Knight Cancer Quantitative Oncology Program

Research output

Research output per year 1980 2016 2017 2018 2019 2020 2021 2022 2023 2024

• 589 Article
• 68 Review article
• 48 Comment/debate
• 27 Conference contribution
• 49 More
  • 20 Chapter
  • 12 Letter
  • 7 Editorial
  • 6 Conference article
  • 3 Short survey
  • 1 Paper

Research output per year

Research output per year

Search results

• 2024

  Activation of coagulation FXI promotes endothelial inflammation and amplifies platelet activation in a nonhuman primate model of hyperlipidemia

  Kohs, T. C. L., Vu, H. H., Jordan, K. R., Parra-Izquierdo, I., Hinds, M. T., Shatzel, J. J., Kievit, P., Morgan, T. K., Yunga, S. T., Ngo, T. T. M., Aslan, J. E., Wallisch, M., Lorentz, C. U., Tucker, E. I., Gailani, D., Lindner, J. R., Puy, C. & McCarty, O. J. T., Jan 2024, In: Research and Practice in Thrombosis and Haemostasis. 8, 1, 102276.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Platelet Activation 100%
  • Hyperlipidemias 91%
  • Primates 84%
  • Inflammation 53%
  • Blood Platelets 30%
  1 Scopus citations

• Automatically pre-screening patients for the rare disease aromatic L-amino acid decarboxylase deficiency using knowledge engineering, natural language processing, and machine learning on a large EHR population

  Cohen, A. M., Kaner, J., Miller, R., Kopesky, J. W. & Hersh, W., Mar 1 2024, In: Journal of the American Medical Informatics Association. 31, 3, p. 692-704 13 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Aromatic amino acid decarboxylase deficiency 100%
  • Natural Language Processing 76%
  • Machine Learning 58%
  • Electronic Health Records 53%
  • Rare Diseases 50%

• Autotaxin–lysolipid signaling suppresses a CCL11–eosinophil axis to promote pancreatic cancer progression

  Bhattacharyya, S., Oon, C., Diaz, L., Sandborg, H., Stempinski, E. S., Saoi, M., Morgan, T., López, C. S., Cross, J. R. & Sherman, M., Feb 2024, In: Nature Cancer. 5, 2, p. 283-298 16 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access
  2 Scopus citations

• Comparison of Immunotherapy versus Targeted Therapy Effectiveness in BRAF-Mutant Melanoma Patients and Use of cGAS Expression and Aneuploidy as Potential Prognostic Biomarkers

  Garrison, Z., Clister, T., Bleem, E., Berry, E. G. & Kulkarni, R., Mar 2024, In: Cancers. 16, 5, 1027.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• DESP demixes cell-state profiles from dynamic bulk molecular measurements

  Youssef, A., Paul, I., Crovella, M. & Emili, A., Mar 25 2024, In: Cell Reports Methods. 4, 3, 100729.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• Dynamic Contrast-Enhanced (DCE) MRI

  Li, X., Huang, W. & Holmes, J. H., Feb 2024, In: Magnetic Resonance Imaging Clinics of North America. 32, 1, p. 47-61 15 p.

  Research output: Contribution to journal › Review article › peer-review
  1 Scopus citations

• Functional delineation of the luminal epithelial microenvironment in breast using cell-based screening in combinatorial microenvironments

  Jokela, T. A., Dane, M. A., Smith, R. L., Devlin, K. L., Shalabi, S., Lopez, J. C., Miyano, M., Stampfer, M. R., Korkola, J. E., Gray, J. W., Heiser, L. M. & LaBarge, M. A., Jan 2024, In: Cellular Signalling. 113, 110958.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Breast 100%
  • Hepatocyte Growth Factor 52%
  • Cell Count 32%
  • Proto-Oncogene Proteins c-sis 31%
  • Epithelial Cells 31%

• High-throughput methylome analysis reveals differential methylation for early and late onset preeclampsia for mothers and their children

  Layman, C. E., Ward, S., Davis, B. A., Nevonen, K. A., Okhovat, M., Rincon, M., Valent, A., Carbone, L. & Thornburg, K. L., Mar 2024, In: Physiological genomics. 56, 3, p. 276-282 7 p.

