Journal publications     (cumulative google scholar citations >100,000)

• Zhou DC et al. (2022) Spatially restricted drivers and transitional cell populations cooperate with the microenvironment in untreated and chemo-resistant pancreatic cancer, Nature Genetics 54(9), 1390-1405.
  
• Storrs EP, Zhou DC, Wendl MC, Wyczalkowski MA et al. (2022) Pollock: Fishing for cell states, Bioinformatics Advances 2(1), art. vbac028.
• Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, and Ding L (2021) Moving pan-cancer studies from basic research toward the clinic, Nature Cancer 2(9), 879-890.
• Sun H et al. (2021) Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment, Nature Comm. 12(1), art. 5086.
• Liu R et al. (2021) Co-evolution of tumor and immune cells during progression of multiple myeloma, Nature Comm. 12(1), art. 2559.
• Huang K et al. (2021) Spatially interacting phosphorylation sites and mutations in cancer, Nature Comm. 12(1), art. 2313.
• Dong G, Wendl MC, Zhang B, Ding L, and Huang KL (2021) AeQTL: eQTL analysis using region-based aggregation of rare genomic variants, Pacific Sympos Biocomput 26, 172-183.
• Wang LB et al. (2021) Proteogenomic and metabolomic characterization of human glioblastoma, Cancer Cell 39(4), 509-528.
• Huang C et al. (2021) Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma, Cancer Cell 39(3), 361-379.
• Han X et al. (2021) MSIsensor-ct: Microsatellite instability detection using cfDNA sequencing data, Briefings in Bioinformatics 22(5), art. 402.
• Cao S et al. (2020) Discovery of driver non-coding splice-site-creating mutations in cancer, Nature Comm. 11(1), art. 5573.
• Bailey MH et al. (2020) Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples, Nature Comm. 11(1), art. 4748.
• Gillette MA et al. (2020) Proteogenomic characterization reveals therapeutic vulnerabilities in lung adenocarcinoma, Cell 182(1), 200-225.
• Rozenblatt-Rosen O et al. (2020) The Human Tumor Atlas Network: Charting tumor transitions across space and time at single-cell resolution, Cell 181(2), 236-249.
• Wang F et al. (2019) Integrated transcriptomic-genomic tool Texomer profiles cancer tissues, Nature Methods 16(5), 401-404.
• Huang KL et al. (2019) Regulated phosphosignaling associated with breast cancer subtypes and druggability, Molec. & Cell. Proteomics 18(8), 1630-1650.
• Sengupta S et al. (2018) Integrative omics analyses broaden treatment targets in human cancer, Genome Med. 10(1), 60.
• Gao Q et al. (2018) Driver fusions and their implications in the development and treatment of human cancers, Cell Reports 23(1), 227-238.
• Jayasinghe RG et al. (2018) Systematic analysis of splice-site-creating mutations in cancer, Cell Reports 23(1), 270-281.
• Huang KL et al. (2018) Pathogenic germline variants in 10,389 adult cancers, Cell 173(2), 355-370.
• Bailey MH et al. (2018) Comprehensive characterization of cancer driver genes and mutations, Cell 173(2), 371-385.
• Ding L et al. (2018) Perspective on oncogenic processes at the end of the beginning of cancer genomics, Cell 173(2), 305-320.
• Wendl MC (2017) Don't tamper with SI-unit consistency (op-ed), Nature 549(7671), 160.
• Wyczalkowski MA et al. (2017) BreakPoint Surveyor: A pipeline for structural variant visualization, Bioinformatics, 33(19), 3121-3122.
• Mashl RJ et al. (2017) GenomeVIP: a cloud platform for genomic variant discovery and interpretation, Genome Res. 27(8), 1450-1459.
• Huang KL et al. (2017) Proteogenomic integration reveals therapeutic targets in breast cancer xenografts, Nature Comm. 8 art. 14864.
• Hoadley KA et al. (2016) Tumor evolution in two patients with basal-like breast cancer: A retrospective genomics study of multiple metastases, PLoS Medicine, 13(12), e1002174.
• Cao S, Wendl MC, Wyczalkowski MA et al. (2016) Divergent viral presentation among human tumors and adjacent normal tissues, Nature Scientific Reports 6, 28294.
• Niu B et al. (2016) Protein structure guided discovery of functional mutations across 19 cancer types, Nature Genetics 48(8), 827-837.
• Wendl MC (2016) Pseudonymous fame (op-ed), Science 351(6280), 1406.
• Ye K et al. (2016) Systematic discovery of complex insertions and deletions in human cancers, Nature Medicine 22(1), 97-104.
• Lu C*, Xie M*, Wendl MC* et al. (2015) Patterns and functional implications of rare germline variants across 12 cancer types, Nature Comm. 6 art. 10086.
• Griffith M et al. (2015) Optimizing cancer genome sequencing and analysis, Cell Systems 1(3), 210-223.
• Kloosterman WP et al. (2015) Characteristics of de novo structural changes in the human genome, Genome Res. 25(6), 792-801.
• Xie M, Lu C, Wang J, McLellan MD, Johnson KJ, Wendl MC et al. (2014) Age-related mutations associated with clonal hematopoietic expansion and malignancies, Nature Medicine 20(12), 1472-1478.
• Ding L et al. (2014) Clonal Architectures and Driver Mutations in Metastatic Melanomas, PLoS One 9(11), e111153.
• Collisson EA et al. (2014) Comprehensive molecular profiling of lung adenocarcinoma, Nature 511(7511), 543-550.
• Ding L, Wendl MC, McMichael J, and Raphael BJ (2014) Expanding the computational toolbox for mining cancer genomes, Nature Rev. Gen. 15(8), 556-570.

