Bader, Gary D.

Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

Rodriguez-Martin, B., Alvarez, E. G., Baez-Ortega, A., Zamora, J., Supek, F., Demeulemeester, J., Santamarina, M., Ju, Y. S., Temes, J., Garcia-Souto, D., et al. (2020) · Nature Genetics

Genomic variations and chromosomal abnormalitiesCancer Genomics and Diagnostics

Cited by 451

Functional genomic landscape of cancer-intrinsic evasion of killing by T cells

Lawson, K. A., Sousa, C. M., Zhang, X., Kim, E., Akthar, R., Caumanns, J. J., Yao, Y., Mikolajewicz, N., Ross, C., Brown, K. R., et al. (2020) · Nature

Cancer Immunotherapy and BiomarkersImmunotherapy and Immune Responses

Cited by 443

Pathguide: a Pathway Resource List

Bader, G. D. (2006) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 435

Too many roads not taken

Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M., & Yu, F. H. (2011) · Nature

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 411

GeneMANIA Prediction Server 2013 Update

Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013) · Nucleic Acids Research

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 396

Quantitative analysis of fitness and genetic interactions in yeast on a genome scale

Baryshnikova, A., Costanzo, M., Kim, Y., Ding, H., Koh, J., Toufighi, K., Youn, J.-Y., Ou, J., San Luis, B.-J., Bandyopadhyay, S., et al. (2010) · Nature Methods

Fungal and yeast genetics researchBioinformatics and Genomic Networks

Cited by 364

Single‐Cell, Single‐Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity

Andrews, T. S., Atif, J., Liu, J. C., Perciani, C. T., Ma, X., Thoeni, C., Slyper, M., Eraslan, G., Segerstolpe, A., Manuel, J., et al. (2022) · Hepatology Communications

Single-cell and spatial transcriptomicsLiver physiology and pathology

Cited by 307

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

Kerrien, S., Orchard, S., Montecchi-Palazzi, L., Aranda, B., Quinn, A. F., Vinod, N., Bader, G. D., Xenarios, I., Wojcik, J., Sherman, D., et al. (2007) · BMC Biology

Bioinformatics and Genomic NetworksAdvanced Proteomics Techniques and Applications

Cited by 266

Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion

Lechman, E. R., Gentner, B., van Galen, P., Giustacchini, A., Saini, M., Boccalatte, F. E., Hiramatsu, H., Restuccia, U., Bachi, A., Voisin, V., et al. (2012) · Cell Stem Cell

Hematopoietic Stem Cell TransplantationMicroRNA in disease regulation

Cited by 208

The multimodality cell segmentation challenge: toward universal solutions

Ma, J., Xie, R., Ayyadhury, S., Ge, C., Gupta, A., Gupta, R., Gu, S., Zhang, Y., Lee, G., Kim, J., et al. (2024) · Nature Methods

Cell Image Analysis TechniquesAdvanced Neural Network Applications

Cited by 154

Pathway information for systems biology

Cary, M. P., Bader, G. D., & Sander, C. (2005) · FEBS Letters

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 152

Single-cell atlas of human liver development reveals pathways directing hepatic cell fates

Wesley, B. T., Ross, A. D. B., Muraro, D., Miao, Z., Saxton, S., Tomaz, R. A., Morell, C. M., Ridley, K., Zacharis, E. D., Petrus-Reurer, S., et al. (2022) · Nature Cell Biology

Single-cell and spatial transcriptomicsLiver physiology and pathology

Cited by 146

cPath: open source software for collecting, storing, and querying biological pathways

Cerami, E. G., Bader, G. D., Gross, B. E., & Sander, C. (2006) · BMC Bioinformatics

Bioinformatics and Genomic NetworksBiomedical Text Mining and Ontologies

Cited by 125

Mapping the Hsp90 genetic interaction network in Candida albicans reveals environmental contingency and rewired circuitry

Diezmann, S., Michaut, M., Shapiro, R. S., Bader, G. D., & Cowen, L. E. (2012) · PLoS Genetics

Heat shock proteins researchFungal and yeast genetics research

Cited by 112

Relapse-Fated Latent Diagnosis Subclones in Acute B Lineage Leukemia Are Drug Tolerant and Possess Distinct Metabolic Programs

Dobson, S. M., García-Prat, L., Vanner, R. J., Wintersinger, J., Waanders, E., Gu, Z., McLeod, J., Gan, O. I., Grandal, I., Payne-Turner, D., et al. (2020) · Cancer Discovery

Acute Lymphoblastic Leukemia researchAcute Myeloid Leukemia Research

Cited by 94

Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

Isserlin, R., Merico, D., Alikhani‐Koupaei, R., Gramolini, A., Bader, G. D., & Emili, A. (2010) · PROTEOMICS

Bioinformatics and Genomic NetworksCardiomyopathy and Myosin Studies

Cited by 63

Ectopic miR-125a expression induces long-term repopulating stem cell capacity in mouse and human hematopoietic progenitors

Wojtowicz, E. E., Lechman, E. R., Hermans, K. G., Schoof, E. M., Wienholds, E., Isserlin, R., van Veelen, P. A., Broekhuis, M. J. C., Janssen, G. M. C., Trotman-Grant, A., et al. (2016) · Cell stem cell

Hematopoietic Stem Cell TransplantationMicroRNA in disease regulation

Cited by 60

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

Narayan, S., Bader, G. D., & Reimand, J. (2016) · Genome Medicine

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 54

MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition

Xie, R., Pang, K., Bader, G. D., & Wang, B. (2023) · 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

Cell Image Analysis TechniquesAdvanced Neural Network Applications

Cited by 17