Review
Biochemistry & Molecular Biology
Violaine Saint-Andre
Summary: The review discusses the main approaches and tools for mapping Transcriptional Regulatory Networks (TRNs) from high-throughput data, highlighting their advantages and limitations. It summarizes the main principles defining the topology and structure-function relationships in TRNs, and presents an overview of the work done to map TRNs from bulk transcriptomic data by methodological approach. Additionally, it touches upon recent modeling of TRNs using different types of molecular data and concludes with expected improvements in the field.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Plant Sciences
Syed Sarfaraz Hussain, Manzar Abbas, Sammar Abbas, Mingke Wei, Ahmed H. El-Sappah, Yuhan Sun, Yun Li, Arthur J. Ragauskas, Quanzi Li
Summary: Alternative splicing in plants regulates gene expression through differential transcriptional modifications, allowing adaptation to environmental stresses and different growth stages. It causes the retention of introns in messenger RNA, leading to the translation of differentially expressed proteins. Additionally, alternative splicing remodels transcription factors at the post-transcriptional level, activating or repressing transcription.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Liu Tian, Tong Liu, Kang-Jian Hua, Xiao-Pan Hu, Bin-Guang Ma
Summary: The transcriptional regulatory network (TRN) is crucial for prokaryotic organisms to receive and respond to environmental information. This study explores the spatial organization characteristics of bacterial TRNs using chromatin interaction data, revealing various stable spatial organization features related to biological functions.
Review
Biochemistry & Molecular Biology
Yakun Li, Lihong Ding, Mei Zhou, Zhixiang Chen, Yanfei Ding, Cheng Zhu
Summary: Cadmium, a highly toxic non-essential heavy metal, can be sensed, transported, and detoxified by plants through specialized mechanisms. Recent studies have identified numerous transporters involved in Cd uptake, transport, and detoxification. However, the intricate transcriptional regulatory networks associated with Cd response are still not fully understood.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Xiaojun Ma, Ashwin Somasundaram, Zengbiao Qi, Douglas J. Hartman, Harinder Singh, Hatice Ulku Osmanbeyoglu
Summary: The study introduces a computational method called SPaRTAN that can link cell-surface receptors with transcription factors to predict the relationships between signaling and transcriptional regulators. Applied to immune cells and tumor infiltrating CD8(+) T cells, the method offers a new approach to developing cell-context-specific maps of the interface between signaling and transcriptional regulators.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Wooseok Seo, Chandsultana Jerin, Hiroyoshi Nishikawa
Summary: Exhausted CD8(+) T cells may be deliberately generated and maintained to provide mild immune responses against chronic infection or cancer, which can be safer over the long term compared to strong immune responses. A specific population of exhausted CD8(+) T cells that behaves like self-renewing stem cells has been identified, suggesting they can be considered progenitors of exhausted CD8(+) T cells. Studies have revealed the regulatory network governing the generation and propagation of exhausted CD8(+) T cells, shedding light on the developmental stages that lead to this subtle but effective immune response.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemical Research Methods
Mengyuan Zhao, Wenying He, Jijun Tang, Quan Zou, Fei Guo
Summary: In this study, a deep learning framework called DGRNS is developed for inferring gene regulatory networks from single-cell transcriptomic data. It effectively identifies the relationships between gene pairs and overcomes the challenges of sparsity and noise in the data. The results show that DGRNS outperforms other methods and discovers novel regulatory relationships with high confidence, which require further research.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Microbiology
Wurihan Wurihan, Yi Zou, Alec M. Weber, Korri Weldon, Yehong Huang, Xiaofeng Bao, Chengsheng Zhu, Xiang Wu, Yaqun Wang, Zhao Lai, Huizhou Fan
Summary: Chlamydia trachomatis, an intracellular bacterium, has a unique developmental cycle with an infectious elementary body and a replicative reticulate body. The temporal control of the transcriptome is important for this cycle. GrgA, a Chlamydia-specific transcription factor, plays a crucial role in transcriptomic expression, along with Euo and HrcA. The regulatory network of these three factors is critical for C. trachomatis growth and development, impacting gene expression, stress response, and virulence factor production.
Article
Computer Science, Artificial Intelligence
Jiyang Bai, Yuxiang Ren, Jiawei Zhang
Summary: This paper proposes a Metric-Guided subgraph learning framework (MeGuide) for GNNs, which utilizes two novel metrics to guide subgraph sampling and mini-batch based training, improving the effectiveness and efficiency of GNNs.
