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Michael C Wendl, PhD - Publications

Affiliations: 
1994- Genetics (McDonnell Genome Institute) Washington University, Saint Louis, St. Louis, MO 
 1999- Mechanical Engineering Washington University, Saint Louis, St. Louis, MO 
 2010- Mathematics Washington University, Saint Louis, St. Louis, MO 
Area:
differential equations, combinatorial probability, fluid mechanics, statistical genetics
Website:
wendl.weebly.com
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Year Citation  Score
2024 Yao L, Krasnick BA, Bi Y, Sethuraman S, Goedegebuure S, Weerasinghe A, Wetzel C, Gao Q, Oyedeji A, Mudd J, Wyczalkowski MA, Wendl M, Ding L, Fields RC. Treatment resistance to melanoma therapeutics on a single cell level. Scientific Reports. 14: 21915. PMID 39300183 DOI: 10.1038/s41598-024-72255-9  0.314
2023 Wu Y, Chen S, Yang X, Sato K, Lal P, Wang Y, Shinkle AT, Wendl MC, Primeau TM, Zhao Y, Gould A, Sun H, Mudd JL, Hoog J, Mashl RJ, et al. Combining the Tyrosine Kinase Inhibitor Cabozantinib and the mTORC1/2 Inhibitor Sapanisertib Blocks ERK Pathway Activity and Suppresses Tumor Growth in Renal Cell Carcinoma. Cancer Research. 83: 4161-4178. PMID 38098449 DOI: 10.1158/0008-5472.CAN-23-0604  0.331
2023 Iglesia MD, Jayasinghe RG, Chen S, Terekhanova NV, Herndon JM, Storrs E, Karpova A, Zhou DC, Al Deen NN, Shinkle AT, Lu RJ, Caravan W, Houston A, Zhao Y, Sato K, ... ... Wendl MC, et al. Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages. Biorxiv : the Preprint Server For Biology. PMID 37961519 DOI: 10.1101/2023.10.31.565031  0.393
2023 Terekhanova NV, Karpova A, Liang WW, Strzalkowski A, Chen S, Li Y, Southard-Smith AN, Iglesia MD, Wendl MC, Jayasinghe RG, Liu J, Song Y, Cao S, Houston A, Liu X, et al. Epigenetic regulation during cancer transitions across 11 tumour types. Nature. PMID 37914932 DOI: 10.1038/s41586-023-06682-5  0.417
2023 Liang WW, Lu RJ, Jayasinghe RG, Foltz SM, Porta-Pardo E, Geffen Y, Wendl MC, Lazcano R, Kolodziejczak I, Song Y, Govindan A, Demicco EG, Li X, Li Y, Sethuraman S, et al. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin. Cancer Cell. PMID 37582362 DOI: 10.1016/j.ccell.2023.07.013  0.387
2023 Li Y, Porta-Pardo E, Tokheim C, Bailey MH, Yaron TM, Stathias V, Geffen Y, Imbach KJ, Cao S, Anand S, Akiyama Y, Liu W, Wyczalkowski MA, Song Y, Storrs EP, ... Wendl MC, et al. Pan-cancer proteogenomics connects oncogenic drivers to functional states. Cell. PMID 37582357 DOI: 10.1016/j.cell.2023.07.014  0.47
2023 Wu Y, Terekhanova NV, Caravan W, Naser Al Deen N, Lal P, Chen S, Mo CK, Cao S, Li Y, Karpova A, Liu R, Zhao Y, Shinkle A, Strunilin I, Weimholt C, ... ... Wendl MC, et al. Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma. Nature Communications. 14: 1681. PMID 36973268 DOI: 10.1038/s41467-023-37211-7  0.405
2023 Yao L, Wang JT, Jayasinghe RG, O'Neal J, Tsai CF, Rettig MP, Song Y, Liu R, Zhao Y, Ibrahim OM, Fiala MA, Fortier JM, Chen S, Gehrs L, Martins Rodrigues F, ... Wendl MC, et al. Single-cell discovery and multi-omic characterization of therapeutic targets in multiple myeloma. Cancer Research. PMID 36779841 DOI: 10.1158/0008-5472.CAN-22-1769  0.416
2022 Yao L, Jayasinghe RG, Lee BH, Bhasin SS, Pilcher W, Doxie DB, Gonzalez-Kozlova E, Dasari S, Fiala MA, Pita-Juarez Y, Strausbauch M, Kelly G, Thomas BE, Kumar SK, Cho HJ, ... ... Wendl MC, et al. Comprehensive Characterization of the Multiple Myeloma Immune Microenvironment Using Integrated scRNA-seq, CyTOF, and CITE-seq Analysis. Cancer Research Communications. 2: 1255-1265. PMID 36969740 DOI: 10.1158/2767-9764.CRC-22-0022  0.334
