Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease by Daisuke Yoshihara, Masanori Kugita, Tamio Yamaguchi, Harold M. Aukema, Hiroki Kurahashi, Miwa Morita, Yoshiyuki Hiki, James P. Calvet, Darren P. Wallace, Takafumi Toyohara, Takaaki Abe, Shizuko Nagao

“…Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes downregulated by PIO treatment. …”
Get full text

Comparative transcriptome analysis revealed gene expression differences in fruits between two Actinidia chinensis cultivars by Lina Guo, Kai Yan, Dan Li, Wanxing Li

“…Meanwhile, 1,915 could be aligned to the GO (Gene Ontology), 551 could be aligned to the KEGG (Kyoto Encyclopedia of Genes and Genomes Pathway), and 2,187 could be aligned to SWISS-PROT (SWISS-PROT Protein Sequence) database, respectively. …”
Get full text

The Impact of Interferon Lambda 3 Gene Polymorphism on Natural Course and Treatment of Hepatitis C by F. Bellanti, G. Vendemiale, E. Altomare, G. Serviddio

“…Very recently, three landmark genome-wide association studies identified single nucleotide polymorphisms near the interleukin 28B (IL28B) region which were more frequent in responders to treatment. …”
Get full text

Comparative Study of Population-based Metaheuristic Algorithms in Case Study of DNA Sequence Assembly by Lala Septem Riza, Yudi Prasetyo, Muhammad Iqbal Zain, Herbert Siregar, Rani Megasari, Topik Hidayat, Diah Kusumawaty, Miftahurrahma Rosyda

“…DNA sequence assembly is the process of combining several short genome sequences to create a longer DNA sequence. …”
Get full text

XGBoost-enhanced ensemble model using discriminative hybrid features for the prediction of sumoylation sites by Salman Khan, Sumaiya Noor, Tahir Javed, Afshan Naseem, Fahad Aslam, Salman A. AlQahtani, Nijad Ahmad

“…Abstract Posttranslational modifications (PTMs) are essential for regulating protein localization and stability, significantly affecting gene expression, biological functions, and genome replication. Among these, sumoylation a PTM that attaches a chemical group to protein sequences—plays a critical role in protein function. …”
Get full text

Advances in plant male sterility for hybrid seed production: an overview of conditional nuclear male sterile lines and biotechnology-based male sterile systems by Naresh Vasupalli, Naresh Vasupalli, Kanakachari Mogilicherla, Kanakachari Mogilicherla, Vahab Shaik, Vahab Shaik, K. R. S. Sambasiva Rao, Shripad R. Bhat, Xinchun Lin, Xinchun Lin

“…Here we review environment-sensitive genic male sterility (EGMS) and biotechnology-based male sterility systems and describe the underlying molecular mechanisms. Advances in crop genomics and discovery of a large number of nuclear genes governing anther/pollen development, which are shared across species, are helping design diverse types of male sterile lines suitable for different crop species and situations. …”
Get full text

SARS-COV-2 viral RNA detection through oligonucleotide-capped nanoporous anodic alumina supports. by Alba López-Palacios, María Nieves Aranda, Isabel Caballos, Andy Hernández-Montoto, Eva Calabuig, María Dolores Gómez-Ruiz, María Ángeles Tormo-Mas, Javier Pemán, Félix Sancenón, Ramón Martínez-Máñez, Elena Aznar, Estela Climent

“…The system is based on NAA that contains a fluorescent dye (Rhodamine B; RhB) and is capped with an oligonucleotide sequence that hybridize specifically a region of SARS-CoV-2 genome. In the presence of RNA from SARS-COV-2 virus, the oligonucleotide of the surface is displaced, uncapping the pores, and producing a delivery of RhB. …”
Get full text

Regulation of viral replication by host restriction factors by Ying Lin, Ying Lin, Ying Lin, Yun Zhu, Yun Zhu, Ling Jing, Ling Jing, Ling Jing, Xiaobo Lei, Xiaobo Lei, Zhengde Xie, Zhengde Xie

“…These cellular proteins inhibit viral replication and spread by impeding essential steps in the viral life cycle, such as viral entry, genome transcription and replication, protein translation, viral particle assembly, and release. …”
Get full text

Gene Technology for Papaya Ringspot Virus Disease Management by Md. Abul Kalam Azad, Latifah Amin, Nik Marzuki Sidik

“…This review discusses the genome and the genetic diversity of PRSV, host range determinants, molecular diagnosis, disease management strategies, the development of transgenic papaya, environmental issues, issues in the adoption of transgenic papaya, and future directions for research.…”
Get full text

Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics by Julia Velz, Lena K. Freudenmann, Gioele Medici, Marissa Dubbelaar, Malte Mohme, David R. Ghasemi, Jonas Scheid, Daniel J. Kowalewski, Angelica B. Patterson, Anna M. Zeitlberger, Katrin Lamszus, Manfred Westphal, Matthias Eyrich, Martina Messing-Jünger, Andreas Röhrig, Harald Reinhard, Kévin Beccaria, Rogeiro B. Craveiro, Beat M. Frey, Martin Sill, Sven Nahnsen, Marie Gauder, Konstantina Kapolou, Manuela Silginer, Tobias Weiss, Hans-Georg Wirsching, Patrick Roth, Michael Grotzer, Niklaus Krayenbühl, Oliver Bozinov, Luca Regli, Hans-Georg Rammensee, Elisabeth J. Rushing, Felix Sahm, Juliane S. Walz, Michael Weller, Marian C. Neidert

