Article
Multidisciplinary Sciences
Teruo Akuta, Daisuke Minegishi, Nobuhide Kido, Keitaro Imaizumi, Shinji Nakaoka, Shin-Ichiro Tachibana, Kenji Hikosaka, Fumi Hori, Masataka Nakagawa, Chiaki Sakuma, Yuki Oouchi, Yu Nakajima, Sohei Tanaka, Tomoko Omiya, Kouki Morikaku, Minori Kawahara, Yoshifumi Tada, Hiroshi Tarui, Takafumi Ueda, Takane Kikuchi-Ueda, Yasuo Ono
Summary: A study developed an immunodiagnostic test based on RNA-seq data to detect scabies in infected animals' skin, which has the potential to accurately diagnose scabies in wildlife and humans.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Mengting Huang, Yixuan Yang, Xingzhao Wen, Weiqiang Xu, Na Lu, Xiao Sun, Jing Tu, Zuhong Lu
Summary: Although single cell RNA sequencing technologies are well developed, acquiring large-scale single cell expression data can still be costly. The study proposes a method of compressing expression profiles from the sample dimension by assigning each cell into multiple pools and demonstrates that expression profiles can be inferred from pool expression data with a overlapping pooling design and compressed sensing strategy. This approach, when combined with plate-based scRNA-seq measurement, maintains superior gene detection sensitivity and individual identity while reducing library costs by half.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Genetics & Heredity
Dhrithi Deshpande, Karishma Chhugani, Yutong Chang, Aaron Karlsberg, Caitlin Loeffler, Jinyang Zhang, Agata Muszynska, Viorel Munteanu, Harry Yang, Jeremy Rotman, Laura Tao, Brunilda Balliu, Elizabeth Tseng, Eleazar Eskin, Fangqing Zhao, Pejman Mohammadi, Pawel P. Labaj, Serghei Mangul
Summary: RNA-seq has become a widely used technology in biology and clinical science due to the development of accurate computational tools by the bioinformatics community. These tools enable the analysis of large amounts of transcriptomic data and help to detect novel exons, assess gene expression, and study alternative splicing. However, it can be challenging to obtain meaningful biological signals from raw RNA-seq data due to the scale of the data and limitations of sequencing technologies. The rapid development of novel computational tools has helped to overcome these challenges and unlock the full potential of RNA-seq.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Baoyi Zhang, Yuhan Fei, Jiejie Feng, Xueai Zhu, Rui Wang, Hanqing Xiao, Hongsheng Zhang, Ji Huang
Summary: This study constructed a comprehensive rice ncRNA co-expression atlas, RiceNCexp, which provides expression information and co-expression analysis tools for rice ncRNAs in multiple tissues/organs.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Yannick Dueren, Johannes Lederer, Li-Xuan Qin
Summary: This study developed a method called DANA to assess the performance of normalization methods for microRNA sequencing data. It can evaluate the effectiveness of normalization in removing handling artifacts and preserving biological signals. DANA can provide guidance for selecting a suitable normalization method.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Melanie Kirsche, Arun Das, Michael C. Schatz
Summary: This paper introduces Sapling, an algorithm for sequence alignment that uses a learned data model to enhance the suffix array and enable faster queries. By investigating different types of data models, providing an analysis of various neural network models, and offering an open-source aligner with a compact, practical piecewise linear model, the authors demonstrate that Sapling outperforms both optimized binary search techniques and multiple widely used read aligners across a variety of genomes. The algorithm achieves a speedup of more than two times while only adding <1% to the memory footprint of the suffix array.
