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Alex H. Wagner, Ph.D. - Publications

Affiliations: 
Interdisciplinary Studies University of Iowa, Iowa City, IA 
Area:
Inherited eye disease
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Krysiak K, Danos AM, Saliba J, McMichael JF, Coffman AC, Kiwala S, Barnell EK, Sheta L, Grisdale CJ, Kujan L, Pema S, Lever J, Ridd S, Spies NC, Andric V, ... ... Wagner AH, et al. CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Research. PMID 36373660 DOI: 10.1093/nar/gkac979  0.37
2022 Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, ... ... Wagner AH, et al. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genetics in Medicine : Official Journal of the American College of Medical Genetics. 24: 1991. PMID 36063163 DOI: 10.1016/j.gim.2022.07.001  0.35
2022 Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, ... ... Wagner AH, et al. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 35101336 DOI: 10.1016/j.gim.2022.01.001  0.369
2021 LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, ... ... Wagner AH, et al. Discovery of clinically relevant fusions in pediatric cancer. Bmc Genomics. 22: 872. PMID 34863095 DOI: 10.1186/s12864-021-08094-z  0.318
2020 Rao S, Pitel B, Wagner AH, Boca SM, McCoy M, King I, Gupta S, Park BH, Warner JL, Chen J, Rogan PK, Chakravarty D, Griffith M, Griffith OL, Madhavan S. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. Jco Clinical Cancer Informatics. 4: 602-613. PMID 32644817 DOI: 10.1200/CCI.19.00169  0.329
2020 Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, et al. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nature Genetics. PMID 32246132 DOI: 10.1038/S41588-020-0603-8  0.455
2020 Alterovitz G, Heale B, Jones J, Kreda D, Lin F, Liu L, Liu X, Mandl KD, Poloway DW, Ramoni R, Wagner A, Warner JL. FHIR Genomics: enabling standardization for precision medicine use cases. Npj Genomic Medicine. 5: 13. PMID 32194985 DOI: 10.1038/S41525-020-0115-6  0.394
2020 Wagner AH, Kiwala S, Coffman AC, McMichael JF, Cotto KC, Mooney TB, Barnell EK, Krysiak K, Danos AM, Walker J, Griffith OL, Griffith M. CIViCpy: A Python Software Development and Analysis Toolkit for the CIViC Knowledgebase. Jco Clinical Cancer Informatics. 4: 245-253. PMID 32191543 DOI: 10.1200/CCI.19.00127  0.302
2020 Horak P, Griffith M, Danos A, Pitel BA, Madhavan S, Liu X, Lee J, Raca G, Li S, Wagner AH, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Abstract 5707: A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations Cancer Research. 80: 5707-5707. DOI: 10.1158/1538-7445.Am2020-5707  0.41
2020 Pitel BA, Rao S, Fitz CDV, Madhavan S, Dientsmann R, Horak P, King I, Mockus SM, Raca G, Rieke DT, Rogan P, Sonkin D, Tamborero D, Vlachos IS, Walsh B, ... ... Wagner AH, et al. Abstract 3222: The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer Cancer Research. 80: 3222-3222. DOI: 10.1158/1538-7445.Am2020-3222  0.454
2020 Wagner AH, Hart RK, Babb L, Freimuth RR, Coffman A, Liang Y, Pitel B, Roy A, Brush M, Lee J, Lu A, Coard T, Rao S, Ritter D, Walsh B, et al. Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium Cancer Research. 80: 1096-1096. DOI: 10.1158/1538-7445.Am2020-1096  0.493
2020 Wagner A, Babb L, Freimuth R, Pitel B, Krysiak K, Roy A, Coard T, Lu A, King I, Sonkin D, Lee J, Raca G, Griffith M, Griffith O, Hart R. 59. Integrating cytogenomic and sequence variants in the GA4GH variation representation specification Cancer Genetics. 244: 22-23. DOI: 10.1016/J.Cancergen.2020.04.063  0.338
