Article
Biotechnology & Applied Microbiology
Fei Zhang, Deborah Velez-Irizarry, Catherine W. Ernst, Wen Huang
Summary: In this study, genome-wide analysis of alternative splicing in skeletal muscle of a Duroc x Pietrain F2 pig population was performed. It was found that the heritability of alternative splicing scores was lower than that of overall gene expression. Additionally, there was little correlation between alternative splicing and overall gene expression. Integration of splice QTL mapping with phenotype QTL mapping identified potential mediators of phenotype QTL effects through alternative splicing.
Review
Biochemistry & Molecular Biology
Sangam L. Dwivedi, Luis Felipe Quiroz, Anireddy S. N. Reddy, Charles Spillane, Rodomiro Ortiz
Summary: Alternative splicing (AS) is a gene regulatory mechanism that modulates gene expression in plants. AS generates multiple mRNAs to regulate transcriptome and proteome diversity. Advances in sequencing and computational methods enable the quantification and visualization of AS-based variation in plant growth, development, and stress tolerance. Understanding and utilizing this variation can enhance climate resilience, productivity, and nutritional quality of staple food crops. AS also contributes to heterosis, plant symbiosis, and the connection between core clock genes and environmental cues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Genetics & Heredity
Kyubin Lee, Doyeong Yu, Daejin Hyung, Soo Young Cho, Charny Park
Summary: In this study, a novel application called ASpediaFI was developed to systematically identify differential alternative splicing (AS) events, co-regulated genes, and pathways. ASpediaFI exhibited strong performance in both simulated and public datasets, demonstrating its ability to effectively detect biologically relevant candidate genes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Review
Behavioral Sciences
M. Gabriela Navas-Zuloaga, Theodore P. Pavlic, Brian H. Smith
Summary: Understanding the origins and maintenance of cognitive variation in animal populations is important for the study of the evolution of cognition. Eusocial-insect colonies serve as a tractable alternative model system to study emergent cognitive-like properties. This review focuses on the individual-scale mechanisms that cause group-level variation in problem-solving abilities.
TRENDS IN COGNITIVE SCIENCES
(2022)
Article
Cell & Tissue Engineering
Jiaqi Wang, Yi Huang, Chen Zhang, Yan Ruan, Yanping Tian, Fengsheng Wang, Yixiao Xu, Meng Yu, Jiangjun Wang, Yuda Cheng, Lianlian Liu, Ran Yang, Jiali Wang, Yi Yang, Jiaxiang Xiong, Yan Hu, Rui Jian, Bing Ni, Wei Wu, Junlei Zhang
Summary: Dax1 is an important component of the transcription factor network in pluripotent mouse embryonic stem cells (ESCs). This study identified 18 new splice variants of Dax1 and compared their protein structures with known Dax1 protein. The expression pattern analysis showed that these novel isoforms were cotranscribed with the known Dax1 protein in ESCs, but exhibited transcriptional heterogeneity and different subcellular localization of the encoded proteins.
STEM CELLS AND DEVELOPMENT
(2023)
Review
Biology
Showkat Ahmad Ganie, Anireddy S. N. Reddy
Summary: When facing environmental stresses, alternative splicing (AS) plays a crucial role in rice by rapidly regulating gene expression to help the plant adapt to various pressures. Studies have shown that AS is important for rice growth and development, especially under stress conditions. Understanding the impact of AS on rice and its pathogens can provide valuable insights for developing stress-resistant rice varieties in the future.
Article
Biology
Mihai Udrescu, Sebastian Mihai Ardelean, Lucretia Udrescu
Summary: Widespread bioinformatics applications rely on the advances in machine learning and comprehensive drug datasets. However, there is much uncertainty in these datasets, which hampers the accuracy of bioinformatics applications. Our analysis shows that the latest drug database versions have dense drug-drug interaction networks, making analysis difficult. On the other hand, the uncertainty in drug-target networks is still present, but complex network analysis methods improve slightly. Future research directions include benchmarking for drug-target interaction prediction and standardization of drug-drug interaction severity.
