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Immunology
Zheng Chen et al.
Summary: This study identified PNOC and LAIR2 as biomarkers for immune infiltration evaluation in cholangiocarcinoma, with PNOC expressed by B cells predicting better patient survival and LAIR2 correlating with worse patient survival. High B cell infiltration levels were associated with better overall survival in cholangiocarcinoma patients. Pathway changes in malignant cell populations were also analyzed in relation to tumor progression.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Microbiology
Jacob T. Nearing et al.
Summary: Advances in DNA sequencing technology have improved researchers' ability to explore human microbiomes, but systemic biases introduced during the process can lead to inconsistent results. Biases begin with sample collection and persist throughout experiments, resulting in observed microbial communities that differ significantly from the true composition. efforts to reduce bias in sequence-based human microbiome studies are ongoing.
Review
Genetics & Heredity
Sadaruddin Chachar et al.
Summary: Studies have shown that DNA 6mA modification plays a significant role in plants, particularly activating gene expression in model plants. However, the occurrence and importance of 6mA in non-model crops remain less understood, presenting an area for further research.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Ruizhi Xiang et al.
Summary: The study compared the performance of different dimensionality reduction methods in scRNA-seq data analysis. t-SNE showed the best accuracy and computing cost, while UMAP demonstrated high stability and preserved the cohesion and separation of cell populations.
FRONTIERS IN GENETICS
(2021)
Article
Oncology
Qingke Duan et al.
Summary: This study used single cell DNA sequencing to uncover genomic variations and clonal evolution in GEJ cancer, revealing significant heterogeneity and subclonal architecture within tumors, as well as two patterns of multi-station lymph node metastasis between primary site and lymph nodes.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Krithika Arumugam et al.
Summary: New long read sequencing technologies show great potential for recovering complete genomes from complex microbial communities, including key functional species relevant for wastewater bioprocesses. The study successfully recovered closed or complete genomes of several important microbial species and circularized plasmids, phages, and small microbial genomes from these communities using long read data.
NPJ BIOFILMS AND MICROBIOMES
(2021)
Review
Biochemistry & Molecular Biology
Sandra Brasil et al.
Summary: Rare diseases affect a large population but treatment options are limited. The development of new technologies accelerates the diagnosis of rare diseases, while epigenetics becomes a promising treatment option. With the help of AI tools, the diagnosis and treatment of rare diseases can be further improved.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Review
Medicine, General & Internal
Andrea Barp et al.
Summary: Neuromuscular disorders are often caused by genetic factors, and genetic testing is crucial for accurate diagnosis, family counseling, and prenatal screening. However, challenges and pitfalls remain in genetic analysis, which clinicians should be aware of.
Letter
Cardiac & Cardiovascular Systems
Luis R. Lopes et al.
CIRCULATION-GENOMIC AND PRECISION MEDICINE
(2021)
Review
Chemistry, Physical
Yingwen Chen et al.
Summary: Cells are fundamental building blocks of biological systems, and studying single cells can provide insights into cell diversity and disease processes. Single-cell RNA sequencing technologies allow cellular heterogeneity to be dissected at unprecedented resolution.
Review
Biochemistry & Molecular Biology
Shi-Xun Ma et al.
Summary: Single-cell and single-nucleus RNA sequencing technologies have advanced the molecular pathogenesis research of neurodegenerative disorders, particularly Parkinson's disease. Despite technical challenges in PD, recent studies have successfully characterized diverse cell-type populations and identified cell type-specific disease associations in PD.
Article
Biochemical Research Methods
Shiyang Zeng et al.
Summary: GLEANER is a web server dedicated to the analysis and visualization of multiomics data related to the mammalian germline cycle, providing a comprehensive collection of transcriptome, DNA methylome, chromatin accessibility, and histone modification characteristics. It displays integrative analysis results for each input gene, genes with correlated transcriptional changes, and overall continuous dynamic trends in the germline cycle.
BMC BIOINFORMATICS
(2021)
Review
Medical Laboratory Technology
Xue Bai et al.
