| A robust benchmark for detection of germline large deletions and insertions JM Zook, NF Hansen, ND Olson, L Chapman, JC Mullikin, C Xiao, ... Nature biotechnology 38 (11), 1347-1355, 2020 | 232 | 2020 |
| Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens Y Wang, N Ghaffari, CD Johnson, UM Braga-Neto, H Wang, R Chen, ... BMC bioinformatics 12, 1-7, 2011 | 157 | 2011 |
| Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture N Ghaffari, A Sanchez-Flores, R Doan, KD Garcia-Orozco, PL Chen, ... Scientific reports 4 (1), 7081, 2014 | 106 | 2014 |
| Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture CD Johnson, JS Carrasco, A Ochoa-Leyva, D Ryan, SV Dindot, ... Nature Publishing Group, 2014 | 106* | 2014 |
| Tissue-specific BMAL1 cistromes reveal that rhythmic transcription is associated with rhythmic enhancer–enhancer interactions JR Beytebiere, AJ Trott, BJ Greenwell, CA Osborne, H Vitet, J Spence, ... Genes & development 33 (5-6), 294-309, 2019 | 99 | 2019 |
| Whole-genome sequencing and genetic variant analysis of a Quarter Horse mare R Doan, ND Cohen, J Sawyer, N Ghaffari, CD Johnson, SV Dindot BMC genomics 13, 1-12, 2012 | 90 | 2012 |
| A robust benchmark for germline structural variant detection JM Zook, NF Hansen, ND Olson, LM Chapman, JC Mullikin, C Xiao, ... BioRxiv, 664623, 2019 | 64 | 2019 |
| Intervention in gene regulatory networks via greedy control policies based on long-run behavior X Qian, I Ivanov, N Ghaffari, ER Dougherty BMC systems biology 3 (1), 1-16, 2009 | 52 | 2009 |
| Modeling the next generation sequencing sample processing pipeline for the purposes of classification N Ghaffari, MR Yousefi, CD Johnson, I Ivanov, ER Dougherty BMC bioinformatics 14, 1-14, 2013 | 42 | 2013 |
| A Colletotrichum graminicola mutant deficient in the establishment of biotrophy reveals early transcriptional events in the maize anthracnose disease interaction MF Torres, N Ghaffari, EAS Buiate, N Moore, S Schwartz, CD Johnson, ... BMC genomics 17, 1-24, 2016 | 35 | 2016 |
| State reduction for network intervention in probabilistic Boolean networks X Qian, N Ghaffari, I Ivanov, ER Dougherty Bioinformatics 26 (24), 3098-3104, 2010 | 35 | 2010 |
| A CoD-based reduction algorithm for designing stationary control policies on Boolean networks N Ghaffari, I Ivanov, X Qian, ER Dougherty Bioinformatics 26 (12), 1556-1563, 2010 | 35 | 2010 |
| The Pacific Biosciences de novo assembled genome dataset from a parthenogenetic New Zealand wild population of the longhorned tick, Haemaphysalis longicornis Neumann, 1901 FD Guerrero, KG Bendele, N Ghaffari, J Guhlin, KR Gedye, KE Lawrence, ... Data in brief 27, 104602, 2019 | 18 | 2019 |
| Selection policy-induced reduction mappings for Boolean networks I Ivanov, P Simeonov, N Ghaffari, X Qian, ER Dougherty IEEE Transactions on Signal Processing 58 (9), 4871-4882, 2010 | 18 | 2010 |
| Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning C Harris, N Ghaffari BMC genomics 9 (2), 1-6, 2008 | 16 | 2008 |
| Evaluating active learning approaches for teaching intermediate programming at an early undergraduate level DK Chakravorty, M Pennings, H Liu, Z Wei, DM Rodriguez, LT Jordan, ... The Journal of Computational Science Education 10 (1), 2019 | 10* | 2019 |
| Identifying the most significant genes from gene expression profiles for sample classification H Al-Mubaid, N Ghaffari 2006 IEEE International Conference on Granular Computing, 655-658, 2006 | 10 | 2006 |
| A CoD-based stationary control policy for intervening in large gene regulatory networks N Ghaffari, I Ivanov, X Qian, ER Dougherty BMC bioinformatics 12 (10), 1-14, 2011 | 7 | 2011 |
| Effectively Extending Computational Training Using Informal Means at Larger Institutions SDL Dhruva K. Chakravorty, Marinus "Maikel" Pennings, Honggao Liu, Zengyu ... Journal of Computational Science Education 10 (1), 40-47, 2019 | 6 | 2019 |
| Examining De Novo transcriptome assemblies via a quality assessment pipeline N Ghaffari, OA Arshad, H Jeong, J Thiltges, MF Criscitiello, BJ Yoon, ... IEEE/ACM Transactions on Computational Biology and Bioinformatics 15 (2 …, 2015 | 6 | 2015 |
