Article
Biochemistry & Molecular Biology
Petri Toronen, Liisa Holm
Summary: The advent of next-generation sequencing technology has resulted in a massive increase in gene catalogs for new genomes, transcriptomes, and metagenomes that require computational inference for functional annotation. PANNZER is a high-throughput functional annotation web server that supports annotation of up to 100,000 protein sequences and provides Gene Ontology annotations and free text description predictions. Two case studies highlight issues related to data quality and method evaluation, arguing that commonly used evaluation metrics and datasets may bias the development of automated function prediction methods.
Article
Biochemistry & Molecular Biology
Yali Wang, Kun Zheng, Xiuqiong Chen, Rui Chen, Yanmei Zou
Summary: The study identified pivotal genes associated with gastric cancer and explored their prognostic significance. COL1A1, THBS2, and SPP1 were found to potentially predict immunotherapy response in GC patients.
BIOSCIENCE REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Ahmed Mohamed, Dharmesh D. Bhuva, Sam Lee, Ning Liu, Chin Wee Tan, Melissa J. Davis
Summary: vissE.Cloud is a webserver for gene-set analysis, offering summarisation and interactive visualisation of GSA results. It allows analysis of gene lists as well as raw single-cell and spatial omics data, making it the first webserver to provide end-to-end gene-set analysis of sub-cellular localised spatial data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Wenhao Jin, Kristopher W. Brannan, Katannya Kapeli, Samuel S. Park, Hui Qing Tan, Maya L. Gosztyla, Mayuresh Mujumdar, Joshua Ahdout, Bryce Henroid, Katherine Rothamel, Joy S. Xiang, Limsoon Wong, Gene W. Yeo
Summary: RNA-binding proteins (RBPs) regulate RNA metabolism and play a role in human diseases. A hybrid ensemble RBP classifier (HydRA) is developed to predict RNA-binding capacity with high specificity and sensitivity using support vector machines (SVMs), convolutional neural networks (CNNs), and Transformer-based protein language models. HydRA can detect known RNA-binding domains (RBDs) and predict uncharacterized RNA-binding associated domains. Experimental validation confirms the RNA-binding activity of HydRA-predicted domains. HydRA accelerates the construction of a comprehensive RBP catalog and expands the diversity of RNA-binding associated domains.
Article
Biochemical Research Methods
Ondrej Vavra, Jakub Beranek, Jan Stourac, Martin Surkovsky, Jiri Filipovic, Jiri Damborsky, Jan Martinovic, David Bednar
Summary: Access pathways are critical for substrate and product transport in enzymes. A Python3 API called pyCaverDock is introduced to enhance the user experience and facilitate ligand transport analysis. This API simplifies the steps needed to use CaverDock and allows for automation of setup processes.
Article
Biochemistry & Molecular Biology
Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Adrian Lopez Martin, Mohamed Mounir, Irmtraud M. Meyer
Summary: RNA structure formation in vivo occurs co-transcriptionally, involving transient RNA structure features that are not part of the final functional structure. COBOLD is a computational method for identifying different classes of transient RNA structure features that can aid or hinder the formation of a known reference RNA structure. It is available as a web-server with dedicated data visualization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Xiaojing Wu, Mingfei Han, Xinyu Song, Song He, Xiaochen Bo, Yunping Zhu
Summary: COMMO is the first web server capable of identifying and analyzing consensus gene functionally related gene modules from different module detection methods. It offers a variety of module detection methods, data sources, and analysis functions, providing a user-friendly solution for precision medicine research.
