Article
Biotechnology & Applied Microbiology
Yan Zhou, Minjiao Peng, Bin Yang, Tiejun Tong, Baoxue Zhang, Niansheng Tang
Summary: In this study, a new deep learning classifier is proposed for large sample scRNA-seq data. The classifier outperforms existing methods in various settings and does not require prior knowledge of the data distribution.
Article
Virology
Solomon Maina, Linda Zheng, Brendan C. Rodoni
Summary: The study developed a targeted genome sequencing (TG-Seq) approach that can detect multiple plant viruses simultaneously with high sensitivity and potential. It successfully detected all expected viral amplicons in mPCR reactions, providing more accurate and detailed virus detection.
Article
Biochemical Research Methods
Ke Xu, ChinWang Cheong, Werner P. Veldsman, Aiping Lyu, William K. Cheung, Lu Zhang
Summary: Single-cell ribonucleic acid sequencing (scRNA-seq) is used to quantify gene expression at the transcriptomic level with single-cell resolution, but excessive missing values in scRNA-seq data impede analysis. IGSimpute is an accurate and interpretable imputation method that outperforms 12 other methods in recovering missing values in scRNA-seq data. It also has applications in denoising gene expression profiles and indicating cellular age.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Jiaxing Chen, ChinWang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K. Cheung, Lu Zhang
Summary: Single-cell RNA sequencing has enabled the reconstruction of cell-type-specific gene regulatory networks with the novel DeepDRIM algorithm, which demonstrated superior performance compared to existing algorithms for both simulated and real scRNA-seq data. The method was robust to varying dropout rates, cell numbers, and training data sizes. DeepDRIM was further applied to analyze cell-type-specific GRN alterations in B cells from COVID-19 patients, revealing potential gene targets associated with coronavirus infection.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Siqi Bao, Ke Li, Congcong Yan, Zicheng Zhang, Jia Qu, Meng Zhou
Summary: This study summarizes the recent advances and applications of deep learning-based methods in the analysis of scRNA-seq data and specific tools, and investigates the future perspectives and challenges of deep learning techniques in the appropriate analysis and interpretation of scRNA-seq data.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Gastroenterology & Hepatology
Liuyang Zhao, Yu Shi, Harry Cheuk-Hay Lau, Weixin Liu, Guangwen Luo, Guoping Wang, Changan Liu, Yasi Pan, Qiming Zhou, Yanqiang Ding, Joseph Jao-Yiu Sung, Jun Yu
Summary: Through ultra-deep metagenomic sequencing, we discovered 1058 novel human gut viruses, including some viral genomes longer than the largest bacteriophage found in humans. Our study also demonstrated that a biomarker panel of 14 novel viruses can differentiate patients with colorectal cancer from controls in a training cohort.
Article
Biochemical Research Methods
Ho-Jin Gwak, Mina Rho
Summary: A hierarchical BERT model named ViBE was developed to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level, outperforming state-of-the-art alignment-based and alignment-free methods for virus identification.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Ahmed Babiker, Heath L. Bradley, Victoria D. Stittleburg, Jessica M. Ingersoll, Autum Key, Colleen S. Kraft, Jesse J. Waggoner, Anne Piantadosi
Summary: Our study found that current broad-spectrum molecular testing algorithms can identify most respiratory viral infections among SARS-CoV-2 PUIs when available and implemented consistently.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Health Care Sciences & Services
Jiong Chen, Xinlei Mi, Jing Ning, Xuming He, Jianhua Hu
Summary: RNA sequencing data are widely used in biomedical research for biomarker discovery. A tail-based test, derived from quantile regression, has been proposed to compare groups in terms of a specific distribution area instead of a single location. Monte Carlo simulation studies show that this test is generally more powerful and robust in detecting differential expression compared to commonly used tests based on the mean or a single quantile.