Summary: The emergence of single-cell sequencing technology has effectively addressed the issue of tumor cell heterogeneity, providing important basis for correctly classifying tumor cells and revealing their molecular level changes.
CLINICA CHIMICA ACTA
(2021)
Article
Biotechnology & Applied Microbiology
Michelle Qiu Carter et al.
Summary: The study revealed significant differences in the methylome between different pathogenic strains of Escherichia coli, with one key reason being the presence of the PstI R-M system. In comparison to deficiency in DNA adenine methylase (Dam), deficiency in the PstI R-M system only had a transcriptional impact on a small number of genes.
Review
Biochemistry & Molecular Biology
Paulius Jonaitis et al.
Summary: Gastric cancer is a common cause of mortality worldwide, with intestinal metaplasia considered a key factor in its development. Recent research has identified various molecular alterations in intestinal metaplasia, some of which show strong associations with the disease and potential for prevention and treatment, though study homogeneity is a key limiting factor.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Khalid Anwar et al.
Summary: Plants face increasing frequencies of multiple abiotic stresses in nature, and their responses to these combined and sequential stresses differ from those triggered by individual stress. Studies have shown that there are interacting signaling pathways between various abiotic stresses, which are crucial for enhancing crops' tolerance to multiple stress combinations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Oncology
Yalan Lei et al.
Summary: Single-cell sequencing is a powerful tool that has revolutionized our understanding of the biological characteristics and dynamics within cancer lesions. Its use in cancer research provides valuable information related to malignant cell landscapes, immune cell interactions, tumor heterogeneity, circulating tumor cells, and underlying mechanisms of tumor behaviors, with bright prospects for diagnosis, targeted therapy, and prognostic prediction among various tumors. Advances in single-cell sequencing will undoubtedly enhance our understanding of tumor biological characteristics and uncover potential precise therapeutic targets for patients in the near future.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Tyler J. Bechtel et al.
Summary: Multicellular organisms rely on physical cell-cell interactions to regulate physiological processes. Understanding the complexity of these interactions has greatly improved insight into cell-cell engagement biology and led to opportunities for therapeutic development. Emerging approaches that combine chemistry and biology technologies effectively interrogate cell-cell interfaces with molecular-level detail.
NATURE CHEMICAL BIOLOGY
(2021)
Review
Genetics & Heredity
Sophia K. Longo et al.
Summary: Integrating single-cell RNA sequencing with spatial transcriptomics allows for the localization of transcriptionally characterized single cells within their native tissue context. While scRNA-seq identifies cell subpopulations within tissue, it does not capture their spatial distribution or reveal local networks of intercellular communication. Recent techniques like multiplexed in situ hybridization and in situ sequencing, defined as high-plex RNA imaging, can help address these limitations. However, the need for approaches to integrate single-cell and spatial data remains, given that no current method provides as complete a scope of the transcriptome as scRNA-seq.
NATURE REVIEWS GENETICS
(2021)
Review
Biotechnology & Applied Microbiology
Dandan Hu et al.
Summary: The study investigates the genetic diversity, genome structure, and population-level differentiation of the rapeseed gene pool in relation to known exotic introgressions. It summarizes progress in gene cloning, trait-marker associations, gene editing, molecular marker-assisted selection, and genome-wide prediction techniques. Future advancements are expected to accelerate genetic diversity manipulation for genomic-based improvement in rapeseed crops.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Review
Oncology
Ariana Cabrera-Licona et al.
Summary: Radiotherapy, along with surgery and systemic chemotherapy, is crucial in the clinical management of cancer, but radioresistance remains a major challenge. Epigenetic mechanisms regulating cancer hallmarks play a key role in the development of radiation resistance, and targeting these mechanisms can enhance treatment effectiveness.
RADIOTHERAPY AND ONCOLOGY
(2021)
Review
Agronomy
Pallavi Sinha et al.
Summary: Integrating genomics technologies and breeding methods to adjust core parameters of the breeder's equation can accelerate the delivery of climate-resilient and nutrient rich crops for future food security. This requires the identification or creation of favorable alleles/haplotypes, the addition of novel alleles for target traits while maintaining genetic diversity, and improvements in selection intensity and criteria. The heritability estimates also play a crucial role in enhancing genetic gains for climate resilience and nutritional traits.