Article
Plant Sciences
Xiaohui Wen, Junzhuo Li, Lili Wang, Chenfei Lu, Qiang Gao, Peng Xu, Ya Pu, Qiuling Zhang, Yan Hong, Luo Hong, He Huang, Huaigen Xin, Xiaoyun Wu, Dongru Kang, Kang Gao, Yajun Li, Chaofeng Ma, Xuming Li, Hongkun Zheng, Zicheng Wang, Yuannian Jiao, Liangsheng Zhang, Silan Dai
Summary: This study reports the chromosome-scale reference genome of a wild chrysanthemum species and reveals the molecular mechanism underlying the diverse capitulum types in chrysanthemums. The findings provide important insights for genetic improvement and developmental studies of chrysanthemums.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Wei Liu, Xu Liao, Ziye Luo, Yi Yang, Mai Chan Lau, Yuling Jiao, Xingjie Shi, Weiwei Zhai, Hongkai Ji, Joe Yeong, Jin Liu
Summary: This paper presents PRECAST, an efficient data integration method for analyzing spatial transcriptomics data from multiple tissue slides with complex batch or biological effects.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Kieran Tebben, Aliou Dia, David Serre
Summary: This study evaluates a reference data set that can be used to estimate the proportions of different stages of malaria parasites in infected human blood samples. This allows for accurate gene expression analysis and correction of biases caused by differences in cell composition.
Article
Biotechnology & Applied Microbiology
Ludvig Bergenstrahle, Bryan He, Joseph Bergenstrahle, Xesus Abalo, Reza Mirzazadeh, Kim Thrane, Andrew L. Ji, Alma Andersson, Ludvig Larsson, Nathalie Stakenborg, Guy Boeckxstaens, Paul Khavari, James Zou, Joakim Lundeberg, Jonas Maaskola
Summary: This method improves the low resolution of spatial transcriptomics by integrating gene expression data with histological images, allowing for higher-resolution expression maps to be inferred. The deep generative model used in this method can predict spatial gene expression solely from histology images.
NATURE BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ying Yu, Wanwan Hou, Yaqing Liu, Haiyan Wang, Lianhua Dong, Yuanbang Mai, Qingwang Chen, Zhihui Li, Shanyue Sun, Jingcheng Yang, Zehui Cao, Peipei Zhang, Yi Zi, Ruimei Liu, Jian Gao, Naixin Zhang, Jingjing Li, Luyao Ren, He Jiang, Jun Shang, Sibo Zhu, Xiaolin Wang, Tao Qing, Ding Bao, Bingying Li, Bin Li, Chen Suo, Yan Pi, Xia Wang, Fangping Dai, Andreas Scherer, Pirkko Mattila, Jinxiong Han, Lijun Zhang, Hui Jiang, Danielle Thierry-Mieg, Jean Thierry-Mieg, Wenming Xiao, Huixiao Hong, Weida Tong, Jing Wang, Jinming Li, Xiang Fang, Li Jin, Joshua Xu, Feng Qian, Rui Zhang, Leming Shi, Yuanting Zheng
Summary: This study established RNA reference materials based on Quartet samples, including four RNA reference materials and ratio-based transcriptome-wide reference datasets between two samples. The results of the study demonstrate that these reference materials can be used to assess and improve the quality of transcriptomic data in clinical and biological settings.
NATURE BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Juliana Costa-Silva, Mariangela Hungria, Douglas S. Domingues, David Menotti, Fabricio Martins Lopes
Summary: This paper provides a comprehensive review of the computational analysis pipeline for differential gene expression analysis from RNA-seq data. It introduces the objectives, methods, and properties of each step, presents a timeline of the computational methods, and discusses the relationships between important tools. The paper serves as a tutorial for beginners and helps established users update their analysis pipelines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Review
Biochemistry & Molecular Biology
Juliana Costa-Silva, Douglas S. Domingues, David Menotti, Mariangela Hungria, Fabricio Martins Lopes
Summary: This paper provides a review of the pipeline for differential expression analysis, discussing the steps, methods, challenges, and tutorial aspects. It aims to guide new entrants and assist established users in updating their analysis pipelines.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Athanasios Alexiou, Dimitrios Zisis, Ioannis Kavakiotis, Marios Miliotis, Antonis Koussounadis, Dimitra Karagkouni, Artemis G. Hatzigeorgiou
Summary: microRNAs are small non-coding RNAs that play central roles in gene expression and various pathological conditions. Next-Generation Sequencing technologies have enabled cost-effective and massive data production, allowing for detailed analysis of miRNA expression. DIANA-mAP is a fully automated computational pipeline that facilitates miRNA NGS data analysis from raw data to differential expression analysis in an easy and efficient manner.
