Dr Jake Lever

  • Lecturer in Natural Language Processing / Information Retrieval (School of Computing Science)
  • Affiliate (School of Cancer Sciences)

email: Jake.Lever@glasgow.ac.uk
pronouns: He/him/his

Room 331, School of Computing Science, Sir Alwyn Williams Building, 18 Lilybank Gardens, Glasgow, G128RZ

Import to contacts

ORCID iDhttps://orcid.org/0000-0001-8198-2939

Biography

I am a Lecturer (Assistant Professor) in the Information, Data and Analysis section in the School of Computing Science. My research focuses on extracting biomedical knowledge from biomedical text (e.g. published research literature) using different natural language processing and machine learning methods. This helps researchers to find important research knowledge and paves the way for representing biological knowledge computationally that artificial intelligence can reason on. I’ve focused in areas of precision medicine which tries to tailor treatment to an individual patient’s genetics and frequently relies on the latest research findings.

Before I moved to Glasgow, I spent two years at Stanford University as a postdoctoral researcher in the Helix Group. I received my Ph.D. in Bioinformatics from the University of British Columbia in Vancouver, Canada where I undertook research at Canada’s Michael Smith Genome Sciences Centre at BC Cancer. I completed my B.Eng. degree at the University of Edinburgh in Software Engineering.

I co-lead the Glasgow AI4BioMed Lab, where we work on natural language processing, knowledge graphs, language models, and more to extract and infer biomedical knowledge. If you'd be interested in working with us, please take a look at this page on the lab website.

Research interests

  • Natural language processing, especially in biomedicine
  • Information extraction
  • Knowledge bases & knowledge inference
  • Applications of machine learning, particularly biomedical
  • Bioinformatics & computational biology

Research Projects | Google Scholar

Publications

List by: Type | Date

Jump to: 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2012
Number of items: 27.

2024

Frayling, E., Lever, J. and McDonald, G. (2024) UoG Siephers at "Discharge Me!": Exploring Ways to Generate Synthetic Patient Notes From Multi-Part Electronic Health Records. In: BioNLP 2024 Workshop, Bangkok, Thailand, 11-16 Aug 2024, pp. 712-718.

Zhang, X., Meng, Z. , Lever, J. and Ho, E. S.L. (2024) Gla-AI4BioMed at RRG24: Visual Instruction-tuned Adaptation for Radiology Report Generation. In: 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024), 23rd BioNLP Workshop, Bangkok, Thailand, 16 August 2024, (Accepted for Publication)

2023

Sosa, D., Hintzen, R., Xiong, B., de Giorgio, A., Fauqueur, J., Davies, M., Lever, J. and Altman, R. B. (2023) Associating biological context with protein-protein interactions through text mining at PubMed scale. Journal of Biomedical Informatics, 145, 104474. (doi: 10.1016/j.jbi.2023.104474) (PMID:37572825)

Krysiak, K. et al. (2023) CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Research, 51(D1), D1230-D1241. (doi: 10.1093/nar/gkac979) (PMID:36373660)

2022

Krysiak, K. et al. (2022) A community approach to the cancer-variant-interpretation bottleneck. Nature Cancer, 3(5), pp. 522-525. (doi: 10.1038/s43018-022-00379-w) (PMID:35624339)

2021

Lever, J. and Altman, R. B. (2021) Analyzing the vast coronavirus literature with CoronaCentral. Proceedings of the National Academy of Sciences of the United States of America, 118(23), 2100766118. (doi: 10.1073/pnas.2100766118) (PMID:34016708)

Wong, M., Previde, P., Cole, J., Thomas, B., Laxmeshwar, N., Mallory, E., Lever, J. , Petkovic, D., Altman, R. B. and Kulkarni, A. (2021) Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive. Journal of Biomedical Informatics, 117, 103732. (doi: 10.1016/j.jbi.2021.103732) (PMID:33737208)

Sosa, D. N., Bimbin, C., Kaushal, A., Lavertu, A., Lever, J. , Rensi, S. and Altman, R. (2021) Repurposing biomedical informaticians for COVID-19. Journal of Biomedical Informatics, 115, 103673. (doi: 10.1016/j.jbi.2021.103673) (PMID:33486067) (PMCID:PMC7825863)

2020

Lever, J. , Altman, R. and Kim, J.-D. (2020) Extending TextAE for annotation of non-contiguous entities. Genomics and Informatics, 18(2), e15. (doi: 10.5808/gi.2020.18.2.e15) (PMID:32634869) (PMCID:PMC7362949)

Lever, J. , Barbarino, J. M., Gong, L., Huddart, R., Sangkuhl, K., Whaley, R., Whirl-Carrillo, M., Woon, M., Klein, T. E. and Altman, R. B. (2020) PGxMine: Text Mining for Curation of PharmGKB. In: 25th Pacific Symposium on Biocomputing, Puako, HI, USA, 03-07 Jan 2020, pp. 611-622.

