Editorial Material
Multidisciplinary Sciences
Luke M. M. Evans, Pamela N. Romero N. Villela
Summary: An analysis of rare genetic variants shows their impact on human traits is mediated through similar biological pathways as common variants, enhancing our understanding of their influence on complex traits.
Editorial Material
Multidisciplinary Sciences
Roser Vento-Tormo, Roser Vilarrasa-Blasi
Summary: The HuBMAP consortium has created spatially resolved cell atlases for the human intestine, kidney, and placenta, providing unprecedented detail for analyzing tissue organization.
Article
Multidisciplinary Sciences
Xia Liu, Minghui Wang, Ao Li
Summary: This study introduces a novel deep-learning framework called PhosVarDeep for predicting phospho-variants, which significantly improves prediction performance through two identical subnetworks and a prediction module. The experimental results demonstrate the effectiveness of this method and its favorable comparison with existing conventional machine learning methods.
Review
Genetics & Heredity
Waleed Iqbal, Wanding Zhou
Summary: Understanding tissue heterogeneity requires analyzing intercellular epigenetic differences at the single-cell level. Recent advances in single-cell DNA methylome profiling have provided the tools to study this heterogeneity in detail. However, these advances also bring challenges in data analysis and interpretation.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Computer Science, Artificial Intelligence
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita
Summary: This paper proposes an effective clustering method for scRNA-seq data, which integrates preprocessing steps and robust cell group identification. The method requires no user input, except for setting thresholds, and outperforms most other existing methods.
KNOWLEDGE-BASED SYSTEMS
(2022)
Review
Biochemical Research Methods
Shangbo Ning, Huiwen Wang, Chen Zeng, Yunjie Zhao
Summary: Cyclin-dependent kinase (Cdk) proteins are important in cell cycle progression and can be targeted for therapy against diseases like cancer. Current Cdk inhibitors lack specificity and often have side effects, making it necessary to identify and study non-catalytic pockets that can interfere with kinase activity. This article summarizes the existing Cdk pockets and their selectivity, introduces a network-based pocket prediction approach called NetPocket, and discusses potential future directions and challenges.
BRIEFINGS IN BIOINFORMATICS
(2022)
News Item
Multidisciplinary Sciences
Ewen Callaway
Summary: Analysis of protein shapes reveals unexpected forms and connections.
Editorial Material
Multidisciplinary Sciences
Anthony J. Hannan
Summary: The study found a link between tandem repeats in DNA and autism spectrum disorder, which could provide insights into other human disorders. Bioinformatic analysis was used to study tandem repeat mutations in autism.
Editorial Material
Multidisciplinary Sciences
David A. Leopold
Summary: The human brain's motor cortex is traditionally seen as a linear map controlling different body parts. However, the discovery of additional functions suggests a different kind of mapping.
Editorial Material
Multidisciplinary Sciences
Miryam Naddaf
Summary: The Human Brain Project is coming to an end in September after a decade. Nature magazine examines its achievements and its troubled past.
Article
Biotechnology & Applied Microbiology
Yanlin Mi, Stefan-Bogdan Marcu, Sabin Tabirca, Venkata V. B. Yallapragada
Summary: In the field of bioinformatics and computational biology, protein structure modelling and analysis is crucial. To address the lack of user-friendly tools, we developed PROFASA, a protein workstation that combines state-of-the-art visualisation techniques with cutting-edge tools for analysis. PROFASA provides a comprehensive platform for protein sequence and structure analysis, simplifying complex workflows and offering customization options.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biology
Hussain Ahmed Chowdhury, Dhruba Kumar Bhattacharyya, Jugal Kumar Kalita
Summary: scRNA-seq data analysis allows for identification of novel cells, specific characterization of known cells, and study of cell heterogeneity. Most clustering methods are influenced by user input, but UICPC shows excellent performance without requiring user input.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Deborah Giordano, Cassiano Langini, Amedeo Caflisch, Anna Marabotti, Angelo Facchiano
Summary: The study compares the structures and flexibility of transglutaminase enzymes from Kutzneria albida (KalbTGase) and Streptomyces mobaraensis (MTGase). It is found that KalbTGase is more rigid and has a more closed catalytic site at room temperature, indicating higher selectivity compared to MTGase. Preliminary results at higher temperature suggest enhanced flexibility of KalbTGase, potentially allowing it to adapt to different substrates, while MTGase shows reduced adaptability and catalytic activity at higher temperatures.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Pediatrics
Edward F. F. Xie, Sarah Hilkert Rodriguez, Bingqing Xie, Mark D'Souza, Gonnah Reem, Dinanath Sulakhe, Dimitra Skondra
Summary: This study aims to identify drugs and chemicals for the treatment of retinopathy of prematurity (ROP) with comprehensive safety profiles and tolerability using a computational bioinformatics approach. By querying relevant literature and gene databases, genes associated with ROP were identified, and compounds with significant associations to these genes were predicted. The study resulted in a list of potential drugs and compounds with therapeutic value for ROP.
