Chris Miller, PhD

I work in the Division of Oncology at Washington University in St. Louis, where I develop and apply computational tools to give us insight into the origins and progression of cancer.

My core research interests include:

Cancer - studying the genomic alterations that result in tumorigenesis

The clonal architecture of tumors and how they evolve in response to therapy

Integrative analysis to place genomic aberrations into a functional context

Effective design and targeting of cancer immunotherapies

Developing open-source software for integrating, mining, and visualizing genomic data

Utilizing technology to drive science communication and collaboration

• PhD, Structural and Computational Biology
  and Molecular Biophysics program
  Baylor College of Medicine
  Mentor: Dr. Aleksandar Milosavljevic
  Thesis: Detection and Integrative Analysis of Genomic Aberrations in Cancer
  (graduated February 2011)
• BS degrees in Biology and Computer Science
  Truman State University
  (graduated May 2005)

* denotes shared first authorship

• Proteomic and Phosphoproteomic Landscapes of Acute Myeloid Leukemia
  Kramer MH, Zhang Q, Sprung R, Day RB, Erdmann-Gilmore P, Li Y, Xu Z, Helton NM, George DR, Mi Y, et al.. Blood. 2022. doi:10.1182/blood.2022016033
• Discovery of a novel genomic alteration that renders leukemic cells resistant to CD19-targeted immunotherapies
  Ghobadi A, Landmann J, Carter A, Cooper ML, Selli ME, Chang J, Baker M, Miller CA, Ferraro F, Chen DY, et al.. Blood Advances. 2022. doi:10.1182/bloodadvances.2022007705
• Convergent clonal evolution of signaling gene mutations is a hallmark of myelodysplastic syndrome progression
  Menssen AJ, Khanna A, Miller CA, Nonavinkere SS, Chang GS, Shao J, Robinson J, O'Laughlin M, Fronick CC, Fulton RS, et al.. Blood Cancer Discovery. 2022. doi:10.1158/2643-3230.BCD-21-0155
• Recurrent transcriptional responses in AML and MDS patients treated with decitabine
  Upadhyay P, Beales J, Shah NM, Gruszczynska A, Miller CA, Petti AA, Ramakrishnan SM, Link DC, Ley TJ, Welch JS. Experimental Hematology. 2022. doi:10.1016/j.exphem.2022.04.002
• Genetic and transcriptional contributions to relapse in normal karyotype acute myeloid leukemia
  Petti AA, Khan SM, Xu Z, Helton N, Fronick CC, Fulton R, Ramakrishnan SM, Nonavinkere SS, Heath SE, Westervelt P, et al.. Blood Cancer Discovery. 2022. doi:10.1158/2643-3230.BCD-21-0050
• DNMT3A overgrowth syndrome is associated with the development of hematopoietic malignancies in children and young adults
  Ferris MA, Smith AM, Heath SE, Duncavage EJ, Oberley M, Freyer D, Wynn R, Douzgou S, Maris JM, Reilly AF, et al.. Blood, The Journal Of The American Society Of Hematology. 2022. doi:10.1182/blood.2021014052
• Decitabine salvage for TP53-mutated, relapsed/refractory acute myeloid leukemia after cytotoxic induction therapy
  Ferraro F, Gruszczynska A, Ruzinova MB, Miller CA, Percival ME, Uy GL, Pusic I, Jacoby MA, Christopher MJ, Kim MY, et al.. Haematologica. 2022. doi:10.3324/haematol.2021.280153
• Efficient Algorithms Unlock Understanding of Clonal Evolution in Cancer
  Miller CA. Blood Cancer Discovery. 2022. doi:10.1158/2643-3230.BCD-22-0036
• Somatic Dnmt3a inactivation leads to slow, canonical DNA methylation loss in murine hematopoietic cells
  Smith AM, Verdoni AM, Abel HJ, Chen DY, Ketkar S, Leight ER, Miller CA, Ley TJ. Iscience. 2022. doi:10.1016/j.isci.2022.104004
• Genomic and transcriptomic somatic alterations of hepatocellular carcinoma in non-cirrhotic livers
  Skidmore ZL, Kunisaki J, Lin Y, Cotto KC, Barnell EK, Hundal J, Krysiak K, Magrini V, Trani L, Walker JR, et al.. Cancer Genetics. 2022. doi:10.1016/j.cancergen.2022.04.002
• Tumor suppressor function of WT1 in acute promyelocytic leukemia
  Christopher MJ, Katerndahl CD, LeBlanc HR, Elmendorf TT, Basu V, Gang M, Menssen AJ, Spencer DH, Duncavage EJ, Ketkar S, et al.. Haematologica. 2022. doi:10.3324/haematol.2021.279601
• Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells
  Wilson ER, Helton NM, Heath SE, Fulton RS, Payton JE, Welch JS, Walter MJ, Westervelt P, DiPersio JF, Link DC, et al.. Leukemia. 2022. doi:10.1038/s41375-021-01476-y
• Immunosuppression and outcomes in adult patients with de novo acute myeloid leukemia with normal karyotypes
  Ferraro F*, Miller CA*, Christensen KA, Helton NM, O’Laughlin M, Fronick CC, Fulton RS, Kohlschmidt J, Eisfeld A, Bloomfield CD, et al.. Proceedings Of The National Academy Of Sciences. 2021. 10.1073/pnas.2116427118
• HPV transcript expression affects cervical cancer response to chemoradiation
  Ruiz FJ, Inkman M, Rashmi R, Muhammad N, Gabriel N, Miller CA, McLellan MD, Goldstein M, Markovina S, Grigsby PW, et al.. Jci Insight. 2021. doi:10.1172/jci.insight.138734
• Bam-readcount-rapid generation of basepair-resolution sequence metrics