THEORETICAL AND APPLIED GENETICS
(2021)
Review
Plant Sciences
Rajeev K. Varshney et al.
Summary: In the future, genomic-assisted breeding (GAB 2.0) will rely on new approaches to manipulate allelic variation for creating novel diversity, optimize crop genomes, and design more climate-smart crop cultivars with higher nutritional value.
TRENDS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Zhixing Feng et al.
Summary: Cellular genetic heterogeneity is common across biological conditions, yet high error rates in long-read sequencing technologies limit their application to this subject. iGDA is introduced as a tool for accurate detection and phasing of minor variants, enabling precise haplotype reconstruction.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Wenqiao He et al.
Summary: This study investigated viral communities in the livers of rats, mice, house shrews, and bats using viral metagenomics and PCR methods, revealing diverse sequences including hepatitis-related viruses. Higher detection rates of pegivirus sequences were found in rat liver tissue and serum samples, while torque teno virus sequences had higher detection rates in rat and house shrew serum samples.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Genetics & Heredity
Aleksandr Bobrovskikh et al.
Summary: Single-cell technology has been mainly used in animals to obtain high-resolution transcriptomic data in the past decade, but there are also efforts to apply this technology in plant tissues. The unique features of plant tissues, such as cell-to-cell communication topology, play a significant role in analyzing single-cell transcriptomic data. Cell-based computational modeling approaches offer new opportunities for summarizing multiscale data in plant research.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Susana Martinez Arbas et al.
Summary: Multi-omic studies have become increasingly prevalent in microbial communities, allowing for a deeper understanding of community structure and function. Longitudinal multi-omic microbiome datasets offer advantages in understanding community dynamics.
FRONTIERS IN GENETICS
(2021)
Review
Genetics & Heredity
Jiajia Liu et al.
Summary: The rapid development of single-cell technologies enables in-depth analysis of cellular heterogeneity, providing valuable insights for understanding complex biological systems and diseases. Machine learning methods play a crucial role in single-cell multi-omics data analysis, but face challenges such as multi-omics integration and data analysis.
FRONTIERS IN GENETICS
(2021)
Review
Oncology
Cristian Scatena et al.
Summary: Recent genomic revolution has shed light on the genetic alterations of cutaneous melanoma, offering new insights and tools for personalized medicine. High-throughput genomic technologies have facilitated the profiling of melanoma, allowing better prediction of biological and clinical behaviors.
FRONTIERS IN ONCOLOGY
(2021)
Review
Oncology
Jingyu Zang et al.
Summary: Advancements in technology have enabled the use of single-cell analysis in characterizing the multicellular ecosystem of UBC, providing insights for more effective immune-based therapies.
FRONTIERS IN ONCOLOGY
(2021)
Review
Agronomy
Ambuj B. Jha et al.
Summary: Pea crops are often affected by various fungal diseases, with traditional breeding methods and next-generation sequencing platforms being key in reducing yield losses. Recent genome studies have enabled rapid identification of genetic loci associated with disease resistance in peas.
Review
Biochemistry & Molecular Biology
Lea D. Schlieben et al.
Summary: Rare diseases collectively impact approximately 350 million people worldwide, with nearly 6,000 distinct rare disorders identified. Whole exome sequencing is improving diagnostic rates, but challenges in variant detection and interpretation remain. RNA sequencing is increasingly being used as a complementary diagnostic tool to enhance detection and interpretation of pathogenic variants, leading to diagnostic rates of 10-35% in rare diseases.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Yu Hu et al.
Summary: LIQA is a tool for long-read RNA sequencing data that quantifies isoform expression and detects differential alternative splicing events, demonstrating high accuracy in various experimental datasets.
Article
Biotechnology & Applied Microbiology
Robin-Lee Troskie et al.
Summary: Pseudogenes, once considered as functionless relics of evolution, are now recognized as a complex and dynamic component of the human transcriptional landscape. This study identified hundreds of novel transcribed pseudogenes expressed in tissue-specific patterns, some of which have intact open reading frames and encode proteins. Deleting the nucleus-enriched pseudogene PDCL3P4 using CRISPR-Cas9 led to perturbations in hundreds of genes, highlighting the potential biological impact of noncoding pseudogenes.
