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Rendong Yang

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Articles 51
Citations 1816
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Recent Articles
1.
Schafer R, Yang R
bioRxiv . 2025 Mar; PMID: 40060661
Efficiently querying genomic intervals is fundamental to modern bioinformatics, enabling researchers to extract and analyze specific regions from large genomic datasets. While various tools have been developed for this purpose,...
2.
Sharifi M, Feng E, Rydzewski N, Taylor A, Sperger J, Shi Y, et al.
Mol Oncol . 2025 Feb; PMID: 39985777
Metastatic castration-resistant prostate cancer (mCRPC) is a heterogeneous disease. Several studies have identified transcriptional subtypes of mCRPC, but comprehensive analysis of prognostic gene expression pathways has been limited. Therefore, we...
3.
Meng Q, Shen J, Ren Y, Liu Q, Wang R, Li Q, et al.
Sci Adv . 2024 Nov; 10(48):eadl2804. PMID: 39602541
DNA repair dysregulation is a key driver of cancer development. Understanding the molecular mechanisms underlying DNA repair dysregulation in cancer cells is crucial for cancer development and therapies. Here, we...
4.
Li Y, Wang T, Guo Q, Ren Y, Lu X, Cao Q, et al.
bioRxiv . 2024 Nov; PMID: 39484530
Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) can significantly distort transcriptome analyses, yet their detection and removal remain challenging due to limitations in existing basecalling models. We present DeepChopper,...
5.
Lawrence J, Seelig D, Demos-Davies K, Ferreira C, Ren Y, Wang L, et al.
Sci Rep . 2024 Oct; 14(1):24819. PMID: 39438583
Over half of all people diagnosed with cancer receive radiation therapy. Moderate to severe radiation dermatitis occurs in most human radiation patients, causing pain, aesthetic distress, and a negative impact...
6.
Pant K, Richard S, Peixoto E, Baral S, Yang R, Ren Y, et al.
Hepatology . 2024 Aug; PMID: 39186465
Background And Aims: The primary cilium, an organelle that protrudes from cell surfaces, is essential for sensing extracellular signals. With disturbed cellular communication and chronic liver pathologies, this organelle's dysfunctions...
7.
Wang S, Stroup E, Wang T, Yang R, Ji Z
Brief Bioinform . 2024 Jul; 25(4). PMID: 39041189
Studies have identified genes and molecular pathways regulating cancer metastasis. However, it remains largely unknown whether metastatic potentials of cancer cells from different lineage types are driven by the same...
8.
Li Y, Yang R
BMC Bioinformatics . 2024 Jun; 25(1):219. PMID: 38898394
Background: With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a...
9.
Schafer R, Guo Q, Yang R
Bioinformatics . 2023 Oct; 39(11). PMID: 37882750
Motivation: Neoantigens, tumor-specific protein fragments, are invaluable in cancer immunotherapy due to their ability to serve as targets for the immune system. Computational prediction of these neoantigens from sequencing data...
10.
Li Y, Yang R
bioRxiv . 2023 Aug; PMID: 37577677
We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive Application Programming Interface (API) design, allowing...