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Review
Medicine, General & Internal
Tomoya Hirota et al.
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects approximately 2.3% of US children aged 8 years and approximately 2.2% of adults. There are no specific biomarkers for diagnosing ASD. Early signs of ASD include lack of response to name, limited use of gestures, and lack of imaginative play. Behavioral interventions are the first-line therapy, while co-occurring psychiatric conditions can be treated with specific behavioral therapy or medication.
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2023)
Article
Biochemistry & Molecular Biology
Wei Xiong Wen et al.
Summary: A comprehensive R package called MARVEL was developed for single-cell splicing analysis. Extensive benchmarking and analysis of publicly available datasets demonstrated the importance and utility of MARVEL in single-cell research, enabling systematic analysis of splicing and gene expression to reveal biological insights.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Damian Szklarczyk et al.
Summary: The STRING database systematically collects and integrates protein-protein interaction information, providing researchers with valuable insights into the functional and regulatory interactions within cells. It offers various data access and analysis tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Alex Bateman et al.
Summary: The UniProt Knowledgebase aims to provide comprehensive, high-quality, and freely accessible protein sequences annotated with functional information. The database has expanded its data processing pipeline and website to accommodate the increasing information content, with over 227 million sequences and plans to include a reference proteome for each taxonomic group. Detailed annotations are extracted from the literature to update or create reviewed entries, while unreviewed entries are supplemented with annotations from automated systems. The new website, https://www.uniprot.org/, offers enhanced user experience and easy access to data, including AlphaFold structures and improved protein subcellular localization visualizations.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Gihanna Galindez et al.
Summary: Molecular interaction networks are the basis for studying the control of biological functions by genes and proteins. Utilizing these networks, researchers have uncovered mechanisms underlying complex diseases. Advancements in omics technologies have enabled large-scale network analysis, and various modeling techniques have proven useful for gaining new insights. This article provides an overview of recent network-based methods and discusses the relevance to biomedical research, highlighting the need for integrative and dynamic network approaches.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Alyssa Soles et al.
Summary: The extracellular matrix (ECM) surrounds cells in the brain and plays important roles in development, the healthy adult brain, and brain diseases. This review discusses the physiological roles of the ECM, its contribution to the pathogenesis of brain disease, and the involvement of gene expression changes, transcriptional factors, and microglia in ECM regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Minoru Kanehisa et al.
Summary: KEGG is a manually curated database resource that integrates various biological objects classified into systems, genomic, chemical, and health information. Through the KEGG identifier and URL links, users can retrieve and browse information for different biological objects, including pathway maps, hierarchy, and genomes. KEGG has also improved KO assignment annotation and included more eukaryotic genomes for better representation of organisms in the taxonomic tree. The taxonomy mapping enables analysis of the conservation of functional and physical links among genes in different organism groups.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ruth L. Seal et al.
Summary: The HUGO Gene Nomenclature Committee (HGNC) is responsible for assigning unique symbols and names to human genes. Their database contains over 43,000 approved gene symbols, including protein-coding genes, pseudogenes, and non-coding RNA genes, which are displayed on their public website along with links to genomic, clinical, and proteomic information.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Sabah Nisar et al.
Summary: Autism-spectrum disorders (ASDs) are developmental disabilities characterized by abnormalities in social behaviors, communication skills, and repetitive behaviors. This review discusses the importance of neuroimaging genetics approaches in understanding the neurobiological mechanisms of ASD and detecting early diagnostic biomarkers. Neuroimaging genetics helps identify ASD-risk genes and elucidate the pathways that confer genetic risk, while integrating artificial intelligence models with neuroimaging data enables accurate diagnosis and biomarker discovery.
MOLECULAR PSYCHIATRY
(2023)
Article
Genetics & Heredity
Suzi A. Aleksander et al.
Summary: The Gene Ontology (GO) knowledgebase is a comprehensive resource that provides information about the functions of genes and gene products. It covers a wide range of organisms and receives updates from a consortium of scientists. The knowledgebase consists of three components: GO, which describes gene functionality; GO annotations, which provide evidence-supported statements about gene products; and GO-CAMs, which are models of molecular pathways. The knowledgebase is continuously updated and reviewed, and guidance is provided to users on how to make the best use of the data.
Article
Psychiatry
Ila Dwivedi et al.
Summary: Opioid use disorder among pregnant women is a growing problem in the US, and the commonly used intervention methadone may have long-term effects on prenatal brain development. Using hCO technology, researchers found that methadone exposure during early cortical development alters transcriptional programs associated with synaptogenesis by modulating extra-synaptic molecular mechanisms. These findings provide new insights into the potential impact of methadone on cognitive and behavioral development and can help improve interventions for maternal opioid addiction.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Psychiatry
Miaomiao Jiang et al.
