Article
Biochemical Research Methods
Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, Markus List
Summary: Cancer is a major cause of death globally, and there is a need for innovative methods to stratify patients and identify biomarkers using molecular data. spongEffects is a novel method that infers subnetworks from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity.
Article
Multidisciplinary Sciences
Yong Shao, Long Zhou, Fang Li, Lan Zhao, Bao-Lin Zhang, Feng Shao, Jia-Wei Chen, Chun-Yan Chen, Xupeng Bi, Xiao-Lin Zhuang, Hong-Liang Zhu, Jiang Hu, Zongyi Sun, Xin Li, Depeng Wang, Iker Rivas-Gonzalez, Sheng Wang, Yun-Mei Wang, Wu Chen, Gang Li, Hui-Meng Lu, Yang Liu, Lukas F. K. Kuderna, Kyle Kai-How Farh, Peng-Fei Fan, Li Yu, Ming Li, Zhi-Jin Liu, George P. Tiley, Anne D. Yoder, Christian Roos, Takashi Hayakawa, Tomas Marques-Bonet, Jeffrey Rogers, Peter D. Stenson, David N. Cooper, Mikkel Heide Schierup, Yong-Gang Yao, Ya-Ping Zhang, Wen Wang, Xiao-Guang Qi, Guojie Zhang, Dong-Dong Wu
Summary: Comparative analysis of primate genomes is crucial for understanding human genetic architecture and primate evolution. This study analyzed the genomes of 50 primate species, including previously underrepresented groups. The results revealed varying rates of genomic rearrangement and gene evolution across primate lineages, with many genes under positive selection playing important roles in primate adaptations.
Article
Chemistry, Physical
Fei Qiu, Yijun Yan, Junlan Zeng, Jian-Ping Huang, Lingjiang Zeng, Wei Zhong, Xiaozhong Lan, Min Chen, Sheng-Xiong Huang, Zhihua Liao
Summary: The study on hyoscyamine dehydrogenase revealed the important role of the AbHDH gene in the biosynthesis of hyoscyamine and provided relevant biochemical and metabolic insights. AbHDH was found to enhance the production of hyoscyamine but did not significantly affect the biosynthesis of hyoscyamine, anisodamine, or scopolamine when suppressed.
Article
Plant Sciences
Danfeng Tang, Changqian Quan, Yang Lin, Kunhua Wei, Shuangshuang Qin, Ying Liang, Fan Wei, Jianhua Miao
Summary: Drought stress significantly affects the growth and development of Mesona chinensis Benth (MCB). However, MCB exhibits resistance to drought through various physiological and molecular mechanisms. Transcriptome analysis reveals the involvement of multiple metabolic pathways and transcription factors in the response of MCB to drought stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Forestry
Hong Zhang, Binrui Chen, Xiaoyi Zhao, Jing Hu, Zhijie Dong, Hui Xiao, Yanwen Yuan, Fei Guo, Yu Wang, Dejiang Ni, Pu Wang
Summary: This study demonstrates the necessity of leaf and light during cuttage by conducting experiments on 24 tea cultivars. Lower net photosynthesis rate is found to promote rooting. Leaf transcriptome analysis of an easy-to-root cultivar reveals differentially expressed genes involved in carbohydrate metabolism, signal transduction, metabolite biosynthesis and transportation during the rooting process.
Article
Agriculture, Dairy & Animal Science
Fangyuan Zeng, Lan Li, Jiaqi Yang, Siqi Liu, Yang Yuan, Chenxu Zhao, Jianguo Wang
Summary: This study investigated the regulatory mechanism of strontium in bovine chondrocytes by analyzing gene and protein expression changes. Transcriptomic and proteomic analyses revealed significant effects of strontium on cell proliferation and differentiation, fat metabolism, inflammation process, and immune responses. These findings provide insights into the functions and application of strontium in ruminants.
Article
Automation & Control Systems
Gerard Biau, Maxime Sangnier, Ugo Tanielian
Summary: This paper presents theoretical advances in WGANs, including discussions on architecture definition, mathematical features, and optimization properties. These features are verified through experiments to illustrate the trade-off effects between the generator and the discriminator.
