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Nidhi Shah
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Year
Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows
N Shah, MG Nute, T Warnow, M Pop
Bioinformatics 35 (9), 1613-1614, 2019
822019
SeqScreen: accurate and sensitive functional screening of pathogenic sequences via ensemble learning
A Balaji, B Kille, AD Kappell, GD Godbold, M Diep, RAL Elworth, Z Qian, ...
Genome biology 23 (1), 133, 2022
312022
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
N Shah, EK Molloy, M Pop, T Warnow
Bioinformatics 37 (13), 1839-1845, 2021
252021
A critical assessment of gene catalogs for metagenomic analysis
S Commichaux, N Shah, J Ghurye, A Stoppel, JA Goodheart, GG Luque, ...
Bioinformatics 37 (18), 2848-2857, 2021
212021
Outlier detection in BLAST hits
N Shah, SF Altschul, M Pop
Algorithms for Molecular Biology 13, 1-9, 2018
182018
Embracing ambiguity in the taxonomic classification of microbiome sequencing data
N Shah, JS Meisel, M Pop
Frontiers in Genetics 10, 1022, 2019
122019
Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up …
JS Meisel, DJ Nasko, B Brubach, V Cepeda-Espinoza, J Chopyk, ...
Microbiome 6, 1-10, 2018
122018
SeqScreen: a biocuration platform for robust taxonomic and biological process characterization of nucleic acid sequences of interest
D Albin, D Nasko, RAL Elworth, J Lu, A Balaji, C Diaz, N Shah, J Selengut, ...
2019 IEEE international conference on bioinformatics and biomedicine (BIBM …, 2019
102019
metagenomeFeatures: an R package for working with 16S rRNA reference databases and marker-gene survey feature data
ND Olson, N Shah, J Kancherla, J Wagner, JN Paulson, H Corrada Bravo
Bioinformatics 35 (19), 3870-3872, 2019
102019
Current state of and future opportunities for prediction in microbiome research: report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019
E Sakowski, G Uritskiy, R Cooper, M Gomes, MR McLaren, JS Meisel, ...
Msystems 4 (5), 10.1128/msystems. 00392-19, 2019
92019
Binnacle: using scaffolds to improve the contiguity and quality of metagenomic bins
HS Muralidharan, N Shah, JS Meisel, M Pop
Frontiers in Microbiology 12, 638561, 2021
72021
NCBI’s virus discovery codeathon: building “FIVE”—The Federated Index of Viral Experiments API index
J Martí-Carreras, AR Gener, SD Miller, AF Brito, CE Camacho, R Connor, ...
Viruses 12 (12), 1424, 2020
42020
Data-driven algorithms for characterizing microbial communities
N Shah
University of Maryland, College Park, 2021
2021
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Articles 1–13