Development and experimental validation of a machine learning model for the prediction of new antimalarials by Mukul Kore, Dimple Acharya, Lakshya Sharma, Shruthi Sridhar Vembar, Sandeep Sundriyal

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Matched pairs demonstrate robustness against inter-assay variability by Jochem Nelen, Horacio Pérez-Sánchez, Hans De Winter, Dries Van Rompaey

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Structural basis of Spliced Leader RNA recognition by the Trypanosoma brucei cap-binding complex by Harald Bernhard, Hana Petržílková, Barbora Popelářová, Kamil Ziemkiewicz, Karolina Bartosik, Marcin Warmiński, Laura Tengo, Henri Gröger, Luciano G. Dolce, Cameron D. Mackereth, Ronald Micura, Jacek Jemielity, Eva Kowalinski

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Metabolic activities are selective modulators for individual segmentation clock processes by Mitsuhiro Matsuda, Jorge Lázaro, Miki Ebisuya

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L’enfant de Mezmaiskaya (Caucase) examiné dans une double perspective paléogénétique et paléoanthropologique by Véronique Barriel, Anne-Marie Tillier

“…The palaeogenetic interpretation is examined in the present article based on data available for modern humans (Anderson et al. 1981; HvrBase; http://www.hvrbase.de) and for three Middle Palaeolithic fossils from Germany (Feildhofer 1 and 2 ; Krings et al. 1997; Krings et al. 1999; Schmitz et al. 2002) and Croatia (Vindija-75-G3/h-203; Krings et al. 2000), which are attributed to the Neanderthal line and those of Pan paniscus and the four sub-species of Pan troglodytes (EMBL and GenBank). The question of the phylogenetic status of the Mezmaiskaya child is examined using both molecular analysis and anthropological arguments.…”
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Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL by Lavinia Arseni, Gianluca Sigismondo, Haniyeh Yazdanparast, Johanne U. Hermansen, Norman Mack, Sibylle Ohl, Verena Kalter, Murat Iskar, Mathias Kalxdorf, Dennis Friedel, Mandy Rettel, Yashna Paul, Ingo Ringshausen, Eric Eldering, Julie Dubois, Arnon P. Kater, Marc Zapatka, Philipp M. Roessner, Eugen Tausch, Stephan Stilgenbauer, Sascha Dietrich, Mikhail M. Savitski, Sigrid S. Skånland, Jeroen Krijgsveld, Peter Lichter, Martina Seiffert

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Genome-Based Virus Taxonomy with the ICTV Database Extension by Shinduck Kang, Young-Chang Kim

“…This virus taxonomy web system was designed specifically to extend the virus taxonomy up to strain and isolation, which was then connected with the NCBI database to facilitate searches for specific viral genes; there are also links to journals provided by the EMBL RESTful API that improves accessibility for academic groups.…”
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Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications by Leyla Garcia, Olga Giraldo, Alexander Garcia, Dietrich Rebholz-Schuhmann

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De novo transcriptome assembly of the Mediterranean sea-rock pool mosquitoes Aedes mariae and Aedes zammitii by Valentina Mastrantonio, Daniele Porretta, Franco Liberati, Roberta Bisconti, Tiziana Castrignanò, Daniele Canestrelli

“…Homology alignments of predicted ORFs showed that 21,842 sequences from Ae. mariae and 21,944 sequences from Ae. zammitii mapped to the Nr, SwissProt, and TrEMBL databases, while 19,208 and 19,393 predicted ORFs, respectively, were functionally annotated using the COG and KEGG databases. …”
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Identification of Diagnostic Genes and Effective Drugs Associated with Osteoporosis Treatment by Single-Cell RNA-Seq Analysis and Network Pharmacology by Zhanyue Zhang, Tingbao Zhang, Liangshuang Zhou, Jianzhong Guan

“…Osteoporosis-related genes were obtained from chEMBL. Cell subpopulations were identified and characterized by scRNA-seq, t-SNE, clusterProfiler, and other computational methods. …”
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Characterization of Halorubrum sfaxense sp. nov., a New Halophilic Archaeon Isolated from the Solar Saltern of Sfax in Tunisia by Hana Trigui, Salma Masmoudi, Céline Brochier-Armanet, Sami Maalej, Sam Dukan

