Transformer-based modeling of Clonal Selection and Expression Dynamics reveals resistance mechanisms in breast cancer by Nathan D Maulding, Jun Zou, Wei Zhou, Ciara Metcalfe, Joshua M Stuart, Xin Ye, Marc Hafner

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Differential gene expression analysis of papillary thyroid carcinoma reveals important genes for lymph node metastasis by Wan Fahmi Wan Mohamad Nazarie, Azliana Mohamad Yusof, Francis Yew Fu Tieng, Nur Fadhlina Mohamad Pakarulrazy, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Nani Harlina Md Latar, Sazuita Saidin, Isa Mohamed Rose, Learn-Han Lee, Nurul-Syakima Ab Mutalib

“…Methods: We employed a bioinformatics pipeline for RNA-Seq analysis in PTC with and without LNM at the gene expression level. …”
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Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing by Delia J. Scoville, Tae Kyu Brian Uhm, Jamie A. Shallcross, Rebecca J. Whelan

“…This data-rich approach, combined with bioinformatics tools, enabled the entire selection process to be characterized. …”
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Tumor Mutation Signature Reveals the Risk Factors of Lung Adenocarcinoma with or Mutation by Jialiang Wang MM, Chang Guo BMed, Jiexiao Wang MM, Xiaopeng Zhang BS, Jian Qi PhD, Xiang Huang MM, Zongtao Hu MM, Hongzhi Wang MM, Bo Hong PhD

“…TMS of LUAD with KRAS and EGFR mutations from the TCGA, OncoSG, and MSK datasets was determined by two bioinformatics tools, namely the “MutationalPatterns” and “FitMS” packages. …”
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Venoms and Extracellular Vesicles: A New Frontier in Venom Biology by Auwal A. Bala, Naoual Oukkache, Elda E. Sanchez, Montamas Suntravat, Jacob A. Galan

“…Recent advancements in isolating and purifying EV cargo, mass spectrometry techniques, and bioinformatics have positioned EVs as potential biomarkers that could elucidate biological signaling pathways and provide valuable information on the relationship between venomous toxins, their mechanisms of action, and the effectiveness of antivenoms. …”
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In silico identification of silent primycin biosynthetic gene clusters within the family Pseudonocardiaceae by Márk Kovács-Valasek, Csaba Fekete, Andrea Kovács-Valasek

“…In the global effort to discover or design new effective antibiotics to fight infectious diseases, the increasingly available multi-omics data with novel bioinformatics tools open up new horizons for the exploration of the genetic potential of bacteria to synthesize bioactive secondary metabolites. …”
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Understanding metastasis mixed-treatment responses through genomic analyses by Susana Garcia-Recio, Paola Zagami, Brooke M. Felsheim, Amy Wheless, Kerry Thomas, Renato Trimarchi, Lisa A. Carey, Charles M. Perou

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Plac8 regulates the fibrogenic ability of cardiac fibroblasts in mice with myocardial infarction by Ting Fu, Jianping Gong, Lei Xu, Ningning Ji

“…This study explored the role of Placenta specific 8 (Plac8) in MI on the basis of single-cell RNA-Seq (scRNA-Seq) data (GSE136088) and micro-array data (GSE153485). Through bioinformatics analysis, Plac8 was finally identified as a key gene related to fibroblasts. …”
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Identification of the CaCRT gene family and function of CaCRT1 under low-temperature stress in pepper (Capsicum annuum L.) by Yanzhuang Wang, Ping Yang, Jian Li, Juan Li, Keyan Zhu, Minkun Pei, Jie Li, Hongbin Du

“…Abstract To explore CRT gene family members and their responses to low-temperature stress, bioinformatics methods were used to identify the CRT gene family in pepper. …”
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CircRNA TUBA1C promotes proliferation and glucose metabolism, and blocks apoptosis of osteosarcoma cells through sponging miR-143-3p by Yi-Bing Liu, Wen-Hao Dai, Jun-Jie Chang, Kang Wei

“…Furthermore, we discovered that miR-143-3p played a reverse role to circTUBA1C in OS cells. Bioinformatics analysis, RNA pull-down assay, and luciferase assay demonstrated that circTUBA1C acted as a sponge for miR-143-3p, blocking its expression in OS cells. …”
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The Role of the Key Differentially Mutated Gene FGFR3 in the Immune Microenvironment of Bladder Cancer by Jun Jiang, Yan Zhan, Jun Li

