Huber, Wolfgang

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 95,106

HTSeq—a Python framework to work with high-throughput sequencing data

Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 21,464

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Genome Biology

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 15,581

The repertoire of mutational signatures in human cancer

Alexandrov, L. B., Kim, J., Haradhvala, N. J., Huang, M. N., Tian Ng, A. W., Wu, Y., Boot, A., Covington, K. R., Gordenin, D. A., Bergstrom, E. N., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,496

Pan-cancer analysis of whole genomes

The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium, Aaltonen, L. A., Abascal, F., Abeshouse, A., Aburatani, H., Adams, D. J., Agrawal, N., Ahn, K. S., Ahn, S.-M., Aikata, H., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 3,064

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A., & Vingron, M. (2002) · Bioinformatics

Gene expression and cancer classificationBioinformatics and Genomic Networks

Cited by 2,440

Detecting differential usage of exons from RNA-seq data

Anders, S., Reyes, A., & Huber, W. (2012) · Genome Research

RNA Research and SplicingGenomics and Phylogenetic Studies

Cited by 1,545

Two independent modes of chromatin organization revealed by cohesin removal

Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature

Genomics and Chromatin DynamicsNuclear Structure and Function

Cited by 1,196

The evolutionary history of 2,658 cancers

Gerstung, M., Jolly, C., Leshchiner, I., Dentro, S. C., Gonzalez, S., Rosebrock, D., Mitchell, T. J., Rubanova, Y., Anur, P., Yu, K., et al. (2020) · Nature

Cancer Genomics and DiagnosticsChromatin Remodeling and Cancer

Cited by 1,057

arrayQualityMetrics—a bioconductor package for quality assessment of microarray data

Kauffmann, A., Gentleman, R., & Huber, W. (2009) · Bioinformatics

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 946

Orchestrating single-cell analysis with Bioconductor

Amezquita, R. A., Lun, A. T. L., Becht, E., Carey, V. J., Carpp, L. N., Geistlinger, L., Marini, F., Rue-Albrecht, K., Risso, D., Soneson, C., et al. (2020) · Nature Methods

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 945

Human haematopoietic stem cell lineage commitment is a continuous process

Velten, L., Haas, S. F., Raffel, S., Blaszkiewicz, S., Islam, S., Hennig, B. P., Hirche, C., Lutz, C., Buss, E. C., Nowak, D., et al. (2017) · Nature Cell Biology

Hematopoietic Stem Cell TransplantationSingle-cell and spatial transcriptomics

Cited by 925

Patterns of somatic structural variation in human cancer genomes

Li, Y., Roberts, N. D., Wala, J. A., Shapira, O., Schumacher, S. E., Kumar, K., Khurana, E., Waszak, S., Korbel, J. O., Haber, J. E., et al. (2020) · Nature

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 867

Gene expression across mammalian organ development

Cardoso-Moreira, M., Halbert, J., Valloton, D., Velten, B., Chen, C., Shao, Y., Liechti, A., Ascenção, K., Rummel, C., Ovchinnikova, S., et al. (2019) · Nature

Developmental Biology and Gene RegulationGenomics and Phylogenetic Studies

Cited by 838

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

Cortés-Ciriano, I., Lee, J. J.-K., Xi, R., Jain, D., Jung, Y. L., Yang, L., Gordenin, D., Klimczak, L. J., Zhang, C.-Z., Pellman, D. S., et al. (2020) · Nature Genetics

Cancer Genomics and DiagnosticsGenomic variations and chromosomal abnormalities

Cited by 712

Transparency and reproducibility in artificial intelligence

Haibe-Kains, B., Adam, G. A., Hosny, A., Khodakarami, F., Massive Analysis Quality Control (MAQC) Society Board of Directors, Shraddha, T., Kusko, R., Sansone, S.-A., Tong, W., Wolfinger, R. D., et al. (2020) · Nature

Explainable Artificial Intelligence (XAI)Ethics and Social Impacts of AI

Cited by 540

Enhancer loops appear stable during development and are associated with paused polymerase

Ghavi-Helm, Y., Klein, F. A., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W., & Furlong, E. E. M. (2014) · Nature

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 536

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

Differential expression analysis for sequence count data

Anders, S., & Huber, W. (2010) · Nature Precedings

Gene expression and cancer classificationGenomics and Phylogenetic Studies

Cited by 328

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

Grubert, F., Zaugg, J. B., Kasowski, M., Ursu, O., Spacek, D. V., Martin, A. R., Greenside, P., Srivas, R., Phanstiel, D. H., Pekowska, A., et al. (2015) · Cell

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 319

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

Ohnishi, Y., Huber, W., Tsumura, A., Kang, M., Xenopoulos, P., Kurimoto, K., Oleś, A. K., Araúzo-Bravo, M. J., Saitou, M., Hadjantonakis, A.-K., et al. (2014) · Nature Cell Biology

Developmental Biology and Gene RegulationPluripotent Stem Cells Research

Cited by 300

Alternative start and termination sites of transcription drive most transcript isoform differences across human tissues

Reyes, A., & Huber, W. (2018) · Nucleic Acids Research

RNA Research and SplicingGenomics and Phylogenetic Studies

Cited by 290

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

Myc Depletion Induces a Pluripotent Dormant State Mimicking Diapause

Scognamiglio, R., Cabezas-Wallscheid, N., Thier, M. C., Altamura, S., Reyes, A., Prendergast, Á. M., Baumgärtner, D., Carnevalli, L. S., Atzberger, A., Haas, S., et al. (2016) · Cell

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 271