Article
Oncology
Jing Yang, Shilin Zhao, Jing Wang, Quanhu Sheng, Qi Liu, Yu Shyr
Summary: Cancer-Immu is a comprehensive platform that integrates various omics data and clinical phenotypes to explore immunogenomic connections. It provides easy access to data and helps researchers translate omics datasets into biological insights and clinical applications.
Review
Oncology
Jamie E. Chaft, Yu Shyr, Boris Sepesi, Patrick M. Forde
Summary: Biomarker-informed clinical trials are pushing the treatment of early-stage lung cancer beyond cytotoxic chemotherapy, with the incorporation of targeted and immunotherapies. Adjuvant osimertinib, preoperative chemoimmunotherapy, and adjuvant immunotherapy could improve outcomes for resectable lung cancer patients, and ongoing or planned studies focusing on biomarkers, immunotherapy, and targeted therapy may further enhance survival.
JOURNAL OF CLINICAL ONCOLOGY
(2022)
Article
Oncology
A. L. Schmidt, C. Labaki, C-Y Hsu, Z. Bakouny, N. Balanchivadze, S. A. Berg, S. Blau, A. Daher, T. El Zarif, C. R. Friese, E. A. Griffiths, J. E. Hawley, B. Hayes-Lattin, V Karivedu, T. Latif, B. H. Mavromatis, R. R. McKay, G. Nagaraj, R. H. Nguyen, O. A. Panagiotou, A. J. Portuguese, M. Puc, M. Santos Dutra, B. A. Schroeder, A. Thakkar, E. M. Wulff-Burchfield, S. Mishra, D. Farmakiotis, Yu Shyr, J. L. Warner, T. K. Choueiri
Summary: This study analyzes the clinical features of cancer patients who develop symptomatic COVID-19 after vaccination. It finds that these patients often have comorbidities and can experience severe and even lethal infections. Hematologic malignancy patients are over-represented among the vaccinated cancer patients who develop symptomatic COVID-19. Therefore, while vaccination remains crucial in protecting vulnerable populations, including cancer patients, those who develop breakthrough infections despite full vaccination still face the risk of severe outcomes.
ANNALS OF ONCOLOGY
(2022)
Article
Oncology
Ziad Bakouny, Chris Labaki, Punita Grover, Joy Awosika, Shuchi Gulati, Chih-Yuan Hsu, Saif Alimohamed, Babar Bashir, Stephanie Berg, Mehmet A. Bilen, Daniel Bowles, Cecilia Castellano, Aakash Desai, Arielle Elkrief, Omar E. Eton, Leslie A. Fecher, Daniel Flora, Matthew D. Galsky, Margaret E. Gatti-Mays, Alicia Gesenhues, Michael J. Glover, Dharmesh Gopalakrishnan, Shilpa Gupta, Thorvardur R. Halfdanarson, Brandon Hayes-Lattin, Mohamed Hendawi, Emily Hsu, Clara Hwang, Roman Jandarov, Chinmay Jani, Douglas B. Johnson, Monika Joshi, Hina Khan, Shaheer A. Khan, Natalie Knox, Vadim S. Koshkin, Amit A. Kulkarni, Daniel H. Kwon, Sara Matar, Rana R. McKay, Sanjay Mishra, Feras A. Moria, Amanda Nizam, Nora L. Nock, Taylor K. Nonato, Justin Panasci, Lauren Pomerantz, Andrew J. Portuguese, Destie Provenzano, Matthew Puc, Yuan J. Rao, Terence D. Rhodes, Gregory J. Riely, Jacob J. Ripp, Andrea Rivera, Erika Ruiz-Garcia, Andrew L. Schmidt, Adam J. Schoenfeld, Gary K. Schwartz, Sumit A. Shah, Justin Shaya, Suki Subbiah, Lisa M. Tachiki, Matthew D. Tucker, Melissa Valdez-Reyes, Lisa B. Weissmann, Michael T. Wotman, Elizabeth M. Wulff-Burchfield, Zhuoer Xie, Yuanchu James Yang, Michael A. Thompson, Dimpy P. Shah, Jeremy L. Warner, Yu Shyr, Toni K. Choueiri, Trisha M. Wise-Draper
Summary: This cohort study found that systemic anticancer therapies, especially IO, in the context of baseline immunosuppression, were associated with severe clinical outcomes and the development of cytokine storm in patients with cancer and COVID-19.