Summary: This study uses bibliometric analysis to describe the current state and trends of autism research over the past decade. It identifies genetics as a widely cited field within autism research, and highlights immune dysbiosis and gut microbiota as new development frontiers since 2015.
FRONTIERS IN PSYCHIATRY
(2023)
Article
Neurosciences
Madhavi Apte et al.
Summary: Autism is a complex spectrum of neurodevelopmental disorders characterized by repetitive and restricted behaviors and interests, as well as social interaction and communication difficulties that manifest in infancy. Over 18 million Indians, according to the National Health Portal of India, and 1 in 160 children worldwide, according to the WHO, are diagnosed with autism spectrum disorders. This review discusses the intricate genetic architecture underlying autism and summarizes the role of proteins likely to be involved in its development, along with the impact of genetic mutations on convergent signaling pathways and brain circuitry development, as well as the role of cognition development and theory of mind in autism and the benefits of cognition-behavior therapy.
IBRO NEUROSCIENCE REPORTS
(2023)
Article
Immunology
Maria Gevezova et al.
Summary: Through the analysis of large-scale gene expression data from 1355 ASD patients and 1110 controls, abnormalities in transcription factors and immune-inflammatory pathways were found in the brains and peripheral blood of ASD patients. These abnormalities lead to impairments in neurodevelopment and social behaviors, and are associated with neuroinflammation and mitochondrial dysfunction induced by viral infections.
BRAIN, BEHAVIOR, & IMMUNITY - HEALTH
(2023)
Review
Behavioral Sciences
Bahman Yousefi et al.
Summary: Autism Spectrum Disorder (ASD) is a severe neurodegenerative syndrome that is related to gut dysbiosis. Dysbiosis leads to increased inflammation, altered neurotransmitter levels, and may contribute to abnormal signaling in ASD. Disruption of the gastrointestinal barrier may increase the risk of ASD. Microbiota influence the functioning of the central nervous system by regulating the quantity and types of bioactive materials transferred from the intestine to the brain.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Marc Gillespie et al.
Summary: The Reactome Knowledgebase, a core resource of Elixir, provides manually curated molecular details of human biological processes, serving as a digital archive and tool for discovering functional relationships. Recent work has expanded annotations of signaling processes, drugs targeting them, infections by coronaviruses, and better analysis tools for high-throughput data and placement of unstudied proteins.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Yoonbee Kim et al.
Summary: Network-based computational approaches are used for efficient disease-gene association prediction. This survey provides an overview of network-based disease-gene association prediction methods and shows that integrative methods perform better.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Maria Gevezova et al.
Summary: This study is the first to link elevated NGF with mitochondrial respiration and altered energy homeostasis in ASD. High levels of NGF may serve as a screening tool to improve early diagnosis and clinical follow-up in ASD.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Chen-Chen Jiang et al.
Summary: Autism spectrum disorder (ASD) is a common and complex neurodevelopmental disorder with a strong genetic basis. Despite the limited understanding of its etiology, risk factors, and disease progression, significant progress has been made in genetics, identifying hundreds of genes associated with a high risk for autism. The involvement of signal transduction molecular events in pathological processes has important implications for precise molecular targeting in autism. This review provides insights into the mechanisms and clinical implications of signal transduction in autism, as well as future challenges and perspectives.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Review
Neurosciences
Atsushi Sato et al.
Summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder associated with the hyperactivation of mTORC1. Through studies on rodent models and clinical trials, mTORC1 inhibitors are considered promising therapeutics for treating ASD associated with mTORC1 activation.
BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Marco Fiorillo et al.
Summary: This study identifies high ATP production by the mitochondrial ATP-synthase as a new therapeutic target for anticancer therapy, particularly for inhibiting tumor progression. ATP-high cancer cells exhibit aggressive phenotypes with increased proliferation, stemness, anchorage-independence, cell migration, invasion, and multi-drug resistance, along with high antioxidant capacity. ATP depletion through targeting ATP5F1C may serve as a promising strategy for preventing metastasis and avoiding treatment failure, making ATP5F1C a potential biomarker and molecular target for future drug development to prevent metastatic disease progression.
CELL DEATH AND DIFFERENTIATION
(2021)
Article
Psychiatry
Richard E. Frye et al.
Summary: This study found that changes in mitochondrial morphology in children with ASD were associated with the activity of ETC complexes and symptom severity. ASD participants with elevated Complex IV activity showed more typical mitochondrial morphology and milder symptoms. Further research is needed to explore the molecular mechanisms behind these unique metabolic changes.
