Van Auken, Kimberly

Combined from CaltechAUTHORS

• Raciti, Daniela and Van Auken, Kimberly M., el al. (2025) Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity; 10.1101/2025.01.06.631539
• Prakash, Sharan J. and Van Auken, Kimberly M., el al. (2024) Correction: Semantic representation of neural circuit knowledge in Caenorhabditis elegans; Brain Informatics; Vol. 11; 13; 10.1186/s40708-024-00226-x
• Aleksander, Suzanne A. and Anagnostopoulos, Anna V., el al. (2024) Updates to the Alliance of Genome Resources central infrastructure; Genetics; Vol. 227; No. 1; iyae049; PMCID PMC11075569; 10.1093/genetics/iyae049
• Sternberg, Paul W. and Van Auken, Kimberly, el al. (2024) WormBase 2024: status and transitioning to Alliance infrastructure; Genetics; Vol. 227; No. 1; iyae050; PMCID PMC11075546; 10.1093/genetics/iyae050
• Markarian, Nicholas and Van Auken, Kimberly M., el al. (2024) Enrichment on steps, not genes, improves inference of differentially expressed pathways; PLOS Computational Biology; Vol. 20; No. 3; e1011968; PMCID PMC10994554; 10.1371/journal.pcbi.1011968
• Hill, David P. and Drabkin, Harold J., el al. (2023) Biochemical pathways represented by Gene Ontology-Causal Activity Models identify distinct phenotypes resulting from mutations in pathways; Genetics; Vol. 225; No. 2; iyad152; PMCID PMC10550311; 10.1093/genetics/iyad152
• Hill, David P. and Drabkin, Harold J., el al. (2023) Identification of Biochemical Pathways Responsible for Distinct Phenotypes Using Gene Ontology Causal Activity Models; PMCID PMC10245817; 10.1101/2023.05.22.541760
• Prakash, Sharan J. and Van Auken, Kimberly M., el al. (2023) Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans; PMCID PMC10168330; 10.1101/2023.04.28.538760
• Agapite, Julie and Albou, Laurent-Philippe, el al. (2022) Harmonizing model organism data in the Alliance of Genome Resources; Genetics; Vol. 220; No. 4; Art. No. iyac022; PMCID PMC8982023; 10.1093/genetics/iyac022
• Grove, Christian and Cain, Scott, el al. (2018) Using WormBase: A Genome Biology Resource for Caenorhabditis elegans and Related Nematodes; ISBN 9781493977369; Eukaryotic Genomic Databases; 399-470; PMCID PMC6424801; 10.1007/978-1-4939-7737-6_14
• Müller, H.-M. and Van Auken, Kimberly M., el al. (2018) Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature; BMC Bioinformatics; Vol. 19; Art. No. 94; PMCID PMC5845379; 10.1186/s12859-018-2103-8
• Lee, Raymond Y. N. and Arnaboldi, Valerio, el al. (2018) WormBase 2017: molting into a new stage; Nucleic Acids Research; Vol. 46; No. D1; D869-D874; PMCID PMC5753391; 10.1093/nar/gkx998
• Mortensen, Jonathan M. and Telis, Natalie, el al. (2016) Is the crowd better as an assistant or a replacement in ontology engineering? An exploration through the lens of the Gene Ontology; Journal of Biomedical Informatics; Vol. 60; 199-209; PMCID PMC4836980; 10.1016/j.jbi.2016.02.005
• Howe, Kevin L. and Bolt, Bruce J., el al. (2016) WormBase 2016: expanding to enable helminth genomic research; Nucleic Acids Research; Vol. 44; No. D1; D774-D780; PMCID PMC4702863; 10.1093/nar/gkv1217
• Wang, Qinghua and Wang, Xiaodong, el al. (2016) Overview of the interactive task in BioCreative V; Database: The Journal of Biological Databases and Curation; Vol. 2016; Art. No. baw119; PMCID PMC5009325; 10.1093/database/baw119