Phaedra Agius
Phaedra Agius
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Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
D Betel, A Koppal, P Agius, C Sander, C Leslie
Genome biology 11, 1-14, 2010
Evaluation of methods for modeling transcription factor sequence specificity
MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, TR Riley, ...
Nature biotechnology 31 (2), 126-134, 2013
Immunogenic neoantigens derived from gene fusions stimulate T cell responses
W Yang, KW Lee, RM Srivastava, F Kuo, C Krishna, D Chowell, ...
Nature medicine 25 (5), 767-775, 2019
Sequence and chromatin determinants of cell-type–specific transcription factor binding
A Arvey, P Agius, WS Noble, C Leslie
Genome research 22 (9), 1723-1734, 2012
Identification of three rheumatoid arthritis disease subtypes by machine learning integration of synovial histologic features and RNA sequencing data
DE Orange, P Agius, EF DiCarlo, N Robine, H Geiger, J Szymonifka, ...
Arthritis & Rheumatology 70 (5), 690-701, 2018
Near universal detection of alterations in CTNNB1 and Wnt pathway regulators in desmoid‐type fibromatosis by whole‐exome sequencing and genomic analysis
AM Crago, J Chmielecki, M Rosenberg, R O'Connor, C Byrne, FG Wilder, ...
Genes, Chromosomes and Cancer 54 (10), 606-615, 2015
Mechanical strain enhances extracellular matrix-induced gene focusing and promotes osteogenic differentiation of human mesenchymal stem cells through an extracellular-related …
DF Ward Jr, RM Salasznyk, RF Klees, J Backiel, P Agius, K Bennett, ...
Stem cells and development 16 (3), 467-480, 2007
Inferring transcriptional and microRNA‐mediated regulatory programs in glioblastoma
M Setty, K Helmy, AA Khan, J Silber, A Arvey, F Neezen, P Agius, JT Huse, ...
Molecular systems biology 8 (1), 605, 2012
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
WJ Chung, P Agius, JO Westholm, M Chen, K Okamura, N Robine, ...
Genome research 21 (2), 286-300, 2011
High Resolution Models of Transcription Factor-DNA Affinities Improve In Vitro and In Vivo Binding Predictions
P Agius, A Arvey, W Chang, WS Noble, C Leslie
PLoS computational biology 6 (9), e1000916, 2010
Integrin-α10 dependency identifies RAC and RICTOR as therapeutic targets in high-grade myxofibrosarcoma
T Okada, AY Lee, LX Qin, N Agaram, T Mimae, Y Shen, R O'Connor, ...
Cancer discovery 6 (10), 1148-1165, 2016
Unexpected similarities between C9ORF72 and sporadic forms of ALS/FTD suggest a common disease mechanism
EG Conlon, D Fagegaltier, P Agius, J Davis-Porada, J Gregory, I Hubbard, ...
Elife 7, e37754, 2018
miR-193b–Regulated Signaling Networks Serve as Tumor Suppressors in Liposarcoma and Promote Adipogenesis in Adipose-Derived Stem Cells
YZ Mazzu, Y Hu, RK Soni, KM Mojica, LX Qin, P Agius, ZM Waxman, ...
Cancer research 77 (21), 5728-5740, 2017
Comparing RNA secondary structures using a relaxed base-pair score
P Agius, KP Bennett, M Zuker
RNA 16 (5), 865-878, 2010
Typing Staphylococcus aureus using the spa gene and novel distance measures
P Agius, B Kreiswirth, S Naidich, K Bennett
IEEE/ACM transactions on computational biology and bioinformatics 4 (4), 693-704, 2007
Histologic and transcriptional evidence of subclinical synovial inflammation in patients with rheumatoid arthritis in clinical remission
DE Orange, P Agius, EF DiCarlo, SZ Mirza, T Pannellini, J Szymonifka, ...
Arthritis & Rheumatology 71 (7), 1034-1041, 2019
Machine learning integration of scleroderma histology and gene expression identifies fibroblast polarisation as a hallmark of clinical severity and improvement
K Showalter, R Spiera, C Magro, P Agius, V Martyanov, JM Franks, ...
Annals of the rheumatic diseases 80 (2), 228-237, 2021
Ranking genes by their co‐expression to subsets of pathway members
P Adler, H Peterson, P Agius, J Reimand, J Vilo
Annals of the New York Academy of Sciences 1158 (1), 1-13, 2009
Bayesian unsupervised learning with multiple data types
P Agius, Y Ying, C Campbell
Statistical applications in genetics and molecular biology 8 (1), 2009
Sequencing and curation strategies for identifying candidate glioblastoma treatments
MO Frank, T Koyama, K Rhrissorrakrai, N Robine, F Utro, AK Emde, ...
BMC medical genomics 12, 1-16, 2019
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