TRANSLATIONAL PSYCHIATRY
(2021)
Review
Oncology
Marco Fiorillo et al.
Summary: The study suggests that high mitochondrial ATP production is a new therapeutic target for cancer treatment, isolating metabolically fit cancer cells with enhanced stem-like properties and invasive abilities. By regulating mitochondrial ATP-synthase, prevention of metastasis in cancer cells is possible.
FRONTIERS IN ONCOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jun Nomura et al.
Summary: The genetic and phenotypic heterogeneity of autism spectrum disorder (ASD) hinders the unified explanation of its complex features. Recent psychiatric genetic studies have identified numerous risk genes and chromosome loci, enabling analysis at the single gene level and utilizing system-level approaches. Comparing data of ASD with other major psychiatric disorders can reveal the unique characteristics of both diseases.
JOURNAL OF NEUROCHEMISTRY
(2021)
Article
Biochemical Research Methods
Apichat Suratanee et al.
Summary: This study established an analysis framework using network topological profiles, machine learning, and statistical analysis to predict human-P. vivax protein associations, successfully identifying potential targets for the treatment of P. vivax malaria. By integrating related data, this analysis efficiently identified potential targets and provided insights into human-parasite protein associations, with the potential for generalizing the model to gain further insights into other diseases in the field of biomedical science.
BIOINFORMATICS AND BIOLOGY INSIGHTS
(2021)
Article
Mathematical & Computational Biology
Panisa Janyasupab et al.
Summary: Disease-related gene prioritization is a crucial pharmaceutical technique, and integrating centrality measures into the traditional ND model can effectively identify new disease-related genes, providing valuable help for biomedical science.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Biochemistry & Molecular Biology
F. Kyle Satterstrom et al.
Editorial Material
Pediatrics
Susan L. Hyman et al.
Article
Genetics & Heredity
Ignazio Stefano Piras et al.
AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS
(2020)
Review
Genetics & Heredity
Cristina Cheroni et al.
Article
Neurosciences
Md Rezanur Rahman et al.
Review
Biochemistry & Molecular Biology
Elena Masini et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Alexander P. Gabrielli et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Review
Neurosciences
Milen Velinov
FRONTIERS IN CELLULAR NEUROSCIENCE
(2019)
Article
Genetics & Heredity
Ryan N. Doan et al.
Article
Biochemistry & Molecular Biology
Wayne Pereanu et al.
NUCLEIC ACIDS RESEARCH
(2018)
Review
Medicine, General & Internal
Karen L. Kotloff et al.
Article
Mathematical & Computational Biology
Changhong Yang et al.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)
Article
Mathematical & Computational Biology
Sezin Kircali Ata et al.
BMC SYSTEMS BIOLOGY
(2018)
Article
Biochemical Research Methods
Apichat Suratanee et al.
BIOINFORMATICS AND BIOLOGY INSIGHTS
(2017)
Review
Behavioral Sciences
Joon Yong An et al.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2016)
Article
Biochemistry & Molecular Biology
Maxim V. Kuleshov et al.
NUCLEIC ACIDS RESEARCH
(2016)
Review
Pharmacology & Pharmacy
Jacopo Meldolesi
PHARMACOLOGICAL RESEARCH
(2016)
Article
Multidisciplinary Sciences
Xiao Ji et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Biochemical Research Methods
Jianxin Wang et al.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2015)
Article
Multidisciplinary Sciences
Angela M. Mabb et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2014)
Article
Biochemistry & Molecular Biology
John E. Walker
BIOCHEMICAL SOCIETY TRANSACTIONS
(2013)
Article
Multidisciplinary Sciences
Ian F. King et al.
Article
Neurosciences
Guomei Tang et al.
NEUROBIOLOGY OF DISEASE
(2013)
Article
Biochemistry & Molecular Biology
Tanya Barrett et al.
NUCLEIC ACIDS RESEARCH
(2013)
Letter
Genetics & Heredity
Brett S. Abrahams et al.
Review
Neurosciences
Janet K. Kern et al.
TRANSLATIONAL NEURODEGENERATION
(2013)
Article
Multidisciplinary Sciences
Stephan J. Sanders et al.
Article
Physics, Multidisciplinary
Huawei Shen et al.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2009)
Article
Biochemistry & Molecular Biology
Saumyendra N. Basu et al.
NUCLEIC ACIDS RESEARCH
(2009)
Article
Biochemistry & Molecular Biology
Amelie Piton et al.
HUMAN MOLECULAR GENETICS
(2008)
Article
Biochemistry & Molecular Biology
P Shannon et al.
