Article
Biochemical Research Methods
Quan Shi, Shiping Liu, Karsten Kristiansen, Longqi Liu
Summary: The FASTQ+ format is specifically designed for single-cell experiments, allowing for optional tags and full compatibility with the FASTQ format. PISA, an open-source software written in C language, provides various utilities for processing single-cell experiment data.
Article
Biology
Cesar Pineiro, Juan C. Pichel
Summary: BigSeqKit is a very complete and ultra-fast toolkit for processing and manipulating large FASTA and FASTQ files. It utilizes a high-performance computing-Big Data framework to parallelize and optimize commands, resulting in significantly faster file manipulation.
Article
Biotechnology & Applied Microbiology
Andrea Telatin, Piero Fariselli, Giovanni Birolo
Summary: FASTA and FASTQ formats are commonly used in bioinformatics, molecular biology, and biochemistry. The SeqFu suite of tools provides a wide range of commands for common and specialist operations in handling these file formats efficiently and is developed for high-performance processing. SeqFu is freely available for users and can be easily implemented in analytical pipelines.
BIOENGINEERING-BASEL
(2021)
Article
Agriculture, Dairy & Animal Science
Andre Moreira Souza, Rodrigo de Andrade Santos Weigert, Elaine Parros Machado de Sousa, Lucas Tassoni Andrietta, Ricardo Vieira Ventura
Summary: This study aims to provide practical directions on storing genomic information and novel phenotypes using a non-relational database. The research investigates different formats of genomic and phenotypic information and highlights the advantages of a centralized database concept. Comparisons with relational database approaches show that non-relational databases have reduced importing time for handling a large number of SNPs.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Computer Science, Information Systems
Robert Bakaric, Damir Korencic, Dalibor Hrsak, Strahil Ristov
Summary: Researchers propose the sFASTQ format, a succinct representation of FASTQ files that can be used without decompression and supports random access. The sFASTQ format can be searched on the disk, eliminating the need for additional memory resources, and has a comparable size to Gzip files. SFQ software is provided for constructing and using the sFASTQ format, with support for various features and compression options.
Article
Chemistry, Analytical
Wiktor Kusmirek
Summary: Nanopore sequencing is a rapidly growing DNA sequencing technology. The basecalling process, which reproduces DNA sequences from the measured current sequence on the nanopores of the sequencer, is a key stage in processing sequencer data. This study compares the estimated quality of nucleotide reconstruction reported by different basecallers and investigates its usage in processing nanopore DNA reads. The results demonstrate variations in estimated quality and the lack of utilization of this information in existing tools.
Article
Biochemical Research Methods
Guillermo Dufort y Alvarez, Gadiel Seroussi, Pablo Smircich, Jose Sotelo-Silveira, Idoia Ochoa, Alvaro Martin
Summary: RENANO is a reference-based lossless data compressor specifically designed for FASTQ files generated with nanopore sequencing technologies, outperforming its predecessor ENANO in base call sequence compression. It shows significant improvements in performance in two different scenarios and overall file compression rates compared to ENANO.
Article
Biochemical Research Methods
Minhyeok Cho, Albert No
Summary: This paper introduces a Fast and Concurrent Lossless Quality scores Compressor (FCLQC) that significantly outperforms baseline compressors in terms of compression and decompression speed while also supporting random access functionality.
BMC BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Toshiya Fujii, Norio Aoyama, Sayuri Kida, Kentaro Taniguchi, Tomomi Yata, Masato Minabe, Motohiro Komaki
Summary: A relationship between periodontitis and liver function has been suggested. This study aimed to clarify the relationship between liver function markers (AST, ALT, and GGT) and the periodontal inflammatory surface area (PISA). The results showed that participants with high PISA scores were more likely to have increased GGT levels, while AST and ALT levels did not differ based on PISA.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Afonso M. Bravo, Athanasios Typas, Jan-Willem Veening
Summary: 2FAST2Q is a versatile and intuitive standalone program that extracts and counts feature occurrences in FASTQ files. It efficiently processes data in microbiology and other fields generating amplicon sequencing data.
Article
Biochemical Research Methods
Hansen Chen, Jianhua Chen, Zhiwen Lu, Rongshu Wang
Summary: CMIC is an adaptive and random access supported compressor for lossless compression of quality score sequences. Our experiments show that our compressor has good performance in terms of compression rates on all the tested datasets. The file sizes can be reduced by up to 21.91% compared with LCQS. In terms of compression speed, CMIC is better than all other compressors on most of the tested cases. In terms of random access speed, CMIC is faster than LCQS, which provides a random access function for compressed quality scores.
