Li Liu
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View article: ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation
ceQTL: A co-expression QTL model to detect a variant that affects transcription factor binding and its target regulation Open
Expression quantitative trait locus (eQTL) mapping is used to identify a functional link between a genomic variant, such as single nucleotide polymorphism (SNP), and gene expression (often close-by pair for cis-eQTL) by linear regression, …
View article: Discovering Condition-specific Cell Populations via Integrative Clustering of Single-cell Data
Discovering Condition-specific Cell Populations via Integrative Clustering of Single-cell Data Open
We present IN tegrative CLustering Of Single cElls (INCLOSE), a novel computational method that integrates single-cell omics data and sample metadata to identify cell populations. INCLOSE analysis of CITE-seq data of acute myeloid leukemia…
View article: HK2 promotes malignant progression of esophageal squamous carcinoma by mediating VDAC1 resistance to mitochondrial apoptosis
HK2 promotes malignant progression of esophageal squamous carcinoma by mediating VDAC1 resistance to mitochondrial apoptosis Open
Background: Esophageal cancer is becoming increasingly common worldwide, and esophageal squamous cell carcinoma is the most predominant type, for which there is no very effective treatment. Hexokinase 2 (HK2) has carcinogenic effects in a …
View article: Precision Probiotics Regulate Blood Glucose, Cholesterol, Body Fat Percentage, and Weight Under Eight-Week High-Fat Diet
Precision Probiotics Regulate Blood Glucose, Cholesterol, Body Fat Percentage, and Weight Under Eight-Week High-Fat Diet Open
Background/Objectives: Poor glycemic control is reaching an epidemic prevalence globally. It is associated with significantly morbid health concerns including retinopathy, neuropathy, nephropathy, cancer, and cardiovascular disease. Probio…
View article: The mitochondrial genome sequence of tachinid fly, <i>Hemyda hertingi,</i> from China
The mitochondrial genome sequence of tachinid fly, <i>Hemyda hertingi,</i> from China Open
Tachinid flies act as key biological vectors in elucidating plant–insect–microbe dynamic interactions. We report the mitochondrial genome sequence of Hemyda hertingi from China. The mitogenome spans 14,775 base pairs in length, with a GC c…
View article: The regulatory role and mechanism of TGFBI on tregs in the immune microenvironment of clear cell renal cell carcinoma
The regulatory role and mechanism of TGFBI on tregs in the immune microenvironment of clear cell renal cell carcinoma Open
Background: Clear cell renal cell carcinoma (ccRCC) is marked by an immunosuppressive tumor microenvironment (TME) dominated by regulatory T cells (Tregs), which facilitate immune evasion. TGFBI, an extracellular matrix protein induced by …
View article: Country-Specific Estimates of Misclassification Rates of Computer-Coded Verbal Autopsy Algorithms
Country-Specific Estimates of Misclassification Rates of Computer-Coded Verbal Autopsy Algorithms Open
Background Computer-coded verbal autopsy (CCVA) algorithms are commonly used to determine individual causes of death (COD) and population-level cause-specific mortality fractions (CSMF), but frequent COD misclassification leads to biased C…
View article: Single-cell Analysis of Intracellular Transport and Expression of Cell Surface Proteins
Single-cell Analysis of Intracellular Transport and Expression of Cell Surface Proteins Open
Intracellular protein transport (ICT) is a tightly regulated process that orchestrates protein localization and expression, ensuring proper cellular function. Dysregulated ICT can lead to aberrant expression of surface proteins involved in…
View article: Extended progression‑free survival after combination treatment with anlotinib and S‑1 in refractory advanced esophageal cancer: A case report
Extended progression‑free survival after combination treatment with anlotinib and S‑1 in refractory advanced esophageal cancer: A case report Open
The rates of survival are low in patients with refractory advanced esophageal cancer in whom chemotherapy, radiotherapy and immunotherapy have failed. In the present report, the case of a 59-year-old male with dysphagia and paraneoplastic …
View article: Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types
Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types Open
Intratumor heterogeneity arises from ongoing somatic evolution complicating cancer diagnosis, prognosis, and treatment. Here we present TEATIME (es t imating e volution a ry events t hrough s i ngle-ti m epoint s e quencing), a novel compu…
View article: Infant Night Sleep Trajectories Differ by Feeding Mode
Infant Night Sleep Trajectories Differ by Feeding Mode Open
View article: Spatially defined intratumoral immune biomarkers predict recurrent versus second primary tumors in non-small cell lung cancer
Spatially defined intratumoral immune biomarkers predict recurrent versus second primary tumors in non-small cell lung cancer Open
View article: Anxiety and burnout in infectious disease nurses: the role of perceived stress and resilience
Anxiety and burnout in infectious disease nurses: the role of perceived stress and resilience Open
Anxiety was identified as a critical risk factor for burnout among nurses in infectious disease units. The relationship between anxiety and burnout was markedly affected by the levels of perceived stress and resilience. Specifically, the d…
View article: Novel Computational and Artificial Intelligence Models in Cancer Research
Novel Computational and Artificial Intelligence Models in Cancer Research Open
The ICIBM 2023 marked the 11th annual conference of its kind, with the ICIBM recently becoming the official conference of the International Association for Intelligent Biology and Medicine (IAIBM), showcasing cutting-edge advancements at t…
