Research Interest Statement:
My primary research interest is in bioinformatics and cancer genomics. I have done analysis and implemented various algorithmson thousands of multiple myeloma samples across a variety of sequencing modalities such as targeted panel, reducedrepresentation bisulfite, whole-genome, whole-exome, RNA, CHiP-Seq, Nanopore WGS, and 10X Genomics WGS.
Ashby C, Rutherford M, Bauer MA, [et al.]. TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use. BMC bioinformatics. 2020 21(1):144. PMID: 32293247. PMCID: PMC7158102.
Bauer MA, Ashby C, Wardell C, [et al.]. Differential RNA splicing as a potentially important driver mechanism in multiple myeloma. Haematologica. 2020. PMID: 32079689.
Boyle EM, Ashby C, Tytarenko R, [et al.]. BRAF and DIS3 Mutations Associate with Adverse Outcome in a Long-term Follow-up of Patients with Multiple Myeloma. Clinical cancer research : an official journal of the American Association for Cancer Research. 2020. PMID: 31988198.
Jones JR, Weinhold N, Ashby C, [et al.]. Clonal evolution in myeloma: the impact of maintenance lenalidomide and depth of response on the genetics and sub-clonal structure of relapsed disease in uniformly treated newly diagnosed patients. Haematologica. 2019 104(7):1440-1450. PMID: 30733268. PMCID: PMC6601103.
Rasche L, Alapat D, Kumar M, [et al., including Ashby C]. Combination of flow cytometry and functional imaging for monitoring of residual disease in myeloma. Leukemia. 2019 33(7):1713-1722. PMID: 30573775. PMCID: PMC6586541.
Mikulasova A, Ashby C, Tytarenko RG, [et al.]. Microhomology-mediated end joining drives complex rearrangements and over expression of MYC and PVT1 in multiple myeloma. Haematologica. 2019. PMID: 31221783.
Ashby C, Tytarenko RG, Wang Y, [et al.]. Poor overall survival in hyperhaploid multiple myeloma is defined by double-hit bi-allelic inactivation of TP53. Oncotarget. 2019 10(7):732-737. PMID: 30774775. PMCID: PMC6366829.
Ashby C, Peterson EA, Bauer M, Johann DJ. A Scalable and Adaptive Approach for NGS Analyses Leveraging High-Performance Computing. Pathological Specimens and Genomics Medicine: Emerging Issues. 2019:248.
Walker BA, Mavrommatis K, Wardell CP, [et al., including Ashby TC]. A high-risk, Double-Hit, group of newly diagnosed myeloma identified by genomic analysis. Leukemia. 2019 33(1):159-170. PMID: 29967379. PMCID: PMC6326953.
Boyle EM, Ashby C, Wardell CP, [et al.]. The genomic landscape of plasma cells in systemic light chain amyloidosis. Blood. 2018 132(26):2775-2777. PMID: 30446495.
Walker BA, Mavrommatis K, Wardell CP, [et al., including Ashby TC]. Identification of novel mutational drivers reveals oncogene dependencies in multiple myeloma. Blood. 2018 132(6):587-597. PMID: 29884741. PMCID: PMC6097138.
Pawlyn C, Loehr A, Ashby C, [et al.]. Loss of heterozygosity as a marker of homologous repair deficiency in multiple myeloma: a role for PARP inhibition?. Leukemia. 2018 32(7):1561-1566. PMID: 29467487. PMCID: PMC6035152.
Causey JL, Ashby C, Walker K, [et al.]. DNAp: A Pipeline for DNA-seq Data Analysis. Scientific reports. 2018 8(1):6793. PMID: 29717215. PMCID: PMC5931599.
Thanendrarajan S, Tian E, Qu P, [et al., including Ashby C]. The level of deletion 17p and bi-allelic inactivation of TP53 has a significant impact on clinical outcome in multiple myeloma. Haematologica. 2017 102(9):e364-e367. PMID: 28550191. PMCID: PMC5685226.
Rasche L, Chavan SS, Stephens OW, [et al., including Ashby C]. Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing. Nature communications. 2017 8(1):268. PMID: 28814763. PMCID: PMC5559527.
Chavan SS, He J, Tytarenko R, [et al., including Ashby C]. Bi-allelic inactivation is more prevalent at relapse in multiple myeloma, identifying RB1 as an independent prognostic marker. Blood cancer journal. 2017 7(2):e535. PMID: 28234347. PMCID: PMC5386330.
Weinhold N, Ashby C, Rasche L, [et al.]. Clonal selection and double-hit events involving tumor suppressor genes underlie relapse in myeloma. Blood. 2016 128(13):1735-44. PMID: 27516441. PMCID: PMC5043128.
Peterson EA, Bauer M, Chavan SS, [et al., including Ashby C]. Enhancing Cancer Clonality Analyses with Integrative Genomics. BMC Bioinformatics. 2015 25(16 Suppl 13):S1.
Chang Z, Li G, Liu J, [et al., including Ashby T]. Bridger: a new framework for de novo transcriptome assembly using RNA-seq data. Genome biology. 2015 16:30. PMID: 25723335. PMCID: PMC4342890.
Ma S, Johnson D, Ashby C, [et al.]. SPARCoC: a new framework for molecular pattern discovery and cancer gene identification. PloS one. 2015 10(3):e0117135. PMID: 25768286. PMCID: PMC4359112.
Peterson EA, Bauer MA, Chavan SS, [et al., including Ashby C]. Enhancing cancer clonality analysis with integrative genomics. BMC bioinformatics. 2015 16 Suppl 13:S7. PMID: 26424171. PMCID: PMC4597064.
Chang Z, Wang Z, Ashby C, [et al.]. eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes. Cancer informatics. 2014 13(Suppl 2):105-12. PMID: 25374455. PMCID: PMC4213194.
Ashby C, Johnson D, Walker K, [et al.]. New enumeration algorithm for protein structure comparison and classification. BMC genomics. 2013 14 Suppl 2:S1. PMID: 23445440. PMCID: PMC3582452.