Article
Biotechnology & Applied Microbiology
Yang Liu, Tao Wang, Bin Zhou, Deyou Zheng
Summary: Integration of multiple single-cell RNA sequencing datasets is improved by creating a common reference space using a new algorithm.
NATURE BIOTECHNOLOGY
(2021)
Review
Urology & Nephrology
Michael S. Balzer, Ziyuan Ma, Jianfu Zhou, Amin Abedini, Katalin Susztak
Summary: Single cell methods have advanced significantly in the past few years, enabling the monitoring of gene and protein expression changes in individual cells. However, data analysis remains a critical bottleneck. This review provides an overview of commonly used analytical tools in the field to help researchers understand challenges and gain insights into typical readouts from single cell datasets in published literature.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Rhonda Bacher, Li-Fang Chu, Cara Argus, Jennifer M. Bolin, Parker Knight, James A. Thomson, Ron Stewart, Christina Kendziorski
Summary: It has been found that equalizing the concentration of cDNA libraries prior to pooling in single-cell RNA-sequencing experiments can improve gene detection rates, enhance biological signals, and reduce technical artifacts. Numerical and in vitro experiments provide evidence to support this finding.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Yue Zhao, Lianbo Yu, Xue Wu, Haoran Li, Kevin R. Coombes, Kin Fai Au, Lijun Cheng, Lang Li
Summary: This study developed a statistical method called CEDA, which integrates gene expression data and CRISPR screening data for identifying essential genes. Compared to existing methods, CEDA shows higher sensitivity in detecting essential genes with moderate sgRNA fold change.
Article
Materials Science, Multidisciplinary
F. Jakobs, T. A. Ostler, C-H Lambert, Y. Yang, S. Salahuddin, R. B. Wilson, J. Gorchon, J. Bokor, U. Atxitia
Summary: This study aims to uncover the thermal single-pulse switching mechanisms in Gd-Fe-Co alloys, presenting experimental evidence and providing a quantitative description of the switching dynamics. Unique element-specific damping parameters were identified as crucial for long picosecond pulse switching, with the potential for switching with pulse durations as long as 15 ps due to Gd's low damping constant. These findings have implications for speeding up dynamics in other contexts involving Gd-Fe-Co alloys, such as domain-wall motion and spin-orbit torque switching in spintronics devices.
Article
Chemistry, Analytical
Fangchi Shao, Joon Soo Park, Guojie Zhao, Kuangwen Hsieh, Tza-Huei Wang
Summary: Developing assays that combine CRISPR/Cas and isothermal nucleic acid amplification is a growing research area, with potential for point-of-care applications. Current research mainly focuses on appending different CRISPR/Cas effectors to isothermal nucleic acid amplification methods, but few studies have integrated both components into single-step assays. We conducted a systematic investigation and found that adding CRISPR/Cas12a enhances signal amplification but hinders recombinase polymerase amplification (RPA). We developed a PAM-free CRISPR/Cas12a-assisted RPA assay that outperforms other assays in design, signal, sensitivity, and speed. Our study provides new insights and can facilitate further advances in CRISPR/Cas-based assays.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Hailin Wei, Tong Han, Taiwen Li, Qiu Wu, Chenfei Wang
Summary: Single-cell CRISPR screens have been widely used to investigate gene regulatory circuits in diverse biological systems. SCREE is a comprehensive and flexible pipeline for the analysis of various types of single-cell CRISPR screens data.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Yiming Lu, Aiqing Yang, Cheng Quan, Yingwei Pan, Haoyun Zhang, Yuanfeng Li, Chengming Gao, Hao Lu, Xueting Wang, Pengbo Cao, Hongxia Chen, Shichun Lu, Gangqiao Zhou
Summary: The authors use single cell RNA sequencing to study the immune cell constituents and localization within human hepatocellular carcinoma, providing insights into the microenvironment of the cancer.
NATURE COMMUNICATIONS
(2022)
Review
Genetics & Heredity
Jun Ding, Nadav Sharon, Ziv Bar-Joseph
Summary: Methods for profiling genes at the single-cell level have greatly advanced our understanding of biological processes and systems. However, time-series single-cell RNA sequencing poses new challenges for analysis and modeling, including determining when and how to profile cells, linking cells across time points, learning continuous trajectories, and integrating different types of data.
