检索结果-内蒙古大学图书馆

Ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

Journal of Proteomics 2025年 317卷

作者： Zheng, Ping Audain, Enrique Webel, Henry Dai, Chengxin Klein, Joshua Hitz, Marc-Phillip Sachsenberg, Timo Bai, Mingze Perez-Riverol, Yasset Chongqing Key Laboratory of Big Data for Bio Intelligence Chongqing University of Posts and Telecommunications Chongqing China Institute of Medical Genetics University Medicine Oldenburg Carl von Ossietzky University Oldenburg Germany The Novo Nordisk Foundation Center for Biosustainability Technical University of Denmark Lyngby Denmark State Key Laboratory of Proteomics Beijing Proteome Research Center National Center for Protein Sciences (Beijing) Beijing Institute of Life Omics Beijing China Program for Bioinformatics Boston University Boston United States Department of Computer Science Applied Bioinformatics University of Tübingen Tübingen Germany Institute for Bioinformatics and Medical Informatics University of Tübingen Tübingen Germany European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Cambridge United Kingdom

Intensity-based absolute quantification (iBAQ) is essential in proteomics as it allows for the assessment of a protein's absolute abundance in various samples or conditions. However, the computation of these values for increasingly large-scale and high-throughput experiments, such as those using DIA, TMT, or LFQ workflows, poses significant challenges in scalability and reproducibility. Here, we present ibaqpy (https://***/bigbio/ibaqpy), a Python package designed to compute iBAQ values efficiently for experiments of any scale. Ibaqpy leverages the Sample and Data Relationship Format (SDRF) metadata standard to incorporate experimental metadata into the quantification workflow. This allows for automatic normalization and batch correction while accounting for key aspects of the experimental design, such as technical and biological replicates, fractionation strategies, and sample conditions. Designed for large-scale proteomics datasets, ibaqpy can also recompute iBAQ values for existing experiments when an SDRF is available. We showcased ibaqpy's capabilities by reanalyzing 17 public proteomics datasets from ProteomeXchange, covering HeLa cell lines with 4921 samples and 5766 MS runs, quantifying a total of 11,014 proteins. In our reanalysis, ibaqpy is a key component in automating reproducible quantification, reducing manual effort and making quantitative proteomics more accessible while supporting FAIR principles for data reuse. Significance: Proteomics studies often rely on intensity-based absolute quantification (iBAQ) to assess protein abundance across various biological conditions. Despite its widespread use, computing iBAQ values at scale remains challenging due to the increasing complexity and volume of proteomics experiments. Existing tools frequently lack metadata integration, limiting their ability to handle experimental design intricacies such as replicates, fractions, and batch effects. Our work introduces ibaqpy, a scalable Python package that lev

关键词： Big data bioinformatics Data integration Proteomics Quantification

来源：评论

学校读者我要写书评

暂无评论

Building a unified model for drug synergy analysis powered by large language models

引用

Nature Communications 2025年第1期16卷 1-17页

作者： Liu, Tianyu Chu, Tinyi Luo, Xiao Zhao, Hongyu Interdepartmental Program in Computational Biology & Bioinformatics Yale University New Haven CT United States Department of Biostatistics Yale University New Haven CT United States Department of Computer Science University of California Los Angeles Los Angeles CA United States

Drug synergy prediction is a challenging and important task in the treatment of complex diseases including cancer. In this manuscript, we present a unified Model, known as BAITSAO, for tasks related to drug synergy prediction with a unified pipeline to handle different datasets. We construct the training datasets for BAITSAO based on the context-enriched embeddings from Large Language Models for the initial representation of drugs and cell lines. After demonstrating the relevance of these embeddings, we pre-train BAITSAO with a large-scale drug synergy database under a multi-task learning framework with rigorous selections of tasks. We demonstrate the superiority of the model architecture and the pre-trained strategies of BAITSAO over other methods through comprehensive benchmark analysis. Moreover, we investigate the sensitivity of BAITSAO and illustrate its promising functions including drug discoveries, drug combinations-gene interaction, and multi-drug synergy predictions. © The Author(s) 2025.

