ESC

Publications

140 publications  ·  60,527 citations  ·  h-index 65  ·  i10-index 113
as of August 2026 (OpenAlex)

* denotes shared first authorship. A complete list is also on Google Scholar.

2026 Consolidation Therapy Based on Mutation Clearance in Acute Myeloid Leukemia
Jacoby MA, Spencer DH, Gao F, Uy GL, Burton T, Heath SE, Du F, O'Laughlin M, Fulton RS, Miller CA, et al.. NEJM Evidence. 2026.
DOI PubMed Cited by 1
2026 pVACtools v6: A comprehensive suite for neoantigen prediction, visualization, and therapy design
Hoang MH, Kiwala S, Richters M, Hendrickson L, Xia H, Schmidt E, Miller CA, Cotto KC, Lichti CF, Skidmore Z, et al.. arXiv. 2026.
arXiv PubMed
2026 Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS
Miller CA, Srivatsan SN, Kramer MH, Ramakrishnan SM, Fronick CC, Fulton RS, Katerndahl CD, Helton NM, Ley TJ, Walter MJ. bioRxiv. 2026.
DOI PubMed
2026 Automating neoantigen selection for personalized cancer vaccine design
Yao JX, Singhal K, Kiwala S, Schmidt E, Goedegebuure S, Miller CA, Xia H, Cotto K, Coffman A, Hoang MH, et al.. medRxiv. 2026.
DOI
2026 Adjuvant personalized multivalent neoantigen DNA vaccination for MGMT unmethylated glioblastoma: a phase 1 trial
Garfinkle EAR, Perales-Linares R, Gimple RC, Livingstone AJ, Roberts KF, Butt OH, Goedegebuure SP, McLellan MD, Chang GS, Hundal J, Miller CA, et al.. Nature Cancer. 2026.
DOI PubMed Cited by 4
2026 Synthetic lethality of decitabine plus ATR inhibition for TP53-mutated AML
Baeten JT, Agashe S, Tabet I, Wooldridge JT, Carter A, Butler JN, Miller CA, Helton N, Quinet A, Johansson KB, et al.. Blood Advances. 2026.
DOI PubMed Cited by 2
2026 Neoadjuvant Endocrine Treatment plus Mammaglobin-A DNA Vaccine Induces Antitumor Immune Responses in the Primary Tumor and Peripheral Blood of Patients with Breast Cancer: Insights from a Phase Ib Clinical Trial
Mishra R, Ademuyiwa F, Yang Y, Herndon J, Li L, Street C, Myers N, Chen I, Zhang X, Hagemann IS, Miller CA, et al.. Cancer Immunology Research. 2026.
DOI PubMed Cited by 1
2025 ImmunoNX: a robust bioinformatics workflow to support personalized neoantigen vaccine trials
Singhal K, Schmidt E, Kiwala S, Goedegebuure SP, Miller CA, Xia H, Cotto KC, Li J, Yao J, Hendrickson L, et al.. arXiv. 2025.
arXiv PubMed
2025 Evaluation of Long-Read Genome Sequencing for Genomic Profiling of Myeloid Cancers
Abel HJ, Mahgoub M, Davarapalli N, Kodgule R, Miller CA, Fulton RS, Fronick C, Markovic C, Heath S, Payton JE, et al.. Journal Of Molecular Diagnostics. 2025.
DOI PubMed Cited by 1
2025 Overexpression of the signaling coordinator GAB2 can play an important role in acute myeloid leukemia progression
Kramer MH, Richardson SN, Li Y, Yin T, Helton NM, George DR, Cai M, Ramakrishnan SM, Katerndahl CD, Miller CA, et al.. Journal Of Clinical Investigation. 2025.
DOI PubMed Cited by 2
2025 Monitoring clonal burden as an alternative to blast count for myelodysplastic neoplasm treatment response
Jacoby MA*, Duncavage ED*, Khanna A*, Chang GS, Nonavinkere Srivatsan S, Miller CA, Gao F, Robinson J, Shao J, Fulton RS, et al.. Leukemia. 2025.