NATURE REVIEWS GENETICS
(2022)
Article
Oncology
Juan Ramon Tejedor, Alfonso Penarroya, Javier Gancedo-Verdejo, Pablo Santamarina-Ojeda, Raul F. Perez, Sara Lopez-Tamargo, Ana Diez-Borge, Juan J. Alba-Linares, Nerea Gonzalez-del-Rey, Rocio G. Urdinguio, Cristina Mangas, Annalisa Roberti, Virginia Lopez, Teresa Morales-Ruiz, Rafael R. Ariza, Teresa Roldan-Arjona, Monica Meijon, Luis Valledor, Maria Jesus Canal, Daniel Fernandez-Martinez, Maria Fernandez-Hevia, Paula Jimenez-Fonseca, Luis J. Garcia-Florez, Agustin F. Fernandez, Mario F. Fraga
Summary: This study utilized a multi-omics approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human colorectal cancer (CRC) samples and colon cancer cell lines. The researchers used CRISPR-Cas9 epigenome editing tools to modulate the DNA methylation status of 56 promoters previously linked with epigenetic repression in CRC and assessed the functional consequences. Overall, the epigenetic modulation had a mild impact on gene expression reactivation and cancer cell viability, but the reactivation of RSPO2 was associated with impaired cell proliferation in p53(-/-) cancer cell lines.
CLINICAL EPIGENETICS
(2023)
Article
Biochemical Research Methods
Jinjin Tian, Jiebiao Wang, Kathryn Roeder
Summary: A new single-cell RNA sequencing data simulator ESCO is proposed in the study, focusing on gene co-expression and evaluating the performance of imputation methods in GCN recovery. The results show that imputation generally helps GCN recovery when data are not too sparse, while simple data aggregating methods are more suitable in the presence of an excessive fraction of zero counts.
Article
Biology
Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann-Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michele Milella, David Chang, Peter Bailey, Nigel B. Jamieson, Fraser Duthie, Marie-Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber L. Johns, John Pearson, Andrew Biankin, Sean M. Grimmond, Nicola Waddell, Katia Nones, Aldo Scarpa
Summary: The study identified three subgroups of PanNETs with distinct methylation patterns and genotype characteristics. The T1 subgroup was enriched for functional tumors and wild-type genotypes, the T2 subgroup had mutations and recurrent chromosomal losses, while the T3 subgroup harbored MEN1 mutations and histological parameters associated with better prognosis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Plant Sciences
Huiyun Yu, Leiyun Yang, Zhan Li, Feng Sun, Bo Li, Shengsong Guo, Yong-Fei Wang, Tong Zhou, Jian Hua
Summary: In situ deletion series generated by CRISPR/Cas9 genome editing identified cis-regulatory elements and potential transcription factors for the expression of the intracellular immune receptor NLR gene SNC1, and revealed the critical role of SNC1 in NLR gene co-expression.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Plant Sciences
Huiyun Yu, Leiyun Yang, Zhan Li, Feng Sun, Bo Li, Shengsong Guo, Yong-Fei Wang, Tong Zhou, Jian Hua
Summary: The transcriptional and post-transcriptional regulation of intracellular immune receptor nucleotide-binding leucine-rich repeats (NLRs) is complex and involves multiple cis-acting elements. The NLR gene SNC1 is a critical regulator of gene expression in the same gene cluster, and its expression is under complex local regulation.