关键词：

来源：评论

学校读者我要写书评

暂无评论

Protein subcellular localization prediction of eukaryotes using a knowledge-based approach

引用

BMC bioinformatics 2009年第SUPPL. 15期10卷 1-13页

作者： Lin, Hsin-Nan Chen, Ching-Tai Sung, Ting-Yi Ho, Shinn-Ying Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei Taiwan Bioinformatics Lab. Institute of Information Science Academia Sinica Taipei Taiwan Institute of Bioinformatics National Chiao Tung University Hsinchu Taiwan

Background: The study of protein subcellular localization (PSL) is important for elucidating protein functions involved in various cellular processes. However, determining the localization sites of a protein through wet-lab experiments can be time-consuming and labor-intensive. Thus, computational approaches become highly desirable. Most of the PSL prediction systems are established for single-localized proteins. However, a significant number of eukaryotic proteins are known to be localized into multiple subcellular organelles. Many studies have shown that proteins may simultaneously locate or move between different cellular compartments and be involved in different biological processes with different roles. Results: In this study, we propose a knowledge based method, called KnowPredsite, to predict the localization site(s) of both single-localized and multi-localized proteins. Based on the local similarity, we can identify the "related sequences" for prediction. We construct a knowledge base to record the possible sequence variations for protein sequences. When predicting the localization annotation of a query protein, we search against the knowledge base and used a scoring mechanism to determine the predicted sites. We downloaded the dataset from ngLOC, which consisted of ten distinct subcellular organelles from 1923 species, and performed ten-fold cross validation experiments to evaluate KnowPredsite's performance. The experiment results show that KnowPredsite achieves higher prediction accuracy than ngLOC and Blast-hit method. For single-localized proteins, the overall accuracy of KnowPredsite is 91.7%. For multi-localized proteins, the overall accuracy of KnowPredsite is 72.1%, which is significantly higher than that of ngLOC by 12.4%. Notably, half of the proteins in the dataset that cannot find any Blast hit sequence above a specified threshold can still be correctly predicted by KnowPredsite. Conclusion: KnowPredsite demonstrates the power of identifying rel

关键词： Proteins

来源：评论

学校读者我要写书评

暂无评论

Correction: Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake

引用

BMC microbiology 2025年第1期25卷 225页

作者： Linton Freund Caroline Hung Talyssa M Topacio Charles Diamond Alyson Fresquez Timothy W Lyons Emma L Aronson Genetics Genomics and Bioinformatics Program University of California Riverside 900 University Ave Riverside CA 92521 USA. lintonfreund@***. Department of Microbiology and Plant Pathology University of California Riverside 900 University Ave Riverside CA 92521 USA. Department of Earth and Planetary Sciences University of California Riverside 900 University Ave Riverside CA 92521 USA.

来源：评论

学校读者我要写书评

暂无评论

Noncovalent Lasso Entanglements are Common in Experimentally Derived Intrinsically Disordered Protein Ensembles and Strongly Influenced by Protein Length and Charge

引用

Journal of Physical Chemistry B 2025年第19期129卷 4682-4691页

作者： Vu, Quyen V. Sitarik, Ian Li, Mai Suan O’Brien, Edward P. Department of Chemistry Pennsylvania State University University ParkPA16802 United States Institute of Physics Polish Academy of Sciences Al. Lotnikow 32/46 Warsaw02-668 Poland Institute for Computational Sciences and Technology Quang Trung Software City Tan Chanh Hiep Ward District 12 Ho Chi Minh City510000 Viet Nam Institute for Computational and Data Sciences Pennsylvania State University University ParkPA16802 United States Bioinformatics and Genomics Graduate Program The Huck Institutes of the Life Sciences Pennsylvania State University University ParkPA16802 United States

Noncovalent lasso entanglements are conformations in which a protein backbone segment forms a loop closed by noncovalent interactions and that loop is threaded one or more times by either the N- or C-terminal segment of the backbone or both. While these entanglements are common in globular proteins, their presence in intrinsically disordered proteins or regions (IDPs/IDRs) remains largely unexplored. Here, we examine whether IDPs/IDRs in their monomeric form populate these conformations and how sequence length and charge composition influence entanglement prevalence. Using experimentally derived IDP/IDR ensembles from the Protein Ensemble Database, we find that 48% (199 of 416) of its entries contain subpopulations with entangled conformations, with 25% of entries having conformational ensembles in which 50% or more are entangled. This includes IDPs such as nuclear pore complex protein Nup153, nonstructural protein V of Hendra virus, and Eukaryotic initiation factor 4F subunit p150. Using molecular simulations, we find that (i) entanglements are most prevalent in weak polyampholytes and polyelectrolytes, and strong polyampholytes but rare in strong polyelectrolytes;(ii) entanglement populations increase with IDP length;(iii) entanglement probability positively correlates with chain compaction;and (iv) most IDPs/IDRs in the human proteome exhibit entangled conformations. A GO enrichment analysis reveals that the entanglement probability correlates with IDP/IDR function and subcellular localization. Thus, these findings indicate that noncovalent lasso entanglements are a widespread structural feature of IDPs/IDRs and have the potential to be biologically relevant. © 2025 American Chemical Society.