STATISTICAL METHODS IN MEDICAL RESEARCH
(2021)
Review
Genetics & Heredity
Matthew Brendel, Chang Su, Zilong Bai, Hao Zhang, Olivier Elemento, Fei Wang
Summary: Single-cell RNA sequencing (scRNA-seq) is widely used to quantify the gene expression profile of thousands of single cells simultaneously. Deep learning techniques have emerged as a promising tool for scRNA-seq data analysis, allowing for the extraction of informative and compact features from noisy and high-dimensional data. This review surveys recent developments in deep learning for scRNA-seq data analysis, highlights key advancements made by deep learning in the analysis pipeline, and discusses the benefits and challenges of applying deep learning to scRNA-seq data.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Tariq Sadad, Raja Atif Aurangzeb, Imran, Mejdl Safran, Sultan Alfarhood, Jungsuk Kim
Summary: This study proposes a genome analysis system that uses advanced deep learning to identify dozens of viruses. The system utilizes nucleotide sequences from the NCBI GenBank database and a BERT tokenizer to extract features. The system consists of a scratch BERT architecture for DNA analysis and a classifier that identifies important features and understands the relationship between genotype and phenotype. The system achieved an accuracy of 97.69% in identifying viral sequences.
Article
Biology
Lulin Huang, Runze Li, Lin Ye, Shanshan Zhang, Huaping Tian, Mingyan Du, Chao Qu, Shujin Li, Jie Li, Mu Yang, Biao Wu, Ran Chen, Guo Huang, Ling Zhong, Hongjie Yang, Man Yu, Yi Shi, Changguan Wang, Houbin Zhang, Wei Chen, Zhenglin Yang
Summary: This study provides a deep understanding of the molecular events in the human retina, revealing regional and age differences in gene expression profiles. Sixty cell sub-types have been identified in the mature human retina with unique markers. Cell-cell interaction analysis shows a rich synaptic connection among retinal cells. The findings of this study contribute to our understanding of the vision system.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Plant Sciences
Annelies Haegeman, Yoika Foucart, Kris De Jonghe, Thomas Goedefroit, Maher Al Rwahnih, Neil Boonham, Thierry Candresse, Yahya Z. A. Gaafar, Oscar P. Hurtado-Gonzales, Zala Kogej Zwitter, Denis Kutnjak, Janja Lamovsek, Marie Lefebvre, Martha Malapi, Irena Mavric Plesko, Serkan Onder, Jean-Sebastien Reynard, Ferran Salavert Pamblanco, Olivier Schumpp, Kristian Stevens, Chandan Pal, Lucie Tamisier, Cigdem Ulubas Serce, Inge van Duivenbode, David W. Waite, Xiaojun Hu, Heiko Ziebell, Sebastien Massart
Summary: High-throughput sequencing of plant tissues is a crucial tool for plant virologists to detect plant viruses. However, during the analysis of the data, researchers often neglect sequences without homologies to viruses, which may contain traces of other pathogens. In this study, we re-analyzed RNA-seq datasets and found non-viral plant pathogens, including fungi, insects, and mites. This highlights the potential of using total RNA-seq data for detecting various plant pathogens.
Article
Multidisciplinary Sciences
Jianshi Jin, Taisaku Ogawa, Nozomi Hojo, Kirill Kryukov, Kenji Shimizu, Tomokatsu Ikawa, Tadashi Imanishi, Taku Okazaki, Katsuyuki Shiroguchi
Summary: Developed a multifunctional robot system ALPS for single-cell RNA sequencing of cells observed under multiple imaging modes. Successfully predicted transcriptome-defined cell phenotypes using cell image-based deep learning. This work provides a new approach to determine live-cell whole transcriptome in real time.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Cell Biology
Charith Raj Adkar-Purushothama, Pavithran Sridharan Iyer, Teruo Sano, Jean-Pierre Perreault
Summary: Viroids are circular, non-coding RNA pathogens that infect plants and trigger the host plant's RNA silencing machinery. A python-based software tool was developed to profile and map sRNAs on circular genomes, showing efficiency in analyzing deep-sequencing data and potentially serving as a key tool for researchers to evaluate sRNA production and profile them on their target RNA species.
Article
Plant Sciences
Kalpana Sharma, Jan Kreuze, Abdulwahab Abdurahman, Monica Parker, Anastase Nduwayezu, Placide Rukundo
Summary: The study identified two RSSC phylotypes, with phylotype II (95.79%) being predominant and phylotype III (4.21%) being less common. Pathogenicity tests showed varying levels of susceptibility among different potato cultivars, with Cultivar Cruza being recommended for planting in fields with a history of BW due to its lower susceptibility to both phylotype II and III strains.
