BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" FitMultiCell: Simulating and parameterizing computational models of multi-scale and multi-cellular processes Motivation: Biological tissues are dynamic and highly organized. Multi-scale models are helpful tools to analyze and understand the processes determining tissue dynamics. These models usually depend on parameters …
Author Archives: Kermit Murray
Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate.
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Ongoing HIV replication in lymph node sanctuary sites in treated patients contributes to the total latent HIV at a very slow rate. Lymph nodes (LNs) may serve as a sanctuary site for HIV viruses due to the heterogeneous distribution …
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches Natural communities are incredibly diverse, and explaining how this biodiversity is even possible remains a central question in ecology. Resource competition is thought to play …
[ASAP] GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] GlycoSLASH: Concurrent Glycopeptide Identification from Multiple Related LC-MS/MS Data Sets by Using Spectral Clustering and Library Searching Journal of Proteome Research DOI: 10.1021/acs.jproteome.3c00066 Sujun Li, Jianhui Zhu, David M. Lubman, He Zhou, and Haixu …
Gas-phase dopant flow to modify nanoLC-MS and nanoESI protein charge
International Journal of Mass Spectrometry ScienceDirect Publication: International Journal of Mass Spectrometry ScienceDirect RSS Gas-phase dopant flow to modify nanoLC-MS and nanoESI protein charge Publication date: May 2023 Source: International Journal of Mass Spectrometry, Volume 487 Author(s): G. Asher Newsome, Timothy P. Cleland February 21, 2023 https://www.sciencedirect.com/science/article/pii/S1387380623000179?dgcid=rss_sd_all
[ASAP] Assessment and Comparison of Database Search Engines for Peptidomic Applications
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Assessment and Comparison of Database Search Engines for Peptidomic Applications Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00307 Eduardo A. De La Toba, Krishna D. B. Anapindi, and Jonathan V. Sweedler February 21, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00307
Integrated Tandem Affinity Protein Purification Using the Polyhistidine Plus Extra 4 Amino Acids (HiP4) Tag System
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Integrated Tandem Affinity Protein Purification Using the Polyhistidine Plus Extra 4 Amino Acids (HiP4) Tag System Abstract Peptide tag systems are a robust biophysical and biochemical method that is widely used for protein …
Fourādimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Fourādimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF Abstract A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation …
LabelāFree Single Cell Proteomics Utilizing Ultrafast LC and MS Instrumentation: A Valuable Complementary Technique to Multiplexing
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. LabelāFree Single Cell Proteomics Utilizing Ultrafast LC and MS Instrumentation: A Valuable Complementary Technique to Multiplexing Abstract The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how …
Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Discovery of multi-state gene cluster switches determining the adaptive mitochondrial and metabolic landscape of breast cancer Adaptive metabolic switches are proposed to underlie conversions between cellular states during normal development as well as in cancer evolution, where they represent …
Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. …
Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, …
Parallelāreaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Parallelāreaction monitoring revealed altered expression of a number of epitranscriptomic reader, writer, and eraser proteins accompanied with colorectal cancer metastasis Abstract RNA contains more than 170 types of chemical modifications, and these modified …
Blood proteome of acute intracranial hemorrhage in infant victims of abusive head trauma
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Blood proteome of acute intracranial hemorrhage in infant victims of abusive head trauma Abstract Abusive head trauma (AHT) is a leading cause of mortality and morbidity in infants. While the reported incidence is …
JUMPptm: Integrated software for sensitive identification of postātranslational modifications and its application in Alzheimer’s disease study
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. JUMPptm: Integrated software for sensitive identification of postātranslational modifications and its application in Alzheimer’s disease study Abstract Background: Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified …
A dataset resource for clinically associated phosphosites in hepatocellular carcinoma
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. A dataset resource for clinically associated phosphosites in hepatocellular carcinoma Abstract Phosphorylation is one of the most common post-translational modifications (PTMs) and is closely related to protein activity and function, playing a critical …
Inādepth analysis of the Sirtuin 5āregulated mouse brain malonylome and succinylome using libraryāfree dataāindependent acquisitions
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Inādepth analysis of the Sirtuin 5āregulated mouse brain malonylome and succinylome using libraryāfree dataāindependent acquisitions Abstract Post-translational modifications (PTMs) dynamically regulate proteins and biological pathways, typically through the combined effects of multiple PTMs. …
Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Yeast cell responses and survival during periodic osmotic stress are controlled by glucose availability Natural environments of living organisms are often dynamic and multifactorial, with multiple parameters fluctuating over time. To better understand how cells respond to dynamically interacting …
Differentiating planteose and raffinose using negative ion mode mass spectrometry
International Journal of Mass Spectrometry ScienceDirect Publication: International Journal of Mass Spectrometry ScienceDirect RSS Differentiating planteose and raffinose using negative ion mode mass spectrometry Publication date: May 2023 Source: International Journal of Mass Spectrometry, Volume 487 Author(s): P. Lijina, B.S. Gnanesh Kumar February 18, 2023 https://www.sciencedirect.com/science/article/pii/S1387380623000180?dgcid=rss_sd_all
[ASAP] Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-Down Proteomics
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Defining the Sarcomeric Proteoform Landscape in Ischemic Cardiomyopathy by Top-Down Proteomics Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00729 Emily A. Chapman, Timothy J. Aballo, Jake A. Melby, Tianhua Zhou, Scott J. Price, Kalina J. Rossler, …