Article
Multidisciplinary Sciences
Xia Yuan, Yi He, Wei Wang
Summary: This study analyzed the expression of COL1A2 in different cancers and found that it was significantly upregulated in colon adenocarcinoma (COAD) and higher expression was associated with poor prognosis. Functional pathway and ceRNA network analysis revealed that LINC00638/hsa-miR-552-3p may serve as a regulatory pathway of COL1A2 in COAD. Furthermore, COL1A2 was found to be positively associated with immune infiltration, suggesting its role in tumor immune escape in COAD.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Wei He, Helen Wang, Yanjun Wei, Zhiyun Jiang, Yitao Tang, Yiwen Chen, Han Xu
Summary: This study developed an integrative prediction method GuidePro that prioritizes sgRNAs in protein knockouts by incorporating multiple factors. Tested on independent datasets, GuidePro demonstrated superior performance in predicting phenotypes caused by protein loss-of-function, suggesting its robustness in various applications of CRISPR/Cas9 knockouts.
Article
Multidisciplinary Sciences
Jun Zhang, Lidong Xu, Jun Gao, Jieyi Li, Xiaokai Zhao, Pengmin Yang, Yujun Ge, Dawei Guo, Zhonghua Liu, Xiyong Wang, Wenchao Gu, Pengli Wang, Xun Hu, Ziying Gong, Daoyun Zhang
Summary: This study aimed to explore the role of CH25H in lung cancer and found that its expression level was significantly reduced in lung adenocarcinoma (LUAD) and associated with worse prognosis. CH25H may affect immune cell infiltration and tumor development, and low expression is correlated with LUAD metastasis.
SCIENTIFIC REPORTS
(2022)
Article
Computer Science, Information Systems
Sawsan Almahmoud, Bassam Hammo, Bashar Al-Shboul, Nadim Obeid
Summary: This paper proposes a hybrid approach using two-level fingerprints to detect illegitimate non-human traffic, and experimental results show that it can effectively detect fake clicks.
MULTIMEDIA TOOLS AND APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Gerard Minuesa, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Ivan Dotu
Summary: MoiRNAiFold is a versatile and user-friendly tool for de novo synthetic RNA design, based on Constraint Programming, with the ability to handle multiple design constraints and quality measures, and improve features for RNA regulation control of gene expression. Demonstrated to outperform any previous software in benchmarking structural RNA puzzles from EteRNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Carlos H. M. Rodrigues, Douglas E. Pires, David B. Ascher
Summary: Protein-protein interactions are crucial in cellular functions and biological processes. Computational methods for assessing the effects of mutations on protein-protein binding affinity are limited to single point mutations, but mmCSM-PPI outperforms existing methods in evaluating changes caused by both single and multiple missense mutations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Alexander R. van Vliet, George N. Chiduza, Sarah L. Maslen, Valerie E. Pye, Dhira Joshi, Stefano De Tito, Harold B. J. Jefferies, Evangelos Christodoulou, Chloe Roustan, Emma Punch, Javier H. Hervas, Nicola O'Reilly, J. Mark Skehel, Peter Cherepanov, Sharon A. Tooze
Summary: ATG9A and ATG2A are essential core members of the autophagy machinery. Researchers have identified the molecular details of their interaction and demonstrated their importance for autophagy using structural modeling and functional activity analysis.
Article
Biochemistry & Molecular Biology
Igor Zwir, Coral Del-Val, Javier Arnedo, Laura Pulkki-Raback, Bettina Konte, Sarah S. Yang, Rocio Romero-Zaliz, Mirka Hintsanen, Kevin M. Cloninger, Danilo Garcia, Dragan M. Svrakic, Nigel Lester, Sandor Rozsa, Alberto Mesa, Leo-Pekka Lyytikainen, Ina Giegling, Mika Kahonen, Maribel Martinez, Ilkka Seppala, Emma Raitoharju, Gabriel A. de Erausquin, Daniel Mamah, Olli Raitakari, Dan Rujescu, Teodor T. Postolache, C. Charles Gu, Joohon Sung, Terho Lehtimaki, Liisa Keltikangas-Jarvinen, C. Robert Cloninger
Summary: Studies suggest that human personality is the integrated expression of three major systems of learning and memory. Research in Finland, Germany, and Korea found that temperament and character are integrated within three disjoint networks regulated by nearly disjoint sets of genetic and environmental influences.
