Forecasting of potential anti-inflammatory targets of some immunomodulatory plants and their constituents using in vitro, molecular docking and network pharmacology-based analysis by Asmaa Khairy, Doaa A. Ghareeb, Ismail Celik, Hala M. Hammoda, Hala H. Zaatout, Reham S. Ibrahim

“…Furthermore, molecular docking analysis of the top hit compounds against the most enriched genes revealed that silibinin had the most stabilized interactions with AKT1, CASP3 and TP53, whereas luteolin and apigenin exhibited the most stabilized interactions with AKT1, PTGS2 and TP53. …”
Get full text

Specific DNA identification of Pheretima in the Naoxintong capsule by Xiaoxiao Zhu, Hoi-Yan Wu, Pang-Chui Shaw, Wei Peng, Weiwei Su

“…The purified PCR products were sequenced and the obtained sequences were identified to species level with top hit of similarity with BLAST against GenBank nucleotide database. …”
Get full text

Metabolic profiling of Lantana camara L. using UPLC-MS/MS and revealing its inflammation-related targets using network pharmacology-based and molecular docking analyses by Alaa A. El-Banna, Reham S. Darwish, Doaa A. Ghareeb, Abdelrahman M. Yassin, Shaymaa A. Abdulmalek, Hend M. Dawood

“…Fifty-seven phytoconstituents were identified in L. camara extract, from which the top hit compounds related to inflammation were ferulic acid, catechin gallate, myricetin and iso-ferulic acid. …”
Get full text

PTPN1 Deficiency Modulates BMPR2 Signaling and Induces Endothelial Dysfunction in Pulmonary Arterial Hypertension by Md Khadem Ali, Xuefei Tian, Lan Zhao, Katharina Schimmel, Christopher J. Rhodes, Martin R. Wilkins, Mark R. Nicolls, Edda F. Spiekerkoetter

“…We further experimentally validated the top hit, PTPN1 (PTP1B), in healthy human pulmonary arterial endothelial cells (PAECs) either silenced by siRNA or exposed to hypoxia and confirmed its relevance to PAH by measuring PTPN1 levels in blood and PAECs collected from PAH patients. …”
Get full text

The Identification of Stemness-Related Genes in the Risk of Head and Neck Squamous Cell Carcinoma by Guanying Feng, Guanying Feng, Feifei Xue, Yingzheng He, Tianxiao Wang, Hua Yuan, Hua Yuan

“…CDK inhibitor was the top hit of potential compounds.ConclusionStemness-related gene expression profiles may be a potential biomarker for HNSCC.…”
Get full text

Environmental and genetic contributors to salivary testosterone levels in infants by Kai eXia, Yang eYu, Mihye eAhn, Hongtu eZhu, Fei eZou, John eGilmore, Rebecca Christine Knickmeyer

“…The top hits in females were two SNPs located upstream of ESR1 (rs3407085 and rs2295190). …”
Get full text

Discovery of Small Molecules for the Reversal of T Cell Exhaustion by Brett S. Marro, Jaroslav Zak, Reza Beheshti Zavareh, John R. Teijaro, Luke L. Lairson, Michael B.A. Oldstone

“…We identify 19 compounds from the ReFRAME drug-repurposing collection that restore cytokine production and enhance the proliferation of exhausted T cells. Analysis of our top hit, ingenol mebutate, a protein kinase C (PKC) inducing diterpene ester, reveals a role for this molecule in overriding the suppressive signaling cascade mediated by IR signaling on T cells. …”
Get full text

TFPI1 mediates resistance to doxorubicin in breast cancer cells by inducing a hypoxic-like response. by Gerald F Davies, Arnie Berg, Spike D L Postnikoff, Heather L Wilson, Terra G Arnason, Anthony Kusalik, Troy A A Harkness

“…A cluster of genes involved in the anticoagulation pathway, with Tissue Factor Pathway Inhibitor 1 (TFPI1) the top hit, was identified. Plasmids overexpressing TFPI1 were utilized, and 1% O2 was used to test the effects of hypoxia on drug resistance. …”
Get full text

Computational biology and in vitro studies for anticipating cancer-related molecular targets of sweet wormwood (Artemisia annua) by Hend Dawood, Ismail Celik, Reham S. Ibrahim

“…Molecular docking analysis of the top hit compounds against the most enriched target proteins showed that 3-(2-methylpropanoyl)-4-cadinene-3,11-diol and O-(2-propenal) coniferaldehyde exhibited the most stabilized interactions. …”
Get full text

Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. by Adam H Freedman, Rena M Schweizer, Diego Ortega-Del Vecchyo, Eunjung Han, Brian W Davis, Ilan Gronau, Pedro M Silva, Marco Galaverni, Zhenxin Fan, Peter Marx, Belen Lorente-Galdos, Oscar Ramirez, Farhad Hormozdiari, Can Alkan, Carles Vilà, Kevin Squire, Eli Geffen, Josip Kusak, Adam R Boyko, Heidi G Parker, Clarence Lee, Vasisht Tadigotla, Adam Siepel, Carlos D Bustamante, Timothy T Harkins, Stanley F Nelson, Tomas Marques-Bonet, Elaine A Ostrander, Robert K Wayne, John Novembre

