| Best practices for single-cell analysis across modalities L Heumos, AC Schaar, C Lance, A Litinetskaya, F Drost, L Zappia, ... Nature Reviews Genetics 24 (8), 550-572, 2023 | 597 | 2023 |
| 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 | 185 | 2020 |
| RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes A Srivastava, H Sarkar, N Gupta, R Patro Bioinformatics 32 (12), i192-i200, 2016 | 142 | 2016 |
| Dissecting the immune suppressive human prostate tumor microenvironment via integrated single-cell and spatial transcriptomic analyses T Hirz, S Mei, H Sarkar, Y Kfoury, S Wu, BM Verhoeven, AO Subtelny, ... Nature communications 14 (1), 663, 2023 | 111 | 2023 |
| 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 | 97 | 2018 |
| Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes T Gao, R Soldatov, H Sarkar, A Kurkiewicz, E Biederstedt, PR Loh, ... Nature Biotechnology 41 (3), 417-426, 2023 | 96 | 2023 |
| Epigenetic regulation during cancer transitions across 11 tumour types NV Terekhanova, A Karpova, WW Liang, A Strzalkowski, S Chen, Y Li, ... Nature 623 (7986), 432-441, 2023 | 75 | 2023 |
| 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 | 75 | 2022 |
| Voronoi game on graphs S Bandyapadhyay, A Banik, S Das, H Sarkar Theoretical Computer Science 562, 270-282, 2015 | 52 | 2015 |
| 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 |
| A Bayesian framework for inter-cellular information sharing improves dscRNA-seq quantification A Srivastava, L Malik, H Sarkar, R Patro Bioinformatics 36 (Supplement_1), i292-i299, 2020 | 22 | 2020 |
| Minnow: a principled framework for rapid simulation of dscRNA-seq data at the read level H Sarkar, A Srivastava, R Patro Bioinformatics 35 (14), i136-i144, 2019 | 20 | 2019 |
| Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets W Mu, H Sarkar, A Srivastava, K Choi, R Patro, MI Love Bioinformatics 38 (10), 2773-2780, 2022 | 17 | 2022 |
| Single-cell analysis of immune and stroma cell remodeling in clear cell renal cell carcinoma primary tumors and bone metastatic lesions S Mei, AM Alchahin, I Tsea, Y Kfoury, T Hirz, NE Jeffries, T Zhao, Y Xu, ... Genome Medicine 16 (1), 1, 2024 | 15 | 2024 |
| Terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data H Sarkar, A Srivastava, HC Bravo, MI Love, R Patro Bioinformatics 36 (Supplement_1), i102-i110, 2020 | 14 | 2020 |
| Accurate, fast and lightweight clustering of de novo transcriptomes using fragment equivalence classes A Srivastava, H Sarkar, L Malik, R Patro arXiv preprint arXiv:1604.03250, 2016 | 13 | 2016 |
| Mapping the topography of spatial gene expression with interpretable deep learning U Chitra, BJ Arnold, H Sarkar, K Sanno, C Ma, S Lopez-Darwin, ... Nature Methods, 1-12, 2025 | 12 | 2025 |
| Social media attributions in the context of water crisis R Sarkar, H Sarkar, S Mahinder, AR KhudaBukhsh arXiv preprint arXiv:2001.01697, 2020 | 12 | 2020 |
| Defining and benchmarking open problems in single-cell analysis MD Luecken, S Gigante, DB Burkhardt, R Cannoodt, DC Strobl, ... Research Square, rs. 3. rs-4181617, 2024 | 10 | 2024 |
| Single-cell analyses of metastatic bone marrow in human neuroblastoma reveals microenvironmental remodeling and metastatic signature S Mei, AM Alchahin, BT Embaie, IM Gavriliuc, BM Verhoeven, T Zhao, X Li, ... JCI insight 9 (6), e173337, 2024 | 6 | 2024 |
Rob PatroAssociate Professor, Department of Computer Science, University of MarylandEmail verificata su cs.umd.edu