BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity Inferring accurate models describing the relationship between genotype and phenotype is necessary in order to understand and predict how mutations …
Author Archives: Kermit Murray
[ASAP] IP-LC-MSMS Enables Identification of Three Tau OâGlcNAcylation Sites as OâGlcNAcase Inhibition Pharmacodynamic Readout in Transgenic Mice Overexpressing Human Tau
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] IP-LC-MSMS Enables Identification of Three Tau OâGlcNAcylation Sites as OâGlcNAcase Inhibition Pharmacodynamic Readout in Transgenic Mice Overexpressing Human Tau Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00822 Sebastiaan Bijttebier, Dina Rodrigues Martins, Liesbeth Mertens, Karolien Grauwen, …
A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology A major goal of cancer biology is to understand the mechanisms underlying tumorigenesis driven by somatically acquired mutations. Existing computational approaches focus on either …
[ASAP] Comparison of Pairwise Venous and Fingertip Plasma Using Quantitative Proteomics Based on Data-Independent Acquisition
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Comparison of Pairwise Venous and Fingertip Plasma Using Quantitative Proteomics Based on Data-Independent Acquisition Journal of Proteome Research DOI: 10.1021/acs.jproteome.3c00081 Ganfei Xu, Jiacheng Lv, Mingjing Huang, Lingli Zhu, Subei Tan, and Chen Ding March …
[ASAP] Identification, Measurement, and Assessment of the Clinical Utility of Human Pancreatic Polypeptide by Liquid ChromatographyâTandem Mass Spectrometry
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Identification, Measurement, and Assessment of the Clinical Utility of Human Pancreatic Polypeptide by Liquid ChromatographyâTandem Mass Spectrometry Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00829 Anthony Maus, Erica M. Fatica, Robert Taylor, Bethany J. Larson, Alicia …
Age-stratified proteomic characteristics and identification of promising precise clinical treatment targets of colorectal cancer
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Age-stratified proteomic characteristics and identification of promising precise clinical treatment targets of colorectal cancer Publication date: 15 April 2023 Source: Journal of Proteomics, Volume 277 Author(s): Qianqian Wang, Yuanchen Zhou, Geyujia Zhou, Geng Qin, Chang Tan, Tengfei Yin, Dongyan Zhao, Shukun Yao March 7, 2023 …
Proteomic analysis reveals CAAP1 negatively correlates with platinum resistance in ovarian cancer
Journal of Proteomics ScienceDirect Publication: Journal of Proteomics ScienceDirect RSS Proteomic analysis reveals CAAP1 negatively correlates with platinum resistance in ovarian cancer Publication date: 15 April 2023 Source: Journal of Proteomics, Volume 277 Author(s): Maowei Ni, Jie Zhou, Wangang Gong, Ruibin Jiang, Xia Li, Wumin Dai, Zhuomin Yin, Zhongbo Chen, Zhiguo Zheng, Jianqing Zhu March …
A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. A gas phase fractionation acquisition scheme integrating ion mobility for rapid diaPASEF library generation Abstract Data independent acquisition (DIA/SWATH) MS is a primary strategy in quantitative proteomics. diaPASEF is a recent adaptation using …
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function. Objective: Bowel movement frequency (BMF) variation has been linked to changes in the composition of the human gut microbiome and to …
Beyond the Genetic Code: A Tissue Code?
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Beyond the Genetic Code: A Tissue Code? The genetic code determines how the precise amino acid sequence of proteins is specified by genomic information in cells. But what specifies the precise histologic organization of cells in plant and animal …
[ASAP] Large-Scale Profiling of Unexpected Tryptic Cleaved Sites at Ubiquitinated Lysines
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Large-Scale Profiling of Unexpected Tryptic Cleaved Sites at Ubiquitinated Lysines Journal of Proteome Research DOI: 10.1021/acs.jproteome.2c00748 Zhen Sun, Weidi Xiao, Naikang Li, Lei Chang, Ping Xu, and Yanchang Li March 6, 2023 http://dx.doi.org/10.1021/acs.jproteome.2c00748
Transcription factor interactions explain the context-dependent activity of CRX binding sites
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Transcription factor interactions explain the context-dependent activity of CRX binding sites The effects of transcription factor binding sites (TFBSs) on the activity of a cis-regulatory element (CRE) depend on the local sequence context. In rod photoreceptors, binding sites for …
Solventâinduced proteome profiling for proteomic quantitation and target discovery of small molecular drugs
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Solventâinduced proteome profiling for proteomic quantitation and target discovery of small molecular drugs Abstract Target identification by modification-free proteomic approaches can potentially reveal the pharmacological mechanism of small molecular compounds. By combining the …
The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" The ups and downs of biological oscillators: A comparison of time-delayed negative feedback mechanisms Many biochemical oscillators are driven by the periodic rise and fall of protein concentrations or activities. A negative feedback loop underlies such oscillations. The feedback …
An integrated workflow for quantitative analysis of the newly synthesized proteome
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" An integrated workflow for quantitative analysis of the newly synthesized proteome The analysis of proteins that are newly synthesized upon a cellular perturbation can provide detailed insight in the proteomic response that is elicited by specific cues. This can …
Identification of proteoforms by topâdown proteomics using twoâdimensional low/low pH reversedâphase liquid chromatographyâmass spectrometry
Proteomics (Wiley) Wiley: PROTEOMICS: Table of Contents Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues. Identification of proteoforms by topâdown proteomics using twoâdimensional low/low pH reversedâphase liquid chromatographyâmass spectrometry Abstract In top-down (TD) proteomics, efficient proteoform separation is crucial to reduce the sample complexity and increase the depth …
Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Leveraging genetic diversity to identify small molecules that reverse mouse skeletal muscle insulin resistance Systems genetics has begun to tackle the complexity of insulin resistance by capitalising on computational advances to study high-diversity populations. "Diversity Outbred in Australia (DOz)" …
Inferring gene regulatory networks using transcriptional profiles as dynamical attractors
BioRxiv bioRxiv Subject Collection: Systems Biology This feed contains articles for bioRxiv Subject Collection "Systems Biology" Inferring gene regulatory networks using transcriptional profiles as dynamical attractors Genetic regulatory networks (GRNs) regulate the flow of genetic information from the genome to expressed messenger RNAs (mRNAs) and thus are critical to controlling the phenotypic characteristics of cells. …
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 …
[ASAP] Electrochemically Etched Tapered-Tip Stainless-Steel Electrospray-Ionization Emitters for Capillary ElectrophoresisâMass Spectrometry
Journal of Proteome Research Journal of Proteome Research: Latest Articles (ACS Publications) latest articles published in Journal of Proteome Research [ASAP] Electrochemically Etched Tapered-Tip Stainless-Steel Electrospray-Ionization Emitters for Capillary ElectrophoresisâMass Spectrometry Journal of Proteome Research DOI: 10.1021/acs.jproteome.3c00076 Jordan T. Aerts, Per E. AndreĚn, and Erik T. Jansson March 3, 2023 http://dx.doi.org/10.1021/acs.jproteome.3c00076