Article
Oncology
Rui Wu, Hao Zhuang, Yu-Kun Mei, Jin-Yu Sun, Tao Dong, Li-Li Zhao, Zhi-Ning Fan, Li Liu
Summary: By combining DEGs and WGCNA, CCNB1 was identified as the hub gene in esophageal cancer, upregulated in tumor tissues, and associated with poor prognosis in esophageal cancer patients with higher expression.
CANCER CELL INTERNATIONAL
(2021)
Article
Oncology
Soazik P. Jamin, Feria Hikmet, Romain Mathieu, Bernard Jegou, Cecilia Lindskog, Frederic Chalmel, Michael Primig
Summary: CT genes are induced in germ cells and play a role in cancer progression. Identifying these genes is challenging due to the diverse sources and time periods of data. A study using RNA profiling analysis identified 478 candidate loci, including known CT genes and novel candidates that may serve as potential therapeutic targets or biomarkers.
MOLECULAR ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ting-You Wang, Qi Liu, Yanan Ren, Sk Kayum Alam, Li Wang, Zhu Zhu, Luke H. Hoeppner, Scott M. Dehm, Qi Cao, Rendong Yang
Summary: Exitron splicing (EIS) functions in cancer by affecting 63% of human coding genes, 95% of which are tumor specific. EIS alters cancer driver genes, leading to gain- or loss-of-function, and also produces neoepitopes that bind to MHC class I or II. Analysis of clinical data shows a correlation between EIS-derived neoantigen load and checkpoint inhibitor response in clear cell renal cell carcinoma.
Article
Cardiac & Cardiovascular Systems
Yuanrong Chen, Chaoling Wu, Xiaoping Wang, Xufeng Zhou, Kunpeng Kang, Zuofeng Cao, Yihong Yang, Yiming Zhong, Genfa Xiao
Summary: This study identified the dysregulated B-cell receptor signaling pathway and novel genes associated with humoral immune response in MCT-induced PAH, providing new insights into the molecular mechanisms underlying inflammation and immunity and offering potential therapeutic targets for treating PAH.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemical Research Methods
Danfeng Lan, Hong-Yan Jiang, Xiaoyang Su, Yan Zhao, Sicheng Du, Ying Li, Rui Bi, Deng-Feng Zhang, Qiuping Yang
Summary: This study identified genes associated with diabetic neuropathy using GWAS data and mouse models, offering the potential for noninvasive early detection of the condition.
COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING
(2021)
Article
Oncology
Csaba Miskey, Lacramioara Botezatu, Nuri A. Temiz, Andreas Gogol-Doering, Aron Bartha, Balazs Gyorffy, David A. Largaespada, Zoltan Ivics, Attila Sebe
Summary: This study identified novel metastasis driver genes in a human breast cancer cell line through an in vitro Sleeping Beauty transposon-based forward genetic screen and an RNA fusion-based candidate gene prediction. The analysis of these genes revealed their association with metastasis related processes and clinical relevance in metastatic breast cancer.
MOLECULAR CANCER RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Zhongli Chen, Biting Liang, Yingfu Wu, Quanzhong Liu, Hongming Zhang, Hao Wu
Summary: This study proposes a network-based method (Netkmeans) for accurately and effectively detecting dysregulated modules in cancer. By constructing a gene network and a comprehensive evaluation function, this method outperforms other methods in terms of statistical significance and biological relevance. Experimental results demonstrate the importance of the dysregulated modules detected by Netkmeans in the development and treatment of cancer.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Malene Blond Ipsen, Ea Marie Givskov Sorensen, Emil Aagaard Thomsen, Simone Weiss, Jakob Haldrup, Anders Dalby, Johan Palmfeldt, Peter Bross, Martin Rasmussen, Jacob Fredsoe, Soren Klingenberg, Mads R. Jochumsen, Kirsten Bouchelouche, Benedicte Parm Ulhoi, Michael Borre, Jacob Giehm Mikkelsen, Karina Dalsgaard Sorensen
Summary: This study identified new genes associated with olaparib resistance in castration-resistant prostate cancer (CRPC) by performing a genome-wide CRISPR-Cas9 knockout screen. Loss of PARP1, ARH3, YWHAE, or UBR5 was found to cause olaparib resistance, and PARP1 or ARH3 knockout led to cross-resistance to other PARP inhibitors. The study also discovered that reduced autophagy may contribute to PARPi resistance. Low ARH3 expression was identified as an independent predictor of recurrence in prostate cancer patients. These findings enhance our understanding of PARPi response in CRPC and propose a new model of PARPi resistance through decreased autophagy.
