1. L. Kubatko and Chifman, J. (2020). Identifiability of speciation times under the multispecies coalescent. bioRxiv doi: https://doi.org/10.1101/2020.11.24.396424
  2. D. Routh, Pullikuth A. K., Jin G., Chifman J., Chou J. W., D’Agostino R. B., Seino Ken-ichiro, Wada H., Print C. G., Zhang W., Lu Y., Miller L. D. (2020). Transcriptomic Features of T Cell-barren Tumors are Conserved Across Diverse Tumor Types. Frontiers in Immunology, 11:57, https://doi.org/10.3389/fimmu.2020.00057
  3. Kubatko and Chifman, J. (2019). An invariants-based method for efficient identification of hybrid species from large-scale genomic data. BMC Evolutionary Biology, 19(1). doi.org/10.1186/s12862-019-1439-7
  4. Blischak, P. D., J. Chifman, A. D. Wolfe, and L. S. Kubatko. (2018). HyDe: a Python Package for Genome-Scale Hybridization Detection, Systematic Biology, syy023, https://doi.org/10.1093/sysbio/syy023
  5. Chifman, J., Arat, S., Deng, Z., Lemler, E., Pino, J. C., Harris, L. A., Kochen, M. A., Lopez, C. F., Akman, S. A., Torti, F. M., Torti, S. V., and Laubenbacher, R. (2017). Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective. PLoS Computational Biology, 13(2), e1005352. https://doi.org/10.1371/journal.pcbi.1005352
  6. Chifman, J., Pullikuth, A., Chou, J. W., Bedognetti, D., & Miller, L. D. (2016). Conservation of immune gene signatures in solid tumors and prognostic implications. BMC Cancer, 16, 911. https://doi.org/10.1186/s12885-016-2948-z
  7. Miller, L. D.,  J. A. Chou, M. A. Black, C. Print, J. Chifman, A. Alistar, T. Putti, X. Zhou, D. Bedognetti, A. Pullikuth, J. Rennhack, E. R. Andrechek, S. Demaria, E. Wang, F. M. Marincola. (2016). Immunogenic subtypes of breast cancer delineated by gene classifiers of immune responsiveness, Cancer Immunology Research. https://doi.org/10.1158/2326-6066.CIR-15-0149
  8. Chifman, J. (2016) Phylogenetic Invariants. In: Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 3, pp. 257–263. Oxford: Academic Press. https://doi.org/10.1016/B978-0-12-800049-6.00216-X
  9. Chifman, J. and L. Kubatko, Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. J. Theor. Biol.374 (2015), 35-47. https://doi.org/10.1016/j.jtbi.2015.03.006
  10. Chifman, J. and L. Kubatko, Quartet inference from SNP data under the coalescent model. Bioinformatics (2014), 30 (23), 3317-3324, https://doi.org/10.1093/bioinformatics/btu530
  11. Chifman, J., R. Laubenbacher, and S. V. Torti. A systems biology approach to iron metabolism. In S. J. Corey, M. Kimmel, and J. N. Leonard, editors, A Systems Biology Approach to Blood, volume 844 of Advances in Experimental Medicine and Biology, pages 201-225. Springer New York (2014). https://doi.org/10.1007/978-1-4939-2095-2_10
  12. Chifman, J., A. Kniss*, P. Neupane*, I. Williams*, B.Leung*, Z. Deng, P. Mendes, V. Hower, F.M. Torti, S.A. Akman, S.V. Torti, and Laubenbacher R. (2012). The core control system of intracellular iron homeostasis: A mathematical model. J. Theor. Biol.300: 91-99. (* Undergraduate students from REU program (VBI, Virginia Tech)). https://doi.org/10.1016/j.jtbi.2012.01.024
  13. Chifman, J., Note on direct products of certain classes of finite groups.Communications in Algebra, (2009) 37:5, 1831-1842.
  14. C. Beidleman, and J. Chifman, The intersection map of subgroups and the classes PSTc, PTcand Tc. Ricerche mat.(2008) 57:301-309.
  15. Chifman, J. and Petrovic, S., Toric ideals of phylogenetic invariants for the general group-based model on claw trees. Proceedings of the Second international conference on Algebraic Biology,(eds. H. Anai, K. Horimoto and T. Kutsia), Springer LNCS, 4545, Springer-Verlag, 307-321, 2007.

Abstracts:

  1. E. D. Routh, J. Chifman, A. Pullikuth, and L. D. Miller. Abstract 4753: Bone morphogenetic protein 7 is a candidate promoter of cancer immune evasion. Cancer Research, 78(13 Supplement):4753–4753, (2018).
  2. Frank Marini, Julia Chifman, Janet Tooze, Candelaria Gomez-Manzano, Karen M. Bussard. Osteoblasts are educated into a tumor-associated stromal cell by disseminated breast cancer cells and mediate breast cancer cell proliferation in the bone microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting (2017); 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl): Abstract nr 5890. doi:10.1158/1538-7445.AM2017-5890.
  3. A. T. Alistar, J. Chifman, R. D’Agostino Jr, and L. D. Miller, Gene expression signatures of effector immune cell abundance are significantly associated with recurrence risk in colon cancer (abstract). Cancer Immunology Research, (1 Supplement): A011-A011, (2016).