“…These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. …”
Get full text

Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data. by Yongsheng Bai, Justin Hassler, Ahdad Ziyar, Philip Li, Zachary Wright, Rajasree Menon, Gilbert S Omenn, James D Cavalcoli, Randal J Kaufman, Maureen A Sartor

“…The 26 nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1α knockout samples. …”
Get full text

Orchestration of Intracellular Circuits by G Protein-Coupled Receptor 39 for Hepatitis B Virus Proliferation by Kaku Goto, Hironori Nishitsuji, Masaya Sugiyama, Nao Nishida, Masashi Mizokami, Kunitada Shimotohno

“…In an RNAi screen of G protein-coupled receptors (GPCRs), GPCR39 (GPR39) appeared as the top hit to facilitate HBV proliferation. Lentiviral overexpression of active GPR39 proteins and an agonist enhanced HBV replication and transcriptional activities of viral promoters, inducing the expression of CCAAT/enhancer binding protein (CEBP)-β (CEBPB). …”
Get full text

Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish by Chun-Hsi Tso, Jen-Leih Wu, Ming-Wei Lu

“…Instead of annotating the BLAST single top hit by a pre-defined gene-to-tag database, we included 500 hits to search related PubMed articles and parse biological terms. …”
Get full text

Inflammatory cell death, PANoptosis, screen identifies host factors in coronavirus innate immune response as therapeutic targets by R. K. Subbarao Malireddi, Ratnakar R. Bynigeri, Raghvendra Mall, Jon P. Connelly, Shondra M. Pruett-Miller, Thirumala-Devi Kanneganti

“…Our screen was validated through the identification of the known MHV receptor Ceacam1 as the top hit, and its deletion significantly reduced viral replication due to loss of viral entry, resulting in a downstream reduction in MHV-induced cell death. …”
Get full text

Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex by Sona Vasudevan, James N. Baraniuk

“…We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1–NXT1 complex. The top hit was ganirelix, with a docking score of −14.49. …”
Get full text

Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs by Lipin Loo, Matthew A. Waller, Cesar L. Moreno, Alexander J. Cole, Alberto Ospina Stella, Oltin-Tiberiu Pop, Ann-Kristin Jochum, Omar Hasan Ali, Christopher E. Denes, Zina Hamoudi, Felicity Chung, Anupriya Aggarwal, Jason K. K. Low, Karishma Patel, Rezwan Siddiquee, Taeyoung Kang, Suresh Mathivanan, Joel P. Mackay, Wolfram Jochum, Lukas Flatz, Daniel Hesselson, Stuart Turville, G. Gregory Neely

“…Here, we use whole-genome CRISPR activation to identify host factors controlling cellular interactions with SARS-CoV-2. Our top hit was a TLR-related cell surface receptor called leucine-rich repeat-containing protein 15 (LRRC15). …”
Get full text

Evaluating the Accuracy of the QCEIMS Approach for Computational Prediction of Electron Ionization Mass Spectra of Purines and Pyrimidines by Jesi Lee, Tobias Kind, Dean Joseph Tantillo, Lee-Ping Wang, Oliver Fiehn

“…Similarity scores between every pair of predicted and experimental spectra revealed that 45% of the compounds were found as the correct top hit when QCEIMS predicted spectra were matched against the NIST17 library of >267,000 EI spectra, and 74% of the compounds were found within the top 10 hits. …”
Get full text

Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants. by Akifumi S Tanabe, Hirokazu Toju

“…In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. …”
Get full text

Epigenome-wide DNA methylation analysis of late-stage mild cognitive impairment by Yi Zhang, Shasha Shen

“…However, previous studies have often pooled EMCI and LMCI patients into a single MCI group, with limited independent investigation into the pathogenesis of LMCI.Methods: In this study, we employed whole-genome methylation association analysis to determine the differences in peripheral blood methylation profiles between 663 cognitive aging (CN) and 554 LMCI patients.Results: Our results revealed 2,333 differentially methylated probes (DMPs) and 85 differentially methylated regions (DMRs) specific to LMCI. The top hit methylation sites or regions were associated with genes such as SNED1, histone deacetylases coding gene HDACs, and HOX and ZNF gene family. …”
Get full text

Mfap4: a promising target for enhanced liver regeneration and chronic liver disease treatment by Viktoriia Iakovleva, Anna Wuestefeld, Agnes Bee Leng Ong, Rong Gao, Neslihan Arife Kaya, May Yin Lee, Weiwei Zhai, Wai Leong Tam, Yock Young Dan, Torsten Wuestefeld

“…We set up an in vivo functional genetic screen to identify such regeneration breaks. As the top hit, we identified Microfibril associated protein 4 (Mfap4). …”
Get full text