• Niu, B et al. (2014) MSIsensor: microsatellite instability detection using paired tumor-normal sequence data, Bioinformatics 30(7), 1015-1016.
• Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC et al. (2014) Integrated analysis of germline and somatic variants in ovarian cancer, Nature Comm. 5 art. 3156.
• Ding L and Wendl MC (2013) Differences that matter in cancer genomics, Nature Biotech. 31(10), 892-893.
• Ding L, Raphael BJ, Chen F, and Wendl MC (2013) Advances for studying clonal evolution in cancer, Cancer Letters 340(2), 212-219.
• Kandoth C et al. (2013) Mutational landscape and significance across 12 major cancer types, Nature 502(7471), 333-339.
• Wendl MC, Kota K, Weinstock GM, and Mitreva M (2013) Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem, J. Math. Biol. 67(5), 1141-1161.
• Chang K et al. (2013) The cancer genome atlas pan-cancer analysis project, Nature Genetics 45(10), 1013-1020.
• Ley TJ et al. (2013) Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia, New England J. Med. 368(22), 2059-2074.
• Altshuler DM et al. (2012) An integrated map of genetic variation from 1,092 human genomes, Nature 491(7422), 56-65.
• Ellis MJ et al. (2012) Whole-genome analysis informs breast cancer response to aromatase inhibition, Nature 486(7403), 353-360.
• Dees ND, Zhang Q, Kandoth C, Wendl MC et al. (2012) MuSiC: Identifying mutation significance in cancer genomes, Genome Res. 22(8), 1589-1598.
• Young MA et al. (2012) Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells, Cell: Stem Cell 10(5), 570-582.
• Matsushita H et al. (2012) Cancer exome analysis reveals a T-cell-dependent mechanism of cancer immunoediting, Nature 482(7385), 400-404.
• Ding L et al. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing, Nature 481(7382), 506-510.
• Bell D et al. (2011) Integrated genomic analyses of ovarian carcinoma, Nature 474(7353), 609-615.
• Wendl MC et al. (2011) PathScan: A tool for discerning mutational significance in groups of putative cancer genes, Bioinformatics 27(12), 1595-1602.
• Ding L, Wendl MC, Koboldt DC, and Mardis ER (2010) Analysis of next-generation genomic data in cancer: Accomplishments and challenges, Hum. Mol. Gen. 19(R2), 188-196.
• Altshuler DM et al. (2010) A map of human genome variation from population-scale sequencing, Nature 467(7319), 1061-1073.
• Ding L et al. (2010) Genome remodelling in a basal-like breast cancer metastasis and xenograft, Nature 464(7291), 999-1005.
• Wendl MC (2009) Technology takes on deadlines for fetal human rights, Nature 458(7235), 147.
• Wendl MC and Wilson RK (2009) The theory of discovering rare variants via DNA sequencing, BMC Genomics 10 art. 485.
• Wendl MC and Wilson RK (2009) Statistical aspects of discerning indel-type structural variation via DNA sequencing alignment, BMC Genomics 10 art. 359.
• Chen K et al. (2009) BreakDancer: An algorithm for high-resolution mapping of genomic structural variation, Nature Methods 6(9), 677-681.
• Ding L et al. (2008) Somatic mutations affect key pathways in lung adenocarcinoma, Nature 455(7216), 1069-1075.
• Chin L et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways, Nature 455(7216), 1061-1068.
• Wendl MC and Wilson RK (2008) Aspects of coverage in medical DNA sequencing, BMC Bioinformatics 9 art. 239.
• Wendl MC (2008) Random covering of multiple one-dimensional finite domains with an application to DNA sequencing, SIAM J. Appl. Math. 68(3), 890-905.
• Wendl MC (2007) H-index: However ranker, citations need context, Nature 449(7161), 403.
• Wendl MC et al. (2007) Design and implementation of a generalized laboratory data model, BMC Bioinformatics 8 art. 362.