JOURNAL OF MACHINE LEARNING RESEARCH
(2021)
Article
Plant Sciences
Wu Yang, Xianya Jiang, Yuelan Xie, Luo Chen, Junliang Zhao, Bin Liu, Shaohong Zhang, Dilin Liu
Summary: Our study identified a total of 768 differentially expressed genes between low-HMRR and high-HMRR accessions, with the up-regulated DEGs in low-HMRR accessions being mainly enriched in metabolic and biosynthetic processes, while the down-regulated DEGs in low-HMRR accessions were mainly concentrated in carbohydrate metabolic processes. Additionally, differential metabolites such as those in the shikimate and pyruvate pathways were integrated into two separate pathways in low-HMRR accessions.
Article
Biochemistry & Molecular Biology
Asad Ullah, Zohra Bano, Shahid Zaman
Summary: Quantitative structure-activity relationship (QSAR) is a method that correlates the biological structural features (topological indices) with pharmacological activity. Topological indices are numerical functions used to predict the growth rate of microorganisms in biological networks. Theoretical assessment of microorganisms helps in vaccine design and discovery by understanding their mechanism of actions. This article investigates the biological properties of two important biological networks (hypertree and its corona product) by obtaining novel topological features and deriving closed formulas for them.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Multidisciplinary
Drew A. Vecchio, Samuel H. Mahler, Mark D. Hammig, Nicholas A. Kotov
Summary: Materials with remarkable properties are structured as percolating nanoscale networks (PNNs), but their complex structures are difficult to describe using traditional methods and lack computational tools to capture patterns. The computational package StructuralGT generates GT descriptions of PNNs from micrographs, allowing rapid analysis of their structures. The GT parameters calculated can be correlated to specific material properties of PNNs for effective materials design.
Article
Genetics & Heredity
Xueting Wang, Qiming Hu, Jiaxi Wang, Lina Lou, Xuewen Xu, Xuehao Chen
Summary: This study provides an in-depth assessment of disease symptoms and biochemical content of cucumber stems infected with the Candidatusphytoplasma asteris strain. The results suggest that changes in plant hormone levels and mineral element composition contribute to phytoplasma infection. Comparative RNA-seq analysis identified several genes related to phenylpropanoid biosynthesis, phenylalanine metabolism, and plant hormone signal transduction that play a role in phytoplasma infection.
Article
Neurosciences
Kanhao Zhao, Boris Duka, Hua Xie, Desmond J. Oathes, Vince Calhoun, Yu Zhang
Summary: The dynamic graph convolutional network (dGCN) improves the diagnostic performance of Attention Deficit Hyperactivity Disorder (ADHD) by learning informative features in brain functional connectome. Visualization of functional abnormal regions and connectivity reveals important brain areas related to ADHD and a positive correlation with symptom severity. The proposed dGCN model shows great potential for precision diagnosis of ADHD and broader applications in studying mental disorders based on brain connectome.
Article
Automation & Control Systems
Yasin Yazicioglu, Mudassir Shabbir, Waseem Abbas, Xenofon Koutsoukos
Summary: This paper studies the strong structural controllability of networks and compares two lower bounds on the dimension of the strong structurally controllable subspace (SSCS). It is found that the distance-based lower bound is usually better than the zero-forcing-based bound when the latter is smaller than the overall network state dimension. Furthermore, a novel bound based on combining these two approaches is introduced, which is always at least as good as, and sometimes strictly greater than, the maximum of the two original bounds.
Article
Multidisciplinary Sciences
Maxime Rageot, Ramadan B. Hussein, Susanne Beck, Victoria Altmann-Wendling, Mohammed I. M. Ibrahim, Mahmoud M. Bahgat, Ahmed M. Yousef, Katja Mittelstaedt, Jean-Jacques Filippi, Stephen Buckley, Cynthianne Spiteri, Philipp W. Stockhammer
Summary: The ability of ancient Egyptians to preserve human bodies through embalming has fascinated people. Through archaeological, philological, and organic residue analyses, this study sheds new light on the embalming practice in ancient Egypt. The analysis of ceramic vessels from a 26th Dynasty embalming workshop revealed the use of specific mixtures of oils, tars, and resins for embalming. The study also highlights the trade networks that provided ancient Egyptian embalmers with foreign substances needed for mummification.
