Accès ouvert
2026
article
OpenAlex
Jiwoong Kim, Shuheng Gan, Harish Jawahar, Ruheng Wang et autres
Background/Objectives: Oxford Nanopore sequencing produces long reads quickly, but most functional profiling tools were developed for short reads or rely on assembly pipelines that are computationally costly and sensitive to long-read error rates. We present NanoPrism, a taxonomy-guided pipeline for rapid functional …
us
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Accès ouvert
2026
article
OpenAlex
Sen Yang, Shidan Wang, Yiqing Wang, Ruichen Rong et autres
Advancements in multi-omics research have demonstrated the potential of integrating human microbiome and metabolomics data to better understand physiological processes and improve prediction accuracy in studies of human health. While conventional models utilizing single-omics data provide valuable perspectives, they often fail to …
us, mm
(code pays fourni par la source)
Accès ouvert
2026
preprint
OpenAlex
Wenling Li, Christina Zarek, Hesuiyuan Wang, Shuheng Gan et autres
Gut microbiota are critical determinants of effective immune checkpoint therapy (ICT), yet the microbial mediators and host mechanisms that enhance antitumor immunity remain poorly understood. Here, we identify the microbiota-derived bile acid taurodeoxycholic acid (TDCA) as a metabolite associated with immune checkpoint …
us
(code pays fourni par la source)
Accès ouvert
2026
preprint
OpenAlex
Jingwei Huang, Kuroush Nezafati, Zhikai Chi, Ruichen Rong et autres
Extracting structured information from clinical notes requires navigating a dense web of interdependent variables where the value of one attribute logically constrains others. Existing Large Language Model (LLM)-based extraction pipelines often struggle to capture these dependencies, leading to clinically inconsistent outputs. We …
Accès ouvert
2026
preprint
OpenAlex
Jingwei Huang, Kuroush Nezafati, Zhikai Chi, Ruichen Rong et autres
Extracting structured information from clinical notes requires navigating a dense web of interdependent variables where the value of one attribute logically constrains others. Existing Large Language Model (LLM)-based extraction pipelines often struggle to capture these dependencies, leading to clinically inconsistent outputs. We …
us
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Danni Luo, Sophie Robertson, Yuanchun Zhan, Ruichen Rong et autres
BACKGROUND: Spatial transcriptomics (ST) enables a high-resolution interrogation of molecular characteristics within specific spatial contexts and tissue morphology. Despite its potential, visualization of ST data is a challenging task due to the complexities in handling, sharing, and visualizing large image datasets together …
us
(code pays fourni par la source)
Accès ouvert
2026
article
OpenAlex
Qiwei Li, Kevin C. Lutz, Shuang Jiang, Andrew Y. Koh et autres
Colorectal cancer (CRC) is a major cause of morbidity and mortality globally. CRC survival is highly dependent upon the stage of disease at diagnosis. Reductions in mortality can be achieved through the detection and treatment of early-stage CRC patients. Optical colonoscopy, which …
us
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Accès ouvert
2025
article
OpenAlex
Katherine A. Stumpf, Miranda Green, Xinying Niu, Dongmei Lu et autres
Background/Objectives: Preterm infants often require increased caloric intake to maintain appropriate growth while in the neonatal intensive care unit (NICU). Emerging evidence suggests that alterations of the gut microbiome may play a role in infant and childhood growth patterns. The fecal microbiome …
us, ca
(code pays fourni par la source)
Accès ouvert
2025
preprint
OpenAlex
Jake Lichterman, Tarun Srinivasan, Ruheng Wang, Chaitanya Dende et autres
Abstract Circadian clocks regulate immunity, yet how they shape the tumor immune microenvironment and influence cancer immunotherapy remains unclear. Here, we show that tumor immune infiltration and immune checkpoint inhibitor efficacy vary by time of day in mice, driven by intrinsic clocks …
us
(code pays fourni par la source)
Accès ouvert
2025
conference-abstract
OpenAlex
Jake Lichterman, Tarun Srinivasan, Ruheng Wang, Chaitanya Dende et autres
Background Immune checkpoint inhibitor therapy (ICT), targeting CTLA-4 and/or PD-1, can induce durable remissions in previously incurable cancers. However, many patients remain refractory or develop resistance. 1–3 The tumor immune microenvironment is a critical determinant of ICT response.4–6 Recent clinical studies suggest …
us
(code pays fourni par la source)
Accès ouvert
2025
article
OpenAlex
Mingyao Pan, Yuhao Tan, Yizhou Tracy Wang, Jing Hu et autres
The interaction between human leukocyte antigens (HLAs) and T cell receptor (TCR) is essential for adaptive immune recognition. While it is known that one TCR can map to multiple HLA alleles, the extent of this cross-reactivity remains poorly understood. Here, we introduce …
us
(code pays fourni par la source)
Accès ouvert
2025
preprint
OpenAlex
Chachrit Khunsriraksakul, Fan Zhang, Lida Wang, Siyuan Chen et autres
Abstract Protein quantitative trait loci (pQTLs) provide insight into the genetic regulation of protein expression and disease biology. We performed a large-scale cross-platform meta-analysis of plasma proteomics, integrating data from over 90,000 individuals across Olink and SomaScan platforms. This effort identified >30,000 …
us
(code pays fourni par la source)