DOI PubMed
2024 Neoantigen DNA vaccines are safe, feasible, and induce neoantigen-specific immune responses in triple-negative breast cancer patients
Zhang X, Goedegebuure SP, Chen MY, Mishra R, Zhang F, Yu YY, Singhal K, Li L, Gao F, Myers NB, Miller CA, et al.. Genome Medicine. 2024.
DOI PubMed Cited by 83
2024 pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection
Xia H, Hoang MH, Schmidt E, Kiwala S, McMichael J, Skidmore ZL, Fisk B, Song JJ, Hundal J, Mooney T, Miller CA, et al.. Genome Medicine. 2024.
DOI PubMed Cited by 11
2024 PML::RARA and GATA2 proteins interact via DNA templates to induce aberrant self-renewal in mouse and human hematopoietic cells
Katerndahl CDS, Rogers ORS, Day RB, Xu Z, Helton NM, Ramakrishnan SM, Miller CA, Ley TJ. Proceedings Of The National Academy Of Sciences. 2024.
DOI PubMed Cited by 7
2023 Proteogenomic analysis reveals cytoplasmic sequestration of RUNX1 by the acute myeloid leukemia-initiating CBFB::MYH11 oncofusion protein
Day RB, Hickman JA, Xu Z, Katerndahl CD, Ferraro F, Ramakrishnan SM, Erdmann-Gilmore P, Sprung RW, Mi Y, Townsend RR, Miller CA, et al.. Journal Of Clinical Investigation. 2023.
DOI PubMed Cited by 12
2024 Rapid and accurate remethylation of DNA in Dnmt3a-deficient hematopoietic cells with restoration of DNMT3A activity
Li Y, Abel HJ, Cai M, LaValle TA, Yin T, Helton NM, Smith AM, Miller CA, Ley TJ. Science Advances. 2024.
DOI PubMed Cited by 8
2024 Molecular responses in decitabine- and decitabine/ venetoclax-treated patients with acute myeloid leukemia and myelodysplastic syndromes
Gruszczynska A, Maiti A, Miller CA, Ramakrishnan SM, Link DC, Uy GL, Petti AA, Hayes K, DiNardo CD, Ravandi F, et al.. Haematologica. 2024.
DOI PubMed Cited by 3
2023 Ultra-Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma
Gomez F, Fisk B, McMichael JF, Mosior M, Foltz JA, Skidmore ZL, Duncavage EJ, Miller CA, Abel H, Li YS, et al.. Cancer Research Communications. 2023.
DOI PubMed Cited by 15
2023 Genomic landscape of TP53-mutated myeloid malignancies
Abel HJ*, Oetjen KA*, Miller CA*, Ramakrishnan SM, Day RB, Helton NM, Fronick CC, Fulton RS, Heath SE, Tarnawsky SP, et al.. Blood Advances. 2023.
DOI PubMed Cited by 32
2023 Induction of cancer neoantigens facilitates development of clinically relevant models for the study of pancreatic cancer immunobiology
Panni UY, Chen MY, Zhang F, Cullinan DR, Li L, James CA, Zhang X, Rogers S, Alarcon A, Baer JM, Miller CA, et al.. Cancer Immunology, Immunotherapy. 2023.
DOI PubMed Cited by 2
2023 Genetic characterization of primary and metastatic high-grade serous ovarian cancer tumors reveals distinct features associated with survival
Kotnik EN, Mullen MM, Spies NC, Li T, Inkman M, Zhang J, Martins-Rodrigues F, Hagemann IS, McCourt CK, Thaker PH, Miller CA, et al.. Communications Biology. 2023.
