Quartet inference from SNP data under the coalescent model J Chifman, L Kubatko Bioinformatics 30 (23), 3317-3324, 2014 | 1073 | 2014 |
Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites J Chifman, L Kubatko Journal of theoretical biology 374, 35-47, 2015 | 261 | 2015 |
HyDe: a Python package for genome-scale hybridization detection PD Blischak, J Chifman, AD Wolfe, LS Kubatko Systematic Biology 67 (5), 821-829, 2018 | 201 | 2018 |
A systems biology approach to iron metabolism J Chifman, R Laubenbacher, SV Torti A Systems Biology Approach to Blood, 201-225, 2014 | 187 | 2014 |
Immunogenic subtypes of breast cancer delineated by gene classifiers of immune responsiveness LD Miller, JA Chou, MA Black, C Print, J Chifman, A Alistar, T Putti, X Zhou, ... Cancer immunology research 4 (7), 600-610, 2016 | 98 | 2016 |
Conservation of immune gene signatures in solid tumors and prognostic implications J Chifman, A Pullikuth, JW Chou, D Bedognetti, LD Miller Bmc Cancer 16, 1-17, 2016 | 72 | 2016 |
An invariants-based method for efficient identification of hybrid species from large-scale genomic data LS Kubatko, J Chifman BMC evolutionary biology 19, 1-13, 2019 | 70 | 2019 |
The core control system of intracellular iron homeostasis: a mathematical model J Chifman, A Kniss, P Neupane, I Williams, B Leung, Z Deng, P Mendes, ... Journal of theoretical biology 300, 91-99, 2012 | 42 | 2012 |
Activated oncogenic pathway modifies iron network in breast epithelial cells: a dynamic modeling perspective J Chifman, S Arat, Z Deng, E Lemler, JC Pino, LA Harris, MA Kochen, ... PLoS computational biology 13 (2), e1005352, 2017 | 26 | 2017 |
Toric Ideals of Phylogenetic Invariants for the General Group-Based Model on Claw Trees K 1,n J Chifman, S Petrović Algebraic Biology: Second International Conference, AB 2007, Castle of …, 2007 | 20 | 2007 |
Bulk and single-cell profiling of breast tumors identifies TREM-1 as a dominant immune suppressive marker associated with poor outcomes AK Pullikuth, ED Routh, KD Zimmerman, J Chifman, JW Chou, MH Soike, ... Frontiers in Oncology 11, 734959, 2021 | 13 | 2021 |
Transcriptomic features of T cell-barren tumors are conserved across diverse tumor types ED Routh, AK Pullikuth, G Jin, J Chifman, JW Chou, RB D'Agostino Jr, ... Frontiers in Immunology 11, 57, 2020 | 10 | 2020 |
Note on direct products of certain classes of finite groups J Chifman Communications in Algebra 37 (5), 1831-1842, 2009 | 7 | 2009 |
Identifiability of speciation times under the multispecies coalescent L Kubatko, A Leonard, J Chifman BioRxiv, 2020.11. 24.396424, 2020 | 6 | 2020 |
A phylogenetic approach to inferring the order in which mutations arise during cancer progression Y Gao, J Gaither, J Chifman, L Kubatko PLOS Computational Biology 18 (12), e1010560, 2022 | 5 | 2022 |
SteadyCellPhenotype: a web-based tool for the modeling of biological networks with ternary logic AC Knapp, L Sordo Vieira, R Laubenbacher, J Chifman Bioinformatics 38 (8), 2369-2370, 2022 | 2 | 2022 |
Immune gene signatures and tumor intrinsic markers delineate novel immunogenic subtypes of breast cancer LD Miller, JW Chou, MA Black, CG Print, E Jimenez, J Chifman, A Alistar, ... Journal for ImmunoTherapy of Cancer 2, 1-3, 2014 | 2 | 2014 |
Assessing how macrophages attain distinct iron handling phenotypes in a tumor via a mathematical model LS Vieira, J Masison, J Adams, S Torti, R Laubenbacher, J Chifman Cancer Research 79 (13_Supplement), 2442-2442, 2019 | 1 | 2019 |
Triggering receptor expressed in myeloid cells 1 (TREM1) is a predictive marker for breast cancer therapeutics AK Pullikuth, J Chifman, ED Routh, J Chou, G Jin, MA Black, LD Miller Cancer Research 78 (13_Supplement), 3791-3791, 2018 | 1 | 2018 |
HyDe: a Python Package for Genome-Scale Hybridization PD BLISCHAK, J CHIFMAN, AD WOLFE, LS KUBATKO | 1 | 2018 |