View article: Advancements in Protein Kinase Inhibitors: From Discovery to Clinical Applications
Advancements in Protein Kinase Inhibitors: From Discovery to Clinical Applications Open
Protein kinases are key mediators of cellular signaling and control cell functions through the phosphorylation of target proteins. They have become major targets for therapeutic agents aimed at treating human diseases, particularly cancer.…
View article: The multifaceted potential of TPT1 as biomarker and therapeutic target
The multifaceted potential of TPT1 as biomarker and therapeutic target Open
View article: Bridging social capital among Facebook users and COVID-19 cases growth in Arizona
Bridging social capital among Facebook users and COVID-19 cases growth in Arizona Open
View article: Body Mass Index Is Associated with Post-Acute Elevations in Biomarkers of Platelet Activation and Inflammation in Unvaccinated Adults Diagnosed with COVID-19 in the Previous 8 Weeks
Body Mass Index Is Associated with Post-Acute Elevations in Biomarkers of Platelet Activation and Inflammation in Unvaccinated Adults Diagnosed with COVID-19 in the Previous 8 Weeks Open
Introduction: Obesity has arisen as a prominent risk factor for COVID-19 severity and long COVID, potentially owed in part to the obesity-induced proinflammatory state. This study aimed to examine relationships among circulat…
View article: Assessing ChatGPT’s Competency in Addressing Interdisciplinary Inquiries on Chatbot Uses in Sports Rehabilitation: Simulation Study
Assessing ChatGPT’s Competency in Addressing Interdisciplinary Inquiries on Chatbot Uses in Sports Rehabilitation: Simulation Study Open
Background ChatGPT showcases exceptional conversational capabilities and extensive cross-disciplinary knowledge. In addition, it can perform multiple roles in a single chat session. This unique multirole-playing feature positions ChatGPT a…
View article: Bioinformatics and biomedical informatics with ChatGPT: Year one review
Bioinformatics and biomedical informatics with ChatGPT: Year one review Open
The year 2023 marked a significant surge in the exploration of applying large language model chatbots, notably Chat Generative Pre‐trained Transformer (ChatGPT), across various disciplines. We surveyed the application of ChatGPT in bioinfo…
View article: Resveratrol activates MAPK/ERK pathway to regulate oestrogen metabolism in type I endometrial cancer
Resveratrol activates MAPK/ERK pathway to regulate oestrogen metabolism in type I endometrial cancer Open
Objective Endometrial cancer (EC) is an oestrogen-dependent tumour, the occurrence of which is closely related to an imbalance of oestrogen homeostasis. Our previous studies explored the effects of Resveratrol(Res) on oestrogen metabolism.…
View article: Genome-wide screening and functional validation of methylation barriers near promoters
Genome-wide screening and functional validation of methylation barriers near promoters Open
CpG islands near promoters are normally unmethylated despite being surrounded by densely methylated regions. Aberrant hypermethylation of these CpG islands has been associated with the development of various human diseases. Although local …
View article: Scientific figures interpreted by ChatGPT: strengths in plot recognition and limits in color perception
Scientific figures interpreted by ChatGPT: strengths in plot recognition and limits in color perception Open
View article: Brain-derived extracellular vesicles mediate systemic coagulopathy and inflammation after traumatic brain injury
Brain-derived extracellular vesicles mediate systemic coagulopathy and inflammation after traumatic brain injury Open
Traumatic brain injury (TBI) can induce systemic coagulopathy and inflammation, thereby increasing the risk of mortality and disability. However, the mechanism causing systemic coagulopathy and inflammation following TBI remains unclear. I…
View article: On the Responsible Use of Chatbots in Bioinformatics
On the Responsible Use of Chatbots in Bioinformatics Open
View article: DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements
DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements Open
Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate …
View article: 178 Tumor neoantigen prioritization from liquid biopsy whole exome sequencing for selected tumor-infiltrating lymphocyte therapy
178 Tumor neoantigen prioritization from liquid biopsy whole exome sequencing for selected tumor-infiltrating lymphocyte therapy Open
Background Adoptive cell transfer (ACT) of neoantigen-reactive tumor-infiltrating lymphocytes (TILs) is an emerging therapeutic modality for solid cancers. A growing body of clinical data in the TIL-ACT field supports the potential for the…
View article: A Mouse-Specific Model to Detect Genes under Selection in Tumors
A Mouse-Specific Model to Detect Genes under Selection in Tumors Open
The mouse is a widely used model organism in cancer research. However, no computational methods exist to identify cancer driver genes in mice due to a lack of labeled training data. To address this knowledge gap, we adapted the GUST (Genes…
View article: Bioinformatics Illustrations Decoded by ChatGPT: The Good, The Bad, and The Ugly
Bioinformatics Illustrations Decoded by ChatGPT: The Good, The Bad, and The Ugly Open
Emerging studies underscore the promising capabilities of large language model-based chatbots in conducting fundamental bioinformatics data analyses. The recent feature of accepting image-inputs by ChatGPT motivated us to explore its effic…
View article: #256 Exosomal MiR-148a-3p serves as tumor suppressor for ovarian cancer
#256 Exosomal MiR-148a-3p serves as tumor suppressor for ovarian cancer Open
Introduction/Background Ovarian cancer (OVCA) develop resistance to cisplatin during treatment. Exosome is associated with chemoresistance in various cancers, whereas such a role in OVCA is not yet clear. Methodology The exosomes were extr…