MOLECULAR PSYCHIATRY
(2021)
Article
Environmental Sciences
Laura C. Terron-Camero, Coral del Val, Luisa M. Sandalio, Maria C. Romero-Puertas
ENVIRONMENTAL POLLUTION
(2020)
Article
Computer Science, Information Systems
Emilio Perez-Bosch Quesada, Rocio Romero-Zaliz, Eduardo Perez, Mamathamba Kalishettyhalli Mahadevaiah, John Reuben, Markus Andreas Schubert, Francisco Jimenez-Molinos, Juan Bautista Roldan, Christian Wenger
Summary: This work evaluates three different RRAM compact models implemented in Verilog-A to replicate a multilevel approach based on the switching capability of experimental devices. The models are integrated in 1T-1R cells to control their analog behavior using compliance current, with four resistance levels simulated and verified for multilevel capability. Additionally, an Artificial Neural Network study is conducted to assess the viability of the multilevel approach in a real scenario.
Article
Computer Science, Information Systems
Rocio Romero-Zaliz, Eduardo Perez, Francisco Jimenez-Molinos, Christian Wenger, Juan B. Roldan
Summary: A comprehensive analysis was conducted on two types of artificial neural networks, revealing that convolutional neural networks (CNN) outperform multilayer perceptrons (MLP) in image recognition processes due to the ability of convolutional layers to extract image features and reduce data complexity.
Review
Biochemistry & Molecular Biology
I. Zwir, C. Del-Val, M. Hintsanen, K. M. Cloninger, R. Romero-Zaliz, A. Mesa, J. Arnedo, R. Salas, G. F. Poblete, E. Raitoharju, O. Raitakari, L. Keltikangas-Jarvinen, G. A. de Erausquin, I. Tattersall, T. Lehtimaki, C. R. Cloninger
Summary: The study reveals significant genetic differences related to creativity and self-awareness between modern humans, chimpanzees, and Neanderthals, which may have arisen from positive selection for characteristics of human well-being and behavioral modernity.
MOLECULAR PSYCHIATRY
(2022)
Article
Computer Science, Information Systems
Eduardo Perez, Antonio Javier Perez-avila, Rocio Romero-Zaliz, Mamathamba Kalishettyhalli Mahadevaiah, Emilio Perez-Bosch Quesada, Juan Bautista Roldan, Francisco Jimenez-Molinos, Christian Wenger
Summary: This study implemented truly discrete and linearly spaced conductive levels in RRAM arrays by tuning programming parameters, significantly reducing device-to-device and cycle-to-cycle variability. The optimized parameters improved precision of VMM results and recognition accuracy of neural network by about 6% compared with non-optimized parameters.
Article
Engineering, Electrical & Electronic
R. Romero-Zaliz, E. Perez, F. Jimenez-Molinos, C. Wenger, J. B. Roldan
Summary: A study on convolutional neural networks (CNNs) was conducted to analyze the effects of quantization and variability of synaptic weights in the network. Different CNN configurations were considered and experimentally quantized and modeled with reference to the conductance levels of fabricated 1T1R structures. Variability in experimental conductance levels was found to be Gaussian distributed and modeled for synaptic weight implementation.
SOLID-STATE ELECTRONICS
(2021)
Article
Computer Science, Information Systems
Rocio Romero-Zaliz, Antonio Cantudo, Eduardo Perez, Francisco Jimenez-Molinos, Christian Wenger, Juan Bautista Roldan
Summary: The study found that CNN performs better when the number of synapses is limited, however, when the number of synapses is reduced and quantized synaptic weights are included, the accuracy of NN significantly decreases, requiring a trade-off between the number of synapses and the NN accuracy.