  Khanna A, Larson DE, Srivatsan SN, Mosior M, Abbott TE, Kiwala S, Ley TJ, Duncavage EJ, Walter MJ, Walker JR, et al.. Arxiv. 2021. doi:arXiv:2107.12817
• Kdm6a Deficiency Restricted to Mouse Hematopoietic Cells Causes an Age-and Sex-dependent Myelodysplastic Syndrome-Like Phenotype
  Tian L, Chavez M, Chang GS, Helton NM, Katerndahl CD, Miller CA, Wartman L. Biorxiv. 2021. doi:10.1101/2021.08.04.455117
• Functional and epigenetic phenotypes of humans and mice with DNMT3A Overgrowth Syndrome
  Smith AM, LaValle TA, Shinawi M, Ramakrishnan SM, Abel HJ, Hill CA, Kirkland NM, Rettig MP, Helton NM, Heath SE, et al.. Nature Communications. 2021. doi:10.1038/s41467-021-24800-7
• Tumor suppressor function of Gata2 in Acute Promyelocytic Leukemia
  Katerndahl CD, Rogers OR, Day RB, Cai MA, Rooney TP, Helton NM, Hoock M, Ramakrishnan SM, Srivatsan SN, Wartman LD, et al.. Blood. 2021. doi:10.1182/blood.2021011758
• Chromosome 8 gain is associated with high-grade transformation in MPNST
  Dehner C, Moon CI, Zhang X, Zhou Z, Miller CA, Xu H, Wan X, Yang K, Mashl J, Gosline SJ, et al.. Jci Insight. 2021. doi:10.1172/jci.insight.146351
• HPV transcript expression affects cervical cancer response to chemoradiation
  Ruiz FJ, Inkman M, Rashmi R, Muhammad N, Gabriel N, Miller CA, McLellan MD, Goldstein M, Markovina S, Grigsby PW, et al.. Jci Insight. 2021. 10.1172/jci.insight.138734
• Genome-wide analysis of focal DNA hypermethylation in IDH-mutant AML samples
  Wilson ER, Helton N, Heath SE, Fulton RS, Miller CA, Payton JE, Welch JS, Walter M, Westervelt P, DiPersio JF, et al.. Biorxiv. 2021. doi:10.1101/2021.03.03.433799
• Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
  Miller CA, Walker JR, Jensen TL, Hooper WF, Fulton RS, Painter JS, Sekeres MA, Ley TJ, Spencer DH, Goll JB, et al.. Biorxiv. 2021. doi:10.1101/2021.05.07.442430
• Genome sequencing as an alternative to cytogenetic analysis in myeloid cancers
  Duncavage EJ, Schroeder MC, O’Laughlin M, Wilson R, MacMillan S, Bohannon A, Kruchowski S, Garza J, Du F, Hughes AE, et al.. New England Journal Of Medicine. 2021. doi:10.1056/NEJMoa2024534
• Enhanced efficacy and increased long-term toxicity of CNS-directed, AAV-based combination therapy for Krabbe disease
  Li Y, Miller CA, Shea LK, Jiang X, Guzman MA, Chandler RJ, Ramakrishnan SM, Smith SN, Venditti CP, Vogler CA, et al.. Molecular Therapy. 2021. doi:10.1016/j.ymthe.2020.12.031
• Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction
  Wells DK, van BMM, Dang KK, Hubbard-Lucey VM, Sheehan KC, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, et al.. Cell. 2020. doi:10.1016/j.cell.2020.09.015
• U2AF1 is a haplo-essential gene required for cancer cell survival
  Wadugu BA, Heard A, Srivatsan SN, Alberti MO, Ndonwi M, Grieb S, Bradley J, Shao J, Ahmed T, Shirai CL, et al.. Biorxiv. 2020. doi:10.1101/2020.06.20.151035
• Accurate neoantigen prediction depends on mutation position relative to patient allele-specific MHC anchor location
  Xia H, McMichael JF, Supabphol S, Richters MM, Basu A, Ramirez CA, Puig-Saus C, Cotto KC, Hundal J, Kiwala S, et al.. Biorxiv. 2020. doi:10.1101/2020.12.08.416271
• HPV-EM: an accurate HPV detection and genotyping EM algorithm
  Inkman MJ, Jayachandran K, Ellis TM, Ruiz F, McLellan MD, Miller CA, Wu Y, Ojesina AI, Schwarz JK, Zhang J. Scientific Reports. 2020. doi:10.1038/s41598-020-71300-7
• Dnmt3a deficiency in the skin causes focal, canonical DNA hypomethylation and a cellular proliferation phenotype
  Chen DY, Ferguson IM, Braun KA, Sutton LA, Helton NM, Ramakrishnan SM, Smith AM, Miller CA, Ley TJ. Proceedings Of The National Academy Of Sciences. 2021. doi:10.1073/pnas.2022760118
• Optimized polyepitope neoantigen DNA vaccines elicit neoantigen-specific immune responses in preclinical models and in clinical translation
  Li L, Zhang X, Wang X, Kim SW, Herndon JM, Becker-Hapak MK, Carreno BM, Myers NB, Sturmoski MA, McLellan MD, et al.. Genome Medicine. 2021. doi:10.1186/s13073-021-00872-4
• Treatment of an aggressive orthotopic murine glioblastoma model with combination checkpoint blockade and a multivalent neoantigen vaccine
  Liu CJ, Schaettler M, Blaha DT, Bowman-Kirigin JA, Kobayashi DK, Livingstone AJ, Bender D, Miller CA, Kranz DM, Johanns TM, et al.. Neuro-oncology. 2020. doi:10.1093/neuonc/noaa050
• Interleukin-15 superagonist (N-803) treatment of PML and JCV in a post--allogeneic hematopoietic stem cell transplant patient
  Oza A, Rettig MP, Powell P, O’Brien K, Clifford DB, Ritchey J, Gehrs L, Hollaway J, Major E, Fehniger TA, et al.. Blood Advances. 2020. doi:10.1182/bloodadvances.2019000664
• The clonal evolution of metastatic colorectal cancer
  Dang HX, Krasnick BA, White BS, Grossman JG, Strand MS, Zhang J, Cabanski CR, Miller CA, Fulton RS, Goedegebuure SP, et al.. Science Advances. 2020. doi:10.1126/sciadv.aay9691
