Article
Computer Science, Artificial Intelligence
Adam Banham, Sander J. J. Leemans, Moe T. Wynn, Robert Andrews, Kevin B. Laupland, Lucy Shinners
Summary: Process mining is a mature discipline that can be applied to various industries, including healthcare. This paper proposes a framework for process mining with exogenous data and introduces new analyses that link exogenous data with process behavior and outcomes. By applying these analyses to healthcare, the study demonstrates how insights about clinical outcomes can be derived from exogenous data.
ARTIFICIAL INTELLIGENCE IN MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
N. M. Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anelia Horvath
Summary: SCReadCounts is a tool for estimating cell-level SNV expression, useful for distinguishing tumor cells, defining gene expression characteristics, and identifying known or novel somatic mutations. The analysis through cell-SNV matrices helps in evaluating SNVs present in a small proportion of cells.
Article
Multidisciplinary Sciences
Kian Soon Hoon, Deborah C. Holt, Sarah Auburn, Peter Shaw, Philip M. Giffard
Summary: This article presents the minSNPs R package, which can optimize the selection of single nucleotide polymorphisms (SNPs) from sequence alignments for discriminating different combinations of sequences or maximizing diversity. The software has fast and flexible mining capabilities, and can present results clearly and comprehensively.
Article
Physiology
Kent M. Reed, Kristelle M. Mendoza, Juan E. Abrahante, Sandra G. Velleman, Gale M. Strasburg
Summary: This study identified unique circRNAs in thermally challenged turkey poults and found significant differential expression between thermal treatments and genetic lines. These findings provide important insights into the potential functional significance of circRNAs in muscle development.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Genetics & Heredity
G. Ramya, Abhijit Mitra, P. K. Vinod
Summary: RNAs are essential in regulating gene expression, and their secondary structures have significant roles. This study identified disease-associated SNPs, known as RiboSNitches, that can alter the pre-mRNA secondary structure. It also demonstrated the potential importance of splice site mutations in alternative splicing. The workflow developed in this study provides a novel approach to predict riboSNitches associated with alternative splicing and enables future experimental validation.
Article
Biotechnology & Applied Microbiology
Igor Ricardo Savoldi, Adriana Mercia Guaratini Ibelli, Mauricio Egidio Cantao, Jane de Oliveira Peixoto, Michele Porto Pires, Marcos Antonio Zanella Mores, Essamai Brizola Lagos, Jader Silva Lopes, Ricardo Zanella, Monica Correa Ledur
Summary: This study identified several variants and genes associated with umbilical hernia in pigs using exome and transcriptome sequencing. The analysis revealed biological processes related to umbilical hernia and highlighted potential candidate genes for further investigation. The combination of exome and transcriptome sequencing provided a better understanding of the molecular mechanisms underlying umbilical hernia in pigs and potentially in other mammals, including humans.
Article
Plant Sciences
Donghyun Jeon, Jin-Baek Kim, Beum-Chang Kang, Changsoo Kim
Summary: This study aimed to identify salt-tolerant genes and SNPs in sorghum through comparative transcriptome analysis. Several potential genes and non-synonymous SNPs associated with salt tolerance were inferred, indicating their potential roles in salt tolerance. Additionally, a specific gene LOC8060874 involved in cyanohydrin beta-glucosyltransferase activity under salt stress was suggested as a key gene associated with salt tolerance.