2019

Lever, J. , Jones, M. R., Danos, A. M., Krysiak, K., Bonakdar, M., Grewal, J. K., Culibrk, L., Griffith, O. L., Griffith, M. and Jones, S. J.M. (2019) Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. Genome Medicine, 11, 78. (doi: 10.1186/s13073-019-0686-y) (PMID:31796060) (PMCID:PMC6891984)

Chun, H.-J. E. et al. (2019) Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration. Cell Reports, 29(8), 2338-2354.e7. (doi: 10.1016/j.celrep.2019.10.013) (PMID:31708418) (PMCID:PMC6905433)

Barbaian, A., Thompson, I. R., Lever, J. , Gagnier, L., Karimi, M. M. and Mager, D. L. (2019) LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. Bioinformatics, 35(19), pp. 3839-3841. (doi: 10.1093/bioinformatics/btz130) (PMID:30793157)

Shen, Y. et al. (2019) Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proceedings of the National Academy of Sciences of the United States of America, 116(38), pp. 19098-19108. (doi: 10.1073/pnas.1813495116) (PMID:31471491) (PMCID:PMC6754609)

Lever, J. , Zhao, E. Y., Grewal, J., Jones, M. R. and Jones, S. J.M. (2019) CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer. Nature Methods, 16(6), pp. 505-507. (doi: 10.1038/s41592-019-0422-y) (PMID:31110280)

2018

Lee, J. J.Y., Gottlieb, M. M., Lever, J. , Jones, S. J.M., Blau, N., van Karnebeek, C. D.M. and Wasserman, W. W. (2018) Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. Journal of Inherited Metabolic Disease, 41(3), pp. 555-562. (doi: 10.1007/s10545-017-0125-4) (PMID:29340838) (PMCID:PMC5959948)

Lever, J. , Gakkhar, S., Gottlieb, M., Rashnavadi, T., Lin, S., Siu, C., Smith, M., Jones, M. R., Krzywinski, M. and Jones, S. J.M. (2018) A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics, 34(4), pp. 652-659. (doi: 10.1093/bioinformatics/btx613) (PMID:29028901)

2017

Anekalla, K. R., Courneya, J.P., Florini, N., Lever, J. , Muchow, M. and Busby, B. (2017) PubRunner: a light-weight framework for updating text mining results. F1000Research, 6, 612. (doi: 10.12688/f1000research.11389.2) (PMID:29152221) (PMCID:PMC5664974)

Lever, J. , Krzywinski, M. and Altman, N. (2017) Principal component analysis. Nature Methods, 14(7), pp. 641-642. (doi: 10.1038/nmeth.4346)

2016

Lever, J. , Krzywinski, M. and Altman, N. (2016) Regularization. Nature Methods, 13(10), pp. 803-804. (doi: 10.1038/nmeth.4014)

Grinshtein, N. et al. (2016) Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells. Oncotarget, 7(37), pp. 59360-59376. (doi: 10.18632/oncotarget.10661) (PMID:27449082) (PMCID:PMC5312317)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Model selection and overfitting. Nature Methods, 13(9), pp. 703-704. (doi: 10.1038/nmeth.3968)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Classification evaluation. Nature Methods, 13(8), pp. 603-604. (doi: 10.1038/nmeth.3945)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Logistic regression. Nature Methods, 13(7), pp. 541-542. (doi: 10.1038/nmeth.3904)

Lever, J. , Jones, M. and Jones, S. J.M. (2016) CancerMine: Knowledge Base Construction for Personalised Cancer Treatment. In: 2016 Joint International Conference on Biological Ontology and BioCreative - Food, Nutrition, Health and Environment for the 9 Billion (ICBO-BioCreative 2016), Corvallis, OR, USA, 01-04 Aug 2016,

2015

Davis, B., Shen, Y., Poon, C. C., Luchman, H. A., Stechishin, O. D., Pontifex, C. S., Wu, W., Kelly, J. J., Blough, M. D. and Terry Fox Research Institute Glioblastoma Consortium, (2015) Comparative genomic and genetic analysis of glioblastoma-derived brain tumor-initiating cells and their parent tumors. Neuro-Oncology, 18(3), pp. 350-360. (doi: 10.1093/neuonc/nov143) (PMID:26245525) (PMCID:PMC4767234)

2012

Lever, J. and Komura, T. (2012) Real-time controllable fire using textured forces. Visual Computer, 28(6-8), pp. 691-700. (doi: 10.1007/s00371-012-0684-1)

This list was generated on Thu Nov 21 03:17:50 2024 GMT.
Jump to: Articles | Conference Proceedings
Number of items: 27.