BMC BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Mahdieh Labani, Amin Beheshti, Nigel H. Lovell, Hamid Alinejad-Rokny, Ali Afrasiabi
Summary: KARAJ is a fast and flexible Linux command-line tool for automating the querying and downloading of a wide range of genomic and transcriptomic sequence data types. It can automate four tasks based on input PMCIDs or access numbers, such as providing dataset summaries, calculating file sizes, generating metadata tables, and downloading supplementary data tables. Additionally, it offers a parallel downloading framework powered by Aspera connect to significantly reduce downloading time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Polymer Science
Cabell B. Eades, Joanna Korpanty, John B. Garrison, Georg M. Scheutz, Sofia L. Goodrich, Nathan C. Gianneschi, Brent S. Sumerlin
Summary: We present a dual-responsive block copolymer system that can control the size and morphology of self-assembled nanostructures through pH-dependent cloud point (Tcp). By incorporating a pH- and temperature-responsive monomer, 2-(dimethylamino)ethyl methacrylate (DMAEMA), in the nanoparticle corona, the relative hydrophilic/hydrophobic block volumes can be controlled. Varying the pH, temperature, and content of DMAEMA, we successfully generated micelles, worms, and vesicles from a single block copolymer composition.
Article
Acoustics
Janek T. Groehl, Lina K. Hacker, Ben Cox, Kris Dreher, Stefan Morscher, Avotra C. Rakotondrainibe, Francois E. Varray, Lawrence Yip, William Vogt, Sarah Bohndeik
Summary: Photoacoustic imaging is a promising modality for patient management, but the lack of uniformity in data formats hinders progress and collaboration. The International Photoacoustic Standardisation Consortium has developed a consensus data format and conversion tools to facilitate data exchange and comparison.
Article
Business
Daniel Martinez-Gautier, Ruben Garrido-Yserte, Maria-Teresa Gallo-Rivera
Summary: The relationship between technology and learning is complex and varies depending on the context and type of use. Access to technology at school and home has a positive impact on learning, but misuse as a distraction can be detrimental. Guidance on technology use is crucial, as it affects the impact of technological devices on learning.
JOURNAL OF BUSINESS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Marc de Manuel, Ross Barnett, Marcela Sandoval-Velasco, Nobuyuki Yamaguchi, Filipe Garrett Vieira, M. Lisandra Zepeda Mendoza, Shiping Liu, Michael D. Martin, Mikkel-Holger S. Sinding, Sarah S. T. Mak, Christian Caroe, Shanlin Liu, Chunxue Guo, Jiao Zheng, Grant Zazula, Gennady Baryshnikov, Eduardo Eizirik, Klaus-Peter Koepfli, Warren E. Johnson, Agostinho Antunes, Thomas Sicheritz-Ponten, Shyam Gopalakrishnan, Greger Larson, Huanming Yang, Stephen J. O'Brien, Anders J. Hansen, Guojie Zhang, Tomas Marques-Bonet, M. Thomas P. Gilbert
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Biochemistry & Molecular Biology
Yunfan Sun, Liang Wu, Yu Zhong, Kaiqian Zhou, Yong Hou, Zifei Wang, Zefan Zhang, Jiarui Xie, Chunqing Wang, Dandan Chen, Yaling Huang, Xiaochan Wei, Yinghong Shi, Zhikun Zhao, Yuehua Li, Ziwei Guo, Qichao Yu, Liqin Xu, Giacomo Volpe, Shuangjian Qiu, Jian Zhou, Carl Ward, Huichuan Sun, Ye Yin, Xun Xu, Xiangdong Wang, Miguel A. Esteban, Huanming Yang, Jian Wang, Michael Dean, Yaguang Zhang, Shiping Liu, Xinrong Yang, Jia Fan
Summary: This study showed that early-relapse hepatocellular carcinoma (HCC) tumors exhibit innate-like CD8(+) T cells with overexpression of KLRB1 (CD161) and a low cytotoxic state, unlike the exhausted state seen in primary HCC. These cells were associated with a worse prognosis. Additionally, potential immune evasion mechanisms were identified in recurrent tumor cells, which dampen dendritic cell antigen presentation and recruit innate-like CD8(+) T cells.
