Yi Qiao

Yi Qiao, PhD

Languages spoken: English

Academic Information

Departments Primary - Biomedical Informatics

Education History

Doctoral Training Boston College
 PhD
Zhejiang University
 BS

Selected Publications

Journal Article

  1. Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT (2024). A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Genome Res, 34(1), 94-105. (Read full article)
  2. Pitman A, Huang X, Marth GT, Qiao Y (2023). quickBAM: a parallelized BAM file access API for high-throughput sequence analysis informatics. Bioinformatics, 39(8). (Read full article)
  3. Groves SM, Ildefonso GV, McAtee CO, Ozawa PMM, Ireland AS, Stauffer PE, Wasdin PT, Huang X, Qiao Y, Lim JS, Bader J, Liu Q, Simmons AJ, Lau KS, Iams WT, Hardin DP, Saff EB, Holmes WR, Tyson DR, Lovly CM, Rathmell JC, Marth G, Sage J, Oliver TG, Weaver AM, Quaranta V (2022). Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer. Cell Syst, 13(9), 690-710.e17. (Read full article)
  4. Black GS, Huang X, Qiao Y, Tarapcsak S, Rogers KA, Misra S, Byrd JC, Marth GT, Stephens DM, Woyach JA (2021). Subclonal evolution of CLL driver mutations is associated with relapse in ibrutinib- and acalabrutinib-treated patients. Blood, 140(4), 401-405. (Read full article)
  5. Guillen KP, Fujita M, Butterfield AJ, Scherer SD, Bailey MH, Chu Z, DeRose YS, Zhao L, Cortes-Sanchez E, Yang CH, Toner J, Wang G, Qiao Y, Huang X, Greenland JA, Vahrenkamp JM, Lum DH, Factor RE, Nelson EW, Matsen CB, Poretta JM, Rosenthal R, Beck AC, Buys SS, Vaklavas C, Ward JH, Jensen RL, Jones KB, Li Z, Oesterreich S, Dobrolecki LE, Pathi SS, Woo XY, Berrett KC, Wadsworth ME, Chuang JH, Lewis MT, Marth GT, Gertz J, Varley KE, Welm BE, Welm AL (2022). A human breast cancer-derived xenograft and organoid platform for drug discovery and precision oncology. Nat Cancer, 3(2), 232-250. (Read full article)
  6. Huang X, Qiao Y, Brady SW, Factor RE, Downs-Kelly E, Farrell A, McQuerry JA, Shrestha G, Jenkins D, Johnson WE, Cohen AL, Bild AH, Marth GT (2021). Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med, 13(1), 170. (Read full article)
  7. Di Sera T, Velinder M, Ward A, Qiao Y, Georges S, Miller C, Pitman A, Richards W, Ekawade A, Viskochil D, Carey JC, Pace L, Bale J, Clardy SL, Andrews A, Botto L, Marth G (2021). Gene.iobio: an interactive web tool for versatile, clinically-driven variant interrogation and prioritization. Sci Rep, 11(1), 20307. (Read full article)
  8. Steely CJ, Russell KL, Feusier JE, Qiao Y, Tavtigian SV, Marth G, Jorde LB (2021). Mobile element insertions and associated structural variants in longitudinal breast cancer samples. Sci Rep, 11(1), 13020. (Read full article)
  9. Nicholas TJ, Cormier MJ, Huang X, Qiao Y, Marth GT, Quinlan AR (2021). OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Genome Med, 13(1), 46. (Read full article)
  10. Ireland AS, Micinski AM, Kastner DW, Guo B, Wait SJ, Spainhower KB, Conley CC, Chen OS, Guthrie MR, Soltero D, Qiao Y, Huang X, Tarapcsk S, Devarakonda S, Chalishazar MD, Gertz J, Moser JC, Marth G, Puri S, Witt BL, Spike BT, Oliver TG (2020). MYC Drives Temporal Evolution of Small Cell Lung Cancer Subtypes by Reprogramming Neuroendocrine Fate. Cancer Cell, 38(1), 60-78.e12. (Read full article)
  11. Ekawade A, Velinder M, Ward A, DiSera T, Miller C, Qiao Y, Marth G (2019). Genepanel.iobio - an easy to use web tool for generating disease- and phenotype-associated gene lists. BMC Med Genomics, 12(1), 190. (Read full article)
  12. Than H, Qiao Y, Huang X, Yan D, Khorashad JS, Pomicter AD, Kovacsovics TJ, Marth GT, OHare T, Deininger MW (2018). Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective. Leukemia, 32(9), 2049-2054. (Read full article)
  13. Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT (2018). Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools. J Clin Transl Sci, 1(6), 381-386. (Read full article)
  14. Brady SW, McQuerry JA, Qiao Y, Piccolo SR, Shrestha G, Jenkins DF, Layer RM, Pedersen BS, Miller RH, Esch A, Selitsky SR, Parker JS, Anderson LA, Dalley BK, Factor RE, Reddy CB, Boltax JP, Li DY, Moos PJ, Gray JW, Heiser LM, Buys SS, Cohen AL, Johnson WE, Quinlan AR, Marth G, Werner TL, Bild AH (2017). Combating subclonal evolution of resistant cancer phenotypes. Nat Commun, 8(1), 1231. (Read full article)
  15. Flygare S, Simmon K, Miller C, Qiao Y, Kennedy B, Di Sera T, Graf EH, Tardif KD, Kapusta A, Rynearson S, Stockmann C, Queen K, Tong S, Voelkerding KV, Blaschke A, Byington CL, Jain S, Pavia A, Ampofo K, Eilbeck K, Marth G, Yandell M, Schlaberg R (2016). Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling. Genome Biol, 17(1), 111. (Read full article)
  16. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT (2014). SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol, 15(8), 443. (Read full article)
  17. Wang L, Yamaguchi S, Burstein MD, Terashima K, Chang K, Ng HK, Nakamura H, He Z, Doddapaneni H, Lewis L, Wang M, Suzuki T, Nishikawa R, Natsume A, Terasaka S, Dauser R, Whitehead W, Adekunle A, Sun J, Qiao Y, Marth G, Muzny DM, Gibbs RA, Leal SM, Wheeler DA, Lau CC (2014). Novel somatic and germline mutations in intracranial germ cell tumours. Nature, 511(7508), 241-5. (Read full article)

Letter

  1. Khorashad JS, Tantravahi SK, Yan D, Mason CC, Qiao Y, Eiring AM, Gligorich K, Hein T, Pomicter AD, Reid AG, Kelley TW, Marth GT, OHare T, Deininger MW (2016). Rapid conversion of chronic myeloid leukemia to chronic myelomonocytic leukemia in a patient on imatinib therapy. [Letter to the editor]. Leukemia, 30(11), 2275-2279. (Read full article)
  2. Miller CA, Qiao Y, DiSera T, DAstous B, Marth GT (2014). bam.iobio: a web-based, real-time, sequence alignment file inspector. [Letter to the editor]. Nat Methods, 11(12), 1189. (Read full article)