2020 Rao S, Ritter D, Danos A, Raca G, Roy A, Krysiak K, Lin W, Barnell E, McCoy M, Pitel B, Sonkin D, Wang J, Hosseini SA, Selvarajah S, King I, ... ... Wagner AH, et al. 46. ClinGen somatic cancer working group: Enhancing standardized interpretation of cancer genetic data for clinical use Cancer Genetics. 244: 17-18. DOI: 10.1016/J.Cancergen.2020.04.050  0.382
2020 Danos A, Krysiak K, Saliba J, Guerra J, Wagner A, McMichael J, Kiwala S, Coffman A, Barnell E, Spies N, Sheta L, Pema S, Kujan L, Clark K, Griffith M, et al. 9. Expansion of the CIViC data model for functional annotation of cancer variants Cancer Genetics. 244: 4. DOI: 10.1016/J.Cancergen.2020.04.013  0.376
2019 Danos AM, Krysiak K, Barnell EK, Coffman AC, McMichael JF, Kiwala S, Spies NC, Sheta LM, Pema SP, Kujan L, Clark KA, Wollam AZ, Rao S, Ritter DI, Sonkin D, ... ... Wagner AH, et al. Standard operating procedure for curation and clinical interpretation of variants in cancer. Genome Medicine. 11: 76. PMID 31779674 DOI: 10.1186/S13073-019-0687-X  0.433
2019 Wagner AH, Griffith M, Griffith OL. Abstract 2478: Cancer genome interpretation with CIViCpy Cancer Research. DOI: 10.1158/1538-7445.Sabcs18-2478  0.392
2019 Griffith OL, Krysiak K, Danos A, Barnell E, Spies N, Ainscough B, Kujan L, Clark K, Pema S, Sheta L, Coffman A, Kiwala S, McMichael J, Wagner A, Griffith M. Solving The Interpretation Bottleneck for Cancer Precision Medicine Pathology. 51: S34. DOI: 10.1016/J.Pathol.2018.12.078  0.338
2019 Krysiak K, Danos A, Wagner A, McMichael J, Kiwala S, Coffman A, Spies N, Kujan L, Barnell E, Sheta L, Pema S, Clark K, Feng Y, Ainscough B, Skidmore Z, et al. 33. Aggregating evidence to determine the clinical significance of cancer variants in the CIViC knowledgebase Cancer Genetics and Cytogenetics. DOI: 10.1016/J.Cancergen.2019.04.039  0.384
2018 Ainscough BJ, Barnell EK, Ronning P, Campbell KM, Wagner AH, Fehniger TA, Dunn GP, Uppaluri R, Govindan R, Rohan TE, Griffith M, Mardis ER, Swamidass SJ, Griffith OL. A deep learning approach to automate refinement of somatic variant calling from cancer sequencing data. Nature Genetics. PMID 30397337 DOI: 10.1038/S41588-018-0257-Y  0.412
2018 Danos AM, Ritter DI, Wagner AH, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca SM, Roy A, Barnell EK, McMichael JF, Kiwala S, Coffman AC, et al. Adapting crowdsourced clinical cancer curation in CIViC to the ClinGen minimum variant level data community-driven standards. Human Mutation. 39: 1721-1732. PMID 30311370 DOI: 10.1002/Humu.23651  0.455
2018 Barnell EK, Ronning P, Campbell KM, Krysiak K, Ainscough BJ, Sheta LM, Pema SP, Schmidt AD, Richters M, Cotto KC, Danos AM, Ramirez C, Skidmore ZL, Spies NC, Hundal J, ... ... Wagner AH, et al. Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30287923 DOI: 10.1038/S41436-018-0278-Z  0.344
2018 Wagner AH, Devarakonda S, Skidmore ZL, Krysiak K, Ramu A, Trani L, Kunisaki J, Masood A, Waqar SN, Spies NC, Morgensztern D, Waligorski J, Ponce J, Fulton RS, Maggi LB, et al. Recurrent WNT pathway alterations are frequent in relapsed small cell lung cancer. Nature Communications. 9: 3787. PMID 30224629 DOI: 10.1038/S41467-018-06162-9  0.321
2018 Danos A, Ritter D, Krysiak K, Sonkin D, Micheel C, McCoy M, Rao S, Raca G, Boca S, Roy A, Sidiropoulos N, Aisner D, Leon A, Wagner A, Li XS, et al. 29. Integrating ClinGen somatic cancer variant description standards into crowdsourced curation technology via CIViC database for ClinVar submission Cancer Genetics and Cytogenetics. 47. DOI: 10.1016/J.Cancergen.2018.04.090  0.364
2018 Wagner A, Walsh B, Sonkin D, Dienstmann R, Li XS, Beckmann JS, Mayfield G, Tamborero D, Lopez-Bigas N, Goecks J, Margolin A, Griffith M, Griffith O. 4. Coordinating variant interpretation knowledgebases improves clinical interpretation of genomic variants in cancers Cancer Genetics and Cytogenetics. 37. DOI: 10.1016/J.Cancergen.2018.04.065  0.449