Article
Oncology
Wei Wang, Yu Zhong, Zhenkun Zhuang, Jiarui Xie, Yueer Lu, Chengzhi Huang, Yan Sun, Liang Wu, Jianhua Yin, Hang Yu, Zhiqiang Jiang, Shanshan Wang, Chunqing Wang, Yuanhang Zhang, Yilin Huang, Chongyin Han, Zhenggang Zhong, Jialin Hu, Ying Ouyang, Huisheng Liu, Mengya Yu, Xiaochan Wei, Dandan Chen, Lizhen Huang, Yong Hou, Zhanglin Lin, Shiping Liu, Fei Ling, Xueqing Yao
Summary: This study utilized two single-cell RNA sequencing technologies to create an atlas of immune and nonimmune cells in colorectal cancer patients, revealing significant differences in the functions and states of B cells at different stages of tumor development. The research provides deeper insights into immune infiltration within CRC and suggests new directions for future immunotherapy research.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Multidisciplinary Sciences
Shang Liu, Biaofeng Zhou, Liang Wu, Yan Sun, Jie Chen, Shiping Liu
Summary: Recent advances in single-cell RNA sequencing have improved our understanding of TILs heterogeneity and cancer progression, but studies on alternative splicing as a regulatory factor remain limited. A new computational tool, DESJ-detection, accurately detects differentially expressed splicing junctions at the single-cell level. Analysis of T cells from HCC identified novel insights into T cell heterogeneity and a potential new cell state pre-activation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Yun-Fan Sun, Liang Wu, Shi-Ping Liu, Miao-Miao Jiang, Bo Hu, Kai-Qian Zhou, Wei Guo, Yang Xu, Yu Zhong, Xiao-Rui Zhou, Ze-Fan Zhang, Geng Liu, Sheng Liu, Ying-Hong Shi, Yuan Ji, Min Du, Nan-Nan Li, Gui-Bo Li, Zhi-Kun Zhao, Xiao-Yun Huang, Li-Qin Xu, Qi-Chao Yu, David H. Peng, Shuang-Jian Qiu, Hui-Chuan Sun, Michael Dean, Xiang-Dong Wang, Wen-Yuan Chung, Ashley R. Dennison, Jian Zhou, Yong Hou, Jia Fan, Xin-Rong Yang
Summary: This study used single-cell RNA sequencing to analyze circulating tumor cells from liver cancer patients, revealing that the transcriptional dynamics of CTCs are associated with stress response, cell cycle, and immune evasion signaling. Additionally, it was identified that CCL5 plays a crucial role in immune evasion of CTCs.
NATURE COMMUNICATIONS
(2021)
Article
Genetics & Heredity
Liang Wu, Miaomiao Jiang, Yuzhou Wang, Biaofeng Zhou, Yunfan Sun, Kaiqian Zhou, Jiarui Xie, Yu Zhong, Zhikun Zhao, Michael Dean, Yong Hou, Shiping Liu
Summary: The single-cell DNA library preparation method developed in this study, known as scDPN, eliminates the need for preamplification and allows for high-throughput CNV detection. It shows lower amplification bias and noise compared to the MDA method, and demonstrates high sensitivity and accuracy in evaluating cell lines and tumor tissues. Additionally, it was used to identify clonal subpopulations in hepatocellular carcinoma (HCC) samples, revealing clonal selection during tumor recurrence. Overall, this approach provides a comprehensive and scalable solution for understanding genome heterogeneity and evolution.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Lei Han, Xiaoyu Wei, Chuanyu Liu, Giacomo Volpe, Zhenkun Zhuang, Xuanxuan Zou, Zhifeng Wang, Taotao Pan, Yue Yuan, Xiao Zhang, Peng Fan, Pengcheng Guo, Yiwei Lai, Ying Lei, Xingyuan Liu, Feng Yu, Shuncheng Shangguan, Guangyao Lai, Qiuting Deng, Ya Liu, Liang Wu, Quan Shi, Hao Yu, Yunting Huang, Mengnan Cheng, Jiangshan Xu, Yang Liu, Mingyue Wang, Chunqing Wang, Yuanhang Zhang, Duo Xie, Yunzhi Yang, Yeya Yu, Huiwen Zheng, Yanrong Wei, Fubaoqian Huang, Junjie Lei, Waidong Huang, Zhiyong Zhu, Haorong Lu, Bo Wang, Xiaofeng Wei, Fengzhen Chen, Tao Yang, Wensi Du, Jing Chen, Shibo Xu, Juan An, Carl Ward, Zongren Wang, Zhong Pei, Chi-Wai Wong, Xiaolei Liu, Huafeng Zhang, Mingyuan Liu, Baoming Qin, Axel Schambach, Joan Isern, Liqiang Feng, Yan Liu, Xiangyu Guo, Zhen Liu, Qiang Sun, Patrick H. Maxwell, Nick Barker, Pura Munoz-Canoves, Ying Gu, Jan Mulder, Mathias Uhlen, Tao Tan, Shiping Liu, Huanming Yang, Jian Wang, Yong Hou, Xun Xu, Miguel A. Esteban, Longqi Liu
Summary: Studying tissue composition and function in non-human primates is crucial for understanding the nature of human species. This study presents a large-scale cell transcriptomic atlas of the non-human primate Macaca fascicularis, providing a vast annotated resource for studying a species closely related to humans. The atlas has been used to reconstruct cell-cell interaction networks, map the distribution of receptors for viruses causing human infectious diseases, and establish potential clinical associations with human genetic diseases.