• Unmasking Intra-tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
  Moon C, Tompkins W, Wang Y, Godec A, Zhang X, Pipkorn P, Miller CA, Dehner C, Dahiya S, Hirbe AC. Genes. 2020. doi:10.3390/genes11050499
• Treatment of an aggressive orthotopic murine glioblastoma model with combination checkpoint blockade and a multivalent neoantigen vaccine
  Liu CJ, Schaettler M, Blaha DT, Bowman-Kirigin JA, Kobayashi DK, Livingstone AJ, Bender D, Miller CA, Kranz DM, Johanns TM, et al.. Neuro-oncology. 2020. doi:10.1093/neuonc/noaa050
• Remethylation of Dnmt3a-/- hematopoietic cells is associated with partial correction of gene dysregulation and reduced myeloid skewing
  Ketkar S, Verdoni AM, Smith AM, Bangert CV, Leight ER, Chen DY, Brune MK, Helton NM, Hoock M, George DR, et al.. Proceedings Of The National Academy Of Sciences. 2020. doi:10.1073/pnas.1918611117
• pVACtools: a computational toolkit to identify and visualize cancer neoantigens
  Hundal J, Kiwala S, McMichael J, Miller CA, Xia H, Wollam AT, Liu CJ, Zhao S, Feng Y, Graubert AP, et al.. Cancer Immunology Research. 2020. doi:10.1158/2326-6066.CIR-19-0401
• A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing
  Petti AA, Williams SR, Miller CA, Fiddes IT, Srivatsan SN, Chen DY, Fronick CC, Fulton RS, Church DM, Ley TJ. Nature Communications. 2019. doi:10.1038/s41467-019-11591-1
• pVACtools: a computational toolkit to identify and visualize cancer neoantigens
  Hundal J, Kiwala S, McMichael J, Miller CA, Wollam AT, Xia H, Liu CJ, Zhao S, Feng Y, Graubert AP, et al.. Biorxiv. 2019. doi:10.1101/501817
• Exome analysis of treatment-related AML after APL suggests secondary evolution.
  Wang T, Jacoby MA, Duncavage EJ, Miller CA, Heath S, Rahme R, Fenaux P, Ades L, Renneville A, Cassinat B, et al.. British Journal Of Haematology. 2019. doi:10.1111/bjh.15681
• Immune escape of relapsed AML cells after allogeneic transplantation
  Christopher MJ, Petti AA, Rettig MP, Miller CA, Chendamarai E, Duncavage EJ, Klco JM, Helton NM, O’Laughlin M, Fronick CC, et al.. New England Journal Of Medicine. 2018. doi:10.1056/NEJMoa1808777
• Smc3 is required for mouse embryonic and adult hematopoiesis
  Wang T, Glover B, Hadwiger G, Miller CA, di MO, Welch JS. Experimental Hematology. 2019. doi:10.1016/j.exphem.2018.11.008
• Shared cell of origin in a patient with Erdheim-Chester disease
  Ghobadi A*, Miller CA*, Li T, O'Laughlin M, Lee Y, Ali M, Westervelt P, DiPersio J, Wartman L. Haematologica. 2019. doi:10.3324/haematol.2019.217794
• Detection of neoantigen-specific T cells following a personalized vaccine in a patient with glioblastoma
  Johanns TM, Miller CA, Liu CJ, Perrin RJ, Bender D, Kobayashi DK, Campian JL, Chicoine MR, Dacey RG, Huang J, et al.. Oncoimmunology. 2019. doi:10.1080/2162402X.2018.1561106
• Mutation clearance after transplantation for myelodysplastic syndrome
  Duncavage EJ, Jacoby MA, Chang GS, Miller CA, Edwin N, Shao J, Elliott K, Robinson J, Abel H, Fulton RS, et al.. New England Journal Of Medicine. 2018. doi:10.1056/NEJMoa1804714
• The prognostic effects of somatic mutations in ER-positive breast cancer
  Griffith OL, Spies NC, Anurag M, Griffith M, Luo J, Tu D, Yeo B, Kunisaki J, Miller CA, Krysiak K, et al.. Nature Communications. 2018. doi:10.1038/s41467-018-05914-x
• Discriminating a common somatic ASXL1 mutation (c. 1934dup; p. G646Wfs* 12) from artifact in myeloid malignancies using NGS.
  Alberti MO, Srivatsan SN, Shao J, McNulty SN, Chang GS, Miller CA, Dunlap JB, Yang F, Press RD, Gao Q, et al.. Leukemia. 2018. doi:10.1038/s41375-018-0193-y
• A case of acute myeloid leukemia with promyelocytic features characterized by expression of a novel RARG-CPSF6 fusion
  Miller CA, Tricarico C, Skidmore ZL, Uy GL, Lee Y, Hassan A, O’Laughlin MD, Schmidt H, Tian L, Duncavage EJ, et al.. Blood Advances. 2018. doi:10.1182/bloodadvances.2017014183
• Somatic mutations in benign breast disease tissue and risk of subsequent invasive breast cancer
  Rohan TE, Miller CA, Li T, Wang Y, Loudig O, Ginsberg M, Glass A, Mardis E. British Journal Of Cancer. 2018. doi:10.1038/s41416-018-0089-7
• Subclones dominate at MDS progression following allogeneic hematopoietic cell transplant
  Jacoby MA, Duncavage EJ, Chang GS, Miller CA, Shao J, Elliott K, Robinson J, Fulton RS, Fronick CC, O’Laughlin M, et al.. Jci Insight. 2018. doi:10.1172/jci.insight.98962]
• An “off-the-shelf” fratricide-resistant CAR-T for the treatment of T cell hematologic malignancies
  Cooper ML, Choi J, Staser K, Ritchey JK, Devenport JM, Eckardt K, Rettig MP, Wang B, Eissenberg LG, Ghobadi A, et al.. Leukemia. 2018. doi:10.1038/s41375-018-0065-5
• Resistance-promoting effects of ependymoma treatment revealed through genomic analysis of multiple recurrences in a single patient
