Avi Srivastava
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Explore the profile of Avi Srivastava including associated specialties, affiliations and a list of published articles.
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21
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Recent Articles
1.
Tiedje V, Vela P, Yang J, Untch B, Boucai L, Stonestrom A, et al.
bioRxiv
. 2024 Oct;
PMID: 39415999
Anaplastic thyroid cancer (ATC) is a clinically aggressive malignancy with a dismal prognosis. Combined BRAF/MEK inhibition offers significant therapeutic benefit in patients with -mutant ATCs. However, relapses are common and...
2.
Hao Y, Stuart T, Kowalski M, Choudhary S, Hoffman P, Hartman A, et al.
Nat Biotechnol
. 2023 May;
42(2):293-304.
PMID: 37231261
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a powerful alternative to unsupervised analysis. However, most reference datasets are constructed from single-cell RNA-sequencing data and cannot be used to...
3.
Mu W, Sarkar H, Srivastava A, Choi K, Patro R, Love M
Bioinformatics
. 2022 May;
38(10):2773-2780.
PMID: 35561168
Motivation: Allelic expression analysis aids in detection of cis-regulatory mechanisms of genetic variation, which produce allelic imbalance (AI) in heterozygotes. Measuring AI in bulk data lacking time or spatial resolution...
4.
Zhang B, Srivastava A, Mimitou E, Stuart T, Raimondi I, Hao Y, et al.
Nat Biotechnol
. 2022 Mar;
40(8):1220-1230.
PMID: 35332340
Technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization, but the sparsity of the measurements and integrating multiple binding maps represent substantial challenges. Here...
5.
He D, Zakeri M, Sarkar H, Soneson C, Srivastava A, Patro R
Nat Methods
. 2022 Mar;
19(3):316-322.
PMID: 35277707
The rapid growth of high-throughput single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies has produced a wealth of data over the past few years. The size, volume and distinctive characteristics...
6.
Stuart T, Srivastava A, Madad S, Lareau C, Satija R
Nat Methods
. 2022 Jan;
19(2):257.
PMID: 34997233
No abstract available.
7.
Stuart T, Srivastava A, Madad S, Lareau C, Satija R
Nat Methods
. 2021 Nov;
18(11):1333-1341.
PMID: 34725479
The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a...
8.
Hao Y, Hao S, Andersen-Nissen E, Mauck 3rd W, Zheng S, Butler A, et al.
Cell
. 2021 Jun;
184(13):3573-3587.e29.
PMID: 34062119
The simultaneous measurement of multiple modalities represents an exciting frontier for single-cell genomics and necessitates computational methods that can define cellular states based on multimodal data. Here, we introduce "weighted-nearest...
9.
Van Buren S, Sarkar H, Srivastava A, Rashid N, Patro R, Love M
Bioinformatics
. 2021 Jan;
37(12):1699-1707.
PMID: 33471073
Motivation: Quantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads...
10.
Soneson C, Srivastava A, Patro R, Stadler M
PLoS Comput Biol
. 2021 Jan;
17(1):e1008585.
PMID: 33428615
Experimental single-cell approaches are becoming widely used for many purposes, including investigation of the dynamic behaviour of developing biological systems. Consequently, a large number of computational methods for extracting dynamic...