wheeler, D., Ally, A., Balasundaram, M., Birol, I., Butterfield, Y. S. N., Chu, A., Chuah, E., & 316 othersChun, H. J. E., Dhalla, N., Guin, R., Hirst, M., Hirst, C., Holt, R. A., Jones, S. J. M., Lee, D., Li, H. I., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Robertson, A. G., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Varhol, R. J., Beroukhim, R., Bhatt, A. S., Brooks, A. N., Cherniack, A. D., Freeman, S. S., Gabriel, S. B., Helman, E., Jung, J., Meyerson, M., Ojesina, A. I., Pedamallu, C. S., Saksena, G., Schumacher, S. E., Tabak, B., Zack, T., Lander, E. S., Bristow, C. A., Hadjipanayis, A., Haseley, P., Kucherlapati, R., Lee, S., Lee, E., Luquette, L. J., Mahadeshwar, H. S., Pantazi, A., Parfenov, M., Park, P. J., Protopopov, A., Ren, X., Santoso, N., Seidman, J., Seth, S., Song, X., Tang, J., Xi, R., Xu, A. W., Yang, L., Zeng, D., Auman, J. T., Balu, S., Buda, E., Fan, C., Hoadley, K. A., Jones, C. D., Meng, S., Mieczkowski, P. A., Parker, J. S., Perou, C. M., Roach, J., Shi, Y., Silva, G. O., Tan, D., Veluvolu, U., Waring, S., Wilkerson, M. D., Wu, J., Zhao, W., Bodenheimer, T., Hayes, D. N., Hoyle, A. P., Jeffreys, S. R., Mose, L. E., Simons, J. V., Soloway, M. G., Baylin, S. B., Berman, B. P., Bootwalla, M. S., Danilova, L., Herman, J. G., Hinoue, T., Laird, P. W., Rhie, S. K., Shen, H., Triche, T., Weisenberger, D. J., Carter, S. L., Cibulskis, K., Chin, L., Zhang, J., Sougnez, C., Wang, M., Getz, G., Dinh, H., Doddapaneni, H. V., Gibbs, R., Gunaratne, P., Han, Y., Kalra, D., Kovar, C., Lewis, L., Morgan, M., Morton, D., Muzny, D., Reid, J., Xi, L., Cho, J., Dicara, D., Frazer, S., Gehlenborg, N., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Liu, Y., Noble, M. S., Stojanov, P., Voet, D., Zhang, H., Zou, L., Stewart, C., Bernard, B., Bressler, R., Eakin, A., Iype, L., Knijnenburg, T., Kramer, R., Kreisberg, R., Leinonen, K., Lin, J., Liu, Y., Miller, M., Reynolds, S. M., Rovira, H., Shmulevich, I., Thorsson, V., Yang, D., Zhang, W., Amin, S., Wu, C. J., Wu, C. C., Akbani, R., Aldape, K., Baggerly, K. A., Broom, B., Casasent, T. D., Cleland, J., Dodda, D., Edgerton, M., Han, L., Herbrich, S. M., Ju, Z., Kim, H., Lerner, S., Li, J., Liang, H., Liu, W., Lorenzi, P. L., Lu, Y., Melott, J., Nguyen, L., Su, X., Verhaak, R., Wang, W., Wong, A., Yang, Y., Yao, J., Yao, R., Yoshihara, K., Yuan, Y., Yung, A. K., Zhang, N., Zheng, S., Ryan, M., Kane, D. W., Aksoy, B. A., Ciriello, G., Dresdner, G., Gao, J., Gross, B., Jacobsen, A., Kahles, A., Ladanyi, M., Lee, W., Lehmann, K. V., Miller, M. L., Ramirez, R., Rätsch, G., Reva, B., Schultz, N., Senbabaoglu, Y., Shen, R., Sinha, R., Sumer, S. O., Sun, Y., Taylor, B. S., Weinhold, N., Fei, S., Spellman, P., Benz, C., Carlin, D., Cline, M., Craft, B., Goldman, M., Haussler, D., Ma, S., Ng, S., Paull, E., Radenbaugh, A., Salama, S., Sokolov, A., Swatloski, T., Uzunangelov, V., Waltman, P., Yau, C., Zhu, J., Hamilton, S. R., Abbott, S., Abbott, R., Dees, N. D., Delehaunty, K., Ding, L., Dooling, D. J., Eldred, J. M., Fronick, C. C., Fulton, R., Fulton, L. L., Kalicki-Veizer, J., Kanchi, K. L., Kandoth, C., Koboldt, D. C., Larson, D. E., Ley, T. J., Lin, L., Lu, C., Magrini, V. J., Mardis, E. R., McLellan, M. D., McMichael, J. F., Miller, C. A., O'Laughlin, M., Pohl, C., Schmidt, H., Smith, S. M., Walker, J., Wallis, J. W., Wendl, M. C., Wilson, R. K., Wylie, T., Zhang, Q., Burton, R., Jensen, M. A., Kahn, A., Pihl, T., Pot, D., Wan, Y., Levine, D. A., Black, A. D., Bowen, J., Frick, J., Gastier-Foster, J. M., Harper, H. A., Helsel, C., Leraas, K. M., Lichtenberg, T. M., McAllister, C., Ramirez, N. C., Sharpe, S., Wise, L., Zmuda, E., Chanock, S. J., Davidsen, T., Demchok, J. A., Eley, G., Felau, I., Sheth, M., Sofia, H., Staudt, L., Tarnuzzer, R., Wang, Z., Yang, L., Zhang, J., Omberg, L., Margolin, A., Raphael, B. J., Vandin, F., Wu, H. T., Leiserson, M. D. M., Benz, S. C., Vaske, C. J., Noushmehr, H., Wolf, D., Veer, L. V. T., Anastassiou, D., Yang, T. H. O., Lopez-Bigas, N., Gonzalez-Perez, A., Tamborero, D., Xia, Z., Li, W., Cho, D. Y., Przytycka, T., Hamilton, M., McGuire, S., Nelander, S., Johansson, P., Jörnsten, R. & Kling, T., Oct 1 2013, In: Nature Genetics. 45, 10, p. 1113-1120 8 p.

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4172 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 othersMcVean, 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. 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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.

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5683 Scopus citations

Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells

Young, M. A., Larson, D. E., Sun, C. W., George, D. R., Ding, L., Miller, C. A., Lin, L., Pawlik, K. M., Chen, K., Fan, X., Schmidt, H., Kalicki-Veizer, J., Cook, L. L., Swift, G. W., Demeter, R. T., Wendl, M. C., Sands, M. S., Mardis, E. R., Wilson, R. K., Townes, T. M., & 1 othersLey, T. J., May 4 2012, In: Cell Stem Cell. 10, 5, p. 570-582 13 p.

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161 Scopus citations

Michael Wendl

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