  Miller CA, Dahiya S, Li T, Fulton RS, Smyth MD, Dunn GP, Rubin JB, Mardis ER. Molecular Case Studies. 2018. doi:10.1101/mcs.a002444
• Lenalidomide results in a durable complete remission in acute myeloid leukemia accompanied by persistence of somatic mutations and a T-cell infiltrate in the bone marrow
  Bansal D, Vij K, Chang GS, Miller CA, DiPersio JF, Vij R, Heath SE, Westervelt P, Welch JS, Fehniger TA. Haematologica. 2018. doi:10.3324/haematol.2017.184168
• Biological and therapeutic implications of multisector sequencing in newly diagnosed glioblastomas
  Mahlokozera T, Vellimana AK, Li T, Mao DD, Zohny ZS, Kim DH, Tran DD, Marcus DS, Fouke SJ, Campian JL, et al.. Neuro-oncology. 2017. doi:10.1093/neuonc/nox232
• Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential
  Wong TN, Miller CA, Jotte MR, Bagegni N, Baty JD, Schmidt AP, Cashen AF, Duncavage EJ, Helton NM, Fiala M, et al.. Nature Communications. 2018. doi:10.1038/s41467-018-02858-0
• Clinical outcomes and differential effects of PI3K pathway mutation in obese versus non-obese patients with cervical cancer
  Grigsby P, Elhammali A, Ruiz F, Markovina S, McLellan MD, Miller CA, Chundury A, Ta NL, Rashmi R, Pfeifer JD, et al.. Oncotarget. 2018. doi:10.18632/oncotarget.23664
• Comprehensive and integrated genomic characterization of adult soft tissue sarcomas
  Network CGAR, et al.. Cell. 2017. doi:10.1016/j.cell.2017.10.014
• Somatic mutations and clonal hematopoiesis in congenital neutropenia
  Xia J, Miller CA, Baty J, Ramesh A, Jotte MR, Fulton RS, Vogel TP, Cooper MA, Walkovich KJ, Makaryan V, et al.. Blood. 2017. doi:10.1182/blood-2017-08-801985
• ClonEvol: clonal ordering and visualization in cancer sequencing
  Dang H, White B, Foltz S, Miller CA, Luo J, Fields R, Maher C. Annals Of Oncology. 2017. doi:10.1093/annonc/mdx517
• Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies
  Cole CB, Russler-Germain DA, Ketkar S, Verdoni AM, Smith AM, Bangert CV, Helton NM, Guo M, Klco JM, O’Laughlin S, et al.. The Journal Of Clinical Investigation. 2017. doi:10.1172/JCI93041
• Comprehensive discovery of noncoding RNAs in acute myeloid leukemia cell transcriptomes
  Zhang J, Griffith M, Miller CA, Griffith OL, Spencer DH, Walker JR, Magrini V, McGrath SD, Ly A, Helton NM, et al.. Experimental Hematology. 2017. doi:10.1016/j.exphem.2017.07.008
• Breast cancer neoantigens can induce CD8 T cell responses and antitumor immunity
  Zhang X, Kim S, Hundal J, Herndon JM, Li S, Petti AA, Soysal SD, Li L, McLellan MD, Hoog J, et al.. Cancer Immunology Research. 2017. doi:10.1158/2326-6066.CIR-16-0264
• Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma
  Krysiak K, Gomez F, White BS, Matlock M, Miller CA, Trani L, Fronick CC, Fulton RS, Kreisel F, Cashen AF, et al.. Blood. 2017. doi:10.1182/blood-2016-07-729954
• Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy
  Uy GL, Duncavage EJ, Chang GS, Jacoby MA, Miller CA, Shao J, Heath S, Elliott K, Reinick T, Fulton RS, et al.. Leukemia. 2016. doi:10.1038/leu.2016.282
• Mutational landscape and response are conserved in peripheral blood of AML and MDS patients during decitabine therapy.
  Duncavage EJ, Uy GL, Petti AA, Miller CA, Lee Y, Tandon B, Gao F, Fronick CC, O'Laughlin M, Fulton RS, et al.. Blood. 2017. doi:10.1182/blood-2016-10-745273
• Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases
  Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, et al.. PLoS Medicine. 2016. doi:10.1371/journal.pmed.1002174
• Endogenous Neoantigen-Specific CD8 T Cells Identified in Two Glioblastoma Models Using a Cancer Immunogenomics Approach
  Johanns TM, Ward JP, Miller CA, Wilson C, Kobayashi DK, Bender D, Fu Y, Alexandrov A, Mardis ER, Artyomov MN, et al.. Cancer Immunology Research. 2016. doi:10.1158/2326-6066
• TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes
  Welch JS, Petti AA, Miller CA, Fronick CC, O’Laughlin M, Fulton RS, Wilson RK, Baty JD, Duncavage EJ, Tandon B, et al.. New England Journal Of Medicine. 2016. doi:10.1056/NEJMoa1605949
• Visualizing tumor evolution with the fishplot package for R
  Miller CA, McMichael J, Dang HX, Maher CA, Ding L, Ley TJ, Mardis ER, Wilson RK. BMC Genomics. 2016. 10.1186/s12864-016-3195-z
• Immunogenomics of Hypermutated Glioblastoma: A Patient with Germline POLE Deficiency Treated with Checkpoint Blockade Immunotherapy
  Johanns TM*, Miller CA*, Dorward IG, Tsien C, Chang E, Perry A, Uppaluri R, Ferguson C, Schmidt RE, Dahiya S, et al.. Cancer Discovery. 2016. doi:10.1158/2159-8290.CD-16-0575
• Truncating Prolactin Receptor Mutations Promote Tumor Growth in Murine Estrogen Receptor-Alpha Mammary Carcinomas
  Griffith OL, Chan SR, Griffith M, Krysiak K, Skidmore ZL, Hundal J, Allen JA, Arthur CD, Runci D, Bugatti M, et al.. Cell Reports. 2016. doi:10.1016/j.celrep.2016.08.076
• Cancer immunogenomics: computational neoantigen identification and vaccine design