2022 Li Y, Lih TM, Dhanasekaran SM, Mannan R, Chen L, Cieslik M, Wu Y, Lu RJ, Clark DJ, Kołodziejczak I, Hong R, Chen S, Zhao Y, Chugh S, Caravan W, ... ... Wendl MC, et al. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell. PMID 36563681 DOI: 10.1016/j.ccell.2022.12.001  0.408
2022 Cui Zhou D, Jayasinghe RG, Chen S, Herndon JM, Iglesia MD, Navale P, Wendl MC, Caravan W, Sato K, Storrs E, Mo CK, Liu J, Southard-Smith AN, Wu Y, Naser Al Deen N, et al. Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer. Nature Genetics. PMID 35995947 DOI: 10.1038/s41588-022-01157-1  0.375
2022 Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA, Karpova A, Wang LB, Li Y, Southard-Smith A, Jayasinghe RG, Yao L, Liu R, Wu Y, Terekhanova NV, Zhu H, Herndon JM, et al. Pollock: fishing for cell states. Bioinformatics Advances. 2: vbac028. PMID 35603231 DOI: 10.1093/bioadv/vbac028  0.321
2021 Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L. Moving pan-cancer studies from basic research toward the clinic. Nature Cancer. 2: 879-890. PMID 35121865 DOI: 10.1038/s43018-021-00250-4  0.464
2021 Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA, Patidar R, Chen L, Wyczalkowski MA, et al. Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature Communications. 12: 5086. PMID 34429404 DOI: 10.1038/s41467-021-25177-3  0.499
2021 Liu R, Gao Q, Foltz SM, Fowles JS, Yao L, Wang JT, Cao S, Sun H, Wendl MC, Sethuraman S, Weerasinghe A, Rettig MP, Storrs EP, Yoon CJ, Wyczalkowski MA, et al. Co-evolution of tumor and immune cells during progression of multiple myeloma. Nature Communications. 12: 2559. PMID 33963182 DOI: 10.1038/s41467-021-22804-x  0.32
2021 Huang KL, Scott AD, Zhou DC, Wang LB, Weerasinghe A, Elmas A, Liu R, Wu Y, Wendl MC, Wyczalkowski MA, Baral J, Sengupta S, Lai CW, Ruggles K, Payne SH, et al. Spatially interacting phosphorylation sites and mutations in cancer. Nature Communications. 12: 2313. PMID 33875650 DOI: 10.1038/s41467-021-22481-w  0.648
2021 Dong G, Wendl MC, Zhang B, Ding L, Huang KL. AeQTL: eQTL analysis using region-based aggregation of rare genomic variants. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 26: 172-183. PMID 33691015  0.491
2021 Wang LB, Karpova A, Gritsenko MA, Kyle JE, Cao S, Li Y, Rykunov D, Colaprico A, Rothstein JH, Hong R, Stathias V, Cornwell M, Petralia F, Wu Y, Reva B, ... ... Wendl MC, et al. Proteogenomic and metabolomic characterization of human glioblastoma. Cancer Cell. PMID 33577785 DOI: 10.1016/j.ccell.2021.01.006  0.429
2021 Han X, Zhang S, Zhou DC, Wang D, He X, Yuan D, Li R, He J, Duan X, Wendl MC, Ding L, Niu B. MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. Briefings in Bioinformatics. PMID 33461213 DOI: 10.1093/bib/bbaa402  0.388
2021 Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieślik M, Chang HY, ... ... Wendl M, et al. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell. PMID 33417831 DOI: 10.1016/j.ccell.2020.12.007  0.354
2020 Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Saksena G, Ellrott K, Wendl MC, et al. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 11: 6232. PMID 33257764 DOI: 10.1038/s41467-020-20128-w  0.485
2020 Cao S, Zhou DC, Oh C, Jayasinghe RG, Zhao Y, Yoon CJ, Wyczalkowski MA, Bailey MH, Tsou T, Gao Q, Malone A, Reynolds S, Shmulevich I, Wendl MC, Chen F, et al. Discovery of driver non-coding splice-site-creating mutations in cancer. Nature Communications. 11: 5573. PMID 33149122 DOI: 10.1038/s41467-020-19307-6  0.465