DOI PubMed Cited by 32
2023 Computational prediction of MHC anchor locations guides neoantigen identification and prioritization
Xia H, McMichael J, Becker-Hapak M, Onyeador OC, Buchli R, McClain E, Pence P, Supabphol S, Richters MM, Basu A, Miller CA, et al.. Science Immunology. 2023.
DOI PubMed Cited by 27
2023 Melanoma in a patient with DNMT3A overgrowth syndrome
Chen DY, Sutton LA, Ramakrishnan SM, Duncavage EJ, Heath SE, Compton LA, Miller CA, Ley TJ. Cold Spring Harbor Molecular Case Studies. 2023.
DOI PubMed Cited by 5
2023 Clonal Hematopoiesis and Risk of Incident Lung Cancer
Tian R, Wiley B, Liu J, Zong X, Truong B, Zhao S, Uddin MM, Niroula A, Miller CA, Mukherjee S, et al.. Journal Of Clinical Oncology. 2023.
DOI PubMed Cited by 87
2023 Combined Kdm6a and Trp53 Deficiency Drives the Development of Squamous Cell Skin Cancer in Mice
Shea LK, Akhave NS, Sutton LA, Compton LA, York C, Ramakrishnan SM, Miller CA, Wartman LD, Chen DY. Journal Of Investigative Dermatology. 2023.
DOI PubMed Cited by 9
2022 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, Miller CA, et al.. Blood. 2022.
DOI PubMed Cited by 130
2022 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 PubMed Cited by 9
2022 Discovery of a novel genomic alteration that renders leukemic cells resistant to CD19-targeted immunotherapies
Ghobadi A, Landmann JH, Carter A, Cooper ML, Selli ME, Chang J, Baker M, Miller CA, Ferraro F, Chen DY, et al.. Blood Advances. 2022.
DOI PubMed Cited by 5
2022 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 PubMed Cited by 20
2022 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, Miller CA, et al.. Cancer Genetics. 2022.
DOI PubMed Cited by 11
2022 Convergent Clonal Evolution of Signaling Gene Mutations Is a Hallmark of Myelodysplastic Syndrome Progression
Menssen AJ, Khanna A, Miller CA, Nonavinkere Srivatsan S, Chang GS, Shao J, Robinson J, O'Laughlin M, Fronick CC, Fulton RS, et al.. Blood Cancer Discovery. 2022.
DOI PubMed Cited by 23
2022 Efficient Algorithms Unlock Understanding of Clonal Evolution in Cancer
Miller CA. Blood Cancer Discovery. 2022.
DOI PubMed
2022 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 PubMed Cited by 3
2022 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, Miller CA, et al.. Journal Of Open Source Software. 2022.
DOI Cited by 145
2022 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, Miller CA, et al.. Blood. 2022.
DOI PubMed Cited by 19
2022 Tumor suppressor function of WT1 in acute promyelocytic leukemia
Christopher MJ, Katerndahl CDS, LeBlanc HR, Elmendorf TT, Basu V, Gang M, Menssen AJ, Spencer DH, Duncavage EJ, Ketkar S, Miller CA, et al.. Haematologica. 2022.
DOI PubMed Cited by 7
2022 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.. Journal Of Molecular Diagnostics. 2022.
DOI PubMed Cited by 43
2022 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 Srivatsan S, Heath SE, Westervelt P, Miller CA, et al.. Blood Cancer Discovery. 2022.
DOI PubMed Cited by 32
2022 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, Miller CA, et al.. Leukemia. 2022.
DOI PubMed Cited by 33
2021 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 AK, Bloomfield CD, et al.. Proceedings Of The National Academy Of Sciences. 2021.
DOI PubMed Cited by 49
2021 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, Miller CA, et al.. Journal Of Clinical Investigation. 2021.
DOI PubMed Cited by 20
2021 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.
DOI PubMed Cited by 9
2021 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, et al.. Blood. 2021.
DOI PubMed Cited by 28
2021 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 PubMed Cited by 23
2021 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, Miller CA, et al.. Nature Communications. 2021.
