User profiles for J. Chifman
Julia ChifmanAssistant 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 …
high levels of iron are detrimental and contribute to a wide range of diseases. Recent …
Quartet inference from SNP data under the coalescent model
… 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 …
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 …
… 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 . …
… 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 …
for researchers studying speciation and phylogeography. Many methods for hybridization …
Immunogenic subtypes of breast cancer delineated by gene classifiers of immune responsiveness
… 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 …
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
… 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 …
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 …
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
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 …
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 …
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
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 …
that there is interdependence between excess iron and increased cancer incidence and …