2020 Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Kelso S, Saksena G, Ellrott K, Wendl MC, Wheeler DA, et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nature Communications. 11: 4748. PMID 32958763 DOI: 10.1038/S41467-020-18151-Y  0.627
2020 Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, ... ... Wendl MC, et al. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell. 182: 200-225.e35. PMID 32649874 DOI: 10.1016/J.Cell.2020.06.013  0.495
2019 Huang KL, Wu Y, Primeau T, Wang YT, Gao Y, McMichael JF, Scott AD, Cao S, Wendl MC, Johnson KJ, Ruggles K, Held J, Payne SH, Davies SR, Dar A, et al. Regulated Phosphosignaling Associated with Breast Cancer Subtypes and Druggability. Molecular & Cellular Proteomics : McP. PMID 31196969 DOI: 10.1074/Mcp.Ra118.001243  0.601
2019 Wang F, Zhang S, Kim TB, Lin YY, Iqbal R, Wang Z, Mohanty V, Sircar K, Karam JA, Wendl MC, Meric-Bernstam F, Weinstein JN, Ding L, Mills GB, Chen K. Integrated transcriptomic-genomic tool Texomer profiles cancer tissues. Nature Methods. PMID 30988467 DOI: 10.1038/S41592-019-0388-9  0.448
2018 Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 174: 1034-1035. PMID 30096302 DOI: 10.1016/J.Cell.2018.07.034  0.562
2018 Sengupta S, Sun SQ, Huang KL, Oh C, Bailey MH, Varghese R, Wyczalkowski MA, Ning J, Tripathi P, McMichael JF, Johnson KJ, Kandoth C, Welch J, Ma C, Wendl MC, et al. Integrative omics analyses broaden treatment targets in human cancer. Genome Medicine. 10: 60. PMID 30053901 DOI: 10.1186/S13073-018-0564-Z  0.51
2018 Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 173: 371-385.e18. PMID 29625053 DOI: 10.1016/J.Cell.2018.02.060  0.541
2018 Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, ... ... Wendl MC, et al. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 173: 355-370.e14. PMID 29625052 DOI: 10.1016/J.Cell.2018.03.039  0.711
2018 Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, ... ... Wendl MC, et al. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 173: 305-320.e10. PMID 29625049 DOI: 10.1016/J.Cell.2018.03.033  0.571
2018 Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, et al. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Reports. 23: 270-281.e3. PMID 29617666 DOI: 10.1016/J.Celrep.2018.03.052  0.559
2018 Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Chen K, ... ... Wendl MC, et al. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Reports. 23: 227-238.e3. PMID 29617662 DOI: 10.1016/J.Celrep.2018.03.050  0.43
2018 Wyczalkowski MA, Bailey MH, Lou C, Hu F, Chen JY, Batra P, McLellan MD, Ding L, Wendl MC. Abstract B11: The MuSiC2 system for discovery and visualization of coding and noncoding cancer drivers Cancer Research. 78. DOI: 10.1158/1538-7445.Pedca17-B11  0.559
2018 Bailey MH, Wang L, Liang W, Foltz S, Dong G, Wendl MC, McLellan M, Hirbe AC, Simpson J, Gerstein M, Ding L. Abstract 419: Reproducibility assessment of mutations calls in exome- and whole-genome sequencing using consensus calling from TCGA and ICGC Cancer Research. 78: 419-419. DOI: 10.1158/1538-7445.Am2018-419  0.631
2018 Jayasinghe RG, Cao S, Gao Q, Wyczalkowski MA, Sengupta S, Walter MJ, Maher C, Wendl MC, Chen F, Eyras E, Lazar AJ, Chen K, Shmulevich I, Ding L. Abstract 2362: Comprehensive portrait of canonical and non-canonical splicing in cancer Cancer Research. 78: 2362-2362. DOI: 10.1158/1538-7445.Am2018-2362  0.598
2017 Wyczalkowski MA, Wylie KM, Cao S, McLellan MD, Flynn J, Huang M, Ye K, Fan X, Chen K, Wendl MC, Ding L. BreakPoint Surveyor: A Pipeline for Structural Variant Visualization. Bioinformatics (Oxford, England). PMID 28582538 DOI: 10.1093/Bioinformatics/Btx362  0.472
