Chaisson, Mark J. P.

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 51,709

A global reference for human genetic variation

The 1000 Genomes Project Consortium, authors, C., Auton, A., Abecasis, G. R., Steering committee, Altshuler, D. M., Durbin, R. M., Abecasis, G. R., Bentley, D. R., Chakravarti, A., et al. (2015) · Nature

Genetic Associations and EpidemiologyForensic and Genetic Research

Cited by 18,247

Towards complete and error-free genome assemblies of all vertebrate species

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., et al. (2021) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 3,097

An integrated map of structural variation in 2,504 human genomes

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature

Genomic variations and chromosomal abnormalitiesGenome Rearrangement Algorithms

Cited by 2,354

A draft human pangenome reference.

Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 1,129

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Chaisson, M. J. P., Sanders, A. D., Zhao, X., Malhotra, A., Porubsky, D., Rausch, T., Gardner, E. J., Rodriguez, O. L., Guo, L., Collins, R. L., et al. (2019) · Nature Communications

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 891

Extensive sequencing of seven human genomes to characterize benchmark reference materials

Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 811

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

Ebert, P., Audano, P. A., Zhu, Q., Rodriguez-Martin, B., Porubsky, D., Bonder, M. J., Sulovari, A., Ebler, J., Zhou, W., Serra Mari, R., et al. (2021) · Science

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 702

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

A robust benchmark for detection of germline large deletions and insertions

Zook, J. M., Hansen, N. F., Olson, N. D., Chapman, L., Mullikin, J. C., Xiao, C., Sherry, S., Koren, S., Phillippy, A. M., Boutros, P. C., et al. (2020) · Nature Biotechnology

Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic Studies

Cited by 418

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

Cited by 350

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

Cited by 343

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

Cited by 333

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson, M. J., Brinza, D., & Pevzner, P. A. (2009) · Genome Research

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 279

Semi-automated assembly of high-quality diploid human reference genomes

Jarvis, E. D., Formenti, G., Rhie, A., Guarracino, A., Yang, C., Wood, J., Tracey, A., Thibaud-Nissen, F., Vollger, M. R., Porubsky, D., et al. (2022) · Nature

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 209

Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads

Human Genome Structural Variation Consortium, Porubsky, D., Ebert, P., Audano, P. A., Vollger, M. R., Harvey, W. T., Marijon, P., Ebler, J., Munson, K. M., Sorensen, M., et al. (2021) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 203

Recombination between heterologous human acrocentric chromosomes

Guarracino, A., Buonaiuto, S., de Lima, L. G., Potapova, T., Rhie, A., Koren, S., Rubinstein, B., Fischer, C., Human Pangenome Reference Consortium, Abel, H. J., et al. (2023) · Nature

Chromosomal and Genetic VariationsGenomic variations and chromosomal abnormalities

Cited by 134

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2021) · The American Journal of Human Genetics

Genomic variations and chromosomal abnormalitiesGenomics and Rare Diseases

Cited by 132

Increased mutation and gene conversion within human segmental duplications

Vollger, M. R., Dishuck, P. C., Harvey, W. T., DeWitt, W. S., Guitart, X., Goldberg, M. E., Rozanski, A. N., Lucas, J., Asri, M., Human Pangenome Reference Consortium, et al. (2023) · Nature

Genomic variations and chromosomal abnormalitiesChromosomal and Genetic Variations

Cited by 104

Analysis and benchmarking of small and large genomic variants across tandem repeats

English, A. C., Dolzhenko, E., Ziaei Jam, H., McKenzie, S. K., Olson, N. D., De Coster, W., Park, J., Gu, B., Wagner, J., Eberle, M. A., et al. (2025) · Nature Biotechnology

Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalities

Cited by 68

Structural variation across 138,134 samples in the TOPMed consortium

Jun, G., English, A., Metcalf, G., Yang, J., Chaisson, M., Pankratz, N., Menon, V., Salerno, W., Krasheninina, O., Smith, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Genomic variations and chromosomal abnormalitiesGenetic Associations and Epidemiology

Cited by 24