2017 Griffith M, Spies NC, Krysiak K, McMichael JF, Coffman AC, Danos AM, Ainscough BJ, Ramirez CA, Rieke DT, Kujan L, Barnell EK, Wagner AH, Skidmore ZL, Wollam A, Liu CJ, et al. CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics. 49: 170-174. PMID 28138153 DOI: 10.1038/Ng.3774  0.423
2017 Griffith O, Griffith M, Tamborero D, Wagner A, Krysiak K, Fitz CDV, Chakravarty D, Cerami E, Elemento O, Schultz N, Margolin A, Lopez-Bigas N. Global integration of knowledgebases for clinical interpretation of cancer variants F1000research. 6. DOI: 10.7490/F1000Research.1113918.1  0.404
2017 Griffith OL, Griffith M, Tamborero D, Wagner AH, Krysiak K, Fitz CDV, Chakravarty D, Cerami E, Elemento O, Schultz N, Margolin A, Lopez-Bigas N. Abstract 2608: Global integration of knowledgebases for clinical interpretation of cancer variants Cancer Research. 77: 2608-2608. DOI: 10.1158/1538-7445.Am2017-2608  0.402
2016 Ainscough BJ, Griffith M, Coffman AC, Wagner AH, Kunisaki J, Choudhary MN, McMichael JF, Fulton RS, Wilson RK, Griffith OL, Mardis ER. DoCM: a database of curated mutations in cancer. Nature Methods. 13: 806-7. PMID 27684579 DOI: 10.1038/Nmeth.4000  0.337
2016 Skidmore ZL, Wagner AH, Lesurf R, Campbell KM, Kunisaki J, Griffith OL, Griffith M. GenVisR: Genomic Visualizations in R. Bioinformatics (Oxford, England). PMID 27288499 DOI: 10.1093/Bioinformatics/Btw325  0.314
2016 Griffith M, Griffith OL, Krysiak K, Skidmore ZL, Christopher MJ, Klco JM, Ramu A, Lamprecht TL, Wagner AH, Campbell KM, Lesurf R, Hundal J, Zhang J, Spies NC, Ainscough BJ, et al. Comprehensive genomic analysis reveals FLT3 activation and a therapeutic strategy for a patient with relapsed adult B lymphoblastic leukemia. Experimental Hematology. PMID 27181063 DOI: 10.1016/J.Exphem.2016.04.011  0.369
2015 Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL, Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR, Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining clinically relevant drug-gene interactions. Nucleic Acids Research. PMID 26531824 DOI: 10.1093/Nar/Gkv1165  0.311
2014 Whitmore SS, Wagner AH, DeLuca AP, Drack AV, Stone EM, Tucker BA, Zeng S, Braun TA, Mullins RF, Scheetz TE. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research. 129: 93-106. PMID 25446321 DOI: 10.1016/J.Exer.2014.11.001  0.46
2013 Braun TA, Mullins RF, Wagner AH, Andorf JL, Johnston RM, Bakall BB, Deluca AP, Fishman GA, Lam BL, Weleber RG, Cideciyan AV, Jacobson SG, Sheffield VC, Tucker BA, Stone EM. Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease. Human Molecular Genetics. 22: 5136-45. PMID 23918662 DOI: 10.1093/Hmg/Ddt367  0.501
2013 Wagner AH, Taylor KR, DeLuca AP, Casavant TL, Mullins RF, Stone EM, Scheetz TE, Braun TA. Prioritization of retinal disease genes: an integrative approach. Human Mutation. 34: 853-9. PMID 23508994 DOI: 10.1002/Humu.22317  0.483
2013 Wagner AH, Anand VN, Wang WH, Chatterton JE, Sun D, Shepard AR, Jacobson N, Pang IH, Deluca AP, Casavant TL, Scheetz TE, Mullins RF, Braun TA, Clark AF. Exon-level expression profiling of ocular tissues. Experimental Eye Research. 111: 105-11. PMID 23500522 DOI: 10.1016/J.Exer.2013.03.004  0.303
2011 DeLuca AP, Wagner AH, Taylor KR, Faga B, Thole D, Sheffield VC, Stone EM, Casavant TL, Scheetz TE, Braun TA. Sequencing and disease variation detection tools and techniques Proceedings of Ieee/Acs International Conference On Computer Systems and Applications, Aiccsa. 80-83. DOI: 10.1109/AICCSA.2011.6126607  0.384
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