2017 Mashl RJ, Scott AD, Huang KL, Wyczalkowski MA, Yoon CJ, Niu B, DeNardo E, Yellapantula VD, Handsaker RE, Chen K, Koboldt DC, Ye K, Fenyö D, Raphael B, Wendl MC, et al. GenomeVIP: a cloud platform for genomic variant discovery and interpretation. Genome Research. PMID 28522612 DOI: 10.1101/Gr.211656.116  0.675
2017 Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, ... ... Wendl MC, et al. Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communications. 8: 15479. PMID 28440318 DOI: 10.1038/Ncomms15479  0.623
2017 Huang KL, Li S, Mertins P, Cao S, Gunawardena HP, Ruggles KV, Mani DR, Clauser KR, Tanioka M, Usary J, Kavuri SM, Xie L, Yoon C, Qiao JW, Wrobel J, ... ... Wendl MC, et al. Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. Nature Communications. 8: 14864. PMID 28348404 DOI: 10.1038/Ncomms14864  0.663
2017 Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Correction: Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. Plos Medicine. 14: e1002222. PMID 28068332 DOI: 10.1371/journal.pmed.1002222  0.419
2016 Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. Plos Medicine. 13: e1002174. PMID 27923045 DOI: 10.1371/Journal.Pmed.1002174  0.491
2016 Cao S, Wendl MC, Wyczalkowski MA, Wylie K, Ye K, Jayasinghe R, Xie M, Wu S, Niu B, Grubb R, Johnson KJ, Gay H, Chen K, Rader JS, Dipersio JF, et al. Divergent viral presentation among human tumors and adjacent normal tissues. Scientific Reports. 6: 28294. PMID 27339696 DOI: 10.1038/Srep28294  0.487
2016 Niu B, Scott AD, Sengupta S, Bailey MH, Batra P, Ning J, Wyczalkowski MA, Liang WW, Zhang Q, McLellan MD, Sun SQ, Tripathi P, Lou C, Ye K, Mashl RJ, ... ... Wendl MC, et al. Protein-structure-guided discovery of functional mutations across 19 cancer types. Nature Genetics. PMID 27294619 DOI: 10.1038/Ng.3586  0.707
2016 Scott AD, Yellapantula VD, Yoon CJ, Wendl M, Tomasson MH, Fiala MA, DiPersio JF, Vij R, Ding L. Uncovering Clonal and Subclonal Druggable Targets in Multiple Myeloma Using Omic Data Blood. 128: 2084-2084. DOI: 10.1182/Blood.V128.22.2084.2084  0.698
2015 Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, et al. Patterns and functional implications of rare germline variants across 12 cancer types. Nature Communications. 6: 10086. PMID 26689913 DOI: 10.1038/Ncomms10086  0.646
2015 Ye K, Wang J, Jayasinghe R, Lameijer EW, McMichael JF, Ning J, McLellan MD, Xie M, Cao S, Yellapantula V, Huang KL, Scott A, Foltz S, Niu B, Johnson KJ, ... ... Wendl MC, et al. Systematic discovery of complex insertions and deletions in human cancers. Nature Medicine. PMID 26657142 DOI: 10.1038/Nm.4002  0.699
2015 Griffith M, Miller CA, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, et al. Optimizing cancer genome sequencing and analysis. Cell Systems. 1: 210-223. PMID 26645048 DOI: 10.7490/F1000Research.1110088.1  0.615
2015 Kloosterman WP, Francioli LC, Hormozdiari F, Marschall T, Hehir-Kwa JY, Abdellaoui A, Lameijer EW, Moed MH, Koval V, Renkens I, van Roosmalen MJ, Arp P, Karssen LC, Coe BP, Handsaker RE, ... ... Wendl MC, et al. Characteristics of de novo structural changes in the human genome. Genome Research. 25: 792-801. PMID 25883321 DOI: 10.1101/Gr.185041.114  0.458
2015 Sengupta S, Ye K, Scott AD, Niu B, Bailey MH, McLellan MD, Wendl MC, Wyczalkowski MA, Ding L. Abstract 61: Sequence and structure-guided approach to identify functional mutations in G-protein coupled receptors Cancer Research. 75: 61-61. DOI: 10.1158/1538-7445.Am2015-61  0.71
2015 Huang K, Wang J, Cao S, Xie M, Jayasinghe R, Ning J, McLellan M, Wendl M, Scott A, Johnson K, Davies S, Fenyö D, Townsend R, Chen F, Parvin J, et al. Abstract 1939: Discovery and proteogenomic investigation of genetic variants in human cancers Cancer Research. 75: 1939-1939. DOI: 10.1158/1538-7445.Am2015-1939  0.709