关键词： Quantum entanglement

来源：评论

学校读者我要写书评

暂无评论

Juntas Contra el Virus del Papiloma Humano: protocol for a pilot randomized controlled trial of an HPV self-sampling intervention for underscreened Latinas

引用

Pilot and feasibility studies 2025年第1期11卷 65页

作者： Carolyn Y Fang Marisol Cora-Cruz Pratistha Koirala Sophia Perez Minzi Li Brian L Egleston Yuku Chen Gina Mantia-Smaldone Omar Martinez Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Ave. Philadelphia PA 19111 USA. carolyn.fang@fccc.edu. Cancer Prevention and Control Program Fox Chase Cancer Center 333 Cottman Ave. Philadelphia PA 19111 USA. Department of Gynecologic Oncology Fox Chase Cancer Center Philadelphia PA USA. Biostatistics and Bioinformatics Facility Fox Chase Cancer Center Philadelphia PA USA. College of Medicine University of Central Florida Orlando FL USA.

BACKGROUND:Rates of cervical cancer incidence and mortality are persistently higher among Latina women in the continental United States (US) and women in Puerto Rico (a US territory) compared with non-Hispanic White (NHW) women. Multiple factors contribute to low participation in cancer screening, including structural barriers (e.g., low access to healthcare services, racism/discrimination, lack of culturally and linguistically adequate information), cultural concerns, and low perceived risk and awareness of cervical cancer. Although community-based education and navigation support can be effective in overcoming some barriers to screening, structural barriers and limited access remain formidable challenges to overcome. Emerging technologies supporting self-sampling for high-risk human papillomavirus (HPV) testing may offer a valuable evidence-based strategy for empowering Latina women to engage in cervical cancer screening. Thus, the objective of this study is to assess the feasibility and acceptability of a novel HPV self-sampling intervention for underscreened Latina women. METHODS:The study will be a randomized controlled feasibility trial involving 100 Latina women who have not received cervical cancer screening within the recommended guidelines. Participants will be randomly assigned to the intervention condition, which includes a synchronous three-session group cervical cancer educational program delivered virtually along with a mailed HPV self-sampling kit (to obtain self-collected cervical samples for HPV testing), or to a comparison condition that involves receipt of the mailed HPV self-sampling kit with written information about cervical cancer screening and nearby clinics. Study assessments will be obtained at baseline (i.e., study entry) and 1-month post-program. The primary outcome of feasibility will be measured through study enrollment and intervention completion. In addition, acceptability of study materials and the self-sampling procedures will be a

关键词： Cervical cancer Human papillomavirus (HPV) Latinas Screening Self-sampling

来源：评论

学校读者我要写书评

暂无评论

Multitissue single-cell analysis reveals differential cellular and molecular sensitivity between fructose and high-fat high-sucrose diets

引用

Cell Reports 2025年第5期44卷 115690页

作者： Chen, Yen-Wei Ahn, In Sook Wang, Susanna Sue-Ming Majid, Sana Diamante, Graciel Cely, Ingrid Zhang, Guanglin Cabanayan, Angelus Komzyuk, Sergey Bonnett, Jack Arneson, Douglas Yang, Xia Department of Integrative Biology & Physiology University of California Los Angeles Los Angeles CA United States Interdepartmental Program of Molecular Toxicology University of California Los Angeles Los Angeles CA United States Interdepartmental Program of Bioinformatics University of California Los Angeles Los Angeles CA United States Department of Molecular and Medical Pharmacology University of California Los Angeles Los Angeles CA United States