FRONTIERS IN PEDIATRICS
(2023)
Article
Immunology
Winston A. Haynes, Kathy Kamath, Rebecca Waitz, Patrick S. Daugherty, John C. Shon
Summary: Identification of antigens associated with antibodies is crucial for understanding immune responses in various disease contexts. Using methods like Serum Epitope Repertoire Analysis (SERA) and Protein-based Immunome Wide Association Study (PIWAS), disease-associated serological antigens can be discovered within any known proteome with high statistical power and accuracy.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Spectroscopy
Kenneth Verheggen, Helge Raeder, Frode S. Berven, Lennart Martens, Harald Barsnes, Marc Vaudel
MASS SPECTROMETRY REVIEWS
(2020)
Article
Biochemical Research Methods
Niels Hulstaert, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, Yasset Perez-Riverol
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Biochemical Research Methods
Tim Van den Bossche, Pieter Verschaffelt, Kay Schallert, Harald Barsnes, Peter Dawyndt, Dirk Benndorf, Bernhard Y. Renard, Bart Mesuere, Lennart Martens, Thilo Muth
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Immunology
Waqas Azeem, Ragnhild Maukon Bakke, Silke Appel, Anne Margrete Oyan, Karl-Henning Kalland
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Biochemical Research Methods
Bram Burger, Marc Vaudel, Harald Barsnes
Summary: Randomization is an effective tool in experimental design for reducing unanticipated confounders, but complete randomization can result in imbalanced designs. Block randomization serves as a method to prevent severe imbalances in sample allocation, addressing both known and unknown confounders. This provides insight into how to effectively organize samples during experimental design, particularly in the context of proteomics research.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Astrid Guldbrandsen, Ragnhild Reehorst Lereim, Mari Jacobsen, Hilde Garberg, Ann Cathrine Kroksveen, Harald Barsnes, Frode S. Berven
CLINICAL PROTEOMICS
(2020)
Article
Multidisciplinary Sciences
Eystein Oveland, Intakhar Ahmad, Ragnhild Reehorst Lereim, Ann Cathrine Kroksveen, Harald Barsnes, Astrid Guldbrandsen, Kjell-Morten Myhr, Lars Bo, Frode S. Berven, Stig Wergeland
Summary: By analyzing two different experimental models of multiple sclerosis using quantitative proteomics in the frontal cortex, new protein alterations were discovered as potential diagnostic, prognostic, or treatment targets. While there were some overlapping proteins between the two models, significant differences were also observed, such as the upregulation of legumain in multiple sclerosis patients, which may be associated with lesion activity.
SCIENTIFIC REPORTS
(2021)
Review
Oncology
Oddmund Nordgard, Rakel Brendsdal Forthun, Morten Lapin, Bjorn Henning Gronberg, Karl Henning Kalland, Reidun Kristin Kopperud, Liv Cecilie Vestrheim Thomsen, Kjersti Tjensvoll, Bjornar Gilje, Bjorn Tore Gjertsen, Randi Hovland
Summary: Liquid biopsies have emerged as a potential new diagnostic tool for solid cancers, with circulating tumor DNA and circulating tumor cells playing key roles in providing detailed information for characterization and treatment. While substantial evidence supports the clinical utility of liquid biopsies in cancer diagnostics, further research is needed for broader application in clinical practice.
