[{"id":88,"date":"2019-03-06T16:32:22","date_gmt":"2019-03-06T16:32:22","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=88"},"modified":"2021-01-17T00:15:43","modified_gmt":"2021-01-17T00:15:43","slug":"publications","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
    \n
  1. L. Kubatko and Chifman, J<\/strong>. (2020). Identifiability of speciation times under the multispecies coalescent.\u00a0bioRxiv\u00a0<\/em>doi:\u00a0https:\/\/doi.org\/10.1101\/2020.11.24.396424<\/a><\/li>\n
  2. D. Routh, Pullikuth A. K., Jin G., Chifman J<\/strong>., 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<\/em>, 11:57, https:\/\/doi.org\/10.3389\/fimmu.2020.00057<\/a><\/li>\n
  3. Kubatko and Chifman, J.<\/strong> (2019). An invariants-based method for efficient identification of hybrid species from large-scale genomic data. BMC Evolutionary Biology, 19<\/em>(1). doi.org\/10.1186\/s12862-019-1439-7<\/li>\n
  4. Blischak, P. D., J.\u00a0Chifman<\/strong>, A. D. Wolfe, and L. S. Kubatko. (2018). HyDe: a Python Package for Genome-Scale Hybridization Detection, Systematic Biology<\/em>, syy023, https:\/\/doi.org\/10.1093\/sysbio\/syy023<\/a><\/li>\n
  5. Chifman, J.,\u00a0<\/strong>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.\u00a0PLoS Computational Biology<\/em>,\u00a013<\/em>(2), e1005352.\u00a0https:\/\/doi.org\/10.1371\/journal.pcbi.1005352<\/a><\/li>\n
  6. Chifman, J., <\/strong>Pullikuth, A., Chou, J. W., Bedognetti, D., & Miller, L. D. (2016). Conservation of immune gene signatures in solid tumors and prognostic implications.\u00a0BMC Cancer<\/em>,\u00a016<\/em>, 911.\u00a0https:\/\/doi.org\/10.1186\/s12885-016-2948-z<\/a><\/li>\n
  7. Miller, L. D., \u00a0J. A. Chou, M. A. Black, C. Print, J. Chifman<\/strong>, 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<\/em>.\u00a0https:\/\/doi.org\/10.1158\/2326-6066.CIR-15-0149<\/a><\/li>\n
  8. Chifman, J<\/strong>. (2016) Phylogenetic Invariants. In: Kliman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 3, pp. 257\u2013263. Oxford: Academic Press.\u00a0https:\/\/doi.org\/10.1016\/B978-0-12-800049-6.00216-X<\/a><\/li>\n
  9. Chifman, J.\u00a0<\/strong>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.<\/em>374\u00a0<\/strong>(2015), 35-47.\u00a0https:\/\/doi.org\/10.1016\/j.jtbi.2015.03.006<\/a><\/li>\n
  10. Chifman, J.\u00a0<\/strong>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<\/a><\/li>\n
  11. Chifman, J.<\/strong>, 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<\/a><\/li>\n
  12. Chifman, J.<\/strong>, A. Kniss*<\/sup>, P. Neupane*<\/sup>, I. Williams*<\/sup>, B.Leung*<\/sup>, 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.<\/em>300: 91-99. (* Undergraduate students from REU program (VBI, Virginia Tech)).\u00a0https:\/\/doi.org\/10.1016\/j.jtbi.2012.01.024<\/a><\/li>\n
  13. Chifman, J.<\/strong>, Note on direct products of certain classes of finite groups.Communications in Algebra<\/em>, (2009) 37:5, 1831-1842.<\/li>\n
  14. C. Beidleman, and J. Chifman<\/strong>, The intersection map of subgroups and the classes PSTc<\/sub>, PTc<\/sub>and Tc<\/sub>. Ricerche mat.<\/em>(2008) 57:301-309.<\/li>\n
  15. Chifman, J.\u00a0<\/strong>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,<\/em>(eds. H. Anai, K. Horimoto and T. Kutsia), Springer LNCS, 4545, Springer-Verlag, 307-321, 2007.<\/li>\n<\/ol>\n

    Abstracts:<\/strong><\/p>\n

      \n
    1. E. D. Routh, J. Chifman,<\/strong> A. Pullikuth, and L. D. Miller. Abstract 4753: Bone\u00a0morphogenetic protein 7 is a candidate promoter of cancer immune evasion. Cancer Research, 78(13 Supplement):4753\u20134753, (2018).<\/li>\n
    2. Frank Marini, Julia Chifman<\/strong>, 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.<\/li>\n
    3. A. T. Alistar, J. Chifman<\/strong>, R. D\u2019Agostino 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).\n
      \n
      \n
      <\/div>\n<\/div>\n<\/div>\n<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"