2015 Jayasinghe RG, Huang K, Ning J, Wyczalkowski M, Lu C, Xie M, Wendl M, McLellan M, Ye K, Ding L. Abstract 1929: Pan-Cancer analysis of the effects of splice-altering variants on mRNA splicing and stability Cancer Research. 75: 1929-1929. DOI: 10.1158/1538-7445.Am2015-1929  0.598
2015 Griffith M, Miller CA, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, et al. Optimizing Cancer Genome Sequencing and Analysis Cell Systems. 1: 210-223. DOI: 10.1016/j.cels.2015.08.015  0.521
2014 Ding L, Kim M, Kanchi KL, Dees ND, Lu C, Griffith M, Fenstermacher D, Sung H, Miller CA, Goetz B, Wendl MC, Griffith O, Cornelius LA, Linette GP, McMichael JF, et al. Clonal architectures and driver mutations in metastatic melanomas. Plos One. 9: e111153. PMID 25393105 DOI: 10.1371/Journal.Pone.0111153  0.807
2014 Xie M, Lu C, Wang J, McLellan MD, Johnson KJ, Wendl MC, McMichael JF, Schmidt HK, Yellapantula V, Miller CA, Ozenberger BA, Welch JS, Link DC, Walter MJ, Mardis ER, et al. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nature Medicine. 20: 1472-8. PMID 25326804 DOI: 10.1038/Nm.3733  0.558
2014 Ding L, Wendl MC, McMichael JF, Raphael BJ. Expanding the computational toolbox for mining cancer genomes. Nature Reviews. Genetics. 15: 556-70. PMID 25001846 DOI: 10.1038/Nrg3767  0.611
2014 Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, et al. Integrated analysis of germline and somatic variants in ovarian cancer. Nature Communications. 5: 3156. PMID 24448499 DOI: 10.1038/Ncomms4156  0.649
2014 Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, Wendl MC, Ding L. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics (Oxford, England). 30: 1015-6. PMID 24371154 DOI: 10.1093/Bioinformatics/Btt755  0.511
2013 Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, et al. Mutational landscape and significance across 12 major cancer types. Nature. 502: 333-9. PMID 24132290 DOI: 10.1038/Nature12634  0.594
2013 Ding L, Wendl MC. Differences that matter in cancer genomics. Nature Biotechnology. 31: 892-3. PMID 24104755 DOI: 10.1038/Nbt.2715  0.592
2013 Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson G, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, ... ... Wendl MC, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia New England Journal of Medicine. 368: 2059-2074. PMID 23634996 DOI: 10.1056/Nejmoa1301689  0.595
2013 Ding L, Raphael BJ, Chen F, Wendl MC. Advances for studying clonal evolution in cancer. Cancer Letters. 340: 212-9. PMID 23353056 DOI: 10.1016/J.Canlet.2012.12.028  0.544
2013 Wendl MC, Kota K, Weinstock GM, Mitreva M. Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem. Journal of Mathematical Biology. 67: 1141-61. PMID 22965653 DOI: 10.1007/S00285-012-0586-X  0.336
2013 Kandoth C, McLellan MD, Miller CA, Lu C, Dees N, Ye K, Niu B, Wendl MC, Wilson RK, Ding L. Abstract LB-239: Mutational and clonal analyses across TCGA cancer types using the MuSiC suite of tools. Cancer Research. 73. DOI: 10.1158/1538-7445.Am2013-Lb-239  0.634
2013 Ding L, Wendl MC. Erratum: Differences that matter in cancer genomics Nature Biotechnology. 31: 1148-1148. DOI: 10.1038/Nbt1213-1148D  0.432
2012 Dees ND, Zhang Q, Kandoth C, Wendl MC, Schierding W, Koboldt DC, Mooney TB, Callaway MB, Dooling D, Mardis ER, Wilson RK, Ding L. MuSiC: Identifying mutational significance in cancer genomes Genome Research. 22: 1589-1598. PMID 22759861 DOI: 10.1101/Gr.134635.111  0.824
