Faculty
Oncology Division
Alphabetical list (active faculty):   
Christopher A. Miller

Christopher A. Miller, PhD

Assistant Professor

Department of Medicine

Oncology Division

Stem Cell Biology

Research Interests

  • Bioinformatics
  • Cancer genomics
  • Tumor evolution
  • Immunogenomics

Contact

  • 314-286-0263 (office)
  • 314-286-1810 (fax)
  • Division of Oncology
    Mail Stop 8007-0057-06
    Washington University
    660 South Euclid Avenue
    St. Louis, MO 63110
  • 6th Floor, Southwest Tower (office)

Original Articles

  • 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 MJ, Freyer D, Wynn R, Douzgou S, Maris JM, Reilly AF, Wu M, Choo F, Fiets RB, Koene S, Spencer DH, Miller CA, Shinawi M, Ley TJ
    Blood 2021 Nov 17; [Epub ahead of print]
  • 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 CDS, Miller CA, Wartman LD
    PLoS One 2021 Nov 15;16(11):e0255706
  • U2af1 Is a Haplo-Essential Gene Required for Hematopoietic Cancer Cell Survival in Mice
    Wadugu BA, Nonavinkere Srivatsan S, Heard A, Alberti MO, Ndonwi M, Liu J, Grieb S, Bradley J, Shao J, Ahmed T, Shirai CL, Khanna A, Fei DL, Miller CA, Graubert TA, Walter MJ
    J Clin Invest 2021 Nov 1;131(21)
  • Tumor Suppressor Function of Gata2 in Acute Promyelocytic Leukemia
    Katerndahl CDS, Rogers ORS, Day RB, Cai MA, Rooney TP, Helton NM, Hoock M, Ramakrishnan SM, Nonavinkere Srivatsan S, Wartman LD, Miller CA, Ley TJ
    Blood 2021 Sep 30;138(13):1148-1161
  • 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, Zhang J, Schwarz JK
    JCI Insight 2021 Aug 23;6(16):e138734
  • Chromosome 8 Gain Is Associated With High-Grade Transformation in MPNST
    Dehner C, Moon CI, Zhang X, Zhou Z, Miller C, Xu H, Wan X, Yang K, Mashl J, Gosline SJ, Wang Y, Zhang X, Godec A, Jones PA, Dahiya S, Bhatia H, Primeau T, Li S, Pollard K, Rodriguez FJ, Ding L, Pratilas CA, Shern JF, Hirbe AC
    JCI Insight 2021 Mar 22;6(6)
  • 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
  • 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, Griffith OL, Griffith M, Miller CA
    ArXiv 2021 Jul 27;arXiv:2107.12817v1
  • 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, Ferraro F, Chen DY, Adak S, Semenkovich CF, Christian DL, Martin JR, Gabel HW, Miller CA, Ley TJ
    Nat Commun 2021 Jul 27;12(1):4549
  • 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, Link DC, Ley TJ, Spencer DH
    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, Walter MJ
    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 AEO, Robinson J, Hughes E, Heath SE, Baty JD, Neidich J, Christopher MJ, Jacoby MA, Uy GL, Fulton RS, Miller CA, Payton JE, Link DC, Walter MJ, Westervelt P, DiPersio JF, Ley TJ, Spencer DH
    N Engl J Med 2021 Mar 11;384(10):924-935
  • 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, Ory DS, Ley TJ, Sands MS
    Mol Ther 2021 Feb 3;29(2):691-701
  • 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, Goedegebuure SP, Johanns TM, Dunn GP, Fehniger TA, Ribas A, Miller CA, Gillanders WE, Griffith OL, Griffith M
    Biorxiv. 2020. doi:10.1101/2020.12.08.416271
  • 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
    Proc Natl Acad Sci U S A 2021 Apr 20;118(16):e2022760118
  • 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, Miller CA, Johanns TM, Tan BR, Dunn GP, Fleming TP, Hansen TH, Goedegebuure SP, Gillanders WE
    Genome Med 2021 Apr 21;13(1):56
  • Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction
    Wells DK, van Buuren MM, Dang KK, Hubbard-Lucey VM, Sheehan KCF, Campbell KM, Lamb A, Ward JP, Sidney J, Blazquez AB, Rech AJ, Zaretsky JM, Comin-Anduix B, Ng AHC, Chour W, Yu TV, Rizvi H, Chen JM, Manning P, Steiner GM, Doan XC, Merghoub T, Guinney J, Kolom A, Selinsky C, Ribas A, Hellmann MD, Hacohen N, Sette A, Heath JR, Bhardwaj N, Ramsdell F, Schreiber RD, Schumacher TN, Kvistborg P, Defranoux NA
    Tumor Neoantigen Selection Alliance (Contributors include: Miller CA)