  Research output: Contribution to journal › Article › peer-review

  • Epigenome 100%
  • Pre-Eclampsia 80%
  • Methylation 72%
  • Mothers 51%
  • Pregnancy 41%

• Imaging of the hepatic arterial infusion pump: Primer for radiologists

  Bonde, A., Fung, A. W., Mayo, S. C., Li, P., Walker, B. S., Jaganathan, S., Mallak, N. & Korngold, E. K., Jan 2024, In: Clinical Imaging. 105, 110022.

  Research output: Contribution to journal › Review article › peer-review

  • Infusion Pumps 100%
  • Radiologists 70%
  • Liver 39%
  • Perfusion Imaging 11%
  • Cholangiocarcinoma 10%

• Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia

  Pino, J. C., Posso, C., Joshi, S. K., Nestor, M., Moon, J., Hansen, J. R., Hutchinson-Bunch, C., Gritsenko, M. A., Weitz, K. K., Watanabe-Smith, K., Long, N., McDermott, J. E., Druker, B. J., Liu, T., Tyner, J. W., Agarwal, A., Traer, E., Piehowski, P. D., Tognon, C. E., Rodland, K. D., & 1 othersGosline, S. J. C., Jan 16 2024, In: Cell Reports Medicine. 5, 1, 101359.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Proteogenomics 100%
  • Acute Myeloid Leukemia 57%
  • Drug 31%
  • Pharmaceutical Preparations 24%
  • quizartinib 22%

• NETosis Is Induced by Complement Component 5a: Implications in the Pathogenesis of Pyoderma Gangrenosum

  Wang, Z., Hornick, N., Vague, M., Yang, D., Keller, J., Kody, S., Leachman, S., Ortega-Loayza, A. G. & Liu, Y., Jan 2024, In: Journal of Investigative Dermatology. 144, 1, p. 184-188.e2

  Research output: Contribution to journal › Article › peer-review
  1 Scopus citations

• Night and Day, Why Radiologists Need Play

  Averill, S. L., Gomez, E. N., Belfi, L. M., Hui, J., Mallak, N. & Chetlen, A., Feb 2024, In: Academic radiology. 31, 2, p. 360-370 11 p.

  Research output: Contribution to journal › Article › peer-review

  • Radiology 100%
  • Workplace 96%
  • Radiologists 92%

• Novel recruitment approaches and operational results for a statewide population Cohort for cancer research: The Healthy Oregon Project

  Zhang, Z., Shafer, A., Johnson-Camacho, K., Adey, A., Anur, P., Brown, K. A., Conrad, C., Crist, R., Farris, P. E., Harrington, C. A., Marriott, L. K., Mitchell, A., O'Roak, B., Serrato, V., Richards, C. S., Spellman, P. T. & Shannon, J., Jan 19 2024, In: Journal of Clinical and Translational Science. 8, 1, e32.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Social Media 100%
  • Smartphone 97%
  • Population 94%
  • Neoplasms 78%
  • Translational Medical Research 45%

• Optimization of Tissue Digestion Methods for Characterization of Photoaged Skin by Single Cell RNA Sequencing Reveals Preferential Enrichment of T Cell Subsets

  Clister, T., Fey, R. M., Garrison, Z. R., Valenzuela, C. D., Bar, A., Leitenberger, J. J. & Kulkarni, R., Feb 2024, In: Cells. 13, 3, 266.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • RNA Sequencing 100%
  • RNA Sequence Analysis 67%
  • T-Lymphocyte Subsets 64%
  • Cell Viability 59%
  • Digestion 55%

• Predicting transcription factor activity using prior biological information

  Yashar, W. M., Estabrook, J., Holly, H. D., Somers, J., Nikolova, O., Babur, O., Braun, T. & Demir, E., Mar 15 2024, In: iScience. 27, 3, 109124.