Article
Genetics & Heredity
Guibing Hu, Junting Feng, Xu Xiang, Jiabao Wang, Jarkko Salojarvi, Chengming Liu, Zhenxian Wu, Jisen Zhang, Xinming Liang, Zide Jiang, Wei Liu, Liangxi Ou, Jiawei Li, Guangyi Fan, Yingxiao Mai, Chengjie Chen, Xingtan Zhang, Jiakun Zheng, Yanqing Zhang, Hongxiang Peng, Lixian Yao, Ching Man Wai, Xinping Luo, Jiaxin Fu, Haibao Tang, Tianying Lan, Biao Lai, Jinhua Sun, Yongzan Wei, Huanling Li, Jiezhen Chen, Xuming Huang, Qian Yan, Xin Liu, Leah K. McHale, William Rolling, Romain Guyot, David Sankoff, Chunfang Zheng, Victor A. Albert, Ray Ming, Houbin Chen, Rui Xia, Jianguo Li
Summary: By studying the genome of lychee, it was found that lychee had undergone two independent domestication events in Yunnan and Hainan, China. The maturity differences between early-maturing and late-maturing lychee cultivars may be regulated by gene deletions. This research is important for understanding the domestication history of lychee and improving lychee and related crops.
Review
Plant Sciences
Yanqing Zhang, Muhammad Waseem, Zaohai Zeng, Jing Xu, Chengjie Chen, Yuanlong Liu, Jixian Zhai, Rui Xia
Summary: MicroRNAs (miRNAs) such as miR482/2118 are small noncoding RNAs of 21-24 nucleotides in length, widely distributed across the plant kingdom. They play essential roles in disease resistance and plant reproduction, with distinct functions in different plant species.
Article
Plant Sciences
Segundo Fuentes, Adrian J. Gibbs, Ian P. Adams, Mohammad Hajizadeh, Jan Kreuze, Adrian Fox, Arnaud G. Blouin, Roger A. C. Jones
Summary: Potato virus V (PVV) originated in the Andes region and only a few isolates spread to other regions. PVV evolved rapidly and shares similar ecological characteristics with Potato virus Y (PVY). Through phylogenetic reconstruction and dating calculations, PVV is estimated to have appeared around 29 BCE and diversified after the potato late blight pandemic in 1853 CE.
Article
Entomology
Veronica Canedo, Waldo Davila, Pablo Carhuapoma, Juergen Kroschel, Jan Kreuze
Summary: The study examined the effect of temperature on the development and reproduction of a parasitoid species, Apanteles subandinus, which is used to control the invasive potato tuber moth. The results showed that the parasitoid could complete its life cycle at temperatures between 15 and 30 degrees C. The optimal temperature for its reproduction was found to be 27 degrees C, while the highest population growth occurred at 26.78 degrees C.
JOURNAL OF APPLIED ENTOMOLOGY
(2022)
Article
Plant Sciences
Jing Liu, Jian Meng, Houbin Chen, Xiaoquan Li, Zuxiang Su, Chengjie Chen, Tong Ning, Zhenting He, Longyu Dai, Chunxiang Xu
Summary: This study identified and analyzed 17 classical MaAGPs and 9 MbAGPs in banana, and investigated their roles in low temperature tolerance. The antigens of JIM13 and LM2 antibodies, as well as classical MaAGP1/2/6/9/16/17, were found to be associated with banana chilling tolerance.
PLANT CELL REPORTS
(2022)
Review
Agronomy
David A. Ramirez, Cecilia Silva-Diaz, Johan Ninanya, Mariella Carbajal, Javier Rinza, Suresh K. Kakraliya, Marcel Gatto, Jan Kreuze
Summary: Rice production is the biggest contributor to plant-based carbon emissions globally, particularly in Asia. Introducing sustainable intensification practices or diversifying with lower-emission crops like potatoes is crucial for mitigating climate change. This study analyzed the impact of potato cultivation under zero/minimum-tillage and/or organic mulching on key performance indicators in Asia. The results showed that potato cultivation under these conditions can increase yield, profitability, nutrient-use efficiency, and water productivity, thanks to significant soil moisture conservation.