    Cell 2020 Oct 29;183(3):818-834e13
  • 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
    Sci Rep 2020 Aug 31;10(1):14340
  • 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, Khanna A, Fei DL, Miller CA, Graubert T, Walter MJ
    Biorxiv. 2020. doi:10.1101/2020.06.20.151035
  • 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, Miller CA, Soon-Shiong P, Rock A, DiPersio JF
    Blood Adv 2020 Jun 9;4(11):2387-2391
  • 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, Fronick CC, Griffith M, Larson DE, Goetz BD, Walker JR, Hawkins WG, Strasberg SM, Linehan DC, Lim KH, Lockhart AC, Mardis ER, Wilson RK, Ley TJ, Maher CA, Fields RC
    Sci Adv 2020 Jun 10;6(24):eaay9691
  • Unmasking Intra-Tumoral Heterogeneity and Clonal Evolution in NF1-MPNST
    Moon CI, Tompkins W, Wang Y, Godec A, Zhang X, Pipkorn P, Miller CA, Dehner C, Dahiya S, Hirbe AC
    Genes (Basel) 2020 May 1;11(5)
  • 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, Dunn GP
    Neuro Oncol 2020 Sep 29;22(9):1276-1288
  • 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, Fronick C, Fulton RS, Ramakrishnan SM, Chang GS, Petti AA, Spencer DH, Miller CA, Ley TJ
    Proc Natl Acad Sci U S A 2020 Feb 11;117(6):3123-3134
  • 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 YY, Graubert AP, Wollam AZ, Neichin J, Neveau M, Walker J, Gillanders WE, Mardis ER, Griffith OL, Griffith M
    Cancer Immunol Res 2020 Mar;8(3):409-420
  • 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
    Nat Commun 2019 Aug 14;10(1):3660
  • 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, Takeshita A, Asou N, Miyazaki Y, Kiyoi H, Ravandi F, Westervelt P, Wartman LD, Welch JS
    Br J Haematol 2019 Jun;185(5):984-987
  • Smc3 Is Required for Mouse Embryonic and Adult Hematopoiesis
    Wang T, Glover B, Hadwiger G, Miller CA, di Martino O, Welch JS
    Exp Hematol 2019 Feb;70:70-84e6
  • Shared Cell of Origin in a Patient With Erdheim-Chester Disease and Acute Myeloid Leukemia
    Ghobadi A*, Miller CA*, Li T, O'Laughlin M, Lee YS, Ali M, Westervelt P, DiPersio JF, Wartman LD (*co-first authorship)
    Haematologica 2019 Aug;104(8):e373-e375
  • 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, Fritsch EF, Gillanders WE, Artyomov MN, Mardis ER, Schreiber RD, Dunn GP
    Oncoimmunology 2019 Jan 25;8(4):e1561106
  • 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, Fulton RS, Wilson RK, Wartman LD, Welch JS, Heath SE, Baty JD, Payton JE, Graubert TA, Link DC, Walter MJ, Westervelt P, Ley TJ, DiPersio JF
    N Engl J Med 2018 Dec 13;379(24):2330-2341
  • 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, Fronick CC, O'Laughlin M, Heath SE, Brendel K, Saba R, Wartman LD, Christopher MJ, Pusic I, Welch JS, Uy GL, Link DC, DiPersio JF, Westervelt P, Ley TJ, Trinkaus K, Graubert TA, Walter MJ
    N Engl J Med 2018 Sep 13;379(11):1028-1041
  • 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, Hundal J, Ainscough BJ, Skidmore ZL, Campbell K, Kumar R, Fronick C, Cook L, Snider JE, Davies S, Kavuri SM, Chang EC, Magrini V, Larson DE, Fulton RS, Liu S, Leung S, Voduc D, Bose R, Dowsett M, Wilson RK, Nielsen TO, Mardis ER, Ellis MJ
