Anupama Jha
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Explore the profile of Anupama Jha including associated specialties, affiliations and a list of published articles.
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19
Citations
284
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Recent Articles
1.
Wu D, Maus N, Jha A, Yang K, Wales-McGrath B, Jewell S, et al.
bioRxiv
. 2025 Feb;
PMID: 39896553
Alternative splicing (AS) of pre-mRNA plays a crucial role in tissue-specific gene regulation, with disease implications due to splicing defects. Predicting and manipulating AS can therefore uncover new regulatory mechanisms...
2.
Wang X, Zhang Y, Ray S, Jha A, Fang T, Hang S, et al.
bioRxiv
. 2025 Jan;
PMID: 39763871
Nuclear DNA is organized into a compact three-dimensional (3D) structure that impacts critical cellular processes. High-throughput chromosome conformation capture (Hi-C) is the most widely used method for measuring 3D genome...
3.
Yang K, Islas N, Jewell S, Wu D, Jha A, Radens C, et al.
Nucleic Acids Res
. 2024 Dec;
53(3).
PMID: 39727154
RNA sequencing (RNA-seq) is widely adopted for transcriptome analysis but has inherent biases that hinder the comprehensive detection and quantification of alternative splicing. To address this, we present an efficient...
4.
Yang K, Islas N, Jewell S, Jha A, Radens C, Pleiss J, et al.
bioRxiv
. 2024 Oct;
PMID: 39386495
RNA-sequencing (RNA-seq) is widely adopted for transcriptome analysis but has inherent biases which hinder the comprehensive detection and quantification of alternative splicing. To address this, we present an efficient targeted...
5.
Jha A, Hristov B, Wang X, Wang S, Greenleaf W, Kundaje A, et al.
bioRxiv
. 2024 Sep;
PMID: 39345598
Three-dimensional nuclear DNA architecture comprises well-studied intra-chromosomal () folding and less characterized inter-chromosomal () interfaces. Current predictive models of 3D genome folding can effectively infer pairwise -chromatin interactions from the...
6.
Fang T, Liu Y, Woicik A, Lu M, Jha A, Wang X, et al.
Bioinformatics
. 2024 Jun;
40(Suppl 1):i471-i480.
PMID: 38940142
Motivation: High-resolution Hi-C contact matrices reveal the detailed three-dimensional architecture of the genome, but high-coverage experimental Hi-C data are expensive to generate. Simultaneously, chromatin structure analyses struggle with extremely sparse...
7.
Jha A, Bohaczuk S, Mao Y, Ranchalis J, Mallory B, Min A, et al.
Genome Res
. 2024 Jun;
34(11):1976-1986.
PMID: 38849157
Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification...
8.
Jha A, Bohaczuk S, Mao Y, Ranchalis J, Mallory B, Min A, et al.
bioRxiv
. 2023 May;
PMID: 37131601
Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification...
9.
Vaquero-Garcia J, Aicher J, Jewell S, Gazzara M, Radens C, Jha A, et al.
Nat Commun
. 2023 Mar;
14(1):1230.
PMID: 36869033
The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and...
10.
Jha A, Quesnel-Vallieres M, Wang D, Thomas-Tikhonenko A, Lynch K, Barash Y
Genome Biol
. 2022 May;
23(1):117.
PMID: 35581644
Background: Cancer is a set of diseases characterized by unchecked cell proliferation and invasion of surrounding tissues. The many genes that have been genetically associated with cancer or shown to...