Articles

Sosa, D., Hintzen, R., Xiong, B., de Giorgio, A., Fauqueur, J., Davies, M., Lever, J. and Altman, R. B. (2023) Associating biological context with protein-protein interactions through text mining at PubMed scale. Journal of Biomedical Informatics, 145, 104474. (doi: 10.1016/j.jbi.2023.104474) (PMID:37572825)

Krysiak, K. et al. (2023) CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase. Nucleic Acids Research, 51(D1), D1230-D1241. (doi: 10.1093/nar/gkac979) (PMID:36373660)

Krysiak, K. et al. (2022) A community approach to the cancer-variant-interpretation bottleneck. Nature Cancer, 3(5), pp. 522-525. (doi: 10.1038/s43018-022-00379-w) (PMID:35624339)

Lever, J. and Altman, R. B. (2021) Analyzing the vast coronavirus literature with CoronaCentral. Proceedings of the National Academy of Sciences of the United States of America, 118(23), 2100766118. (doi: 10.1073/pnas.2100766118) (PMID:34016708)

Wong, M., Previde, P., Cole, J., Thomas, B., Laxmeshwar, N., Mallory, E., Lever, J. , Petkovic, D., Altman, R. B. and Kulkarni, A. (2021) Search and visualization of gene-drug-disease interactions for pharmacogenomics and precision medicine research using GeneDive. Journal of Biomedical Informatics, 117, 103732. (doi: 10.1016/j.jbi.2021.103732) (PMID:33737208)

Sosa, D. N., Bimbin, C., Kaushal, A., Lavertu, A., Lever, J. , Rensi, S. and Altman, R. (2021) Repurposing biomedical informaticians for COVID-19. Journal of Biomedical Informatics, 115, 103673. (doi: 10.1016/j.jbi.2021.103673) (PMID:33486067) (PMCID:PMC7825863)

Lever, J. , Altman, R. and Kim, J.-D. (2020) Extending TextAE for annotation of non-contiguous entities. Genomics and Informatics, 18(2), e15. (doi: 10.5808/gi.2020.18.2.e15) (PMID:32634869) (PMCID:PMC7362949)

Lever, J. , Jones, M. R., Danos, A. M., Krysiak, K., Bonakdar, M., Grewal, J. K., Culibrk, L., Griffith, O. L., Griffith, M. and Jones, S. J.M. (2019) Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. Genome Medicine, 11, 78. (doi: 10.1186/s13073-019-0686-y) (PMID:31796060) (PMCID:PMC6891984)

Chun, H.-J. E. et al. (2019) Identification and analyses of extra-cranial and cranial rhabdoid tumor molecular subgroups reveal tumors with cytotoxic T cell infiltration. Cell Reports, 29(8), 2338-2354.e7. (doi: 10.1016/j.celrep.2019.10.013) (PMID:31708418) (PMCID:PMC6905433)

Barbaian, A., Thompson, I. R., Lever, J. , Gagnier, L., Karimi, M. M. and Mager, D. L. (2019) LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq. Bioinformatics, 35(19), pp. 3839-3841. (doi: 10.1093/bioinformatics/btz130) (PMID:30793157)

Shen, Y. et al. (2019) Comprehensive genomic profiling of glioblastoma tumors, BTICs, and xenografts reveals stability and adaptation to growth environments. Proceedings of the National Academy of Sciences of the United States of America, 116(38), pp. 19098-19108. (doi: 10.1073/pnas.1813495116) (PMID:31471491) (PMCID:PMC6754609)

Lever, J. , Zhao, E. Y., Grewal, J., Jones, M. R. and Jones, S. J.M. (2019) CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer. Nature Methods, 16(6), pp. 505-507. (doi: 10.1038/s41592-019-0422-y) (PMID:31110280)

Lee, J. J.Y., Gottlieb, M. M., Lever, J. , Jones, S. J.M., Blau, N., van Karnebeek, C. D.M. and Wasserman, W. W. (2018) Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis. Journal of Inherited Metabolic Disease, 41(3), pp. 555-562. (doi: 10.1007/s10545-017-0125-4) (PMID:29340838) (PMCID:PMC5959948)

Lever, J. , Gakkhar, S., Gottlieb, M., Rashnavadi, T., Lin, S., Siu, C., Smith, M., Jones, M. R., Krzywinski, M. and Jones, S. J.M. (2018) A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics, 34(4), pp. 652-659. (doi: 10.1093/bioinformatics/btx613) (PMID:29028901)