    Nat Commun 2018 Sep 4;9(1):3476
  • 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, Ding L, Heusel JW, Duncavage EJ, Walter MJ
    Leukemia 2018 Aug;32(8):1874-1878
  • 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 YS, Hassan A, O'Laughlin MD, Schmidt H, Tian L, Duncavage EJ, Griffith M, Griffith OL, Welch JS, Wartman LD
    Blood Adv 2018 Jun 12;2(11):1295-1299
  • 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 (*co-first authorship)
    Br J Cancer 2018 Jun;118(12):1662-1664
  • 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, Heath SE, Pusic I, Welch JS, Link DC, DiPersio JF, Westervelt P, Ley TJ, Graubert TA, Walter MJ
    JCI Insight 2018 Mar 8;3(5)
  • 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, Gehrs LN, Prior JL, Achilefu S, Miller CA, Fronick CC, O'Neal J, Gao F, Weinstock DM, Gutierrez A, Fulton RS, DiPersio JF
    Leukemia 2018 Sep;32(9):1970-1983
  • 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
    Cold Spring Harb Mol Case Stud 2018 Apr 2;4(2)
  • 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 Jun;103(6):e270-e273
  • Cellular Stressors Contribute to the Expansion of Hematopoietic Clones of Varying Leukemic Potential
    Wong TN, Miller CA, Jotte MRM, Bagegni N, Baty JD, Schmidt AP, Cashen AF, Duncavage EJ, Helton NM, Fiala M, Fulton RS, Heath SE, Janke M, Luber K, Westervelt P, Vij R, DiPersio JF, Welch JS, Graubert TA, Walter MJ, Ley TJ, Link DC
    Nat Commun 2018 Jan 31;9(1):455
  • Biological and Therapeutic Implications of Multisector Sequencing in Newly Diagnosed Glioblastoma
    Mahlokozera T, Vellimana AK, Li T, Mao DD, Zohny ZS, Kim DH, Tran DD, Marcus DS, Fouke SJ, Campian JL, Dunn GP, Miller CA, Kim AH
    Neuro Oncol 2018 Mar 27;20(4):472-483
  • Somatic Mutations and Clonal Hematopoiesis in Congenital Neutropenia
    Xia J, Miller CA, Baty J, Ramesh A, Jotte MRM, Fulton RS, Vogel TP, Cooper MA, Walkovich KJ, Makaryan V, Bolyard AA, Dinauer MC, Wilson DB, Vlachos A, Myers KC, Rothbaum RJ, Bertuch AA, Dale DC, Shimamura A, Boxer LA, Link DC
    Blood 2018 Jan 25;131(4):408-416
  • 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, Fulton RS, DeWees T, Schwarz JK
    Oncotarget 2017 Dec 23;9(3):4061-4073
  • 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, Primeau T, Myers N, Vickery TL, Sturmoski M, Hagemann IS, Miller CA, Ellis MJ, Mardis ER, Hansen T, Fleming TP, Goedegebuure SP, Gillanders WE
    Cancer Immunol Res 2017 Jul;5(7):516-523
  • 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, Fronick C, Fulton R, Chang GS, Petti AA, Miller CA, Ley TJ
    J Clin Invest 2017 Oct 2;127(10):3657-3674
  • ClonEvol: Clonal Ordering and Visualization in Cancer Sequencing
    Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA
    Ann Oncol 2017 Dec 1;28(12):3076-3082
  • Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
    Cancer Genome Atlas Research Network (Contributors include: Miller CA)
    Cell 2017 Nov 2;171(4):950-965