Article
Genetics & Heredity
Lu Zhang, Jie Song, Lvchun Peng, Weijia Xie, Shifeng Li, Jihua Wang
Summary: In this study, the molecular mechanism of cold-induced dormancy in Rhododendron floral buds was investigated using transcriptome data profiling and co-expression network analysis. The results revealed the crucial roles of endogenous hormones, carbohydrate metabolism, oxidative species, and proteins in regulating floral bud dormancy. Potential structural genes and transcription factors related to dormancy were identified, providing valuable candidates for further research on the molecular mechanisms of floral bud dormancy in Rhododendron species.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Alon Bartal, Alexander Lachmann, Daniel J. B. Clarke, Allison H. Seiden, Kathleen M. Jagodnik, Avi Ma'ayan
Article
Neurosciences
Zhihong Chen, Cameron J. Herting, James L. Ross, Ben Gabanic, Montse Puigdelloses Vallcorba, Frank Szulzewsky, Megan L. Wojciechowicz, Patrick J. Cimino, Ravesanker Ezhilarasan, Erik P. Sulman, Mingyao Ying, Avi Ma'ayan, Renee D. Read, Dolores Hambardzumyan
Article
Immunology
Jens Eberlein, Bennett Davenport, Tom T. Nguyen, Francisco Victorino, Kevin Jhun, Verena van der Heide, Maxim Kuleshov, Avi Ma'ayan, Ross Kedl, Dirk Homann
JOURNAL OF IMMUNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Minji Jeon, Kathleen M. Jagodnik, Eryk Kropiwnicki, Daniel J. Stein, Avi Ma'ayan
Summary: While many genes are associated with pain, the molecular mechanisms are largely unknown. A machine learning model was trained to predict new pain targets, showing promising results for identifying novel drug targets and pathways. This approach provides a foundation for future experimental exploration in developing safer and more effective analgesics.
Article
Multidisciplinary Sciences
Evan Austin, Eugene Koo, Alexander Merleev, Denis Torre, Alina Marusina, Guillaume Luxardi, Andrew Mamalis, Roslyn Rivkah Isseroff, Avi Ma'ayan, Emanual Maverakis, Jared Jagdeo
Summary: Red light phototherapy can improve skin fibrosis by regulating extracellular matrices, proliferation, and cellular responses to oxygen-containing compounds. The study found that red light therapy may have anti-fibrotic effects by increasing the expression of MMP1 and PRSS35.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Maxim Kuleshov, Zhuorui Xie, Alexandra B. K. London, Janice Yang, John Erol Evangelista, Alexander Lachmann, Ingrid Shu, Denis Torre, Avi Ma'ayan
Summary: KEA3 is a webserver application used to predict upstream kinases and analyze data from proteomics and phosphoproteomics studies. The background database of KEA3 contains measured and predicted kinase-substrate interactions. Studies show that integrating kinase-substrate and kinase-protein interactions across data sources improves the recovery of the expected kinase.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Alexander Lachmann, Zhuorui Xie, Avi Ma'ayan
Summary: This paper introduces an algorithm called blitzGSEA, which significantly improves gene set enrichment analysis. Compared to previous methods, blitzGSEA allows for faster calculations and more accurate estimation of small P-values.
Article
Biochemical Research Methods
Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan
Summary: DrugShot is a web-based server application that provides ranked lists of drugs and small molecules relevant to biomedical search terms. By integrating PubMed abstracts and LINCS L1000 signatures, DrugShot can predict additional drugs and small molecules associated with the search term.