  Hundal J, Miller CA, Griffith M, Griffith OL, Walker J, Kiwala S, Graubert A, McMichael J, Coffman A, Mardis ER. . 2016. doi:10.1101/sqb.2016.81.030726
• Targeted sequencing informs the evaluation of normal karyotype cytopenic patients for low-grade myelodysplastic syndrome
  Duncavage E, O'Brien J, Vij K, Miller CA, Chang G, Shao J, Jacoby M, Heath S, Janke M, Elliott K, et al.. Leukemia. 2016. doi:10.1038/leu.2016.247
• Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers
  Miller CA, Gindin Y, Lu C, Griffith OL, Griffith M, Shen D, Hoog J, Li T, Larson DE, Watson M, et al.. Nature Communications. 2016. doi:10.1038/ncomms12498
• Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B-lymphoblastic leukemia
  Griffith M, Griffith OL, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, et al.. Experimental Hematology. 2016. doi:10.1016/j.exphem.2016.04.011
• Cancer immunogenomics: computational neoantigen identification and vaccine design
  Hundal J, Miller CA, Griffith M, Griffith OL, Walker J, Kiwala S, Graubert A, McMichael J, Coffman A, Mardis ER. . 2016. 10.1101/sqb.2016.81.030726
• ATRX in diffuse gliomas with its mosaic/heterogeneous expression in a subset
  Purkait S, Miller CA, Kumar A, Sharma V, Pathak P, Jha P, Sharma MC, Suri V, Suri A, Sharma B, et al.. Brain Pathology. 2016. doi:10.1111/bpa.12364
• Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation
  Gellert P, Segal CV, Gao Q, L{\'o}pez-Knowles E, Martin L, Dodson A, Li T, Miller CA, Lu C, Mardis ER, et al.. Nature Communications. 2016. doi:c10.1038/ncomms13294
• A common founding clone with TP53 and PTEN mutations gives rise to a concurrent germ cell tumor and acute megakaryoblastic leukemia
  Lu C, Riedell P, Miller CA, Hagemann IS, Westervelt P, Ozenberger BA, O'Laughlin M, Magrini V, Demeter RT, Duncavage EJ, et al.. Molecular Case Studies. 2016. doi:10.1101/mcs.a000687
• A genomic analysis of Philadelphia chromosome-negative AML arising in patients with CML
  Krysiak K, Christopher M, Skidmore Z, Demeter R, Magrini V, Kunisaki J, O'laughlin M, Duncavage E, Miller CA, Ozenberger B, et al.. Blood Cancer Journal. 2016. doi:10.1038/bcj.2016.18
• Patterns and functional implications of rare germline variants across 12 cancer types
  Lu C, Xie M, Wendl MC, Wang J, McLellan MD, Leiserson MD, Huang K, Wyczalkowski MA, Jayasinghe R, Banerjee T, et al.. Nature Communications. 2015. doi:10.1038/ncomms10086
• Rapid expansion of preexisting nonleukemic hematopoietic clones frequently follows induction therapy for de novo AML
  Wong TN, Miller CA, Klco JM, Petti A, Demeter R, Helton NM, Li T, Fulton RS, Heath SE, Mardis ER, et al.. Blood. 2016. doi:10.1182/blood-2015-10-677021
• Genomic analysis of germ line and somatic variants in familial myelodysplasia/acute myeloid leukemia
  Churpek JE, Pyrtel K, Kanchi K, Shao J, Koboldt D, Miller CA, Shen D, Fulton R, O’Laughlin M, Fronick C, et al.. Blood. 2015. doi:10.1182/blood-2015-04-641100
• Optimizing Cancer Genome Sequencing and Analysis
  Griffith M*, Miller CA*, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, Walker JR, Dang HX, Trani L, Larson DE, et al.. Cell Systems. 2015. doi:10.1016/j.cels.2015.08.015
• Association Between Mutation Clearance After Induction Therapy and Outcomes in Acute Myeloid Leukemia
  Klco JM*, Miller CA*, Griffith M, Petti A, Spencer DH, Ketkar-Kulkarni S, Wartman LD, Christopher M, Lamprecht TL, Helton NM, et al.. Jama. 2015. doi:10.1001/jama.2015.9643
• Genome Modeling System: A Knowledge Management Platform for Genomics
  Griffith M, Griffith OL, Smith SM, Ramu A, Callaway MB, Brummett AM, Kiwala MJ, Coffman AC, Regier AA, Oberkfell BJ, et al.. PLoS Comput Biol. 2015. doi:10.1371/journal.pcbi.1004274
• Whole exome sequencing reveals the order of genetic changes during malignant transformation and metastasis in a single patient with NF1-plexiform neurofibroma
  Hirbe A, Dahiya SM, Miller CA, Li T, Fulton R, Zhang X, McDonald S, DeSchryver K, Duncavage E, Walrath J, et al.. Clinical Cancer Research. 2015. doi:10.1158/1078-0432.CCR-14-3049
• Genetic Heterogeneity of Induced Pluripotent Stem Cells: Results from 24 Clones Derived from a Single C57BL/6 Mouse
  Li C, Klco JM, Helton NM, George DR, Mudd JL, Miller CA, Lu C, Fulton R, O'Laughlin M, Fronick C, et al.. PLoS One. 2015. doi:10.1371/journal.pone.0120585
• Epigenomic analysis of the HOX gene loci reveals mechanisms that may control canonical expression patterns in AML and normal hematopoietic cells
  Spencer D, Young M, Lamprecht T, Helton N, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter R, Miller CA, et al.. Leukemia. 2015. doi:10.1038/leu.2015.6
• Functional Heterogeneity of Genetically Defined Subclones in Acute Myeloid Leukemia