Article
Biochemistry & Molecular Biology
Waqas Azeem, Ragnhild Maukon Bakke, Benjamin Gabriel, Silke Appel, Anne Margrete Oyan, Karl-Henning Kalland
Summary: Research indicates that axitinib and nitazoxanide did not significantly inhibit beta-catenin signaling in monocyte-derived dendritic cells, but exhibited lower cytotoxicity. Axitinib stimulated various aspects of dendritic cell function, such as IL12-p70 secretion, and countered IL-10 secretion.
Article
Biotechnology & Applied Microbiology
Ksenia Lavrichenko, Stefan Johansson, Inge Jonassen
Summary: Different high-throughput genome technologies have varying abilities in detecting copy number variants (CNVs), with long-read platforms being able to detect CNVs in genomic regions inaccessible to arrays or short reads. The reproducibility of CNV detection within each technology is strongly linked to other CNV evidence measures. Additionally, the public database frequency profiles for CNVs vary depending on the technology the database was built on.
Article
Pharmacology & Pharmacy
Yaping Hua, Xing Yuan, Yun-heng Shen, Jinxin Wang, Waqas Azeem, Shuo Yang, Alexandra Gade, Seyed Mohammad Lellahi, Anne Margrete oyan, Xisong Ke, Wei-dong Zhang, Karl-Henning Kalland
Summary: Our drug discovery model has identified two novel STAT3 SH2 domain inhibitors, which show potential for treating cancers with hyper-activated STAT3.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Waqas Azeem, Jan Roger Olsen, Margrete Reime Hellem, Yaping Hua, Kristo Marvyin, Xisong Ke, Anne Margrete oyan, Karl-Henning Kalland
Summary: This study investigated the role of GATA2 in prostate epithelial cells and found that exogenous GATA2 protein was rapidly degraded and its expression could be rescued by proteasome inhibitors. The inhibition of proteasome also induced the transcription of AR mRNA and luminal marker genes in prostate cells. Different intrinsic mechanisms restricted the expression of GATA2 in these cells. These findings suggest the existence of crucial cofactors for AR mRNA expression and luminal differentiation at the proteolytic level.
Article
Immunology
Seyed Mohammad Lellahi, Waqas Azeem, Yaping Hua, Benjamin Gabriel, Kristin Paulsen Rye, Hakon Reikvam, Karl-Henning Kalland
Summary: Conventional type 1 dendritic cells (cDC1) and conventional type 2 dendritic cells (cDC2) are being considered as alternative options to monocyte-derived dendritic cells (moDCs) in cancer immunotherapy. However, the low numbers of cDCs in peripheral blood and their extensive spontaneous apoptosis and death in culture within 24hrs pose challenges. The study found that GM-CSF improved the viability of both cDC1 and cDC2, while Flt3-L and IL-4 specifically increased the viability of cDC1 and cDC2, respectively. Combinations of these three cytokines further improved the viability of both cDCs at different time points.
FRONTIERS IN IMMUNOLOGY
(2023)
Meeting Abstract
Immunology
Dag Heiro Yi, Waqas Azeem, Anne Margrete Oyan, Karl Henning Kalland, Silke Appel
EUROPEAN JOURNAL OF IMMUNOLOGY
(2021)
Article
Cell & Tissue Engineering
Manoj K. Gupta, Heidrun Vethe, Samir Softic, Tata Nageswara Rao, Vilas Wagh, Jun Shirakawa, Harald Barsnes, Marc Vaudel, Tomozumi Takatani, Sevim Kahraman, Masaji Sakaguchi, Rachael Martinez, Jiang Hu, Yngvild Bjorlykke, Helge Raeder, Rohit N. Kulkarni
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)
