Shadow enhancers are pervasive features of developmental regulatory networks E Cannavò, P Khoueiry, DA Garfield, P Geeleher, T Zichner, ... Current Biology 26 (1), 38-51, 2016 | 263 | 2016 |
Rules governing selective protein carbonylation E Maisonneuve, A Ducret, P Khoueiry, S Lignon, S Longhi, E Talla, ... PloS one 4 (10), e7269, 2009 | 176 | 2009 |
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program O Tassy, D Dauga, F Daian, D Sobral, F Robin, P Khoueiry, D Salgado, ... Genome research 20 (10), 1459-1468, 2010 | 128 | 2010 |
Ten simple rules for organizing an unconference A Budd, H Dinkel, M Corpas, JC Fuller, L Rubinat, DP Devos, ... PLoS computational biology 11 (1), e1003905, 2015 | 70 | 2015 |
A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites P Khoueiry, U Rothbächer, Y Ohtsuka, F Daian, E Frangulian, A Roure, ... Current Biology 20 (9), 792-802, 2010 | 60 | 2010 |
Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity P Khoueiry, C Girardot, L Ciglar, PC Peng, EH Gustafson, S Sinha, ... Elife 6, e28440, 2017 | 46 | 2017 |
Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse and relevance for personalized medicine C Dupain, AC Harttrampf, Y Boursin, M Lebeurrier, W Rondof, ... Molecular Therapy 27 (1), 200-218, 2019 | 30 | 2019 |
Biggest challenges in bioinformatics JC Fuller, P Khoueiry, H Dinkel, K Forslund, A Stamatakis, J Barry, A Budd, ... EMBO reports 14 (4), 302-304, 2013 | 23 | 2013 |
A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis MJ Gilchrist, D Sobral, P Khoueiry, F Daian, B Laporte, I Patrushev, ... Developmental Biology 404 (2), 149-163, 2015 | 22 | 2015 |
BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity P Khoueiry, A Ward Gahlawat, M Petretich, AM Michon, D Simola, E Lam, ... Epigenetics & Chromatin 12, 1-18, 2019 | 20 | 2019 |
The Role of Chromatin Accessibility in cis-Regulatory Evolution PC Peng, P Khoueiry, C Girardot, JP Reddington, DA Garfield, ... Genome biology and evolution 11 (7), 1813-1828, 2019 | 20 | 2019 |
The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection J Liu, RR Viales, P Khoueiry, JP Reddington, C Girardot, EEM Furlong, ... Genome research 31 (9), 1573-1581, 2021 | 14 | 2021 |
Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5 H Auger, C Lamy, M Haeussler, P Khoueiry, P Lemaire, JS Joly Developmental biology 329 (2), 364-373, 2009 | 12 | 2009 |
Prognostic significance of O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation and isocitrate dehydrogenase-1 (IDH-1) mutation in glioblastoma multiforme … Z Ayoub, F Geara, M Najjar, Y Comair, N Khoueiry-Zgheib, P Khoueiry, ... Clinical Neurology and Neurosurgery 182, 92-97, 2019 | 4 | 2019 |
Uncovering a novel role of focal adhesion and interferon-gamma in cellular rejection of kidney allografts at single cell resolution A Halawi, AB El Kurdi, KA Vernon, Z Solhjou, JY Choi, AJ Saad, ... Frontiers in Immunology 14, 1139358, 2023 | 2 | 2023 |
TempoMAGE: a deep learning framework that exploits the causal dependency between time-series data to predict histone marks in open chromatin regions at time-points with missing … M Hallal, M Awad, P Khoueiry Bioinformatics 37 (23), 4336-4342, 2021 | 2 | 2021 |
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates A El-Kurdi, GA Khalil, G Khazen, P Khoueiry BMC bioinformatics 21, 1-8, 2020 | 2 | 2020 |
Correlation of genetic alterations by whole-exome sequencing with clinical outcomes of glioblastoma patients from the Lebanese population FS Saadeh, RZ Morsi, A El-Kurdi, G Nemer, R Mahfouz, M Charafeddine, ... Plos one 15 (11), e0242793, 2020 | 2 | 2020 |
Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population P Khoueiry, G Fakhri, R Akel, M El Assaad, R Mahfouz, F Khuri, H Chami, ... Journal of Thoracic Disease 11 (6), 2383, 2019 | 2 | 2019 |
A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements S Idriss, M Hallal, A El-Kurdi, H Zalzali, I El-Rassi, EA Ehli, CM Davis, ... Genome Research 33 (2), 269-282, 2023 | 1 | 2023 |