“…Despite recent advances in integrated genomics, the prognosis in children with high-risk medulloblastoma remains devastating, and new tumor-specific therapeutic approaches are needed. …”
Get full text

Online COVID-19 Infection Diagnoses via Chest X-Ray Images using Alexnet Deep Learning Model by Ali Heidari, Hamidreza Erfanian

“…As the virus causes inflammation in the infected patient's lung, it is possible to diagnose whether one is infected or not using his/her CXR image. in contrast to other tests which mostly are based on the virus genome, this test is not time-consuming and it is reliable against new strains of the virus. …”
Get full text

Phylogenomic approaches reveal a robust time-scale phylogeny of the Terminal Fusarium Clade by Andrés Felipe Lizcano Salas, Jorge Duitama, Silvia Restrepo, Adriana Marcela Celis Ramírez

“…To achieve this objective, we performed a phylogenomic analysis using the available genomes in GenBank and ran eight different pipelines. …”
Get full text

Microbial phenolic metabolites 3-(3′,4′-dihydroxyphenyl)propanoic acid and 3′,4′-dihydroxyphenylacetic acid prevent obesity in mice fed with high-fat diet by Wanbing Chen, Ruonan Liu, Xiaoling Zhu, Qun Lu, Hong Yang, Rui Liu

“…Surprisingly, the 16S rRNA sequencing and UHPLC-Q-TOF/MS demonstrated that DHPA and DHAA only slightly disturbed the intestinal microbiome, but significantly altered the urine metabolome of HFD mice mainly by regulating pentose and glucuronate interconversion, tyrosine metabolism, pentose phosphate and tricarboxylic acid (TCA) cycle as indicated by metabolic pathway analysis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Correlation analysis revealed that the differential metabolites are strongly associated with body weight, blood glucose, insulin level, and superoxide dismutase (SOD) enzyme activity. …”
Get full text

Glioblastoma Multiforme Stem Cells by Irena Dimov, Deasanka Tasic-Dimov, Irena Conic, Vladisav Stefanovic

“…The rapidly emerging focus on cancer stem cells embodies a paradigm shift in our understanding of tumor pathogenesis, while the development of powerful genome-wide screening techniques has provided cause for optimism related to the development of more reliable therapies primarily targeting GBM stem cells (GBMSCs). …”
Get full text

A network medicine approach to investigating ME/CFS pathogenesis in severely ill patients: a pilot study by Li-Yuan Hung, Chan-Shuo Wu, Chia-Jung Chang, Peng Li, Kimberly Hicks, Joshua J. Dibble, Braxton Morrison, Chimere L. Smith, Ronald W. Davis, Wenzhong Xiao

“…By utilizing a network analysis on whole genome sequencing (WGS) data from the Severely Ill Patient Study (SIPS), we identified ME/CFS-associated proteins and delineated the corresponding network-level module, termed the SIPS disease module, together with its relevant pathways. …”
Get full text

A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing by John Ziegler, Jaclyn F. Hechtman, Satshil Rana, Ryan N. Ptashkin, Gowtham Jayakumaran, Sumit Middha, Shweta S. Chavan, Chad Vanderbilt, Deborah DeLair, Jacklyn Casanova, Jinru Shia, Nicole DeGroat, Ryma Benayed, Marc Ladanyi, Michael F. Berger, Thomas J. Fuchs, A. Rose Brannon, Ahmet Zehir

“…Abstract Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. …”
Get full text

FOX DOMESTICATION: MOLECULAR MECHANISMS INVOLVED IN SELECTION FOR BEHAVIOR by L. N. Trut, Yu. E. Herbeck, A. V. Kharlamova, R. G. Gulevich, A. V. Kukekova

“…Additional resources were developed to analyze the molecular nature of differences in the behavior of these unique foxes: the meiotic map of the fox genome was constructed, crosses of tame and aggressive animals obtained informative segregating subpopulations, and the formerly applied method of quantification of behavioral phenotypes was improved. …”
Get full text

Non-targeted Metabolomic Analysis of Differences in the Composition of Different Rice Varieties for Baijiu Production by LIU Maoke, TIAN Xinhui, LIU Yao, TANG Yuming, QIN Jian, FENG Jun, LIU Chengyuan

“…Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differential metabolites identified 16 significantly differential biological pathways (P < 0.05), of which 14 were assigned to metabolic functions, including those related to Baijiu brewing such as galactose metabolism, the biosynthesis of unsaturated fatty acids, fatty acid biosynthesis, and butanoate metabolism. …”
Get full text

Multi‐omics graph convolutional networks for digestive system tumour classification and early‐late stage diagnosis by Lin Zhou, Zhengzhi Zhu, Hongbo Gao, Chunyu Wang, Muhammad Attique Khan, Mati Ullah, Siffat Ullah Khan

“…A rigorous experimental evaluation was undertaken on the DST dataset from The Cancer Genome Atlas to scrutinise the efficacy of the MGTCN model. …”
Get full text

The clinical utility of circulating human papillomavirus across squamous cell carcinomas by Karen-Lise G. Spindler, Anne V. Jakobsen, Jesper G. Eriksen, Lars Fokdal, Marianne Nordsmark, Lise B. J. Thorsen, Karen L. Wind, Anna C. Lefevre, Jens Overgaard

“…In HPV associated cancers, HPV is integrated into the tumor genome and can consequently be detected in the circulating fragments of the tumor DNA. …”
Get full text