BMC BIOINFORMATICS
(2022)
Article
Dermatology
Alexandros Onoufriadis, Laura E. Proudfoot, Chrysanthi Ainali, Denis Torre, Maria Papanikolaou, Tuntas Rayinda, Ellie Rashidghamat, Retno Danarti, Jemima E. Mellerio, Avi Ma'ayan, John A. McGrath
Summary: This study identified gene expression profiles and pathways in RDEB wounds, identifying potential drugs or compounds to restore wound healing. The findings highlight the clinical value of reverse transcriptomics data analysis in RDEB and the potential of this approach in discovering or repurposing drugs for other diseases.
EXPERIMENTAL DERMATOLOGY
(2022)
Article
Cell Biology
Edmund Charles Jenkins, Mrittika Chattopadhyay, Maria Gomez, Denis Torre, Avi Ma'ayan, Miguel Torres-Martin, Daniela Sia, Doris Germain
Summary: A major limitation in breast cancer research using mouse models is that most mice develop estrogen receptor-alpha (ER alpha)-negative mammary tumors, while in humans, the majority of breast cancers are ER alpha-positive. However, a new study using an inducible mouse model revealed that mammary tumors in young mice are ER alpha-negative, while they are ER alpha-positive in aged mice. The study also identified genes involved in the activation of ER alpha axis and the regulation of UPR stress responses in aged female-derived mammary tumors. These findings suggest that aging alters the oncogenic trajectory towards ER alpha-positive breast cancer subtype.
Article
Cell Biology
J. B. Daniel Clarke, W. Alison Rebman, Jinshui Fan, J. Mark Soloski, N. John Aucott, Avi Ma'ayan
Summary: This study analyzed differential gene expression in peripheral blood cells of patients with acute Lyme disease and post-treatment Lyme disease using RNA sequencing, revealing an inflammatory signature in post-treatment patients distinct from those with acute disease. By extracting gene sets and analyzing feature importance, a potential biomarker set was identified for distinguishing healthy individuals from those with acute or post-treatment Lyme disease.
CELL REPORTS MEDICINE
(2022)
Article
Cell Biology
Eden Z. Deng, Reid H. Fleishman, Zhuorui Xie, Giacomo B. Marino, Daniel J. B. Clarke, Avi Ma'ayan
Summary: To identify potential targets for selective identification and removal of senescent cells, gene expression signatures of senescent cells were compared to normal human tissues and cell types. A gene set called SenoRanger, composed of 301 genes, was established based on consensus analysis. Pathway analysis confirmed the potential role of SenoRanger genes in aging and senescence-related processes. Overall, SenoRanger provides solid hypotheses for identifying and removing senescent cells.
Article
Biochemistry & Molecular Biology
Giacomo B. Marino, Michael Ngai, Daniel J. B. Clarke, Reid H. Fleishman, Eden Z. Deng, Zhuorui Xie, Nasheath Ahmed, Avi Ma'ayan
Summary: GeneRanger is a web server that integrates data from multiple atlases to provide information about gene and protein expression in normal human cells, tissues, and cell lines. TargetRanger, on the other hand, compares uploaded RNA-seq data to expression levels across atlases to identify highly expressed genes in the input that are lowly expressed in normal human cells and tissues. Both servers offer visualization through box and scatter plots, as well as interactive tables.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Nhi Nguyen, Daniel J. B. Clarke, Avi Ma'ayan
Summary: Enrichr-KG is a knowledge graph database and web-server application that integrates gene set libraries from Enrichr for comprehensive enrichment analysis and visualization. The graphical representation of cross-library results allows users to uncover hidden associations between genes and annotated enriched terms from different datasets and resources. Enrichr-KG currently offers 26 gene set libraries from various categories including transcription, pathways, ontologies, diseases/drugs, and cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan
Summary: lncHUB2 is a web server database that provides extensive information about the function and regulation of human and mouse lncRNAs, including secondary structure fold, related publications, correlated coding genes and lncRNAs, visualized gene network, predicted phenotypes, participation in biological processes and pathways, predicted transcription factors, disease associations, subcellular localization information, expression patterns, and predicted regulators. Overall, lncHUB2 is a valuable resource for hypothesis generation in future studies.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)