INTERNATIONAL JOURNAL OF INTELLIGENT SYSTEMS
(2022)
Article
Geriatrics & Gerontology
Xianzhong Zhang, Guanglou Zhu, Fengmin Zhang, Dingye Yu, Xuyang Jia, Bingwei Ma, Weizhe Chen, Xinyu Cai, Lingzhou Mao, Chengle Zhuang, Zhen Yu
Summary: This study identified an immune-related transcriptional regulatory network in sarcopenia using RNA-seq data analysis. The PAX5-SERPIAN5-PI3K/Akt axis was suggested as a potential mechanism for sarcopenia, with B cells playing a vital role in this signal transduction. Trichostatin A was identified as a potential medicine for sarcopenia.
Article
Engineering, Multidisciplinary
Zhongzheng Tang, Luning Wang, Qian Xu, Kejie Lu, Jianping Wang, Kui Wu, Xiaohua Jia
Summary: A key challenge in Internet measurement is accurately and effectively measuring end-to-end performance. This study proposes a scalable network inference framework called SNIFF, which monitors the end-to-end performance of a set of paths over time by exploring key features and developing non-uniform sampling strategies.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2022)
Article
Immunology
Feng Shan, Anthony R. Cillo, Carly Cardello, Daniel Y. Yuan, Sheryl R. Kunning, Jian Cui, Caleb Lampenfeld, Asia M. Williams, Alexandra P. Mcdonough, Arjun Pennathur, James D. Luketich, John M. Kirkwood, Robert L. Ferris, Tullia C. Bruno, Creg J. Workman, Panayiotis V. Benos, Dario A. A. Vignali
Summary: Research identified an activated Tregs subpopulation expressing multiple tumor necrosis factor receptor genes in head and neck squamous cell carcinoma tumors, associated with worse prognosis. The transcription factor BATF plays a central role in limiting excessive activation and promoting the survival of activated T-regs. Additionally, a suite of surface molecules reflective of the BATF-driven transcriptional network on intratumoral T-regs was identified.
SCIENCE IMMUNOLOGY
(2021)
Article
Immunology
Zhaoqi Zhang, Elhusseny A. Bossila, Ling Li, Songnian Hu, Yong Zhao
Summary: This study used RNA-seq data to analyze transcriptome profiles and cell metabolism during monocyte development, revealing important genes and pathways involved in this process. The findings provide valuable insights into the dynamics of monocyte development in bone marrow.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Jian-Fei Kuang, Chao-Jie Wu, Yu-Fan Guo, Dirk Walther, Wei Shan, Jian-Ye Chen, Lin Chen, Wang-Jin Lu
Summary: This study conducted temporal gene expression analyses to investigate the gene regulatory network involved in banana fruit ripening, identifying 25 transcription factors as prime candidates to regulate the ripening process by modulating different ripening-related pathways. This provides a basis for targeted manipulation of fruit ripening to achieve higher banana yield and reduced losses in commercialization.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Softya Sebastian, Swarup Roy, Jugal Kalita
Summary: Inference of large-scale gene regulatory networks is crucial for understanding gene interactions. Existing methods are limited to small networks, so parallel computing is proposed to construct large networks. A generic parallel framework is proposed which can infer large networks without re-engineering existing methods, and has been tested on various inference methods with good results. Finally, a gene network associated with Alzheimer's Disease was successfully inferred using the framework, revealing hub genes related to the disease.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Jing Zhang, Jason Liu, Donghoon Lee, Shaoke Lou, Zhanlin Chen, Gamze Gursoy, Mark Gerstein
BMC BIOINFORMATICS
(2020)
Article
Multidisciplinary Sciences
Michael P. Snyder, Thomas R. Gingeras, Jill E. Moore, Zhiping Weng, Mark B. Gerstein, Bing Ren, Ross C. Hardison, John A. Stamatoyannopoulos, Brenton R. Graveley, Elise A. Feingold, Michael J. Pazin, Michael Pagan, Daniel A. Gilchrist, Benjamin C. Hitz, J. Michael Cherry, Bradley E. Bernstein, Eric M. Mendenhall, Daniel R. Zerbino, Adam Frankish, Paul Flicek, Richard M. Myers
Article
Multidisciplinary Sciences
Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lecuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigo, Peggy J. Farnham, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, Zhiping Weng
Article
Multidisciplinary Sciences
Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gursoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T. Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R. Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J. Klein, Michael Snyder, David M. Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X. Shirley Liu, Kevin P. White, Mark Gerstein
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Donghoon Lee, Jing Zhang, Jason Liu, Mark Gerstein
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Biochemical Research Methods
Jing Zhang, Jason Liu, Patrick McGillivray, Caroline Yi, Lucas Lochovsky, Donghoon Lee, Mark Gerstein
BMC BIOINFORMATICS
(2020)
Article
Biochemical Research Methods
Zhanlin Chen, Jing Zhang, Jason Liu, Zixuan Zhang, Jiangqi Zhu, Donghoon Lee, Min Xu, Mark Gerstein
Summary: Researchers have developed an efficient and scalable scATAC-seq simulation method called SCAN-ATAC-Sim, which uses down-sampled bulk ATAC-seq data to simulate experiments with known cell type labels. This method utilizes a tunable signal-to-noise ratio and independent sampling without replacement to account for the diploid genome.