2012 Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, ... ... Wendl MC, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 486: 353-60. PMID 22722193 DOI: 10.1038/Nature11143  0.589
2012 Young MA, Larson DE, Sun CW, George DR, Ding L, Miller CA, Lin L, Pawlik KM, Chen K, Fan X, Schmidt H, Kalicki-Veizer J, Cook LL, Swift GW, Demeter RT, ... Wendl MC, et al. Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells. Cell Stem Cell. 10: 570-82. PMID 22542160 DOI: 10.1016/J.Stem.2012.03.002  0.579
2012 Matsushita H, Vesely MD, Koboldt DC, Rickert CG, Uppaluri R, Magrini VJ, Arthur CD, White JM, Chen YS, Shea LK, Hundal J, Wendl MC, Demeter R, Wylie T, Allison JP, et al. Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting. Nature. 482: 400-4. PMID 22318521 DOI: 10.1038/Nature10755  0.377
2012 Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, ... ... Wendl MC, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 481: 506-10. PMID 22237025 DOI: 10.1038/Nature10738  0.646
2012 Ellis MJ, Li D, Shen D, Luo J, Suman VJ, Wallis JW, Tine BAV, Hoog J, Crowder RJ, Snider JE, Ballman K, Chen K, Koboldt DC, Schierding WS, McMichael JF, ... ... Wendl MC, et al. Abstract LB-423: Whole genome comparisons of pre- and post- aromatase inhibitor treatment in estrogen receptor positive breast cancer Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Lb-423  0.459
2011 Bell D, Berchuck A, Birrer M, Chien J, Cramer DW, Dao F, Dhir R, Disaia P, Gabra H, Glenn P, Godwin AK, Gross J, Hartmann L, Huang M, Huntsman DG, ... ... Wendl M, et al. Integrated genomic analyses of ovarian carcinoma Nature. 474: 609-615. PMID 21720365 DOI: 10.1038/Nature10166  0.807
2011 Wendl MC, Wallis JW, Lin L, Kandoth C, Mardis ER, Wilson RK, Ding L. PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics (Oxford, England). 27: 1595-602. PMID 21498403 DOI: 10.1093/Bioinformatics/Btr193  0.588
2010 Ding L, Wendl MC, Koboldt DC, Mardis ER. Analysis of next-generation genomic data in cancer: Accomplishments and challenges Human Molecular Genetics. 19: R188-R196. PMID 20843826 DOI: 10.1093/Hmg/Ddq391  0.594
2010 Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, ... ... Wendl MC, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature. 464: 999-1005. PMID 20393555 DOI: 10.1038/Nature08989  0.8
2009 Wendl MC, Wilson RK. The theory of discovering rare variants via DNA sequencing. Bmc Genomics. 10: 485. PMID 19843339 DOI: 10.1186/1471-2164-10-485  0.358
2009 Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nature Methods. 6: 677-81. PMID 19668202 DOI: 10.1038/Nmeth.1363  0.588
2009 Wendl MC, Wilson RK. Statistical aspects of discerning indel-type structural variation via DNA sequence alignment. Bmc Genomics. 10: 359. PMID 19656394 DOI: 10.1186/1471-2164-10-359  0.339
2008 Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K, Sougnez C, Greulich H, Muzny DM, Morgan MB, Fulton L, Fulton RS, Zhang Q, Wendl MC, Lawrence MS, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 455: 1069-75. PMID 18948947 DOI: 10.1038/Nature07423  0.648
2008 McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, Yung WKA, Bogler O, Weinstein JN, VandenBerg S, Berger M, ... ... Wendl MC, et al. Comprehensive genomic characterization defines human glioblastoma genes and core pathways Nature. 455: 1061-1068. PMID 18772890 DOI: 10.1038/Nature07385  0.671
2008 Wendl MC, Wilson RK. Aspects of coverage in medical DNA sequencing. Bmc Bioinformatics. 9: 239. PMID 18485222 DOI: 10.1186/1471-2105-9-239  0.457
2007 Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Research. 17: 659-66. PMID 17416743 DOI: 10.1101/Gr.6151507  0.534