Article
Microbiology
Zyanya Mayoral-Pena, Victor Lazaro-Vidal, Juan Fornoni, Roberto Alvarez-Martinez, Etzel Garrido
Summary: This study confirms that the bacteriome of plants influences the bacteriome of herbivorous insects. Shared genera were found between plants and insects, but their abundances differed significantly. Functional inferences showed that the insect samples had a significant abundance of xenobiotics degradation and metabolism, while the plant samples had a significant abundance of biosynthesis of secondary metabolites. Co-abundance patterns were found to be important in the insect but not in the plant.
Article
Computer Science, Artificial Intelligence
Antonio Longa, Giulia Cencetti, Bruno Lepri, Andrea Passerini
Summary: This study introduces a technique based on egocentric temporal neighborhoods to extract temporal motifs in temporal networks, bypassing the graph isomorphism problem and enabling the algorithm to mine larger motifs. By focusing on the temporal dynamics of interactions of specific nodes, the method allows for the extraction of interpretable temporal motifs.
DATA MINING AND KNOWLEDGE DISCOVERY
(2022)
Article
Biochemistry & Molecular Biology
Miya John, Caroline E. Ford
Summary: This study systematically examined the expression of transcript variants of ROR1/2 genes and found their expression in non-diseased tissues. The results suggest that the expression of ROR1/2 in healthy human tissues should be carefully considered for safety assessment of targeted therapy.
Review
Biochemistry & Molecular Biology
Zhaoshi Bai, Yaling Peng, Xinyue Ye, Zhixian Liu, Yupeng Li, Lingman Ma
Summary: This review provides an overview of the evolving relationship between autophagy and cancer treatment, discussing the different functions of autophagy and its interaction with various cell death modes, as well as the effects of autophagy inhibition or activation in different contexts.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B
(2022)
Article
Multidisciplinary Sciences
Robert Leech, Reinder Vos De Wael, Frantisek Vasa, Ting Xu, R. Austin Benn, Robert Scholz, Rodrigo M. Braga, Michael P. Milham, Jessica Royer, Boris C. Bernhardt, Emily J. H. Jones, Elizabeth Jefferies, Daniel S. Margulies, Jonathan Smallwood
Summary: Recent theories of cortical organisation propose that the spatial arrangement of brain regions determines their functional features. Association cortex, located farthest from action and perception systems, is interwoven with adjacent regions exhibiting different functional connectivity patterns. The study findings show that function changes more gradually with distance in sensory-motor cortex compared to association cortex. Importantly, systems within the same type of cortex exhibit similar profiles. The differentiation between primary and association cortex lies in how function changes over space, highlighting the importance of topographical features in estimating their contribution to cognition and behavior.
NATURE COMMUNICATIONS
(2023)
Article
Food Science & Technology
Mizuki Hirai, Ryo Kobori, Ryo Doge, Issei Tsuji, Akiko Saito
Summary: This study explores a method of concentrating polyphenol compounds using the interaction between gelatin and catechol structures. It was found that gelatin can efficiently adsorb polyphenol compounds while retaining their functionality.
Article
Plant Sciences
Gurnoor Singh, Evangelia A. Papoutsoglou, Frederique Keijts-Lalleman, Bilyana Vencheva, Mark Rice, Richard G. F. Visser, Christian W. B. Bachem, Richard Finkers
Summary: This study developed a pipeline using natural language processing on biological literature to generate knowledge networks, focusing on the flesh color trait of potato. The time-based analysis of these networks revealed connections between the trait and a candidate gene, demonstrating the potential of network-assisted hypothesis generation in scientific research.