Article
Environmental Sciences
Yang Lan, Cheng Teng Ng, Choon Nam Ong, Liya E. Yu, Boon Huat Bay
Summary: This study investigated the effects of PM2.5 exposure on differentiated human small airway epithelial cells, highlighting the importance of using the advanced ALI model over submerged cultures. Transcriptomic analysis revealed changes in multiple signaling pathways involved in inflammation and apoptosis, suggesting that reduction of ambient PM2.5 concentrations could have a protective effect on respiratory health in humans.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Oncology
Duo Liu, Jingjing Zhu, Dan Zhou, Emily G. Nikas, Nikos T. Mitanis, Yanfa Sun, Chong Wu, Nicholas Mancuso, Nancy J. Cox, Liang Wang, Stephen J. Freedland, Christopher A. Haiman, Eric R. Gamazon, Jason B. Nikas, Lang Wu
Summary: The study combines transcriptome-wide association study and validation to identify candidate genes potentially involved in prostate cancer development. Analysis revealed 573 genes associated with prostate cancer risk, including 451 novel genes and 122 previously reported genes.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Biotechnology & Applied Microbiology
Zhichi Zeng, Sichen Zhang, Wenyan Li, Baoshan Chen, Wenlan Li
Summary: This study investigated the molecular mechanism of cold tolerance in rice through transcriptome analysis. It found that hormone-mediated defense response plays an important role in protecting rice plants from physiological damage under low-temperature stress. The study also provided a potential regulatory mechanism for the cold stress and recovery of rice cultivars and identified candidate central genes.
Article
Biochemistry & Molecular Biology
Hesam Montazeri, Mairene Coto-Llerena, Gaia Bianco, Ehsan Zangene, Stephanie Taha-Mehlitz, Viola Paradiso, Sumana Srivatsa, Antoine de Weck, Guglielmo Roma, Manuela Lanzafame, Martin Bolli, Niko Beerenwinkel, Markus von Fluee, Luigi M. Terracciano, Salvatore Piscuoglio, Charlotte K. Y. Ng
Summary: Systematic perturbation screens provide resources for identifying cancer driver genes, requiring specialized computational tools for processing data from perturbation of many genes in few cell lines. APSiC is a statistical framework developed for identifying novel cancer genes and effectors in perturbation screens, demonstrated through analysis of the DRIVE project. The analysis of DRIVE using APSiC is available as a web portal, providing a valuable resource for discovery of cancer genes.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Rajendra P. Pangeni, Ivonne Olivaries, David Huen, Vannessa C. Buzatto, Timothy P. Dawson, Katherine M. Ashton, Charles Davis, Andrew R. Brodbelt, Michael D. Jenkinson, Ivan Bieche, Lu Yang, Farida Latif, John L. Darling, Tracy J. Warr, Mark R. Morris
Summary: Brain metastases are common in breast tumors, but the role of epigenetic gene dysregulation in this process is not well understood. Through methylation array analysis, we identified dysregulated genes in breast to brain metastases, which may occur at early or later stages of tumor evolution. These epigenetic changes can also be detected in the serum of patients.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Sergio Lario, Maria J. Ramirez-Lazaro, Anna Brunet-Vega, Maria Vila-Casadesus, Ana M. Aransay, Juan J. Lozano, Xavier Calvet
Summary: This study identified co-expression modules and differential gene expression in dyspeptic patients at different stages of the Correa pathway using weighted gene co-expression network analysis (WGCNA). The results provide valuable information for understanding the pathogenesis and progression of precancerous lesions of gastric cancer (PLGC).