PLANT CELL AND ENVIRONMENT
(2022)
Review
Biochemical Research Methods
Guanjing Hu, Corrinne E. Grover, Mark A. Arick, Meiling Liu, Daniel G. Peterson, Jonathan F. Wendel
Summary: This study presents an analytical workflow using cotton genus as an example to evaluate various bioinformatic methods at different stages of RNA-seq analysis for understanding polyploid expression evolution. The findings suggest that EAGLE-RC and GSNAP-PolyCat quantification pipelines outperform others, representing homoeolog expression and co-expression divergence well. This work highlights the importance of examining homoeolog read ambiguity to avoid potential artifacts affecting the understanding of duplicate gene expression in polyploids.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Lingfei Wang, Tom Michoel
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Astronomy & Astrophysics
Lingfei Wang, Ernestas Pukartas, Anupam Mazumdar
JOURNAL OF COSMOLOGY AND ASTROPARTICLE PHYSICS
(2013)
Article
Astronomy & Astrophysics
Lingfei Wang, Anupam Mazumdar
Article
Astronomy & Astrophysics
Anupam Mazumdar, Lingfei Wang
Article
Astronomy & Astrophysics
Changhong Li, Lingfei Wang, Yeuk-Kwan E. Cheung
PHYSICS OF THE DARK UNIVERSE
(2014)
Article
Biochemistry & Molecular Biology
Deepti Vipin, Lingfei Wang, Guillaume Devailly, Tom Michoel, Anagha Joshi
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2018)
Article
Multidisciplinary Sciences
Lingfei Wang, Tom Michoel
ROYAL SOCIETY OPEN SCIENCE
(2019)
Article
Genetics & Heredity
Lingfei Wang, Pieter Audenaert, Tom Michoel
FRONTIERS IN GENETICS
(2019)
Article
Multidisciplinary Sciences
Kwontae You, Lingfei Wang, Chih-Hung Chou, Kai Liu, Toru Nakata, Alok Jaiswal, Junmei Yao, Ariel Lefkovith, Abdifatah Omar, Jacqueline G. Perrigoue, Jennifer E. Towne, Aviv Regev, Daniel B. Graham, Ramnik J. Xavier
Summary: This study used single-cell RNA sequencing and genome-scale CRISPR screening to reveal the transcriptional states and functional roles associated with adaptive and terminal UPR in the mouse intestinal epithelium. It identified QRICH1 as a key effector of the UPR pathway, controlling a transcriptional program associated with translation and secretory networks crucial for cell fate in response to pathological ER stress.
Article
Biochemical Research Methods
Lingfei Wang, Nikolaos Trasanidis, Ting Wu, Guanlan Dong, Michael Hu, Daniel E. E. Bauer, Luca Pinello
Summary: Gene regulatory networks (GRNs) play crucial roles in cell function and identity, and undergo dynamic rewiring in development and disease. However, challenges in GRN inference persist, including dynamic rewiring, causal inference, feedback loop modeling, and context specificity. To tackle these challenges, researchers develop Dictys, a dynamic GRN inference and analysis method that combines various single-cell assays and probabilistic modeling to improve accuracy and reproducibility in GRN reconstruction. Dictys allows the inference and comparative analysis of context-specific and dynamic GRNs, providing unique insights into development and uncovering regulatory relationships. It is a freely available Python package that facilitates the probabilistic modeling of gene regulatory networks using single-cell multiomics data.
Article
Endocrinology & Metabolism
Sean Bankier, Lingfei Wang, Andrew Crawford, Ruth A. Morgan, Arno Ruusalepp, Ruth Andrew, Johan L. M. Bjorkegren, Brian R. Walker, Tom Michoel
Summary: Genome-wide association meta-analysis identified a genetic association between plasma cortisol, cardiovascular disease, and the SERPINA6/SERPINA1 locus. The study explored the mechanisms by which variations in corticosteroid-binding globulin (CBG) lead to cardiovascular disease using transcriptomic data and causal inference. The findings suggest that liver CBG production may perturb cortisol-regulated gene networks in peripheral tissues and promote cardiovascular disease.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lingfei Wang, Qian Zhang, Qian Qin, Nikolaos Trasanidis, Michael Vinyard, Huidong Chen, Luca Pinello
Summary: This article summarizes recent and popular computational methods for trajectory inference and cell fate prediction, revealing previously unknown transitional cell types and differentiation processes. Future challenges and opportunities in the development of new methods for reconstructing differentiation trajectories and inferring cell fates are also described.
CURRENT OPINION IN SYSTEMS BIOLOGY
(2021)
Article
Cell Biology
Kimberly L. Carey, Geraldine L. C. Paulus, Lingfei Wang, Dale R. Balce, Jessica W. Luo, Phil Bergman, Ianina C. Ferder, Lingjia Kong, Nicole Renaud, Shantanu Singh, Maria Kost-Alimova, Beat Nyfeler, Kara G. Lassen, Herbert W. Virgin, Ramnik J. Xavier
Article
Astronomy & Astrophysics
Anupam Mazumdar, Lingfei Wang
JOURNAL OF COSMOLOGY AND ASTROPARTICLE PHYSICS
(2013)