  • 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, Reineck T, Fulton RS, Fronick CC, O'Laughlin M, Ganel L, Abboud CN, Cashen AF, DiPersio JF, Wilson RK, Link DC, Welch JS, Ley TJ, Graubert TA, Westervelt P, Walter MJ
    Leukemia 2017 Apr;31(4):872-881
  • 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, Carson KR, Berrien-Elliott MM, Bartlett NL, Griffith M, Griffith OL, Fehniger TA
    Blood 2017 Jan 26;129(4):473-483
  • 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, Trissal M, Link DC, Dang HX, Larson DE, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Klco JM, Mardis ER, Ley TJ, Wilson RK, Maher CA
    Exp Hematol 2017 Nov;55:19-33
  • 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 YS, Tandon B, Gao F, Fronick CC, O'Laughlin M, Fulton RS, Wilson RK, Jacoby MA, Cashen AF, Wartman LD, Walter MJ, Westervelt P, Link DC, DiPersio JF, Ley TJ, Welch JS
    Blood 2017 Mar 9;129(10):1397-1401
  • 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 BS, Fulton RS, Kale SS, Dahiya S, Sarkar C
    Brain Pathol 2017 Mar;27(2):138-145
  • 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, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER
    PLoS Med 2016 Dec 6;13(12):e1002174
  • 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, Schreiber RD, Dunn GP
    Cancer Immunol Res 2016 Dec;4(12):1007-1015
  • 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, Lee YS, Wartman LD, Uy GL, Ghobadi A, Tomasson MH, Pusic I, Romee R, Fehniger TA, Stockerl-Goldstein KE, Vij R, Oh ST, Abboud CN, Cashen AF, Schroeder MA, Jacoby MA, Heath SE, Luber K, Janke MR, Hantel A, Khan N, Sukhanova MJ, Knoebel RW, Stock W, Graubert TA, Walter MJ, Westervelt P, Link DC, DiPersio JF, Ley TJ
    N Engl J Med 2016 Nov 24;375(21):2023-2036
  • 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 Nov 7;17(1):880
  • 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, Ansstas G, Mardis ER, Dunn GP (*co-first authorship)
    Cancer Discov 2016 Nov;6(11):1230-1236
  • 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, Miceli AP, Schmidt H, Trani L, Kanchi KL, Miller CA, Larson DE, Fulton RS, Vermi W, Wilson RK, Schreiber RD, Mardis ER
    Cell Rep 2016 Sep 27;17(1):249-60
  • 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
    Cold Spring Harb Symp Quant Biol 2016;81:105-111
  • Targeted Sequencing Informs the Evaluation of Normal Karyotype Cytopenic Patients for Low-Grade Myelodysplastic Syndrome
    Duncavage EJ, O'Brien J, Vij K, Miller CA, Chang GS, Shao J, Jacoby MA, Heath S, Janke MR, Elliott K, Fulton RS, Fronick C, O'Laughlin M, Westervelt P, Ley TJ, Wilson RK, Walter MJ
    Leukemia 2016 Dec;30(12):2422-2426
  • Impact of Mutational Profiles on Response of Primary Oestrogen Receptor-Positive Breast Cancers to Oestrogen Deprivation
    Gellert P, Segal CV, Gao Q, Lopez-Knowles E, Martin LA, Dodson A, Li T, Miller CA, Lu C, Mardis ER, Gillman A, Morden J, Graf M, Sidhu K, Evans A, Shere M, Holcombe C, McIntosh SA, Bundred N, Skene A, Maxwell W, Robertson J, Bliss JM, Smith I, Dowsett M
    POETIC Trial Management Group and Trialists

