Genetic regulatory signatures underlying islet gene expression and type 2 diabetes A Varshney, LJ Scott, RP Welch, MR Erdos, PS Chines, N Narisu, ... Proceedings of the National Academy of Sciences 114 (9), 2301-2306, 2017 | 201 | 2017 |
Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D A Viñuela, A Varshney, M van de Bunt, RB Prasad, O Asplund, A Bennett, ... Nature communications 11 (1), 4912, 2020 | 102 | 2020 |
Glycosylation of plasma IgG in colorectal cancer prognosis E Theodoratou, K Thaçi, F Agakov, MN Timofeeva, J Štambuk, ... Scientific reports 6 (1), 28098, 2016 | 98 | 2016 |
Multiomic profiling identifies cis-regulatory networks underlying human pancreatic β cell identity and function N Lawlor, EJ Marquez, P Orchard, N Narisu, MS Shamim, A Thibodeau, ... Cell reports 26 (3), 788-801. e6, 2019 | 71 | 2019 |
Quantification, dynamic visualization, and validation of bias in ATAC-seq data with ataqv P Orchard, Y Kyono, J Hensley, JO Kitzman, SCJ Parker Cell systems 10 (3), 298-306. e4, 2020 | 63 | 2020 |
Genome-wide association study of response to methotrexate in early rheumatoid arthritis patients JC Taylor, T Bongartz, J Massey, B Mifsud, A Spiliopoulou, IC Scott, ... The pharmacogenomics journal 18 (4), 528-538, 2018 | 54 | 2018 |
Improving prediction of risk of hospital admission in chronic obstructive pulmonary disease: application of machine learning to telemonitoring data P Orchard, A Agakova, H Pinnock, CD Burton, C Sarran, F Agakov, ... Journal of medical Internet research 20 (9), e263, 2018 | 45 | 2018 |
GeneImp: fast imputation to large reference panels using genotype likelihoods from ultralow coverage sequencing A Spiliopoulou, M Colombo, P Orchard, F Agakov, P McKeigue Genetics 206 (1), 91-104, 2017 | 38 | 2017 |
Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits P Orchard, N Manickam, C Ventresca, S Vadlamudi, A Varshney, V Rai, ... Genome Research 31 (12), 2258-2275, 2021 | 30 | 2021 |
Genetic effects on liver chromatin accessibility identify disease regulatory variants KW Currin, MR Erdos, N Narisu, V Rai, S Vadlamudi, HJ Perrin, JR Idol, ... The American Journal of Human Genetics 108 (7), 1169-1189, 2021 | 28 | 2021 |
Chromatin information content landscapes inform transcription factor and DNA interactions R D’Oliveira Albanus, Y Kyono, J Hensley, A Varshney, P Orchard, ... Nature Communications 12 (1), 1307, 2021 | 25 | 2021 |
BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning T Liu, L Mi, J Xiong, P Orchard, Q Yu, L Yu, XY Zhao, ZX Meng, ... Nature Communications 11 (1), 2379, 2020 | 23 | 2020 |
Influence of genetic variants on gene expression in human pancreatic islets–implications for type 2 diabetes A Viñuela, A Varshney, M van de Bunt, RB Prasad, O Asplund, A Bennett, ... BioRxiv, 655670, 2019 | 17 | 2019 |
Cell specificity of human regulatory annotations and their genetic effects on gene expression A Varshney, H VanRenterghem, P Orchard, AP Boyle, ML Stitzel, D Ucar, ... Genetics 211 (2), 549-562, 2019 | 17 | 2019 |
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data T Qin, C Lee, S Li, RG Cavalcante, P Orchard, H Yao, H Zhang, S Wang, ... Genome Biology 23 (1), 105, 2022 | 12 | 2022 |
Bayesian inference in sparse gaussian graphical models P Orchard, F Agakov, A Storkey arXiv preprint arXiv:1309.7311, 2013 | 12 | 2013 |
Genome-wide chromatin accessibility and transcriptome profiling show minimal epigenome changes and coordinated transcriptional dysregulation of hedgehog signaling in Danforth’s … P Orchard, JS White, PE Thomas, A Mychalowych, A Kiseleva, J Hensley, ... Human Molecular Genetics 28 (5), 736-750, 2019 | 11 | 2019 |
Discriminative mixtures of sparse latent fields for risk management F Agakov, P Orchard, A Storkey Artificial Intelligence and Statistics, 10-18, 2012 | 11 | 2012 |
A transcription start site map in human pancreatic islets reveals functional regulatory signatures A Varshney, Y Kyono, VR Elangovan, C Wang, MR Erdos, N Narisu, ... Diabetes 70 (7), 1581-1591, 2021 | 10 | 2021 |
FixItFelix: improving genomic analysis by fixing reference errors S Behera, J LeFaive, P Orchard, M Mahmoud, LF Paulin, J Farek, ... Genome biology 24 (1), 31, 2023 | 8 | 2023 |