Article
Biochemistry & Molecular Biology
Artur Wnorowski, Jakub Wojcik, Maciej Maj
Summary: The study found that GPR55 is predominantly regulated in the context of immune activation, indicating its role in response to pathogens and immune cell lineage determination. There is almost no overlap between the experimental conditions affecting GPR55 expression and those modulating agonist production. Enhanced capacity to synthesize LPI in various types of tumors suggests cancer cells can hijack GPR55's motility-related activity to increase aggressiveness. Conditions favoring accumulation of PACAP-derived peptides differ from those for LPI, suggesting a different function of the two agonist classes and a possible signaling bias.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Daniel E. Platt, Hovig Artinian, Francis Mouzaya, Wissam Khalil, Francois G. Kamar, Elizabeth Matisoo-Smith, Francesc Calafell, Nassim Nicolas Taleb, Pierre Zalloua
Summary: There are 18 different religious communities living in Lebanon, showing genetic isolation and autosomal clustering. Analysis of Y-chromosome STR and SNP data reveals a Levantine branching around 5000 years ago and distinct genetic components in the North Lebanese Mountain Maronite community. The Levantine L1b group split from the Caucasus ancestral group around 7300 years ago, with cultural barriers marked by the transmission of L1b lineages.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Genetics & Heredity
Qihan Long, Yangyang Yuan, Miaoxin Li
Summary: The RNA-SSNV framework allows for the accurate identification of expressed somatic mutations and enables a more insightful analysis of cancer driver genes and carcinogenic mechanisms.
FRONTIERS IN GENETICS
(2022)
Review
Agriculture, Dairy & Animal Science
Seungmee Lee, Melissa E. Baker, Michael Clinton, Sarah E. Taylor
Summary: Despite recent advances in imaging and epidemiological data analysis, musculoskeletal injuries remain a welfare issue in racehorses. Studies on miRNA profiling in horses have yet to reliably predict fractures, highlighting the need for well-designed future studies that account for variations in sample size, exercise, and normalization methods.
Article
Oncology
Maxim Sorokin, Alexander Gorelyshev, Victor Efimov, Evgenia Zotova, Marianna Zolotovskaia, Elizaveta Rabushko, Denis Kuzmin, Alexander Seryakov, Dmitry Kamashev, Xinmin Li, Elena Poddubskaya, Maria Suntsova, Anton Buzdin
Summary: The study compared TMB levels deduced from WES and RNAseq profiles of the same FFPE biosamples, suggesting the potential of RNA sequencing in TMB assessment. Application of machine learning improved accuracy, indicating that RNA sequencing can be used for high-quality discrimination of tumors with high and low TMB levels.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Elizaveta Rabushko, Maxim Sorokin, Maria Suntsova, Alexander P. Seryakov, Denis Kuzmin, Elena Poddubskaya, Anton A. Buzdin
Summary: This study identified potential clinically relevant RTK fusions by annotating RNAseq reads, providing a basis for automatic annotation of 3' RTK fusions using FFPE RNAseq profiles.
Article
Biochemistry & Molecular Biology
Yu Ding, Ma-Yin Wang, Ding-Hai Yang, Dai-Cheng Hao, Wei-Shi Li, Peng Ling, Shang-Qian Xie
Summary: This study identified the genes involved in flower color formation in Phalaenopsis at the transcription level and found that the biosynthesis of secondary metabolites pathway plays a key role in color formation.
Article
Genetics & Heredity
Frederic Jehl, Fabien Degalez, Maria Bernard, Frederic Lecerf, Laetitia Lagoutte, Colette Desert, Manon Coulee, Olivier Bouchez, Sophie Leroux, Behnam Abasht, Michele Tixier-Boichard, Bertrand Bed'hom, Thierry Burlot, David Gourichon, Philippe Bardou, Herve Acloque, Sylvain Foissac, Sarah Djebali, Elisabetta Giuffra, Tatiana Zerjal, Frederique Pitel, Christophe Klopp, Sandrine Lagarrigue
Summary: RNA-seq data is a valuable yet unexploited resource for detecting SNPs and genotypes in various populations, especially in livestock species. This study compared SNP calling results using RNA-seq data in two chicken populations, proposing thresholds for genotype calling consistency and demonstrating the potential of RNA-seq data for gene expression regulation and population genetic analysis.