Article
Food Science & Technology
Yuwan Liu, Xiaojing Li, Shangyuan Sang, David Julian McClements, Long Chen, Jie Long, Aiquan Jiao, Jinpeng Wang, Xueming Xu, Zhengyu Jin, Chao Qiu
Summary: In this study, soybean peptide-succinic acid-modified cyclodextrin nanoparticles were successfully prepared and their structure and properties were investigated. The optimal SPT/SACD mass ratio and SPT average molecular weight were found to be 2:1 and 300 Da, respectively. The prepared nanoparticles exhibited good uniformity and their interaction with enzymes was found to alter the enzyme protein structure and enhance the inhibitory effect of EGCG on the enzyme.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biochemical Research Methods
Jin-Dong Kim, Jung-jae Kim, Xu Han, Dietrich Rebholz-Schuhmann
BMC BIOINFORMATICS
(2015)
Article
Biochemical Research Methods
Anika Oellrich, Nigel Collier, Tudor Groza, Dietrich Rebholz-Schuhmann, Nigam Shah, Olivier Bodenreider, Mary Regina Boland, Ivo Georgiev, Hongfang Liu, Kevin Livingston, Augustin Luna, Ann-Marie Mallon, Prashanti Manda, Peter N. Robinson, Gabriella Rustici, Michelle Simon, Liqin Wang, Rainer Winnenburg, Michel Dumontier
BRIEFINGS IN BIOINFORMATICS
(2016)
Article
Computer Science, Information Systems
Jan A. Kors, Simon Clematide, Saber A. Akhondi, Erik M. van Mulligen, Dietrich Rebholz-Schuhmann
JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION
(2015)
Article
Mathematical & Computational Biology
Nigel Collier, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2015)
Article
Mathematical & Computational Biology
Senay Kafkas, Jee-Hyub Kim, Xingjun Pi, Johanna R. McEntyre
JOURNAL OF BIOMEDICAL SEMANTICS
(2015)
Article
Mathematical & Computational Biology
Senay Kafkas, Xingjun Pi, Nikos Marinos, Francesco Talo, Andrew Morrison, Johanna R. McEntyre
JOURNAL OF BIOMEDICAL SEMANTICS
(2015)
Article
Mathematical & Computational Biology
Yasar Khan, Muhammad Saleem, Muntazir Mehdi, Aidan Hogan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
JOURNAL OF BIOMEDICAL SEMANTICS
(2017)
Article
Mathematical & Computational Biology
Ali Hasnain, Qaiser Mehmood, Syeda Sana e Zainab, Muhammad Saleem, Claude Warren, Durre Zehra, Stefan Decker, Dietrich Rebholz-Schuhmann
JOURNAL OF BIOMEDICAL SEMANTICS
(2017)
Article
Biochemical Research Methods
Chen Li, Maria Liakata, Dietrich Rebholz-Schuhmann
BRIEFINGS IN BIOINFORMATICS
(2014)
Article
Biochemical Research Methods
Catia M. Machado, Dietrich Rebholz-Schuhmann, Anat. Freitas, Francisco M. Couto
BRIEFINGS IN BIOINFORMATICS
(2015)
Review
Pharmacology & Pharmacy
Dietrich Rebholz-Schuhmann, Christoph Grabmueller, Silvestras Kavaliauskas, Samuel Croset, Peter Woollard, Rolf Backofen, Wendy Filsells, Dominic Clark
DRUG DISCOVERY TODAY
(2014)
Article
Biochemistry & Molecular Biology
Yuci Gou, Florian Graff, Oliver Kilian, Senay Kafkas, Jyothi Katuri, Jee-Hyub Kim, Nikos Marinos, Johanna McEntyre, Andrew Morrison, Xingjun Pi, Philip Rossiter, Francesco Talo, Vid Vartak, Lee-Ann Coleman, Craig Hawkins, Anna Kinsey, Sami Mansoor, Victoria Morris, Rob Rowbotham, David Chaplin, Ross MacIntyre, Yogesh Patel, Sophia Ananiadou, William J. Black, John McNaught, Rafal Rak, Andrew Rowley
NUCLEIC ACIDS RESEARCH
(2015)
Review
Mathematical & Computational Biology
Robert Hoehndorf, Melissa Haendel, Robert Stevens, Dietrich Rebholz-Schuhmann
JOURNAL OF BIOMEDICAL SEMANTICS
(2014)
Proceedings Paper
Computer Science, Information Systems
Alokkumar Jha, Muntazir Mehdi, Yasar Khan, Qaiser Mehmood, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
DATA MANAGEMENT AND ANALYTICS FOR MEDICINE AND HEALTHCARE
(2017)
Proceedings Paper
Linguistics
Johannes Hellrich, Simon Clematide, Udo Hahn, Dietrich Rebholz-Schuhmann
LREC 2014 - NINTH INTERNATIONAL CONFERENCE ON LANGUAGE RESOURCES AND EVALUATION
(2014)