Article
Oncology
Elisa Diaz de la Guardia-Bolivar, Rocio Barrios-Rodriguez, Igor Zwir, Jose Juan Jimenez-Moleon, Coral del Val
Summary: Prostate cancer is a highly heterogeneous tumor with limited prognostic markers. This study identified new genes associated with PCa progression, some of which have anti-tumoral activity and may serve as potential early markers for the disease.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Plant Sciences
Laura C. Terron-Cameron, M. Angeles Pelaez-Vico, A. Rodriguez-Gonzalez, Coral del Val, Luisa M. Sandalio, Maria C. Romero-Puertasl
Summary: Reactive oxygen species (ROS) act as secondary messengers that activate signal transduction and alter gene expression. The chemical identity and subcellular origin of ROS determine the transcriptome response. Transcriptomic studies on altered ROS metabolism in plant peroxisomes reveal common transcriptional footprints involved in metabolic pathways, gene regulation, and plant responses to abiotic stresses. Human orthologs of peroxisomal-dependent proteins are associated with cancer pathologies. Peroxisomal footprints provide valuable insights into peroxisomal functions in cellular metabolism under normal and stress conditions.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Salih Kafkas, Xiaokai Ma, Xingtan Zhang, Hayat Topcu, Rafael Navajas-Perez, Ching Man Wai, Haibao Tang, Xuming Xu, Mortaza Khodaeiaminjan, Murat Guney, Aibibula Paizila, Harun Karci, Xiaodan Zhang, Jing Lin, Han Lin, Roberto de la Herran, Carmelo Ruiz Rejon, Jerson Alexander Garcia-Zea, Francisca Robles, Coral del Val Munoz, Agnes Hotz-Wagenblatt, Xiangjia Jack Min, Hakan Ozkan, Elmira Ziya Motalebipour, Hatice Gozel, Nergiz Coban, Nesibe Ebru Kafkas, Andrej Kilian, HuaXing Huang, Xuanrui Lv, Kunpeng Liu, Qilin Hu, Ewelina Jacygrad, William Palmer, Richard Michelmore, Ray Ming
Summary: By sequencing the genomes of Pistacia vera, we have discovered genes related to sex determination and cultivation traits, which will accelerate the improvement of pistachio cultivars and rootstocks.
PLANT COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Igor Zwir, Javier Arnedo, Alberto Mesa, Coral del Val, Gabriel A. de Erausquin, C. Robert Cloninger
Summary: The resting-state functional connectivity (rsFC) of the human brain provides stable measures of individual differences in perceptual, cognitive, emotional, and social functioning. This study investigates whether the rsFC of the prefrontal cortex is associated with vulnerability to psychosis and related personality configurations. The results suggest that different patterns of rsFC in specific networks relate to biopsychosocial aspects of psychosis, and these differences are influenced by temperament and character traits.
MOLECULAR PSYCHIATRY
(2023)
Article
Multidisciplinary Sciences
Miikael Lehtimaki, Binisha H. H. Mishra, Coral Del-Val, Leo-Pekka Lyytikainen, Mika Kahonen, C. Robert Cloninger, Olli T. T. Raitakari, Reijo Laaksonen, Igor Zwir, Terho Lehtimaki, Pashupati P. P. Mishra
Summary: This study used an unsupervised machine learning method called PGMRA to discover the genotype-lipidome relations in a Finnish population. The researchers found 93 statistically significant lipidome-genotype relations, which contained a total of 5977 SNPs across 3164 genes. Twenty nine of these relations represented distinct subgroups with unique SNPs and participants. Pathway enrichment analysis identified 30 significantly enriched biological processes related to plasma lipid metabolism. These findings have implications for precision medicine research.
SCIENTIFIC REPORTS
(2023)
Meeting Abstract
Oncology
G. Di Stefano, E. Chteinberg, H. Loeffler-Wirth, S. Hillebrecht, R. Wagener, D. Abramov, B. Burkhardt, A. Louissant, H. Horn, A. Mottok, I. Oschlies, W. Klapper, K. Schafernak, Y. Zhang, C. Del-Val, A. Rosenwald, H. Binder, G. Ott, L. Leoncini, Reiner Siebert