Michael Wendl

2024

The Fall and Rise of Water

Wendl, M. C., 2024, (Accepted/In press) In: College Mathematics Journal.

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

2023

Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma

Wu, Y., Chen, S., Yang, X., Sato, K., Lal, P., Wang, Y., Shinkle, A. T., Wendl, M. C., Primeau, T. M., Zhao, Y., Gould, A., Sun, H., Mudd, J. L., Hoog, J., Mashl, R. J., Wyczalkowski, M. A., Mo, C. K., Liu, R., Herndon, J. M. & Davies, S. R. & 19 others, Liu, D., Ding, X., Evrard, Y. A., Welm, B. E., Lum, D., Koh, M. Y., Welm, A. L., Chuang, J. H., Moscow, J. A., Meric-Bernstam, F., Govindan, R., Li, S., Hsieh, J., Fields, R. C., Lim, K. H., Ma, C. X., Zhang, H., Ding, L. & Chen, F., Dec 15 2023, In: Cancer research. 183, 24, p. 4161-4178 18 p.

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

Open Access

Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

Wu, Y., Terekhanova, N. V., Caravan, W., Naser Al Deen, N., Lal, P., Chen, S., Mo, C. K., Cao, S., Li, Y., Karpova, A., Liu, R., Zhao, Y., Shinkle, A., Strunilin, I., Weimholt, C., Sato, K., Yao, L., Serasanambati, M., Yang, X. & Wyczalkowski, M. & 22 others, Zhu, H., Zhou, D. C., Jayasinghe, R. G., Mendez, D., Wendl, M. C., Clark, D., Newton, C., Ruan, Y., Reimers, M. A., Pachynski, R. K., Kinsinger, C., Jewell, S., Chan, D. W., Zhang, H., Chaudhuri, A. A., Chheda, M. G., Humphreys, B. D., Mesri, M., Rodriguez, H., Hsieh, J. J., Ding, L. & Chen, F., Dec 2023, In: Nature communications. 14, 1, 1681.

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

Open Access

13 Scopus citations

Epigenetic regulation during cancer transitions across 11 tumour types

Terekhanova, N. V., Karpova, A., Liang, W. W., Strzalkowski, A., Chen, S., Li, Y., Southard-Smith, A. N., Iglesia, M. D., Wendl, M. C., Jayasinghe, R. G., Liu, J., Song, Y., Cao, S., Houston, A., Liu, X., Wyczalkowski, M. A., Lu, R. J. H., Caravan, W., Shinkle, A. & Naser Al Deen, N. & 24 others, Herndon, J. M., Mudd, J., Ma, C., Sarkar, H., Sato, K., Ibrahim, O. M., Mo, C. K., Chasnoff, S. E., Porta-Pardo, E., Held, J. M., Pachynski, R., Schwarz, J. K., Gillanders, W. E., Kim, A. H., Vij, R., DiPersio, J. F., Puram, S. V., Chheda, M. G., Fuh, K. C., DeNardo, D. G., Fields, R. C., Chen, F., Raphael, B. J. & Ding, L., Nov 9 2023, In: Nature. 623, 7986, p. 432-441 10 p.

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

Open Access

19 Scopus citations

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

Clinical Proteomic Tumor Analysis Consortium, Li, Y., Wu, Y., Lu, R. J. H., Chen, S., Zhao, Y., Caravan, W., Calinawan, A., Wyczalkowski, M. A., Wendl, M. C., Reimers, M. A., Pachynski, R., Van Tine, B. A., Chen, F., Ding, L. & Hsieh, J., Jan 9 2023, In: Cancer Cell. 41, 1, p. 139-163.e17

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

Open Access

64 Scopus citations

Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Clinical Proteomic Tumor Analysis Consortium, Sep 11 2023, In: Cancer Cell. 41, 9, p. 1567-1585.e7

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

Open Access

13 Scopus citations

Pan-cancer proteogenomics connects oncogenic drivers to functional states

Clinical Proteomic Tumor Analysis Consortium, Aug 31 2023, In: Cell. 186, 18, p. 3921-3944.e25

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

Open Access

24 Scopus citations

Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Yao, L., Wang, J. T., Jayasinghe, R. G., O’Neal, J., Tsai, C. F., Rettig, M. P., Song, Y., Liu, R., Zhao, Y., Ibrahim, O. M., Fiala, M. A., Fortier, J. M., Chen, S., Gehrs, L., Rodrigues, F. M., Wendl, M. C., Kohnen, D., Shinkle, A., Cao, S. & Foltz, S. M. & 12 others, Zhou, D. C., Storrs, E., Wyczalkowski, M. A., Mani, S., Goldsmith, S. R., Zhu, Y., Hamilton, M., Liu, T., Chen, F., Vij, R., Ding, L. & DiPersio, J. F., Apr 15 2023, In: Cancer research. 83, 8, p. 1214-1233 20 p.