  Research output: Contribution to journal › Article › peer-review

  Open Access

• RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration

  Olson, H. M., Maxfield, A., Calistri, N. L., Heiser, L. M., Qian, W., Knaut, H. & Nechiporuk, A. V., Jan 2024, In: Development (Cambridge). 151, 1, dev201898.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Cell Movement 100%
  • Zebrafish 93%
  • Myosin Type II 42%
  • Cell Polarity 37%
  • RNA Sequence Analysis 34%

• Second site reversion of HIV-1 envelope protein baseplate mutations maps to the matrix protein

  Alfadhli, A., Romanaggi, C. A., Barklis, R. L. & Barklis, E., Feb 2024, In: Journal of virology. 98, 2

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Genetic Suppression 100%
  • Human immunodeficiency virus 1 87%
  • genetic suppression 70%
  • HIV-1 62%
  • tail 59%

• Structurally divergent and recurrently mutated regions of primate genomes

  Mao, Y., Harvey, W. T., Porubsky, D., Munson, K. M., Hoekzema, K., Lewis, A. P., Audano, P. A., Rozanski, A., Yang, X., Zhang, S., Yoo, D. A., Gordon, D. S., Fair, T., Wei, X., Logsdon, G. A., Haukness, M., Dishuck, P. C., Jeong, H., del Rosario, R., Bauer, V. L., & 14 othersFattor, W. T., Wilkerson, G. K., Mao, Y., Shi, Y., Sun, Q., Lu, Q., Paten, B., Bakken, T. E., Pollen, A. A., Feng, G., Sawyer, S. L., Warren, W. C., Carbone, L. & Eichler, E. E., Mar 14 2024, In: Cell. 187, 6, p. 1547-1562.e13

  Research output: Contribution to journal › Article › peer-review

  Open Access
  1 Scopus citations

• The Reactome Pathway Knowledgebase 2024

  Milacic, M., Beavers, D., Conley, P., Gong, C., Gillespie, M., Griss, J., Haw, R., Jassal, B., Matthews, L., May, B., Petryszak, R., Ragueneau, E., Rothfels, K., Sevilla, C., Shamovsky, V., Stephan, R., Tiwari, K., Varusai, T., Weiser, J., Wright, A., & 4 othersWu, G., Stein, L., Hermjakob, H. & D'Eustachio, P., Jan 5 2024, In: Nucleic acids research. 52, D1, p. D672-D678

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Knowledge Bases 100%
  • Community Networks 63%
  • Catalogs 51%
  • Proteome 43%
  • Biological Phenomena 40%
  10 Scopus citations

• txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility

  Zhang, H., Mulqueen, R. M., Iannuzo, N., Farrera, D. O., Polverino, F., Galligan, J. J., Ledford, J. G., Adey, A. C. & Cusanovich, D. A., Dec 2024, In: Genome biology. 25, 1, 78.

  Research output: Contribution to journal › Article › peer-review

  Open Access
• 2023

  #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

  Dommer, A., Casalino, L., Kearns, F., Rosenfeld, M., Wauer, N., Ahn, S. H., Russo, J., Oliveira, S., Morris, C., Bogetti, A., Trifan, A., Brace, A., Sztain, T., Clyde, A., Ma, H., Chennubhotla, C., Lee, H., Turilli, M., Khalid, S., Tamayo-Mendoza, T., & 32 othersWelborn, M., Christensen, A., Smith, D. G. A., Qiao, Z., Sirumalla, S. K., O’Connor, M., Manby, F., Anandkumar, A., Hardy, D., Phillips, J., Stern, A., Romero, J., Clark, D., Dorrell, M., Maiden, T., Huang, L., McCalpin, J., Woods, C., Gray, A., Williams, M., Barker, B., Rajapaksha, H., Pitts, R., Gibbs, T., Stone, J., Zuckerman, D. M., Mulholland, A. J., Miller, T., Jha, S., Ramanathan, A., Chong, L. & Amaro, R. E., Jan 2023, In: International Journal of High Performance Computing Applications. 37, 1, p. 28-44 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Aerosol 100%
  • Severe Acute Respiratory Syndrome 99%
  • Microscopy 94%
  • Aerosols 76%
  • Viruses 75%
  19 Scopus citations

• Accessible high-throughput single-cell whole-genome sequencing with paired chromatin accessibility

  Queitsch, K., Moore, T. W., O'Connell, B. L., Nichols, R. V., Muschler, J. L., Keith, D., Lopez, C., Sears, R. C., Mills, G. B., Yardımcı, G. G. & Adey, A. C., Nov 20 2023, In: Cell Reports Methods. 3, 11, 100625.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Whole Genome Sequencing 100%
  • Genomics 89%
  • Chromatin 75%
  • Throughput 59%
  • Reagents 29%