Anekalla, K. R., Courneya, J.P., Florini, N., Lever, J. , Muchow, M. and Busby, B. (2017) PubRunner: a light-weight framework for updating text mining results. F1000Research, 6, 612. (doi: 10.12688/f1000research.11389.2) (PMID:29152221) (PMCID:PMC5664974)

Lever, J. , Krzywinski, M. and Altman, N. (2017) Principal component analysis. Nature Methods, 14(7), pp. 641-642. (doi: 10.1038/nmeth.4346)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Regularization. Nature Methods, 13(10), pp. 803-804. (doi: 10.1038/nmeth.4014)

Grinshtein, N. et al. (2016) Small molecule epigenetic screen identifies novel EZH2 and HDAC inhibitors that target glioblastoma brain tumor-initiating cells. Oncotarget, 7(37), pp. 59360-59376. (doi: 10.18632/oncotarget.10661) (PMID:27449082) (PMCID:PMC5312317)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Model selection and overfitting. Nature Methods, 13(9), pp. 703-704. (doi: 10.1038/nmeth.3968)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Classification evaluation. Nature Methods, 13(8), pp. 603-604. (doi: 10.1038/nmeth.3945)

Lever, J. , Krzywinski, M. and Altman, N. (2016) Logistic regression. Nature Methods, 13(7), pp. 541-542. (doi: 10.1038/nmeth.3904)

Davis, B., Shen, Y., Poon, C. C., Luchman, H. A., Stechishin, O. D., Pontifex, C. S., Wu, W., Kelly, J. J., Blough, M. D. and Terry Fox Research Institute Glioblastoma Consortium, (2015) Comparative genomic and genetic analysis of glioblastoma-derived brain tumor-initiating cells and their parent tumors. Neuro-Oncology, 18(3), pp. 350-360. (doi: 10.1093/neuonc/nov143) (PMID:26245525) (PMCID:PMC4767234)

Lever, J. and Komura, T. (2012) Real-time controllable fire using textured forces. Visual Computer, 28(6-8), pp. 691-700. (doi: 10.1007/s00371-012-0684-1)

Conference Proceedings

Frayling, E., Lever, J. and McDonald, G. (2024) UoG Siephers at "Discharge Me!": Exploring Ways to Generate Synthetic Patient Notes From Multi-Part Electronic Health Records. In: BioNLP 2024 Workshop, Bangkok, Thailand, 11-16 Aug 2024, pp. 712-718.

Zhang, X., Meng, Z. , Lever, J. and Ho, E. S.L. (2024) Gla-AI4BioMed at RRG24: Visual Instruction-tuned Adaptation for Radiology Report Generation. In: 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024), 23rd BioNLP Workshop, Bangkok, Thailand, 16 August 2024, (Accepted for Publication)

Lever, J. , Barbarino, J. M., Gong, L., Huddart, R., Sangkuhl, K., Whaley, R., Whirl-Carrillo, M., Woon, M., Klein, T. E. and Altman, R. B. (2020) PGxMine: Text Mining for Curation of PharmGKB. In: 25th Pacific Symposium on Biocomputing, Puako, HI, USA, 03-07 Jan 2020, pp. 611-622.

Lever, J. , Jones, M. and Jones, S. J.M. (2016) CancerMine: Knowledge Base Construction for Personalised Cancer Treatment. In: 2016 Joint International Conference on Biological Ontology and BioCreative - Food, Nutrition, Health and Environment for the 9 Billion (ICBO-BioCreative 2016), Corvallis, OR, USA, 01-04 Aug 2016,

This list was generated on Thu Nov 21 03:17:50 2024 GMT.

Grants

  • NIH U24 Biomedical Knowledgebase: Extracting the clinical impact of cancer mutations from research literature with natural language processing (with Profs Obi & Malachi Griffith at WashU and Prof Alex Wagner at Nationwide Children's Hospital)
  • EPSRC New Horizons: Safe Information Extraction of Patient Histories (with Dr Graham MacDonald and Prof Iadh Ounis)

Supervision

  • Zhai, Zihao
    Understanding the structure and content of tables in published manuscripts by integrating the tabular data with free text
  • Zhang, Xi
    Generative Multi-modal BioMedical Natural Language Modelling

Teaching

I teach the undergraduate Honours Text As Data course (COMPSCI 4074/5096) that covers natural language processing methods from the basics up to large language models. I also teach as part of the Generative Pre-trained Transformers short course available through Coursera.

Research datasets

Jump to: 2022
Number of items: 1.

2022

Lever, J. (2022) PGxMine. [Data Collection]

This list was generated on Thu Nov 21 03:17:51 2024 GMT.