• Wendl MC (2007) Algebraic correction methods for computational assessment of clone overlaps in DNA fingerprint mapping, BMC Bioinformatics 8 art. 127.
• Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, and Mardis ER (2007) PolyScan: Automatic indel and SNP detection in human resequence data, Genome Res. 17(5), 659-66.
• Mitreva M, Wendl MC, Martin J, Wylie T et al. (2006) Codon usage patterns in nematoda: Analysis based on over 25 million codons in thirty-two species, Genome Biol. 7 art. 75.
• Wendl MC (2006) A general coverage theory for shotgun DNA sequencing, J. Comp. Biol. 13(6), 1177-1196.
• Wendl MC (2006) Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing, Bull. Math. Biol. 68(1), 179-196.
• Wendl MC (2005) Bioweapons could kill more in one strike than guns, Nature 437(7056), 192.
• Wendl MC (2005) The question of forbidden knowledge, Science 308(5728), 1549.
• Wendl MC and Barbazuk WB (2005) Extension of Lander-Waterman theory for sequencing filtered DNA libraries, BMC Bioinformatics 6 art. 245.
• Mikkelsen TJ et al. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome, Nature 437(7055), 69-87.
• Wendl MC (2005) Probabilistic assessment of clone overlaps in DNA fingerprint mapping via a priori models, J. Comp. Biol. 12(3), 283-297.
• Hillier LW et al. (2005) Generation and annotation of the DNA sequences of human chromosomes 2 and 4, Nature 434(7034), 724-731.
• Int. Human Genome Sequence Consortium (2004) Finishing the euchromatic sequence of the human genome, Nature 431(7011), 931-945.
• Wendl MC and Yang SP (2004) Gap statistics for whole genome shotgun DNA sequencing projects, Bioinformatics 20(10), 1527-1534.
• Wendl MC (2003) Collision probability between sets of random variables, Stat. Prob. Lett. 64(3), 249-254.
• Hillier LW et al. (2003) The DNA sequence of human chromosome 7, Nature 424(6945), 157-164.
• Wendl MC and Dooling DJ (2003) Open-source answer to bibliography problem, Nature 424(6952), 995.
• Wendl MC and Waterston RH (2002) Generalized gap model for bacterial artificial chromosome  clone fingerprint mapping and shotgun sequencing, Genome Res. 12(12), 1943-1949.
• Waterston RH et al. (2002) Initial sequencing and comparative analysis of the mouse genome, Nature 420(6915), 520-562.
• Wendl MC and Agarwal RK (2002) Viscous dissipation in finite thin-gap Couette devices, J. Heat Trans. 124(1), 200-203.
• Wendl MC (2001) Mathematical analysis of coaxial disk cellular shear loading devices, Rev. Sci. Instr. 72(11), 4212-4217.
• Wendl MC, Marra MA et al. (2001) Theories and applications for sequencing randomly selected clones, Genome Res. 11(2), 274-280.
• Wendl MC, Korf I, Chinwalla AT, and Hillier LW (2001) Automated processing of raw DNA sequence data, IEEE Eng. Med. Biol. 20(4), 41-48.
• Lander ES et al. (2001) Initial sequencing and analysis of the human genome, Nature 409(6822), 860-921.
• Wendl MC and Agarwal RK (2000) Couette flow profiles for two non-classical Taylor-Couette cells, J. Fluids Eng. 122(2), 435-438.
• Wendl MC (1999) General solution for the Couette flow profile, Phys. Rev. E 60(5), 6192-6194.
• Wendl MC (1999) A method for obtaining benchmark Navier-Stokes solutions, Int. J. Num. Meth. Fluids, 31(3), 657-660.
• C elegans Sequencing Consortium (1998) Genome sequencing of the nematode C elegans: A platform for investigating biology, Science 282(5396), 2012-2018.
• Wendl MC, Dear S, Hodgson D, and Hillier LW (1998) Automated sequence preprocessing in a large-scale sequencing environment, Genome Res. 8(9), 975-984.
• Ewing B, Hillier LW, Wendl MC, and Green P (1998) Base-calling of automated sequencer traces using PHRED: I. Accuracy assessment, Genome Res. 8(3), 175-185.
• Wendl MC (1997) Computer testing not yet mature, APTA Bull. 12(16), 16.