Article
Biotechnology & Applied Microbiology
Zhaoran Zhou, Christiane Eichner, Frank Nilsen, Inge Jonassen, Michael Dondrup
Summary: A gene co-expression network-based approach was used to identify important genes associated with the moulting and development of the salmon louse. RNA interference experiments confirmed the essential role of a RAB1A-like gene in the development of the salmon louse, suggesting the approach could be generalized to identify important genes in other organisms.
Article
Biology
Harald Oey, Martha Zakrzewski, Kanwar Narain, K. Rekha Devi, Takeshi Agatsuma, Sujeevi Nawaratna, Geoffrey N. Gobert, Malcolm K. Jones, Mark A. Ragan, Donald P. McManus, Lutz Krause
Article
Microbiology
Harald Oey, Martha Zakrzewski, Kerstin Gravermann, Neil D. Young, Pasi K. Korhonen, Geoffrey N. Gobert, Sujeevi Nawaratna, Shihab Hasan, David M. Martinez, Hong You, Martin Lavin, Malcolm K. Jones, Mark A. Ragan, Jens Stoye, Ana Oleaga, Aidan M. Emery, Bonnie Webster, David Rollinson, Robin B. Gasser, Donald P. McManus, Lutz Krause
Article
Oncology
K. Nones, J. Johnson, F. Newell, A. M. Patch, H. Thorne, S. H. Kazakoff, X. M. de Luca, M. T. Parsons, K. Ferguson, L. E. Reid, A. E. McCart Reed, S. Srihari, V Lakis, A. L. Davidson, P. Mukhopadhyay, O. Holmes, Q. Xu, S. Wood, C. Leonard, J. Beesley, J. M. Harris, D. Barnes, A. Degasperi, M. A. Ragan, A. B. Spurdle, K. K. Khanna, S. R. Lakhani, J. Pearson, S. Nik-Zainal, G. Chenevix-Trench, N. Waddell, P. T. Simpson
ANNALS OF ONCOLOGY
(2019)
Review
Ecology
Raul A. Gonzalez-Pech, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
TRENDS IN ECOLOGY & EVOLUTION
(2019)
Review
Zoology
Cornelia Jaspers, Sebastian Fraune, A. Elizabeth Arnold, David J. Miller, Thomas C. G. Bosch, Christian R. Voolstra, Maja Adamska, Tracy Ainsworth, Eldon Ball, Chloe Boote, David Bourne, Nicholas J. Butterfield, Cheong Xin Chan, Ira Cooke, Peter F. Cowman, Aaron Darling, Simon K. Davy, Amin Mohamed, Katharina Fabricius, Sofia Fortunato, Alejandra Hernandez, Mia Hoogenboom, Aurelie Moya, Lucia Pita, Mark A. Ragan, Steven J. Robbins, Natalia R. Andrade, Kazuhiro Sakamaki, Verena Schoepf, Thorsten Seemann, Chuya Shinzato, Jaroslaw Stolarski, Jan Strugnell, Shunichi Takahashi, Sen-Lin Tang, Nicole Webster, Brooke Whitelaw, Hua Ying
Review
Zoology
Ira Cooke, Oliver Mead, Casey Whalen, Chloe Boote, Aurelie Moya, Hua Ying, Steven Robbins, Jan M. Strugnell, Aaron Darling, David Miller, Christian R. Voolstra, Maja Adamska, Tracy Ainsworth, Natalia R. Andrade, A. Elizabeth Arnold, Eldon Ball, David Bourne, Thomas C. G. Bosch, Nicholas J. Butterfield, Cheong Xin Chan, Peter F. Cowman, Simon K. Davy, Katharina Fabricius, Sofia Fortunato, Sebastian Fraune, Alejandra Hernandez, Mia Hoogenboom, Cornelia Jaspers, Amin Mohamed, Lucia Pita, Mark A. Ragan, Kazuhiro Sakamaki, Verena Schoepf, Torsten Seemann, Chuya Shinzato, Jaroslaw Stolarski, Shunichi Takahashi, Sen-Lin Tang, Nicole Webster, Brooke Whitelaw
Article
Microbiology