“…Therefore, strain ETD6 represents a novel species of the genus Halorubrum, for which the name Hrr. sfaxense sp. nov. is proposed. The Genbank EMBL-EBI accession number is GU724599.…”
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Identification of dequalinium as a potent inhibitor of human organic cation transporter 2 by machine learning based QSAR model by Fumihiro Yamane, Kenji Ikemura, Masayoshi Kondo, Manami Ueno, Masahiro Okuda

“…In the present study, we established a machine learning-based quantitative structure–activity relationship (QSAR) model for hOCT2 inhibitors based on the public ChEMBL database and explored novel hOCT2 inhibitors among the FDA-approved drugs. …”
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The expanded genome of Hexamita inflata, a free-living diplomonad by Zeynep Akdeniz, Michal Havelka, Michal Stoklasa, Alejandro Jiménez-González, Vojtěch Žárský, Feifei Xu, Courtney W. Stairs, Jon Jerlström-Hultqvist, Martin Kolísko, Jan Provazník, Staffan Svärd, Jan O. Andersson, Jan Tachezy

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Fecal microbiota transplantation to prevent acute graft-versus-host disease: pre-planned interim analysis of donor effect by Swetha Reddi, Liliia Senyshyn, Maryam Ebadi, Daniel Podlesny, Samuel S. Minot, Ted Gooley, Amanda J. Kabage, Geoffrey R. Hill, Stephanie J. Lee, Alexander Khoruts, Armin Rashidi

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Effect of Acetyl tributyl citrate on bone metabolism based on network toxicology and molecular docking technology by Xuan Lin, Kun Lin, Yue Lai, Qingping Peng, Miao Xu, Yiting Xu, Jialin Yang, Huan Liu, Jianlin Shen

“…Leveraging the exhaustive exploration of databases such as ChEMBL, STITCH, GeneCards, and OMIM, we have identified a comprehensive list of 164 potential targets intimately associated with both ATBC and bone metabolism. …”
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Nicotinic α7 receptors on cholinergic neurons in the striatum mediate cocaine-reinforcement, but not food reward by Michael Fritz, Michael Fritz, Michael Fritz, Priscila Batista Rosa, Daniel Wilhelms, Daniel Wilhelms, Maarit Jaarola, Johan Ruud, David Engblom, Anna M. Klawonn, Anna M. Klawonn, Anna M. Klawonn, Anna M. Klawonn

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Better understanding the phenotypic effects of drugs through shared targets in genetic disease networks by Elena Díaz-Santiago, Aurelio A. Moya-García, Jesús Pérez-García, Raquel Yahyaoui, Raquel Yahyaoui, Christine Orengo, Florencio Pazos, James R. Perkins, James R. Perkins, James R. Perkins, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea, Juan A. G. Ranea

“…Gaining traction in this field is the use of disease data linking genes with pathological phenotypes and combining this with drugtarget interaction data.MethodsWe introduce methodology to associate drugs with effects, both intended and adverse, using a tripartite network approach that combines drug-target and target-phenotype data, in which targets can be represented as proteins and protein domains.ResultsWe were able to detect associations for over 140,000 ChEMBL drugs and 3,800 phenotypes, represented as Human Phenotype Ontology (HPO) terms. …”
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Integrating pharmacogenomics and cheminformatics with diverse disease phenotypes for cell type-guided drug discovery by Arda Halu, Sarvesh Chelvanambi, Julius L. Decano, Joan T. Matamalas, Mary Whelan, Takaharu Asano, Namitra Kalicharran, Sasha A. Singh, Joseph Loscalzo, Masanori Aikawa

“…Using these networks and a large-scale disease-gene network consisting of 569 disease signatures from the Enrichr database, we calculate Pathophenotypic Congruity Scores (PACOS) between input gene signatures and drug perturbation signatures and combine these scores with cheminformatic data from ChEMBL to prioritize drugs. We benchmark our approach by calculating area under the receiver operating characteristic curves (AUROC) for 73 gene sets from the Molecular Signatures Database (MSigDB) using target gene expression profiles from the Comparative Toxicogenomics Database (CTD). …”
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