    Nat Commun 2016 Nov 9;7:13294
  • 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, Davies SR, Hunt K, Suman VJ, Snider J, Walsh T, Colditz GA, DeSchryver K, Wilson RK, Mardis ER, Ellis MJ
    Nat Commun 2016 Aug 9;7:12498
  • 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, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, Larson DE, Heath SE, Fronick C, O'Laughlin S, Fulton RS, Magrini V, McGrath S, Smith SM, Miller CA, Maher CA, Payton JE, Walker JR, Eldred JM, Walter MJ, Link DC, Graubert TA, Westervelt P, Kulkarni S, DiPersio JF, Mardis ER, Wilson RK, Ley TJ
    Exp Hematol 2016 Jul;44(7):603-13
  • 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, Griffith M, Griffith OL, Wartman LD
    Cold Spring Harb Mol Case Stud 2016 Jan;2(1):a000687
  • A Genomic Analysis of Philadelphia Chromosome-Negative AML Arising in Patients With CML
    Krysiak K, Christopher MJ, Skidmore ZL, Demeter RT, Magrini V, Kunisaki J, O'Laughlin M, Duncavage EJ, Miller CA, Ozenberger BA, Griffith M, Wartman LD, Griffith OL
    Blood Cancer J 2016 Apr 8;6:e413
  • 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, Westervelt P, DiPersio JF, Walter MJ, Welch JS, Graubert TA, Wilson RK, Ley TJ, Link DC
    Blood 2016 Feb 18;127(7):893-7
  • Genomic Analysis of Germ Line and Somatic Variants in Familial Myelodysplasia/Acute Myeloid Leukemia
    Churpek JE, Pyrtel K, Kanchi KL, Shao J, Koboldt D, Miller CA, Shen D, Fulton R, O'Laughlin M, Fronick C, Pusic I, Uy GL, Braunstein EM, Levis M, Ross J, Elliott K, Heath S, Jiang A, Westervelt P, DiPersio JF, Link DC, Walter MJ, Welch J, Wilson R, Ley TJ, Godley LA, Graubert TA
    Blood 2015 Nov 26;126(22):2484-90
  • 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 KL, Wyczalkowski MA, Jayasinghe R, Banerjee T, Ning J, Tripathi P, Zhang Q, Niu B, Ye K, Schmidt HK, Fulton RS, McMichael JF, Batra P, Kandoth C, Bharadwaj M, Koboldt DC, Miller CA, Kanchi KL, Eldred JM, Larson DE, Welch JS, You M, Ozenberger BA, Govindan R, Walter MJ, Ellis MJ, Mardis ER, Graubert TA, Dipersio JF, Ley TJ, Wilson RK, Goodfellow PJ, Raphael BJ, Chen F, Johnson KJ, Parvin JD, Ding L
    Nat Commun 2015 Dec 22;6:10086
  • 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, Demeter RT, Wendl MC, McMichael JF, Austin RE, Magrini V, McGrath SD, Ly A, Kulkarni S, Cordes MG, Fronick CC, Fulton RS, Maher CA, Ding L, Klco JM, Mardis ER, Ley TJ, Wilson RK (*co-first authorship)
    Cell Syst 2015 Sep 23;1(3):210-223
  • 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, Duncavage EJ, Payton JE, Baty J, Heath SE, Griffith OL, Shen D, Hundal J, Chang GS, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Larson DE, Kulkarni S, Ozenberger BA, Welch JS, Walter MJ, Graubert TA, Westervelt P, Radich JP, Link DC, Mardis ER, DiPersio JF, Wilson RK, Ley TJ (*co-first authorship)
    JAMA 2015 Aug 25;314(8):811-22
  • 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, Sanderson GE, Mooney TP, Nutter NG, Belter EA, Du F, Long RL, Abbott TE, Ferguson IT, Morton DL, Burnett MM, Weible JV, Peck JB, Dukes A, McMichael JF, Lolofie JT, Derickson BR, Hundal J, Skidmore ZL, Ainscough BJ, Dees ND, Schierding WS, Kandoth C, Kim KH, Lu C, Harris CC, Maher N, Maher CA, Magrini VJ, Abbott BS, Chen K, Clark E, Das I, Fan X, Hawkins AE, Hepler TG, Wylie TN, Leonard SM, Schroeder WE, Shi X, Carmichael LK, Weil MR, Wohlstadter RW, Stiehr G, McLellan MD, Pohl CS, Miller CA, Koboldt DC, Walker JR, Eldred JM, Larson DE, Dooling DJ, Ding L, Mardis ER, Wilson RK
    PLoS Comput Biol 2015 Jul 9;11(7):e1004274
  • Whole Exome Sequencing Reveals the Order of Genetic Changes During Malignant Transformation and Metastasis in a Single Patient With NF1-Plexiform Neurofibroma