Review
Biotechnology & Applied Microbiology
Ruqian Lyu et al.
Summary: Genetic maps are essential for understanding disease genetics and evolutionary processes. Single-cell gamete sequencing has the potential to combine the advantages of short-read sequencing with the ability to build personalized genetic maps, opening up a new space in personalized genetics.
Review
Biochemistry & Molecular Biology
Stefan Graw et al.
Summary: This article discusses the increasing demand for merging biological features to study a system as a whole, due to advancements in next-generation sequencing and mass spectrometry. Technological limitations such as sample preparation steps, material amount required for sequencing, and sequencing depth requirements need to be addressed. The development of data integration methods, considerations for each data feature, limitations in gene and protein abundance, and the influence of the microbiome on gene and protein expression are important aspects in studying multi-omics data integration.
Review
Parasitology
Libia Zulema Rodriguez-Anaya et al.
Summary: This review explores the sequenced genomes of pathogens like Naegleria fowleri, Acanthamoeba spp. and Balamuthia mandrillaris, highlighting the significance of comparative genomics and differential gene/protein expression analyses in identifying unique genes and pathways related to pathogenicity. The integration of omics data provides insights into the molecular complexity required for understanding virulence factors and potential advancements in therapy design and medical diagnosis.
Review
Oncology
Zhaoqi Liu et al.
Summary: This review summarizes the latest computational approaches to studying alternative splicing in cancer and highlights the current limitations of popular tools in this field. Additionally, some of the current computational challenges in characterizing the role of alternative splicing in cancer are discussed.
Review
Fisheries
Sandra Infante-Villamil et al.
Summary: As the human population grows and the demand for high-quality protein increases, aquaculture must enhance productivity by improving resource utilization efficiency and managing microbial diversity to enhance animal health and, ultimately, productivity.
REVIEWS IN AQUACULTURE
(2021)
Review
Genetics & Heredity
Erick Armingol et al.
Summary: Intercellular interactions and communication can be inferred from RNA sequencing data, such as ligand-receptor pairs, which has led to new insights and methodologies for studying cell-cell interactions.
NATURE REVIEWS GENETICS
(2021)
Editorial Material
Pathology
Season Wong
EXPERT REVIEW OF MOLECULAR DIAGNOSTICS
(2020)
Editorial Material
Biochemical Research Methods
Chenxu Zhu et al.
Article
Clinical Neurology
Sorina Gorcenco et al.
PARKINSONISM & RELATED DISORDERS
(2020)
Article
Multidisciplinary Sciences
Alexandro E. Trevino et al.
Review
Microbiology
Lauren Davey et al.
CURRENT OPINION IN MICROBIOLOGY
(2020)
Review
Cell Biology
Xin Shao et al.
Article
Biochemistry & Molecular Biology
Rizqah Kamies et al.
Review
Oncology
Ivana Jovcevska
FRONTIERS IN ONCOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Oleg N. Reva et al.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Review
Biochemistry & Molecular Biology
Martin Philpott et al.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2020)
Review
Biochemical Research Methods
Muhammad Munir Iqbal et al.
Article
Biochemical Research Methods
Lucile Broseus et al.
Article
Biochemistry & Molecular Biology
Zheng-Hui Zhao et al.
Review
Infectious Diseases
Aimaiti Yasen et al.
INFECTION GENETICS AND EVOLUTION
(2020)
Article
Genetics & Heredity
Luotong Wang et al.
FRONTIERS IN GENETICS
(2020)
Article
Allergy
Dongmei Li et al.
ALLERGY AND ASTHMA PROCEEDINGS
(2020)
Review
Biotechnology & Applied Microbiology
Anne-Kristin Kaster et al.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2020)
Editorial Material
Oncology
Ansam Sinjab et al.
Article
Biochemistry & Molecular Biology
Bo Cao et al.