• Advances in Early Detection of Melanoma and the Future of At-Home Testing

  Garrison, Z. R., Hall, C. M., Fey, R. M., Clister, T., Khan, N., Nichols, R. & Kulkarni, R. P., Apr 2023, In: Life. 13, 4, 974.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • melanoma 100%
  • Melanoma 71%
  • artificial intelligence 41%
  • mortality 40%
  • testing 33%
  2 Scopus citations

• A framework for considering prior information in network-based approaches to omics data analysis

  Somers, J., Fenner, M., Kong, G., Thirumalaisamy, D., Yashar, W. M., Thapa, K., Kinali, M., Nikolova, O., Babur, Ö. & Demir, E., Nov 2023, In: Proteomics. 23, 21-22, 2200402.

  Research output: Contribution to journal › Review article › peer-review

  Open Access

  • Information Services 100%
  • Mechanics 93%
  • Data Analysis 61%
  • Information Systems 45%
  • Datasets 32%

• A Framework for Evaluating the Technical Performance of Multiparameter Quantitative Imaging Biomarkers (mp-QIBs)

  Obuchowski, N. A., Huang, E., deSouza, N. M., Raunig, D., Delfino, J., Buckler, A., Hatt, C., Wang, X., Moskowitz, C., Guimaraes, A., Giger, M., Hall, T. J., Kinahan, P. & Pennello, G., Feb 2023, In: Academic radiology. 30, 2, p. 147-158 12 p.

  Research output: Contribution to journal › Review article › peer-review

  • Biomarkers 100%
  • Phenotype 92%
  • Medicine 56%
  9 Scopus citations

• Allele-Specific Gene Regulation, Phenotypes, and Therapeutic Vulnerabilities in Estrogen Receptor Alpha-Mutant Endometrial Cancer

  Blanchard, Z., Rush, C. M., Arnesen, S., Vahrenkamp, J. M., Rodriguez, A. C., Jarboe, E. A., Brown, C., Chang, M. E. K., Flory, M. R., Mohammed, H., Modzelewska, K., Lum, D. H. & Gertz, J., Oct 1 2023, In: Molecular Cancer Research. 21, 10, p. 1023-1036 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Estrogen Receptor alpha 100%
  • Endometrial Neoplasms 88%
  • Alleles 63%
  • Phenotype 51%
  • Mutation 38%

• An altered extracellular matrix–integrin interface contributes to Huntington’s disease-associated CNS dysfunction in glial and vascular cells

  Hernandez, S. J., Lim, R. G., Onur, T., Dane, M. A., Smith, R., Wang, K., Jean, G. E. H., Reyes-Ortiz, A., Devlin, K., Miramontes, R., Wu, J., Casale, M., Kilburn, D., Heiser, L. M., Korkola, J. E., Van Vactor, D., Botas, J., Thompson-Peer, K. L. & Thompson, L. M., May 1 2023, In: Human molecular genetics. 32, 9, p. 1483-1496 14 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Huntington Disease 100%
  • Neuroglia 79%
  • Blood Vessels 52%
  • Integrins 42%
  • Induced Pluripotent Stem Cells 33%
  2 Scopus citations

• Analysis and modeling of cancer drug responses using cell cycle phase-specific rate effects

  Gross, S. M., Mohammadi, F., Sanchez-Aguila, C., Zhan, P. J., Liby, T. A., Dane, M. A., Meyer, A. S. & Heiser, L. M., Dec 2023, In: Nature communications. 14, 1, 3450.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Drug Design 100%
  • drugs 87%
  • cancer 81%
  • Cell Cycle 68%
  • cycles 57%
  1 Scopus citations

• Analysis methods and clinical applications of circulating cell-free DNA and RNA in human blood

  Wagner, J. T., Briand, J. & Ngo, T. T. M., Sep 27 2023, Cutting-edge Technologies in Biological Sensing and Analysis. River Publishers, p. 33-94 62 p.

