| Alignment and mapping methodology influence transcript abundance estimation A Srivastava, L Malik, H Sarkar, M Zakeri, F Almodaresi, C Soneson, ... Genome biology 21, 1-29, 2020 | 157 | 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 | 118 | 2018 |
| 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 | 91 | 2018 |
| Rainbowfish: a succinct colored de Bruijn graph representation F Almodaresi, P Pandey, R Patro bioRxiv, 138016, 2017 | 80 | 2017 |
| 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 | 47 | 2020 |
| PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index F Almodaresi, M Zakeri, R Patro Bioinformatics 37 (22), 4048-4055, 2021 | 34 | 2021 |
| Improved data-driven likelihood factorizations for transcript abundance estimation M Zakeri, A Srivastava, F Almodaresi, R Patro Bioinformatics 33 (14), i142-i151, 2017 | 33 | 2017 |
| Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis L Malik, F Almodaresi, R Patro Bioinformatics 34 (19), 3265-3272, 2018 | 17 | 2018 |
| AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite G Skoufos, F Almodaresi, M Zakeri, JN Paulson, R Patro, ... Genome biology 23 (1), 39, 2022 | 15 | 2022 |
| 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 | 15* | 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 | 13* | 2022 |
| 17th International Workshop on Algorithms in Bioinformatics (WABI 2017) B Alipanahi, L Salmela, SJ Puglisi, M Muggli, C Boucher, MS Bayzid, ... Schloss Dagstuhl-Leibniz-Zentrum für Informatik GmbH, 2017 | 6 | 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 | | 2020 |
Rob PatroAssociate Professor, Department of Computer Science, University of MarylandVerified email at cs.umd.edu