FRONTIERS IN GENETICS
(2021)
Correction
Genetics & Heredity
Yuan Yuan, Young Seok Ju, Youngwook Kim, Jun Li, Yumeng Wang, Christopher J. Yoon, Yang Yang, Inigo Martincorena, Chad J. Creighton, John N. Weinstein, Yanxun Xu, Leng Han, Hyung-Lae Kim, Hidewaki Nakagawa, Keunchil Park, Peter J. Campbell, Han Liang
Article
Ophthalmology
A. Brantley Milam, Katherine S. Peters, Emilio Rivera, Cassandra Warden, Paula A. Harlow, Sabrina L. Mitchell, M. Wade Calcutt, David C. Samuels
Summary: This study aimed to investigate the differences in six arginine-related and citrulline-related metabolites between patients with type 2 diabetes and diabetic retinopathy. The results showed that plasma levels of arginine and citrulline were significantly elevated in patients with diabetic retinopathy.
AMERICAN JOURNAL OF OPHTHALMOLOGY
(2022)
Editorial Material
Genetics & Heredity
David C. Samuels, Hui Yu, Yan Guo
Summary: Variant annotation is a crucial step in selecting candidates for further investigation. Recent annotation methods focus on empirically generated data, rather than theoretical predictions. These methods have the advantage of utilizing large amounts of experimental data, but also come with their own limitations.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Jingjing Qi, Hongxiang Sun, Yao Zhang, Zhengting Wang, Zhenzhen Xun, Ziyi Li, Xinyu Ding, Rujuan Bao, Liwen Hong, Wenqing Jia, Fei Fang, Hongzhi Liu, Lei Chen, Jie Zhong, Duowu Zou, Lianxin Liu, Leng Han, Florent Ginhoux, Yingbin Liu, Youqiong Ye, Bing Su
Summary: This study provides insights into the interaction between FAP(+) fibroblasts and SPP1(+) macrophages in colorectal cancer, suggesting a potential therapeutic strategy to improve immunotherapy by disrupting this interaction.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Gaoyang Wang, Zuozhong Xie, Juan Su, Meishan Chen, Yanhua Du, Qian Gao, Guanxiong Zhang, Hailun Zhang, Xiang Chen, Hong Liu, Leng Han, Youqiong Ye
Summary: This study provides an in-depth analysis of immune-related alternative polyadenylation in cancer, identifying alternative polyadenylation events that may play a role in immune modulation and immunotherapy efficacy.
Article
Cell Biology
Marzia Savini, Andrew Folick, Yi-Tang Lee, Feng Jin, Andre Cuevas, Matthew C. Tillman, Jonathon D. Duffy, Qian Zhao, Isaiah A. Neve, Pei-Wen Hu, Yong Yu, Qinghao Zhang, Youqiong Ye, William B. Mair, Jin Wang, Leng Han, Eric A. Ortlund, Meng C. Wang
Summary: This study reveals the importance of lysosomes as a signaling hub in coordinating metabolism and aging, as well as the role of lysosomal signaling in promoting longevity through inter-tissue communication. Lysosomal lipolysis in peripheral adipose depots produces polyunsaturated fatty acids (PUFAs) and activates a signaling pathway in neurons that extends lifespan. The polyunsaturated fatty acid dihomo-gamma-linolenic acid and the lipid chaperone LBP-3 play key roles in this fat-to-neuron lipid signaling pathway.
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Adam L. Sanders, Jake N. Hermanson, David C. Samuels, Lars Plate, Charles R. Sanders
Summary: Genetic missense tolerance ratio (MTR) analysis evaluates the segments in protein-encoding transcripts in the human population. This analysis can identify genes with zero-tolerance segments, which may be associated with underexplored human biology and diseases. In this study, MTR analysis was conducted on 20,000 protein-encoding human genes, and 257 genes were found to have at least one segment with an MTR score of 0. Among these genes, a collection of proteins involved in RNA splicing showed the highest functional enrichment.