    Hirbe AC, Dahiya S, Miller CA, Li T, Fulton RS, Zhang X, McDonald S, DeSchryver K, Duncavage EJ, Walrath J, Reilly KM, Abel HJ, Pekmezci M, Perry A, Ley TJ, Gutmann DH
    Clin Cancer Res 2015 Sep 15;21(18):4201-11
  • 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, Wilson RK, Ley TJ
    PLoS One 2015 Mar 23;10(3):e0120585
  • Role of TP53 Mutations in the Origin and Evolution of Therapy-Related Acute Myeloid Leukaemia
    Wong TN, Ramsingh G, Young AL, Miller CA, Touma W, Welch JS, Lamprecht TL, Shen D, Hundal J, Fulton RS, Heath S, Baty JD, Klco JM, Ding L, Mardis ER, Westervelt P, DiPersio JF, Walter MJ, Graubert TA, Ley TJ, Druley TE, Link DC, Wilson RK
    Nature 2015 Feb 26;518(7540):552-5
  • Enforced Differentiation of Dnmt3a-Null Bone Marrow Leads to Failure With c-Kit Mutations Driving Leukemic Transformation
    Celik H, Mallaney C, Kothari A, Ostrander EL, Eultgen E, Martens A, Miller CA, Hundal J, Klco JM, Challen GA
    Blood 2015 Jan 22;125(4):619-28
  • Epigenomic Analysis of the HOX Gene Loci Reveals Mechanisms That May Control Canonical Expression Patterns in AML and Normal Hematopoietic Cells
    Spencer DH, Young MA, Lamprecht TL, Helton NM, Fulton R, O'Laughlin M, Fronick C, Magrini V, Demeter RT, Miller CA, Klco JM, Wilson RK, Ley TJ
    Leukemia 2015 Jun;29(6):1279-89
  • Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia
    Engle EK, Fisher DA, Miller CA, McLellan MD, Fulton RS, Moore DM, Wilson RK, Ley TJ, Oh ST
    Leukemia 2015 Apr;29(4):869-76
  • Clonal Architectures and Driver Mutations in Metastatic Melanomas
    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, Sondak VK, Fields RC, Ley TJ, Mule JJ, Wilson RK, Weber JS
    PLoS One 2014 Nov 13;9(11):e111153
  • Age-Related Mutations Associated With Clonal Hematopoietic Expansion and Malignancies
    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, Dipersio JF, Chen F, Wilson RK, Ley TJ, Ding L
    Nat Med 2014 Dec;20(12):1472-8
  • Caspase-9 Is Required for Normal Hematopoietic Development and Protection From Alkylator-Induced DNA Damage in Mice
    Lu EP, McLellan M, Ding L, Fulton R, Mardis ER, Wilson RK, Miller CA, Westervelt P, DiPersio JF, Link DC, Walter MJ, Ley TJ, Graubert TA
    Blood 2014 Dec 18;124(26):3887-95
  • 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, Ellis MJ, Schierding W, DiPersio JF, Ley TJ, Mardis ER, Wilson RK, Ding L (*co-first authorship)
    PLoS Comput Biol 2014 Aug 7;10(8):e1003665
  • Clonal Architecture of Secondary Acute Myeloid Leukemia Defined by Single-Cell Sequencing
    Hughes AE, Magrini V, Demeter R, Miller CA, Fulton R, Fulton LL, Eades WC, Elliott K, Heath S, Westervelt P, Ding L, Conrad DF, White BS, Shao J, Link DC, DiPersio JF, Mardis ER, Wilson RK, Ley TJ, Walter MJ, Graubert TA
    PLoS Genet 2014 Jul 10;10(7):e1004462
  • 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, Eades WC, Link DC, Graubert TA, Walter MJ, Mardis ER, Dipersio JF, Wilson RK, Ley TJ
    Cancer Cell 2014 Mar 17;25(3):379-92
  • 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, Ley TJ
    Cancer Cell 2014 Apr 14;25(4):442-54
  • 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, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L
    Nat Commun 2014;5:3156
  • Response to 'Genomic Landscapes and Clonality of De Novo AML'
    Miller CA, Wilson RK, Ley TJ
    N Engl J Med 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, Leiserson MD, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L
    Nature 2013 Oct 17;502(7471):333-9
  • The Cancer Genome Atlas Pan-Cancer Analysis Project
    Cancer Genome Atlas Research Network (Contributors include: Miller CA)
    Nat Genet 2013 Oct;45(10):1113-20
  • 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, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK
    Nat Methods 2013 Dec;10(12):1209-10
  • 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, Ding L, Griffith OL, Miller C, Larson D, Fulton RS, Harrison M, Mooney T, McMichael JF, Luo J, Tao Y, Goncalves R, Schlosberg C, Hiken JF, Saied L, Sanchez C, Giuntoli T, Bumb C, Cooper C, Kitchens RT, Lin A, Phommaly C, Davies SR, Zhang J, Kavuri MS, McEachern D, Dong YY, Ma C, Pluard T, Naughton M, Bose R, Suresh R, McDowell R, Michel L, Aft R, Gillanders W, DeSchryver K, Wilson RK, Wang S, Mills GB, Gonzalez-Angulo A, Edwards JR, Maher C, Perou CM, Mardis ER, Ellis MJ
    Cell Rep 2013 Sep 26;4(6):1116-30
  • 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, Leonard JR, Guha A, Miller CA, Ding L, Mardis ER
    Genome Res 2013 Mar;23(3):431-9
  • Clonal Diversity of Recurrently Mutated Genes in Myelodysplastic Syndromes
    Walter MJ, Shen D, Shao J, Ding L, White BS, Kandoth C, Miller CA, Niu B, McLellan MD, Dees ND, Fulton R, Elliot K, Heath S, Grillot M, Westervelt P, Link DC, DiPersio JF, Mardis E, Ley TJ, Wilson RK, Graubert TA
    Leukemia 2013 Jun;27(6):1275-82
  • Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
    Cancer Genome Atlas Research Network (Contributors include: Miller C)
    N Engl J Med 2013 May 30;368(22):2059-74
  • 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, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, Hundal J, Cook LL, Swift GW, Reed JP, Alldredge PA, Wylie TN, Walker JR, Watson MA, Heath SE, Shannon WD, Varghese N, Nagarajan R, Payton JE, Baty JD, Kulkarni S, Klco JM, Tomasson MH, Westervelt P, Walter MJ, Graubert TA, DiPersio JF, Ding L, Mardis ER, Wilson RK
    Cell 2012 Jul 20;150(2):264-78
  • Background Mutations in Parental Cells Account for Most of the Genetic Heterogeneity of Induced Pluripotent Stem Cells
    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, Sands MS, Mardis ER, Wilson RK, Townes TM, Ley TJ
    Cell Stem Cell 2012 May 4;10(5):570-82
  • 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 Res 2012 Mar;22(3):568-76
  • Whole-Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition
    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, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER
    Nature 2012 Jun 10;486(7403):353-60
  • 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, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, Shannon WD, Payton JE, Kulkarni S, Westervelt P, Walter MJ, Graubert TA, Mardis ER, Wilson RK, DiPersio JF
    Nature 2012 Jan 11;481(7382):506-10
  • 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, Albert I
    PLoS Comput Biol 2011 Oct;7(10):e1002216
  • Long-Range Massively Parallel Mate Pair Sequencing Detects Distinct Mutations and Similar Patterns of Structural Mutability in Two Breast Cancer Cell Lines
    Hampton OA, Koriabine M, Miller CA, Coarfa C, Li J, Den Hollander P, Schoenherr C, Carbone L, Nefedov M, Ten Hallers BF, Lee AV, De Jong PJ, Milosavljevic A
    Cancer Genet 2011 Aug;204(8):447-57
  • Discovering Functional Modules by Identifying Recurrent and Mutually Exclusive Mutational Patterns in Tumors
    Miller CA, Settle SH, Sulman EP, Aldape KD, Milosavljevic A
    BMC Med Genomics 2011 Apr 14;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 Jan 31;6(1):e16327
  • 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 Nov 23;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 Hollander P, Miller CA, Delgado DA, Li J, Coarfa C, Harris RA, Richards S, Scherer SE, Muzny DM, Gibbs RA, Lee AV, Milosavljevic A
    Genome Res 2009 Feb;19(2):167-77
  • Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways
    Cancer Genome Atlas Research Network (Contributors include: Miller CA)
    Nature 2008 Oct 23;455(7216):1061-8