      L. Kubatko and Chifman, J. (2020). Identifiability of speciation times under the multispecies coalescent.\u00a0bioRxiv\u00a0doi:\u00a0https:\/\/doi.org\/10.1101\/2020.11.24.396424 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.,… Continue Reading →<\/a><\/p>\n","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":5,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-88","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/88","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=88"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/88\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=88"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":85,"date":"2019-03-06T16:20:06","date_gmt":"2019-03-06T16:20:06","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=85"},"modified":"2021-06-11T03:43:45","modified_gmt":"2021-06-11T03:43:45","slug":"students","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/students\/","title":{"rendered":"Research Students"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-85","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/85","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=85"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/85\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=85"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":84,"date":"2019-03-06T16:19:32","date_gmt":"2019-03-06T16:19:32","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=84"},"modified":"2021-06-11T03:42:50","modified_gmt":"2021-06-11T03:42:50","slug":"phylogenetic-models-and-inference-methods","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/phylogenetic-models-and-inference-methods\/","title":{"rendered":"Phylogenetic models"},"content":{"rendered":"

       <\/p>\n

       <\/p>\n","protected":false},"excerpt":{"rendered":"

         <\/p>\n","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":3,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-84","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/84","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=84"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/84\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=84"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":44,"date":"2019-03-05T21:41:44","date_gmt":"2019-03-05T21:41:44","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=44"},"modified":"2022-06-10T17:33:55","modified_gmt":"2022-06-10T17:33:55","slug":"modeling-of-molecular-networks","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/modeling-of-molecular-networks\/","title":{"rendered":"Molecular networks"},"content":{"rendered":"\t\t

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      Lorem ipsum dolor sit amet, consectetur adipiscing elit. Ut elit tellus, luctus nec ullamcorper mattis, pulvinar dapibus leo.<\/p>\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t

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      \n\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\"\"\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t<\/div>\n\t\t\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t
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      \n\t\t\t\t\t\t\t<\/div>\n\t\t<\/div>\n\t\t\t\t\t<\/div>\n\t\t<\/section>\n\t\t\t\t<\/div>\n\t\t","protected":false},"excerpt":{"rendered":"

      Lorem ipsum dolor sit amet, consectetur adipiscing elit. Ut elit tellus, luctus nec ullamcorper mattis, pulvinar dapibus leo.<\/p>\n","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-44","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/44","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=44"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/44\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=44"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":28,"date":"2019-03-05T20:25:13","date_gmt":"2019-03-05T20:25:13","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=28"},"modified":"2019-03-07T19:24:55","modified_gmt":"2019-03-07T19:24:55","slug":"home","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/","title":{"rendered":"Home"},"content":{"rendered":"

      I have joined the Department of Mathematics and Statistics at American University in August 2016 as an Assistant Professor. Prior to this appointment I\u00a0was a Postdoctoral Research Fellow at the Mathematical Biosciences Institute at The Ohio State University, a Postdoctoral Fellow in the Department of Cancer Biology at the Wake Forest University School of Medicine and a Visiting Scholar at the Virginia Bioinformatics Institute at Virginia Tech.<\/p>\n

      My\u00a0research interests include systems biology and its application to molecular networks, the estimation of species-level phylogenies using novel mathematical techniques, and application of methods from evolutionary biology to cancer evolution.<\/p>\n","protected":false},"excerpt":{"rendered":"

      I have joined the Department of Mathematics and Statistics at American University in August 2016 as an Assistant Professor. Prior to this appointment I\u00a0was a Postdoctoral Research Fellow at the Mathematical Biosciences Institute at The Ohio State University, a Postdoctoral… Continue Reading →<\/a><\/p>\n","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-28","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/28","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=28"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/28\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=28"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":2,"date":"2019-03-05T18:02:36","date_gmt":"2019-03-05T18:02:36","guid":{"rendered":"http:\/\/edspace.american.edu\/chifman\/?page_id=2"},"modified":"2021-06-11T03:44:54","modified_gmt":"2021-06-11T03:44:54","slug":"contact","status":"publish","type":"page","link":"https:\/\/edspace.american.edu\/chifman\/contact\/","title":{"rendered":"Contact"},"content":{"rendered":"

      Julia Chifman<\/h3>\n

      \"\"<\/h3>\n

      American University
      \nCAS – Math and Statistics
      \nDon Myers Building – 208D
      \n4400 Massachusetts Avenue NW
      \nWashington, DC 20016-8050<\/p>\n

      \n

       <\/p>\n","protected":false},"excerpt":{"rendered":"

      Julia Chifman American University CAS – Math and Statistics Don Myers Building – 208D 4400 Massachusetts Avenue NW Washington, DC 20016-8050  <\/p>\n","protected":false},"author":2798,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-2","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/2","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/users\/2798"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/comments?post=2"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/pages\/2\/revisions"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/chifman\/wp-json\/wp\/v2\/media?parent=2"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}]