  Klco JM, Spencer DH, Miller CA, Griffith M, Lamprecht TL, O’Laughlin M, Fronick C, Magrini V, Demeter RT, Fulton RS, et al.. Cancer Cell. 2014. doi:10.1016/j.ccr.2014.01.031
• The R882H DNMT3A mutation associated with AML dominantly inhibits wild-type DNMT3A by blocking its ability to form active tetramers
  Russler-Germain DA, Spencer DH, Young MA, Lamprecht TL, Miller CA, Fulton R, Meyer MR, Erdmann-Gilmore P, Townsend RR, Wilson RK, et al.. Cancer Cell. 2014. doi:10.1016/j.ccr.2014.02.010
• Integrated analysis of germline and somatic variants in ovarian cancer
  Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, et al.. Nature Communications. 2014. doi:10.1038/ncomms4156
• SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution
  Miller CA*, White BS*, Dees ND, Griffith M, Welch JS, Griffith OL, Vij R, Tomasson MH, Graubert TA, Walter MJ, et al.. PLoS Comput Biol. 2014. doi:10.1371/journal.pcbi.1003665
• Response to 'Genomic Landscapes and Clonality of De Novo AML'
  Miller CA, Wilson RK, Ley TJ. New England Journal Of Medicine. 2013. doi:10.1056/NEJMc1308782
• Mutational landscape and significance across 12 major cancer types
  Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, et al.. Nature. 2013. doi:10.1038/nature12634
• The cancer genome atlas pan-cancer analysis project
  Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM, Network CGAR, et al.. Nature Genetics. 2013. doi:10.1038/ng.2764
• DGIdb: mining the druggable genome
  Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, et al.. Nature Methods. 2013. doi:10.1038/nmeth.2689
• Endocrine-Therapy-Resistant ESR1 Variants Revealed by Genomic Characterization of Breast-Cancer-Derived Xenografts
  Li S, Shen D, Shao J, Crowder R, Liu W, Prat A, He X, Liu S, Hoog J, Lu C, et al.. Cell Reports. 2013. doi:10.1016/j.celrep.2013.08.022
• Somatic neurofibromatosis type 1 (NF1) inactivation characterizes NF1-associated pilocytic astrocytoma
  Gutmann DH, McLellan MD, Hussain I, Wallis JW, Fulton LL, Fulton RS, Magrini V, Demeter R, Wylie T, Kandoth C, et al.. Genome Research. 2013. doi:10.1101/gr.142604.112
• Clonal diversity of recurrently mutated genes in myelodysplastic syndromes
  Walter M, Shen D, Shao J, Ding L, White B, Kandoth C, Miller CA, Niu B, McLellan M, Dees N, et al.. Leukemia. 2013. doi:10.1038/leu.2013.58
• Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
  The Cancer Genome Atlas Research Network. New England Journal Of Medicine. 2013. doi:10.1056/NEJMoa1301689
• The Origin and Evolution of Mutations in Acute Myeloid Leukemia
  Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, et al.. Cell. 2012. doi:10.1016/j.cell.2012.06.023
• Background mutations in parental cells account for most of the genetic heterogeneity of induced pluripotent stem cells
  Young MA, Larson DE, Sun C, George DR, Ding L, Miller CA, Lin L, Pawlik KM, Chen K, Fan X, et al.. Cell Stem Cell. 2012. doi:10.1016/j.stem.2012.03.002
• VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
  Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. Genome Research. 2012. doi:10.1101/gr.129684.111
• Whole-genome analysis informs breast cancer response to aromatase inhibition
  Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van TBA, Hoog J, Goiffon RJ, Goldstein TC, et al.. Nature. 2012. doi:10.1038/nature11143
• Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
  Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, et al.. Nature. 2012. doi:10.1038/nature10738
• BioStar: an online question & answer resource for the bioinformatics community
  Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, et al.. PLoS Computational Biology. 2011. doi:10.1371/journal.pcbi.1002216
• Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines
  Hampton OA, Miller CA, Koriabine M, Li J, Den HP, Carbone L, Nefedov M, Ten HBF, Lee AV, De JPJ, et al.. Cancer Genetics. 2011. doi:10.1016/j.cancergen.2011.07.009
• Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors
  Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A. BMC Medical Genomics. 2011. doi:10.1186/1755-8794-4-34
• ReadDepth: a parallel R package for detecting copy number alterations from short sequencing reads
  Miller CA, Hampton O, Coarfa C, Milosavljevic A. PLoS One. 2011. doi:10.1371/journal.pone.0016327
• Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing
  Coarfa C, Yu F, Miller CA, Chen Z, Harris RA, Milosavljevic A. BMC Bioinformatics. 2010. doi:10.1186/1471-2105-11-572
• A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome
  Hampton OA, Den HP, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, et al.. Genome Research. 2009. doi:10.1101/gr.080259.108
• Comprehensive genomic characterization defines human glioblastoma genes and core pathways
  McLendon R, Friedman A, Bigner D, Van MEG, Brat DJ, Mastrogianakis GM, Olson JJ, Mikkelsen T, Lehman N, Aldape K, et al.. Nature. 2008. doi:10.1038/nature07385