Article
Multidisciplinary Sciences
Shanshan Wang, Jiarui Xie, Xuanxuan Zou, Taotao Pan, Qichao Yu, Zhenkun Zhuang, Yu Zhong, Xin Zhao, Zifei Wang, Rui Li, Ying Lei, Jianhua Yin, Yue Yuan, Xiaoyu Wei, Longqi Liu, Shiping Liu, Huanming Yang, Liang Wu
Summary: This study investigates the molecular mechanisms underlying metastasis in hepatocellular carcinoma (HCC) using single-cell transcriptomic, proteomic, and chromatin accessibility data. The researchers found that the prevalence of a mesenchymal state and levels of cell proliferation are linked to metastatic potential in HCC cell lines. They also identified a rare hypoxic subtype with increased glycolysis capacity and higher metastatic potential. Furthermore, they identified a 14-gene panel representing the hypoxia signature, which could serve as a prognostic index.
Article
Genetics & Heredity
Wenhui Wang, Yan Chen, Liang Wu, Yi Zhang, Seungyeul Yoo, Quan Chen, Shiping Liu, Yong Hou, Xiao-ping Chen, Qian Chen, Jun Zhu
Summary: Our study revealed high heterogeneity of HCC tumor cells in terms of both HBV integrations and CNVs. Two HBV integration hotspots were found across cells, and cells from multiple tumor sites shared some HBV integration and CNV patterns.
BMC MEDICAL GENOMICS
(2022)
Review
Genetics & Heredity
Shuangsang Fang, Bichao Chen, Yong Zhang, Haixi Sun, Longqi Liu, Shiping Liu, Yuxiang Li, Xun Xu
Summary: The development of spatial transcriptomics technologies has revolutionized genetic research, enabling the study of cell subsets in different environments and organs. This has brought about the need for computational approaches to interpret the large-scale data generated by these technologies, but algorithms specifically designed for this purpose are still in their early stages.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Ying Lei, Mengnan Cheng, Zihao Li, Zhenkun Zhuang, Liang Wu, Yunong Sun, Lei Han, Zhihao Huang, Yuzhou Wang, Zifei Wang, Liqin Xu, Yue Yuan, Shang Liu, Taotao Pan, Jiarui Xie, Chuanyu Liu, Giacomo Volpe, Carl Ward, Yiwei Lai, Jiangshan Xu, Mingyue Wang, Hao Yu, Haixi Sun, Qichao Yu, Chunqing Wang, Chi Wai Wong, Wei Liu, Liangzhi Xu, Jingkuan Wei, Dandan Chen, Zhouchun Shang, Guibo Li, Kun Ma, Le Cheng, Fei Ling, Tao Tan, Kai Chen, Bosiljka Tasic, Michael Dean, Weizhi Ji, Huanming Yang, Ying Gu, Miguel A. Esteban, Yuxiang Li, Ao Chen, Yuyu Niu, Hongkui Zeng, Yong Hou, Longqi Liu, Shiping Liu, Xun Xu
Summary: This study utilizes single-cell transcriptomic and chromatin accessibility data, along with spatial enhanced resolution omics-sequencing, to conduct a detailed investigation of cell type and regulatory features in the prefrontal cortex, primary motor cortex, and primary visual cortex of cynomolgus monkey brain. The study identifies area-specific chromatin accessible sites and their targeted genes, reveals genes related to specialized functions, compares oligodendrocyte trajectories between macaque and human, and maps genetic variants and gene perturbations of human diseases to NHP cortical cells.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Gui-Ming Li, Guo-Zhong Xiao, Peng-Fei Qin, Xing-Yang Wan, Yuan-Ji Fu, Yi-Hui Zheng, Min-Yi Luo, Dong-Lin Ren, Shi-Ping Liu, Hua-Xian Chen, Hong-Cheng Lin
Summary: There are significant differences in the tumor microenvironment (TME) between young-onset colorectal cancer (yCRC) and old-onset colorectal cancer (oCRC). The TME of yCRC is more immunosuppressive, with malignant cells playing a crucial role.
Article
Biochemical Research Methods
Quan Shi, Shiping Liu, Karsten Kristiansen, Longqi Liu
Summary: The FASTQ+ format is specifically designed for single-cell experiments, allowing for optional tags and full compatibility with the FASTQ format. PISA, an open-source software written in C language, provides various utilities for processing single-cell experiment data.
