User profiles for J. Chifman

Julia Chifman

Assistant Professor, Department of Mathematics and Statistics, American University
Verified email at american.edu
Cited by 2077

A systems biology approach to iron metabolism

J Chifman, R Laubenbacher, SV Torti - A Systems Biology Approach to …, 2014 - Springer
Iron is critical to the survival of almost all living organisms. However, inappropriately low or
high levels of iron are detrimental and contribute to a wide range of diseases. Recent …

Quartet inference from SNP data under the coalescent model

J Chifman, L Kubatko - Bioinformatics, 2014 - academic.oup.com
… where p ^ i j k l is the frequency with which we observe the event { X 1 = i , X 2 = j , X 3 = k ,
X 4 = l } in the data where L 1 = { 1 , 2 } and L 2 = { 3 , 4 } ⁠. A key observation is that this can …

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable …

J Chifman, L Kubatko - Journal of theoretical biology, 2015 - Elsevier
… π i Q ij = π j Q ji . The intuition of the model is that a pair of states i and j have the same basic
… by μ l , but the rate of moving to state j depends also on the frequency of state j, given by π j . …

HyDe: a Python package for genome-scale hybridization detection

PD Blischak, J Chifman, AD Wolfe… - Systematic …, 2018 - academic.oup.com
The analysis of hybridization and gene flow among closely related taxa is a common goal
for researchers studying speciation and phylogeography. Many methods for hybridization …

Immunogenic subtypes of breast cancer delineated by gene classifiers of immune responsiveness

LD Miller, JA Chou, MA Black, C Print, J Chifman… - Cancer immunology …, 2016 - AACR
… A–J, Kaplan–Meier plots are shown for each gene marker in IBE and IBD tumor subtypes …
A–J, Kaplan–Meier plots are shown for each gene marker in IBE and IBD tumor subtypes …

[HTML][HTML] Conservation of immune gene signatures in solid tumors and prognostic implications

J Chifman, A Pullikuth, JW Chou, D Bedognetti… - Bmc Cancer, 2016 - Springer
… m represent specific clusters of probe sets for breast, colon, lung, ovarian and prostate
datasets, respectively, then we computed all possible combinations of the following form B i ∩C j

[HTML][HTML] An invariants-based method for efficient identification of hybrid species from large-scale genomic data

LS Kubatko, J Chifman - BMC evolutionary biology, 2019 - Springer
… A full description of the computations required for this model are given in Chifman and
Kubatko (2015) [60], and we do not review them here. Finally, we write the site pattern probability …

[HTML][HTML] Bulk and single-cell profiling of breast tumors identifies TREM-1 as a dominant immune suppressive marker associated with poor outcomes

…, J Chifman, JW Chou, MH Soike, G Jin, J Su… - Frontiers in …, 2021 - frontiersin.org
Background Triggering receptor expressed on myeloid cells (TREM)-1 is a key mediator of
innate immunity previously associated with the severity of inflammatory disorders, and more …

The core control system of intracellular iron homeostasis: a mathematical model

J Chifman, A Kniss, P Neupane, I Williams… - Journal of theoretical …, 2012 - Elsevier
Iron is a metal essential for cellular metabolism. However, excess iron available for reactions
contributes to the formation of dangerous reactive oxygen species, such as the hydroxyl …

[HTML][HTML] Activated oncogenic pathway modifies iron network in breast epithelial cells: a dynamic modeling perspective

J Chifman, S Arat, Z Deng, E Lemler… - PLoS computational …, 2017 - journals.plos.org
Dysregulation of iron metabolism in cancer is well documented and it has been suggested
that there is interdependence between excess iron and increased cancer incidence and …