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Books and Theses
- 2020
[b1]Fatemeh Almodaresi:
Algorithms and Data Structures for Indexing, Querying, and Analyzing Large Collections of sequencing Data in the presence or Absence of a Reference. University of Maryland, College Park, MD, USA, 2020
Journal Articles
- 2022
- [j6]Fatemeh Almodaresi
, Jamshed Khan, Sergey Madaminov, Michael Ferdman, Rob Johnson, Prashant Pandey, Rob Patro:
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation. Bioinform. 38(12): 3155-3163 (2022) - 2021
- [j5]Fatemeh Almodaresi, Mohsen Zakeri, Rob Patro:
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index. Bioinform. 37(22): 4048-4055 (2021) - 2020
- [j4]Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro:
An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using de Bruijn Graph Search. J. Comput. Biol. 27(4): 485-499 (2020) - 2018
- [j3]Fatemeh Almodaresi, Hirak Sarkar, Avi Srivastava, Rob Patro:
A space and time-efficient index for the compacted colored de Bruijn graph. Bioinform. 34(13): i169-i177 (2018) - [j2]Laraib Malik, Fatemeh Almodaresi, Rob Patro:
Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis. Bioinform. 34(19): 3265-3272 (2018) - 2017
- [j1]Mohsen Zakeri, Avi Srivastava, Fatemeh Almodaresi, Rob Patro:
Improved data-driven likelihood factorizations for transcript abundance estimation. Bioinform. 33(14): i142-i151 (2017)
Conference and Workshop Papers
- 2019
- [c4]Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro:
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search. RECOMB 2019: 1-18 - 2018
- [c3]Prashant Pandey, Fatemeh Almodaresi, Michael A. Bender, Michael Ferdman, Rob Johnson, Rob Patro:
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index. RECOMB 2018: 271-273 - 2017
- [c2]Fatemeh Almodaresi, Lyle H. Ungar, Vivek Kulkarni, Mohsen Zakeri, Salvatore Giorgi, H. Andrew Schwartz:
On the Distribution of Lexical Features at Multiple Levels of Analysis. ACL (2) 2017: 79-84 - [c1]Fatemeh Almodaresi, Prashant Pandey, Rob Patro:
Rainbowfish: A Succinct Colored de Bruijn Graph Representation. WABI 2017: 18:1-18:15
Coauthor Index
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