Article
Biotechnology & Applied Microbiology
Jiakun Zheng, Chengjie Chen, Guanliang Li, Peike Chen, Yuanlong Liu, Rui Xia
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Plant Sciences
Maria David, Moctar Kante, Segundo Fuentes, Raul Eyzaguirre, Federico Diaz, Bert De Boeck, Robert O. M. Mwanga, Jan Kreuze, Wolfgang J. Gruneberg
Summary: This study aimed to develop a precise phenotyping protocol for Sweet Potato Virus Disease (SPVD), identify new SPVD-resistant genotypes, and standardize the early stages of SPVD resistance screening. The results showed that the modified serological analysis successfully identified resistant clones, which were further validated in field experiments. This improved method can expedite the development of resistant varieties and provide reliable data for marker-assisted selection.
Article
Plant Sciences
Jan F. Kreuze, Wilmer J. Cuellar, P. Lava Kumar, Prasanna Boddupalli, Aman B. Omondi
Summary: Plant viruses pose a serious threat to crop production worldwide, but advancements in sequencing technology, amplification methods, and modeling have provided opportunities for improved understanding and preparedness. International collaboration and funding have enabled the application of these technologies in low- and middle-income countries to enhance surveillance and response against plant viral threats.
Article
Agronomy
Kwame Ogero, Haile Selassie Okuku, Bramwel Wanjala, Margaret McEwan, Conny Almekinders, Jan Kreuze, Paul Struik, Rene van der Vlugt
Summary: Viruses pose a significant challenge to sweet potato production in Tanzania. The use of virus-tested seed vines through a formal seed system is suggested as a strategy to tackle this issue. However, the performance of these virus-tested seed vines after several seasons of on-farm propagation is unknown. The study evaluated the performance of virus-tested and farmer-sourced seed vines for susceptible and tolerant sweet potato varieties over five seasons, revealing the prevalence of different viruses and their impact on yield.
Article
Entomology
Marc Sporleder, Heidy Gamarra, Pablo Carhuapoma, Luis Goicochea, Juergen Kroschel, Jan Kreuze
Summary: The sweetpotato whitefly, Bemisia tabaci MEAM1, is a significant insect pest that affects a wide range of plants and transmits various viruses. Understanding its population growth potential with respect to temperature is crucial for predicting its range and designing effective pest management strategies.
ENVIRONMENTAL ENTOMOLOGY
(2023)
Article
Plant Sciences
Robert Alvarez-Quinto, Melody Amao, Giovanna Muller, Segundo Fuentes, Samuel Grinstead, Irazema Fuentes-Bueno, Annelien Roenhorst, Marcel Westenberg, Marleen Botermans, Jan Kreuze, Dimitre Mollov
Summary: A new torradovirus species called potato rugose stunting virus (PotRSV) was detected in potatoes from Peru, the United States, and the Netherlands. The virus has high sequence identity to an unknown isometric virus associated with potato rugose stunting disease in Peru. The genome of PotRSV consists of two RNA segments, with RNA1 encoding a replication-related polyprotein and RNA2 encoding a movement protein and capsid proteins.
Article
Agronomy
Kwame Ogero, Haile Selassie Okuku, Margaret McEwan, Conny Almekinders, Jan Kreuze, Paul Struik, Rene van der Vlugt
Summary: The use of insect-proof net tunnels can reduce virus infection in sweetpotato seed produced by decentralized seed producers. This study compared the effect of ratoon cropping technique on vine production in net tunnels and open fields for two varieties of virus-tested sweetpotato. The ratoon cropping technique produced more vines than the replanting technique, but also led to higher virus incidences in plants grown in the open fields, particularly for the Mataya variety. The study recommends using the ratoon cropping technique in net tunnels and the replanting technique in open fields to control virus infections.
EXPERIMENTAL AGRICULTURE
(2023)
Article
Biochemistry & Molecular Biology
Tong Ning, Chengjie Chen, Ganjun Yi, Houbin Chen, Yudi Liu, Yanjie Fan, Jing Liu, Shule Chen, Sixuan Wei, Zexuan Li, Yehuan Tan, Zhenting He, Chunxiang Xu
Summary: This study reveals the dynamic changes of HG in banana fruit development and ripening, as well as its correlation with fruit expansion, peel firmness, and epitope levels of antibodies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