NUCLEIC ACIDS RESEARCH
(2020)
Review
Virology
I-Na Lu et al.
Review
Biochemistry & Molecular Biology
Mauro Belli et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Review
Genetics & Heredity
Yang Li et al.
TRENDS IN GENETICS
(2020)
Article
Biology
Samuel J. Modlin et al.
Review
Medicine, Research & Experimental
Shuai Men et al.
MEDICAL SCIENCE MONITOR
(2020)
Article
Virology
Ludivine Brandt et al.
ANNUAL REVIEW OF VIROLOGY, VOL 7, 2020
(2020)
Article
Biochemistry & Molecular Biology
Yaru Zhang et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Article
Biochemistry & Molecular Biology
Anca F. Savulescu et al.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2020)
Review
Biology
Lisa N. Waylen et al.
COMMUNICATIONS BIOLOGY
(2020)
Article
Infectious Diseases
Jie Zhang et al.
CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY
(2020)
Article
Biochemical Research Methods
Yufang Qin et al.
PLOS COMPUTATIONAL BIOLOGY
(2020)
Review
Plant Sciences
Junzhong Liu et al.
FRONTIERS IN PLANT SCIENCE
(2020)
Review
Genetics & Heredity
Tingting Guo et al.
FRONTIERS IN GENETICS
(2020)
Article
Biotechnology & Applied Microbiology
Jose A. Campoy et al.
Review
Biotechnology & Applied Microbiology
Yu Shangguan et al.
Review
Oncology
Zhe Dai et al.
BIOMARKER RESEARCH
(2020)
Article
Biochemistry & Molecular Biology
Robert A. Gaultney et al.
NUCLEIC ACIDS RESEARCH
(2020)
Article
Microbiology
Meng Zhang et al.
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Richard I. Kuo et al.
Review
Genetics & Heredity
Lachlan F. MacBean et al.
CURRENT GENETIC MEDICINE REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
C. Anthony Scott et al.
Review
Biotechnology & Applied Microbiology
Shanika L. Amarasinghe et al.
Review
Biochemistry & Molecular Biology
Nicholas A. Bokulich et al.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2020)
Review
Plant Sciences
Ovidiu Paun et al.
Article
Multidisciplinary Sciences
Samuel G. Rodriques et al.
Article
Biochemical Research Methods
Mahdi Heydari et al.
BMC BIOINFORMATICS
(2019)
Review
Environmental Sciences
Nele Horemans et al.
ENVIRONMENTAL POLLUTION
(2019)
Review
Biochemistry & Molecular Biology
Lu Wen et al.
Review
Genetics & Heredity
John Beaulaurier et al.
NATURE REVIEWS GENETICS
(2019)
Editorial Material
Genetics & Heredity
Matthew S. Hestand et al.
Review
Chemistry, Analytical
Yanling Song et al.
Article
Biotechnology & Applied Microbiology
Miten Jain et al.
NATURE BIOTECHNOLOGY
(2018)
Review
Genetics & Heredity
A. -L. Schang et al.
Article
Multidisciplinary Sciences
Sarah L. Castro-Wallace et al.
SCIENTIFIC REPORTS
(2017)
Article
Biodiversity Conservation
Christoph Bleidorn
SYSTEMATICS AND BIODIVERSITY
(2016)
Article
Multidisciplinary Sciences
Patrik L. Stahl et al.
Article
Biotechnology & Applied Microbiology
Paul Muir et al.
Article
Biochemistry & Molecular Biology
Evan Z. Macosko et al.
Article
Multidisciplinary Sciences
Spyros Darmanis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Review
Biochemistry & Molecular Biology
G. Barry
MOLECULAR PSYCHIATRY
(2014)
Article
Neurosciences
Jeremy J. Day et al.
NATURE NEUROSCIENCE
(2013)
Article
Multidisciplinary Sciences
Rashel V. Grindberg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2013)
Article
Multidisciplinary Sciences
Fatih Ozsolak et al.
Review
Nutrition & Dietetics
C. J. Seal et al.
BRITISH JOURNAL OF NUTRITION
(2008)
Article
Biochemical Research Methods
Arjun Raj et al.