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

Open Access

11 Scopus citations

2022

Comprehensive Characterization of the Check for updates Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis

Yao, L., Jayasinghe, R. G., Lee, B. H., Bhasin, S. S., Pilcher, W., Doxie, D. B., Gonzalez-Kozlova, E., Dasari, S., Fiala, M. A., Pita-Juarez, Y., Strausbauch, M., Kelly, G., Thomas, B. E., Kumar, S. K., Cho, H. J., Anderson, E., Wendl, M., Dawson, T., D’souza, D. & Oh, S. T. & 17 others, Cheloni, G., Li, Y., DiPersio, J. F., Rahman, A. H., Dhodapkar, K. M., Kim-Schulze, S., Vij, R., Vlachos, I. S., Mehr, S., Hamilton, M., Auclair, D., Kourelis, T., Avigan, D., Dhodapkar, M. V., Gnjatic, S., Bhasin, M. K. & Ding, L., 2022, In: Cancer research communications. 2, 10, p. 1255-1265 11 p.

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

Open Access

12 Scopus citations

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health

Stanford TDA, University of Connecticut TMC, University of Michigan TDA, University of Minnesota TMC, University of Pittsburgh TMC, University of Washington TDA, Washington University TMC, Yale TMC, SenNet Consortium, Writing Group, Brown University TDA, Buck Institute for Research on Aging TMC/TDA, Consortium Organization and Data Coordinating Center (CODCC), Columbia TMC, Duke University TMC, Massachusetts General Hospital TDA, Mayo Clinic TDA & National Institute of Health (NIH), Dec 2022, In: Nature Aging. 2, 12, p. 1090-1100 11 p.

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

Open Access

37 Scopus citations

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

1 Scopus citations

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 others, Fulton, 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

85 Scopus citations

2021

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 others, Fulton, 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

75 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

63 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

122 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

16 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

325 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

193 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

11 Scopus citations

2020

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

PCAWG Tumor Subtypes and Clinical Translation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 728.

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

Open Access

127 Scopus citations

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

PCAWG Consortium, PCAWG Drivers and Functional Interpretation Working Group & PCAWG-Structural Variation Working Group, Feb 6 2020, In: Nature. 578, 7793, p. 102-111 10 p.

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

Open Access

361 Scopus citations

Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

PCAWG Drivers and Functional Interpretation Group & PCAWG Consortium, Dec 1 2020, In: Communications Biology. 3, 1, 56.

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

Open Access

145 Scopus citations

Combined burden and functional impact tests for cancer driver discovery using DriverPower

PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 734.

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

Open Access

25 Scopus citations

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

PCAWG-Structural Variation Working Group & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 331-341 11 p.

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

Open Access

389 Scopus citations

Comprehensive molecular characterization of mitochondrial genomes in human cancers

PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 342-352 11 p.

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

Open Access

232 Scopus citations

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

19 Scopus citations

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

PCAWG-Structural Variation Working Group & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 294-305 12 p.

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

Open Access

151 Scopus citations

Divergent mutational processes distinguish hypoxic and normoxic tumours

PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 737.

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

Open Access

84 Scopus citations

Genomic basis for RNA alterations in cancer

PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group & PCAWG Consortium, Feb 6 2020, In: Nature. 578, 7793, p. 129-136 8 p.

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

Open Access

261 Scopus citations

Genomic footprints of activated telomere maintenance mechanisms in cancer

PCAWG-Structural Variation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 733.

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

Open Access

75 Scopus citations

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

PCAWG Transcriptome Working Group, PCAWG-Structural Variation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 736.

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

Open Access

49 Scopus citations

Inferring structural variant cancer cell fraction

PCAWG Consortium & PCAWG Evolution and Heterogeneity Working Group, Dec 1 2020, In: Nature communications. 11, 1, 730.

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

Open Access

29 Scopus citations

Integrative pathway enrichment analysis of multivariate omics data

PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 735.

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

Open Access

111 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

1699 Scopus citations

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

PCAWG-Structural Variation Working Group & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 306-319 14 p.

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

Open Access

241 Scopus citations

Pathway and network analysis of more than 2500 whole cancer genomes

PCAWG Drivers and Functional Interpretation Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 729.

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

Open Access

66 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

400 Scopus citations

Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig

PCAWG Evolution and Heterogeneity Working Group & PCAWG Consortium, Dec 1 2020, In: Nature communications. 11, 1, 731.

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

Open Access

29 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

27 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

59 Scopus citations

The landscape of viral associations in human cancers

PCAWG Pathogens & PCAWG Consortium, Mar 1 2020, In: Nature Genetics. 52, 3, p. 320-330 11 p.

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

Open Access

240 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 others, Chen, 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

11 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

1287 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

378 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 others, Ding, L., Jul 27 2018, In: Genome medicine. 10, 1, 60.

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

Open Access

15 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

543 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

240 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

173 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

Michael Wendl

Research output

Search results