• Genomic and Transcriptional evolution of AML at single-cell resolution
  Institute of Medical Informatics - Münster, Germany (2021)
• Sequencing, Variant Calling, and Cancer Genomics
  Genomics Education Partnership (GEP) Workshop (2020)
• Tumor Heterogeneity and Evolution
  Genomics in Medicine Seminar Series (2019)
• Characterizing genomic responses to cancer immunotherapy
  Genome Informatics (2016)
• Genomic insights into tumor evolution and therapy response
  Festival of Genomics Boston (2016)
• Assessing tumor heterogeneity and tracking clonal clearance in response to therapy
  Genome Informatics (2015)
• Ultra-deep whole-genome sequencing reveals clinically relevant low-frequency subclones in an acute myeloid leukemia
  The Cancer Genome Atlas Symposium (2014)
• SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution and therapy resistance
  Personal Genomes & Pharmacogenomics (2013)
• Multi-dimensional clustering of mutations from heterogeneous tumors offers insight into clonal architecture, tumor evolution, and response to therapy
  The Cancer Genome Atlas Steering Committee Meeting (2013)
• Assessing Tumor Heterogeneity and Tracking Clonal Evolution Using Whole Genome or Exome Sequencing
  The Cancer Genome Atlas Scientific Symposium (2012) link
• An Image Analytic Approach to Characterizing Vasculogenic Networks
  Presentation: Truman State University Student Research Symposium (2005)