Metabolic syndrome (MetS), a conglomerate of dysregulated metabolic traits that vary between individuals, is partially driven by modern diets high in fat, sucrose, or fructose and their interactions with host genes in metabolic tissues. To elucidate the roles of individual tissues and cell types in diet-induced MetS, we performed single-cell RNA sequencing on the hypothalamus, liver, adipose tissue, and small intestine of mice fed high-fat high-sucrose (HFHS) or fructose diets. We found that hypothalamic neurons were sensitive to fructose, while adipose progenitor cells and macrophages were responsive to HFHS. Ligand-receptor analysis revealed lipid metabolism and inflammation networks among peripheral tissues driven by HFHS, while both diets stimulated synaptic remodeling within the hypothalamus. mt-Rnr2, a top responder to both diets, mitigated diet-induced MetS by stimulating thermogenesis. Our study demonstrates that HFHS and fructose diets have differential cell type and network targets but also share regulators such as mt-Rnr2 to affect MetS risk. © 2025 The Author(s)

关键词： adipose stromal vascular fraction CP: Metabolism fructose diet high-fat high-sucrose diet hypothalamus liver metabolic syndrome single-cell RNA-seq small intestine SVF tissue crosstalk

来源：评论

学校读者我要写书评

暂无评论

consexpressionR: an R package for consensus differential gene expression analysis

arXiv

引用

arXiv 2025年

作者： Costa-Silva, Juliana Menotti, David Lopes, Fabricio M. Department of Informatics Federal University of Paraná Rua Coronel Francisco Heráclito dos Santos 100 Paraná81531-990 Brazil Department of Computer Science Bioinformatics Graduate Program Federal University of Technology - Paraná Av. Alberto Carazzai 1640 - Cornélio Procópio ParanáPostal code: 86300-000 Brazil

Motivation: Bulk RNA-Seq is a widely used method for studying gene expression across a variety of contexts. The significance of RNA-Seq studies has grown with the advent of high-throughput sequencing technologies. Computational methods have been developed for each stage of the identification of differentially expressed genes. Nevertheless, there are few studies exploring the association between different types of methods. In this study, we evaluated the impact of the association of methodologies in the results of differential expression analysis. By adopting two data sets with qPCR data (to gold-standard reference), seven methods were implemented and assessed in R packages (EBSeq, edgeR, DESeq2, limma, SAMseq, NOISeq, and Knowseq), which was performed and assessed separately and in association. The results were evaluated considering the adopted qPCR data. Results: Here, we introduce consexpressionR, an R package that automates differential expression analysis using consensus of at least seven methodologies, producing more assertive results with a significant reduction in false positives. Availability: consexpressionR is an R package available via Source code and support are available at GitHub (https://***/costasilvati/consexpressionR). © 2025, CC BY-NC-ND.

关键词：

来源：评论

学校读者我要写书评

暂无评论

CD19 CAR-T With Axicabtagene Ciloleucel in R/R Large B-Cell Lymphoma With/Without Prior Autologous Stem Cell Transplant

引用

Clinical Lymphoma, Myeloma and Leukemia 2025年第6期25卷 432-439页

作者： Chen, David T. Goloubeva, Olga Rapoport, Aaron P. Dahiya, Saurabh Atanackovic, Djordje Hardy, Nancy Kocoglu, Mehmet Lutfi, Forat Alkhaldi, Hanan Claiborne, John Preston Lee, Seung Tae Kline, Kathryn Law, Jennie Y. Yared, Jean A. Division of Hematology/Oncology Department of Medicine Greenebaum Comprehensive Cancer Center University of Maryland Medical Center University of Maryland School of Medicine Baltimore MD United States Department of Epidemiology and Public Health Division of Biostatistics and Bioinformatics University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine Baltimore MD United States Transplantation & Cellular Therapy Program Division of Hematology/Oncology Department of Internal Medicine Greenebaum Comprehensive Cancer Center University of Maryland Medical Center University of Maryland School of Medicine Baltimore MD United States Sidney Kimmel Comprehensive Cancer Center Johns Hopkins University School of Medicine Baltimore MD United States

