Noushin Ghaffari
Noushin Ghaffari
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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
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
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
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
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
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
A robust benchmark for germline structural variant detection
JM Zook, NF Hansen, ND Olson, LM Chapman, JC Mullikin, C Xiao, ...
BioRxiv, 664623, 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
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
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
State reduction for network intervention in probabilistic Boolean networks
X Qian, N Ghaffari, I Ivanov, ER Dougherty
Bioinformatics 26 (24), 3098-3104, 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
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
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
Biomarker discovery across annotated and unannotated microarray datasets using semi-supervised learning
C Harris, N Ghaffari
BMC genomics 9 (2), 1-6, 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
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
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
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
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
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