David L Wheeler's research while affiliated with National Institutes of Health and other places

... All virus-associated contigs were derived from SMV. Of the SMV-associated contigs, we selected viral contigs with sizes greater than 9000 bp to identify SMV sequences that covered all open reading frames (ORFs) using the NCBI ORFfinder [32]. ...

... In this review, we summarize the methods of sORF identification used in plant studies and discuss the challenges and caveats in plant sORF identification and possible solutions for future studies. sORF identification through sequence conservation As functional ORFs are conserved across genomes, early attempts at sORF identification were primarily based on sequence similarities using sequence alignment tools, such as BLAST (Altschul et al., 1997), coupled with ORF Finder (Wheeler et al., 2002), assuming that the functional sORFs would also have been preserved by natural selection ( Figure 1A). For example, a total of 26 groups of conserved uORFs were identified in O. sativa and A. thaliana using uORF-Finder (Hayden and Jorgensen, 2007). ...

... Despite their clinical relevance to familial PD, 6,29 these variants are relatively rare in the overall population, thus, not being considered polymorphisms (minor allele frequency <1%). 67 A study comparing the frequency of A53T in the general population with those occurring in four independent Italian PD families provides strong genetic evidence that this mutation is associated with familial phenotypes of PD. 68 Furthermore, genetic characterization in German kindred revealed that A30P participates in rare forms of ADPD. 69 Variant E46K was the third ASYN mutation to be described leading to ADPD, which was first identified in Spanish kindred. ...

... Genome curation involves multifaceted activities such as data use at different levels thatUsing state-of-the-art experimental methods, scientists generate, collect, and use genomic data to develop theories, models, and to perform integrative analysis (Stathias et al., 2018;Chen et al., 2011;Hong et al., 2016). These data are available in a variety of formats and organized and curated, but the quality of curation largely relies on the metadata schemas and tools that support the discovery, selection, retrieval, evaluation, and analysis of genomic data (Rapp and Wheeler, 2005). While metadata schemas and data management tools exist for genomic data curation and preservation (Klimke et al., 2011;Kottmann et al., 2008), they share a minimum consensus on certain data elements requirements, and are typically done on an ad hoc basis. ...

... For this study, we utilized the primary online resources were NCBI, NCBI-CDD, PDB, AlphaFold database, UniProt, VectorBuilder, and the SWISS-MODEL server [23][24][25][26][27][28] . Here the GROMACS software was employed for MD simulation studies of the protein structure [29]. ...

... The partial sequences of 26S rRNA obtained were analyzed using the Basic Local Alignment Search Tool (BLAST 2.2.26) algorithm [20], accessible on GenBank [21], using the non-redundant nucleotide database [22]. Only alignments with an identity match greater than 95% were considered for identification purposes. ...

... Identifi cation of microorganisms with ecological similarities. A comprehensive review of the existing scientifi c literature was conducted through the PubMed repository (https://pubmed.ncbi.nlm.nih.gov/ ) at the Na-tional Center for Biotechnology Information (NCBI) to identify microorganisms with ecological characteristics similar to Y. enterocolitica, specifi cally those that are soil-borne and possess pathogenicity [22]. ...

... The specificity of the primers and probes was checked using BLAST (https: //www.ncbi.nlm.nih.gov/tools/primer-blast/, accessed on 22 September 2023) [30,31]. ...

... A literature search was performed in PubMed [35] for relevant studies published before 16 February, 2023. The specific search strategy was as follows: (i) the title or abstract of the literature must contain the keywords 'EGFR mutation' and 'non-small cell lung cancer', (ii) the title or abstract of the literature must contain at least one approved EGFR-TKI agent, including 'tyrosine kinase inhibitors', 'gefitinib', 'erlotinib', 'icotinib', 'afatinib', 'osimertinib', 'olmutinib', 'dacomitinib', 'almonertinib' and 'furmonertinib' and (iii) the full text of the literature must contain the keywords about drug responses. ...

... Gen-Bank serves as a repository for annotated nucleotide sequence data, containing 2.5 × 10 11 bases from 2.0 × 10 8 sequences. BioProject, formerly known as GenomeProject, provides Whole-Genome Sequencing (WGS) data for over 130,000 sequencing projects, representing approximately 20,000 species [79]. These databases are essential resources for researchers working in the fields of genomics and bioinformatics. ...