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Avi Srivastava, Ph.D.
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Wistar Institute Assistant Professor of Genetics
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Department: Genetics
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Graduate Group Affiliations
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Contact information
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3601 Spruce St. Rm 218-E
33 Philadelphia, PA
Philadelphia, PA 19104
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33 Philadelphia, PA
Philadelphia, PA 19104
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Office: 2158983995
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Email:
asrivastava@wistar.org
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asrivastava@wistar.org
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Publications
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Education:
21 a Ph.D. 22 (Computational Biology) c
2f Stony Brook University, 2019.
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Permanent link21 a Ph.D. 22 (Computational Biology) c
2f Stony Brook University, 2019.
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15e Our lab focuses on research in three key areas. (1) we design innovative single-cell technologies to explore cellular heterogeneity. (2) we develop high-throughput probabilistic models to quantify single-cell measurements accurately. (3) we apply novel methods to study alternative splicing and chromatin dynamics in hematopoietic disruption.
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11 Keywords:
6b Single-cell Biology, Computational Biology, Alternative splicing, Chromatin dynamics, Hematopoiesis
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43 Rotation Projects: Please get in touch with Avi for details.
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Description of Research Expertise
23 Research Interest:15e Our lab focuses on research in three key areas. (1) we design innovative single-cell technologies to explore cellular heterogeneity. (2) we develop high-throughput probabilistic models to quantify single-cell measurements accurately. (3) we apply novel methods to study alternative splicing and chromatin dynamics in hematopoietic disruption.
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6b Single-cell Biology, Computational Biology, Alternative splicing, Chromatin dynamics, Hematopoiesis
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43 Rotation Projects: Please get in touch with Avi for details.
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141 Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F; Single-cell Best Practices Consortium; Schiller HB, Theis FJ.: Best practices for single-cell analysis across modalities. Nat Rev Genet 2023.
ff Zhang B, Srivastava A, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R.: Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. Nat Biotechnol 2022.
f8 He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R.: Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 2022.
f3 Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI.: Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics 37: 1699-1707, Jul 2021.
1a9 Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R.: Integrated analysis of multimodal single-cell data. Cell 184: 3573-3587, Jun 2021.
c3 Stuart T, Srivastava A, Madad S, Lareau CA, Satija R.: Single-cell chromatin state analysis with Signac. Nat Methods 2021.
118 Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R.: Alignment and mapping methodology influence transcript abundance estimation. Genome Biol 21: 239, Sep 2020.
e8 Zhu A, Srivastava A, Ibrahim JG, Patro R, Love MI.: Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Res 47: e105, Oct 2019.
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Selected Publications
130 Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R.: Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat Biotechnol 2024.141 Heumos L, Schaar AC, Lance C, Litinetskaya A, Drost F, Zappia L, Lücken MD, Strobl DC, Henao J, Curion F; Single-cell Best Practices Consortium; Schiller HB, Theis FJ.: Best practices for single-cell analysis across modalities. Nat Rev Genet 2023.
ff Zhang B, Srivastava A, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R.: Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. Nat Biotechnol 2022.
f8 He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R.: Alevin-fry unlocks rapid, accurate and memory-frugal quantification of single-cell RNA-seq data. Nat Methods 2022.
f3 Van Buren S, Sarkar H, Srivastava A, Rashid NU, Patro R, Love MI.: Compression of quantification uncertainty for scRNA-seq counts. Bioinformatics 37: 1699-1707, Jul 2021.
1a9 Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R.: Integrated analysis of multimodal single-cell data. Cell 184: 3573-3587, Jun 2021.
c3 Stuart T, Srivastava A, Madad S, Lareau CA, Satija R.: Single-cell chromatin state analysis with Signac. Nat Methods 2021.
118 Srivastava A, Malik L, Sarkar H, Zakeri M, Almodaresi F, Soneson C, Love MI, Kingsford C, Patro R.: Alignment and mapping methodology influence transcript abundance estimation. Genome Biol 21: 239, Sep 2020.
e8 Zhu A, Srivastava A, Ibrahim JG, Patro R, Love MI.: Nonparametric expression analysis using inferential replicate counts. Nucleic Acids Res 47: e105, Oct 2019.
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