Transcriptional brain networks and their key regulators across the human lifespan by Wehrspaun, CC

“…Enrichment for predicted miRNA response elements that are often shared among the ion channel/transporter genes, along with increased co-expression of this gene set, indicated that the extended 3’UTRs could serve as a hub for an endogenous competitive RNA network. …”

Positively-Coated Nanofiltration Membranes for Lithium Recovery from Battery Leachates and Salt-Lakes: Ion Transport Fundamentals and Module Performance by Foo, Zi Hao, Liu, Suwei, Kanias, Lucy, Lee, Trent R., Heath, Samuel M., Tomi, Yasuhiro, Miyabe, Tomotsugu, Keten, Sinan, Lueptow, Richard M., Lienhard, John H.

“…This study examines polyamide NF membranes coated with polyelectrolytes enriched with ammonium groups to maintain high monovalent cation selectivity in hypersaline conditions. …”
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Transcriptome alterations of vascular smooth muscle cells in aortic wall of myocardial infarction patients by Wongsurawat, Thidathip, Woo, Chin Cheng, Giannakakis, Antonis, Lin, Xiao Yun, Cheow, Esther Sok Hwee, Lee, Chuen Neng, Richards, Mark, Sze, Siu Kwan, Nookaew, Intawat, Sorokin, Vitaly, Kuznetsov, Vladimir Andreevich

“…Prediction Analysis of Microarray (PAM) identified genes that significantly discriminated the two groups of samples. …”
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Functional homogeneity and specificity of topological modules in human proteome by Kaalia, Rama, Rajapakse, Jagath Chandana

“…Conclusions: The topological modules ranked using specificity scores show high enrichment with gene sets of known functions. Physical interactions in PPIN contribute to high specificity of the topological modules of the human proteome whereas functional interactions contribute to high homogeneity of the modules. …”
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Using machine learning to discover candidate localised transcripts from microscopy and genome-wide bioinformatics data by Kiourlappou, M

“…I find that the group of predicted genes is highly enriched in terms involving localisation, transport and cell protrusions. …”

The Evolution of Galaxies and Clusters at High Spatial Resolution with Advanced X-ray Imaging Satellite (AXIS) by Russell, Helen R., Lopez, Laura A., Allen, Steven W., Chartas, George, Choudhury, Prakriti Pal, Dupke, Renato A., Fabian, Andrew C., Flores, Anthony M., Garofali, Kristen, Hodges-Kluck, Edmund, Koss, Michael J., Lanz, Lauranne, Lehmer, Bret D., Li, Jiang-Tao, Maksym, W. Peter, Mantz, Adam B., McDonald, Michael, Miller, Eric D., Mushotzky, Richard F., Qiu, Yu, Reynolds, Christopher S., Tombesi, Francesco, Tozzi, Paolo, Trindade-Falcão, Anna, Walker, Stephen A., Wong, Ka-Wah, Yukita, Mihoko, Zhang, Congyao

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Establishment of an experimental system to analyse extracellular vesicles during apoplastic fungal pathogenesis by Hearfield, Nathaniel, Brotherton, Dominik, Gao, Zedi, Inal, Jameel, Stotz, Henrik U.

“…Enrichment analysis of gene ontology terms provided evidence for involvement of glucan and chitin metabolism as well as catalase and peptidase activities. …”
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REST targets JAK–STAT and HIF-1 signaling pathways in human Down syndrome brain and neural cells by Huang, Tan, Fakurazi, Sharida, Cheah, Pike-See, Ling, King-Hwa

“…Gene expression datasets generated from healthy controls and DS samples of human brain tissues, cerebral organoids, NPC, neurons, and astrocytes were retrieved from the Gene Ontology (GEO) and Sequence Read Archive (SRA) databases. …”
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Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation by Li, Guoliang, Ruan, Xiaoan, Auerbach, Raymond K., Sandhu, Kuljeet Singh, Zheng, Meizhen, Wang, Ping, Poh, Huay Mei, Goh, Yufen, Lim, Joanne, Zhang, Jingyao, Sim, Hui Shan, Peh, Su Qin, Mulawadi, Fabianus Hendriyan, Ong, Chin Thing, Orlov, Yuriy L., Hong, Shuzhen, Zhang, Zhizhuo, Landt, Steve, Raha, Debasish, Euskirchen, Ghia, Wei, Chia-Lin, Ge, Weihong, Wang, Huaien, Davis, Carrie, Fisher-Aylor, Katherine I., Mortazavi, Ali, Gerstein, Mark, Gingeras, Thomas, Wold, Barbara, Sun, Yi, Cheung, Edwin, Liu, Edison, Sung, Wing-Kin, Snyder, Michael, Ruan, Yijun, Fullwood, Melissa Jane

“…Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. …”
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Towards understanding genome regulation via high-resolution analysis of chromatin accessibility by Dai, L

“…<p>Next generation sequencing has been used to in functional genomics to rep- resent specific aspects of chromatin structure, DNA-protein interactions and the epigenome, enriching the knowledge of the non-coding genome which plays significantly roles in gene regulation but is vaguely understood. …”