educational research & STEM outreach publications

• Wendl MC (2022) Spam calls and number blocking, Chalkdust, 16, in press.
  
• Wendl MC (2021) An odd card trick, Chalkdust, 14, 44-50.

book chapter, Reviews, and other Miscellaneous publications

• Wendl MC (2022)  Männerchor, Ernst Herzwurm, and the 38–th Sängerfest in St. Louis, DKV Rundschreiben 22(2), 14-21.
  
• Wendl MC et al. (2005) Genome assembly, In Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Ed. PFR Little, Wiley, vol 3, 1047-1058.
• Wendl MC et al. (2005) The mouse genome sequencing project: An overview, Ch. 16 in The Mouse in Animal Genetics and Breeding Research, Ed. EJ Eisen, World Scientific, pp. 341-352.
• Wendl MC, Chinwalla AT, and Hillier LW (2003) Software for genomic sequencing, Ch. 12 in Genome Mapping and Sequencing, Ed. I Dunham, Horizon Scientific Press, pp. 357-395.
• Wendl MC and Agarwal RK (2003) Mass conservation and the accuracy of non-staggered grid incompressible flow schemes, In Numerical Simulations of Incompressible Flows, Ed. MM Hafez, World Scientific, pp. 86-97.
• Wendl MC (2001) Mathematics and numeracy, In Encyclopedia of the United States in the Nineteenth Century, Ed. P Finkelman, Scribner's, vol 2, pp. 273-274.

graduate school work

• Wendl MC (1990) Jet-induced mixing of propellant in partially filled tanks in a reduced gravity environment, Master's Thesis.
  
• Wendl MC (1994) A pressure-based finite-volume time-stepping algorithm for the numerical simulation of incompressible flows, Doctoral Dissertation  (metadata in the NASA ADS database).