|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 (8), R90, 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
|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
|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
|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
|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
|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 Comput Biol 6 (9), e1000916, 2010
|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
|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
|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
|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
|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
|Comparing RNA secondary structures using a relaxed base-pair score|
P Agius, KP Bennett, M Zuker
RNA 16 (5), 865-878, 2010
|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
|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
|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), 1-16, 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, 2020