2007 Ley TJ, DiPersio J, Ding L, Ries R, Magrini V, Payton J, McGrath S, Walter M, Wylie T, Dunford-Shore B, Chen K, McLellan M, Wendl M, Dooling D, Cook L, et al. Sequencing an Acute Myeloid Leukemia (AML) Genome with “Next Generation” Technologies. Blood. 110: 205-205. DOI: 10.1182/Blood.V110.11.205.205  0.58
2006 Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biology. 7: R75. PMID 26271136 DOI: 10.1186/Gb-2006-7-8-R75  0.581
2006 Wendl MC. A general coverage theory for shotgun DNA sequencing. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 1177-96. PMID 16901236 DOI: 10.1089/Cmb.2006.13.1177  0.406
2006 Wendl MC. Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing. Bulletin of Mathematical Biology. 68: 179-96. PMID 16794926 DOI: 10.1007/S11538-005-9021-4  0.391
2006 Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP. Codon usage patterns in Nematoda: Analysis based on over 25 million codons in thirty-two species Genome Biology. 7. DOI: 10.1186/gb-2006-7-8-r75  0.485
2005 Wendl MC, Barbazuk WB. Extension of Lander-Waterman theory for sequencing filtered DNA libraries. Bmc Bioinformatics. 6: 245. PMID 16216129 DOI: 10.1186/1471-2105-6-245  0.343
2005 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, ... ... Wendl MC, et al. Initial sequence of the chimpanzee genome and comparison with the human genome Nature. 437: 69-87. PMID 16136131 DOI: 10.1038/Nature04072  0.405
2005 Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, ... ... Wendl MC, et al. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature. 434: 724-31. PMID 15815621 DOI: 10.1038/Nature03466  0.612
2004 Wendl MC, Yang SP. Gap statistics for whole genome shotgun DNA sequencing projects. Bioinformatics (Oxford, England). 20: 1527-34. PMID 14962917 DOI: 10.1093/Bioinformatics/Bth120  0.354
2003 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, ... ... Wendl MC, et al. The DNA sequence of human chromosome 7. Nature. 424: 157-64. PMID 12853948 DOI: 10.1038/Nature01782  0.636
2002 Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, ... ... Wendl MC, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 420: 520-62. PMID 12466850 DOI: 10.1038/Nature01262  0.634
2002 Wendl MC, Waterston RH. Generalized gap model for bacterial artificial chromosome clone fingerprint mapping and shotgun sequencing Genome Research. 12: 1943-1949. PMID 12466299 DOI: 10.1101/Gr.655102  0.562
2001 Wendl MC, Korf I, Chinwalla AT, Hillier LW. Automated processing of raw DNA sequence data Ieee Engineering in Medicine and Biology Magazine. 20: 41-48. PMID 11494768 DOI: 10.1109/51.940044  0.365
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Wendl MC, et al. Initial sequencing and analysis of the human genome. Nature. 409: 860-921. PMID 11237011 DOI: 10.1038/35057062  0.618
2001 Wendl MC, Marra MA, Hillier LW, Chinwalla AT, Wilson RK, Waterston RH. Theories and applications for sequencing randomly selected clones Genome Research. 11: 274-280. PMID 11157790 DOI: 10.1101/Gr.133901  0.602
2001 Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, Fitzhugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, ... ... Wendl MC, et al. Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) Nature. 412: 565-566. DOI: 10.1038/35087627  0.402
1998 Wendl MC, Dear S, Hodgson D, Hillier L. Automated sequence preprocessing in a large-scale sequencing environment. Genome Research. 8: 975-84. PMID 9750196 DOI: 10.1101/Gr.8.9.975  0.369
1998 Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Research. 8: 175-85. PMID 9521921 DOI: 10.1101/Gr.8.3.175  0.368
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