Background: Anti-CD19 CAR-T therapy has been a breakthrough in treatment of primary refractory or relapsed large B-cell lymphoma (r/r LBCL) and is poised to supplant previous second line of high dose chemotherapy and autologous stem cell transplantation (HDT/ASCT). However, in clinical practice, high risk patients with chemoimmunotherapy sensitive disease continue to receive salvage chemoimmunotherapy or cannot access CAR-T in a timely manner and thus may still proceed to HDT/ASCT. Little is known about clinical outcomes of CAR-T in patients who receive HDT/ASCT compared to those who are transplant-naïve. Design: We conducted a retrospective study of patients with r/r LBCL who previously underwent HDT/ASCT or were transplant-naïve (n = 97) and received axicabtagene ciloleucel after at least 2 prior therapy lines between 1/1/2018 to 12/31/2021. Primary endpoint was progression-free survival (PFS). Secondary endpoints were overall survival (OS), nonrelapse mortality (NRM), and cumulative incidence of relapse/progression. Results: 82 (84.5%) patients were transplant-naïve and 15 (15.5%) previously received HDT/ASCT. No differences were found in the incidence of high-grade cytokine release syndrome or immune effector cell-associated neurotoxicity syndrome, length of hospital admission, or incidence of cytopenia at day 30. 90-day response, PFS, OS, cumulative incidence of relapse/progression, and NRM were not different. Factors that adversely affected outcomes were prior bridging therapy, elevated LDH or thrombocytopenia at time of lymphodepleting chemotherapy, and worse ECOG performance status. Conclusion: Prior treatment with HDT/ASCT does not compromise the safety and efficacy of anti-CD19 CAR-T therapy, suggesting a continued role for HDT/ASCT in treatment of select patients with r/r DLBCL. © 2024

关键词： Autologous HCT Axi-cel CAR-T DLBCL HSCT

来源：评论

学校读者我要写书评

暂无评论

Integrating computational and experimental insights into osmolyte-driven activation of Geobacillus kaustophilus L-asparaginase for acrylamide mitigation

引用

Journal of Molecular Liquids 2025年 423卷

作者： Özdemir, F.İnci Servili, Burak Demirtaş, Özge Şükür, Gözde Tülek, Ahmet Yildirim, Deniz Gebze Technical University Department of Molecular Biology and Genetics Kocaeli Gebze41400 Turkey Kadir Has University of Science and Engineering Bioinformatics and Genetics Program İstanbul Fatih35430 Turkey Iğdır University Postgraduate Education Institute Department of Bioengineering and Sciences Iğdır Merkez76000 Turkey Cukurova University Faculty of Ceyhan Engineering Department of Chemical Engineering Adana Ceyhan01950 Turkey

Osmolytes play a critical role in enhancing the stability and activity of enzymes for industrial applications. This study systematically investigated the effects of various osmolytes on the activity, optimal pH, temperature, stability, metal ion effects, storage, and acrylamide mitigation performance of L-asparaginase from the thermophilic Geobacillus kaustophilus (GkASNase). The experimental findings were further supported by computationally integrated tools such as homology modeling, docking, and molecular dynamics (MD) simulations. Among the selected osmolytes (maltose, sorbitol, trehalose, glycine, and sucrose), GkASNase showed the highest stability during 30 days of storage in the presence of maltose and arginine. Maltose increased GkASNase activity approximately 2-fold at 37 °C and 55 °C. In the presence of osmolytes, the Km values of GkASNase decreased and the Vmax values increased compared to controls at 37 °C and 55 °C. In the presence of osmolytes, the acrylamide mitigation performance of GkASNase increased by 1.7-fold in a 15 min reaction. The computational analysis indicates that L-asparagine as substrate enhances protein compactness and stability, while arginine as osmolyte increases flexibility and optimizes water distribution around the enzyme. These findings provide novel insights into enzyme stabilization that have implications for therapeutic and biotechnological applications. © 2025 Elsevier B.V.

关键词： Maltose

来源：评论

学校读者我要写书评

暂无评论

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案：

请选择收藏分类：

通借通还

建议与咨询 留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

时间限定

文献类型

馆藏选择

核心期刊

语言

文献类型

帮助

文字说明：

检索规则说明：

检索范例：

分类表

所选分类

限定检索结果

文献类型

馆藏范围

日期分布

学科分类号

主题

机构

作者

语言

请选择保存的检索档案： 新增检索档案 确定 取消

请选择收藏分类： 新增自定义分类 确定 取消

通借通还

建议与咨询留下您的常用邮箱和电话号码，以便我们向您反馈解决方案和替代方法

请选择保存的检索档案：

请选择收藏分类：