Article
Biochemical Research Methods
Shaoke Lou, Tianxiao Li, Jason Liu, Mark Gerstein
Summary: This study developed an Amazon Alexa skill called Gene Tracer, which allows users to query gene information using voice interaction and provides a genome browser-like visualization experience, offering users a more flexible way to acquire knowledge.
Article
Biochemical Research Methods
Zhanlin Chen, Jing Zhang, Jason Liu, Yi Dai, Donghoon Lee, Martin Renqiang Min, Min Xu, Mark Gerstein
Summary: DECODE is a deep learning model trained on large-scale functional assays to accurately predict cell-type-specific enhancers and achieve precise boundary detection through an object detection framework. It outperforms state-of-the-art enhancer prediction methods in transgenic mouse validation, condensing annotations and increasing conservation scores.
Article
Sport Sciences
Garrett Ash, Matthew Stults-Kolehmainen, Michael A. Busa, Allison E. Gaffey, Konstantinos Angeloudis, Borja Muniz-Pardos, Robert Gregory, Robert A. Huggins, Nancy S. Redeker, Stuart A. Weinzimer, Lauren A. Grieco, Kate Lyden, Esmeralda Megally, Ioannis Vogiatzis, LaurieAnn Scher, Xinxin Zhu, Julien S. Baker, Cynthia Brandt, Michael S. Businelle, Lisa M. Fucito, Stephanie Griggs, Robert Jarrin, Bobak J. Mortazavi, Temiloluwa Prioleau, Walter Roberts, Elias K. Spanakis, Laura M. Nally, Andre Debruyne, Norbert Bachl, Fabio Pigozzi, Farzin Halabchi, Dimakatso A. Ramagole, Dina C. Janse van Rensburg, Bernd Wolfarth, Chiara Fossati, Sandra Rozenstoka, Kumpei Tanisawa, Mats Boerjesson, Jose Antonio Casajus, Alex Gonzalez-Aguero, Irina Zelenkova, Jeroen Swart, Gamze Gursoy, William Meyerson, Jason Liu, Dov Greenbaum, Yannis P. Pitsiladis, Mark B. Gerstein
Summary: This paper summarizes the outcomes of a discussion on guiding standards for consumer sport and fitness wearables (CSFWs), including key facilitators and barriers for participation by manufacturers and stakeholder priorities. Participants generally agreed to adopt Keadle et al.'s standard pathway for testing devices, but did not reach a consensus on the prioritization of these steps. The focus was on creating a networking hub to connect companies, consumers, and researchers for flexible guidance in navigating the heterogeneity, multi-tiered development, dynamicity, and uncertainty of the CSFW field.
Article
Biochemical Research Methods
Jason Liu, Daniel J. Spakowicz, Garrett Ash, Rebecca Hoyd, Rohan Ahluwalia, Andrew Zhang, Shaoke Lou, Donghoon Lee, Jing Zhang, Carolyn Presley, Ann Greene, Matthew Stults-Kolehmainen, Laura M. Nally, Julien S. Baker, Lisa M. Fucito, Stuart A. Weinzimer, Andrew Papachristos, Mark Gerstein
Summary: The development of mobile-health technology, utilizing biomedical sensors, has the potential to revolutionize personalized medicine and provide quantitative information to aid healthcare decisions. The Bayesian structural time series framework offers a robust method for evaluating the impact of interventions in biomedical sensor data, with time-dependent confidence intervals for personalized assessment.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Guan Wang, Traci Kitaoka, Ali Crawford, Qian Mao, Andrew Hesketh, Fergus M. Guppy, Garrett Ash, Jason Liu, Mark B. Gerstein, Yannis P. Pitsiladis
Summary: This study compared two RNA-seq and two microarray platforms for transcriptome-wide quantification of differential gene expression in healthy individuals administered recombinant human erythropoietin. Results showed that the total RNA DNB-seq generated a large number of target genes compared to other platforms, with pathway enrichment analyses revealing genes not only related to erythropoiesis and oxygen transport, but also to a wide range of other functions such as tissue protection and immune regulation. The study established a knowledge base of genes relevant to EPO biology through cross-platform comparisons and validation.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P. White, Mark Gerstein
Article
Biotechnology & Applied Microbiology
Jing Zhang, Jason Liu, Donghoon Lee, Jo-Jo Feng, Lucas Lochovsky, Shaoke Lou, Michael Rutenberg-Schoenberg, Mark Gerstein