Article
Cell Biology
Mengting Shen, Shengli Li, Yiming Zhao, Yizhe Liu, Zhen Liu, Lin Huan, Yejun Qiao, Lu Wang, Leng Han, Zhiao Chen, Xianghuo He
Summary: Liver cancer stemness is closely related to tumour malignancy, and this study identifies the transcription factor ARID3A as a key regulator of stemness in liver cancer. ARID3A interacts with CEP131 and activates KDM3A, leading to the upregulation of downstream genes associated with embryonic stem cell signature and promoting liver cancer metastasis. The ARID3A/CEP131-KDM3A regulatory circuit may serve as a prognostic indicator and potential therapeutic target for liver cancer.
CELL DEATH & DISEASE
(2022)
Review
Cell Biology
Hang Ruan, Peng-Cheng Wang, Leng Han
Summary: Circular RNAs (circRNAs) are a class of non-coding RNAs that have a closed circular structure. The biological significance of circRNAs has long been underestimated, but recent advancements in sequencing technology have allowed for extensive exploration of their functions in complex diseases, particularly human cancers. This review provides an overview of circRNA detection methods, data resources, and functional studies related to human complex diseases, as well as discussing the potential advantages of utilizing advanced sequencing approaches for interpreting full-length circRNAs.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2023)
Editorial Material
Immunology
Gang Chen, Shengtao Zhou, Chaoyang Sun, Leng Han
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Katherine M. Stefanski, Geoffrey C. Li, Justin T. Marinko, Bruce D. Carter, David C. Samuels, Charles R. Sanders
Summary: Cellular and biophysical studies were conducted to investigate the effects of the T118M PMP22 variation leading to CMT disease. It was found that T118M PMP22 reduces surface-trafficked PMP22 without forming toxic intracellular aggregates, explaining the incomplete disease penetrance and mild neuropathy observed in WT/T118M CMT cases. Additionally, a statistically significant association between the T118M mutation and the occurrence of carpal tunnel syndrome was identified.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Clinical Neurology
Lori Schirle, David C. Samuels, Annika Faucon, Nancy J. Cox, Stephen Bruehl
Summary: This study employed a genome-wide poly-genic risk score approach to evaluate genetic influences on 8 common chronic overlapping pain conditions. The findings suggest a shared polygenic influence potentially involving central sensitization mechanisms across these conditions. This study provides evidence supporting future research on biomarkers and risk assessment.
Article
Genetics & Heredity
Mingqiang Wang, Wankun Deng, David C. C. Samuels, Zhongming Zhao, Lukas M. M. Simon
Summary: Genetic variation in the mitochondrial genome is important and related to human diseases. Single-cell RNA sequencing (scRNAseq) has become a popular technique to study transcriptomics at the cellular level. However, the study of mitochondrial variants using scRNAseq data has been limited. In this study, we developed an R package called MitoTrace to analyze mitochondrial genetic variation in scRNAseq data and demonstrated its effectiveness in recovering genetic variants in different datasets.
Review
Medicine, Research & Experimental
Xiao Zhou, Xiang Chen, Leng Han, Hong Liu
Summary: Immune checkpoint proteins are crucial for tumor cells to evade immune surveillance, and inhibiting them has shown efficacy in tumor treatment. However, immune-related adverse events are a common occurrence in patients receiving immune checkpoint blockade therapy, requiring further investigation into the underlying mechanisms.
Article
Multidisciplinary Sciences
Youqiong Ye, Yongchang Zhang, Nong Yang, Qian Gao, Xinyu Ding, Xinwei Kuang, Rujuan Bao, Zhao Zhang, Chaoyang Sun, Bingying Zhou, Li Wang, Qingsong Hu, Chunru Lin, Jianjun Gao, Yanyan Lou, Steven H. Lin, Lixia Diao, Hong Liu, Xiang Chen, Gordon B. Mills, Leng Han
Summary: Research has shown that immune checkpoint blockade therapies are effective in treating cancer, with changes in immune features in patients after initiation of treatment. The immune activation score based on dynamic alteration of interleukins can accurately predict immunotherapy efficacy.