Letter
Cardiac & Cardiovascular Systems
Kaushik Amancherla, Juan Qin, Michelle L. Hulke, Ryan D. Pfeiffer, Vineet Agrawal, Quanhu Sheng, Yaomin Xu, Kelly H. Schlendorf, JoAnn Lindenfeld, Ravi V. Shah, Jane E. Freedman, Nathan R. Tucker, Javid Moslehi
CIRCULATION-HEART FAILURE
(2023)
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
Oncology
Eric M. Lander, Katherine C. Rappazzo, Li-Ching Huang, Jiun-Ruey Hu, Heidi Chen, Yu Shyr, Vandana G. Abramson
Summary: This novel study investigates the relationship between HER2 amplification and pathologic complete response (pCR) following neoadjuvant anti-HER2 dual therapy without chemotherapy. The results show a positive association between the HER2/CEP17 FISH ratio and pCR.
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.
Article
Medicine, Research & Experimental
Evan A. Clark, Edward Ryan R. Talatala, Wenda Ye, Ruth J. Davis, Samuel L. Collins, Alexander T. Hillel, Marisol Ramirez-Solano, Quanhu Sheng, Celestine N. Wanjalla, Simon A. Mallal, Alexander Gelbard
Summary: This study found that SGS cases do not have lower diversity in adaptive immune response compared to healthy controls. Interestingly, both in health and disease, the TCR repertoire contains a restricted number of high frequency clonotypes that do not significantly overlap between individuals.
Article
Oncology
Jing Wang, Hua-Chang Chen, Quanhu Sheng, T. Renee Dawson, Robert J. Coffey, James G. Patton, Alissa M. Weaver, Yu Shyr, Qi Liu
Summary: Through a systematic assessment of small RNA sequencing, we identified the quality, technical, and potential biological biases introduced by different EV isolation methods and the enrichment of specific small RNA types in EVs. The findings from this study provide guidance for quality control of EV small RNA-seq, selection of EV isolation techniques, and enhance the interpretation of small RNA contents and preferential loading in EVs.
Article
Oncology
Kristina Fanucci, Mary Jo Pilat, Derek Shyr, Yu Shyr, Scott Boerner, Jing Li, Diane Durecki, Jan Drappatz, Vinay Puduvalli, Frank Scott Lieberman, Javier Gonzalez, Pierre Giglio, S. Percy Ivy, Ranjit S. Bindra, Antonio Omuro, Patricia LoRusso
Summary: A multicenter study evaluated the efficacy of olaparib monotherapy in patients with IDH1/2-mutant gliomas. The study showed that olaparib monotherapy can produce prolonged disease stabilization in patients with grade 2/3 histology, but not in patients with grade 4 histology. This suggests potential clinical benefit of olaparib monotherapy in select populations.
CANCER RESEARCH COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Li-Ching Huang, Lindsey K. Stolze, Hua-Chang Chen, Alexander Gelbard, Yu Shyr, Qi Liu, Quanhu Sheng
Summary: Single-cell sequencing is widely used for studying cellular heterogeneity, and sample multiplexing is an important technique that allows for increased capacity, decreased costs, and minimized batch effects. The crucial step in analyzing multiplexed data is demultiplexing, which assigns cells to individual samples. Accurate demultiplexing is essential to avoid misleading characterization.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Respiratory System
Emily Pei-Ying Lin, Li-Ching Huang, Jennifer Whisenant, Sally York, Travis Osterman, Jennifer Lewis, Wade Iams, Emily Skotte, Amanda Cass, Chih-Yuan Hsu, Yu Shyr, Leora Horn
Summary: This study shows that influenza vaccination (FV) does not increase toxicity for patients with advanced thoracic cancer on immune checkpoint inhibitors (ICIs) and is associated with a decreased risk of grade 3-5 immune-related adverse events (IRAEs). However, FV does not have a statistically significant impact on survival times.