BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Identifying drug effects in a cardiac model of electrophysiology using kernel-based parameter estimation methods Computational models of cardiac electrophysiology hold great potential in the drug discovery process to bridge the gap between in vitro and in vivo preclinical trials. …
Author Archives: Kermit Murray
[ASAP] Detection and Isolation of Circulating Tumor Cells from Breast Cancer Patients Using CUB Domain-Containing Protein 1
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Detection and Isolation of Circulating Tumor Cells from Breast Cancer Patients Using CUB Domain-Containing Protein 1 Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00739 Kai Bartkowiak, Parinaz Mossahebi Mohammadi, Sebastian Gärtner, Marcel Kwiatkowski, Antje Andreas, Maria …
[ASAP] Microprotein Dysregulation in the Serum of Patients with Atrial Fibrillation
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Microprotein Dysregulation in the Serum of Patients with Atrial Fibrillation Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00622 Zheng Zhang, Tao Tian, Ni Pan, Yi Wang, Mingbo Peng, Xinbo Zhao, Zhenwei Pan, and Cuihong Wan March …
Corrigendum to “The explorations of dynamic interactions of paxillin at the focal adhesions” [Biochimica et Biophysica Acta(BBA) – Proteins and Proteomics 1870/10 (2022) 140825]
Biochimica et Biophysica Acta – Proteins and Proteomics ScienceDirect Publication: Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics ScienceDirect RSS Corrigendum to “The explorations of dynamic interactions of paxillin at the focal adhesions” [Biochimica et Biophysica Acta(BBA) – Proteins and Proteomics 1870/10 (2022) 140825] Publication date: 1 July 2023 Source: Biochimica et Biophysica Acta …
Leveraging gene correlations in single cell transcriptomic data
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leveraging gene correlations in single cell transcriptomic data Many approaches have been developed to overcome technical noise in single cell (and single nucleus) RNA-sequencing (scRNAseq). As researchers dig deeper into data–looking for rare cell types, subtleties of cell states, …
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Proteins and Metabolites fingerprints of Gestational Diabetes Mellitus forming Protein‐Metabolite Interactomes are its potential biomarkers
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Proteins and Metabolites fingerprints of Gestational Diabetes Mellitus forming Protein‐Metabolite Interactomes are its potential biomarkers Abstract Gestational diabetes mellitus (GDM) is a consequence of glucose intolerance with an inadequate production of insulin that …
Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Comparative analysis between RNA-seq and single-molecule RNA FISH indicates that the pyrimidine nucleobase idoxuridine (IdU) globally amplifies transcriptional noise Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability, but the physiological roles of noise have remained difficult to determine …
Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops Lineage-defining transcription factors form densely interconnected circuits in chromatin occupancy assays, but the functional significance of these networks remains underexplored. We reconstructed the functional topology …
MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters SUMMARY: Low-affinity interactions among multivalent biomolecules may lead to the formation of molecular complexes that undergo phase transitions to become extra-large clusters. Characterizing the physical properties of these clusters is …
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A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A data-driven Boolean model explains memory subsets and evolution in CD8+ T cell exhaustion T cells play a key role in a variety of immune responses, including infection and cancer. Upon stimulation, naive CD8+ T cells proliferate and differentiate …
[ASAP] Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Definitive Screening Designs to Optimize Library-Free DIA-MS Identification and Quantification of Neuropeptides Journal of Proteome Research DOI: 10.1021/acs.jproteome.3c00088 Ashley Phetsanthad, Austin V. Carr, Lauren Fields, and Lingjun Li March 16, 2023 http://dx.doi.org/10.1021/acs.jproteome.3c00088
[ASAP] Serum Bile Acid Metabolites Predict the Therapeutic Effect of Mesalazine in Patients with Ulcerative Colitis
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Serum Bile Acid Metabolites Predict the Therapeutic Effect of Mesalazine in Patients with Ulcerative Colitis Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00820 Qiaoli Sun, Yingjue Tang, Liang Dai, Zhipeng Tang, Wenjun Zhou, Tao Wu, and …
Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2′3′ cGAMP reveals various signaling axes impacted by cyclic dinucleotides
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Proteomic and phosphoproteomic analyses of Jurkat T-cell treated with 2′3′ cGAMP reveals various signaling axes impacted by cyclic dinucleotides Publication date: 15 May 2023 Source: Journal of Proteomics, Volume 279 Author(s): Kenneth I. Onyedibe, Rodrigo Mohallem, Modi Wang, Uma K. Aryal, Herman O. Sintim March …
Editorial Board: Proteomics 6’23
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Editorial Board: Proteomics 6’23 PROTEOMICS, Volume 23, Issue 6, March 2023. March 15, 2023 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370042?af=R
Front Cover
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Front Cover Cover Image © Wiley-VCH GmbH. The image is part of a figure in the article DOI: 10.1002/pmic.201900203 by Lei Li, Yong Jiang et al. March 15, 2023 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370041?af=R
Standard abbreviations
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Standard abbreviations PROTEOMICS, Volume 23, Issue 6, March 2023. March 15, 2023 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370044?af=R
Molecular methods to study protein trafficking between organs
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Molecular methods to study protein trafficking between organs Abstract Interorgan communication networks are key regulators of organismal homeostasis, and their dysregulation is associated with a variety of pathologies. While mass spectrometry proteomics identifies …
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Contents: Proteomics 6’23
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Contents: Proteomics 6’23 PROTEOMICS, Volume 23, Issue 6, March 2023. March 15, 2023 https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202370043?af=R
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. …
In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" In silico agent-based modeling approach to characterize multiple in vitro tuberculosis infection models In vitro models of Mycobacterium tuberculosis (Mtb) infection are a valuable tool to examine host-pathogen interactions and screen drugs. With the development of more complex in …