Statistical methods and analyses in autoimmune diseases by Inshaw, J

“…</p> <p>Finally, I performed an ImmunoChip-wide meta-analysis of 59, 974 individuals, approxi- mately twice the sample size of the previous largest T1D genetic analysis, and identified 74 chromosome regions associated with T1D, including 22 novel regions. I fine mapped each region and confirmed that prioritised variants were enriched in open chromatin re- gions in lymphoid cells. …”

New insights into the genetic etiology of Alzheimer’s disease and related dementias by Bellenguez, C, Küçükali, F, Jansen, IE, Amin, N, Ahmad, S, Lovestone, S, Smith, AD, Warden, D, Wilcock, G, Laitinen, T, van Duijn, CM

“…Gene prioritization in the new loci identified 31 genes that were suggestive of new genetically associated processes, including the tumor necrosis factor alpha pathway through the linear ubiquitin chain assembly complex. …”

Lipid regulation of exocytosis by Zhang, Jing

“…Exocytosis is a finely tuned program in which the secretory vesicles are directed to fuse with plasma membrane and discharge neurotransmitter or hormone content to the extracellular space. …”
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Identification of genetic effects underlying type 2 diabetes in South Asian and European populations by Loh, Marie, Zhang, Weihua, Ng, Hong Kiat, Schmid, Katharina, Lamri, Amel, Tong, Lin, Meraj Ahmad, Lee, Jung-Jin, Ng, Maggie C. Y., Petty, Lauren E., Spracklen, Cassandra N., Takeuchi, Fumihiko, Md. Tariqul Islam, Jasmine, Farzana, Kasturiratne, Anuradhani, Muhammad Kibriya, Mohlke, Karen L., Paré, Guillaume, Prasad, Gauri, Mohammad Shahriar, Chee, Miao Ling, de Silva, H. Janaka, Engert, James C., Gerstein, Hertzel C., Mani, K. Radha, Sabanayagam, Charumathi, Vujkovic, Marijana, Wickremasinghe, Ananda R., Wong, Tien Yin, Yajnik, Chittaranjan S., Salim Yusuf, Habibul Ahsan, Bharadwaj, Dwaipayan, Anand, Sonia S., Below, Jennifer E., Boehnke, Michael, Bowden, Donald W., Chandak, Giriraj R., Cheng, Ching-Yu, Kato, Norihiro, Mahajan, Anubha, Sim, Xueling, McCarthy, Mark I., Morris, Andrew P., Kooner, Jaspal S., Saleheen, Danish, Chambers, John C.

“…We identify 21 novel genetic loci for significant association with T2D (P = 4.7 × 10-8 to 5.2 × 10-12), to the best of our knowledge at the point of analysis. The loci are enriched for regulatory features, including DNA methylation and gene expression in relevant tissues, and highlight CHMP4B, PDHB, LRIG1 and other genes linked to adiposity and glucose metabolism. …”
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A rapid CRISPR competitive assay for in vitro and in vivo discovery of potential drug targets affecting the hematopoietic system by Shen, Yunbing, Jiang, Long, Iyer, Vaishnavi Srinivasan, Raposo, Bruno, Dubnovitsky, Anatoly, Boddul, Sanjaykumar V., Kasza, Zsolt, Wermeling, Fredrik

“…Such mixed genotypes complicate analysis of the role of the targeted gene in the studied cell population. Here, we present a rapid and universal experimental approach to functionally analyze a CRISPR-targeted cell population that does not involve generating clonal lines. …”
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Evolution of an extracellular pathogen recognition mechanism in Solanaceae by Kourelis, J

“…First, I present a review and meta-analysis of the molecular mechanisms by which <em>R</em> gene products function, thereby identifying nine molecular mechanisms conferring pathogen resistance in plants. …”

Identification of alternative-splicing events in human monocyte differentiation by Sim, Donald Yuhui

“…During this project, 31 out of 47 splicing events were successfully validated, with SRRM2-regulated splicing events achieving a 92% validation rate. Additionally, gene set enrichment analysis (GSEA) also revealed potential perturbations in anti-viral, amino acid metabolism and intracellular signalling pathways by the knockdown of these splicing factors. …”
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In-vitro validation of potential modulators of non-alcoholic fatty liver disease (NAFLD) by Tang, Daryl Woon Tat

“…This study aims to identify genes that enhance hepatocyte survival and regeneration in NAFLD. …”
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Characterizing the interplay between super enhancers and chromatin interactions in cancer by Choudhary, Ruchi

“…Using HiChIP experiments in five human cell lines, we discovered multiple transcription factor (TF) clusters regulating chromatin interactions between SEs/enhancers and promoters, with one hub enriched in c-MYC and YY1. …”
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Real‐time imaging of dynamic cell reprogramming with nanosensors by Wiraja, Christian, Yeo, David Chenloong, Tham, Khek-Chian, Chew, Sharon Wan Ting, Lim, Xinhong, Xu, Chenjie

“…Tracking the dynamic expression of four pivotal biomarkers (i.e., THY1, E-CADHERIN, OCT4, and GATA4 mRNA), nanosensor signal showed great agreement with polymerase chain reaction and gene reporter imaging (R2 > 0.9). Overall, such facile, versatile nanosensor enables real-time monitoring of low-frequency reprogramming events, thereby useful for high-throughput assessment, optimization, and biomarker-specific cell enrichment.…”
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