“…In this work, we downloaded the RNA-seq expression profiles and somatic mutation data of 433 bladder cancer cases from The Cancer Genome Atlas (TCGA) and then employed a comprehensive bioinformatics approach to evaluate them. Firstly, the expression profiles were used to predict the scores and then the content of immune and stromal cells via the estimate package in R software. …”
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New insights on genetic background of major diabetic vascular complications by Zuira Tariq, Salah Abusnana, Bashair M. Mussa, Hala Zakaria

“…Results The number of genetic findings for diabetes and diabetic complications has over doubled due to the discovery of novel genomics data, including bioinformatics and the aggregation of global cohort studies. …”
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Identification of Allergenic Tropomyosins with Known and Unknown Sequences in Seafood Products by Marta Godlewska, Piotr Minkiewicz, Małgorzata Darewicz, Anna Iwaniak

“…Our results show that bioinformatics analysis (especially using Unipept program) may be a viable tool supporting LC-MS/MS experiments aimed at the detection of allergens.…”
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Clinical Significance of NKD Inhibitor of WNT Signaling Pathway 1 (NKD1) in Glioblastoma by Lijun Li, Ruiying Gao, Weizhong Huangfu, Fang Zhang, Ruixia Wang

“…Immune cell enrichment in glioblastoma and its correlation with NKD1 level was finally assessed using bioinformatics analyses. Results. NKD1 shows a lower expression level in glioblastoma compared to that in the normal brain or other glioma subtypes, which is independently correlated to a worse prognosis in both the TCGA cohort and our retrospective cohort. …”
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The Potential Impact of HNRNPA2B1 on Human Cancers Prognosis and Immune Microenvironment by Tao Huang, Gang Zhu, Fan Chen

“…We further validated the bioinformatic findings using immunohistochemistry techniques. …”
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Deoxycholic Acid Could Induce Apoptosis and Trigger Gastric Carcinogenesis on Gastric Epithelial Cells by Quantitative Proteomic Analysis by Yanyan Shi, Ying Wei, Ting Zhang, Jing Zhang, Ye Wang, Shigang Ding

“…Using liquid chromatographic/tandem mass spectrometric (LC-MS/MS) methods, 134 upregulated proteins and 214 downregulated proteins were identified in the bile acid treated GES-1 cells. Bioinformatics analysis revealed the interactions and signaling networks of these differentially expressed proteins. …”
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Pulse protein quality and derived bioactive peptides by Matthew G. Nosworthy, Matthew G. Nosworthy, Bianyun Yu, L. Irina Zaharia, Gerardo Medina, Nii Patterson

“…Additionally, the use of proteomics platforms, such as mass spectrometry, in combination with bioinformatics tools, enables the identification and characterization of bioactive peptides in pulse crops. …”
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A Method for Detecting Overlapping Protein Complexes Based on an Adaptive Improved FCM Clustering Algorithm by Caixia Wang, Rongquan Wang, Kaiying Jiang

“…The protein complex has attracted significant attention in bioinformatics as a critical substance in life activities. …”
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Systematic functional analysis and potential application of a serine protease from cold-adapted Planococcus bacterium by Weijun Leng, Xiaoyun Wu, Xianghui Qi, Hongying Liu, Li Yuan, Ruichang Gao

“…In this study, a gene encoding serine protease (PmSpr288) from cold-adapted bacterium, namely Planococcus maritimus XJ11, was cloned and overexpressed in Escherichia coli BL21 (DE3). Bioinformatics analysis revealed that PmSpr288 belongs to serine protease S8 superfamily with a classical catalytic triad comprised by the Asp49, His86 and Ser251. …”
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Long noncoding RNA DHRS4 antisense RNA 1 suppresses osteosarcoma cell proliferation and promotes apoptosis through a competitive endogenous RNA mechanism by Zhouzhou Tang, Zhihao Li, Guofeng Wu, Jianjun Li, Jianye Tan, Lixin Zhu

“…The potential mechanism of DHRS4-AS1 was examined through bioinformatics analysis and rescue experiments. DHRS4-AS1 was downregulated in OS cell lines. …”
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