• Instructor - Advanced Sequencing Technologies & Bioinformatics Analysis, Cold Spring Harbor Laboratory course (2021-)
• Co-organizer - WUSTL Bioinformatics Workshop
  
  • full academic year course, developed curriculum, recruited faculty
  • delivered lectures on sequencing, informatics, somatic variant calling, bisulfite sequencing and analysis, bash, HPC/LSF/Docker, Tumor Heterogeneity, etc
• Lecturer - High-Throughput Biology: From Sequence to Networks - CSHL/CBW Course (2019)
• WUSTL Bioinformatics Workshops (2017-present)
  
  • Workshop Co-organizer
  • Lectures on Bash, Docker/LSF/HPC, DNA Alignment, Variant Calling, Tumor Heterogeneity, etc
• Lecturer - Research Explorations in Genomics (2020)
• Lecturer - Human Genetics (2019-20)
• Lecturer - Computational Statistical Genetics (2017-19)
• Lecturer - Investigating Eukaryotic Genomes (2015-2017)
• Lecturer - Molecular Basis of Heredity (2015)
• Computer Aided Discovery Methods (2007 and 2008)
  co-developer of the course and taught computational labs on:
  • Studies of genome variation
  • Transcriptional regulatory pathways
• Computational Mathematics for Biomedical Scientists (2008)
  • Teaching Assistant
• Advanced Topics: Quantitative Biology (2005)
  • Teaching Assistant

Ad-hoc reviewer for Bioinformatics, Cancer Cell, Genome Biology, PLoS Computational Biology, Nucleic Acids Research, Nature Communications, BMC Evolutionary Biology.
Grant reviewer for Dutch Cancer Society (KWF Kankerbestrijding)
Grant reviewer for Siteman Cancer Center Investment Program