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • RNA 100%
  • DNA 85%
  • Blood 76%
  • Alzheimer's Disease 45%
  • Oncology 39%

• A phosphoinositide switch mediates exocyst recruitment to multivesicular endosomes for exosome secretion

  Liu, D. A., Tao, K., Wu, B., Yu, Z., Szczepaniak, M., Rames, M., Yang, C., Svitkina, T., Zhu, Y., Xu, F., Nan, X. & Guo, W., Dec 2023, In: Nature communications. 14, 1, 6883.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Phosphatidylinositol 4-Phosphate 100%
  • secretions 84%
  • Phosphoinositide 83%
  • Phosphatidylinositol 3-Phosphate 73%
  • Exosomes 71%
  4 Scopus citations

• Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors

  Braun, T. P., Estabrook, J., Schonrock, Z., Curtiss, B. M., Darmusey, L., Macaraeg, J., Enright, T., Coblentz, C., Callahan, R., Yashar, W., Taherinasab, A., Mohammed, H., Coleman, D. J., Druker, B. J., Demir, E., Lusardi, T. A. & Maxson, J. E., Feb 2023, In: Leukemia. 37, 2, p. 478-487 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Comb and Wattles 100%
  • Granulocyte Precursor Cells 90%
  • RNA Polymerase II 80%
  • Myelopoiesis 24%
  • Histone Code 19%

• Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

  O’Connell, B. L., Nichols, R. V., Pokholok, D., Thomas, J., Acharya, S. N., Nishida, A., Thornton, C. A., Co, M., Fields, A. J., Steemers, F. J. & Adey, A. C., 2023, In: Genome Research. 33, 2, p. 208-217 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Atlases 100%
  • Chromatin 82%
  • Transposases 26%
  • Workflow 13%
  • Costs and Cost Analysis 11%
  2 Scopus citations

• Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)

  PCAWG Consortium, May 2023, In: Nature genetics. 55, 5, p. 892 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Seoul 100%
  • Mitochondrial Genome 98%
  • Korea 80%
  • Genome 52%
  • Neoplasms 25%
  1 Scopus citations

• Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing (Nature Genetics, (2020), 52, 3, (331-341), 10.1038/s41588-019-0576-7)

  PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1076 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Chromothripsis 100%
  • Whole Genome Sequencing 67%
  • Genome 39%
  • Neoplasms 18%

• Author Correction: The landscape of viral associations in human cancers (Nature Genetics, (2020), 52, 3, (320-330), 10.1038/s41588-019-0558-9)

  PCAWG Pathogens & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1077 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Genome 100%
  • Neoplasms 47%
  • Germany 32%
  • Infections 17%

• Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x)

  PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1078 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Mitochondrial Genome 100%
  • Genome 53%
  • Neoplasms 25%

• Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6)

  The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E39

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Genome 100%
  • Neoplasms 47%
  1 Scopus citations

• Author Correction: The evolutionary history of 2,658 cancers (Nature, (2020), 578, 7793, (122-128), 10.1038/s41586-019-1907-7)

  PCAWG Evolution & Heterogeneity Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E42

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • History 100%
  • Genome 90%
  • Neoplasms 42%
  1 Scopus citations

• Author Correction: Patterns of somatic structural variation in human cancer genomes (Nature, (2020), 578, 7793, (112-121), 10.1038/s41586-019-1913-9)

  PCAWG Structural Variation Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E38

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Human Genome 100%
  • Genome 64%
  • Neoplasms 30%
  2 Scopus citations

• Author Correction: The repertoire of mutational signatures in human cancer (Nature, (2020), 578, 7793, (94-101), 10.1038/s41586-020-1943-3)

  PCAWG Mutational Signatures Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E41

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access
  2 Scopus citations

• Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition (Nature Genetics, (2020), 52, 3, (306-319), 10.1038/s41588-019-0562-0)

  PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1080 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Genome 100%
  • Medicine 53%
  • Neoplasms 47%
  • Baltimore 47%
  • Quebec 44%
  1 Scopus citations

• Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes (Nature, (2020), 578, 7793, (102-111), 10.1038/s41586-020-1965-x)

  PCAWG Drivers and Functional Interpretation Working Group, PCAWG Structural Variation Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E40

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Genome 100%
  • Sweden 72%
  • Neoplasms 47%
  • Biological Science Disciplines 45%
  • Computational Biology 34%
  1 Scopus citations

• Author Correction: Supervised learning of high-confidence phenotypic subpopulations from single-cell data (Nature Machine Intelligence, (2023), 5, 5, (528-541), 10.1038/s42256-023-00656-y)

