Haussler, David

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

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Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes

Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., & Haussler, D. (2003) · Proceedings of the National Academy of Sciences

Genome Rearrangement AlgorithmsGenomic variations and chromosomal abnormalities

Cited by 850

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D., & Stuart, J. M. (2010) · Bioinformatics

Bioinformatics and Genomic NetworksCancer Genomics and Diagnostics

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Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

Putnam, N. H., O'Connell, B. L., Stites, J. C., Rice, B. J., Blanchette, M., Calef, R., Troll, C. J., Fields, A., Hartley, P. D., Sugnet, C. W., et al. (2016) · Genome Research

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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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

The UCSC Genome Browser database: 2014 update

Karolchik, D., Barber, G. P., Casper, J., Clawson, H., Cline, M. S., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical Research

Cited by 670

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell

Adrenal and Paraganglionic TumorsChromatin Remodeling and Cancer

Cited by 657

Integrative Molecular Characterization of Malignant Pleural Mesothelioma

Hmeljak, J., Sanchez-Vega, F., Hoadley, K. A., Shih, J., Stewart, C., Heiman, D., Tarpey, P., Danilova, L., Drill, E., Gibb, E. A., et al. (2018) · Cancer Discovery

Occupational and environmental lung diseasesIntraperitoneal and Appendiceal Malignancies

Cited by 618

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

Pollen, A. A., Bhaduri, A., Andrews, M. G., Nowakowski, T. J., Meyerson, O. S., Mostajo-Radji, M. A., Di Lullo, E., Alvarado, B., Bedolli, M., Dougherty, M. L., et al. (2019) · Cell

Neurogenesis and neuroplasticity mechanismsPluripotent Stem Cells Research

Cited by 600

Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis

Fiddes, I. T., Lodewijk, G. A., Mooring, M., Bosworth, C. M., Ewing, A. D., Mantalas, G. L., Novak, A. M., van den Bout, A., Bishara, A., Rosenkrantz, J. L., et al. (2018) · Cell

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 595

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., et al. (2020) · Nature

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 586

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

Shafin, K., Pesout, T., Lorig-Roach, R., Haukness, M., Olsen, H. E., Bosworth, C., Armstrong, J., Tigyi, K., Maurer, N., Koren, S., et al. (2020) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 567

Key parameters of tumor epitope immunogenicity revealed through a consortium approach improve neoantigen prediction

Wells, D. K., van Buuren, M. M., Dang, K. K., Hubbard-Lucey, V. M., Sheehan, K. C. F., Campbell, K. M., Lamb, A., Ward, J. P., Sidney, J., Blazquez, A. B., et al. (2020) · Cell

vaccines and immunoinformatics approachesCancer Immunotherapy and Biomarkers

Cited by 538

Forces shaping the fastest evolving regions in the human genome

Pollard, K. S., Salama, S. R., King, B., Kern, A. D., Dreszer, T., Katzman, S., Siepel, A., Pedersen, J. S., Bejerano, G., Baertsch, R., et al. (2006) · PLoS Genetics

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

Jacobs, F. M. J., Greenberg, D., Nguyen, N., Haeussler, M., Ewing, A. D., Katzman, S., Paten, B., Salama, S. R., & Haussler, D. (2014) · Nature

Chromosomal and Genetic VariationsGenomics and Chromatin Dynamics

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The Human Pangenome Project: a global resource to map genomic diversity

Wang, T., Antonacci-Fulton, L., Howe, K., Lawson, H. A., Lucas, J. K., Phillippy, A. M., Popejoy, A. B., Asri, M., Carson, C., Chaisson, M. J. P., et al. (2022) · Nature

Genomics and Phylogenetic StudiesGenetic Associations and Epidemiology

Cited by 494

The UCSC Genome Browser database: 2018 update

Casper, J., Zweig, A. S., Villarreal, C., Tyner, C., Speir, M. L., Rosenbloom, K. R., Raney, B. J., Lee, C. M., Lee, B. T., Karolchik, D., et al. (2018) · Nucleic Acids Research

Genomics and Phylogenetic StudiesGenetics, Bioinformatics, and Biomedical Research

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Dense sampling of bird diversity increases power of comparative genomics

Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., et al. (2020) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

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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

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Pangenomics enables genotyping of known structural variants in 5202 diverse genomes

Sirén, J., Monlong, J., Chang, X., Novak, A. M., Eizenga, J. M., Markello, C., Sibbesen, J. A., Hickey, G., Chang, P.-C., Carroll, A., et al. (2021) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Green, R. E., Braun, E. L., Armstrong, J., Earl, D., Nguyen, N., Hickey, G., Vandewege, M. W., St. John, J. A., Capella-Gutiérrez, S., Castoe, T. A., et al. (2014) · Science

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

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High-resolution comparative analysis of great ape genomes

Kronenberg, Z. N., Fiddes, I. T., Gordon, D., Murali, S., Cantsilieris, S., Meyerson, O. S., Underwood, J. G., Nelson, B. J., Chaisson, M. J. P., Dougherty, M. L., et al. (2018) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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Pangenome graph construction from genome alignments with Minigraph-Cactus

Hickey, G., Monlong, J., Ebler, J., Novak, A. M., Eizenga, J. M., Gao, Y., Human Pangenome Reference Consortium, Abel, H. J., Antonacci-Fulton, L. L., Asri, M., et al. (2024) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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Long-read sequence assembly of the gorilla genome

Gordon, D., Huddleston, J., Chaisson, M. J. P., Hill, C. M., Kronenberg, Z. N., Munson, K. M., Malig, M., Raja, A., Fiddes, I., Hillier, L. W., et al. (2016) · Science

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

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