DOI PubMed Cited by 49
2021 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 PubMed Cited by 8
2021 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, et al.. Genome Medicine. 2021.
DOI PubMed Cited by 68
2021 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 PubMed Cited by 47
2021 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, Miller CA, et al.. New England Journal Of Medicine. 2021.
DOI PubMed Cited by 301
2021 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 PubMed Cited by 51
2020 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, et al.. Cell. 2020.
DOI PubMed Cited by 551
2020 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 PubMed Cited by 81
2020 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 PubMed Cited by 11
2020 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, et al.. Blood Advances. 2020.
DOI PubMed Cited by 14
2020 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 PubMed Cited by 81
2020 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. 2020.
DOI PubMed Cited by 13
2020 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, et al.. Cancer Immunology Research. 2020.
DOI PubMed Cited by 302
2020 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, Miller CA, et al.. Proceedings Of The National Academy Of Sciences. 2020.
DOI PubMed Cited by 36
2019 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 PubMed Cited by 239
2019 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 L. Haematologica. 2019.
DOI PubMed Cited by 18
2019 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 PubMed Cited by 2
2019 Smc3 is required for mouse embryonic and adult hematopoiesis
Wang T, Glover B, Hadwiger G, Miller CA, di Martino O, Welch JS. Experimental Hematology. 2019.
DOI PubMed Cited by 20
2019 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 PubMed Cited by 75
2018 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 PubMed Cited by 477
2018 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 PubMed Cited by 124
2018 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 PubMed Cited by 143
2018 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 PubMed Cited by 32
2018 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, Miller CA, et al.. Leukemia. 2018.
DOI PubMed Cited by 397
2018 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, et al.. Blood Advances. 2018.
DOI PubMed Cited by 33
2018 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 PubMed Cited by 25
2018 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 PubMed Cited by 2
2018 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 Harbor Molecular Case Studies. 2018.
DOI PubMed Cited by 17
2018 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 PubMed Cited by 61
2018 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, et al.. Nature Communications. 2018.
DOI PubMed Cited by 199
2018 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, Miller CA, et al.. Neuro-oncology. 2018.
DOI PubMed Cited by 58
2018 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, et al.. Blood. 2018.
DOI PubMed Cited by 123
2018 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 PubMed Cited by 19
2017 ClonEvol: clonal ordering and visualization in cancer sequencing
Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA. Annals Of Oncology. 2017.
DOI PubMed Cited by 188
2017 Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
The Cancer Genome Atlas Network. Cell. 2017.
DOI PubMed Cited by 1,096
2017 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 PubMed Cited by 11
2017 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, Miller CA, et al.. Journal Of Clinical Investigation. 2017.
DOI PubMed Cited by 89
2017 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, Miller CA, et al.. Cancer Immunology Research. 2017.
DOI PubMed Cited by 92
2017 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, et al.. Leukemia. 2017.
DOI PubMed Cited by 106
2017 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, et al.. Blood. 2017.
DOI PubMed Cited by 59
2017 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 PubMed Cited by 187
2016 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 PubMed Cited by 108
2016 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 PubMed Cited by 106
2016 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 PubMed Cited by 796
2016 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.
DOI PubMed Cited by 185
2016 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 PubMed Cited by 299
2016 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 Harbor Symposia On Quantitative Biology. 2016.
DOI PubMed Cited by 24
2016 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, Miller CA, et al.. Cell Reports. 2016.
DOI PubMed Cited by 28
2016 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, et al.. Leukemia. 2016.
DOI PubMed Cited by 6
2016 Impact of mutational profiles on response of primary oestrogen receptor-positive breast cancers to oestrogen deprivation
Gellert P, Segal CV, Gao Q, López-Knowles E, Martin LA, Dodson A, Li T, Miller CA, Lu C, Mardis ER, et al.. Nature Communications. 2016.