Steven J. Robbins, Caitlin M. Singleton, Cheong Xin Chan, Lauren F. Messer, Aileen U. Geers, Hua Ying, Alexander Baker, Sara C. Bell, Kathleen M. Morrow, Mark A. Ragan, David J. Miller, Sylvain Foret, Christian R. Voolstra, Gene W. Tyson, David G. Bourne, Eldon Ball, Roger Beeden, Michael Berumen, Manuel Aranda, Timothy Ravasi, Pim Bongaerts, Ove Hoegh-Guldberg, Ira Cooke, Bill Leggat, Susan Sprungala, Anna Fitzgerald, Catherine Shang, Petra Lundgren, Theresa Fyffe, Francesco Rubino, Madeleine van Oppen, Karen Weynberg, Sara C. Bells
NATURE MICROBIOLOGY
(2019)
Article
Biology
Timothy G. Stephens, Raul A. Gonzalez-Pech, Yuanyuan Cheng, Amin Mohamed, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Article
Environmental Sciences
Amin R. Mohamed, Cheong Xin Chan, Mark A. Ragan, Jia Zhang, Ira Cooke, Eldon E. Ball, David J. Miller
ENVIRONMENTAL MICROBIOLOGY REPORTS
(2020)
Article
Biology
Raul A. Gonzalez-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, Sarah Shah, Katherine E. Dougan, Michael D. A. Fortuin, Remi Lagorce, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Summary: Genome sequences of Symbiodiniaceae are still scarce due to their large genome sizes and unique genome features. This study presented de novo genome assemblies of seven members of the genus Symbiodinium, revealing high sequence and structural divergence among different lineages, with some Symbiodinium isolates showing comparable divergence to distinct genera of Symbiodiniaceae.
Article
Biochemistry & Molecular Biology
Pim Bongaerts, Ira R. Cooke, Hua Ying, Dagmar Wels, Stijn den Haan, Alejandra Hernandez-Agreda, Christopher A. Brunner, Sophie Dove, Norbert Englebert, Gal Eyal, Sylvain Foret, Mila Grinblat, Kyra B. Hay, Saki Harii, David C. Hayward, Yu Lin, Mihaljevi C. Morana, Aurelie Moya, Paul Muir, Frederic Sinniger, Patrick Smallhorn-West, Gergely Torda, Mark A. Ragan, Madeleine J. H. van Oppen, Ove Hoegh-Guldberg
Summary: DNA sequencing studies are challenging the notion that the diversity of coral species is accurately described. Research has found that coral species can have ecological and phenotypic differences even if they are morphologically similar. This discovery highlights the potential role of temporal reproductive isolation in driving ecological and phenotypic divergence in coral species.
Review
Biochemistry & Molecular Biology
Katherine E. Dougan, Raul A. Gonzalez-Pech, Timothy G. Stephens, Sarah Shah, Yibi Chen, Mark A. Ragan, Debashish Bhattacharya, Cheong Xin Chan
Summary: Modern microbial taxonomy often relies on single or concatenated marker genes for classification. However, using whole-genome data can provide more accurate classification, especially for microbial eukaryotes.
TRENDS IN MICROBIOLOGY
(2022)
Meeting Abstract
Plant Sciences
Katherine E. Dougan, Raul A. Gonzalez-Pech, Timothy G. Stephens, Sarah Shah, Yibi Chen, Mark A. Ragan, Debashish Bhattacharya, Cheong Xin Chan
Article
Multidisciplinary Sciences
Ira Cooke, Hua Ying, Sylvain Foret, Pim Bongaerts, Jan M. Strugnell, Oleg Simakov, Jia Zhang, Matt A. Field, Mauricio Rodriguez-Lanetty, Sara C. Bell, David G. Bourne, Madeleine J. H. van Oppen, Mark A. Ragan, David J. Miller
Article
Biochemical Research Methods
Guillaume Bernard, Cheong Xin Chan, Yao-ban Chan, Xin-Yi Chua, Yingnan Cong, James M. Hogan, Stefan R. Maetschke, Mark A. Ragan
BRIEFINGS IN BIOINFORMATICS
(2019)