Fatemeh Almodaresi
Fatemeh Almodaresi
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Cited by
Cited by
Alignment and mapping methodology influence transcript abundance estimation
A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ...
Genome biology 21 (1), 1-29, 2020
Mantis: a fast, small, and exact large-scale sequence-search index
P Pandey, F Almodaresi, MA Bender, M Ferdman, R Johnson, R Patro
Cell systems 7 (2), 201-207. e4, 2018
Rainbowfish: a succinct colored de Bruijn graph representation
F Almodaresi, P Pandey, R Patro
bioRxiv, 138016, 2017
A space and time-efficient index for the compacted colored de Bruijn graph
F Almodaresi, H Sarkar, A Srivastava, R Patro
Bioinformatics 34 (13), i169-i177, 2018
An efficient, scalable, and exact representation of high-dimensional color information enabled using de Bruijn graph search
F Almodaresi, P Pandey, M Ferdman, R Johnson, R Patro
Journal of Computational Biology 27 (4), 485-499, 2020
Improved data-driven likelihood factorizations for transcript abundance estimation
M Zakeri, A Srivastava, F Almodaresi, R Patro
Bioinformatics 33 (14), i142-i151, 2017
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
F Almodaresi, M Zakeri, R Patro
Bioinformatics 37 (22), 4048-4055, 2021
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis
L Malik, F Almodaresi, R Patro
Bioinformatics 34 (19), 3265-3272, 2018
On the distribution of lexical features at multiple levels of analysis
F Almodaresi, L Ungar, V Kulkarni, M Zakeri, S Giorgi, HA Schwartz
Proceedings of the 55th Annual Meeting of the Association for Computational …, 2017
An incrementally updatable and scalable system for large-scale sequence search using the Bentley–Saxe transformation
F Almodaresi, J Khan, S Madaminov, M Ferdman, R Johnson, P Pandey, ...
Bioinformatics 38 (12), 3155-3163, 2022
AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite
G Skoufos, F Almodaresi, M Zakeri, JN Paulson, R Patro, ...
Genome biology 23 (1), 1-27, 2022
17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
F Almodaresi, P Pandey, R Patro
Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik, 88, 15, 2017
Algorithms and Data Structures for Indexing, Querying, and Analyzing Large Collections of Sequencing Data in the Presence or Absence of a Reference
F Almodaresi
University of Maryland, College Park, 2020
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Articles 1–13