DOI PubMed Cited by 44
2016 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 PubMed Cited by 72
2017 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, et al.. Brain Pathology. 2017.
DOI PubMed Cited by 23
2016 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, Miller CA, et al.. Experimental Hematology. 2016.
DOI PubMed Cited by 58
2016 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, et al.. Blood Cancer Journal. 2016.
DOI PubMed Cited by 18
2016 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.. Cold Spring Harbor Molecular Case Studies. 2016.
DOI PubMed Cited by 20
2016 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 PubMed Cited by 107
2015 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, Miller CA, et al.. Nature Communications. 2015.
DOI PubMed Cited by 316
2015 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, et al.. Blood. 2015.
DOI PubMed Cited by 241
2015 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 PubMed Cited by 209
2015 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, et al.. Clinical Cancer Research. 2015.
DOI PubMed Cited by 56
2015 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 PubMed Cited by 347
2015 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, Miller CA, et al.. PLoS Computational Biology. 2015.
DOI PubMed Cited by 90
2015 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 PubMed Cited by 17
2015 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, et al.. Nature. 2015.
DOI PubMed Cited by 894
2015 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.
DOI PubMed Cited by 96
2014 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, et al.. Nature Medicine. 2014.
DOI PubMed Cited by 1,911
2014 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, et al.. Blood. 2014.
DOI PubMed Cited by 24
2014 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, et al.. PLoS One. 2014.
DOI PubMed Cited by 89
2015 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, et al.. Leukemia. 2015.
DOI PubMed Cited by 130
2015 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.
DOI PubMed Cited by 47
2014 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 Computational Biology. 2014.
DOI PubMed Cited by 500
2014 Comprehensive molecular profiling of lung adenocarcinoma
Cancer Genome Atlas Research Network. Nature. 2014.
DOI PubMed Cited by 5,923
2014 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, et al.. PLoS Genetics. 2014.
DOI PubMed Cited by 138
2014 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 PubMed Cited by 465
2014 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 PubMed Cited by 408
2014 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, Miller CA, et al.. Nature Communications. 2014.
DOI PubMed Cited by 305
2013 Genomic landscapes and clonality of de novo AML
Miller CA, Wilson RK, Ley TJ. New England Journal Of Medicine. 2013.
DOI PubMed Cited by 71
2013 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, Miller CA, et al.. Nature. 2013.
DOI PubMed Cited by 4,558
2013 The cancer genome atlas pan-cancer analysis project
The Cancer Genome Atlas Research Network. Nature Genetics. 2013.
DOI PubMed Cited by 9,759
2013 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, et al.. Nature Methods. 2013.
DOI PubMed Cited by 574
2013 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, Miller CA, et al.. Cell Reports. 2013.
DOI PubMed Cited by 630
2013 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, Miller CA, et al.. Genome Research. 2013.
DOI PubMed Cited by 127
2013 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, et al.. Leukemia. 2013.
DOI PubMed Cited by 281
2013 Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia
The Cancer Genome Atlas Research Network. New England Journal Of Medicine. 2013.
DOI PubMed Cited by 5,207
2012 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 PubMed Cited by 1,579
2012 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, et al.. Cell Stem Cell. 2012.
DOI PubMed Cited by 197
2012 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 PubMed Cited by 5,376
2012 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, Miller CA, et al.. Nature. 2012.
DOI PubMed Cited by 1,036
2012 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 PubMed Cited by 2,028
2011 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 PubMed Cited by 103
2011 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, et al.. Cancer Genetics. 2011.
DOI PubMed Cited by 19
2011 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 PubMed Cited by 141
2011 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 PubMed Cited by 237
2010 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 PubMed Cited by 54
2009 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, et al.. Genome Research. 2009.
DOI PubMed Cited by 132
2008 Comprehensive genomic characterization defines human glioblastoma genes and core pathways
Cancer Genome Atlas Network. Nature. 2008.
DOI PubMed Cited by 7,860