| 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 | 137 | 2020 |
| Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data D He, M Zakeri, H Sarkar, C Soneson, A Srivastava, R Patro Nature Methods 19 (3), 316-322, 2022 | 42 | 2022 |
| Improved data-driven likelihood factorizations for transcript abundance estimation M Zakeri, A Srivastava, F Almodaresi, R Patro Bioinformatics 33 (14), i142-i151, 2017 | 31 | 2017 |
| Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification H Sarkar, M Zakeri, L Malik, R Patro Proceedings of the 2018 ACM International Conference on Bioinformatics …, 2018 | 26 | 2018 |
| PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index F Almodaresi, M Zakeri, R Patro Bioinformatics 37 (22), 4048-4055, 2021 | 25 | 2021 |
| 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 | 12* | 2017 |
| 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 | 8 | 2022 |
| A like-for-like comparison of lightweight-mapping pipelines for single-cell RNA-seq data pre-processing M Zakeri, A Srivastava, H Sarkar, R Patro bioRxiv, 2021.02. 10.430656, 2021 | 4 | 2021 |
| Sigmoni: classification of nanopore signal with a compressed pangenome index VS Shivakumar, OY Ahmed, S Kovaka, M Zakeri, B Langmead bioRxiv, 2023 | 3 | 2023 |
| SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty EY Wu, NP Singh, K Choi, M Zakeri, M Vincent, GA Churchill, ... Genome biology 24 (1), 165, 2023 | 3 | 2023 |
| Accounting for fragments of unexpected origin improves transcript quantification in RNA-seq simulations focused on increased realism A Srivastava, M Zakeri, H Sarkar, C Soneson, C Kingsford, R Patro bioRxiv, 2021.01. 17.426996, 2021 | 2 | 2021 |
| r-indexing without backward searching O Ahmed, A Baláž, NK Brown, L Depuydt, A Goga, A Petescia, M Zakeri, ... arXiv preprint arXiv:2312.01359, 2023 | | 2023 |
| r-indexing without backward searching L Depuydt, O Ahmed, A Baláž, NK Brown, A Goga, A Petescia, M Zakeri, ... arXiv e-prints, arXiv: 2312.01359, 2023 | | 2023 |
| Movi: a fast and cache-efficient full-text pangenome index M Zakeri, NK Brown, OY Ahmed, T Gagie, B Langmead bioRxiv, 2023 | | 2023 |
| Optimizing the Accuracy of Lightweight Methods for Short Read Alignment and Quantification M Zakeri University of Maryland, College Park, 2021 | | 2021 |
Rob PatroAssociate Professor, Department of Computer Science, University of MarylandVerified email at cs.umd.edu