  Ren, T., Chen, C., Danilov, A. V., Liu, S., Guan, X., Du, S., Wu, X., Sherman, M. H., Spellman, P. T., Coussens, L. M., Adey, A. C., Mills, G. B., Wu, L. Y. & Xia, Z., Jun 2023, In: Nature Machine Intelligence. 5, 6, p. 676 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • HTML 100%
  • Supervised learning 87%
  • Display devices 63%

• Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes (Nature Biotechnology, (2020), 38, 3, (288-292), 10.1038/s41587-019-0360-3)

  PCAWG Technical Working Group & PCAWG Consortium, Apr 2023, In: Nature biotechnology. 41, 4, p. 577 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Biotechnology 100%
  • Human Genome 82%
  • Genomics 81%
  • Genome 53%
  • HTML 47%

• Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (Nature Genetics, (2020), 52, 3, (294-305), 10.1038/s41588-019-0564-y)

  PCAWG Structural Variation Working Group & PCAWG Consortium, Jun 2023, In: Nature genetics. 55, 6, p. 1079 1 p.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Chromatin 100%
  • Genome 76%
  • Neoplasms 36%

• Author Correction: Genomic basis for RNA alterations in cancer (Nature, (2020), 578, 7793, (129-136), 10.1038/s41586-020-1970-0)

  PCAWG Transcriptome Core Group, PCAWG Transcriptome Working Group & PCAWG Consortium, Feb 16 2023, In: Nature. 614, 7948, p. E37

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • RNA 100%
  • Genome 97%
  • Agriculture 55%
  • Neoplasms 46%
  • France 45%

• Author Correction: The amniotic fluid proteome changes across gestation in humans and rhesus macaques (Scientific Reports, (2023), 13, 1, (17039), 10.1038/s41598-023-44125-3)

  Shorey-Kendrick, L. E., Crosland, B. A., Spindel, E. R., McEvoy, C. T., Wilmarth, P. A., Reddy, A. P., Zientek, K. D., Roberts, V. H. J., D’Mello, R. J., Ryan, K. S., Olyaei, A. F., Hagen, O. L., Drake, M. G., McCarty, O. J. T., Scottoline, B. P. & Lo, J. O., Dec 2023, In: Scientific Reports. 13, 1, 17640.

  Research output: Contribution to journal › Comment/debate › peer-review

  Open Access

  • Amniotic Fluid 100%
  • Macaca mulatta 97%
  • Proteome 96%
  • Pregnancy 55%

• Automated deep-learning system in the assessment of MRI-visible prostate cancer: comparison of advanced zoomed diffusion-weighted imaging and conventional technique

  Hu, L., Fu, C., Song, X., Grimm, R., von Busch, H., Benkert, T., Kamen, A., Lou, B., Huisman, H., Tong, A., Penzkofer, T., Choi, M. H., Shabunin, I., Winkel, D., Xing, P., Szolar, D., Coakley, F., Shea, S., Szurowska, E., Guo, J. Y., & 3 othersLi, L., Li, Y. H. & Zhao, J. G., Dec 2023, In: Cancer Imaging. 23, 1, 6.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Deep Learning 100%
  • Prostatic Neoplasms 57%
  • Artifacts 19%
  • ROC Curve 11%
  • Noise 6%
  2 Scopus citations

• Automated large volume sample preparation for vEM

  Stempinski, E. S., Pagano, L., Riesterer, J. L., Adamou, S. K., Thibault, G., Song, X., Chang, Y. H. & López, C. S., Jan 2023, Volume Electron Microscopy. Narayan, K., Narayan, K., Collinson, L. & Verkade, P. (eds.). Academic Press Inc., p. 1-32 32 p. (Methods in Cell Biology; vol. 177).

  Research output: Chapter in Book/Report/Conference proceeding › Chapter

  • Electron Microscopy 100%
  • Electron Scanning Microscopy 75%
  • Electrons 61%
  • Research Personnel 54%
  • Hazardous Substances 54%
  1 Scopus citations

• Biology-inspired graph neural network encodes reactome and reveals biochemical reactions of disease

  Burkhart, J. G., Wu, G., Song, X., Raimondi, F., McWeeney, S., Wong, M. H. & Deng, Y., Jul 14 2023, In: Patterns. 4, 7, 100758.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Neural Networks 100%
  • Graph 79%
  • Future Studies 31%
  • Genotype 25%
  • Cancer 24%
  2 Scopus citations